Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 5187 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 3766 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 5182 SARS 1350 COVID-19 518 patient 390 CoV-2 367 ACE2 359 covid-19 309 RNA 198 Fig 191 MERS 189 China 174 PCR 148 figure 137 cell 115 protein 114 virus 106 RBD 64 CoV 62 infection 61 IFN 54 Wuhan 53 Coronavirus 52 respiratory 51 drug 47 vaccine 45 disease 42 IL-6 40 TMPRSS2 39 Health 38 human 37 HCQ 36 case 36 ELISA 35 clinical 33 dna 33 HIV 32 Hong 31 child 31 Kong 30 coronavirus 28 HLA 27 severe 27 health 27 PPE 25 ICU 25 ARDS 24 study 23 acute 23 CD8 23 3CL 22 viral Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 118364 patient 78025 infection 73662 cell 72033 virus 67978 % 60714 protein 60617 study 58995 coronavirus 55263 disease 46819 case 29270 syndrome 27900 response 27341 treatment 27294 antibody 25845 analysis 24944 sample 24915 datum 24704 day 24099 time 23708 risk 23524 result 22476 receptor 22311 symptom 22109 drug 21110 transmission 20232 level 19651 outbreak 19139 effect 18913 test 18757 health 18708 vaccine 17998 lung 17873 system 17871 pandemic 17503 number 17118 group 17023 author 16679 model 16290 gene 16128 rate 15850 host 15765 figure 15746 sequence 15626 activity 15515 factor 15341 expression 15194 pneumonia 15152 control 14808 assay 14615 use Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 190929 SARS 107772 CoV-2 69264 COVID-19 41718 al 36803 CoV 32956 et 31962 . 24952 ACE2 23441 RNA 20553 China 14761 PCR 14187 MERS 13935 Coronavirus 13581 S 13471 Fig 11267 Wuhan 10037 de 9991 RT 8740 Health 8326 • 8202 T 7656 M 7407 C 7389 Table 7307 RBD 6424 Disease 5742 la 5273 IFN 5117 CT 4760 March 4759 East 4731 N 4699 y 4693 S1 4647 II 4537 IL-6 4485 Middle 4449 IgG 4382 sha 4223 TMPRSS2 3870 World 3849 IgM 3774 J 3771 HIV 3744 ARDS 3731 Hong 3719 el 3650 DOI 3611 Kong 3549 Syndrome Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 51846 we 43157 it 13756 they 7994 i 5071 them 2936 he 1955 us 1841 she 1078 itself 953 you 822 one 729 themselves 150 him 129 me 125 her 74 ourselves 63 mg 49 nsp10 44 himself 36 ours 36 mcr-9 33 oneself 32 em 30 his 27 yourself 26 herself 25 nsp15 23 myself 23 covid-19 19 s 19 mrnas 17 ha3 15 nsp7 14 's 11 ≥100 11 igg1 10 p3ile 10 mine 10 imagej 10 iga1 10 https://doi.org/10.1101/2020.08 10 https://doi.org/10.1101/2020.06.02.20120345 9 ya 9 u 9 cft 8 theirs 7 impdh2 6 rrbd-15 6 qag-2 6 pdcs Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 576727 be 119542 have 57432 use 34941 show 30162 include 25332 report 22713 associate 22558 base 19190 bind 18969 increase 18091 infect 18053 do 17445 find 16034 suggest 15976 identify 15833 cause 14193 provide 14109 compare 14092 follow 13393 perform 13170 develop 12776 induce 12326 test 12231 confirm 12002 reduce 11955 require 11857 detect 11525 observe 11303 consider 11267 indicate 10680 relate 10427 make 10267 lead 9753 know 9380 describe 9163 contain 8739 treat 8635 result 8611 present 8468 give 8467 demonstrate 8434 inhibit 8226 need 8179 determine 8144 express 8049 occur 7985 remain 7812 involve 7737 reveal 7724 obtain Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 52000 not 49283 respiratory 46070 viral 41779 severe 41198 - 38373 clinical 38217 high 37427 also 33017 acute 31784 human 31558 other 25714 more 23993 covid-19 22257 such 19625 positive 19547 however 19211 low 17728 novel 17606 immune 17418 well 16842 first 16704 different 16334 only 16009 most 14676 specific 14052 potential 13227 new 13197 early 12799 available 12328 further 12073 non 12017 as 11900 anti 11893 inflammatory 11819 negative 11067 antiviral 10608 large 10596 important 10502 several 10277 infectious 10223 possible 10144 significant 9616 similar 9529 many 9517 therefore 9132 molecular 9067 thus 8502 single 8352 effective 8299 then Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 5186 most 2678 least 2626 high 2198 good 1658 Most 1065 large 817 low 603 late 405 great 296 early 259 bad 247 strong 245 close 155 big 147 short 128 long 95 small 86 near 80 steep 71 young 67 new 57 old 53 fast 40 common 39 safe 36 simple 27 weak 22 poor 22 easy 19 deadly 17 few 14 Least 13 hard 13 deep 12 wide 11 sick 10 quick 9 n(t 9 dark 8 tough 8 mild 8 fine 8 broad 8 N95s 7 slow 7 severe 7 postt 7 nonsevere 7 heavy 6 tremeGENE Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 10823 most 2116 least 358 well 48 hard 41 worst 40 highest 18 long 10 lowest 9 early 7 fast 4 ha3g 4 close 3 vrna 3 shortest 3 greatest 3 furthest 3 -tag 2 ® 2 topmost 2 oldest 2 latest 2 fewest 2 cfdna 2 8his 2 -hla 1 ß1b 1 www.womenshealthconf.org 1 top-100 1 slowest 1 poorest 1 nab 1 mir-1273d 1 leftmost 1 inhibitionofsars 1 ifn)-alpha 1 http://metascape.org/gp/index.html#/main/step1 1 easiest 1 cov-2 1 aunps 1 -uk 1 -rapamycin 1 -not 1 -j 1 -i 1 -human 1 -detect 1 -conh 1 -3.9 Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 2848 doi.org 223 orcid.org 195 www.who.int 136 github.com 95 www.cdc.gov 87 www 83 www.ncbi.nlm.nih.gov 62 www.gisaid.org 56 creativecommons.org 42 coronavirus.jhu.edu 39 clinicaltrials.gov 37 www.rcsb.org 32 www.frontiersin.org 29 www.mdpi.com 29 www.fda.gov 28 www.worldometers.info 27 creat 26 www.biomedcentral.com 26 nextstrain.org 25 www.ebi.ac.uk 25 tools.iedb.org 24 dx.doi.org 22 pubs.acs.org 22 doi 18 www.nature.com 18 crdd.osdd.net 17 www.cbs.dtu.dk 17 creativecommons 16 covid19.who.int 16 artic.network 14 blast.ncbi.nlm.nih.gov 13 www.proteinatlas.org 12 swissmodel.expasy.org 11 pubchem.ncbi.nlm.nih.gov 11 bit.ly 10 www.who 10 www.dovepress.com 10 mc.manuscriptcentral.com 9 wwwnc.cdc.gov 9 www.medrxiv.org 9 www.epicentro.iss.it 9 www.ecdc.europa.eu 9 www.ddg-pharmfac.net 9 bigd.big.ac.cn 8 www.nhc.gov.cn 8 www.chictr.org.cn 8 www.bmj.com 8 www.biorxiv.org 8 web.expasy.org 8 apps.who.int Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 147 http://doi.org/10.1101 110 http://doi.org/10.1101/2020.04 106 http://doi.org/10 86 http://www 40 http://www.gisaid.org/ 32 http://doi.org 27 http://doi.org/10.1101/2020.09.07.20187666 27 http://creat 26 http://coronavirus.jhu.edu/map.html 24 http://doi.org/10.1101/2020.02 23 http://doi.org/10.1101/2020.11.04.20225888 23 http://creativecommons.org/licenses/by/4.0/ 22 http://doi.org/10.1101/2020.03.04.20031112 22 http://doi 21 http://doi.org/10.1101/2020.09.28.20203257 21 http://doi.org/10.1101/2020.02.03.20020263 20 http://doi.org/10.1101/2020.07.06.20147082 19 http://doi.org/10.1101/2020.08.07.20170258 19 http://doi.org/10.1101/2020.05.14.20102491 18 http://doi.org/10.1101/2020.06.28.20141945 18 http://doi.org/10.1101/2020.04.14.20060160 18 http://doi.org/10.1101/2020.03.04.20029538 18 http://creativecommons.org/ 17 http://www.who.int/ 17 http://doi.org/10.1101/2020.11.04.20226282 17 http://creativecommons 16 http://www.gisaid.org 16 http://doi.org/10.1101/2020.11.05.20226555 16 http://doi.org/10.1101/2020.08.23.20180125 15 http://www.worldometers.info/coronavirus/ 15 http://doi.org/10.1101/2020.11.02.20224485 15 http://doi.org/10.1101/2020.10.26.20219907 15 http://doi.org/10.1101/2020.10.15.20213108 15 http://doi.org/10.1101/2020.09.03.20187732 15 http://doi.org/10.1101/2020.08.24.20180877 15 http://doi.org/10.1101/2020.07.27.20162321 14 http://www.ncbi.nlm.nih.gov/ 14 http://doi.org/10.1101/2020.10.11.20210849 14 http://doi.org/10.1101/2020.10.09.20209858 14 http://doi.org/10.1101/2020.10.03.20205278 14 http://doi.org/10.1101/2020.09.03.20179598 14 http://doi.org/10.1101/2020.08.20.20178541 14 http://doi.org/10.1101/2020.08.18.20177303 14 http://doi.org/10.1101/2020.05.28.20116400 14 http://doi.org/10.1101/2020.05.24.20111963 14 http://doi.org/10.1101/2020 13 http://www.who.int/emergencies/diseases/novel-coronavirus-2019 13 http://www.rcsb.org/ 13 http://www.biomedcentral.com/1471-2105/15/333 13 http://doi.org/10.1101/2020.11.10.20229146 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 7 support@bmj.com.visi 4 research@f1000.com 4 journals.permissions@oup.com 3 consortiumcontact@cogconsortium.uk 2 support@bmj.com 2 qincf@bmi.ac.cn 2 ovidstudie@usz.ch 2 lung-network@humancellatlas.org 2 josemariabarrioslopez@gmail.com 2 jassi2param@gmail.com 2 ewilson@gastro.org 2 ciii@cpha.ca 2 shivsarin@gmail.com 1 zouzui1980@163.com 1 zlshi@wh.iov.cn 1 zkontos@ioi-investment.com 1 zhengw@musc.edu 1 zhaoyunhe@medmail.com.cn 1 zhangxiaoyuprc@163.com 1 zhangxiaoyu@shphc.org.cn 1 ykhan@datamonitor.com 1 yee_sin_leo@ttsh.com.sg 1 yangyuan@tmu.edu.tw 1 yangxiuhong@ncst.edu.cn 1 xgkong@hvri.ac.cn 1 wwahyunawang@gmail.co 1 wvadot@ch-annecygenevois.fr 1 wuhaibing@shphc.org.cn 1 wolfram.henn@uks.eu 1 wlan66@126.com 1 wenqiangyu@fudan.edu.cn 1 wei_xu@ttsh.com.sg 1 wangyc@nifdc.org.cn 1 wangchaofu@126.com 1 walgate@scienceanalysed.com 1 vonbrunn@mvp.uni-muenchen.de 1 vjimenezy@salud.madrid.org 1 vivek.gupta@mq.edu.au 1 vishwa.dixit@yale.edu 1 unurhayati@ina-respond.net 1 underthelens@bioch.ox.ac.uk 1 toshiiba@juntendo.ac.jp 1 tmandelclausen@health.ucsd.edu 1 thilagavathir@yahoo.com 1 testai@uic.edu 1 teshima@med.hokudai.ac.jp 1 teresa.lambe@ndm.ox.ac.uk 1 teresa.desoto@salud.madrid.org 1 sxdevara@texaschildrens.org 1 subhadip.basu@jadavpuruniversity.in Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 319 coronavirus indicating person 201 data are available 188 cov-2 infected patients 165 cells were then 161 patients did not 146 study did not 121 study has several 118 studies have also 109 cov-2 is not 97 study are available 88 patient did not 85 ace2 is also 85 patients tested positive 79 cov-2 test results 78 studies did not 77 covid-19 is not 76 samples were then 73 infection causes neuronal 73 infection is not 73 patients were more 73 samples were positive 71 patients were not 68 covid-19 is higher 67 cov-2 is highly 65 virus is not 63 patients were also 61 samples were negative 61 virus was not 60 coronavirus causing severe 57 cov-2 infected individuals 57 patients are more 57 samples were also 56 cov-2 has not 55 ace2 is highly 55 covid-19 is still 55 patients were male 55 study was not 53 protein is also 53 rna was not 52 cov-2 is more 52 results are consistent 49 cov-2 was not 49 data were available 48 cov-2 is still 48 patients do not 48 studies are necessary 47 cov-2 is also 46 data do not 46 patients are not 46 patients were positive Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 19 study had no role 14 data were not available 13 data are not available 11 cov-2 is not yet 10 response is not as 9 cases was not enough 9 infection is not yet 8 cov-2 has not yet 8 rna does not necessarily 7 covid-19 is not only 7 data are not yet 6 cov-2 are not yet 6 cov-2 is not detectable 6 infection has not yet 6 study are not publicly 6 virus has not yet 6 virus is not yet 5 ace2 is not only 5 cov-2 is not clear 5 data are not sufficient 5 data have not yet 5 disease is not yet 5 infection is not clear 5 infection is not well 5 patient had no fever 5 patient had no history 5 patient had no significant 5 patients have not yet 5 protein is not essential 5 results showed no significant 5 studies have not yet 5 study found no significant 4 % had no comorbidities 4 cells did not significantly 4 cov-2 is not as 4 cov-2 is not completely 4 cov-2 is not only 4 covid-19 are not fully 4 covid-19 is not well 4 covid-19 is not yet 4 infection does not significantly 4 infections are not yet 4 patients had no history 4 patients had no symptoms 4 response was not significantly 4 results do not necessarily 4 results were not available 4 rna was not detectable 4 studies showed no significant 4 study found no difference A rudimentary bibliography -------------------------- id = cord-298989-qk0k2lmz author = , Umesh title = Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target date = 2020-05-13 keywords = CoV-2; SARS; ligand summary = title: Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. SARS-CoV-2 main protease, a potential drug target, crystal structure (PDB-ID: 6Y84) was available and used for docking simulation and identification of potential drug molecule form Indian spices. Details of various kinds of interaction shown between the amino acids near the active site of SARS-CoV-2 main protease along with their respective inhibitor constant (Ki) and biological source and binding energy. Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study doi = 10.1080/07391102.2020.1763202 id = cord-282449-7mxp3sdy author = A, Amouroux title = Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date = 2020-05-04 keywords = PCR; SARS summary = Abstract COVID-19 can severely affect pregnant women and the issue of vertical transmission of sars-cov-2 has also emerged. Sars-cov-2 could be recovered by real-time (RT) PCR from nasal and throat swabs, sputum and feces of symptomatic patients including neonates but not from vaginal swabs, amniotic fluid, placenta, cord blood, neonatal blood or breast milk. Detection rates of real-time PCR and the interpretation of IgM and IgG antibodies levels in cord and neonatal blood are discussed in relation with the immaturity of the fetal and neonatal immune system. Based upon RT-PCR identification of SARS-CoV-2 virus, early reports from China suggested that intrauterine vertical transmission was unlikely 1 . Total (Ab) and IgG antibodies seem to be acquired over 2 weeks'' in infected individuals from the onset of symptoms and the introduction of SARS-CoV-2 serology is a rapidly evolving field of research and much-needed aid in the management of the pandemic. doi = 10.1016/j.ajog.2020.04.039 id = cord-308615-4fobikeh author = AKTAS, Busra title = Gut-lung axis and dysbiosis in COVID-19 date = 2020-06-21 keywords = COVID-19; SARS summary = Although SARS-CoV-2 mainly causes lung infection, gastrointestinal symptoms described in COVID-19 patients and detection of the viral RNA in feces of infected patients drove attentions to a possible fecal-oral transmission route of SARS-CoV-2. This review points out the role of dysbiosis of the gut microbiota involving in sepsis, on the severity of SARS-CoV-2 infection. Due to the common symptoms, indicating respiratory tract disease, of patients infected with SARS-CoV-2, the main organ effected by the COVID-19 seems to be lung. In addition to the data detecting viral RNA in feces previously, these results suggest that SARS-CoV-2 infection does not remain with the respiratory tract only and the gastrointestinal system contribute to the course of the disease as well. However, with the limited data until today, it is hard to propose a fecal-oral transmission route to explain the enteric symptoms in COVID-19 patients and claim that SARS-CoV-2 pass through stomach and reach intestine to infect the intestinal cells as enteric viruses accomplish. doi = 10.3906/biy-2005-102 id = cord-279435-ffgd2ets author = ALBalawi, Hani B title = COVID-19: Precautionary Guidelines for Ophthalmologists date = 2020-06-25 keywords = COVID-19; SARS; patient summary = Healthcare providers, particularly ophthalmologists, are at high risk of a COVID-19 infection through unprotected contact with eye secretions during routine ophthalmic examinations that involve the use of direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that allows for close doctor-patient contact. In fact, ophthalmologists are at high risk of contracting the COVID-19 virus through unprotected eye contact with secretions during routine ophthalmic examinations with direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that has close doctor-patient contact. A three-stage control measure to reduce the transmission of the virus in the ophthalmology department in Hong Kong was based on text messaging to reschedule refill visits [6] ; a triage to identify patients with fever, conjunctivitis, and respiratory symptoms; asking those who recently traveled to areas infected with the virus to postpone their ophthalmology visits for 14 days; and the avoidance of micro-aerosol generating procedures, nasal endoscopy, and operations under general anesthesia. doi = 10.7759/cureus.8815 id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 keywords = HMPV; HRV; PCR; RNA; RSV; SARS; child; infection; respiratory; virus summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. doi = 10.1016/b978-0-443-06668-9.50064-8 id = cord-273726-24mi50rv author = Aaroe, Ashley title = Potential Neurologic and Oncologic Implications of the Novel Coronavirus date = 2020-04-16 keywords = SARS summary = It is one of seven coronaviruses that are known to infect humans, along with SARS-CoV1, MERS-CoV, and four endemic species that cause cold-like symptoms (229E, OC43, NL63 and HKU1). Human coronavirus species have been detected in CNS samples of patients with MS as early as the 1980s in autopsy studies [3] , and also in the CSF of children with acute disseminated encephalomyelitis. A similar phenomenon may be evident in SARS-CoV2, as an estimated 63% of COVID-19 patients develop lymphopenia, and recent data shows a trend to worsened lymphopenia in patients with CNS symptoms compared with those without [5] . A preliminary report describes a case of acute myelitis following SARS-CoV2 infection [9] . Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. Acute myelitis after SARS-CoV-2 infection: a case report. The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients doi = 10.1093/neuonc/noaa096 id = cord-340581-ngwgb3y0 author = Abassi, Zaid title = ACE2, COVID-19 Infection, Inflammation, and Coagulopathy: Missing Pieces in the Puzzle date = 2020-10-06 keywords = ACE2; Ang; SARS summary = Angiotensin-converting enzyme is expressed on the plasma membranes of various cell types, including alveolar and intestinal epithelia, vascular endothelial cells in the heart, kidney, and testis, and on macrophages, where it catalyzes the production of Ang 1-7 and its likely paracrine activity (Crackower et al., 2002; Hamming et al., 2007; Santos et al., 2008; Clarke and Turner, 2012; Abassi et al., 2020c) . In this context, testosterone has been described to induce ACE2 expression, the receptor entry of the SARS-CoV-2 infection, but also exerts protective effect against lung injury (Kuba et al., 2005) . FIGURE 2 | Physiology of coronavirus disease 2019 (COVID 19) homing to target host cells expressing ACE2: viral spike-domains enable attachment to cellmembrane-bound ACE2. Thus, viral cellular invasion and replication, initially facilitated by ACE2 and in particular under conditions characterized by enhanced ACE2 expression, later lead to diminution of cell membrane-attached ACE2, and likely increase circulating sACE2 (Figures 2, 3) . doi = 10.3389/fphys.2020.574753 id = cord-257820-4qmajxtb author = Abate, Giulia title = Impact of COVID-19 on Alzheimer’s Disease Risk: Viewpoint for Research Action date = 2020-08-21 keywords = ACE2; Alzheimer; SARS summary = On the other hand, we cannot exclude that, in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) positive subjects, the virus infection could have long-term consequences, leading to chronic medical conditions such as dementia and neurodegenerative disease. Based on the belief that the tissue distribution of host receptors are generally consistent with the tropism of the virus [35] , ACE2 expression and its modulation in CNS might aid in dissecting the invasion rate and distribution of SARS-CoV-2 in the brain area. Recently, in the UK Biobank Community Cohort (n = 451,367), the ApoE e4e4 (homozygous) genotype was also found associated with an increased risk of severe COVID-19 infection, independent of preexisting dementia, cardiovascular disease, and type-2 diabetes [81] . All of these hypotheses about the theoretical impact of SARS-CoV-2 brain infection on Alzheimer''s disease risk are summarized Table 1 . Theoretical impact of SARS-CoV-2 brain infection on Alzheimer''s disease risk. AD, Alzheimer''s disease; Aβ, Beta-amyloid; ACE2, Angiotensin-Converting Enzyme 2; NO, nitric oxide. doi = 10.3390/healthcare8030286 id = cord-288403-m6qe57he author = Abbas, K. M. title = Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa date = 2020-05-26 keywords = Africa; SARS; covid-19 summary = First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month Covid-19 risk period without catch-up campaigns. Specifically, we conducted a benefit-risk analysis of vaccine-preventable deaths averted by sustaining routine childhood immunisation in comparison to excess Covid-19 deaths from SARS-CoV-2 infections acquired by visiting routine vaccination service delivery points. The central estimates for benefit-risk ratio at the household level show the child deaths averted by continuing the routine childhood immunisation programmes (1-dose MCV1, RCV1, MenA, YFV for 9-month-old children) per excess Covid-19 death caused by SARS-CoV2 infections acquired in the vaccination service delivery points. doi = 10.1101/2020.05.19.20106278 id = cord-322789-9elfpx0e author = Abbaspour Kasgari, Hamideh title = Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial date = 2020-08-19 keywords = COVID-19; SARS; group summary = title: Evaluation of the efficacy of sofosbuvir plus daclatasvir in combination with ribavirin for hospitalized COVID-19 patients with moderate disease compared with standard care: a single-centre, randomized controlled trial 29 We therefore conducted a randomized controlled trial in adult patients hospitalized with COVID-19 in Ghaem Shahr Razi Hospital to evaluate the efficacy and safety of sofosbuvir and daclatasvir in combination with ribavirin compared with standard care. This study was a single-centre, randomized clinical trial to evaluate the effectiveness of sofosbuvir/daclatasvir with ribavirin against controls who received standard of care for COVID-19 at the time of the study. This randomized trial found that the combination of sofosbuvir/ daclatasvir/ribavirin compared with standard care showed limited clinical improvement in moderate COVID-19 patients. To our knowledge, this is the first clinical trial of sofosbuvir/ daclatasvir/ribavirin in COVID-19 patients; however, there are limitations to our study. doi = 10.1093/jac/dkaa332 id = cord-285486-99trkti1 author = Abd-Elsalam, Sherief title = Hydroxychloroquine in the Treatment of COVID-19: A Multicenter Randomized Controlled Study date = 2020-08-14 keywords = COVID-19; HCQ; SARS summary = Univariate logistic regression analysis showed that HCQ treatment was not significantly associated with decreased mortality in COVID-19 patients. So, adding HCQ to standard care did not add significant benefit, did not decrease the need for ventilation, and did not reduce mortality rates in COVID-19 patients. 1. Hydroxychloroquine group: This group included 97 patients who received HCQ 400 mg twice daily (in day 1) followed by 200 mg tablets twice daily added to the standard of care treatment adopted by the Egyptian MOH for 15 days. 18 Although cardiac toxicity is a known adverse event requiring monitoring during treatment, HCQ showed promise in treating SARS-CoV-2-infected patients with multiple comorbidities including coronary artery disease. 12 studied the change in symptom severity over 14 days in nonhospitalized patients between HCQ and control groups and did not find any significant difference (P = 0.12). doi = 10.4269/ajtmh.20-0873 id = cord-298722-rmibv5z7 author = Abdel-latif, Rania G title = Statin therapy and SAR-COV-2: an available and potential therapy? date = 2020-05-07 keywords = SARS summary = 4 In fact, some observational data suggest that moderate dose statin therapy was associated with lower mortality among patients with influenza pneumonia. 9 Host ACE2 receptors utilized by SARS-CoV-2 might be potential targets for viral therapeutic intervention. 10 Clinical studies are encouraged to investigate the effect of ACE2 expression in protection against respiratory distress and the role of statin therapy for this postulated hypothesis. Further clinical studies are warranted to evaluate the efficacy of statin therapy against COVID-19 and determine the effective therapeutic dose. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region, Italy Cardiovascular implications of fatal outcomes of patients with coronavirus disease 2019 (COVID-19) Statins reduce the expression of proinflammatory cytokines in influenza A virus infected CrFK cells A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury doi = 10.1093/ehjcvp/pvaa050 id = cord-347516-linjv64o author = Abdelaziz, Osama S. title = Neuropathogenic human coronaviruses: A review date = 2020-07-20 keywords = SARS; neurological summary = authors: Abdelaziz, Osama S.; Waffa, Zuraiha However, there are reports of neurological findings in HCoV infections, particularly in patients infected with the novel severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) amid Coronavirus disease 2019 (COVID‐19) pandemic. 26, 29 Reports of neuromusculoskeletal disorders, complicating HCoV infections and COVID-19, postulate that myopathies and neuropathies are a result of the significantly elevated inflammatory cytokines in patients'' sera leading to virus-induced immune damage. 20, 24, 32, 33 This primary neurotropism could be further supported by the recent reports of the occurrence of olfactory and/or taste disorders, as early atypical manifestations of SARS-CoV-2, which may precede the onset of full-blown clinical COVID-19 in more than onethird of patients. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome doi = 10.1002/rmv.2118 id = cord-330994-6nu7utu1 author = Abdelrheem, Doaa A. title = The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation date = 2020-10-01 keywords = 3TNT; SARS; compound; study summary = title: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. [6] So, we study the inhibitory effect of some bioactive compounds obtained from natural sources against SARS-CoV-2-3CLpro and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT). The crystal structures of SARS-CoV-2-3CLpro (PDB code: 6LU7) and main proteases of SARS-Coronavirus (Mpro) with (PDB IDs: 2GTB and 3TNT) were downloaded from the Protein Data Bank (www.pdb.org), and any heteroatoms and water molecules were removed before molecular docking studies. Based on our molecular docking analysis we found that among all studied compounds, caulerpin has the highest binding affinity against all studied receptors 6LU7, 3TNT, and 2GTB with compared to some proposed antiviral drug currently used in COVID-19 treatment. doi = 10.1080/10934529.2020.1826192 id = cord-337302-fpz2jfuj author = Abdihamid, Omar title = The Landscape of COVID-19 in Cancer Patients: Prevalence, Impacts, and Recommendations date = 2020-09-23 keywords = COVID-19; China; SARS; cancer; patient summary = 21 Similar to cases seen during the MERS-outbreak where having cancer was identified as a risk factor for MERS-CoV mortality, the COVID-19 pandemic also poses threats to cancer patients. 23 In one of the early data by Yu et al published in JAMA Oncology, the infection rate of SARS-CoV-2 in cancer patients from Wuhan, China, was at 0.79% (12 of 1524 patients; 95% CI, 0.31.2%). 15 In a retrospective cohort study of 28 COVID-19infected cancer patients with laboratory-confirmed COVID-19 from three hospitals in China, a total of 15 (53.6%) patients had severe outcomes with a mortality rate of 28.6%. Patients'' age, tumor type, underlying comorbidities, stage of the disease, and treatment type all affect the risk and outcomes of contracting SARS-CoV-2 in cancer patients. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.2147/cmar.s272008 id = cord-299422-s5evsj96 author = Abdollahi, Alireza title = The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types date = 2020-05-23 keywords = ABO; SARS; blood summary = CONCLUSION: Similar to several previous studies about other viral diseases'' association with ABO histo-blood groups, we have concluded that an individual''s ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. Previous researches have proved the potential role of ABO blood groups on a host''s genetic susceptibility to various viral diseases such as influenza, Ebola, enteric viruses, and SARS-CoV infections (8) (9) (10) (11) (12) . In the present study, 397 COVID-19 patients and 500 normal controls were analyzed to evaluate the association of the ABO histo-blood group phenotypes with COVID-19 disease in the Iranian population. Further studies are required to determine the exact mechanism through which ABO blood group influences COVID-19 susceptibility, which could be helpful in patient management and disease control. However, our results were discordant regarding the ABO histo-blood antigens which make people susceptible to COVID-19 (AB versus A histo-blood group phenotype in Iran and China, respectively). doi = 10.30699/ijp.2020.125135.2367 id = cord-319184-voc0eqb9 author = Abduljalil, Jameel M. title = Laboratory diagnosis of SARS-CoV-2: available approaches and limitations date = 2020-06-14 keywords = CoV-2; SARS summary = Clinical 397 evaluation of the cobas SARS-CoV-2 test and a diagnostic platform switch during 48 398 hours in the midst of the COVID-19 pandemic Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-406 19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro Rapid and visual detection of 2019 458 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal 459 amplification assay Transcription Loop-Mediated Isothermal Amplification Assays Targeting SARS-CoV-2 Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of 467 SARS-CoV-2 Development of a reverse 469 transcription-loop-mediated isothermal amplification as a rapid early-detection method for 470 novel SARS-CoV-2 Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Development and clinical application of a 500 rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Novel Antigen-Based Rapid Detection Test for the Diagnosis of SARS-CoV-2 in Serological immunochromatographic 525 approach in diagnosis with SARS-CoV-2 infected COVID-19 patients doi = 10.1016/j.nmni.2020.100713 id = cord-031061-48xwfr9i author = Abdullah, Abdullah title = Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 date = 2020-08-16 keywords = SARS; convalescent; covid-19 summary = title: Innate Immune-mediated Antiviral Response to SARS-CoV-2 and Convalescent sera a potential Prophylactic and Therapeutic Agent to Tackle COVID-19 The convalescent sera of the recovered COVID-19 patients are containing antiviral neutralizing antibodies and is used therapeutically for infected individuals by SARS-CoV-2 and for the purpose of prophylaxis in exposed individuals. Three SARS-CoV-1 infected patients were treated with 500ml of convalescent sera, the reduction in viral titer and mortality were recorded (39) . Three MERS infected patients were also treated with Convalescent or Passive antibody therapy, two of them produce nAbs and remaining one not (40) , this study highlights the limitation in using of convalescent sera it means that the recovered individual may not have enough titer of nAbs (41) . The available information on the use of convalescent sera or passive immunization for the treatment of SARS-CoV-2 suggests that early administration of convalescent serum reduces viral abundance and was found safe. doi = 10.1093/abt/tbaa019 id = cord-280939-d478p8u6 author = Abe, Kento T. title = A simple protein-based surrogate neutralization assay for SARS-CoV-2 date = 2020-10-02 keywords = ACE2; ELISA; RBD; SARS; Supplemental summary = Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). SARS-CoV-2 ELISAs are performed by immobilizing a recombinantly produced viral antigen (such as the spike trimer or RBD) ( Figure 1B and Supplemental Figures 1 and 2; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.142362DS1) (see Methods) onto multiwell plastic plates that are then incubated with diluted patient serum or plasma samples. doi = 10.1172/jci.insight.142362 id = cord-336870-nirg3269 author = Abebe, Endeshaw Chekol title = The newly emerged COVID-19 disease: a systemic review date = 2020-07-08 keywords = COVID-19; China; SARS summary = The novel COVID-19 infection, caused by a beta coronavirus called SARS-CoV-2, is a new outbreak that has been emerged in Wuhan, China in December 2019. i. If a patient with a severe acute respiratory infection (fever, cough, and requiring admission to hospital), and with no other etiology that fully explains the clinical presentation and a history of travel to or residence in a country/area or territory reporting local transmission during the 14 days prior to symptom onset, OR ii. It is caused by a novel beta-coronavirus, resulting from genetic recombination, called SARS-CoV-2, The most common symptoms of COVID-19 are fever, cough, and dyspnea. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.1186/s12985-020-01363-5 id = cord-315641-bzfrd7xj author = Abenavoli, Fabio Massimo title = Plastic Surgery in the Age of Coronavirus date = 2020-06-16 keywords = China; Italy; SARS summary = [24] [25] [26] The ability of the Chinese authorities to build hospital facilities for infected patients within a very short time appeared to be a test of "strength." However, little attention was paid to the conclusions that should have been drawn about how to assist new patients during the emergency situation. Severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2), which results in a high percentage of infected patients, has been enormously difficult to manage. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study From SARS to COVID-19: a previously unknown SARS-related coronavirus (SARS-CoV-2) of pandemic potential infecting humans-call for a One Health approach 2019-nCoV (Wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness Isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-nCoV) outbreak doi = 10.1097/gox.0000000000002957 id = cord-033311-e5axxrm1 author = Abenza Abildúa, M.J. title = Myopathy associated with serious SARS-CoV-2 infection() date = 2020-10-07 keywords = SARS summary = 1,2 Reports of neurological symptoms associated with the infection are increasingly frequent, and include cases of Guillain-Barré syndrome, stroke, intraparenchymal haemorrhage, and cerebral thrombosis. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] We present the case of a 45-year-old woman with no relevant history who was admitted to the ICU due to severe respiratory insufficiency secondary to bilateral pneumonia, with positive nasal swab PCR results for SARS-CoV-2; therefore, the patient met the World Health Organization criteria for COVID-19. The muscle study showed positive sharp waves at rest, reduced motor unit potential amplitude and duration, and no polyphasia, especially in the abductor digiti minimi and the tibialis anterior (Fig. 2) . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS-CoV2 infection: causality or coincidence? Guillain-Barré syndrome associated with SARS-CoV2 Patients with COVID-19 and neurological manifestations show indetectable SARS-CoV2 doi = 10.1016/j.nrleng.2020.07.004 id = cord-324856-hf969tav author = Abir, Tanvir title = Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys date = 2020-07-21 keywords = Bangladesh; COVID-19; Cov-2; SARS summary = title: Factors Associated with the Perception of Risk and Knowledge of Contracting the SARS-Cov-2 among Adults in Bangladesh: Analysis of Online Surveys Since the sheer illness of the whole country is sufficient to destroy the health care system, this current study is to examine changes of individual perception of risk for contracting SARS-Cov-2, and the awareness level in Bangladesh during the early and late lockdowns implemented by the government of Bangladesh. In this study, males who were worried about contracting SARS-Cov-2 were more likely to perceive themselves as being at high risk of contracting the infection, as well as those who did not quarantine themselves or only did so at the request of the public health officers. Moreover, in India, it was found that a higher level of knowledge on COVID-19 was associated with the high-risk perception of contracting the infection during the consistent lockdown period [28] . doi = 10.3390/ijerph17145252 id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 keywords = HLA; SARS; epitope; protein summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach doi = 10.1101/2020.10.14.339689 id = cord-353523-gwud4bb7 author = Abobaker, Anis title = The Eye: A Possible New Route of Infection in COVID-19 date = 2020-07-27 keywords = SARS summary = 1 This might indicate that the eye is not a potential target for coronaviruses; however, this does not rule out the possibility that the conjunctiva and the ocular mucous membrane could act as a port of entry to CoVs to the upper respiratory tract given the close anatomical proximity and the similar epithelial receptors. There is evidence that lack of eye protection in clinical settings increased the risk of infection of the severe acute respiratory disease (SARS) caused by SARS-CoV. The low frequency of conjunctivitis and corneal involvement in COVID-19 patients could be explained with the fact that the level of ACE2 expression in ocular tissues is much less compared with other organs, such as the lungs and kidneys. SARS-CoV-2 has been detected by PCR in conjunctival swabs taken from COVID-19 patients with conjunctivitis as well as patients without ocular LETTER TO THE EDITOR manifestations. SARS-CoV-2 in the ocular surface of COVID-19 patients doi = 10.1017/dmp.2020.270 id = cord-284398-rhfwbyav author = Aboubakr, Hamada A. title = Stability of SARS‐CoV‐2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review date = 2020-07-14 keywords = SARS; covid-19 summary = In another study, aerosolized SARS-CoV-2 retained its infectivity for a period of 16h at room temperature and the authors concluded that the virus can be considered as an airborne pathogen (Fears et al., 2020 and was infectious after 72 hr of aerosolization (Ijaz, Brunner, Sattar, Nair, & Johnson-Lussenburg, 1985) . In the first study, SARS-CoV-2 retained its infectivity for 4 days but was completely decayed after 7 days on plastic surface at room temperature and 65% RH (Chin et al., 2020) . Although this study reported longer virus survival, it has been shown that the survivability of SARS-CoV-1 on plastic surface is drastically affected by increases in temperature and RH as described below. In another study, a this virus with a higher initial load (5.5 log TCID 50 ) retained its infectivity for 4 days and was completely inactivated after 7 days on stainless steel at room temperature and RH of 65% (Chin et al., 2020) . doi = 10.1111/tbed.13707 id = cord-340687-99ad1rwq author = Abourida, Yassamine title = Management of Severe COVID-19 in Pregnancy date = 2020-07-27 keywords = COVID-19; SARS; patient summary = The scarcity of data concerning pregnant patients gravely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) makes their management difficult, as most of the reported cases in the literature present mild pneumonia symptoms. Herein, we outline a case of severe COVID-19 infection in a pregnant woman abruptly rupturing her membranes and undergoing cesarean delivery. Herein, we report the case of a healthy parturient infected with SARS-CoV-2 in her third trimester, whose condition deteriorated leading to premature rupture of membranes, a premature birth via a caesarian delivery, and neonatal death. It is noteworthy that recent reports highlighted elevated SARS-CoV-2 antibody levels (IgM and IgG) and abnormal cytokine test results 2 hours after birth in a neonate born to a mother with COVID-19 via a caesarian delivery, whereas RT-PCR tests on nasopharyngeal swabs taken were negative [20] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn doi = 10.1155/2020/8852816 id = cord-264915-g5ar0pwb author = Abrams, Rory M.C. title = Severe rapidly progressive Guillain-Barré syndrome in the setting of acute COVID-19 disease date = 2020-07-27 keywords = GBS; SARS summary = There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS). We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss diagnostic and management issues and complications that may warrant special consideration in similar patients. There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of Guillain-Barré syndrome (GBS) (Guidon and Amato 2020) . We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss management dilemmas that may warrant special attention in similar patients. doi = 10.1007/s13365-020-00884-7 id = cord-331790-0w0pjjg1 author = Abu Jawdeh, Bassam G. title = COVID-19 in Kidney Transplantation: Outcomes, Immunosuppression Management and Operational Challenges date = 2020-07-17 keywords = COVID-19; KTR; SARS summary = This review summarizes the published COVID-19 literature as it relates to outcomes and immunosuppression management in kidney transplant recipients. These multiple studies have elucidated that COVID-19 is a systemic disease that often manifests with gastrointestinal (GI) symptoms, liver injury, cardiac involvement, encephalitis, atypical stroke, acute kidney injury (AKI) in addition to endothelial cell injury and coagulopathy -the likely mediators of multi-organ involvement (3) (4) (5) (6) (7) (8) . In a 36-patient study, the median age was 60 years, 72% were male, 39% were African American and 75% received deceased-donor kidney transplants (DDKT)(9). Notably, the Columbia transplant program adopts an early steroid withdrawal strategy, however their sample was enriched with patients on prednisone maintenance (67%) which confirms the plausible role of enhanced immunosuppression as a susceptibility factor. doi = 10.1053/j.ackd.2020.07.004 id = cord-287459-k9x3z2h1 author = Abu-Farha, Mohamed title = The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date = 2020-05-17 keywords = COVID-19; SARS; lipid; viral summary = Since lipids play a crucial function in the viral life cycle, we asked whether drugs targeting lipid metabolism, such as statins, can be utilized against SARS-CoV-2 and other viruses. Similarly, increased expression of age-dependent phospholipase A2 group IID (PLA2G2D), an enzyme that usually contributes to anti-inflammatory/pro-resolving lipid mediator expression, resulted in worsened outcomes in aged mice infected with SARS-CoV, suggesting that inhibition of such factor could represent a potential therapeutic option [36] . Of high relevance to this review and the ongoing COVID-19 pandemic is the role of lipid rafts in viral entry into the host cells. Taken together, these studies suggest a beneficial impact for statins and potentially other lipid-lowering drugs such as PCSK9 inhibitors for treatment of COVID-19, especially that of the most severely infected people which are suffering from cardiovascular disease and diabetes [55] . doi = 10.3390/ijms21103544 id = cord-262090-nbxzyjvf author = Acharya, Arpan title = SARS-CoV-2 Infection Leads to Neurological Dysfunction date = 2020-05-23 keywords = SARS; covid-19 summary = A number of neurological disease complications have been seen following infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Such central nervous system (CNS) signs and symptoms linked to laboratory-confirmed SARS-CoV-2 infection is often life threatening. As cardio-respiratory impairments could reflect brainstem dysfunction it may, in part, be responsible for ARDS as frequently occurs as a cause of COVID-19 mortality among SARS-CoV-2 infected patients (Netland et al. As the impaired ability to smell and test are a common manifestation of respiratory neurotropic viral invasion of the olfactory system, we suspect there is a possibility that SARS-CoV-2 can infect the olfactory system and may enter the CNS using the olfactory pathway. A retrospective study substantiates this, wherein, 36.4% of patients out of 214 confirmed cases of SARS-CoV-2 have been documented to present with varying degree of neurological manifestations that include skeletal muscle injury, delirium and acute cerebrovascular disease (Fig. 2) . doi = 10.1007/s11481-020-09924-9 id = cord-276350-lcl9jn35 author = Acharya, Dhiraj title = Dysregulation of type I interferon responses in COVID-19 date = 2020-05-26 keywords = IFN; SARS summary = In a mouse model of SARS-CoV infection, local IFN responses in the lungs were delayed relative to peak viral replication, which impeded virus clearance and was associated with the development of CRS 5 . By contrast, IFNAR inhibition enhanced the recruitment of neutrophils to the lungs in MERS-CoV-infected mice, leading to elevated production of pro-inflammatory cytokines 6 . While patients with severe COVID-19 showed profound depletion and functional exhaustion of NK cells 8 , it is unclear whether this NK cell dysfunction is due to dysregulation of IFN responses. It is thus tempting to speculate that the deficient or dysregulated IFN responses elicited by SARS-CoV-2 infection may influence the generation of T reg cells during the recovery phase of COVID-19. Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice doi = 10.1038/s41577-020-0346-x id = cord-315982-iuez41zj author = Achdout, Hagit title = COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date = 2020-10-30 keywords = DMSO; SARS; assay; cell; plate summary = title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. The COVID Moonshot project has focused on progressing early fragment-screening results into potent compounds with activity against both the main protease and the virus. The rationales for each design include docking-based approaches, by-eye structure-based designs, machine learning approaches, crawling of the past literature on SARS and MERS compounds, and other general medicinal-chemistry insights that can be visualised at https://postera.ai/covid. At 24 h post-seeding, cell culture medium was discarded, cells were washed twice with PBS and infected with SARS-CoV-2 at an MOI of 0.01 in the presence of six concentrations of the inhibitors (25 M -0.06 M). doi = 10.1101/2020.10.29.339317 id = cord-266307-w56rii2p author = Acheampong, Desmond Omane title = Male Predisposition to Severe COVID-19: Review of Evidence and Potential Therapeutic Prospects date = 2020-09-09 keywords = ACE2; ADT; SARS; covid-19; female summary = The sex hormones, estrogens and androgens which exist in varying functional levels respectively in females and males are cited as the underlying cause for the differential immune response to COVID-19. In this review efforts are made to expand understanding and explain the possible roles of the immune system, the sex hormones and the angiotensin-converting enzyme (ACE) systems in male bias to severe COVID-19. Hence, females known for producing high-level estrogen will be better protected against infections including COVID-19 compared to their male counterparts. Hence, women are better protected against viral infections and for that matter the severe COVID-19 due to the over-expression of TLR7 in females compared to their male counterparts. This explains J o u r n a l P r e -p r o o f why prolong inflammation is very common in males infected with SARS-CoV-2 virus compared to females, and could be one of the factors that promote severe COVID-19 in men. doi = 10.1016/j.biopha.2020.110748 id = cord-280819-z6ucnwk0 author = Achilonu, Ikechukwu title = Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach date = 2020-09-02 keywords = COVID-19; SARS; drug; ligand summary = title: Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach The SARS-CoV-2 main protease (M(pro)) is an attractive target towards discovery of drugs to treat COVID-19 because of its key role in virus replication. Using 6Y2G and the prior knowledge that protease inhibitors could eradicate COVID-19, we designed a computational study aimed at identifying FDA-approved drugs that could interact with M(pro). We used HTVS, induced-fit ligand docking and molecular dynamics simulation studies to identify additional classes of plausible FDA-approved drugs as possible drug candidate to treat COVID-19. In conclusion, we have used a computational approach which includes HTVS, IFD, MM/GBSA free binding energy calculations and MD simulation to study potential drug candidates for COVID-19. Targeting the SARS-CoV-2 main protease using FDA-approved Isavuconazonium, a P2-P3 α-ketoamide derivative and Pentagastrin: an in-silico drug discovery approach Ikechukwu Achilonu 1 * doi = 10.1016/j.jmgm.2020.107730 id = cord-293304-kakxmc14 author = Achutha, A. S. title = Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors date = 2020-09-22 keywords = HCQ; SARS; cys145; energy summary = The interactions with the active site residues especially with Cys145 and His41, which are involved in catalytic diad for proteolysis, make these compounds potent main protease inhibitors. Molecular docking studies with the 3CL pro protein were performed to analyze the drug likeness as well as to correlate the binding energy of the docked complex with various physicochemical properties of the active molecules, which will aid in the design of new anti-COVID-19 medicatives. By using the formulated regression Model 2, we predicted the binding energy of some primaquine analogs obtained from the literature and PubChem database and then carried out their molecular docking studies on 3CL pro target to check the inhibitory potency of the ligands, given in Table 4 . Thirty molecules that showed lower binding energies were subjected to molecular docking analysis to identify the potent 3CL pro inhibitors (Supplementary Figure S5) . doi = 10.1021/acs.jproteome.0c00683 id = cord-292050-x3isowrt author = Ackerman, Emily E. title = Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning date = 2020-09-26 keywords = HIN; SARS; SCARB1 summary = Based on network topology and controllability, 16 proteins involved in translation, cellular transport, cellular stress, and host immune response are predicted as regulators of the SARS-CoV-2 infected cell. Screenings of experimentally verified SARS-CoV-2 interacting host proteins [7] have elucidated key infection mechanisms which, when compared to drug databases, have predicted a range of possible targets for repurposing. To assess whether the robust controllability classifications of the driver and virus interacting proteins are a result of the network''s connectivity structure, a randomization analysis was performed as developed in previous work [11] . The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. The eight critical virus interacting proteins of the HIN become intermittent in the VIN, losing some control over infected network regulation. doi = 10.3390/v12101087 id = cord-271915-nvilxnzl author = Adachi, D. title = Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date = 2004-12-01 keywords = PCR; SARS summary = The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada. This single-tube RT-PCR is based on consensus primers targeting conserved regions of coronavirus genome sequences and allows for the detection and species identification of several coronaviruses including SARS-HCoV, with high analytical sensitivity. Aliquots of a 10-fold serial RNA dilution prepared from a lung biopsy sample of a patient with SARS (see Section 2) were used to compare our assay with the RealArt HPA coronavirus RT-PCR (Artus GmbH). doi = 10.1016/j.jviromet.2004.07.008 id = cord-271419-v6dfel3l author = Adachi, Shun title = Commentary: Origin and evolution of pathogenic coronaviruses date = 2020-04-21 keywords = RNA; SARS summary = Among viruses, some coronaviruses (CoVs) are notorious for causing the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The said article has successfully predicted today''s COVID-19 outbreak by pointing out that novel pathogenic variants will readily emerge from very diversified severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) of the bat origin through their close coexistence and high genetic recombination ability (Figure 1) . Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. Thus, to consider the origin of new pathogens and the prevention of their transmission to humans, and control of the viruses, not only studies on SARS-CoV, MERS-CoV, and SARS-CoV-2, but also those on their relatives SARSr-CoVs and MERSr-CoVs are recommendable for bats tracked for the ecology and evolution. doi = 10.3389/fimmu.2020.00811 id = cord-296331-i4hyzqcv author = Adapa, Sreedhar title = COVID-19 Pandemic Causing Acute Kidney Injury and Impact on Patients With Chronic Kidney Disease and Renal Transplantation date = 2020-06-04 keywords = AKI; CRRT; SARS; covid-19; patient summary = COVID-19 infection causes acute kidney injury (AKI) and is an independent risk factor for mortality. The impact of COVID-19 infection on chronic kidney disease (CKD) and renal transplant patients is also discussed in the manuscript. Acute kidney injury (AKI) was seen in 5-15% of the cases infected with SARS-CoV and MERS-CoV, and had a higher mortality rate of 60-90% as per the literature [12] . We summarized the finding from multiple studies including patient characteristics, co-morbidities, incidence of AKI in general as well as ICU/severely ill patients, number of patients requiring continuous renal replacement therapy (CRRT), extracorporeal membrane oxygenation (ECMO) and mortality in Table 2 [9-11, 13, 19, 22-24, 26-32] . Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.14740/jocmr4200 id = cord-027649-6xn9swsq author = Addetia, Amin title = Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates date = 2020-06-23 keywords = SARS summary = title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates Sequence reads were trimmed using Trimommatic v0.38 (5) , aligned to the SARS-CoV-2 reference genome (NC_045512.2) using BBMap (https://sourceforge.net/projects/bbmap/), trimmed of synthetic PCR primers using Primerclip (https://github.com/swiftbiosciences/primerclip) if appropriate, and visualized in Geneious v11.1.4 (6) . Interestingly, ORF6 of SARS-CoV-2 interacts with the mRNA export proteins NUP98 and RAE1, and may inhibit cellular translation (10) . We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization An 81 nucleotide deletion in SARS-CoV Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein A SARS-CoV-2 protein interaction map reveals targets for drug repurposing A 227-nucleotide deletion beginning at nt 27,524 was identified in b) WA-UW-5812 and resulted in the fusion of ORF7a and ORF7b. doi = 10.1016/j.jcv.2020.104523 id = cord-336022-b2fwktld author = Addetia, Amin title = Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate date = 2020-08-14 keywords = August; SARS; international summary = Only three 34 crewmembers tested seropositive prior to the boat''s departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Only three 34 crewmembers tested seropositive prior to the boat''s departure in initial serological 35 screening and also had neutralizing and spike-reactive antibodies in follow-up assays. Prior to the ship''s departure, crewmembers were screened for active SARS-CoV-2 182 infection by RT-PCR, or for serological evidence of prior or ongoing infection using the 183 Abbott Architect assay which detects antibodies against the viral nucleoprotein (N). . https://doi.org/10.1101/2020.08.13.20173161 doi: medRxiv preprint observed in humans who have been infected with SARS-CoV-2 within the previous few 198 months (29, 34, 35) . . https://doi.org/10.1101 pre-departure Abbot Architect anti-N serological screening, since only individuals 335 positive in that screening were subjected to additional serological assays for anti-spike 336 and neutralizing antibodies. doi = 10.1101/2020.08.13.20173161 id = cord-336585-19vwpjkt author = Adem, Şevki title = Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19 date = 2020-08-22 keywords = COVID-19; SARS summary = Based upon these results, we have screened a library of caffeic acid derivatives (CAFDs) (Figure 1 ) for the identification of novel natural anti-COVID-19 compounds against various SARS-CoV-2 drug targets including COVID-19 M pro (6LU7), SARS-CoV-2 S2 subunit (6LXT), Nsp15 endoribonuclease (6VWW), SARS-CoV-2 spike ectodomain open state structure (6VYB), and SARS-CoV-2 spike closed state glycoprotein structure (6VXX). Our results present in silico-based identification of khainaoside C, 6-O-Caffeoylarbutin, khainaoside B, khainaoside C and vitexfolin A as potent modulators of COVID-19 M pro , Nsp15, coronavirus fusion protein, spike open state and closed state structure respectively. Based on these in-silico results, khainaoside C, calceolarioside B, vitexfolin A, calceolarioside C and scrophuloside B exhibited best binding potential with COVID-19 virus Figure 2B represents residual wise van der Waals interactions, piNelfinavir which possess MolDock score of -148.413 The interactions of these compounds with amino acid residues of target protein are shown in Figure 3A . doi = 10.1016/j.phymed.2020.153310 id = cord-315193-z6v6s46n author = Adhikari, Nilanjan title = Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches date = 2017-07-14 keywords = QSAR; SARS; compound; table summary = In the present report, quantitative structure-activity relationships (QSARs) techniques have been explored to understand the relation between the SARS-CoV 3CL pro and HRV 3C pro enzyme inhibitory activity with the physicochemical and structural properties of these inhibitors developed till now. (2008) reported some cinanserin analogs as SARS-CoV 3CL pro inhibitors (Table 11 .18), for which the QSAR model obtained was as shown by Eq. (2013b) reported a series of dipeptide-type SARS-CoV 3CL protease inhibitors (Table 11 .27) whose activity was shown to be controlled by the molar refractivity (CMR) and the polar volume (Pol Vol) of the compounds [Eq. QSAR models exhibited that the physicochemical parameters, such as dipole moment, PSA, polar volume, hydrophobicity, molar refractivity, SA, and molecular volume of the compounds play a crucial role in controlling both SARS-CoV 3CL pro and HRV 3C pro inhibitory activities. doi = 10.1016/b978-0-12-809712-0.00011-3 id = cord-341701-zropd3mo author = Adhikari, Subash title = A high-stringency blueprint of the human proteome date = 2020-10-16 keywords = Chr; Fig; SARS; hpp; human; pe1; protein; proteome summary = During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. • Be a focal point for life sciences researchers, pathologists, clinicians and industry communities seeking to translate and leverage proteomic and proteogenomic data to improve human health through: (i) greater understanding of the molecular mechanisms of common and rare diseases, (ii) identification of pathophysiological changes to generate disease and wellness diagnostic biomarkers, and (iii) development of new effective and safe personalized therapeutics. The HPP Ab Resource Pillar, ostensibly led by the Human Protein Atlas (HPA; www.proteinatlas.org), was initiated in 2003 and uses Ab-based strategies to analyse spatio-temporal aspects of the proteome 39 . Community encouragement to identify biological data that complement high-stringency MS strategies to accelerate discovery and understanding of human proteome PE2,3,4 missing proteins. doi = 10.1038/s41467-020-19045-9 id = cord-298693-x25r0gtt author = Advani, Sonali D. title = Are we forgetting the “universal” in universal masking? Current challenges and future solutions date = 2020-07-16 keywords = SARS summary = Overall, HCP compliance with protective measures such as universal masking often correlates with the level of risk they perceive. Earlier this year, public health authorities pointed out a lack of evidence related to the use of universal masking by the general public to prevent acquisition of SARS-CoV-2. Inconsistent, contradictory and unclear advice from public health authorities has contributed to widespread confusion about the utility of universal masking in preventing the spread of SARS-COV-2 (response efficacy). COVID-19 fatigue, a term that describes drift in following preventative measures as this pandemic goes on, is an important cause of poor compliance with policies related to universal masking. Finally, we need clear, simple, and consistent messaging from public health authorities for successful implementation of universal masking policies. Our goal should be to focus on the simple message of universal masking to prevent the transmission of SARS-CoV-2. doi = 10.1017/ice.2020.333 id = cord-323596-dh7oh54z author = Advani, Sonali D. title = Assessing severe acute respiratory coronavirus virus 2 (SARS-CoV-2) preparedness in US community hospitals: A forgotten entity date = 2020-10-07 keywords = SARS; hospital summary = Several differences in hospital preparedness for SARS-CoV-2 emerged with respect to personal protective equipment conservation strategies, protocols related to testing, universal masking, and restarting elective procedures. Hence, we conducted a cross-sectional survey of SARS-CoV-2 preparedness among community hospitals in southeastern United States. The survey included 13 questions related to PPE availability, crisis capacity strategies to extend and reuse PPE, policies related to restarting surgeries, testing prior to elective surgery and prior to transfer to extended care facilities, universal masking, and daily screening of hospital staff. In addition, 80% of hospitals reported an adequate supply of N95 respirators, face shields, and googles, likely due to use of crisis capacity strategies to extend, reuse, and reprocess these PPE. We found several differences in community hospital preparedness for SARS-CoV-2 with respect to type of conservation strategies used to preserve PPE, protocols related to testing, masking, and restarting elective procedures. doi = 10.1017/ice.2020.1238 id = cord-354762-3a3a3ku9 author = Afsar, Cigdem Usul title = SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES date = 2020-06-02 keywords = IFN; SARS summary = title: SARS-CoV-2 (COVID-19): INTERFERON-EPSILON MAY BE RESPONSIBLE OF DECREASED MORTALITY IN FEMALES IFN is particularly expressed in epithelial cells and it is essential in skin and mucosal immunity (lung, intestines and reproductive tissues) of all African and Asian pangolin species (Choo and others, 2016) . IFN, like the other type I IFNs, might be responsible of decreased mortality in females because of its antiviral effects. The JAK/STAT pathway responds to type I IFN secreted from neighboring cells and SARS-CoV proteins have been shown to affect this pathway before (Frieman and Baric, 2008) . JAK-STAT signal blocking by baricitinib (a selective JAK1 and JAK2 inhibitor) produces an impairment of IFN-mediated antiviral response, with a potential facilitating effect on the evolution of SARS-CoV-2 infection. Interferon-epsilon protects the female reproductive tract from viral and bacterial infection doi = 10.1016/j.jri.2020.103154 id = cord-253777-h8wy0coq author = Afshar, Hale title = Evolution and resolution of brain involvement associated with SARS- CoV2 infection: A close Clinical – Paraclinical follow up study of a case date = 2020-05-21 keywords = SARS; covid-19 summary = We report a para-infectious encephalitis patient with clinical, laboratory, and imaging findings during evolution and convalescence phase of coronavirus infection. Herein we report a case with clinical (including respiratory and neurological), laboratory, chest Computed Tomography and Brain Magnetic Resonance Imaging (B-MRI) findings during evolution and convalescence phase which can illuminate the natural history of similar cases. These results led to the diagnosis of para-infectious encephalitis associated with COVID-19 and treatment with IVIg continued to a total dosage of 3g/kg of body weight (250g total) which resulted in considerable improvement in consciousness, but discontinued because of headaches (day 28). Our patient before diagnosis of neurologic involvement had received IVIg (25 g/day for three days) as a part of treatment for COVID-19 severe pulmonary involvement; and after the CNS lesions were established, it was reinstituted and due to very good clinical and radiological response, we decided to continue IVIg therapy until complete recovery, unless there is a complication. doi = 10.1016/j.msard.2020.102216 id = cord-253970-sbj869yy author = Agarwal, Amit title = Neurological emergencies associated with COVID-19: stroke and beyond date = 2020-08-11 keywords = COVID-19; SARS; patient summary = There is limited knowledge on the neurologic manifestations of COVID-19 at present, with a wide array of neurological complications reported, ranging from ischemic stroke to acute demyelination and encephalitis. The second subset of neurological presentation involves a response to the cytokine storm and multi-system inflammation including acute demyelination, vasculitis, necrotizing encephalopathy, and posterior reversible encephalopathy syndrome. Table 1 provides a summary of the most common (1) vascular complications with stroke secondary to arterial or venous thrombosis, related to the known hypercoagulable state seen in COVID [4, 5, 14] , and (2) much broader gamut including diffuse leukoencephalopathy, acute demyelination, posterior reversible encephalopathy syndrome (PRES), necrotizing encephalopathy, and focal cytotoxic edema, primarily seen as a consequence of systemic inflammation and cytokine storm seen with COVID-19 [6] [7] [8] [9] [10] [11] [12] [13] . The most common neurological presentation reported has been ischemic stroke, secondary to arterial or venous thrombosis, because of the hypercoagulable state associated with COVID-19. doi = 10.1007/s10140-020-01837-7 id = cord-280996-anq680a1 author = Agarwal, Arnav title = High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission date = 2020-06-15 keywords = HFNC; SARS; covid-19; high; patient summary = title: High-flow nasal cannula for acute hypoxemic respiratory failure in patients with COVID-19: systematic reviews of effectiveness and its risks of aerosolization, dispersion, and infection transmission Review 1: we synthesized results from randomized-controlled trials (RCTs) comparing HFNC to conventional oxygen therapy (COT) in critically ill patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. Conclusions High-flow nasal cannula may reduce the need for invasive ventilation and escalation of therapy compared with COT in COVID-19 patients with acute hypoxemic respiratory failure. We conducted two rapid systematic reviews commissioned by the WHO to summarize the evidence for the efficacy, safety, and risk of aerosol generation and infection transmission during HFNC use among patients with acute hypoxemic respiratory failure due to COVID-19. doi = 10.1007/s12630-020-01740-2 id = cord-306465-7kevsl1z author = Agarwal, Krishna Mohan title = Study and Overview of the Novel Corona Virus Disease (COVID-19) date = 2020-09-06 keywords = COVID-19; Coronavirus; SARS summary = In December 2019, a new disease with pneumonia-like symptoms was spreading throughout Wuhan in China which was entitled as novel coronavirus disease or COVID -19 caused by the virus SARS CoV-2. The current global pandemic is caused by the "novel coronavirus disease (2019-nCoV) or severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) popularly known as COVID19 Hunan seafood market was sealed, on 7 th January roughly a week after China''s notification of a possible outbreak the disease was confirmed to be the novel coronavirus disease or COVID-19 which has more than 95% homology with bat coronavirus and almost 70% similarity to the SARS CoV-1 Flatten the curve is a statement used during healthcare emergencies, its basic concept is to limit the spread of the virus such that at any given time during a pandemic the total number of patients required to be hospitalized is less than the maximum capacity of the state''s health infrastructure. doi = 10.1016/j.sintl.2020.100037 id = cord-336702-2qa4u8gv author = Agarwal, Sangya title = Harnessing CAR T-cell Insights to Develop Treatments for Hyperinflammatory Responses in Patients with COVID-19 date = 2020-04-17 keywords = COVID-19; SARS summary = Consistent with HLH, accumulations of macrophages are found in the lungs of patients with COVID-19 ( 9 ) , and HLH has previously been reported in patients with SARS, MERS, and other severe systemic viral infections. Drug treatments used for HLH/MAS and ARDS may also be effective in treating patients with COVID-19. Thus, an urgent need emerges to uncover therapies that may be effective for patients with SARS-CoV-2 infection. Thus, if properly timed in patients after exposure to virus, CSA could serve as a broad-spectrum inhibitor to control SARS-CoV-2 infection and decrease the magnitude of cytokine release. This shows not only the coincidence of treatments that modulate dysfunctional host immune responses, but also the potential complications with overlapping SARS-CoV-2 infections and cancer immunotherapies. This is important because comorbidities from CRS due to CAR T-cell therapy and HLH-like symptoms due to SARS-CoV 2 infection could be fatal. doi = 10.1158/2159-8290.cd-20-0473 id = cord-262361-3f09z5pf author = Agbelele, Penance title = Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case date = 2020-07-30 keywords = SARS summary = title: Use of chest CT-scan images to differentiate between SARS-CoV-2 infection and fat embolism: a clinical case The authors present the case of a young man victim of a traffic accident during the SARS-CoV-2 confinement, having presented a fracture of the femoral shaft that was soon complicated by respiratory failure with oxygen desaturation. This case demonstrates the difficulty of differential interpretation of CT images between fatty embolism and SARS-CoV-2 infection. However, no study has investigated the specific features of CT scans to differentiate fat embolism syndrome from SARS-Cov-2 infection. His condition was further complicated by acute respiratory failure with CT images that may suggest either SARS-Cov-2 infection or a fatty embolism or both. Upon our patient''s arrival during the pandemic, he presented with fever (38°C) and oxygen desaturation (88%) strongly suggestive of a SARS-CoV-2 infection, especially since the signs of fat embolism occur on average at H39 [11, 12] . doi = 10.1016/j.radcr.2020.07.071 id = cord-275506-3t5gf66c author = Agbuduwe, Charles title = Hematolological Manifestations of COVID‐19: From Cytopenia to Coagulopathy date = 2020-07-14 keywords = COVID-19; SARS; patient; severe summary = [45] A retrospective study of COVID-19 patients admitted to ICU identified DVT in 25% with advanced age, lower lymphocyte counts and elevated D-dimers being significant risk factors. [63] Currently, the evidence base for the clinical management of COVID-19 is mostly limited to case series and other relatively small observational studies of hospitalised patients. Similar to findings in SARS patients, [64] lymphopenia is the most commonly reported hematological abnormality in COVID-19 and recent data shows that it can be predictive of disease severity. The use of convalescent plasma may, in addition, provide neutralising antibodies against SARS-CoV-2 and a small-scale clinical trial has reported modest but encouraging results in severely-ill but not in critical COVID-19 patients. In view of the increased thrombotic risk associated with COVID-19, prophylactic anticoagulation with low Accepted Article molecular weight heparin is recommended for all hospitalised patients with the disease and clinical trials are needed to investigate the role of more intensive anticoagulation and other experimental therapies. doi = 10.1111/ejh.13491 id = cord-305788-z75yv88e author = Agergaard, Charlotte Nielsen title = Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date = 2020-09-28 keywords = SARS summary = Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. doi = 10.1016/j.ijid.2020.09.1442 id = cord-269871-w41o1krr author = Aggarwal, Shyam title = High Viral Load and Poor Ventilation: Cause of High Mortality From COVID-19 date = 2020-07-25 keywords = SARS summary = Low viral load in the nasal cavity due to open air ventilation is a plausible reason for this difference. As a result, people living in developed countries tend to build up high viral load in their nasal cavity and nasopharynx. These factors indicate a strong association between high viral load and poor ventilation, which, in turn, leads to high mortality from COVID-19 in developed Western nations. In this article, we have tried to explain that poor ventilation and subsequent buildup of high viral load could be a reason for such a drastic difference in mortality rates among these two groups of countries. 2 These studies suggest an association of high viral load in nasal cavity and nasopharynx with the severity of the disease. For this reason, the viral load in the nasal cavity and the nasopharynx could be lower and result in a less severe disease. doi = 10.1177/1010539520944725 id = cord-297132-lhfa9fl5 author = Aghagoli, Ghazal title = Neurological Involvement in COVID-19 and Potential Mechanisms: A Review date = 2020-07-13 keywords = ACE2; COVID-19; CoV-2; SARS; patient summary = In this review, we synthesize a range of clinical observations and initial case series describing potential neurologic manifestations of COVID-19 and place these observations in the context of coronavirus neuro-pathophysiology as it may relate to SARS-CoV-2 infection. The novel 2019 coronavirus disease (COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) results in a variety of symptoms including fever, cough, and fatigue [1] . The Kawasaki-like syndrome that is now described in young patients following COVID-19 infection and associated with a hyper-inflammatory state is further suggestive of a vascular inflammatory potential of SARS-CoV-2 [48, 49] . Once established in the CNS, SARS-CoV, the virus responsible for Severe Acute Respiratory Syndrome (SARS), has been shown to be capable of inducing rapid transneuronal spread and death of infected neurons in transgenic mice models expressing human ACE2 receptors [63] . doi = 10.1007/s12028-020-01049-4 id = cord-298535-wmxlu3l1 author = Agnihothram, Sudhakar title = Evaluation of Serologic and Antigenic Relationships Between Middle Eastern Respiratory Syndrome Coronavirus and Other Coronaviruses to Develop Vaccine Platforms for the Rapid Response to Emerging Coronaviruses date = 2013-11-18 keywords = HKU; MERS; SARS; VRP summary = In this article, we use alphavirus replicon vaccine vectors to express a panel of recombinant S and N proteins from distantly related alphacoronaviruses and betacoronaviruses, including MERS-CoV and other subgroup 2c CoVs. Using mouse polyclonal antisera and recombinant proteins, we compare the cross-reactivity and neutralization titers of these antisera between distantly related human and bat CoVs. Our results indicate that the S glycoprotein but not the N protein is the major determinant of the neutralizing antibody response to MERS-CoV; that the N proteins of CoVs only cross-react within but not between subgroups; that little if any cross-neutralization or cross-reactivity exists between the S proteins of CoVs within subgroup 2c or any other subgroup; and that cross-neutralization and cross-reactive patterns were validated with the convalescent-phase serum sample from a patient infected with MERS-CoV Hu/England-N1/2012 and a donor panel of human antisera against 3 different HCoVs. Our approach provides critical reagents, antisera, and recombinant virus vaccines that allow for rapid diagnosis of and intervention against MERS-CoV and other zoonotic CoVs that emerge in the future. doi = 10.1093/infdis/jit609 id = cord-334495-7y1la856 author = Agricola, Eustachio title = Heart and Lung Multimodality Imaging in COVID-19 date = 2020-06-24 keywords = COVID-19; CXR; LUS; SARS; patient summary = From a clinical point of view, cardiac involvement during COVID-19 may present a wide spectrum of severity ranging from subclinical myocardial injury to well-defined clinical entities (myocarditis, myocardial infarction, pulmonary embolism and heart failure), whose incidence and prognostic implications are currently largely unknown due to a significant lack of imaging data. The use of integrated heart and lung multimodality imaging plays a central role in different clinical settings and is essential in diagnosis, risk stratification and management of COVID-19 patients. In this context, the use of multiple diagnostic imaging techniques may apply to both heart and lung to provide an integrated assessment of cardiac and pulmonary function and to refine diagnosis, risk stratification and management of COVID-19 patients. patients not requiring ICU, when clinical presentation and biomarker alterations suggest acute-onset myocardial inflammation, if the diagnosis is likely to impact on management, CMR may be considered to confirm acute myocarditis, after exclusion of alternative relevant clinical conditions, including ACS and HF, by means of other rapidly available imaging modalities (i.e. cardiac CT scan or TTE). doi = 10.1016/j.jcmg.2020.05.017 id = cord-352935-kb0i58z1 author = Aguila, Enrik John T. title = Repurposed GI Drugs in the Treatment of COVID-19 date = 2020-06-29 keywords = SARS summary = A recent drug research in Germany has shown that omeprazole interfered viral formation of SARS-CoV-2 beyond therapeutic plasma concentrations at 8 µM [6] . To date, there is still little knowledge on the potential of famotidine and omeprazole as repurposed drugs to treat COVID-19. In their letter, Aguila and colleagues provide an insight into commonly used acid suppressants such as famotidine and omeprazole as the potential agents for drug repurposing against COVID-19. The role of famotidine in interfering maturation of SARS-CoV-2 by inhibiting 2-chymotrypsin-like protein and reduction in inflammation needs to be studied. The authors also note that omeprazole at therapeutic concentration increased the anti-SARS-CoV-2 effects of remdesivir and aprotinin. Therefore, there is a theoretical concern that the use of H2-blockers and PPIs could diminish or abolish the neutralizing effects of gastric acid on SARS-CoV-2, which could potentially increase the risk of GI manifestations and severity in COVID-19. doi = 10.1007/s10620-020-06430-z id = cord-333089-ufyzqgqk author = Aguilar-Pineda, Jorge Alberto title = Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date = 2020-07-29 keywords = ACE2; RBD; SARS; figure; protein summary = Based on the structural complementarity and steric impediments between the S protein and human ACE2 (hACE2) protein membranes, we mapped the glycosylation sites of both models [21] [22] [23] [24] and performed molecular dynamics simulations (MDS) by 250 ns to stabilize the glycosylated SARS-CoV2 spike (S) and hACE2 complex (suppl. Given the possibility that occupancy at glycosylated residues or S-RBD binding sites by estrogens could modify the affinity of the SARS-CoV2 virus and alter entry into the cell thereby reducing infectivity, we sought to further examine these interactions using a range of complementary experimental approaches (see Table S1 ). In an effort to explore the potential protective effects of female sex hormones against SARS-CoV-2 infection, we examined the impact of estradiol (17β-diol) and a dietary-derived phytoestrogen (S-equol) on hACE2 structure and protein expression by a combination of in silico modeling, in vitro, and in vivo analysis. doi = 10.1101/2020.07.29.227249 id = cord-281512-79g22dk6 author = Aguirre, A. Alonso title = Illicit Wildlife Trade, Wet Markets, and COVID‐19: Preventing Future Pandemics date = 2020-07-05 keywords = SARS; animal; market summary = This article will explore the connections among the current pandemic, live-animal markets, the spread of animal-related diseases, and the illicit wildlife trade and will include a set of policy recommendations prescribed to prevent future outbreaks stemming from these issues. It further explains "the identification of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in civet cats and other wild animals in live animal markets suggests that this novel human pathogen emerged as a result of an interspecies transmission" (Poon et al., 2005 (Poon et al., , p. The devastation resulting from the spread of COVID-19 could potentially serve as a future warning for what is to come, if practices such as illicit wildlife trade and wet markets are allowed to continue on a global scale. Research must focus on the central causes of the spread of zoonotic diseases such as illicit wildlife trade and wet markets. doi = 10.1002/wmh3.348 id = cord-337599-dyxfsojh author = Ahamad, Shakir title = Primed for Global Coronavirus Pandemic: Emerging Research and Clinical Outcome date = 2020-09-19 keywords = COVID-19; SARS; severe summary = Under such circumstances, drug repurposing has emerged as a realistic and effective strategy to counter the virus menace in the short run, and several antiviral and antimalarial medicines are currently in different stages of clinical trials. Researchers are also experimenting with nutrients, vitamins, monoclonal antibodies, and convalescent plasma as immunity boosters against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This report presents a critical analysis of the global clinical trial landscape for COVID-19 with an emphasis on the therapeutic agents and vaccines currently being tested at pandemic speed. 166 The Institute of Biotechnology, AMMS, China, registered a randomized, double-blind, 167 placebo-controlled Phase-II clinical trial of recombinant novel coronavirus (2019-nCOV) 168 vaccine (adenovirus vector) in healthy adults aged 18 and above on April 10, 2020, (Table1, 169 Entry 6). Clinical study for safety and efficacy of Favipiravir in the treatment of novel 924 coronavirus pneumonia (COVID-19) Genentech Announces FDA Approval of Clinical Trial for Actemra to Treat 1093 Hospitalized Patients with Severe COVID-19 Pneumonia doi = 10.1016/j.ejmech.2020.112862 id = cord-266948-n7sltd1b author = Ahamed, Jasimuddin title = Severe aortic stenosis patient risk during the COVID-19 pandemic date = 2020-09-14 keywords = COVID-19; SARS summary = The patient risk assessment typically includes patient age and surgical risk; however, given the increased general risk of the procedure and that SARS-CoV-2 infection can be an additional and very dangerous comorbidity, suggesting the less invasive TAVR should be considered. 5 AS patients therefore may have increased risk for developing thromboembolic complications during the valve replacement procedure or during subsequent hospitalisation and recovery if they are infected with SARS-CoV-2. In fact, a recent study showed that a prosthetic aortic graft thrombosis patient died from COVID-19 and that anticoagulant and thrombectomy procedure were unsuccessful. 5 Therefore, direct thrombin inhibitors should be considered for AS patients who test positive for SARS-CoV-2, since both COVID-19 and AS procedure can increase the risk of thrombosis. Studies in animals have suggested that inhibitors of this system can upregulate ACE2 expression, which led some investigators to postulate that patients receiving those inhibitors may be at high risk of contracting a SARS-CoV-2 infection, which needs to be validated experimentally. doi = 10.1136/openhrt-2020-001355 id = cord-328471-oz99upzz author = Ahmad, Jamshaid title = SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date = 2020-07-23 keywords = FDA; RNA; SARS summary = In this global health emergency, drug repurposing (or repositioning) is one of the fast track option that involves screening of existing FDA approved drugs for the identification of potential molecules that can disrupt the function of key proteins of the SARS-CoV-2 and can be used for treatment against COVID-19. Whereas, Demoxytocin showed ten H-bonds with both active site Asp760 and Asp761 and other key residues e.g. Trp617, Tyr619, Lys621, Ser682, Glu811, Lys621, Tyr619, Trp617, Ser682 and Glu811 with dock score -9.68kcal/mol and ligand efficiency of -0.142 (Supplementary Figure S3) . Colistin (polymyxin E, polypeptide antibiotics) showed most of the H-bonding with Lys551, Trp617, Tyr619, Asp618, Ser682, Asp684, Asn691, and both catalytic residues i.e. Asp760, Asp761, with a docking score of -9.24kcal/mol and ligand efficiency of -0.113 (Supplementary Figure S5) . Examorelin, Lypressin, Ornipressin, and Colistin are also common drugs in both form of RdRp. Only one H-bond with His810 and other non-covalent interactions were observed for Examorelin showed a docking score of -12.139 kcal/mol and ligand efficiency of -0.187. doi = 10.1016/j.heliyon.2020.e04502 id = cord-315611-xbj41ekc author = Ahmad, Mohammed title = Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date = 2020-07-14 keywords = Dependent; GTP; Polymerase; RNA; SARS summary = Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. 20−22 In this report, using computer-aided homology modeling, docking, and molecular simulations, we have predicted the protein structure and probable small-molecule inhibitors against SARS-CoV2 RdRp (CoV2-RdRp). Taking together the aforementioned interaction and comparison of the model and experimentally determined structures, we propose the probable initiation complex of CoV2-RdRp bound to RNA and GTP molecules in Figure 2D . Molecular Dynamics simulation studies of the native and ligand-bound complexes of CoV2-RdRp. MD (Molecular dynamics) simulations were performed for the modelled structure of the RdRp protein and docked complexes for the GTP, lead optimized, and FIH compounds for a 50 ns time period. doi = 10.1021/acsomega.0c02096 id = cord-258624-041cf99j author = Ahmad, Sajjad title = Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics date = 2020-05-23 keywords = COVID-19; MEPVC; SARS; epitope; protein; vaccine summary = title: Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. In order to estimate the MMPBSA binding free energies for the receptors and multi-epitope peptide vaccine construct, the MMPBSA.py module [56] of AMBER16 was castoff. The B-cell epitopes predicted for the vaccine candidates were in the following order: nine for Nsp8 and 3C-like proteinase, five for Nsp9, eight for Nsp10, 34 for spike glycoprotein and surface glycoprotein, and four for ORF1ab polyprotein| partial. Molecular interactions and binding conformation of the designed MEPVC with TLR3 and TLR4 innate immune receptors were deciphered via a protein-peptide docking approach. The dynamic simulations of the human immune system in response to the designed vaccine construct were deciphered through C-immsim server [40] . doi = 10.1016/j.ejps.2020.105387 id = cord-295051-upyar7en author = Ahmadian, Elham title = Covid‐19 and kidney injury: Pathophysiology and molecular mechanisms date = 2020-10-06 keywords = ACE2; AKI; SARS; covid-19 summary = The SARS‐CoV‐2‐induced kidney damage is expected to be multifactorial; directly it can infect the kidney podocytes and proximal tubular cells and based on an angiotensin‐converting enzyme 2 (ACE2) pathway it can lead to acute tubular necrosis, protein leakage in Bowman''s capsule, collapsing glomerulopathy and mitochondrial impairment. 6, 7 The initial impact might be the direct role of the virus on the renal parenchyma mediated by activating the angiotensin-converting enzyme 2 (ACE2), which functions as a SARS-CoV-2 receptor. 22 Altogether, these reports clarify that kidney cells are targeted by SARS-CoV-2 and new strategies are needed to treat Covid-19 to prevent organ infection and dysfunction. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Coronavirus disease 19 infection does not result in acute kidney injury: an analysis of 116 hospitalized patients from Wuhan, China Acute kidney injury in SARS-CoV-2 infection: direct effect of virus on kidney proximal tubule cells doi = 10.1002/rmv.2176 id = cord-336049-n3swuykg author = Ahmed, Mubbasheer title = Multisystem inflammatory syndrome in children: A systematic review date = 2020-09-04 keywords = COVID-19; MIS; SARS summary = INTERPRETATION: Multisystem inflammatory syndrome is a new pediatric disease associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is dangerous and potentially lethal. However, in early May 2020, investigators from South Thames Retrieval Service in London, UK published a report describing eight severely ill pediatric patients presenting in hyperinflammatory shock with multiorgan involvement [6] Specifically, the children manifested with high fever, rash, conjunctivitis, peripheral edema, and gastrointestinal symptoms. We included patients with COVID-19 to reinforce to the healthcare community and public the differences in the clinical presentation, to highlight the degree of systemic inflammation in MIS-C, and to iterate the differences in treatment and outcome between the two diseases. Data collected from the studies included demographics, number of patients, signs and symptoms, laboratory markers, imaging results, medications, and outcomes. Cardiac MRI of children with multisystem inflammatory syndrome (MIS-C) associated with COVID-19: case series doi = 10.1016/j.eclinm.2020.100527 id = cord-312722-talu4geh author = Ahmed, Nausheen title = COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient date = 2020-06-13 keywords = SARS; covid-19 summary = title: COVID-19 presenting as a viral exanthem and detected during admission prescreening in a hematopoietic cell transplant recipient 3, 4 As a result of the high mortality in this population, the American Society of Transplantation and Cellular Therapy (ASTCT) recently published guidelines on March 18, 2020, suggesting universal testing of patients before admission for cellular therapy or stem cell transplant to mitigate the risk of transmission and outbreaks in transplant wards. 5 Accordingly, at our institution a policy to screen all patients planned for HCT or cellular therapy the day prior to admission with a nasopharyngeal swab real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2 infection was implemented. 8 The skin rash, such as livedo reticularis and petechial rash have been reported, but our patient''s positive SARS-CoV-2 test and biopsy suggest Covid-19 may also cause a more classic viral exanthem. doi = 10.1016/j.htct.2020.06.002 id = cord-308499-xqmguqyi author = Ahmed, Sakir title = Reply to Rheumatologists’ perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? date = 2020-05-09 keywords = SARS summary = title: Reply to Rheumatologists'' perspective on coronavirus disease 19: is heparin the dark horse for COVID-19? Heparin has multiple possible mechanisms of action which may support its use for COVID-19. SARS coronavirus strain HSR1 multiplication can be directly inhibited by heparin as evidenced by reduction of viral plaques by 50% on addition of heparin to Vero cell cultures [3] . One of the mechanisms of inhibition of cellular entry of SARS coronavirus is via lactoferrin binding [4] . SARS-CoV-2 entry into a cell via the ACE2 receptor leads to shedding of this receptor [6] . Furthermore, RAAS (renin-angiotensin-aldosterone system) activation is linked to thrombosis by multiple mechanisms [9] . Therefore, ACE2 downregulation by SARS-CoV-2 may lead to enhanced thrombosis. To summarize, SARS-CoV-2 can possibly activate the RAAS axis via ACE2 shedding and promote thrombosis. The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 receptor binding domain undergoes conformational change upon heparin binding. doi = 10.1007/s10067-020-05145-w id = cord-290445-vb53bih9 author = Ahmed, Shiek SSJ title = Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date = 2020-04-23 keywords = Fig; SARS; protein summary = Secondly, the viral replication machinery network from SET-B with 332 seed proteins extended to 1486 neighboring proteins with 11438 interacting edges which representing the mechanism attributed to evasion of the SARS-CoV2 genome into the host. Similarly, the viral replication machinery network was acquired with 1522 proteins with 9747 interacting edges showing the complex SARS-CoV-2 mechanism in the human lungs. These common molecules represent the inter-connecting mechanism involved in the transcription machinery, immune response, cell growth and/or maintenance, transport, metabolism, protein metabolism, cell communication and signal transduction that activated upon virus binding and has been subsequently utilized for viral replication process (S5 Table) Also mapping with other viral infection dataset, 50 hub proteins of the replication machinery network have noticed in influenza virus infection (S4 Table) , which suggests SARS-CoV2 and influenza may have a similar mode of host infection machinery [17] . The molecular pathways of interconnecting protein hubs could be the intermediate phase that connects the receptor activation mechanism and viral replication process (Fig 10) . doi = 10.1101/2020.04.20.050138 id = cord-333174-g10kvc0c author = Ahmed, Sinthyia title = Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 date = 2020-07-28 keywords = Mpro; Raltegravir; Remdesivir; SARS summary = title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro. In this study, we employ drug repurposing approach to identify potential candidates which can bind and interact with RdRp and Mpro proteins of SARS-CoV-2. doi = 10.1080/07391102.2020.1796804 id = cord-334299-0zn1z7rc author = Ahmed, Warish title = Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date = 2020-09-30 keywords = RNA; SARS summary = title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In view of this need, we recommend methodological and quality assurance approaches for SARS-CoV-2 RNA detection in 158 wastewater using molecular methods. doi = 10.1016/j.coesh.2020.09.003 id = cord-262673-j2ot35lt author = Ahmed-Hassan, Hanaa title = Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date = 2020-08-18 keywords = COVID-19; IFN; MERS; SARS; cell; respiratory summary = Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells doi = 10.3389/fimmu.2020.01979 id = cord-336671-vfq5ft08 author = Ai, Jing-Wen title = Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date = 2020-03-16 keywords = PCR; SARS summary = Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19. doi = 10.1080/22221751.2020.1738905 id = cord-298991-5qae0ege author = Aiello, Francesco title = Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date = 2020-05-18 keywords = COVID-19; PCR; SARS summary = SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients'' conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. This systematic review will firstly attempt to analyse the current knowledge on SARS-CoV-2 colonization of ocular and periocular tissues and secretions (i.e., cornea, conjunctiva, lacrimal sac, and tears), in order elucidate if conjunctival transmission occurs, and secondarily aims to propose a potential diagnostic tool in the evaluation of suspected, infected patients. Due to the scant evidence, both original articles, editorials, letters, and reviews providing evidence (i.e., prevalence, anecdotal report) about SARS-CoV-2 colonization of ocular and periocular tissues and secretions were all included in the study. This systematic review analysed 252 SARS-CoV-2infected patients globally who underwent conjunctival swab, and demonstrates the prevalence of ocular conjunctivitis complicating the course of COVID-19 to be as high as 32% (12 patients out 38) , differently as what Lu et al. doi = 10.1038/s41433-020-0926-9 id = cord-272113-j82z4q8x author = Akaji, Kenichi title = Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease date = 2020-08-27 keywords = 3CL; CoV; SARS; inhibitor summary = Instead of an exhaustive survey of the inhibitors [21] , we provide an overview of several typical inhibitors, and our recent efforts for the rational design of new scaffolds are discussed based on the inhibitory mechanism and structural interactions with SARS-CoV 3CL pro . Following the interaction with the active center of the SARS-CoV 3CL pro , the nucleophilic Cys145 thiolate generated by a proton-withdrawing effect caused by His41 at the catalytic dyad promotes a typical 1,4-addition to the α,β-unsaturated structure of the Michael acceptor ( Figure 3 ). These data also indicate that the corresponding S1 pocket of the SARS-CoV 3CL pro might accept a simple ring structure containing heteroatoms at this specific interaction site, which provides a clue to our design of a potent substrate-based inhibitor described later in this review. doi = 10.3390/molecules25173920 id = cord-353229-k3zerr83 author = Akca, Ummusen Kaya title = Kawasaki-like disease in children with COVID-19 date = 2020-09-16 keywords = COVID-19; Kawasaki; SARS summary = Herein, we report the characteristics of four patients with Kawasaki-like phenotype associated with COVID-19 from Turkey and analyze the features of similar published cases through a systematic literature review. Diagnosis of complete KD was based on the criteria of the American Heart Association (AHA): the presence of fever for at least 5 days accompanied by the presence of at least four of the following five findings: bilateral non-exudative conjunctival injection, unilateral cervical lymphadenopathy, changes in the lips and oral cavity, skin rash, and changes in extremities, including indurative angioedema and desquamation [18] . Children with persistent fever, inflammation (neutrophilia, high CRP, and lymphopenia), and single or multi-organ dysfunction have been identified in the UK as "Pediatric Multisystem Inflammatory Syndrome in relation to SARSCoV-2 (PMIS-TS)" regardless of the SARS-CoV-2 RT-PCR test results [73] . Pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort doi = 10.1007/s00296-020-04701-6 id = cord-320466-l7017jis author = Akgun, Emel title = Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date = 2020-10-20 keywords = ELANE; MPO; PRTN3; SARS summary = Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified up-regulated proteins Myeloperoxidase, Myeloblastin, Neutrophil Elastase, Cathepsin G, and Azurocidin (MPO, PRTN3, ELANE, CTSG, and AZU1) in nasooropharyngeal swab samples are discussed to highlight the molecular mechanism changes in the site of infection. Pathway analysis of the significantly altered protein levels between COVID-19 positive and negative patients'' naso-oropharyngeal swab samples were analyzed using the STRING online database. In SARS-CoV-2 patients'' naso-oropharyngeal samples, we have identified azurophilic granule (AG) proteins like Myeloperoxidase (MPO), elastase (ELANE), cathepsin G (CTSG), azurocidin 1 (AZU1) and proteinase 3 (PRTN3) to be highly overexpressed. The alterations of various proteins in SARS-CoV-2 infected patients'' naso-oropharyngeal samples depict the molecular changes that govern the host antiviral defense system. doi = 10.1371/journal.pone.0240012 id = cord-325293-nwxtyrpl author = Akhtar, Hubba title = COVID-19 (SARS-CoV-2) Infection in Pregnancy: A Systematic Review date = 2020-07-30 keywords = COVID-19; SARS summary = INTRODUCTION: To review published studies related to the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with pregnancy, foetal, and neonatal outcomes during coronavirus disease 2019 (COVID-19) pandemic in a systematic manner. This study was done according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method identifying published literature on COVID-19 and its potential impact on pregnancy and neonates. The comprehensive literature search was carried out with PubMed, Medline, Scopus, Cochrane database, and Google Scholar, using key MeSH words, which include "COVID-19," "Pregnancy," "Coronavirus 2019," "Newborn," "Foetus," "Neonate," "vertical transmission," and "outcomes." All published articles have been reviewed, and the findings have been included in this study. [6] Clinical analysis of 10 neonates born to mothers with 2019-nCoV pneumonia 9 10 (2 twins) Fever (8) Intrauterine distress (6) Shortness of breath (6) Infections (4) (3) PROM (3) Fever (2) NRDS (2) Sore throat (1) (3) Dyspnoea (1) Sore throat (1) NVD (1) Diarrhoea (1) Unknown as still pregnant (4) Yu et al. doi = 10.1159/000509290 id = cord-291644-5y0ioety author = Akiyama, Tomohiro title = The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond date = 2020-08-29 keywords = COVID-19; IFMC; Japan; SARS; blood; increase summary = title: The Natural-Mineral-Based Novel Nanomaterial IFMC Increases Intravascular Nitric Oxide without Its Intake: Implications for COVID-19 and beyond Since the long-term continuous measurement of intravascular NO was impossible, complementary tests were conducted to determine whether IFMC could increase the surface temperature, blood flow rate, velocity and vessel diameter in the human body. The present study confirmed that the natural-mineral-based novel nanomaterial IFMC, with a size of tens of nanometres (Figure 1 ), could induce an increase of intravascular NO (Figure 3) , vasodilation (vessel diameter) and blood flow rate in a living body (Figure 4) , as well as an increase of the surface temperature of a hand including fingers ( Figure 5 ). To summarise, our inter-and trans-disciplinary approach revealed that the natural-mineral-based novel nanomaterial IFMC can induce an increase of intravascular NO, vasodilation and blood flow rate, as well as an increase of hand surface temperature in a living body. doi = 10.3390/nano10091699 id = cord-313603-y8p9bmph author = Akter, Shahina title = Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh date = 2020-09-24 keywords = Bangladesh; SARS summary = title: Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. After generating a FASTA file from the FASTQ files using the DRAGEN software, it was found that the complete genome sequences of the Bangladeshi SARS-CoV-2 strains (BCSIR_ NILMRC_006, BCSIR_NILMRC_007, and BCSIR_NILMRC_008) have linear RNAs of 29,892 bp, 29,823 bp, and 29,758 bp, respectively, with an average GC content of 39%. The sequences of these SARS-CoV-2 genomes from Bangladesh were submitted to the GISAID database (accession no. We extend special thanks to Architect Yeafesh Osman, Honorable Minister of Science and Technology. Anwar Hossain, Senior Secretary, Ministry of Science and Technology. doi = 10.1128/mra.00764-20 id = cord-302195-25gjbyi1 author = Al Huraimel, Khalid title = SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date = 2020-07-15 keywords = RNA; SARS; covid-19 summary = This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. There is no conclusive evidence for aerosol or faecal-oral transmission of SARS-CoV-2 despite several researchers considering them as plausible routes that may explain the high infectivity and global spread of COVID-19 (Chen et al., 2020; van Doremalen et al., 2020; Wang et al., 2020a) . From the literature studied, concerns of COVID-19 infection through environmental contact pertain mainly to areas that lack proper sanitation and wastewater treatment, lack adequate solid waste management infrastructure, in areas where raw sewage is discharged directly into natural water bodies, and in cities where air pollution is problematic.  Robust evidence is needed to assess impact of air pollution, solid waste management, and sewage contamination of water bodies on COVID-19 spread and infectivity. doi = 10.1016/j.scitotenv.2020.140946 id = cord-304617-5ozf18lg author = Al-Khafaji, Khattab title = Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 date = 2020-05-15 keywords = CoV-2; Mpro; SARS; drug summary = The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. The got protein-drug complex structures from covalent docking were submitted to MD simulations (saquinavir, ritonavir, and remdesivir with SARS-CoV-2 Mpro). The effect of drug-protein interactions upon dynamics of biological system is a fundamental in drug discovery thereby we used RMSD to investigate the influence of saquinavir, ritonavir, and remdesivir upon the stability of SARS-CoV-2 Mpro. One of the more noteworthy findings in this study is that MD simulation analysis that saquinavir, ritonavir, and remdesivir can form stable interaction inside the binding site of SARS-CoV-2 Mpro. doi = 10.1080/07391102.2020.1764392 id = cord-330384-yujbcwg5 author = Al-Mulla, Fahd title = A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date = 2020-05-16 keywords = ACE2; Fig; SARS; TMPRSS2 summary = The increased cleavage activity of this protease was suggested to diminish viral recognition by neutralizing antibodies and by activating SARS spike (S) protein for virus-cell fusion 11 and facilitates the active binding of SARS-CoV-2 through ACE2 receptor, which is a risk factor for a more serious COVID-19 presentation [8] [9] [10] . Recent studies, assessed the genetic variations and eQTL (expression quantitative trait locus) expression profiles in the candidate genes ACE2, TMPRSS2, and FURIN to demonstrate the sex and population-wise differences that may influence the pathogenicity of SARS-CoV-2 9, [15] [16] [17] [18] [19] . Therefore, we screened the genetic variations and eQTL expression of the SARS-CoV-2 candidate genes, ACE2, TMPRSS2 and FURIN in three Middle Eastern populations: Kuwaiti, Iranian, and Qatari and compared them to available MAF data in the gnomAD database 41 . doi = 10.1101/2020.05.16.099176 id = cord-275191-lgze4zex author = Al-Sadeq, Duaa W. title = The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date = 2020-07-02 keywords = SARS; asymptomatic; covid-19 summary = AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. doi = 10.1016/j.ijid.2020.06.098 id = cord-354398-f3cg8gi1 author = Al-Saud, Haya title = Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date = 2020-09-20 keywords = COV-2; RNA; SARS summary = The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. We validated the modified Invitrogen Forensic DNA Purification kit in extracting in-laboratory propagated SARS-COV-2 RNA by conducting manual and automated extractions on titrations from 15 000 copies to 60 copies of SARS-COV-2 followed by RT-qPCR methods: the commercially available TaqPath One-Step qRT-QP-CR kit (using the N, S, and ORF1b genes) and primers and probes from Metabion, Germany to establish an inhouse RT-qPCR assay based on E, RdRp2 and RdRp4 gene detection as per recommended SARS-COV-2 testing from CDC and WHO. doi = 10.5144/0256-4947.2020.373 id = cord-291248-0kuc9jv9 author = Al-Sehemi, Abdullah G. title = Potential of NO donor furoxan as SARS-CoV-2 main protease (M(pro)) inhibitors: in silico analysis date = 2020-07-08 keywords = SARS; X77; figure summary = Herein, we evaluated the phenyl furoxan, a well-known exogenous NO donor to identify the possible potent inhibitors through in silico studies such as molecular docking as per target analysis for candidates bound to substrate binding pocket of SARS-COV-2 M(pro). In the present study to validate the molecular docking, MD simulation and MM-PBSA results, crystal structure of M(pro) bound to experimentally known inhibitor X77 was used as control and the obtained results are presented herein. Docking analysis of the studied furoxan derivatives were found to have similar binding ability to SARS-CoV-2 M pro as compared to reported inhibitors. Residue wise decomposition results confirms that the interacting residues from binding pocket of SARS-CoV-2 M pro as obtained from docking analysis (Table 1 ) also shows significantly higher energetic contribution in binding with potent furoxan derivatives 22, 26 in comparison to control ( Figure 10A -C). doi = 10.1080/07391102.2020.1790038 id = cord-294349-ps3qlho2 author = Al-Sharif, Eman title = Ocular tropism of coronavirus (CoVs): a comparison of the interaction between the animal-to-human transmitted coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV, CoV-229E, NL63, OC43, HKU1) and the eye date = 2020-09-03 keywords = COVID-19; MERS; SARS; ocular; patient summary = PURPOSE: Several studies have reported conflicting results on ocular manifestations and transmission of coronavirus disease 2019 (COVID-19) whose causative virus, SARS-CoV-2, belongs to the coronavirus family, the seventh recognized as a human pathogen and the third causing a severe clinical syndrome. Coronavirus disease 2019, known as COVID-19, is an emerging infection which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first reported in Wuhan city, China, late in December 2019 [4] . Clinical ocular manifestations were absent in all SARS-CoV-1 patients, and viral RNA was detected in the conjunctival secretions and tears in three cases out of 120 (2.5%) with a range of 0-8% [6] [7] [8] [9] . Similarly, a small study testing the conjunctival secretions and tears (collected twice over 2-3 days) of 30 confirmed COVID-19 patients demonstrated the presence of viral RNA (in both samples) in one patient only who also showed clinical signs of conjunctivitis [12] . doi = 10.1007/s10792-020-01575-2 id = cord-345019-i7zm9bt1 author = Al-Waleedi, Ali Ahmed title = The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date = 2020-10-29 keywords = SARS; Yemen; case summary = A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. For early detection of SARS-CoV-2 in Yemen, as in other countries, a case definition, active surveillance, and contact tracing were required [10, 11] . The first 2 months after confirmation of the SARS-CoV-2 epidemic in Yemen was characterized by a 57% hospitalization rate in the southern and eastern parts of the country included in The First 2 Months of the SARS-CoV-2 Epidemic in Yemen our study, 63% of deaths occurring in individuals aged <60 years, confirmatory testing of <50% of the suspected cases, and majority of cases were not related to a defined chain of transmission. doi = 10.1371/journal.pone.0241260 id = cord-289364-p31gt533 author = AlFehaidi, Alanoud title = A case of SARS-CoV-2 re-infection date = 2020-10-25 keywords = SARS summary = Different reports have proposed the reactivation of SARS-CoV-2 infection, with 2 RT-PCR positive results following resolving symptoms and interim RT-PCR negative results [4] [5] [6] [7] [8] [9] [10] [11] . Early studies reported that re-detectable positive virus nucleic acid among patients with SARS-CoV-2 with an average duration of 15 days from discharge to a re-positive results 13 . Patients in those early reports did not show signs of infection with the second positive results and had negative swab results within one week later. The COCOREC (Collaborative study COvid RECurrences) study suggested that recurrence of infection is likely if the patient has two confirmed SARS-CoV-2 RT-PCR positive results over 15 days apart with one major clinical sign and no other cause to explain the symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report doi = 10.1016/j.jinf.2020.10.019 id = cord-309582-ihrj84hr author = AlNaamani, Khalid title = Medical research during the COVID-19 pandemic date = 2020-08-06 keywords = COVID-19; SARS; trial summary = Despite the dedication of enormous resources, the advancement in health care systems and collaboration between different investigators across the world, only a small number of patients over the last decade have in fact benefited from clinical research performed during different outbreaks of respiratory viruses such as was the case for the severe acute respiratory syndrome (SARS), the HIN1 flu virus (swine flu) or the Middle East Respiratory Syndrome. An example of unpublished results that need to be widely acknowledged because of a negative outcome leading to early termination is that of a Brazilian study (CloroCovid19 ) which was a parallel, double-blind, randomized, phase IIb clinical trial, which started on March 23, 2020, aiming to assess safety and efficacy of Chloroquine diphosphate (CQ) in the treatment of hospitalized patients with severe respiratory syndrome secondary to SARS-CoV-2 infection. doi = 10.12998/wjcc.v8.i15.3156 id = cord-104435-y7mxyein author = Alabdulmonem, Waleed title = COVID-19: A global public health disaster date = 2020 keywords = SARS summary = [4] As compared to the previous CoVs, the infectivity rate of SARS-CoV-2 is comparatively much higher, and the mode of transmission of this deadly virus is primarily by respiratory droplets from an infected individual to others through coughing, sneezing within a distance up to 6 feet, or touching of infected surfaces, where the viral particles are present. [9] The transmission of virus can be decreased to a large extent by adopting strict infection control policies, which are basically a team base efforts and everyone has to play their roles. [8, 9] Being an enveloped virus, SARs-CoV-2 is comparatively easy to disinfect; therefore, hands hygiene plays a vital preventive tool from getting infected, washing hands frequently with soap and water or using alcohol-based hand sanitizers to disinfect hands have strongly been recommended by the WHO. Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica) doi = nan id = cord-333080-qytwbsne author = Alahari, Suresh K. title = SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date = 2020-07-28 keywords = RNA; SARS summary = Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. Developing functional computational models and networks to predict potential SARS-CoV -miRNA/lncRNA association may benefit not only the understanding of COVID-19 mechanism at the noncoding RNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis, and prevention. Since multiple ways of interaction between miRNAs, lncRNAs, and mRNA have been reported to play key roles in determining the cellular functions during viral infection, it is essential to discover these interactions in an integrated fashion to comprehensively decipher the networks and key regulatory noncoding-RNA hubs underpinning the pathology of SARS-CoV. Our in-silico analysis has built a network of protein-protein interaction between the Human SARS coronavirus (SARS-CoV) and host proteome (Figure 1) , as well as strong miRNA-mRNA-lncRNA crosstalk ( Figure 4 and Table 2 ) possibly modulating the human response to the viral infection. doi = 10.1016/j.biopha.2020.110548 id = cord-338755-f5g2r4n9 author = Alam, Nawsad title = A spike with which to beat COVID-19? date = 2020-05-15 keywords = SARS summary = This month''s Under the Lens discusses how structural studies of the SARS-CoV-2 spike glycoprotein might guide a path towards a vaccine. Coronavirus spikes have been structurally characterized before, in particular for SARS-CoV and MERS-CoV, two related viruses that have caused epidemics of respiratory disease. Shortly after this, the first structure of a neutralizing antibody bound to the RBD of the spike glycoprotein showed that SARS-CoV-reactive antibodies could neutralize the new virus 3 , and polyclonal antibody sera against SARS-CoV also proved effective 1 . Two spike-based vaccine-design strategies, developed for SARS-CoV, should be applicable. To generate the most effective neutralizing antibody responses, vaccinated individuals should generate antibodies to the pre-fusion spike, thus preventing ACE2 binding and cell entry. For this reason, structure-guided mutations have been designed that fix the SARS-CoV spike into this pre-fusion state 4 . Stabilized SARS-CoV-2 spikes, designed using this method, are therefore promising for a vaccine. doi = 10.1038/s41579-020-0383-2 id = cord-324619-y7gilopu author = Alam, S.B. title = Severe acute respiratory syndrome coronavirus‐2 may be an underappreciated pathogen of the central nervous system date = 2020-07-15 keywords = BBB; CNS; COVID-19; SARS; patient summary = In this review, we examine some of the most recent data of COVID-19-associated neurological disease and the possibility that SARS-CoV-2 may be infecting the CNS. suggested that since SARS-CoV-2 shared significant similarities to severe acute respiratory syndrome coronavirus (SARS-CoV), it was entirely possible that SARS-CoV-2 could similarly penetrate the brain and CNS of infected patients through synapses in the medullary cardiorespiratory center and thereby cause respiratory failure (5) . Similar to these neurotropic HCoVs, SARS-CoV-2 infection in the lungs of some COVID-19 patients may also lead to entry into the CNS and this could occur via two main pathways: i) infection of peripheral nerves and retrograde axonal transport; and/or ii) hematogenous spread and infection of the cells of the blood-brain barrier. In this review, we have extrapolated information from other neurotropic viruses to make some predictions and it is clear that SARS-CoV-2 has the potential to infect the CNS and cause long-term neurologic damage in COVID-19 patients. doi = 10.1111/ene.14442 id = cord-316083-f1h2j6jx author = Alamri, Ahmad title = nan date = 2020-05-21 keywords = SARS; patient summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the origin of the current pandemic of coronavirus disease 2019 (COVID-19) that was identified in hospitalized patients in Wuhan, China, in December 2019 [1] . She reported a total anosmia with an associated dysgeusia that started on the 21 st of March, with no rhinorrhea, no stuffy nose, no fever, no dyspnea, no myalgia nor fatigue, and no swollen lymph nodes on the clinical examination and no other We started olfactory training for both patients, with different aliments like vanilla, lavender, spices and coffee. Here, we have two cases of confirmed SARS-CoV-2 infection, both having isolated anosmia; with a probable context of a worker to worker transmission (with an interval of the onset of symptoms around 24 hours). The fact that both cases were physicians working in the same structure with a possible worker to worker transmission could justify systematic (or focused) screening of health care providers which could drastically minimize the health worker-patient transmission by applying the necessary measures (like home confinement). doi = 10.1016/j.lpm.2020.104027 id = cord-308786-e6rv5csl author = Alamri, Mubarak A. title = Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date = 2020-08-28 keywords = SARS summary = In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL(pro), that can be further developed as potential pan-PL(pro) based broad-spectrum antiviral drugs. Conclusively, the reported SARS-CoV-2 PL(pro) specific compounds could serve as seeds for developing potent pan-PL(pro) based broad-spectrum antiviral drugs against deadly human coronaviruses. Interestingly, the functionally 176 well-conserved catalytic triad residues within the catalytic pockets of PL pro among SARS183 Integrated computational methods comprising virtual high throughput screening, molecular 184 docking, and MD simulation are a significant approach for the exploration of potential 185 inhibitors against a target protein [22, 28, 78, 86] . Pharmacoinformatics and 655 molecular dynamics simulation studies reveal potential covalent and FDA-approved 656 inhibitors of SARS-CoV-2 main protease 3CLpro An integrated structure-based computational approach identified potential inhibitors of SARS-CoV-2 PL pro doi = 10.1016/j.jpha.2020.08.012 id = cord-311415-wwwqqvca author = Alamri, Mubarak A. title = Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) date = 2020-06-24 keywords = GBSA; SARS summary = title: Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro) Molecular dynamics (MD) simulations were utilized to investigate the binding mode of the potential inhibitors at the active site of SARS-CoV-2 main protease. Since the active site of SARS-CoV-2 main protease contains a catalytic cysteine, it is possible to target it with covalently binding compounds. In order to investigate the binding mode of the most promising hit compounds inside the active site of SARS-CoV-2 3CL pro , molecular dynamics (MD) simulations of each complex were performed for a period of 50 ns. (C-E) Representation of the chemical reaction of the reactive thiol group of Cys145 with the reactive nucleophilic group of the hit compounds, and the corresponding covalently docked poses (green sticks) inside the substrate-binding site of SARS-CoV-2 3CL pro (white ribbon presentation, ligand-interacting amino acids are shown in sticks). In Silico discovery of novel inhibitors against main protease (Mpro) of SARS-CoV-2 using pharmacophore and molecular docking based virtual screening from ZINC database doi = 10.1080/07391102.2020.1782768 id = cord-323397-5yop6clu author = Albalate, M. title = Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date = 2020-04-30 keywords = COVID19; PCR; SARS summary = El objetivo de este trabajo es describir la experiencia del primer mes de pandemia por SARS-Cov2 en una unidad hospitalaria de hemodiálisis (HD) que atiende al 2º distrito madrileño con más en incidencia de COVID19 (casi 1000 pacientes en 100000 h). Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19 , de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. doi = 10.1016/j.nefro.2020.04.005 id = cord-278839-uu2wlpmp author = Alberca, Ricardo Wesley title = Pregnancy, Viral Infection, and COVID-19 date = 2020-07-07 keywords = COVID-19; MERS; SARS; infection; maternal; pregnancy summary = In 2009, during the H1N1 flu pandemic, an increased ratio of female to male cases was verified, in which pregnant women developed more complications, as severe acute respiratory syndrome, and higher mortality compared to the general population (30, 31) . Additionally, infection by the Lassa virus in pregnant women shows high levels of placental replication, and the risk of maternal-fetal mortality increases with the duration of pregnancy (38, 39) . At first, contagion occurred through contact with some infected animals but, soon there were the first reports of human-to-human transmission (93), The virus was identified as belonging to the coronaviridae family and was designated SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) (94). Chen and collaborators, verified alteration in calcium and albumin levels in the blood of pregnant women with SARS-CoV-2 infection (124) , which could potentially increase the severity in COVID-19 (125) . doi = 10.3389/fimmu.2020.01672 id = cord-321568-okvt1fg3 author = Alberca, Ricardo Wesley title = Perspective: The Potential Effects of Naringenin in COVID-19 date = 2020-09-25 keywords = COVID-19; NAR; Naringenin; SARS summary = Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic by the World Health Organization in March 2020. Among many compounds, naringenin (NAR) a flavonoid present in citrus fruits has been investigated for antiviral and anti-inflammatory properties like reducing viral replication and cytokine production. In this perspective, we summarize NAR potential anti-inflammatory role in COVID-19 associated risk factors and SARS-CoV-2 infection. Naringenin (NAR) is an important natural flavonoid present in citrus fruits, like grapefruit (43.5 mg/100 mL) and oranges (2.13 mg/100 mL) (19), with a high analgesic, anti-oxidant, anti-inflammatory, anti-tumoral, and anti-viral effect (20-23) (Figure 1) . Further investigations and clinical trials are needed to help understand the role of NAR consumption in humans during a viral infection, especially in SARS-CoV-2 infection and COVID-19. doi = 10.3389/fimmu.2020.570919 id = cord-268492-0rbmqarx author = Alberer, Martin title = Cats and kids: how a feline disease may help us unravel COVID-19 associated paediatric hyperinflammatory syndrome date = 2020-09-02 keywords = FIP; SARS summary = The RCPCH and CDC have published a case definition and scientists refer to this novel but still very rare severe clinical condition in children as "paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2" (PIMS-TS). While reflecting on this syndrome and its characteristic features, some interesting similarities come to mind when comparing the clinical course of PIMS-TS cases and the specific features of a disease in cats called feline infectious peritonitis (FIP) caused by the feline coronavirus (FCoV), an alphacoronavirus [2] . On this note, it would be of great interest to see whether mutations in the viral genome, particularly in regions affecting the S-protein of SARS-CoV-2, could lead to a change in cell tropism enabling the virus to more effectively infect and replicate within human monocytes/macrophages subsequently leading to the clinical picture of PIMS-TS. doi = 10.1007/s15010-020-01515-3 id = cord-352196-rpyoeg9n author = Alberici, Federico title = A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. date = 2020-05-08 keywords = ARDS; SARS summary = title: A report from the Brescia Renal COVID Task Force on the clinical characteristics and short-term outcome of hemodialysis patients with SARS-CoV-2 infection. The main clinical characteristics of the overall MHD population with SARS-CoV2 infection and the subgroups managed as outpatient or in hospital are shown in Table 2 . In our cohort including four centers of the "Brescia Renal COVID task force", we have identified 94 patients with SARS-CoV-2 infection. The finding of worse outcome of hemodialysis patients with SARS-CoV-2 infection may be explained by high prevalence of comorbidities as well as other risk factors related to end stage renal disease per se (2). Management of Patients on Dialysis and With Kidney Transplantation During the SARS-CoV-2 (COVID-19) Pandemic in Brescia A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia doi = 10.1016/j.kint.2020.04.030 id = cord-264828-6w13xo2a author = Albini, Adriana title = The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies date = 2020-05-19 keywords = ACE-2; SARS; ace summary = Older COVID-19-affected patients with cardiovascular comorbidities exhibit a more severe clinical course and a worse prognosis, with many of them being also treated with ARBs or ACE-Is. Another confounding factor is cigarette smoking, which has been reported to increase ACE-2 expression in both experimental models and humans. 4. Renin-angiotensin-aldosterone system (RAAS)-interfering drugs are likely to affect ACE-2 receptor-SARS-CoV-2 interaction dynamics within lung, heart, vascular, kidney and gut tissues [5, 19] , while it is still not completely elucidated how such interactions are relevant to the clinical course of cardiovascular comorbidities in patients with COVID-19 [29] . Consequently, the up-regulation of human ACE-2 induced by RAAS-antagonists in SARS-CoV-2-infected patients could be clinically useful, due to the cardiovascular protection elicited by the increased activity of angiotensin(1-7), thereby attenuating angiotensin II effects on vasoconstriction and sodium retention [31, 34] . doi = 10.1007/s11739-020-02364-6 id = cord-304742-ytf2ilw4 author = Albini, Adriana title = The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based antihypertensive therapies—reply date = 2020-07-14 keywords = ACE-2; SARS summary = The transmembrane protease serine 2 TMPRSS2, an androgendependent enzyme, acts in reinforcing the ACE-2 receptor activity in allowing cell entry to a number of viral pathogens as well as to SARS-CoV-2 as reported in our Point of View [2] . Yet in trisomy 21 individuals a TMPRSS2 protease overexpression has been documented, as mentioned in the comment of Dr De Cauwer [1] , with this leading to an increased viral infection''s rate of susceptible host''s cells and tissues. In conclusion, the interesting comment by Dr De Cauwer points out the complex interactions between ACE-2 and TMPRSS2 with reference to the clinical course of CoViD-19 as well as to SARS-CoV-2 infection''s pathogenic evolution and severity degree in given population segments of infected individuals, like male individuals and Down syndromeaffected patients [1] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACEinhibitor-and angiotensin II receptor blocker-based cardiovascular therapies: comment The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies doi = 10.1007/s11739-020-02436-7 id = cord-310304-f28tjmi8 author = Alcendor, Donald J. title = Racial Disparities-Associated COVID-19 Mortality among Minority Populations in the US date = 2020-07-30 keywords = ACE2; COPD; SARS; covid-19 summary = Maintaining glycemic control in COVID-19 patients is essential, as hyperglycemia could affect pulmonary function, the immune response to infection, and the development of the pro-inflammatory cytokine storm associated with more severe clinical disease ( Figure 1 ). Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Patients who clinically present with normal or high blood pressure may be subject to undue complications related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, upon infection with SARS-CoV-2 the ACE2 protein serves as the entry receptor for the virus and is internalized in the endosome with SARS-CoV-2 during membrane fusion and uptake by Hypothetical model of uncontrolled blood pressure in patients with hypertension and increased risk for complications due to COVID-19. Longstanding health disparities such as diabetes, hypertension, CVD, and pulmonary disease among minority populations in the US may serve to predispose these communities to SARS-CoV-2 infection and increased risk for clinically severe COVID-19. doi = 10.3390/jcm9082442 id = cord-282421-yialyuav author = Alcoba-Florez, Julia title = Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date = 2020-08-01 keywords = SARS summary = In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. doi = 10.1016/j.ijid.2020.07.058 id = cord-297708-uocs65sl author = Alders, N. title = COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected date = 2020-08-22 keywords = August; PIMS; SARS summary = Four distinct groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile illnesses with or without extra-pulmonary organ dysfunction (21%). The relative paucity of data describing SARS-CoV-2 in the paediatric population mandates a broad-arching approach to pandemic planning with preparations put in place to manage a heterogeneous population of patients presenting with a range of single and multi-organ pathology of varying severity. . https://doi.org/10.1101/2020.08.20.20178541 doi: medRxiv preprint Methods All patients aged ≤ 18 years with positive respiratory or nasal SARS-CoV-2 RT-PCR and/or serum IgG (Epitope Diagnostics Inc. TM ) up to 19 th May 2020. Four distinct clinical groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile/viral illness with or without single organ dysfunction (21%). doi = 10.1101/2020.08.20.20178541 id = cord-311965-3x3tjzhi author = Alexander, Jan title = Early Nutritional Interventions with Zinc, Selenium and Vitamin D for Raising Anti-Viral Resistance Against Progressive COVID-19 date = 2020-08-07 keywords = COVID-19; SARS; vitamin; zinc summary = Adequate supply of zinc, selenium, and vitamin D is essential for resistance to other viral infections, immune function, and reduced inflammation. Clinical and subclinical micronutrient deficiencies common in older adults are known to contribute to decreased immune function and age-related diseases [11] , implying that nutritional management is essential to reduce the risk of severe infection [12] . In view of a lack of clinical data on preventive and/or therapeutic efficiency of the nutritive adequacy of selenium, zinc, and vitamin D in COVID-19, we, in the present narrative review, discussed recent clinical data on the role of these micronutrients in the protection against bronchopulmonary infections, as well as the existing indications of their impact on COVID-19. We did a literature search for the period 2010-2020 on PubMed, Medline, and Google Scholar with the keywords of SARS, SARS-CoV-2, COVID 19, coronavirus, micronutrients (zinc, selenium, vitamin D), immune system, inflammation, prevention, and treatment. doi = 10.3390/nu12082358 id = cord-322660-bis2arbu author = Alexander, Regi title = Guidance for the Treatment and Management of COVID‐19 Among People with Intellectual Disabilities date = 2020-06-10 keywords = COVID-19; England; SARS; care; people summary = The guidelines cover specific issues associated with hospital passports, individual COVID‐19 care plans, the important role of families and carers, capacity to make decisions, issues associated with social distancing, ceiling of care/treatment escalation plans, mental health and challenging behavior, and caring for someone suspected of contracting or who has contracted SARS‐CoV‐2 within community or inpatient psychiatric settings. These teams provide a range of care and support to people with IDs, while during the current pandemic there will be an increased focus upon providing TABLE 1 Group at risk because they are clinically vulnerable due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection who need particularly stringent social distancing measures Issues associated with diagnostic overshadowing, the views of parents, family members and carers, the required reasonable adjustments, communication needs, specialist mental health support, anticipatory care plans, any end-of-life or do not attempt cardiopulmonary resuscitation (DNACPR) discussions should be reported. doi = 10.1111/jppi.12352 id = cord-319780-rfj9t99r author = Alexander, S.P.H. title = A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date = 2020-05-01 keywords = ACE2; COVID-19; MERS; RNA; SARS; TMPRSS2; cell; link; protein summary = Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.1111/bph.15094 id = cord-270588-c9rxmo44 author = Algarroba, Gabriela N. title = Visualization of SARS-CoV-2 virus invading the human placenta using electron microscopy date = 2020-05-13 keywords = SARS summary = We present a case of rapid clinical deterioration in a woman at 28 weeks'' gestation due to 36 severe COVID-19 infection. Using electron microscopy to evaluate for potential viral transmission in the 37 placenta, we visualized and identified coronavirus virions invading into syncytiotrophoblasts in placental 38 All placentas from COVID-19 positive mothers are submitted for gross and histologic 70 evaluation in our institution. In this case, the placenta was submitted to the pathology laboratory 71 without fixative; fresh tissue was taken, using appropriate personal protective gear, under the Fisher 72 Ten representative, 3 mm thick tissue sections were 76 submitted from the placental parenchyma, membranes and umbilical cord for histologic evaluation. Preterm delivery 125 in pregnant woman with critical COVID-19 pneumonia and vertical transmission Clinical characteristics and intrauterine 130 vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective 131 review of medical records Evidence for and against 133 vertical transmission for SARS-CoV-2 (COVID-19) doi = 10.1016/j.ajog.2020.05.023 id = cord-349838-p6vfzbla author = Algwaiz, Ghada title = Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR''s Health Services and International Studies Committee date = 2020-07-24 keywords = COVID-19; HCT; PCR; SARS; patient summary = Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. While acknowledging all aforementioned challenges and taking into account current recommendations or guidelines issued by the American Society for Transplantation and Cellular Therapy (ASTCT) and the European Society for Blood and Marrow Transplantation (EBMT) (which are WBMT members), herein, we aim at providing a consensus among the authors from WBMT and CIBMTR''s HSIS committee and other HCT experts who represent multiple continents and allude to the current worldwide threat to HCT patient from the COVID-19 pandemic (7, 8) . doi = 10.1016/j.bbmt.2020.07.021 id = cord-314901-b18vy7dc author = Ali, Elrazi title = A Case of Fulminant Liver Failure in a 24-Year-Old Man with Coinfection with Hepatitis B Virus and SARS-CoV-2 date = 2020-10-13 keywords = SARS summary = Patient: Male, 24-year-old Final Diagnosis: Acute kidney injury • coagulopathy • liver failure • SARS-CoV-2 Symptoms: Cough • fever Medication: — Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases OBJECTIVE: Unusual clinical course BACKGROUND: Coronavirus disease 2019 (COVID-19) is a newly emerging disease that is still not fully characterized. CONCLUSIONS: It is uncommon for SARS-CoV-2 infection with mild respiratory symptoms to result in severe systemic disease and organ failure. We report an unusual case of acute hepatitis B infection with concomitant SARS-CoV-2 leading to fulminant hepatitis, multiorgan failure, and death. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been a central health concern worldwide for the last 6 months. Similarly, patients with chronic liver disease, including patients with chronic hepatitis B infection co-occurring with SARS-CoV-2 infection, had more severe illness and poor outcomes [17] . Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection doi = 10.12659/ajcr.925932 id = cord-296762-sc6crkkw author = Ali, Fedaa title = ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date = 2020-08-20 keywords = SARS summary = title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity Here, we combined ACE2 coding variants analysis in different populations and computational chemistry calculations to probe the effects on SARS-CoV-2/ACE2 interaction. Furthermore, the structure of ACE2 was trimmed by removing residues from P733 to the end of The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-108 2/ACE2 were compared between single mutated and WT protein at pH =7 ( Fig. 2A) . Based on our calculations, G211R mutant is shown to induce the largest increase 112 in the binding energy between SARS-CoV-2 and ACE2, where the binding is more favorable by 113 ~ 7.6 Kcal/mol than the WT. SARS-CoV-2/ACE2 interface in the 123 WT protein and corresponding mutants is showed to be a dominated by van der Waals 124 interactions, which accounts for more than 60% of the interaction energy. doi = 10.1016/j.bbrep.2020.100798 id = cord-344236-qp3ianzf author = Ali, Fedaa title = ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date = 2020-05-08 keywords = ACE2; SARS summary = Classical electrostatic calculations based on solving Poisson-Boltzmann (PB) equation is used to investigate the interaction energies between SARS-CoV-2 and ACE2 for different mutated ACE2 structures. In an attempt to better understand the susceptibility of different populations to infection by SARS-CoV-2, we gathered data on ACE2 missense variants from different projects and databases that aggregate allele frequencies (AF). These projects and databases included Single Nucleotide Polymorphism Database (dbSNP) 12, 13 , 1000 genomes project phase 3 (1KGP3) 14 , Allele Frequency Aggregator (ALFA project) a , Exome Aggregation Consortium (ExAC) 15 SARS-CoV-2 was reported to bind to human ACE2 via different ACE2 residues; Q24, D30, H34, Y41, Q42, M82, K353 and R357 5 . The electrostatic and the van der Waal contribution to the interaction energies of SARS-CoV-2/ACE2 were compared between single mutated and WT protein at pH =7 (Table 1 ). doi = 10.1101/2020.05.08.084384 id = cord-297878-c4cq92x8 author = Ali, Mohammed title = ST-Elevation Myocardial Infarction in a 27-Year-Old Male With COVID-19 date = 2020-09-11 keywords = COVID-19; SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that led to a global public health emergency causing coronavirus disease 2019 (COVID-19). Here we present a case of a very young 27-year-old patient without any past history of hypertension, coronary artery disease, or any risk factors for coronary artery disease except obesity, who developed STEMI while in the hospital. Here we present a case of ST-elevation myocardial infarction (STEMI) in a very young 27-year-old African American patient who was admitted for respiratory 1 2 1 3, 4 failure secondary to COVID-19. revealed that STEMI was the presenting clinical manifestation in 24 out of 28 COVID-19 patients who were diagnosed with an STEMI. COVID-19 has now been associated with increased cardiovascular injury and even more so in patients with severe disease. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Cardiac involvement in a patient with coronavirus disease 2019 (COVID-19) doi = 10.7759/cureus.10384 id = cord-255474-7fq9culd author = Alifano, Marco title = Renin-angiotensin system at the heart of COVID-19 pandemic date = 2020-04-16 keywords = ACE2; COVID-19; SARS summary = We decided to use the analogy of a play and speculate about the possible impact in this tragedy of 1) air pollution via the interference of nitrogen dioxide on ACE2 expression; 2) the dual role of nicotine; 3) the hypothetical involvement of ACE2 polymorphisms, the relationships of which with ethnic factors and susceptibility to cardiovascular disease seems intriguing; 4) the impact on the severity of infection of hypertension and related medications acting on the renin/angiotensin system, and, finally, 5) the possible helpful role of chloroquine, thanks to its capacity of modifying ACE2 affinity to the viral spike protein by altering glycosylation. 6 Although concurrent cardiovascular disease might explain increased mortality in a severe infection responsible for respiratory failure and deterioration of cardiac function, the observations on hypertension warrant urgent speculation and reflection, while waiting for results of large-scale studies evaluating the independent value of each risk factor. doi = 10.1016/j.biochi.2020.04.008 id = cord-355924-8sk9al0n author = Allam, Loubna title = Targeting the GRP78-Dependant SARS-CoV-2 Cell Entry by Peptides and Small Molecules date = 2020-10-21 keywords = GRP78; SARS; Spike; protein summary = Here, we report potential inhibitors comprising small molecules and peptides that could interfere with the interaction of SARS-CoV-2 and its target cells by blocking the recognition of the GRP78 cellular receptor by the viral Spike protein. For this purpose, a targeted analysis of the expression of candidate genes involved in SARS-CoV-2 infection confirmed the presence of the GRP78 protein in vitro in epithelial cells of the human respiratory tract and lung tissue. In this direction, our study focused on the repositioning of approved drugs as well as the investigation of other bioactive compounds that may prevent the penetration of SARS-CoV-2 into host cells by targeting the region of GRP78 that is required for the interaction with the Spike protein of the virus. Inhibition of the interaction between the spike protein SARS-CoV-2 and the receptor by blocking the GRP78 is a strategy interesting to identify drugs that decrease the rate of viral infection. doi = 10.1177/1177932220965505 id = cord-272602-rywg9mek author = Allison, James R title = Evaluating aerosol and splatter following dental procedures: addressing new challenges for oral healthcare and rehabilitation date = 2020-09-23 keywords = Dental; SARS; aerosol; splatter summary = A number of authors have used microbiological methods to study bacterial contamination from aerosol and splatter following dental procedures, either by air sampling 21, 32, 33 , swabbing of contaminated surfaces 34, 35 , or most commonly, by collection directly onto culture media [36] [37] [38] [39] . Many studies are small and report only one repetition of a single procedure, and some have only examined contamination of the operator and assistant; a number of studies which have measured spatial distribution of aerosol and splatter have only done so to a limited distance from the source. We present initial data on three dental procedures (high-speed air-turbine, ultrasonic scaler, and 3-in-1 spray use) and examine the effect of dental suction and the presence of an assistant on aerosol and splatter distribution. doi = 10.1111/joor.13098 id = cord-291047-mpahl77t author = Alm, Erik title = Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 date = 2020-08-13 keywords = Alexander; GISAID; Matthew; Nextstrain; SARS; clade summary = We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2. In this report, we applied the available nomenclatures to the European subset of the GISAID dataset to describe broad geographical and temporal trends in the distribution of SARS-CoV-2 genetic clades during the first half of 2020 and we discuss potential genomic surveillance objectives at the European level. doi = 10.2807/1560-7917.es.2020.25.32.2001410 id = cord-303111-iv4lzpev author = Almazán, Fernando title = Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date = 2014-12-19 keywords = BAC; RNA; SARS summary = Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. doi = 10.1016/j.virusres.2014.09.006 id = cord-103659-wpwfqhp2 author = Almqvist, J. title = Neurological manifestations of coronavirus infections: a systematic review date = 2020-09-01 keywords = COVID-19; SARS; September; patient; preprint summary = In order to optimize diagnostic workup of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we systematically reviewed neurological and neuroradiological manifestations of SARS-CoV-2 and all other known human coronavirus species (HCoV). . https://doi.org/10.1101/2020.08.26.20182196 doi: medRxiv preprint symptoms/complications, neuropathological findings and/or neuroimaging findings associated to acute or prior coronavirus infection. Several case reports, comprising a total of 11 patients, described neurological complications in SARS-CoV-1, among them critical illness neuro-/myopathy, seizures, persistent sleeping difficulties, persistent anosmia, delirium and generalized pain (Table e-6). Several common neurological symptoms among SARS-CoV-2 patients have been described in these studies, such as fatigue (44 -64% of patients), 42 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Retrospective Observational Study of Brain Magnetic Resonance Imaging Findings in Patients with Acute SARS-CoV-2 Infection and Neurological Manifestations doi = 10.1101/2020.08.26.20182196 id = cord-305704-grzrkff9 author = Almutairi, Abdulelah title = Dermatological Manifestations in Patients With SARS-CoV-2: A Systematic Review date = 2020-07-28 keywords = CoV-2; SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been initially defined as a disease of the respiratory tract; however, with the increasing number of patients and announcing that the virus became a pandemic, new systemic clinical manifestations are observed, including dermatological manifestations. The following step was filtering the results to include only original research studies investigating the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. The results were then filtered to include only original research studies examining the different types of skin and dermatological clinical manifestations in patients with SARS-CoV-2. After searching the abstracts and reviewing the eligibility criteria in identified potential abstracts, a total of seven studies [14] [15] [16] [17] [18] [19] [20] were considered as eligible to be included in the present systematic review, covering a total of 555 patients with SARS-CoV-2 who had dermatological symptoms in the form of skin lesions. doi = 10.7759/cureus.9446 id = cord-353659-wtacr6qj author = Almutairi, Nawaf title = Coronavirus Disease‐2019 with Dermatologic Manifestations and Implications: An Unfolding Conundrum date = 2020-05-09 keywords = COVID-19; SARS summary = As a nosocomial infection for hospital and nursing home patients and health care workers, it represents an extraordinary challenge. Lungs are the most severely affected organ by COVID-19 because the virus enters the host cells via the integral membrane protein angiotensin-converting enzyme 2 (ACE2), which is attached to cellular membranes in the lungs, arteries, heart, kidney, and intestines. A study of 663 COVID-19 patients from Wuhan, China stressed that patients more than 60 years old and those with chronic diseases were at enhanced risk of severe COVID-19, and more likely to die (43). Clinical Characteristics of Coronavirus Disease 2019 in China Prevalence of venous thromboembolism in patients with severe novel coronavirus pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.1111/dth.13544 id = cord-333696-3ci9re9a author = Alomari, Safwan O. title = COVID-19 and the Central Nervous System date = 2020-08-04 keywords = SARS; acute; covid-19; patient summary = Li and colleagues (2020) have suggested that SARS-CoV-2 can enter the brain, and it might be the cause of the respiratory failure in patients with COVID-19 [25] . Recently, Olds & Kabbani (2020) raised the question of nicotine associated neurological comorbidity in COVID19 patients depending on published evidence that the viral target receptor J o u r n a l P r e -p r o o f ACE2 is expressed in the brain and functionally interacts with nAChRs [29, 30] . This was the first reported case of MERS associated with coronavirus infection, which adds to the expanding list of differential diagnoses to be considered in a COVID-19 patient with neurological signs, most notably; cerebellar ataxia and disturbance in consciousness [49, 52, 53] . Laboratory work-up was negative for influenza, with the diagnosis of COVID-19 made by detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) PCR. doi = 10.1016/j.clineuro.2020.106116 id = cord-349690-hgdjbeht author = Alonso, Fábio de O. Martinez title = Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report date = 2020-08-14 keywords = SARS summary = title: Recurrence of SARS‐CoV‐2 infection with a more severe case after mild COVID‐19, reversion of RT‐qPCR for positive and late antibody response: case report Although cases vary in terms of serological data, timing of reactivation and clinics, patients who retested positive to SARS-CoV-2 generally have a mild or asymptomatic course 5, 6 , which is perhaps the result of some level of immunity, while symptomatic reactivation is rare but may happen 7 . Our patient, on the other hand, presented a more potent form of COVID-19 after more than 40 days from the first mild infection, and with a detectable antibody response only after the second infectious episode. In this paper, we describe a COVID-19 recurrence from a mild to a moderate form after convalescence, with RT-qPCR turning positive and antibody detection after more severe symptoms. Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report doi = 10.1002/jmv.26432 id = cord-280914-6k8gpp4y author = Alpaslan Kocamemi, B. title = First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey date = 2020-05-06 keywords = SARS; covid-19 summary = SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. SARS-CoV-2, Covid-19, sewage, wastewater, RT-qPCR, virus concentration, PEG SARS-CoV-2 virus titers of manhole were higher than inlet of WWTPs. Terkos wastewater sample has the highest Case number (person)/WWTP flow (m3/d), but SARS-CoV-2 virus was not detected. So far, ultracentrifugation [6] , Polyethylene glycol 8000 (PEG 8000) adsorption [5] , electronegative membrane [3] and ultrafiltration [3, 4, 8] methods were used for SARS-CoV-2 concentration from wastewater samples. Time course quantitative detection of SARS-CoV-2 in Parisian wastewaters correlates with COVID-19 confirmed cases doi = 10.1101/2020.05.03.20089417 id = cord-287321-1ro10ujr author = Alpaydin, Aylin Ozgen title = Clinical and Radiological Diagnosis of Non‐SARS‐CoV‐2 Viruses in the Era of Covid‐19 Pandemic date = 2020-08-08 keywords = COVID-19; SARS summary = INTRODUCTION: Following the announcement of first coronavirus disease 2019 (COVID‐19) case on March 11, 2020, in Turkey we aimed to report the co‐infection rates, and the clinical, laboratory, radiological distinctive features of viral pneumonia caused by viruses other than severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The spectrum of SARS-CoV-2 originated human disease named as coronavirus disease 2019 (COVID19) changes from little to no symptoms to severe pneumonia and acute respiratory distress syndrome 4 . Under these conditions; it was aimed to report the co-infection rates, the prevalence, clinical, laboratory and radiological characteristics of non-SARS-CoV-2 respiratory pathogens in a teaching hospital organized as a pandemic hospital immediately at the beginning of the pandemic in Turkey. Radiological assessments for the more frequently identified Non-SARS-CoV-2 pathogens (both metapneumovirus and rhinovirus) were compatible with indeterminate or atypical for COVID-19 disease. Some clinical, laboratory and especially radiological findings may aid in the differential diagnosis of non-SARS-CoV-2 pathogens from COVID-19. doi = 10.1002/jmv.26410 id = cord-305956-l02xdq87 author = Alqahtani, Saleh A title = Liver injury in COVID-19: The current evidence date = 2020-05-26 keywords = COVID-19; SARS; liver summary = These reports highlighted that beyond severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a complicated course of the disease or even viral infection itself can lead to involvement of other organs and multiorgan failure. The current review summarizes the pathophysiology and potentially specific role of COVID-19 in liver disease based on the available data and case series published, ahead of print and non-peer-reviewed preprints as of 2 April. In this study, 47.3% of the discharged patients showed elevated LFTs at baseline, and 23.7% developed abnormalities during hospitalization, suggesting emerging liver injury from drugs or during the course of the infection. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: A single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series doi = 10.1177/2050640620924157 id = cord-281552-zfjy3m3i author = Alsaadi, Entedar A. J. title = Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus date = 2020-09-22 keywords = MHV; SARS; protein summary = Here, we test E-derived peptides for membrane binding activity in vitro and confirm those identified as positive in the context of the full length protein expressed in two different cell types. Relative densitometry of the HSP and LSP bands revealed significant differences among the mutants with regard to their localisation to the different membrane fractions of E expressing insect cells ( Figure 5B ) and confirmed a role for the amphipathic MHV CoV E 50-64 peptide in membrane interaction. An amphipathic helix, EPTM, detected in the post-TM region of E, was suggested by bioinformatics analysis and assessed for direct membrane interaction in vitro by binding to GUVs. For comparison, the predicted E protein TM domain, ETM, and an established membrane active peptide from the influenza M2 protein were also included. Following expression of the complete E protein with mutations in the same identified peptide, altered membrane binding in two distinct cell types, mammalian and insect, was apparent. doi = 10.3390/v12091054 id = cord-321855-7b1c2xdh author = Alshami, Alanoud title = Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date = 2020-10-30 keywords = COV-2; PCR; SARS summary = title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. doi = 10.1371/journal.pone.0241258 id = cord-289612-4x5t4c5u author = Alsuliman, Tamim title = COVID-19 paraclinical diagnostic tools: Updates and future trends date = 2020-06-20 keywords = COVID-19; PCR; RNA; SARS; patient summary = Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases doi = 10.1016/j.retram.2020.06.001 id = cord-306351-ka6asw3m author = Alsuliman, Tamim title = A review of potential treatments to date in COVID-19 patients according to the stage of the disease date = 2020-05-30 keywords = COVID-19; HCQ; SARS; clinical; patient summary = Several trials of Remdesivir treatment on few patients in the United States have shown early promising benefits in cases with severe pneumonia [33, 34] . On the other hand, data emerging from other ongoing Chinese trials have demonstrated that CQ phosphate is superior to a control treatment in the following areas: pneumonia exacerbation inhibition, imaging findings improvement, virus negative conversion promoting, and disease course shortening [62] . For example, clinical data from reliable randomized controlled studies are still missing, and data published to date lacks homogeneity in terms of recommended dose concentration, treatment duration, and severity of patient illness [58] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The experience of clinical immunologists from China doi = 10.1016/j.retram.2020.05.004 id = cord-263840-1t4ykc01 author = Altay, Ozlem title = Current status of COVID-19 therapies and drug repositioning applications date = 2020-06-20 keywords = COVID-19; SARS; drug summary = Summary The rapid and global spread of a new human coronavirus (SARS-CoV-2) has produced an immediate urgency to discover promising targets for treatment of COVID-19. Here, we review current information concerning the global health issue of COVID-19 including promising approved drugs and ongoing clinical trials for prospective treatment options. At the genome 60 level, SARS-CoV-2 has 79·5% homology to SARS CoVCoV-2 and other coronaviruses, and its relative ease of sample acquisition and study, it has been widely 75 accepted that drug repositioning is a promising approach to make available an effective, safety-assured 76 treatment in a timely manner. In this review, we summarize diagnosis approaches, risk groups, available 77 treatment options, and drug repositioning studies related to COVID-19. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 525 2019 (COVID-19): The experience of clinical immunologists from China doi = 10.1016/j.isci.2020.101303 id = cord-294912-xl0wzi16 author = Alteri, Claudia title = Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date = 2020-09-08 keywords = CoV-2; SARS; covid-19 summary = Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72–345). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients. In this study, the presence of SARS-CoV-2 genome was evaluated in 55 SARS-CoV-2 rtPCR negative nasopharyngeal swabs from COVID-19 suspected patients thanks to a quantitative ad hoc designed assay based on ddPCR. This proof-of-concept study shows that an in-house ddPCR-based assay can allow an efficient detection of SARS-CoV-2 at low copy number in symptomatic cases resulted negative by standard rtPCR. doi = 10.1371/journal.pone.0236311 id = cord-235691-en6fgilb author = Althouse, Benjamin M. title = Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2 date = 2020-05-27 keywords = COVID-19; SARS summary = In Figure 2 we show an example by utilizing a stochastic branching process model with both Poisson and SARS-CoV-1 like NB distribution (k = 0.16) under the same mean R 0 = 2.6 26 , with different population sizes ranging from small clusters of 10 like households to large ones of 10 6 like city-wide. Because they play an important role in the spread of infection, hotspots pose an opportunity for surveillance and control: focusing on facilities and activities known to sustain hotspots, such as healthcare facilities, nursing homes, prisons, meat-packing plants, homeless shelters, schools, mass gatherings, as well as those places with closed, poorly circulated environments, can provide efficient ways to identify potential SSEs before they happen, therefore, potentially reducing a substantial amount of transmission in the population. Multiple lines of evidence at the individual-and population-level strongly indicate the role of SSEs in the transmission dynamics of SARS-CoV-2 and that we should not overlook the heterogeneity in numbers of secondary infections 57 . doi = nan id = cord-030999-27wennun author = Altmann, Daniel M title = Adaptive immunity to SARS-CoV-2 date = 2020-07-09 keywords = SARS; antibody; response summary = The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. Since many key questions about durability of the antibody response and about correlates of protection have been hard to address in this short timeframe, there has been value in recourse to the coronavirus immunology literature, especially in relation to SARS and MERS [16] [17] [18] [19] . Experience to date with SARS-CoV-2 suggests that this may not prove to be an infection that throws up insurmountable confounders to vaccine design-approaches that can safely and durably elicit neutralizing antibody look likely to work. Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals doi = 10.1093/oxfimm/iqaa003 id = cord-270858-ozvdz9ew author = Altmann, Daniel M title = What policy makers need to know about COVID-19 protective immunity date = 2020-04-27 keywords = SARS; covid-19 summary = Strategies in various countries that aim to stagger return to work on the basis of disease severity risk and age do not take account of how exposing even lower-risk individuals, such as young people with no comorbidities, to the virus so as to increase herd immunity can still result in pandemic spread. A caveat is that most studies, either of SARS survivors or of COVID-19 patients, have focused on people who were hospitalised and had severe, symptomatic disease. Anecdotal reports of reinfection from China and South Korea should be regarded with caution because some individuals who seemed to have cleared SARS-CoV-2 infection and tested negative on PCR might nevertheless have harboured persistent virus. 16 On the basis of this estimated R 0 , the herd immunity calculation suggests that at least 60% of the population would need to have protective immunity, either from natural infection or vaccination. doi = 10.1016/s0140-6736(20)30985-5 id = cord-315666-ngozukzj author = Altundag, Aytug title = Olfactory Cleft Measurements and COVID-19–Related Anosmia date = 2020-10-13 keywords = SARS summary = OBJECTIVE: This study aimed to investigate the differences in olfactory cleft (OC) morphology in coronavirus disease 2019 (COVID-19) anosmia compared to control subjects and postviral anosmia related to infection other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RESULTS: This study showed 3 major findings: the right and left OC widths were significantly wider in anosmic patients due to SARS-CoV-2 (group 1) or OD due to non–SARS-CoV-2 viral infection (group 2) when compared to healthy controls. Exclusion criteria for groups 1 and 2 were age younger than 18 years, pregnancy, normosmia detected on Sniffin'' Sticks olfactory test (a threshold discrimination identification [TDI] score of .30.5), acute and/or chronic rhinosinusitis or other acute/chronic nasal disease, nasal polyposis, allergic or idiopathic rhinitis, posttraumatic olfactory loss, severe turbinate hypertrophy or nasal septum deviation affecting the air passage, malignancy history, and a history of nasal or paranasal surgery. doi = 10.1177/0194599820965920 id = cord-310184-qth1y88o author = Alunno, Alessia title = Storm, typhoon, cyclone or hurricane in patients with COVID-19? Beware of the same storm that has a different origin date = 2020-05-18 keywords = COVID-19; SARS; cytokine summary = Some of the articles being published during the severe acute respiratory syndrome–coronavirus (SARS-CoV)-2 pandemic highlight a link between severe forms of coronavirus disease 2019 (COVID-19) and the so-called cytokine storm, also with increased ferritin levels. Some patients with coronavirus 2019 disease (COVID-19) develop a fully blown secondary haemophagocytic lymphohistiocytosis (sHLH), whereas others, despite a consistent release of pro-inflammatory cytokines, do not fulfil sHLH criteria but still show some features resembling the phenotype of the hyperferritinemic syndrome. Other immunomodulating agents like IL-1 or IL-6 inhibitors are only recommended in selected cases including the macrophage activation syndrome (MAS), a subtype of sHLH associated with systemic juvenile idiopathic arthritis (sJIA), adult-onset Still''s disease (AOSD) and other autoimmune disorders. doi = 10.1136/rmdopen-2020-001295 id = cord-033592-j1c2brb4 author = Alvarez Bravo, G. title = Encefalitis anti-NMDA-R secundaria a infección por SARS-CoV-2 Anti–NMDA receptor encephalitis secondary to SARS-CoV-2 infection date = 2020-10-09 keywords = SARS; nmdar summary = Coronavirus disease 2019 (COVID-19), which is caused by infection with the SARS-CoV-2 coronavirus and has caused a global pandemic, presents a wide spectrum of manifestations ranging from asymptomaticity to severe infection causing systemic failure and death. We present the case of a patient with anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis secondary to SARS-CoV-2 infection. 3 In this case, we suspect that SARS-CoV-2 infection acted as a trigger for the onset of anti-NMDAR encephalitis. 4, 5 Identifying autoimmune phenomena in patients with COVID-19 has enabled us to detect some immune-mediated neurological conditions, such as Guillain-Barré syndrome, acute necrotising encephalitis, myelitis, limbic encephalitis, and multiple cranial neuropathy associated with SARS-CoV-2 infection. [6] [7] [8] This case illustrates the slow clinical progression of a patient with anti-NMDAR encephalitis and COVID-19. To our knowledge, this is the first case of anti-NMDAR encephalitis associated with COVID-19. doi = 10.1016/j.nrleng.2020.07.011 id = cord-355560-vsxe97xs author = Alves, Amanda Mandarino title = SARS-CoV-2 leading to Acute Pancreatitis: an unusual presentation date = 2020-09-15 keywords = SARS; acute summary = During SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) pandemic, the etiologic agent of COVID-19, several studies described the involvement of other tissues besides the respiratory tract, such as the gastrointestinal tract. Diagnosing acute pancreatitis secondary to SARS-CoV-2 infection is challenging due to the need to rule out other etiologies as well the notable heterogeneous presentations. The mechanisms of pancreatic injury in SARS-CoV-2 infection include direct cytopathic effects or indirect systemic inflammatory and immune-mediated cellular responses, resulting in organ damage or secondary enzyme abnormalities [1] . This case report describes a patient with COVID-19 that developed severe acute pancreatitis. ACE2 receptor is highly expressed in pancreatic islet cells [16] , therefore SARS-CoV-2 infection can theoretically cause islet damage resulting in acute diabetes [7] . ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection doi = 10.1016/j.bjid.2020.08.011 id = cord-276267-77903fld author = Al‐Ani, Aysha H. title = Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient date = 2020-05-26 keywords = COVID-19; IBD; SARS; patient; risk summary = 6 Consequently, there is a concern that IBD patients are at greater risk of developing COVID-19 and at increased risk of progressing to a more severe clinical course or even death compared to the general population. 18 Furthermore, there is a recent case report of a possible SARS-CoV-2 gastrointestinal infection causing acute haemorrhagic colitis and signalling COVID-19 disease. Clinical assessment of risk factors for infection in inflammatory bowel disease patients Protection of 318 inflammatory bowel disease patients from the outbreak and rapid spread of COVID-19 infection in Wuhan Risk of infection with methotrexate therapy in inflammatory diseases: a systematic review and meta-analysis Comparative risk of serious infections with biologic and/or immunosuppressive therapy in patients with inflammatory bowel diseases: a systematic review and meta-analysis Infection-related hospitalizations are associated with increased mortality in patients with inflammatory bowel diseases Respiratory tract infections in patients with inflammatory bowel disease: safety analyses from vedolizumab clinical trials doi = 10.1111/apt.15779 id = cord-331147-numz9onx author = Al‐Kofahi, Mahmoud title = Finding the Dose for Hydroxychloroquine Prophylaxis for COVID‐19: The Desperate Search for Effectiveness date = 2020-06-01 keywords = SARS summary = Our aim was to identify possible hydroxychloroquine dosing regimens through simulation in those at high risk of infections by optimizing exposures above the in vitro generated half maximal effective concentration (EC(50)) and to help guide researchers in dose‐selection for COVID‐19 prophylactic studies. 8 We simulated the current FDA approved dosing for malaria treatment (800 mg followed by 400 mg at 6, 24, and 48 hours after the initial dose, a total of 3 days) and prophylaxis (400 mg weekly) and other regimens, such as those tested in recent COVID-19 trials (i.e., 400 mg/day for 5 days or 200 mg 3 times daily for 6 days). For the FDA recommended treatment dose of malaria (800 mg loading dose followed by 400 mg daily for a total of 3 days), simulations predicted 89% of subjects would have troughs above the target on day 1, however, this number dropped to 7% by day 14 post-exposure after the start of prophylaxis ( Table 1) . doi = 10.1002/cpt.1874 id = cord-283716-tleh9323 author = Amatore, F. title = SARS‐CoV‐2 infection presenting as a febrile rash date = 2020-05-27 keywords = SARS summary = The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide.1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The World Health Organization (WHO) has declared that Coronavirus disease 2019 (Covid-19) is a public health emergency of international concern as it continues to spread worldwide. 1 After a median incubation period of 4 days, fever and cough are the two most common manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. [3] [4] [5] [6] [7] [8] [9] Herein, we describe a febrile rash as the only clinical manifestation of SARS-CoV-2 infection in a patient free from pulmonary symptoms. Firstly, Covid-19 disease can present with a distinctive rash, which is histologically similar but clinically different to classic viral exanthemata. doi = 10.1111/jdv.16528 id = cord-269909-1cso5cl4 author = Amatya, Shaili title = Management of newborns exposed to mothers with confirmed or suspected COVID-19 date = 2020-05-21 keywords = COVID-19; China; SARS; mother; newborn summary = The unexpectedly high asymptomatic carrier rates reported from other institutions as well as prolonged face-to-face patient care required during labor and delivery drove this decision, allowing for judicious personal protective equipment (PPE) use and decreased potential exposure for both healthcare workers and newborns. Several reports, based on expert opinion, have recommended that DCC not be performed in neonates born to mothers with confirmed or suspected COVID-19 in order to reduce the risk of secondary transmission [15, 47, 49] . For resuscitation of premature, high-risk, and newborns with anomalies born to mothers with cinfirmed or suspected COVID-19, a fully donned neonatal resuscitation team enters the room upon delivery. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Neonatal resuscitation and postresuscitation care of infants born to mothers with suspected or confirmed SARS-CoV-2 infection doi = 10.1038/s41372-020-0695-0 id = cord-275452-ymimvoq9 author = Ameen, Fuad title = Covid-19 pandemic outburst in Saudi Arabia: A Glimpse date = 2020-07-30 keywords = March; SARS; covid-19 summary = This short review report very briefly highlights covid-19 syndromes; propagation; Middle East outburst, natural products as cure for viral diseases, probable psychosomatic effects, protective measures and Islamic wisdom. Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . Existing pandemic eruption of infections with SARS-CoV2 has been phrased as coronavirus disease 2019 (covid-19) . The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. The rapid global widespread of novel covid-19 viruses lead to World Health Organization (WHO) to declare outbreak as pandemic. -q (2020) Traditional Chinese medicine is a resource for drug discovery against 2019 novel coronavirus (SARS-CoV-2) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1016/j.sjbs.2020.07.026 id = cord-293415-u9onutny author = Amendola, A. title = Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression date = 2020-11-10 keywords = ACE2; SARS; cell summary = title: Human cardiac stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression Our findings indicate that human cardiac stromal cells have a susceptibility to SARS-CoV-2 infection and produce variable viral yields depending on the extent of cellular ACE2 receptor expression. The susceptibility of the myocardial tissue to SARS-CoV-2 infection Tavazzi et al., 2020) has been inferred based on the expression of the Angiotensin-Converting Enzyme-2 (ACE2) receptor in various cardiac cell types (Zou et al., 2020) , and the evidence that the virus interacts with this receptor via the Spike (S) protein, as a main cellular docking/internalization site . Together, these results highlight an additional cardiac pathogenesis mechanism by SARS-CoV-2 independent of ACE2 expression, consisting of substantial upregulation of genes involved in response to viral infection, intercellular virus transmission and related to innate immunity signaling and fibrotic activation. doi = 10.1101/2020.11.06.20226423 id = cord-270951-6nq3jwgr author = Amerio, Paolo title = COVID‐19 and psoriasis: Should we fear for patients treated with biologics? date = 2020-05-05 keywords = COVID-19; SARS summary = One of question is if psoriasis patients treated with immunomodulating and immunosuppressive drugs have to discontinue their treatment in the midst of fears for the infection and its consequences. Previous coronaviruses outbreaks reports, current published evidences on pathogenesis and on clinical reports of COVID infection in immunosuppressed patients are used to make a scientifically based decision. 3 Recently some concern over the possibility that cytokine directed immunosuppressive treatment may be a risk factor for SARS-CoV-2 infection in psoriasis patients has been expressed. Given the potential role of proinflammatory cytokines in the pathogenesis of SARS and MERS severe disease, also ant inflammatory drugs have been suggested as novel treatments in these diseases. High levels of IL-2, IL-7, GM-CSF, MIP1-α, and TNF-α have also been correlated with disease severity in SARS-CoV-2 infected patients. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): the perspectives of clinical immunologists from China doi = 10.1111/dth.13434 id = cord-306365-7cydmgn2 author = Ami, Yasushi title = Co‐infection of respiratory bacterium with severe acute respiratory syndrome coronavirus induces an exacerbated pneumonia in mice date = 2008-04-01 keywords = SARS summary = Our results show that both low-virulent Pp infection, and administration of LPS derived from Escherichia coli, induced elastase in the lungs and enhanced the replication of SARS-CoV, resulting in exacerbation of the respiratory disease caused by SARS-CoV infection and a high mortality rate. Thus, mice co-infected with Pp + Fr-mo developed severe respiratory disease, suggesting the possibility that elastase produced by Pp infection exacerbated infection by SARS-CoV adapted to mice. An important condition for sustaining high titers beyond four days p.i. would be that of high replication in the lungs in an early phase of infection, which could be facilitated by elastase induced by Pp. These data suggest that severe respiratory disease caused by co-infection of Pp and mouse-adapted SARS-CoV is attributable to the high replication of virus in the lungs, for which the elastase produced by Pp infection is probably responsible. doi = 10.1111/j.1348-0421.2008.00011.x id = cord-283956-zgrtux7i author = Amin, Sk. Abdul title = Fight against novel coronavirus: A perspective of medicinal chemists date = 2020-06-12 keywords = COVID-19; CoV-2; Mpro; SARS; drug summary = Like other RNA viruses, the functional significance of this Mpro or chymotrypsin-like protease (3CLpro) of SARS-CoV-2 emerges as an attractive drug target for the development of anti-viral agents. A group of scientists from the Cairo University, Egypt predicted COVID-19 spike binding site to a cell-surface receptor namely Glucose Regulated Protein 78 (GRP78) by employing structural bioinformatics in combination with protein-protein docking [55] . An early virtual screening (VS) study of FDA approved drugs (retrieved from Selleckchem Inc.) against the first resolved SARS-CoV-2 Mpro crystal structure (PDB: 6LU7) was performed. In another study, Elfiky [67] reported SARS-CoV-2 RdRp targeted molecular docking study of some anti-polymerase drugs which have been approved for use against various viruses. This study deals with the information currently available on potential targets for therapeutic invention and screening of new compounds or drug repurposing against SARS-CoV-2 (Figure 8 ). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 doi = 10.1016/j.ejmech.2020.112559 id = cord-297323-l3f12hg4 author = Amor, Sandra title = Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date = 2020-09-26 keywords = COVID-19; Coronavirus; RNA; SARS; severe summary = Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. These subsequently induce expression of type I IFNs (IFNα/β) and interferon stimulated genes (ISGs) [figure 2] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. Likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to SARS-CoV-2 infection, [ Table 4 ; (101) (102) (103) (104) (105) (106) (107) (108) (109) (110) (111) (112) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection doi = 10.1111/cei.13523 id = cord-314663-8cf0jci9 author = Ampuero, M. title = SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results. date = 2020-07-03 keywords = SARS summary = This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool. The goal of this study was to detect SARS-CoV-2 in sewage samples in Santiago, Chile. doi = 10.1101/2020.07.02.20145177 id = cord-289574-engwi8h3 author = An, Peng-jiao title = Biochemical indicators of coronavirus disease 2019 exacerbation and the clinical implications date = 2020-05-23 keywords = COVID-19; IL-6; SARS; patient summary = Accumulating evidence suggested that the progression of COVID-19 is associated with lymphopenia and excessive inflammation, and a subset of severe cases might exhibit cytokine storm triggered by secondary hemophagocytic lymphohistiocytosis (sHLH). Previously, it has been found that the serum levels of pro-inflammatory cytokines [IFN-γ, IL-1, IL-6, IL-12, and transforming growth factor-β (TGF-β)], and chemokines (CCL2, CXCL9, CXCL10, and IL-8) in SARS-CoV infected patients were higher than those in healthy individuals. Procalcitonin (PCT), released by bacterial infectious tissues under the irritation of pro-inflammatory cytokines, is a more specific marker of serious bacterial infection compared to C-reactive protein (CRP) and IL-6 [111] PCT-based strategy has been applied to guide antibiotic use in ICU or emergency wards, since the serum PCT levels in patients with severe bacterial infections are much higher than those with simple viral infections or non-specific inflammatory diseases [111] [112] [113] . The definition and risks of Cytokine Release Syndrome-Like in 11 COVID-19-Infected Pneumonia critically ill patients: Disease Characteristics and Retrospective Analysis doi = 10.1016/j.phrs.2020.104946 id = cord-321231-zlpa3x2x author = Anand, Pratima title = Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India date = 2020-09-10 keywords = COVID; SARS; mother; neonate summary = title: Clinical profile, viral load, management and outcome of neonates born to COVID 19 positive mothers: a tertiary care centre experience from India The study was conducted to describe the clinical profile of neonates born to mothers who tested positive for COVID 19 infection and to determine the association of neonatal COVID 19 status and viral load with maternal clinical status and viral load. • In this study on a limited number of neonates, maternal viral load of COVID 19 (E and RdRp cycle thresholds) was not associated with severity of illness or COVID 19 positivity in neonates. Neonates born to COVID 19 positive mothers and requiring NICU care for any reason (comorbidity like prematurity, low birth weight, or transient tachypnoea of neonate) were nursed in separate designated NICU in COVID block. doi = 10.1007/s00431-020-03800-7 id = cord-277137-k3jj5vom author = Anand, Praveen title = SARS-CoV-2 strategically mimics proteolytic activation of human ENaC date = 2020-05-26 keywords = ACE2; ENaC; SARS summary = We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site, absent in any previous coronavirus sequenced, resulting in the striking mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). Although the furin-like cleavage motifs can be found in other viruses (Coutard et al., 2020) , the exact mimicry of human ENaC-a cleavage site raises the specter that SARS-CoV-2 may be hijacking the protease network of ENaC-a for viral activation. The overlap of the cell-types expressing ACE2 and ENaC-a, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. SARS-CoV-2 then exploits enzymes called proteases to cut, or cleave, its spikes at a specific site which allows the virus to infiltrate the host cell. show that the spike proteins on SARS-CoV-2 may have the same sequence of amino acids at its cut site as a human epithelial channel protein called ENaC-a. doi = 10.7554/elife.58603 id = cord-348635-1pb2ag9j author = Anand, Praveen title = SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date = 2020-04-30 keywords = ACE2; SARS summary = We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry of an identical FURIN-cleavable peptide on the human epithelial sodium channel α-subunit (ENaC-α). We extrapolate that the evolution of SARS-CoV-2 into a global coronavirus pandemic may be in part due to its targeted mimicry of human ENaC and hijack of the associated host proteolytic network. The overlap of the cell-types expressing ACE2 and ENaC-ɑ, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. In order to extrapolate the tissue tropism of SARS-CoV-2 from the lens of the host proteolytic network, we assessed the co-expression of these proteases concomitant with the viral receptor ACE2 and ENaC-ɑ (Figure 2) . doi = 10.1101/2020.04.29.069476 id = cord-272010-kc0gi3cj author = Anand, Sai Priya title = Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins date = 2020-09-29 keywords = ACE2; CoV-2; SARS summary = The viral entry of SARS-CoV-2 depends on an interaction between the receptor-binding domain of its trimeric spike glycoprotein and the human angiotensin-converting enzyme 2 (ACE2) receptor. One potential therapeutic target receiving significant attention is the interaction between the SARS-CoV-2 spike (S) glycoprotein and its receptor, human angiotensin-converting enzyme 2 (ACE2). To better understand the interactions between membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins with their receptor, human ACE2, we sought to determine the cooperativity of ACE2 within the respective trimers. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2 doi = 10.3390/v12101104 id = cord-328865-ekgqdjlk author = Anand, Shuchi title = Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study date = 2020-09-25 keywords = SARS; USA; hispanic; population summary = METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). 12 Testing remainder plasma from monthly samples obtained for routine care of patients on dialysis for SARS-CoV-2 antibodies therefore represents a practical approach to a population-representative surveillance strat egy, 13 informing risks faced by a susceptible population while ensuring representation from racial and ethnic minorities. In our analysis of seroprevalence of SARS-CoV-2 spike protein receptor binding antibodies from a nationwide representative sample of patients receiving dialysis, we find that despite the USA contemporaneously leading the world in the numbers of diagnosed cases, overall, fewer than 10% of US adults had evidence of seroconversion in July, 2020. doi = 10.1016/s0140-6736(20)32009-2 id = cord-267610-bzbr9ios author = Anastassopoulou, Cleo title = SARS-CoV-2 transmission, the ambiguous role of children and considerations for the reopening of schools in the fall date = 2020-09-03 keywords = COVID-19; SARS; child summary = In agreement with this reasoning, data suggest that SARS-CoV-2 infections in children involve the upper rather than the lower respiratory tract, the typical site of severe COVID-19 disease where ACE2 receptors are more abundant [29] . In this respect, a large prospective NIH-funded study of 6000 people from 2000 US families in 11 cities, called human epidemiology and response to SARS-CoV-2, will help determine the incidence of novel coronavirus infection in children in the USA and whether rates differ between children who have asthma or other allergic conditions and children who do not [45] . School children are nonetheless anticipated to contribute to the community transmission of SARS-CoV-2 through their large numbers of daily social contacts, some of which are intergenerational, with older age groups where the risk for more severe illness is increased. doi = 10.2217/fmb-2020-0195 id = cord-302163-0jav84zw author = Anastassopoulou, Cleo title = Human genetic factors associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity date = 2020-10-22 keywords = ACE2; SARS; TMPRSS2; covid-19 summary = We searched PubMed/MEDLINE for all Englishlanguage original articles or reviews reporting on potential associations between human genetic factors and susceptibility to SARS-CoV-2 infection or COVID-19 severity, up to August 12, 2020 (with updating as of September 11, 2020, during the revision of the manuscript). The search was performed using all combinations of terms related to the novel coronavirus and the disease (e.g., "SARS-CoV-2," "2019-nCoV," and "COVID-19") on the one hand, and terms concerning susceptibility to infection or disease severity (e.g., "polymorphisms," "allelic variation," "genetic predisposition," "genotype," "clinical outcome") as well as the names of individual genes in which relevant polymorphisms were found (e.g., "TLR7," "ACE2"), on the other. A recently published comparative genetic analysis of approximately 81,000 human genomes across different populations suggested possible associations of coding region variants of ACE2 and TMPRSS2 with COVID-19 susceptibility, severity, and clinical outcomes [49] . doi = 10.1186/s40246-020-00290-4 id = cord-259084-lwh3rww4 author = Anderson, Cole title = Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date = 2020-05-22 keywords = SARS summary = title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations. This protocol allows for 35 the rapid detection of SARS-CoV-2 RNA from clinical specimens such as, nasopharyngeal and 36 oropharyngeal swabs, sputum, bronchoalveolar lavage, and tracheal aspirates. 43 In this study, we examined the feasibility of pooling nasopharyngeal swab specimens submitted 44 for COVID-19 testing using the CDC 2019-nCoV RT-PCR diagnostic panel without compromising 45 Specimens were submitted to 54 the Virology laboratory at Landstuhl Regional Medical Center for routine SARS-CoV-2 testing 55 using the CDC 2019-nCoV RT-PCR assay. Pooling nasopharyngeal/throat swab specimens to increase testing 176 capacity for influenza viruses by PCR doi = 10.1101/2020.05.22.110932 id = cord-279584-9x1d1kp1 author = Anderson, E. M. title = Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection date = 2020-11-10 keywords = OC43; SARS summary = Finally, we completed a series of studies using 36 serum collected from COVID-19 patients to determine if antibodies reactive to hCoVs are 37 boosted upon SARS-CoV-2 infections. We completed ELISAs to quantify levels of pre-pandemic SARS-CoV-2-reactive IgG 42 antibodies in 204 human serum samples collected in 2017. We completed ELISAs to quantify levels of pre-pandemic hCoV-reactive IgG antibodies 69 in all 204 human serum samples collected in 2017. We 74 completed full antibody titrations to directly compared levels of hCoV antibodies in a subset of 75 pre-pandemic samples from individuals who either did (n=12) or did not (n=51) possess cross-76 reactive SARS-CoV-2 antibodies (Figure 1f-h) . Our study demonstrates that ~23% of individuals possessed SARS-CoV-2 cross-reactive 137 serum antibodies prior to the COVID-19 pandemic. We compared antibody titers in 296 pre-pandemic serum samples from individuals who did and did not have a subsequent PCR-297 confirmed SARS-CoV-2 infection. doi = 10.1101/2020.11.06.20227215 id = cord-346544-kk7qyn4w author = Andersson, M. title = SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date = 2020-05-26 keywords = RNA; SARS summary = Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. . https://doi.org/10.1101/2020.05.21.20105486 doi: medRxiv preprint prevalence of vRNA detection in blood, serum or plasma, noting whether this attribute was correlated with clinical or laboratory phenotypes of disease, and recording Ct values when these were reported. We collected 212 serum samples through the microbiology department at Oxford University Hospitals NHS Foundation Trust, OUH NHSFT, comprising adults with a diagnosis of COVID-19, confirmed by SARS-CoV-2 detection by a clinical diagnostic microbiology laboratory using RT-PCR on a respiratory swab, classified in three groups as follows: Based on a systematic review of the literature, together with our own data, we estimate that SARS-CoV-2 RNA may be present at low copy numbers in ~10% of blood samples obtained from individuals with COVID-19 prior to day 28, most of which arise at earlier timepoints and in the setting of more severe disease. doi = 10.1101/2020.05.21.20105486 id = cord-333713-nz36i2oa author = Andonegui-Elguera, Sergio title = Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism date = 2020-06-18 keywords = COVID-19; SARS summary = Results Alterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, NK cells, T CD4+ cell and macrophages. Conclusions In summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. Therefore, in the present work we carried out comprehensive and stringent transcriptomic metanalysis of SARS-CoV-2 infected bronchoalveolar cells and peripheral blood mononuclear cells to unveil the molecular alterations caused by viral infection as well as deconvolution analysis to identify the immune cell profiles in COVID-19 patients. Using molecular deconvolution analysis, we identified the presence of neutrophils, NK cells, T CD4+ lymphocytes and macrophages infiltrating the lungs of COVID-19 patients, consistently our findings with the previously reported (14) . doi = 10.1016/j.arcmed.2020.06.011 id = cord-321027-64y43o0y author = Andreano, Emanuele title = Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date = 2020-05-09 keywords = SARS summary = The SARS-CoV-2 spike glycoprotein (S-protein) has a pivotal role in viral pathogenesis and it is 63 considered the main target to elicit potent neutralizing antibodies and the focus for the development 64 of therapeutic and prophylactic tools against this virus (3, 4) . Results shown in Table 1 and Figure 1 show that, among the seven donors 97 included in this study, six were able to produce high titers of SARS-CoV-2 S-protein specific 98 antibodies and in particular donors R-042, R-122 and R-188 showed the highest virus neutralizing 99 titers. In the case of SARS-CoV-2, where so far we do not have any effective therapeutic nor prophylactic 154 interventions, mAbs have the possibility to become one of the first drugs that can be used for 155 immediate therapy of any patient testing positive for the virus, and even to provide immediate 156 protection from infection in high risk populations. doi = 10.1101/2020.05.05.078154 id = cord-321369-xzu2faol author = Andreano, Emanuele title = Extremely potent human monoclonal antibodies from convalescent Covid-19 patients date = 2020-10-07 keywords = Fig; SARS; antibody summary = By single cell sorting 4277 SARS-CoV-2 spike protein specific memory B cells from 14 Covid-19 survivors, 453 neutralizing antibodies were identified and 220 of them were expressed as IgG. The three most potent monoclonal antibodies identified were able to neutralize the wild type and D614G mutant viruses with less than 10 ng/mL and are good candidates for the development of prophylactic and therapeutic tools against SARS-CoV-2. As for the authentic virus neutralization assay, supernatants containing naturally produced IgG or IgA were tested for their ability to protect the layer of Vero E6 cells from the cytopathic effect triggered by SARS-CoV-2 infection (Fig. S2) . This work describes a systematic screening of memory B cells from convalescent people to identify extremely potent human monoclonal antibodies against the spike protein of the SARS-CoV-2 virus, to be used for prevention and therapy of Covid-19. doi = 10.1101/2020.10.07.328302 id = cord-335156-l4jie8g6 author = Andreozzi, Fabio title = Eosinopenia and COVID-19 patients: So specific ? date = 2020-06-27 keywords = SARS summary = key: cord-335156-l4jie8g6 title: Eosinopenia and COVID-19 patients: So specific ? cord_uid: l4jie8g6 For the prediction of positive SARS-CoV-2 cases (diagnosis based on RT-PCR), eosinopenia has a sensitivity of 74.7% and specificity of 68.7% with the area under the curve AUC of 0.717. Up until end of March 20, Seasonal Influenza and COVID-19 were simultaneously present in Europe. We reviewed the laboratory results of two cohorts of SARS-CoV-2 (N = 50) and Influenza A (N = 41) patients (diagnosis confirmed by RT PCR). As such from the above, we can reach to the conclusion that complete eosinopenia is a common finding in both COVID-19 and Seasonal Influenza infections. Thus result could imply that eosinopenia could be considered as a potential biological indicator of either Influenza or SARS-COV-2 infections. Eosinopenia and elevated C-reactive protein facilitate triage of COVID-19 patients in fever clinic: a retrospective casecontrol study Co-infection with SARS-CoV-2 and influenza a virus in patient with pneumonia doi = 10.1016/j.eclinm.2020.100439 id = cord-261662-d0tg9i90 author = Andres, Cristina title = Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date = 2020-06-08 keywords = SARS summary = title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. Because of the importance of the S protein, we carried out a deep-sequencing study of the S gene in upper respiratory tract samples from 18 patients with mild or severe SARS-CoV-2 disease. The fact that the truncated S protein was present in only a low percentage of the entire viral quasispecies suggests that natural selection may have designed a favorable equilibrium in which a limited number of deleted virions are generated to balance virus production with infection of new cells during disease progression. doi = 10.1101/2020.06.03.129585 id = cord-259808-82drb14x author = Andrews, Paul L R title = COVID‐19, nausea, and vomiting date = 2020-10-05 keywords = ACE2; COVID-19; SARS; nausea; vomiting summary = Considering the likely effects of SARS-CoV-2 on the digestive tract (discussed further), a relationship between symptoms such as nausea/vomiting and diarrhea would not be unexpected but identifying the time of onset of each postinfection is essential to assessing their relative relevance for diagnosis. There are no formal studies at present so we have reviewed the effects of SARS-CoV-2 (and other coronaviruses) on the digestive tract in the light of knowledge of the established mechanisms of nausea and vomiting; this is the same approach that has been used to understand the pathogenesis of other symptoms (e.g. diarrhoea 10 ). We hypothesize that SARS-CoV-2 would induce acute (first few days postinfection) nausea and vomiting by causing the release of key hormones from the enteroendocrine cells (EECs) in the mucosa of the upper GI tract or after gaining direct entry into the blood, by acting directly within the brainstem. doi = 10.1111/jgh.15261 id = cord-202687-z17knvts author = Angelina, Emilio title = Drug Repurposing to find Inhibitors of SARS-CoV-2 Main Protease date = 2020-06-26 keywords = OTC; SARS summary = [11] In another study, Jin and colleagues identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of SARS-CoV-2 M pro in complex with this compound. Moreover, another recent crystallographic fragment screening against SARS-CoV-2 M pro that has been deposited in the Protein Data Bank (DOI: 10.2210/pdb5rgj/pdb ) also might help to find structural determinants for ligand anchoring within the enzyme binding cleft. Up to date, more than 100 structures of SARS-CoV-2 M pro with ligands bound at the enzyme binding cleft, have been released. While different fragments bind to different regions of SARS-CoV-2 M pro binding cleft, there are two interaction sites at the enzyme S1 sub-pocket that are targeted by most fragments. In this work we have performed a virtual screening of FDA approved drugs for repurposing as potential inhibitors of SARS-CoV-2 main protease M pro . doi = nan id = cord-270348-5804ffwx author = Angelino, Andrew F. title = Design and implementation of a regional inpatient psychiatry unit for asymptomatic SARS-CoV-2 positive patients. date = 2020-07-02 keywords = PPE; SARS; patient; unit summary = To prevent COVID-19 outbreaks in our units, we next decided to require universal nasal swab testing for SARS-CoV-2 for all medically asymptomatic patients being admitted to psychiatric units 3 . Second, we realized that we needed to decide where to care for SARS-CoV-2 positive, medically asymptomatic patients with mental illnesses who required hospitalization-those without symptoms of COVID-19. In light of the above, we concluded it would best serve our patients if we developed an inpatient psychiatric unit capable of accepting SARS-CoV-2 infected patients without COVID-19 symptoms, or with mild enough symptoms that they would not require medical hospitalization. Further, it is highly beneficial for continuity of care if the patient requires transfer to a medical COVID-19 unit that the psychiatrist be able to follow them there and maintain the psychiatric treatments as indicated. doi = 10.1016/j.psym.2020.06.018 id = cord-024130-kgzegwon author = Ankita title = COVID-19: An Ophthalmological Update date = 2020-04-30 keywords = COVID-19; SARS; patient summary = doi = 10.1007/978-981-15-4814-7_8 id = cord-267373-nzxbogga author = Antinori, Spinello title = Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status date = 2020-05-11 keywords = ICU; IDW; SARS summary = title: Compassionate remdesivir treatment of severe Covid-19 pneumonia in intensive care unit (ICU) and Non-ICU patients: Clinical outcome and differences in post_treatment hospitalisation status This prospective (compassionate), open-label study of remdesivir, which was conducted at Luigi Sacco Hospital, Milan, Italy, between February 23 and March 20, 2020, involved patients with SARS-CoV-2 pneumonia aged ≥18 years undergoing mechanical ventilation or with an oxygen saturation level of ≤94% in air or a National Early Warning Score 2 of ≥4. Patients were eligible to receive remdesivir for compassionate use if they were a male or non-pregnant female aged >18 years, had SARS-CoV-2 infection confirmed by a positive reverse-transcriptase polymerase chain reaction (RT-PCR) test of a respiratory tract sample and pneumonia confirmed by a chest X-ray or computed tomography (CT) scan, and were mechanically ventilated or had an oxygen saturation (SaO2) level of <94% in room air or a National Early Warning Score (NEWS)2 of  4 [19] . doi = 10.1016/j.phrs.2020.104899 id = cord-345827-yo3uq03v author = Antiochia, Riccarda title = Developments in biosensors for CoV detection and future trends date = 2020-10-28 keywords = MERS; SARS; SPR; biosensor summary = Since MERS and COVID-19 are highly contagious diseases with the potential to cause a pandemic, in absence of a specific vaccine or effective therapeutic drugs, it is of extreme importance to find rapid and accurate detection methods for control and prevention of virus spread. Current methods used for screening and diagnosis of novel COVID-19 are based on three different approaches: SARS-CoV-2 antigen detection in nasopharyngeal secretions through molecular biology techniques, computed tomography, and SARS-CoV-2 antibody analysis in serum using immunoassay methods (Carter et al., 2020) . According to the Food and Drug Administration (FDA) Emergency Use Authorizations (EUAs) for COVID-19 diagnostics, in addition to the most common ELISA method, there are two serological assays used for the detection of antibodies generated against SARS-CoV-2, the chemiluminescence immunoassays (CLIA) and the lateral flow immunoassays (LFIA). Biosensors based on specific biomolecular interactions offer an alternative and reliable solution to current methods for clinical diagnosis of COVID-19, due to their high sensitivity, low-cost, easy to use and possibility of POC utilization. doi = 10.1016/j.bios.2020.112777 id = cord-295548-o877eog6 author = Antonio, G.E title = Imaging in Severe Acute Respiratory Syndrome (SARS) date = 2003-10-21 keywords = HRCT; SARS summary = HRCT is an important tool for early diagnosis in patients with a high clinical suspicion and a negative initial chest radiograph [8] . (1) the majority (108/138, 78%) of patients had air-space opacification of various extent on the chest radiograph at presentation, (2) the right lung was more affected than the left (82/108, 76% versus 67/108, 62%), (3) the lower zone (70/108, 65%) and peripheral lung fields (81/108, 75%) were commonly involved, (4) unifocal involvement (59/108, 55%) was more common at presentation, high fever (.388C), AND cough or breathing difficulty, AND one or more of the following exposures during the 10 days prior to onset of symptoms: close contact with a person who is a suspect or probable case of SARS; history of travel, to an area with recent local transmission of SARS; residing in an area with recent local transmission of SARS. doi = 10.1016/s0009-9260(03)00308-8 id = cord-355734-pz64534w author = Antonio-Villa, Neftali Eduardo title = Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date = 2020-09-28 keywords = Mexico; SARS; covid-19 summary = Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. doi = 10.1093/cid/ciaa1487 id = cord-309729-nd48uh8e author = Antunes, Adriane E.C. title = Potential contribution of beneficial microbes to face the COVID- 19 pandemic date = 2020-07-24 keywords = COVID-19; SARS; gut; microbiota; probiotic summary = Then, dietary strategies for the promotion of the gut microbiota, and thus the strengthening of the immune system associated with the gut, include increased consumption of fiber and prebiotics (Holscher, 2017) , and incorporating fermented foods (Marco et al., 2017) , and probiotics (Zmora, Suez, & Elinav, 2019) into the diet. There is scientific evidence about the ability of probiotics to promote gut immunity (Sánchez et al., 2017) and, for the moment, a modest evidence of their role in reducing the severity of acute upper respiratory tract infections (AURTI) (Hao, Dong, & Wu, 2015) . In a context of impoverished and threatened intestinal microbiota, the consumption of home-made fermented foods (yoghurt, kefir, sauerkraut, kombucha) or the incorporation into the diet of commercial products containing probiotics and prebiotics, as food or food supplements, is part of a comprehensive nutritional strategy to enhance the function of the gut microbiota, to promote mucosal immunity and potentially upper respiratory tract immunity, to be potentially better prepared to face viral or bacterial infections caused by respiratory syndromes. doi = 10.1016/j.foodres.2020.109577 id = cord-268329-apl6n6jl author = Antunes, Douglas Eulálio title = Will cases of leprosy reaction increase with COVID-19 infection? date = 2020-07-17 keywords = SARS; covid-19 summary = The coronavirus disease 2019 (COVID-19)-caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus (betaCoV)-emerged for the first time as an outbreak of pneumonia in Wuhan, China, and it is now spreading to several countries around the world [1] . Some studies of SARS-CoV-2 infection have reported the presence of a cytokine storm syndrome and a subgroup of patients who progressed to severe forms of the disease, expressing a pro-inflammatory profile in plasma with IL-2, IL-7, TNF-α, and others as significant complications, such as occurs in T1R [10, 11] . In both reactions, we warn of the possible effect that COVID-19 infection may have on the number of cases of these immunological events because the presence of infection is an important risk factor for triggering leprosy reactions [8] . Another disturbing factor, which may contribute to the susceptibility of those affected by leprosy reactions, are the treatments implemented during these events that interfere with the inflammatory response of these patients. doi = 10.1371/journal.pntd.0008460 id = cord-349089-ta07bho2 author = Antushevich, Hanna title = Interplays between inflammasomes and viruses, bacteria (pathogenic and probiotic), yeasts and parasites date = 2020-09-22 keywords = AIM2; IL-18; SARS; activation; cell; inflammasome; nlrp3 summary = For example, in in vitro experiments on human primary neurons (HPNs) and microglial cells (HFMG) collected from healthy patients, it was discovered that treatment of the cells with HIV ssRNA40 (specific GU-rich single-stranded RNA from the HIV long terminal repeat region) activates the NLRP3 inflammasome and increases the expression and extracellular secretion of pro-inflammatory cytokines (IL-1β, IL-18) and neurotoxic cytokines (TNF-α, IL-1α, C1q). Another report has shown that HIV-1 induces the expression of NLRP3 inflammasome and IL-1β secretion in dendritic cells from healthy individuals but not HIV-1-infected patients, suggesting that inflammasome activation contributes to disease progression [23] . Based on the strong inflammatory potential of the NLRP3 inflammasome during infections caused by MERS-and SARS-CoVs, inhibition of the NLRP3 inflammasome activity may attenuate the cytokine storm and be a therapeutic target in the treatment of tissue inflammation in SARS patients [33, 41] . doi = 10.1016/j.imlet.2020.09.004 id = cord-338751-2eo7ityc author = Anzalone, Nicoletta title = Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients date = 2020-06-06 keywords = MRI; SARS summary = title: Multifocal laminar cortical brain lesions: a consistent MRI finding in neuro-COVID-19 patients They are part of a series of 21 patients presenting with neurological symptoms studied with brain MRI with otherwise no significant imaging findings. Although the predominantly parieto-occipital distribution of the lesions recalls posterior reversible encephalopathy syndrome (PRES) [5] , the prevalent cortical involvement and diffusion MRI pattern are not typical of PRES. More recently, evidence of direct viral infection of the endothelial cell and diffuse endothelial inflammation has been reported, resulting Fig. 1 Forty-seven-year-old man diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. Multiple, cortical areas of punctiform and gyriform FLAIR and DWI hyperintensity (arrows) in both parietal lobes, with no ADC changes Fig. 2 Fifty-four-year-old woman diagnosed with COVID-19 and presenting neurological signs of agitation and spatial disorientation after weaning from mechanical ventilation. doi = 10.1007/s00415-020-09966-2 id = cord-311566-x8n1bbwn author = Aouidate, Adnane title = Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation date = 2020-06-18 keywords = SARS; figure summary = As we are running of time and the virus is spreading quickly, we have screened the CAS COVID-19 Antiviral Compound Dataset, which includes $50000 chemical compounds against 3CLpro and RNA-dependent RNA polymerase (RdRp) using computational methods and ligand and structure based screening and in this study, we report the identification of different compounds with CAS IDs (2001083-69-6, 2001083-68-5, 63248-75-9, 264621-13-8, 1025098-90-1, 1253912-09-2) as potent inhibitors of 3CLpro and (833463-10-8, 833463-11-9, 833465-33-1, 2001083-69-6, 833463-19-7, 833464-45-2) as potent inhibitors RNA-dependent RNA-polymerase (RdRp), most compounds are 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives, the analysis of SARS-CoV-2 main protease and RNAdependent RNA polymerase binding sites reveals are combinations of hydrophobic, hydrophilic and charged residues holding with hydrogen bonds in excess, therefore, the 1,3,5triazine that is aligned centrally in both proteins binding pockets could be a good choice to occupy the central part of the molecules to be substituted by different hydrophobic, hydrophilic and charged fragments. doi = 10.1080/07391102.2020.1779130 id = cord-274439-y9jrdg5n author = Aoyama, Kazuyoshi title = Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model date = 2020-07-27 keywords = SARS summary = title: Estimating the risk of SARS-CoV-2 transmission to pediatric anesthesiologists: a microsimulation model A Through the interface, users can define inputs such as surgical statistics, including percent change of surgical caseload, and constraint on the number of available N95 respirators to model expected resource utilization at the individual hospital level, community level, or provincial level. Beginning on 16 March 2020, our quaternary-care children''s hospital performed only emergent and urgent surgeries (e.g., cancer surgery), including 236 cases during the first three weeks after the pandemic was declared. We estimated that cancelling elective surgeries during those three weeks reduced the cumulative incidence of SARS-CoV-2 transmission to an anesthesiologist by more than six times (2.1% with cancellation compared with 13.5% without cancellation) (Figure) . 5 Although we considered aerosol transmission and environmental contamination of SARS-CoV-2 in the model, we did not account for transmission risks among HCWs in operating rooms, which is our future work. The user can tune the transmission risk in the model when new data emerge. SARS-CoV-2 Infection in children doi = 10.1007/s12630-020-01771-9 id = cord-300978-busx8w6s author = Apetrii, Mugurel title = A brand-new cardiorenal syndrome in the Coronavirus Disease- 2019 (COVID-19) setting date = 2020-06-04 keywords = ACE2; COVID-19; SARS summary = Although the pandemic outbreak of coronavirus disease-2019 (COVID-19) targets preferentially patient''s lungs, recent data have documented that COVID-19 causes myocarditis, acute myocardial infarction, exacerbation of heart failure and acute kidney injury. Studies show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similar to its predecessor SARS-CoV, engages angiotensin-converting enzyme 2 (ACE2) as the entry receptor. In patients with SARS-CoV-2 infection, the most important features that suggest myocardial injury are electrocardiogram changes and troponin elevation coupled with echocardiography showing signs of subclinical left ventricular diastolic impairment or even reduced ejection fraction (EF) in severe cases [11] , with a higher likelihood of the need for mechanical ventilation in those with reduced EF, as was seen during previous coronavirus outbreaks [9] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection doi = 10.1093/ckj/sfaa082 id = cord-319955-spnykv96 author = Arafah, Azher title = S1 Subunit and Host Proteases as Potential Therapeutic Avenues for the Treatment of COVID-19 date = 2020-05-21 keywords = SARS summary = Abstract The novel corona virus (SARS-CoV-2) that causes severe acute respiratory syndrome, now called COVID-19 initially originated in Wuhan city of China and later spread across borders and infected more than two million people and killed over 2.9 lakh people all over the globe. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. Some reports have found and confirmed that SARS-CoV-2 like others SARS-CoVs utilizes angiotensin converting enzyme-2 receptor for making entry into target cell by binding to the receptor with its S1 subunit and employing host cell proteases for cleaving S2 subunit at S2′ in order to fuse with cell membrane. doi = 10.1016/j.arcmed.2020.05.013 id = cord-343340-zi0rfidc author = Aragón‐Caqueo, Diego title = Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date = 2020-05-03 keywords = SARS; test summary = The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. Therefore, the aim of this study is to provide a mathematical model to estimate the optimum number of pooled samples according to the specific prevalences of positive tests in a particular country context, in order to save as many tests as possible and cover as many people as possible, knowing that if a group tests out positive, all the individuals of the sample would have to be individually tested. This article proposed a simple and landed model to estimate the most optimum group number to implement pool testing strategy for SARS-CoV-2, according to the specific historical positive tests prevalence for a determined healthcare context. doi = 10.1002/jmv.25929 id = cord-336227-0j0nbm9k author = Aranda‐Abreu, Gonzalo Emiliano title = Use of amantadine in a patient with SARS‐CoV‐2 date = 2020-06-24 keywords = SARS summary = Due to a persistent cough, 500 mg of azithromycin was added for three days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time PCR test for SARS-Cov-2 which was positive. Due to a persistent cough, 500 mg of azithromycin was added for 3 days, but the symptoms continued, and he had to go to his community hospital, where he got a pharyngeal exudate, to do a real-time polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was positive. Asymptomatic family members (wife and daughter 54 and 33 years old, respectively) positive for SARS-CoV-2 were prescribed amantadine 100 mg twice daily for 14 days as a preventive measure. Family members (wife and daughter) who were in contact with the patient and also tested positive for SARS-CoV-2 took amantadine 1 100 mg twice a day for 14 days and did not develop symptoms. doi = 10.1002/jmv.26179 id = cord-347048-qqft4yc9 author = Araten, David J. title = Mild Clinical Course of COVID-19 in 3 Patients Receiving Therapeutic Monoclonal Antibodies Targeting C5 Complement for Hematologic Disorders date = 2020-09-12 keywords = COVID-19; SARS summary = CASE REPORTS: Case 1 is a 39-year-old woman with an approximately 20-year history of paroxysmal nocturnal hemoglobinuria (PNH), who had recently been switched from treatment with eculizumab to ravulizumab prior to SARS-CoV-2 infection. Case 2 is a 54-year-old woman with a cadaveric renal transplant for lupus nephritis, complicated by thrombotic microangiopathy, who was maintained on eculizumab, which she started several months before she developed the SARS-CoV-2 infection. CONCLUSIONS: We see no evidence of increased susceptibility to SARS-CoV-2 in these patients on anti-complement therapy, which might actually have accounted for the mild course of infection. We now have the opportunity to report on 3 patients who were on therapeutic anti-complement therapy at the time they became infected with the SARS-CoV-2 virus. The mild cases of SARS-CoV-2 infection in these 3 patients may have been related to anti-complement therapy, as suggested by preclinical models and reports of other patients who have received anti-complement therapy for COVID-19. doi = 10.12659/ajcr.927418 id = cord-287488-h102xn29 author = Araujo, Danielle Bastos title = SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date = 2020-10-23 keywords = Brazil; RNA; SARS; Vero summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. doi = 10.1590/0074-02760200342 id = cord-254886-fl5ar971 author = Arav, Y. title = Understanding the indoor pre-symptomatic transmission mechanism of COVID-19 date = 2020-05-17 keywords = SARS; hand summary = The model explicitly tracks the dynamics of contact and airborne transmission between individuals indoors, and was validated against the observed fundamental attributes of the epidemic, the secondary attack rate (SAR) and serial interval distribution. We provide evidence that a combination of rather easy to implement measures of frequent hand washing, cleaning fomites and avoiding physical contact decreases the risk of infection by an order of magnitude, similarly to wearing masks and gloves. In fact, pre-symptomatic transmission was recently referred to as the Achilles'' heel of COVID-19 pandemic control, as symptom-based detection of infection is less effective in comparison to the control of the SARS epidemic in 2003 (7) . We decided to examine five HBMs: Washing hands, cleaning fomites, maintaining social distancing (i.e avoiding physical contact), wearing a mask and 6 All rights reserved. Frequent hand washing and fomite cleaning coupled with avoiding physical contact result in a similar risk for infection as wearing gloves and a mask. doi = 10.1101/2020.05.12.20099085 id = cord-319900-16osnnga author = Arcadepani, Felipe B. title = The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil date = 2020-07-02 keywords = SARS summary = title: The SARS-Cov-2 threat in Cracolândia, an open-air drug use scene in Brazil All these issues make these individuals a high-risk group for infected by SARS-Cov-2 as they present several clinical (including pulmonary) comorbidities and social conditions that, besides posing difficulties for disease prevention, may play a role in hampering their immunological responses and general health. The population living or frequenting outdoor scenes lack adequate support from the Brazilian Public Health System, and the current pandemic adds more urgency to specific policies to address their susceptibility to this and other diseases. A pandemic that requires social isolation, especially for high-risk populations, turns this existing necessity into an emergency measure, taking into account basic public health principles and human rights. Health care facilities must provide treatment for their clinical comorbidities, focusing particularly on primary conditions such as hypertension and diabetes, which may be highly underdiagnosed among people who frequently use crackcocaine and are highly vulnerable to severe cases of COVID-19. doi = 10.1016/j.drugpo.2020.102835 id = cord-345754-mgixsfcc author = Arena, Patrick J. title = Race, COVID-19 and deaths of despair date = 2020-07-31 keywords = SARS summary = 1 The higher burden of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection and COVID-19 mortality among ethnic and racial minorities does not appear to be explained by biological factors, but instead by longstanding discriminatory societal and historical factors whereby the simple fact of belonging to a specific race/ethnicity limits access to education and wealth and precipitates exposure to the criminal justice system and poor health outcomes. COVID-19 morbidity and mortality is influenced by specific pre-existing health conditions, such as diabetes, hypertension, heart disease, food insecurity and lack of health insurance, all of which are highly prevalent among ethnic and racial minority groups, such as Black, Latinx and Native American populations in the United States (US). Similarly, a recent systematic review suggested that Black, Asian, and minority ethnic (BAME) individuals had a higher risk of SARS-CoV-2 infection and also experienced worse clinical outcomes than White individuals. Although some public health officials are taking concrete steps to address COVID-19 disparities among impacted ethnic groups, 8 data on the effectiveness of lockdowns on BAME communities is lacking. doi = 10.1016/j.eclinm.2020.100485 id = cord-323489-ro7kbnu3 author = Arenas, María Dolores title = Protection of nephrology health professionals during the COVID-19 pandemic date = 2020-10-06 keywords = COVID-19; SARS; healthcare; patient summary = There are a number of reasons why the protection of healthcare professionals has to be one of the main objectives in the SARS-CoV-2 pandemic: 1) They are necessary to guarantee the continuity of care; 2) They have a high risk of contagion due to their front-line exposure to infected patients; and 3) They may act as transmission vehicles in their day-to-day work to patients, other colleagues, and members of their families and the community. a Special care or protective measures for medical, nursing and auxiliary staff who work daily with haemodialysis patients As has previously been described in other publications 3,10 , the main protection measures for healthcare professionals and patients in haemodialysis units are: 1) adequate information for patients attending the centre in terms of maintaining a safe distance from fellow patients in waiting rooms and ambulances, and in the use of surgical masks and frequent hand washing; 2) early detection of patients suspected to be infected on arrival at the unit (questionnaires about symptoms or close contacts, taking temperature), and if highly suspect, taking a nasopharyngeal swab for PCR testing. doi = 10.1016/j.nefroe.2020.06.018 id = cord-310239-mmvuij3k author = Arentz, Susan title = Clinical significance summary: Preliminary results of a rapid review of zinc for the prevention and treatment of SARS-CoV-2 and other acute viral respiratory infections date = 2020-08-01 keywords = CoV-2; SARS; infection; zinc summary = Indirect evidence from systematic reviews have found zinc supplementation is effective for the prevention of acute respiratory infections in young children and zinc lozenges may reduce the duration of the common cold in adults. As of the 9 June 2020, the preliminary findings of a rapid review of zinc for the prevention or treatment Pending any definitive evidence, clinicians might consider assessing the zinc status of people with chronic disease co-morbidities and older adults as part of a SARS-CoV-2 clinical work-up, as both groups have a higher risk of zinc deficiency/insufficiency and poorer outcomes from SARS-CoV-2. The primary objective of this rapid review was to assess the effects of zinc on the incidence, duration and severity of acute upper or lower respiratory tract infections caused by SARS-CoV-2 infection in people of any age and of any zinc status when used as a preventive supplement or as a therapy. doi = 10.1016/j.aimed.2020.07.009 id = cord-294666-xlyuhzo9 author = Arguin, Paul M. title = Health Communication during SARS date = 2004-02-17 keywords = CDC; SARS summary = Timely health communication, along with surveillance, quarantine, isolation, and travel restrictions, figured prominently among the tools the Centers for Disease Control and Prevention (CDC) used to help contain the outbreak. By the end of September 1994, CDC had produced six documents to distribute to public health officials: an outbreak notice; a plague advisory for travelers to India; a plague alert notice handed to passengers arriving from India, which described the symptoms of plague and urged them to seek medical attention if they developed a febrile illness within 7 days; recommendations for treatment and prophylaxis; guidelines for diagnosis and biosafety; and a review article in the Morbidity and Mortality Weekly Report. Kennedy International Airport on flights from India), the departments of health in New York City and New York State supplemented CDC''s surveillance plan by using two approaches to disseminate information to heighten awareness of plague, focusing on emergency department physicians. doi = 10.3201/eid1002.030812 id = cord-347734-0z2kin6r author = Armann, J. P. title = Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates date = 2020-07-17 keywords = CoV-2; SARS summary = title: Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates However, there is reason to believe that children play a less significant role in SARS-CoV-2 transmission compared to influenza, making control measures focused on this age group less effective: Most countries-including Germany-report a much lower proportion of cases in children compared to their population size 4-6 . The findings from this unique study in older students and their teachers indicate that the prevalence of IgG antibodies against SARS-CoV-2 remains extremely low after the first wave of the corona pandemic in Germany. In fact, 5 of the 12 participants with antibodies against SARS-CoV-2 had a personal or household history of COVID-19, yielding a ratio of unidentified to identified cases of 2.4, which is much smaller than that previously assumed by some authors 9 . doi = 10.1101/2020.07.16.20155143 id = cord-356264-q0yqnlyl author = Armijos-Jaramillo, Vinicio title = SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-03-23 keywords = RBD; SARS; selection; site summary = With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene, and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. All these experiments were performed again using the S-protein genes of a shorter list of accessions and more distantly related (broad dataset) to SARS-COV-2 (AY304488, AY395003, DQ412043, FJ882957, KY417144, MG772933, MG772934, MN908947, NC_004718) to test the reproducibility of the predicted branches and sites under positive selection. Modeling results suggest that interference with the hot spot 353 could be and effective strategy for inhibiting the recognition of the RBD of the SARS-COV-2 spike protein by its human host receptor ACE2 and hence prevent infections. doi = 10.1101/2020.03.21.001933 id = cord-323324-h2a25xym author = Armijos‐Jaramillo, Vinicio title = SARS‐CoV‐2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date = 2020-05-07 keywords = ACE2; RBD; SARS summary = With this analysis, we determine a region inside the receptor‐binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor ACE2. In the case of SARS-CoV, ACE2 binding was found to be a critical determinant for the range of hosts the virus can infect, and key amino acid residues in the RBD were identified to be essential for ACE2-mediated SARS-CoV infection and adaptation to humans (Li et al., 2005 (Li et al., , 2006 . We employ a multidisciplinary approach to look for evidence of diversifying selection on the S-protein gene and model the interactions between human ACE2 (hACE2) and the RBD of selected coronavirus strains, which ultimately afforded us novel insights detailing virus and host cell interactions. Additionally, important hACE2-binding residues in the RBD from SARS-COV-2 obtained from the crystallography and structure determination performed by Shang et al. doi = 10.1111/eva.12980 id = cord-289813-kq3ayyip author = Arnaez, Juan title = The Impact of the Current SARS-CoV-2 Pandemic on Neonatal Care date = 2020-04-30 keywords = SARS; care summary = These changes mainly impact several key points: (1) the organization and workflow of the neonatal unit, (2) parent-infant bonding and family-centered care, and (3) stress-related consequences in health professionals (Figure 1) . The contingency plans required by the circumstances in the current SARS-CoV-2 outbreak scenario must not let us forget that restrictions on parental contact and interventions in the care of infants may entail costs to the families in addition to the loss of opportunities for the newborn to adapt to the extrauterine environment and advance in neurodevelopment. Importantly, health-workers should rely positively on the contingency plans and help parents to reduce their fear and encourage them to participate in their children''s care. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes A contingency plan for the management of the 2019 novel coronavirus outbreak in neonatal intensive care units doi = 10.3389/fped.2020.00247 id = cord-265155-jbvrcjx8 author = Aroniadis, Olga C. title = Current Knowledge and Research Priorities in the Digestive Manifestations of COVID-19 date = 2020-04-22 keywords = SARS; covid-19 summary = Herein we discuss the known digestive manifestations of COVID-19 and their potential implications, important questions that remain unanswered, and what gastroenterologists should know to care for affected patients and contribute to extinguishing the pandemic. This is based on: 1) a high incidence (in some reports) of digestive symptoms among infected patients, 1-4 2) expression of Angiotensin Converting Enzyme 2 (ACE2) receptors -the viral target for cellular entry -throughout the digestive system, 1,2 3) presence of viral RNA in the stool of infected patients [1] [2] [3] 5 , and 4) prior experience with the 2003 SARS-coronavirus and the 2012 Middle Eastern Respiratory Syndrome (MERS)-coronavirus, both of which are known to infect and injure the GI tract. Multiple studies have confirmed the presence of SARS-nCoV-2 RNA in the stool of COVID-19 patients, including some who never tested positive in the upper respiratory tract. Digestive Symptoms in COVID-19 Patients with Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes doi = 10.1016/j.cgh.2020.04.039 id = cord-350733-0zghspb8 author = Aronson, Jeffrey K. title = The use of mechanistic reasoning in assessing coronavirus interventions date = 2020-07-15 keywords = EBM+; MERS; SARS; mechanism summary = RATIONALE: Evidence‐based medicine (EBM), the dominant approach to assessing the effectiveness of clinical and public health interventions, focuses on the results of association studies. That treatment for hypertension is a risk factor for severe disease in the case of SARS-CoV-2 suggests that altering hypertension treatment might alleviate disease, but the mechanisms are complex, and it is essential to consider and evaluate more than one mechanistic hypothesis (Section 3). This strategy makes much use of evidence from mechanistic studies: evidence that the drug has some action against the novel virus in the laboratory, both in vitro and in vivo in experimental animals, is used to justify the decision to use the treatment clinically. Some evidence, for instance, supports a behavioural mechanism known as the "intention-behaviour gap," 53 In sum, the explicit and systematic assessment of mechanistic studies is essential for the development of effective vaccination programs in a given context. doi = 10.1111/jep.13438 id = cord-334321-3c10ecgd author = Arora, S. title = Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India date = 2020-06-20 keywords = SARS summary = Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks. doi = 10.1101/2020.06.18.20135277 id = cord-318048-6nvi63rq author = Arshad, Usman title = Prioritisation of Anti‐SARS‐Cov‐2 Drug Repurposing Opportunities Based on Plasma and Target Site Concentrations Derived from their Established Human Pharmacokinetics date = 2020-05-21 keywords = Cmax; SARS; drug summary = An indication of the degree to which candidate drugs are expected to accumulate in lung (a presumed site of primary efficacy and for prevention of SARS-CoV-2 infection) was provided by calculation of unbound Accepted Article lung to plasma tissue partition coefficient (K p U lung ) according to the methodology of Rodgers and Rowland (20-22). All rights reserved Simulated exposure relative to reported anti-SARS-CoV-2 activity in lung and other tissues Lung K p U was simulated for all molecules for which the necessary physicochemical properties and in vitro drug binding information were available. The rank order of lung Cmax/EC 90 ratio was chloroquine > atazanavir (ritonavir boosted) > tipranavir (ritonavir boosted) > hydroxychloroquine > mefloquine > ivermectin > lopinavir (ritonavir boosted) > azithromycin > nitazoxanide > ritonavir > gilteritinib > amodiaquine > imatinib > oxprenolol (data excluded due to this analysis only being possible for 33 of the 56 drugs). doi = 10.1002/cpt.1909 id = cord-276345-xsjh3766 author = Arshad, Yasir title = Detection of SARS-CoV-2 in ophthalmic secretions in Pakistan: A preliminary report date = 2020-08-25 keywords = SARS summary = All 35 oropharyngeal swab samples were detected positive for SARS CoV-2, however out of total 35 conjunctival swab samples, 3(8.5%) were detected positive by using real-time RT-PCR. There was no ocular manifestation observed among patients with positive conjunctival specimens and similar information has already been reported by the previous study [4] . Results of the present study support the evidence that ophthalmic secretions may not be the main source of transmission for the novel SARS-CoV-2, but the role of eye in the transmission of this highly contagious virus must not be ignored. In 2004, SARScoronavirus was detected from tear samples in 37.5% positive cases and in another study, positivity of SARS-CoV-2 from conjunctival swabs was 16.6% which contributed to the evidence of eye as a carrier [6, 7] . SARS-CoV-2 in the ocular surface of COVID-19 patients. New evidence of SARS-CoV-2 transmission through the ocular surface. Evaluation of ocular symptoms and tropism of SARS-CoV-2 in patients confirmed with COVID-19 doi = 10.1016/j.jinf.2020.08.035 id = cord-352849-vd62r8qu author = Artesi, M. title = Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome date = 2020-05-03 keywords = SARS summary = Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals, while also clearing essential staff to continue work. At the current time a number of RT-PCR tests have been developed to identify SARS-CoV-2, targeting multiple regions in the viral genome. Out of the 186 SARS-CoV-2 genomes we have sequenced, only these four samples carry a SNP at position 26340. Vogels et al [17] also identified this 3 base change as well as other SNPs in primer/probe binding sites from a number of RT-PCR assays for SARS-CoV-2. The cobas® E-gene assay may use an alternate primer probe combination that is more sensitive to the presence of the SNP, alternatively it may target the same positions as the Corman et al. . https://doi.org/10.1101/2020.04.28.20083337 doi: medRxiv preprint However, our ability to show that each individual carries a genetically identical virus demonstrates the potential whole genome sequencing has for tracking chains of transmission. doi = 10.1101/2020.04.28.20083337 id = cord-324531-lpoelp91 author = Artesi, Maria title = A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date = 2020-09-22 keywords = PCR; SARS summary = title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. The cobas system (Roche) implements a dual-target assay to detect SARS-CoV-2, with qRT-PCRs targeting both the ORF1ab region and the E gene (see Fig. S1 in the supplemental material). We speculated that these samples carried a common variant that interfered with the E gene qRT-PCR and carried out whole-genome sequencing of the viruses using the Artic Network protocol (17) . doi = 10.1128/jcm.01598-20 id = cord-336364-2ust3qoq author = Artigas, Laura title = In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date = 2020-10-02 keywords = ARD; SARS; protein; set summary = title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). doi = 10.1371/journal.pone.0240149 id = cord-257456-15bm9psj author = Arumugam, Arunkumar title = A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date = 2020-09-24 keywords = PCR; RNA; SARS summary = Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. To further improve the speed of a diagnostic assay, we and others tested using untreated or heat-inactivated samples added directly to one-step RT-PCR master mixes without an RNA extraction step [6, [13] [14] [15] [16] [17] [18] [19] . Prior to COVID-19 emerged as a global pandemic, we have tested the feasibility of circumventing the sample preparation steps by adding a few microliters of the unprocessed sample (in VTM) directly into the RT-qPCR assay master mix targeting InfA, InfB, and RSV. doi = 10.3390/diagnostics10100739 id = cord-283109-ka3n9pft author = Arumugam, Arunkumar title = The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date = 2020-04-08 keywords = SARS summary = Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. Using Inf and RSV clinical specimens, we successfully performed RT-qPCR reactions by simply adding a few microliters of the unprocessed sample in viral transport medium (VTM) directly into the RT-qPCR assay master mix. We next tested whether the RNA from SARS-CoV-2 can be detected by directly spiking samples of the non-replicative recombinant virus particles (SeraCare AccuPlex SARS-CoV-2 reference material) in VTM to master mix without an extraction step. As shown in Fig. 3 , the SARS-CoV-2 RNA from directly spiked samples was successfully detected by the RT-qPCR reaction without a nucleic acid extraction step (N1 target shown). doi = 10.1101/2020.04.06.028811 id = cord-351038-k2m6woow author = Arun Krishnan, R. title = COVID-19: Current Trends in Invitro Diagnostics date = 2020-06-27 keywords = COVID-19; PCR; SARS summary = Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. The limitation of rRT-PCR to detect COVID-19 past infection and the progress of the disease, increases the importance of serological assays. Currently COVID-19 antigen LFIA test is under development which will offer more sensitive and specific result for COVID-19 diagnosis and will detect the viral antigen in 3 days of infection [22] . have developed an enzyme linked immunosorbent assay for the detection of COVID-19 IgM and IgG antibody from serum sample. The complexity, cost effectiveness and limitations of nucleic acid based diagnostic tools, impetus the innovative development of well standardized, high sensitive, specific and low cost serological assays for COVID-19 diagnosis. Evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). doi = 10.1007/s12291-020-00906-5 id = cord-353742-k4gxww2c author = Arévalo, AP title = Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date = 2020-11-02 keywords = SARS summary = SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. The objective of this study was to test the ivermectin drug in a murine model of coronavirus infection using a type 2 family RNA coronavirus similar to SARS-CoV2, the mouse hepatitis virus (MHV). Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). In conclusion, ivermectin seems to be effective to diminish MHV viral load and disease in mice, being a useful model for further understanding new therapies against coronavirus diseases. doi = 10.1101/2020.11.02.363242 id = cord-309200-t2xugb8l author = Asadi, Sima title = The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? date = 2020-04-03 keywords = COVID-19; SARS summary = (2005) established that hospitalized patients infected with SARS during the 2003 epidemic emitted viable aerosolized virus into the air. Recent work on influenza (another viral respiratory disease) has established that viable virus can indeed be emitted from an infected individual by breathing or speaking, without coughing or sneezing (Yan et al. In regard to virology, information is required about the average viral titer in the respiratory fluid and the emitted aerosol particles, as well as the minimum infectious dose for COVID-19 in susceptible individuals. But given the large numbers of expiratory particles known to be emitted during breathing and speech, and given the clearly high transmissibility of COVID-19, a plausible and important hypothesis is that a face-to-face conversation with an asymptomatic infected individual, even if both individuals take care not to touch, might be adequate to transmit Note that the key word in the last sentence was "might." Many urgent questions about aerosol transmission and COVID-19 must be answered. doi = 10.1080/02786826.2020.1749229 id = cord-306819-otabtxin author = Asensio-Samper, JM title = Recomendaciones Prácticas Para El Manejo Del Paciente Con Dolor Crónico Durante La Pandemia De COVID-19 date = 2020-09-02 keywords = COVID-19; SARS summary = Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. Dentro de estas recomendaciones que incluyen las Unidades de Tratamiento del Dolor, los pacientes con sospecha o infección confirmada por SARS-CoV-2 pueden encontrase en situación de espera para consulta medica o técnicas invasivas para manejo de dolor crónico refractario a otras terapias. En las Unidades de Tratamiento del Dolor, los casos en los que se establece la necesidad de manejo preferente de pacientes en situación de crisis sanitaria, incluyendo pandemia COVID-19, son aquellos casos no subsidiarios de atención mediante telemedicina, es decir, aquellos casos refractarios a tratamiento médico convencional que requieran evaluación clínica especializada y alta probabilidad de realización de procedimiento invasivo para control del dolor, el cual podrá ser realizado en formato de "acto único". doi = 10.1016/j.redar.2020.08.005 id = cord-218886-lqme2j8n author = Asghari, Aref title = Fast Accurate Point of Care COVID-19 Pandemic Diagnosis Enabled Through Advanced Lab-on-a-Chip Optical Biosensors: Opportunities and Challenges date = 2020-08-01 keywords = Fig; SARS; SPR; biosensor summary = Primarily, an optical biosensor translates the capture of the target analyte in a measurable alteration of a light property, such as refractive index (RI), intensity or resonance shift, through different methods such as resonators and interferometers ( Fig. 2 ). The sensing transduction signals in Optical label-free biosensing platform functions based on miniscule changes in refractive index resulting from the attachment of biomolecules to the immobilized bioreceptors. On the other hand, by simply depositing a gold layer, the device concept can be used for a surface plasmon resonance, which can improve the LOD even further 71 In order to maximize the sensitivity of the waveguide-based biosensor, the speed of light can be reduced even further. Graphene unique electrical properties has also been exploited effectively to develop different transistor based label-free biosensors including COVID-19 detection system 39 (fig 18.a) . doi = nan id = cord-322672-gjph61cq author = Ashok, Vishnu title = Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis date = 2020-08-25 keywords = COVID-19; SARS summary = title: Case report: high-grade atrioventricular block in suspected COVID-19 myocarditis A few cases of concurrent myocarditis have been reported, but the extent of cardiac complications with the SARS-CoV-2 strain of coronavirus is still largely unknown. Myocarditis and non-specific cardiac arrhythmias have been reported in a few cases of COVID-19, but this is the first reported case of a high-grade atrioventricular conduction block with SARS-CoV-2 infection. 7 In the European Study of the Epidemiology and Treatment of Inflammatory Heart Disease, 18% of the 3055 patients in the study had high-grade arrhythmias including complete heart block. Since the onset of the current pandemic, cases of myocarditis in patients with COVID-19 have been reported. In a case series of 150 patients with COVID-19 conducted in Wuhan City, China, 7% of the reported 68 deaths (5 deaths) were attributed to myocarditis with circulatory failure; however, their pre-morbid cardiac status was unclear. doi = 10.1093/ehjcr/ytaa248 id = cord-271648-m2c5bvuj author = Ashour, Hossam M. title = Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date = 2020-03-04 keywords = China; CoV; MERS; RNA; SARS summary = Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model doi = 10.3390/pathogens9030186 id = cord-326305-mjd5agvf author = Ashraf, Mohammad Ali title = The application of direct viral cytopathic hypothesis to design drug trials in the battle against COVID-19 date = 2020-08-15 keywords = SARS summary = As previously shown, clathrin-mediated endocytosis is the main pathway for virus entry, while doublemembrane vesicles formation and autophagy in the host cell is the mechanism for viral replication [14] . Imatinib, a protein-tyrosine kinase inhibitor that inhibits the BCR-ABL tyrosine kinase which is approved to treat chronic myeloid leukemia by inhibiting ABL oncogenetic pathway has previously shown success in disrupting the viral entry mechanism of both SARS-CoVand MERS-CoV into the cell; hence, it can also be considered as a potentially useful drug to treat patients with severe forms of COVID-19. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor doi = 10.1007/s40199-020-00368-3 id = cord-255883-mz6nyisw author = Asif, Muhammad title = COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date = 2020-08-14 keywords = COVID-19; CoV-2; RNA; SARC; SARS summary = Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. An in vitro study conducted by Hoffmann and colleagues revealed that SARC-CoV-2 depends on cellular serine protease (TMPRSS2) for S proteins priming which are known to interact with human ACE2 receptors in the lungs and facilitate entry into the cells. The authors opted the following keywords to find relevant studies: "essential oils", "antiviral", "COVID-19", "SARC-CoV-2", "bronchodilation", "immunomodulatory'''', "anti-inflammatory'''', "corona virus''''. Thus, on the basis of these docking and in vitro studies, it is proposed that garlic essential oils and their isolated constituents, especially DAS, have potential to prevent the entry of virus into host cells as well as to activate molecular antioxidant pathways that decrease the secretions of culprit pro-inflammatory cytokines. Essential oils have long been known to have anti-inflammatory, antioxidant, immunomodulatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2. doi = 10.1007/s10787-020-00744-0 id = cord-268468-036i1082 author = Asif, Muhammad title = The role of biosensors in COVID-19 outbreak date = 2020-09-18 keywords = COVID-19; CoV-2; PCR; SARS summary = In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. In this outbreak, three different types of diagnosis tests are being used including (i) chest CT scan along with clinical indications, (ii) RNA detection using RT-PCR assay and (iii) lateral flow assays, full automatic chemiluminescence method, enzyme-linked immunosorbent assay (ELISA) for the determination of antibodies [5] . In this review, we have summarized the biosensor based technologies which are able to detect SARS-CoV-2 effectively. The peptide monolayer was successfully coated on SPR biosensor and further functionalized with virus nucleocapsid protein which was finally able to detect SARS-CoV-2 antibodies at nanomolar level. The sensing aptitude of the biosensor was evaluated employing antigen protein, self-cultured virus, and nasopharyngeal swab samples taken from people infected with COVID-19 pneumonia. doi = 10.1016/j.coelec.2020.08.011 id = cord-317429-pp6hb4q5 author = Aslam, Saima title = COVID-19: Yet another coronavirus challenge in transplantation date = 2020-03-14 keywords = COVID-19; SARS summary = A novel coronavirus, severe acute respiratory syndrome −coronavirus-2 (SARS-CoV-2), causing a severe acute respiratory syndrome with its disease designated as COVID-19, emerged from its epicenter in Wuhan, China, in December 2019 and is now a global pandemic. 7 report on the presentation and outcome of 2 microbiologically confirmed COVID-19 cases in heart transplantation detected in the Hubei Province in China. These 2 patients apparently were part of a community of at least 200 heart transplant survivors in that region and presented with variable severity of disease (one mild and another with more severe manifestations requiring a prolonged hospitalization); however, both survived the event. It is important to note that the clinical presentations were not distinct from those described in non-immunosuppressed individuals, and the patient with severe disease presented with a viral prodrome, displayed the typical findings on CT scan imaging, and progressed to clinical hypoxia. In summary, the novel coronavirus and its disease, COVID-19, require thoughtful approaches for the prevention, mitigation, timely detection, and appropriate therapeutic intervention for our vulnerable patients. doi = 10.1016/j.healun.2020.03.007 id = cord-323148-rsjocuh3 author = Assaad, Souad title = Risk of death of cancer patients presenting with severe symptoms of infection, with or without documented COVID-19 date = 2020-09-06 keywords = SARS summary = The striking observation of our series is the high risk of death (actuarial survival close to 20% at day 28) of cancer patients who did not demonstrate detectable SARS-COV-2 using the standard Cobas test. The high death rates of RT-PCR negative cancer patients observed in our series may result from a sensitivity of SARS-COV-2 diagnostic assays (false negativity), and also other undocumented infections in the context of patients with a progressive cancer. From these different series and works, it can be concluded that cancer patients under active treatment are at high risk of lethal complications when presenting with symptoms resembling those of COVID -19 and requiring hospitalisation even in the absence of documented SARS-COV-2 infection. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR The impact of the COVID-19 pandemic on cancer deaths due to delays in diagnosis in England, UK: a national, population-based, modelling study doi = 10.1016/j.ejca.2020.08.018 id = cord-256508-ce59ovan author = Asselah, Tarik title = COVID-19: discovery, diagnostics and drug development date = 2020-10-08 keywords = COVID-19; China; CoV-2; RNA; SARS; infection; patient summary = To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals doi = 10.1016/j.jhep.2020.09.031 id = cord-338689-4u1ezk64 author = Ata, Fateen title = COVID-19 presenting with diarrhoea and hyponatraemia date = 2020-06-07 keywords = COVID-19; SARS summary = We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. We present a young man with diarrhoea, abdominal pain and hyponatraemia who turned out to be positive for COVID-19. COVID-19 is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ► We recommend studies to evaluate the effectiveness of stool PCR for severe acute respiratory syndrome coronavirus 2 if initial nasopharyngeal PCR is negative and suspicion remains high. 4 Gastrointestinal symptoms such as diarrhoea, abdominal pain and vomiting have been previously seen with acute viral respiratory infections and reported recently as rare manifestations of COVID-19. 15 Our patient had acute hyponatraemia, abdominal pain and diarrhoea with minimal Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical and virological factors associated with gastrointestinal symptoms in patients with acute respiratory infection: a two-year prospective study in general practice medicine doi = 10.1136/bcr-2020-235456 id = cord-268140-s5lailkp author = Atal, Shubham title = IL-6 Inhibitors in the Treatment of Serious COVID-19: A Promising Therapy? date = 2020-06-13 keywords = COVID-19; IL-6; SARS; patient summary = Considering the proven role of cytokine dysregulation in causing this hyperinflammation in the lungs with IL-6 being a key driver, particularly in seriously ill COVID-19 patients, it is crucial to further explore selective cytokine blockade with drugs like the IL-6 inhibitors tocilizumab, sarilumab, and siltuximab. Considering the proven role of cytokine dysregulation in serious COVID-19 and interleukin (IL)-6 being the key driver of this hyperinflammation, which can cause multi-organ failure, a series of clinical trials with IL-6 inhibitors like tocilizumab, sarilumab and siltuximab are underway. Another Italian Phase II open-label trial (NCT04315480) with tocilizumab 8 mg/kg single dose is being conducted in patients with severe multifocal interstitial pneumonia due to COVID-19 to evaluate its role in the virus-induced cytokine storm, in blocking deterioration of lung function or even promoting a rapid improvement of clinical conditions, preventing naso-tracheal intubation and/or death [51] . doi = 10.1007/s40290-020-00342-z id = cord-295431-p9iy7uaf author = Atangana, Ernestine title = Facemasks simple but powerful weapons to protect against COVID-19 spread: Can they have sides effects? date = 2020-09-30 keywords = COVID-19; China; SARS; concentration; figure summary = Climatic factors including climate temperature, humidity, wind speed have played some crucial role in respect to the transition of the ongoing pandemic COVID-19, caused by the severe acute respiratory syndrome coronavirus2 (SARS-COV-2) and patient''s recovery and the death rate across the globe. With all these results in hand, there is a clear evidence that the wind could be a carrier of droplets containing concentration of COVID-19, while some case studied have been done for indoor and outdoor exposure with a wind speed of 2km/h, no mathematical model has been suggested to see in general how far such droplets could be transported. It was also observed that the transport followed a crossover behaviour, where during the first period, the transport followed a fading memory process but later a power law behaviour, with no steady state, this was very interesting as this shows that, when the COVID-19 infected person sneezed there were no wind effect, thus concentration released in the air with initial speed was able to spread like in the results described in [66] see Figure 8 below. doi = 10.1016/j.rinp.2020.103425 id = cord-323131-l726qv1g author = Atogebania, Julius Wedam title = An Invited Commentary on ‘ Evidence Based Management Guideline for the COVID-19 Pandemic- Review article’ date = 2020-04-23 keywords = SARS summary = COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. AUTHOR SUMMARY: To date over one(1) million persons have been affected indicating exponential spread of the disease and more rigorous implementation and adherence to more strengthen restrictions of social distancing would mitigate the spread of the pandemic disease and may prove to be even tedious. Abstract COVID 19 been declared recently as a pandemic, to date has affected over 1,8881,365 with over 119,403 deaths in accordance to the global pandemic Real-Time Report. COVID-19 has recently been declared a pandemic by WHO • Increased cases globally have highlighted the need for updated management guidelines • Currently, supportive management is the first-line treatment • New medical therapies are currently in phase 1 and 2 trials • Invited Commentary'' Evidence doi = 10.1016/j.ijsu.2020.04.050 id = cord-344006-0iq9s94n author = Atzrodt, Cassandra L. title = A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date = 2020-05-23 keywords = COVID-19; CRISPR; RNA; SARS; vaccine; virus summary = All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . doi = 10.1111/febs.15375 id = cord-327349-rxb6zfoc author = Au, Lewis title = Cancer, COVID-19, and antiviral immunity: the CAPTURE study date = 2020-09-03 keywords = COVID-19; SARS; cancer; patient summary = Inherent perturbations on cell subsets (e.g. lymphoid and myeloid malignancies), or therapy-induced impact on immune states (e.g. immune checkpoint blockade) may provide opportunities to understand contributions of distinct immune compartments and key regulators of the anti-SARS-CoV-2 response. Herein, we aim to provide an overview of knowledge to-date of the clinical features of COVID-19 observed in cancer patients, as well as potential impact of cancer and anti-cancer interventions on the immune response to SARS-CoV-2. However, what has been critically missing in cohort and registry reports to date are data on 1) the true prevalence of SARS-CoV-2 infection in the cancer population, given population screening has not been widely implemented; and 2) the experience of those who remain well (uninfected, asymptomatic or subclinically affected), to determine the drivers of mortality and the absolute risks of severe adverse events within the cancer community as a whole. A longitudinal understanding of the degree to which the immunocompromised states of cancer patients impact infection, viral clearance, clinical course of COVID-19, and subsequent generation of long-term immunity is needed. doi = 10.1016/j.cell.2020.09.005 id = cord-256075-fudeaq7y author = Audo, Andrea title = Acute Pulmonary Embolism in SARS-CoV-2 Infection Treated with Surgical Embolectomy date = 2020-04-28 keywords = SARS summary = We report the first case of SARS-CoV-2 complicated by massive pulmonary embolism underwent successfully surgical embolectomy. We believe that maintaining the same pro-active attitude suggested by current Guidelines might help in reducing morality and improving survival in SARS-COV-2/patients. SARS-CoV-2 infected patients usually experience fever, dry cough, fatigue and worsening dyspnoea with interstitial pneumonia that in up to 3-5% might unfortunately evolve in a severe acute respiratory distress syndrome (ARDS) requiring endotracheal intubation (ETI) and mechanical ventilation. Due to the severe ARDS unresponsive to assisted non-invasive ventilation the patient underwent ETI and was transferred to an isolation ward of the intensive care unit (ICU); the infection of SARS-CoV-2 virus was confirmed thereafter by an RT-PCR assay of a nasal swab. We are now facing this unexpected severe SARS-CoV-2 pandemic, but maintaining the same proactive attitude suggested by current Guidelines or routine standard of care might help in reducing morality rate and improving survival also in SARS-CoV-2 infected patients. doi = 10.1016/j.athoracsur.2020.04.013 id = cord-268034-7id7sfsu author = Auerswald, Heidi title = Assessment of Inactivation Procedures for SARS-CoV-2 date = 2020-05-28 keywords = CoV-2; SARS summary = This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10. The buffers used in this lysis step yield varying results [11, 13, 15, 16] ; however, unlike 224 previous studies [11] , this study found that AVL buffer alone was successfully able to fully 225 inactivate up to 5 log10 of virus from three different primary isolates of SARS-CoV-2. Previous 234 studies have shown that GITC-lysis buffers are able to inactivate SARS-CoV-2 samples [11, 12] ; 235 however, the addition of Triton-X may be necessary for complete inactivation [11] . Therefore, formaldehyde treatment does not appear to be a 247 solution for increased molecular SARS-CoV-2 testing; however, it does remain a viable alternative 248 for sample inactivation or disinfection. doi = 10.1101/2020.05.28.120444 id = cord-300791-417tzufc author = Austin, Zubin title = Pharmacy practice in times of civil crisis: The experience of SARS and “the blackout” in Ontario, Canada date = 2007-10-16 keywords = SARS; blackout; pharmacist; pharmacy summary = OBJECTIVES: The objectives were to describe and analyze the impact of 2 major crises (the severe acute respiratory syndrome [SARS] outbreak, and the electrical system failure ["blackout"]) on pharmacy practice and pharmacists in Toronto, Canada. RESULTS: Five key themes emerged from this research: (1) during times of crisis, pharmacies become frontline health care facilities, (2) a vacuity of leadership/lack of utility of emergency preparedness guidelines and policies, (3) role of and reliance on experience and professional judgment, (4) importance of documentation, and (5) the importance of "teamness" in enabling successful adaptation during times of crisis. In order to participate in this study, pharmacists were required to have been practicing as a pharmacist in a direct patient-care setting in Toronto for at least 25 h/wk during March 2003 to June 2003 (SARS) and August 2004 (blackout). doi = 10.1016/j.sapharm.2006.09.001 id = cord-276147-30buoweg author = Avancini, Joao title = Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil date = 2020-09-15 keywords = SARS summary = authors: Avancini, Joao; Miyamoto, Denise; Arnone, Marcelo; Villas-Boas Gabbi, Tatiana; Ferreira, Paula Silva; Neta, Cyro Festa; Sanches, Jose Antonio title: Absence of specific cutaneous manifestations of SARS-Cov-2 in a reference center in Brazil cord_uid: 30buoweg Contents of the manuscript have not been previously published and are not currently submitted elsewhere. All listed authors have seen and approved of the manuscript and will sign off on any subsequent manuscript revisions. To the editor: We read with interest the letters from the New York City report regarding the absence of COVID toes lesions on their patients and the recommendation of caution when concluding that cutaneous findings are specifically due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cutaneous manifestations in patients with COVID-19: a preliminary review of an emerging issue Classification of the cutaneous manifestations of COVID-19: a rapid prospective nationwide consensus study in Spain with 375 cases doi = 10.1016/j.jaad.2020.09.030 id = cord-299346-f13xly6q author = Awad, Mohamed E. title = Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic date = 2020-04-10 keywords = PPE; SARS; covid-19; patient summary = title: Perioperative Considerations in Urgent Surgical Care of Suspected and Confirmed Coronavirus Disease 2019 Orthopaedic Patients: Operating Room Protocols and Recommendations in the Current Coronavirus Disease 2019 Pandemic To reduce the occupational risk in treating suspected or confirmed COVID-19 urgent orthopaedic patients, recommended precautions and preventive actions (triage area, ED consultation room, induction room, operating room, and recovery room) are reviewed. HCPs in high-risk areas should adhere to infection prevention and control practices, which includes the appropriate use of engineering controls (negative pressure rooms), administrative controls, and personal protective equipment (PPE) ( 6 Per CDC recommendations, a clinically suspected/ confirmed COVID-19 patient should wear a cloth face covering, over nose, and mouth and a surgical mask should be reserved for HCP and first responders. It is recommended for an environmental services worker to increase the Flowchart demonstrating the the recommended use of personal protective equipment for different activities at various settings managing suspected/clinically Coronavirus disease 2019 patients. doi = 10.5435/jaaos-d-20-00227 id = cord-343082-46lo7xtx author = Awasthi, Ankit title = OUTBREAK of novel corona virus disease (COVID-19): Antecedence and aftermath date = 2020-07-25 keywords = COVID-19; Kumar; SARS summary = Studies also confirm that flu shots are not efficient in the fight against COVID-19 as the patients continue to suffer despite the treatment (https://www.wsj.com/articles/gilead-sciences-offers-experimental-drug-for-coronavirustreatments-testing-11580511519).In the meantime, Thai health officials claimed to have successfully handled the infection with acocktail of antiviral drugs that include lopinavir and ritonavir under the name "Kaetra" along with flu medication oseltamivir. In 2016, this drug was used as an emergency aid for the Ebola virus outbreak.A clinical trial involving 80 participants (in Shenzhen city) demonstrated chest symptoms improvement in patients of COVID-19 treated with favipiravir. Favipiravirhas been reported to be effective, without any obvious side-effects, in helping coronavirus patients recover.In another study carried out in China, two mild and two severe COVID-19 associated pneumonia patients were treated with combined Western and Chinese medicine treatment (Lopinavir/ritonavir/arbidol/ShufengJiedu Capsule). In recent clinical studies the use of steroidal drug Dexamethasone has been very effective to treat patients suffering from COVID-19. doi = 10.1016/j.ejphar.2020.173381 id = cord-266036-qhlo99l7 author = Axell-House, Dierdre B. title = The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date = 2020-08-31 keywords = PCR; SARS; Table; test summary = OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. doi = 10.1016/j.jinf.2020.08.043 id = cord-343148-rp3kmd80 author = Ayatollahi, Parisa title = Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection date = 2020-09-17 keywords = CSF; SARS summary = title: Possible Autoimmune Encephalitis with Claustrum Sign in case of Acute SARS-CoV-2 Infection On the third day of admission, new behavioral changes appeared including elated mood, inappropriate laughing, anxiety, and insomnia, leading to treatment with clonazepam, risperidone, and sertraline, in addition to sodium divalproex. Repeat brain MRI showed signal hyperintensities on fluidattenuated inversion recovery (FLAIR) and T2-weighted sequences in the claustrum bilaterally, which were not present on the initial scan 2 weeks earlier. Follow-up MRI 1 month after the abnormal scan showed near-complete resolution of the claustrum hyperintensities ( Figure 2 ). [1] [2] [3] The MRI abnormality ("the claustrum sign") may extend to external/extreme capsules and insular cortices 3 and typically resolves in weeks or months. The finding of the claustrum sign on brain MRI, not previously reported in a COVID-19 patient, [4] [5] [6] [7] [8] provides further support for the idea that acute SARS-CoV-2 infection may present as an autoimmune encephalitis. doi = 10.1017/cjn.2020.209 id = cord-352281-9huyb4cs author = Ayoub, Houssein H. title = Age could be driving variable SARS-CoV-2 epidemic trajectories worldwide date = 2020-04-17 keywords = SARS summary = We aimed here to answer this question and to estimate for each country (with a population ≥1 million), region, and globally, 0 R , and the rate per 100 persons (out of the total population by the end of the epidemic cycle) of each of the cumulative number of incident infections, mild infections, severe and/or critical disease cases, and deaths, in addition to the number of days needed for the national epidemic to reach its incidence peak (a measure of how fast the epidemic will grow). 13.20059253 doi: medRxiv preprint Figure S11 : Sensitivity analysis assessing the impact of a 50% increase in the susceptibility to SARS-CoV-2 infection among those aged <30 years on our estimates for the basic reproduction number, R0, for the select countries presented in the main text. doi = 10.1101/2020.04.13.20059253 id = cord-310042-9z8rkzq8 author = Aysha, Al‐Ani title = Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date = 2020-07-12 keywords = COVID-19; IBD; SARS; infection summary = This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. A significant proportion of IBD patients are treated with long-term immunomodulator/immunosuppressive therapy which potentially places them at increased risk of infections and associated complications. Practitioners and patients alike are therefore concerned about the risk and implications of COVID-19 infection in the IBD patient, despite a paucity of evidence supporting an altered predisposition to disease or more severe disease course. Despite concerns regarding immunosuppression and consequent predisposition to infection, there is no evidence to suggest increased infection rates of COVID-19 in IBD patients to date. 8, 9 Hence, expert consensus currently is that patients with IBD do not appear to be at increased risk of SARS-CoV-2 infection compared with the general population. 2 • Reducing disease activitythere is evidence that moderate to severe disease activity increases the risk of infection in IBD patients. doi = 10.1111/imj.14889 id = cord-274839-r4jg6wac author = Azam, Faizul title = An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α date = 2020-11-02 keywords = IVM; Nsp9; SARS summary = Therefore, the current study seeks to employ molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) analysis and molecular dynamics simulation studies for decrypting the binding mode, key interacting residues as well as mechanistic insights on IVM interaction with 15 potential drug targets associated with COVID-19 as well as IMPα. Among all COVID-19 targets, the non-structural protein 9 (Nsp9) exhibited the strongest affinity to IVM showing −5.30 kcal/mol and −84.85 kcal/mol binding energies estimated by AutoDock Vina and MM-GBSA, respectively. Therefore, in this study, molecular docking, molecular mechanics generalized Born surface area (MM-GBSA) and molecular dynamics protocols have been exploited to investigate the binding interactions between IVM and 15 potential drug targets associated with COVID-19 as well as IMPa co-crystallized with NS5 fragment. doi = 10.1080/07391102.2020.1841028 id = cord-355039-qi4fwqbc author = Azar, William S. title = COVID-19 and diabetes mellitus: how one pandemic worsens the other date = 2020-08-02 keywords = ACE2; AMPK; COVID-19; IL-6; SARS; patient summary = In this review, we elucidate suggested mechanisms underlying the increased susceptibility of patients with diabetes to infection with SARS-CoV-2 with a more severe COVID-19 disease. The different studies presented suggest that patients with diabetes may not only be prone to a more severe COVID-19 disease, but also to an increased risk of infection with SARS-CoV-2. Although plausible hypotheses for the increased risk of COVID-19 infection in patients with diabetes and other chronic diseases like hypertension are still under investigation, ACE2 seems to play a key role in the association between COVID-19 and DM [60] (Table 1 ). suggested that higher ACE2 expression in the lungs increased susceptibility to SARS-CoV-2 infection with more severe complications and was causally correlated with diabetes [68] . In this review, we describe three potential mechanisms underlying the increased susceptibility of patients with diabetes to a more severe COVID-19 disease, leading to higher morbidity and mortality. doi = 10.1007/s11154-020-09573-6 id = cord-342569-ja96xfns author = Azer, Samy A. title = COVID-19: Pathophysiology, diagnosis, complications and Investigational therapeutics date = 2020-08-05 keywords = COVID-19; CoV-2; SARS; patient summary = On 31 December 2019, the Chinese authorities reported to the World Health Organisation (WHO) an emerging of a novice coronavirus, currently the virus is known as SARS-CoV-2 and the disease name is coronavirus-19 disease (COVID19) , that has emerged in patients from Wuhan city, Hubel Province [1] . Recently it was debated that targeting the Notch signalling to prevent SARS-CoV-2 infection and interfering with the progression of COVID-19associated heart and lungs disease pathogenesis [13] . It is not clear whether the observed SARS-CoV-2-associated liver injury is cause by direct viral injury or related to hepatoxic drugs, coexisting systemic inflammatory changes, sepsis, respiratory distress syndrome-induced hypoxia, and multiple organ failure [18] . In patients with type 2 diabetes mellitus who are infected with COVID-19, it is important to remember that two receptor proteins ACE-2 and dipeptidyl peptidase-4 (DPP-4) are test can detect IgM, and IgG antibodies against SARS-CoV-2 in the serum, plasma, and whole blood [23] . doi = 10.1016/j.nmni.2020.100738 id = cord-297870-m7n43k4p author = Azevedo, Rafael Bellotti title = Covid-19 and the cardiovascular system: a comprehensive review date = 2020-07-27 keywords = ACE2; COVID-19; SARS; patient summary = Moreover, as in other respiratory infections, preexisting CV diseases and risk factors can increase the severity of COVID-19, leading to the aggravation and decompensation of chronic underlying cardiac pathologies as well as acute-onset of new cardiac complications [3] , highlighting that myocardial injury can be present in approximately 12% of hospitalized patients with SARS-CoV-2 infection [1] . Within the CV manifestations of COVID-19, we can highlight four different aspects: (a) CV risk factors and established CV disease is associated with a worse prognosis, (b) appearance of acute CV complications in previously healthy individuals, (c) promising therapies with antimalarials and antivirals present important CV side effects, and (d) questioning the safety of the use of renin-angiotensin-aldosterone system (RAAS) inhibitors regarding an increased risk of COVID-19 [1] . doi = 10.1038/s41371-020-0387-4 id = cord-332153-fczf3lzc author = Azkur, Ahmet Kursat title = Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19 date = 2020-05-12 keywords = CD8; COVID-19; SARS; patient summary = In this review, we aim to improve our understanding on the immune response and immunopathological changes in patients linked to detoriating clinical conditions such as, cytokine storm, acute respiratory distress syndrome, autopsy findings and changes in acute phase reactants and serum biochemistry in COVID‐19. The IgM, IgA and IgG type virus‐specific antibodies levels are important measurements to predict population immunity against this disease and whether cross‐reactivity with other coronaviruses is taking place.High viral‐load during the first infection and repeated exposure to virus especially in healthcare workers can be an important factor for severity of disease. It should be noted that many aspects of severe patients are unique to COVID‐19 and are rarely observed in other respiratory viral infections, such as severe lymphopenia and eosinopenia, extensive pneumonia and lung tissue damage, a cytokine storm leading to acute respiratory distress syndrome and multiorgan failure. doi = 10.1111/all.14364 id = cord-335802-1kiqfy68 author = Azoulay, Elie title = Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset date = 2020-08-11 keywords = ICU; SARS; patient summary = METHODS: In a multicentre retrospective study, we included 379 COVID-19 patients admitted to four ICUs between 20 February and 24 April 2020 and categorised according to time from disease onset to ICU admission. To test the hypothesis that COVID-19-related critical illness differs according to time from viral symptom onset to ICU admission, we assessed patient characteristics and outcomes in a cohort of 379 critically ill patients admitted to four university-affiliated hospitals in Paris. This study collecting data from 379 COVID-19 patients showed that mortality decreased with increasing time from viral symptom onset to ICU admission. Mortality was significantly higher in patients admitted to the ICU within a week after viral symptom onset, independently from acute illness severity at ICU admission. Second, the excess mortality in patients admitted to the ICU within 7 days after viral symptom onset was associated with an increased prevalence of non-respiratory injury and, more specifically, of acute kidney and myocardial injury. doi = 10.1007/s00134-020-06202-3 id = cord-343523-xb4ee5r5 author = Azouz, Haya title = COVID-19 in an Infant with Congenital Adrenal Hyperplasia: A Case Report date = 2020-10-05 keywords = SARS summary = Herein, we present a case of a 5-week-old infant with congenital adrenal hyperplasia who acquired SARS-CoV-2 and recovered with minimal medical support. Unlike 10% to 33% of the adult population, only 5.7% to 20% of known pediatric patients with SARS-CoV-2 infection required hospitalizations. We present a case report of an infant with a prior diagnosis of congenital adrenal hyperplasia (CAH) who was found to have SARS-CoV-2 infection. Since the start of the SARS-CoV-2 pandemic, several studies have been published pertaining to clinical presentation in various age groups, possible management options and its implications in patients with other comorbidities. To our knowledge, this is the first case report of SARS-CoV-2 infection in an infant with underlying adrenal insufficiency secondary to CAH. Our patient presented with fever and irritability that was worrisome given his age, the current pandemic and his underlying adrenal insufficiency. Interestingly, a prior case report of a 2-week-old infant with SARS-CoV-2 noted skin and soft tissue infection. doi = 10.1177/2333794x20958933 id = cord-355567-60sfv60p author = Azuma, Kenichi title = Environmental factors involved in SARS-CoV-2 transmission: effect and role of indoor environmental quality in the strategy for COVID-19 infection control date = 2020-11-03 keywords = COVID-19; CoV-2; Japan; SARS; air; ventilation summary = Recently, 36 researchers insisted on the potential risk of indoor airborne transmission of SARS-CoV-2 and the importance of sufficient and effective ventilation, particle filtration, and air sterilization as infection control measures inside buildings [43] . Therefore, the MHLW published a document titled "Prevention of the COVID-19 Clusters" Abbreviation: SARS-CoV severe acute respiratory syndrome coronavirus Fig. 1 Traditional Japanese office building HVAC systems: a a centralized HVAC system; and b a centralized ventilation system with an individual air-conditioning system on March 1, 2020 [94] , showing the need for adequate ventilation in buildings because a ventilation standard for infection control has not been established in general buildings in Japan and the characteristics of indoor spaces where the clusters occurred might include poor ventilation and crowding. doi = 10.1186/s12199-020-00904-2 id = cord-257732-3xuy6tbn author = Azzi, Lorenzo title = Saliva is a reliable tool to detect SARS-CoV-2 date = 2020-04-14 keywords = COVID-19; SARS; patient summary = OBJECTIVES: This study analyzed salivary samples of COVID-19 patients and compared the results with their clinical and laboratory data. At present, Real Time reverse transcription Polymerase Chain Reaction (rRT-PCR) on respiratory specimens represents the gold standard test for detection of SARS-CoV-2 infection. 10 , 11 Sputum and oropharyngeal secretions have recently been suggested as a possible target for the molecular diagnosis of COVID-19, 12 and salivary droplets represent the main source of the human-to-human transmission of the SARS-CoV-2 infection when social distance is less than 2 m. There were not significant differences regarding the clinical and anamnestic history between males and females, with the only exception of the values of serum LDH, which were higher in the female patients'' haematochemical analyses carried out on the day of saliva collection ( p = 0.025). doi = 10.1016/j.jinf.2020.04.005 id = cord-352296-rpjehijd author = Azzi, Lorenzo title = Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern date = 2020-05-11 keywords = SARS summary = title: Two cases of COVID‐19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern During our research, we found two patients out of 25 subjects (i.e., 8%) affected by COVID-19 with different degrees of severity, who showed positive salivary results on the same days when their pharyngeal or bronchoalveolar swabs proved to be negative . These findings, together with those reported by the F I G U R E 1 The temporal line of the clinical course in the two patients shows how their salivary samples tested positive, while the pharyngeal or bronchoalveolar swabs were negative on the same day (Patient 1 on March 19) or during the interval between two consecutive salivary swabs (Patient 2, March 23-28) Chinese colleagues on sputum, rise the concern about how to manage these patients before hospital discharging. Two cases of COVID-19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: A rising concern doi = 10.1111/odi.13368 id = cord-306108-ja0wyr5w author = B K, Anupama title = A Review of Acute Myocardial Injury in Coronavirus Disease 2019 date = 2020-06-03 keywords = COVID-19; SARS; injury; patient summary = Although SARS-CoV-2 infection predominantly causes pulmonary complications, such as pneumonia and ARDS, the disease has also been associated with a variety of cardiovascular complications, including acute myocardial injury, myocarditis, arrhythmia, heart failure, and venous thromboembolism [6] . Hence, one potential explanation for the higher likelihood of acquiring infection, and the increased risk of severe disease and adverse outcomes in patients with COVID-19 with pre-existing CVD, maybe the elevated secretion of ACE2 in these patients, thus making them more susceptible to direct viral damage to cardiac myocytes [33] ; but, this has not yet been demonstrated in pathology studies. In a single-center, retrospective cohort study including 188 patients with COVID-19 in Wuhan, China, conducted to explore whether heart injury occurred during COVID-19 on admission and later increased mortality, approximately 11.2% of patients had high-sensitivity cardiac troponin I (hs-TnI) exceeding the clinical upper normal limit on admission. doi = 10.7759/cureus.8426 id = cord-311918-gifwg2ho author = BENDER, Whitney R. title = Universal Testing for SARS-CoV-2 in Two Philadelphia Hospitals: Carrier Prevalence and Symptom Development Over Two Weeks date = 2020-09-11 keywords = SARS; woman summary = Objectives To describe the prevalence of positive SARS-CoV-2 tests among asymptomatic pregnant women at two Philadelphia obstetric hospitals, characterize the clinical course of those testing positive, and report symptom development among all women tested in the two weeks post-hospitalization. 242 (78.1%) and 213 (68.7%) of the 310 women who were SARS-CoV-2 negative at time of initial hospitalization were reached for telephone follow-up at one and two weeks post-admission, respectively. Conclusions The asymptomatic positive SARS-CoV-2 test rate among an obstetric population in Philadelphia differed between two hospitals and was lower than described in other geographic regions. The objectives of this study are to describe the prevalence of positive SARS-Cov-2 tests 123 at time of admission for delivery among asymptomatic pregnant women in Philadelphia within 124 two large academic hospitals, characterize the in-hospital clinical course for those who tested 125 positive, and report the development of viral symptoms in all women tested for two weeks 126 after hospital discharge. doi = 10.1016/j.ajogmf.2020.100226 id = cord-319855-78xmxymu author = BR, Bharath title = In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19 date = 2020-07-01 keywords = ACE2; RBD; SARS summary = The three molecules streptomycin, ciprofloxacin, and GA had low interaction penalties and displayed better interactions with the ACE2 binding site on the RBD of SARS-CoV-2-S, as shown in Figure 8A -C, respectively. Further, in the RMSF plot for the RBD domain of the GA/SARS-CoV-2-S complex, shown in Figure 11C , the RMSF at loop region was 6.3Å with a high number of ligand contacts (green-coloured vertical bars), justifying the interactions seen in molecular docking. In the protein-ligand contact plot for the streptomycin/ SARS-CoV-2-S complex, shown in Figure 12A , residues Glu493 and Lys544 showed maximum interactions fractions, i.e. 0.20 facilitated by hydrogen bonds and water bridges. In the protein-ligand contact plot for the ciprofloxacin/ SARS-CoV-2-S complex shown in Figure 12B , residues Phe465, Tyr482, Tyr498, and Phe499 were seen to have the interactions fractions 0.75, 0.6, 0.35 and 0.39 respectively facilitated by hydrophobic, hydrogen bonds and water bridges. doi = 10.12688/f1000research.24143.1 id = cord-342625-31fe1neb author = Baba, Hiroaki title = Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide date = 2020-07-01 keywords = COVID-19; SARS summary = The patient who continued iguratimod therapy without dose reduction was treated with ciclesonide had an uneventful clinical course, but prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed after resolution of symptoms. The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly across the world, yet investigations of in patients with rheumatologic disease taking disease-modifying antirheumatic drugs (DMARDs) with immunomodulatory or immunosuppressive effects remain scarce [1] . Here we report a case of COVID-19 in a patient with rheumatoid arthritis taking iguratimod, who had prolonged viral RNA presence. A woman in her 40s with rheumatoid arthritis treated with iguratimod 25 mg twice a day was admitted to Tohoku University Hospital, Sendai, Japan, with a diagnosis of COVID-19 based on real-time reverse transcription polymerase chain reaction (real-time RT-PCR) with primers that target the N2 gene of SARS-CoV-2 as described previously [2] from nasopharyngeal swabs and sputum. doi = 10.1016/j.jiac.2020.06.022 id = cord-330338-i6ozygkp author = Babacic, H. title = Global between-countries variance in SARS-CoV-2 mortality is driven by reported prevalence, age distribution, and case detection rate date = 2020-06-02 keywords = CFR; SARS summary = Objective: To explain the global between-countries variance in number of deaths per million citizens (nDpm) and case fatality rate (CFR) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The derived explanators age-adjusted infection fatality rate (IFRadj) and case detection rate (CDR) were estimated for each country based on a SARS-CoV-2 model of China. (9) Studies suggest that the reported number of cases per million citizens (nCpm) is probably lower than the true number of infected individuals, and that this contributes to the varying CFR between countries.(5,6) CFR appears higher than the true infection fatality rate (IFR), i.e. the true proportion of individuals with a SARS-CoV-2 infection who will die in the population regardless of whether they are confirmed or not. The aim of this study was to test two mathematical hypotheses that explain the global between-countries variance in SARS-CoV-2 mortality expressed as nDpm and CFR on real data. doi = 10.1101/2020.05.28.20114934 id = cord-268622-3jireyep author = Babadaei, Mohammad Mahdi Nejadi title = The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets date = 2020-06-01 keywords = ACE2; COVID-19; SARS summary = Researchers have reported some useful information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leading to CoV disease 2019 (COVID-19). Indeed, these outcomes have elucidated the principal mechanism that the oral cavity is basically in higher risk to SARS-CoV-2 infection and showed a piece of conformation for the ongoing inhibition approach in clinical implementation It has been also revealed that in addition to causing fever and respiratory symptoms, COVID-19 resulted in gastrointestinal disorders including diarrhoea, vomiting and some pains in abdominal part . Figure 2C also shows the SARS-CoV-2 infection-related sensitive organs which can explain about the non-respiratory symptoms identified in COVID-19 patients . According to a report from China, the fatality is observed in older people as well as patients with hypertension, chronic lung disease, diabetes, and CVDs. One of the most likely mechanisms by which COVID-19 can causes lung and cardiac damage is through the SARS-CoV-2 binding to ACE2 receptors. doi = 10.1080/07391102.2020.1767211 id = cord-312740-2ro2p77q author = Babadaei, Mohammad Mahdi Nejadi title = Development of remdesivir repositioning as a nucleotide analog against COVID-19 RNA dependent RNA polymerase date = 2020-05-20 keywords = MERS; RDV; SARS summary = A broad-spectrum of antiviral agents are being currently evaluated in clinical trials, and in this review, we specifically focus on the application of Remdesivir (RVD) as a potential anti-viral compound against Middle East respiratory syndrome (MERS) -CoV, SARS-CoV and SARS-CoV-2. First, we overview the general information about SARS-CoV-2, followed by application of RDV as a nucleotide analogue which can potentially inhibits RNA-dependent RNA polymerase of COVs. Afterwards, we discussed the kinetics of SARSor MERS-CoV proliferation in animal models which is significantly different compared to that in humans. With Having a considerable number of people worldwide infected with COVID-19, scientists have identified a number of cases of broad-spectrum antiviral agents (BSAAs) that could serve as potential candidates for the treatment of the viral diseases (Andersen et al., 2020; Ianevski et al., 2018) . Corona virus SARS-CoV-2 disease COVID-19: Infection, prevention and clinical advances of the prospective chemical drug therapeutics doi = 10.1080/07391102.2020.1767210 id = cord-306835-juitltpi author = Babaei, Fatemeh title = Curcumin (a constituent of turmeric): New treatment option against COVID‐19 date = 2020-09-06 keywords = ACE2; ALI; COVID-19; SARS; curcumin summary = The keywords used for the search were as follows: coronavirus-19, COVID-19, SARS-CoV-2, curcumin, Curcuma longa, turmeric, curcumin and antiviral, curcumin and anti-inflammatory, curcumin and antipyretic, curcumin and lung, curcumin and acute lung injury, curcumin and fatigue, curcumin and antioxidant, curcumin and ARDS, curcumin and bradykinin, curcumin and fibrosis, curcumin and Interleukin-6 (IL-6), curcumin and tumor necrosis factor-alpha (TNF-α), curcumin and NF-κB, curcumin and Toll-like receptors (TLRs), curcumin and antiapoptotic. AA: arachidonic acid, ALI: acute lung injury, AP-1: activator protein 1, BK: bradykinin, ACE2: angiotensin-converting enzyme 2, Ang II: angiotensin II, ARDS: acute respiratory distress syndrome, Cas-3: caspase 3, COX: cyclooxygenase, CXCL: chemokine (C-X-C motif) ligand, 12-HPETE: 12-hydroperoxyeicosatetraenoic acid, JNK: c-Jun N-terminal kinase, 12 LOX: 12-lipoxygenase, MMP: matrix metalloproteinase NF-κB: nuclear factor kappa-light-chain-enhancer of activated B cells, MAPK: mitogen-activated protein kinase, PAI-1: plasminogen activator inhibitor-1, PLA2: phospholipase A2, PG: prostaglandin, SMAD3: mothers against decapentaplegic homolog 3, TGF-β1: transforming growth factor-beta 1, TNF-α: tumor necrosis factor-α, TLR: Toll-like receptor, TRPA1: transient receptor potential channel subfamily vanilloid member 1, TRPV1: transient receptor potential channel subfamily A member 1 mechanisms that curcumin may be useful to prevent or treat the ARDS. doi = 10.1002/fsn3.1858 id = cord-229246-qgp7ksq8 author = Babino, Andres title = Masks and COVID-19: a causal framework for imputing value to public-health interventions date = 2020-06-09 keywords = SARS summary = In this paper, we aim to fill this gap by testing the hypothesis that the policy change regarding masks by the CDC (and local governments) decreased the number of positive cases in the states of Connecticut (CT), Massachusetts (MA), New York (NY), Rhode Island (RI), and Virginia (VA). The data from RI is harder to interpret because stay-at-home orders and masks guidelines happened close in time, and data from before April are unreliable (with less than 500 tests a day). The framework that we presented is data-driven, and therefore it relies on only a handful of hypotheses as compared to other methods For example, the counterfactual analysis relies on one hypothesis: the log-odds are piecewise linear (see Eq. 6 in the supplementary material)without the need to assume any of the hypotheses of the SIR model. doi = nan id = cord-127741-h23w89h2 author = Babuji, Yadu title = Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release date = 2020-05-28 keywords = SARS; smile; source summary = In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. For example, these data now include the 2D and 3D molecular descriptors, computed molecular fingerprints, 2D images representing the molecule, and canonical simplified molecular-input line-entry system (SMILES) [6] structural representations to speed development of machine learning models. We expect forthcoming data releases to extend to molecular conformers; incorporate the results of natural language processing extractions of drugs from COVID-related literature; provide the results of molecular docking simulations against SARS-CoV-2 viral and host proteins; and include the trained machine learning models that the team is building to identify top candidates for running various, more expensive calculations. doi = nan id = cord-275708-17cz3agx author = Babyn, Paul S. title = Severe acute respiratory syndrome (SARS): chest radiographic features in children date = 2003-11-18 keywords = Hong; Kong; SARS; Toronto summary = CONCLUSION: In pediatric cases, SARS manifests with nonspecific radiographic features making radiological differentiation difficult, especially from other commonly encountered childhood respiratory viral illnesses causing airspace disease. This article presents the initial chest radiographic findings collated from 62 children diagnosed as probable or suspect SARS cases during the recent SARS outbreak in Toronto, Singapore, and Hong Kong. Keywords Chest AE Severe acute respiratory syndrome (SARS) AE Radiography AE CT AE Children the following signs and symptoms: fever, chills, body ache, cough, sore throat, rhinorrhea, dyspnea, tachypnea, crackles, headache, dizziness, hypoxemia, malaise, myalgia, rigor, lethargy, and gastrointestinal symptoms including vomiting and diarrhea. In general, fever and cough were the most common clinical presentation amongst younger pediatric SARS cases (age<10 years), whereas, in addition to these symptoms, headache, myalgia, sore throat, chills, and/or rigor were reported in older patients (age ‡10 years). doi = 10.1007/s00247-003-1081-8 id = cord-312736-bm6t2bxz author = Bach, Paxton title = Innovative strategies to support physical distancing among individuals with active addiction date = 2020-05-27 keywords = SARS summary = In response to these dual crises, health authorities have implemented policy changes to provide new tools to practitioners who treat patients with substance use disorders, circumventing previous barriers to treatment, such as inadequate access and prohibitively regimented medication management. In British Columbia, an epicentre of the overdose epidemic in Canada, unique steps are being taken to mitigate risk for people who use drugs in the context of SARS-CoV-2. Clinical guidance published by the British Columbia Centre on Substance Use in collaboration with the provincial Ministry of Health has, for the first time, proposed an approach to prescribing these medications to patients with active substance use disorders who are thought to be at high risk for SARS-CoV-2. People with substance use disorders face compounded risk in the context of SARS-CoV-2, and implementing physical distancing measures among this population presents unique challenges. doi = 10.1016/s2215-0366(20)30231-5 id = cord-292462-zbjig3pt author = Backhaus, Andreas title = Common Pitfalls in the Interpretation of COVID-19 Data and Statistics date = 2020-06-07 keywords = COVID-19; SARS summary = Daily data releases on confi rmed COVID-19 cases and deaths provide information on the course of the pandemic. In its simplest form, the case fatality rate divides the total number of confi rmed deaths by COVID-19 by the to-Forum hence be lower than the IFR (and the CFR). Recall that the computation of the CFR only requires the total number of confi rmed deaths by COVID-19 and the total number of confi rmed cases of infections with SARS-CoV-2. Italy and South Korea are among those countries that have published demographic characteristics of their confi rmed cases comparatively early and consistently over the course of the pandemic. Consequently, the IFR divides the total number of confi rmed deaths by COVID-19 by the total number of infections with SARS-CoV-2. doi = 10.1007/s10272-020-0893-1 id = cord-256385-g1wcfrfi author = Badraoui, Riadh title = Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 date = 2020-08-05 keywords = ACE2; ARDS; COVID-19; SARS summary = title: Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 A better understood of ARDS key features and the pathophysiological injuries of the pulmonary parenchyma are linked to lessons learned from previous severe diseases associated previous coronaviruses outbreaks (especially SARS-CoV and MERS-CoV) and more the ongoing SARS-CoV-2. The novel coronavirus, finally named as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and it''s inducing Coronavirus Disease 2019 (COVID-19) (Gorbalenya et al., 2020; Khailany et al., 2020) . While SARS-CoV-2 induces mild symptoms in several infected patients (low pathogenic), it can also be associated with a fast onset of widespread infection in the lungs worsened in an acute respiratory distress syndrome (ARDS) . Lessons learned from previous severe diseases caused by coronaviruses outbreaks (SARS-CoV and MERS-CoV) and more recently SARS-CoV-2 lead to a better understood of ARDS key features associated COVID-19. doi = 10.1080/07391102.2020.1803139 id = cord-294295-sd5893ii author = Badua, Christian Luke D.C. title = Genomic and Proteomic Mutation Landscapes of SARS‐CoV‐2 date = 2020-09-24 keywords = SARS; figure; mutation summary = The overall frequency and densities of mutations in the genes and proteins of SARS‐CoV‐2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. Altogether, approximately similar proportions of nucleotide change types were observed between genomes among the geographical areas collected from December-March 2020 versus December-May 2020 ( Figure 3B , 3C). All in all, the ORF7b gene/protein was observed to have no mutations in all geographical region and between the study timepoints, therefore this gene may be potentially conserved in SARS-CoV-2. In conclusion, this study highlights the importance of the characterization of both nucleotide and amino acid mutation landscape in SAR-CoV-2 to identify hotspots and coldspots that may be significant in the effectivity of diagnostic tools and treatment options for COVID-19, over the different areas worldwide as the pandemic continues. doi = 10.1002/jmv.26548 id = cord-274788-oyk8js16 author = Bae, Sanghyuk title = Epidemiological Characteristics of COVID-19 Outbreak at Fitness Centers in Cheonan, Korea date = 2020-08-05 keywords = Korea; SARS; Zumba summary = BACKGROUND: In February 2020, a coronavirus disease 2019 (COVID-19) outbreak was reported in fitness centers in Cheonan, Korea. We determined the epidemiological characteristics of confirmed cases of SARS-CoV-2 infection, and estimated the time-dependent reproduction number to assess the transmission dynamics of the infection. In this report, we describe the epidemiological characteristics of the COVID-19 outbreak at fitness centers in Cheonan, Korea, based on the official epidemiological investigation, and document the effectiveness of contact tracing and isolation at containing the outbreaks. In the present study, we described epidemiological characteristics of a COVID-19 outbreak in fitness centers in Cheonan, Korea from February 24 to March 13, 2020. A previous epidemiological investigation of an outbreak in a single call center in Seoul, Korea reported that 99.8% of traced contacts had been tested. doi = 10.3346/jkms.2020.35.e288 id = cord-294788-9usyb1nn author = Baek, Woong Kee title = A Comprehensive Review of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-05-03 keywords = COVID-19; Epub; SARS; cell; patient summary = Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus strain that causes coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China in December 2019. It is suspected that the acute respiratory distress syndrome (ARDS)-like picture in SARS-CoV-2-infected patients is precipitated and worsened by the excess monocytes in response to GM-CSF, which is released by rapidly activated CD4+T-cell lineage [17] . have reported that the cytokine profile and the trend of the inflammatory markers of SARS-CoV-2-infected patients present similarly to the secondary hemophagocytic lymphohistiocytosis (sHLH), whose severe clinical presentation is related to the cytokine storm [23] . There is no consensus yet on how to treat SARS-CoV-2-infected patients who present with a wide spectrum of clinical symptoms and severity. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Epub ahead of print) doi = 10.7759/cureus.7943 id = cord-260886-v1ei9im8 author = Baggett, Travis P. title = COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing date = 2020-04-15 keywords = SARS summary = Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. In mid-March, 2020, Boston Health Care for the Homeless Program (BHCHP), in partnership with city and state public health agencies and community partners, created a COVID-19 response strategy that included front-door symptom screening at area shelters, expedited referrals for SARS-CoV-2 testing and isolation for those with respiratory symptoms, dedicated treatment settings for COVID-positive individuals, and detailed contact tracing of confirmed cases. With support from the Massachusetts Department of Public Health (MDPH), BHCHP rapidly conducted polymerase chain reaction (PCR) testing for SARS-CoV-2 along with focused symptom assessments among all guests residing at the shelter over a 2-day period. doi = 10.1101/2020.04.12.20059618 id = cord-259869-kwzsdhrr author = Baghizadeh Fini, Maryam title = Oral saliva and CVID-19 date = 2020-05-27 keywords = COVID-19; SARS; saliva summary = Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable. Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable in a dental office. The analysis of saliva in COVID-19 cases can help to explain the pathogenesis because epithelial oral cavity cells demonstrated ample expression of the Angiotensin-Converting Enzyme 2 (ACE2) receptor that plays a critical role in allowing SARS-CoV-2 to enter the cells [4] . SARS-CoV-2 in the lower and upper respiratory tract reaches the oral cavity along with the liquid droplets; SARS-CoV-2 in the blood may enter the mouth through the gingival crevicular fluid; and major and minor infection of the salivary gland, with the ensuing release of particles into the saliva through salivary ducts [7] . Detection of SARS-CoV-2 in Saliva and Characterization of Oral Symptoms in COVID-19 Patients. doi = 10.1016/j.oraloncology.2020.104821 id = cord-276414-kicu0tv5 author = Bahadur Gurung, Arun title = In silico screening of FDA approved drugs reveals ergotamine and dihydroergotamine as potential coronavirus main protease enzyme inhibitors date = 2020-06-10 keywords = FDA; SARS summary = Interestingly, the anti-migraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. In the present study, we have explored the possibilities of FDA approved drugs as potential inhibitors of the coronavirus main protease, a therapeutically important drug target playing a salient role in the maturation and processing of the viral polyproteins and are vital for viral replication and transcription. Interestingly, the antimigraine drugs such as ergotamine and its derivative, dihydroergotamine were found to bind to all the three target enzymes within the Cys-His catalytic dyad cleft with lower binding energies as compared to the control inhibitors (α-ketoamide 13b, SG85 and GC813) and the molecules are held within the pocket through a good number of hydrogen bonds and hydrophobic interactions. doi = 10.1016/j.sjbs.2020.06.005 id = cord-265221-qtkwciym author = Bahadur, Gulam title = SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date = 2020-06-03 keywords = PCR; SARS summary = It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. raising equal concerns for embryo and fetal development (Colaco et al., 2020) .In males, ACE2 receptor sites have been reported in testicular tissue which then have the capability to harbour SARS-CoV-2 virus and eventual shedding into the semen and hence its implication in sexual transmission, early pregnancy or early in utero embryonic development. Studies analysing SARS-CoV-2 in seminal fluid or testicular biopsies have so far lacked appropriate controls and patients suffered from predominantly mild infections and tested several weeks after the infection, thereby increasing the complexity of result interpretation. Also no SARS-CoV-2 was detected in expressed prostatic secretion (EPS) of 18 confirmed Covid-19 infected patients and 5 strongly suspected cases but absent semen analyses. doi = 10.1016/j.rbmo.2020.05.014 id = cord-313379-6sa6oc6u author = Bahar, B. title = Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children date = 2020-08-07 keywords = August; SARS summary = title: Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children 14 We report viral and antibody testing results from our 95 pediatric patient population in order to contribute to a better understanding of timing of viral 96 clearance and antibody production in children with In addition to the RT-PCR results, qualitative and quantitative serologic testing results, age and 107 sex were also included in the data extracts. In this study, we demonstrated that IgG class antibodies directed against S1 and S2 228 glycoproteins could be detected in blood samples of children before viral clearance. . https://doi.org/10.1101/2020.08.06.20162446 doi: medRxiv preprint A strength of our study was the inclusion of patients from multiple pediatric age groups with 262 sequential PCR testing, which allowed comparison between age groups and sex serologic assays for SARS-CoV-2 are still in early phases of development. doi = 10.1101/2020.08.06.20162446 id = cord-290277-ndfoppoq author = Bahl, Prateek title = Airborne or droplet precautions for health workers treating COVID-19? date = 2020-04-16 keywords = SARS; droplet summary = World Health Organization (WHO) has issued guidelines for contact and droplet precautions for Healthcare Workers (HCWs) caring for suspected COVID-19 patients, whilst the US Centre for Disease Control (CDC) has recommended airborne precautions. We aimed to review the evidence for horizontal distance travelled by droplets and the guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) on respiratory protection for COVID-19. We aimed to review the evidence supporting the rule of 1 m (≈3 ft) spatial separation for droplet precautions in the context of guidelines issued by the World Health Organization (WHO), US Center for Diseases Control (CDC) and European Centre for Disease Prevention and Control (ECDC) for HCWs on respiratory protection for COVID-19. Interim Infection Prevention and Control Recommendations for Hospitalized Patients with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) doi = 10.1093/infdis/jiaa189 id = cord-030934-t7akdu6x author = Bahrami, Afsane title = Genetic and pathogenic characterization of SARS-CoV-2: a review date = 2020-08-26 keywords = ACE2; COVID-19; CoV-2; SARS; Wuhan; coronavirus summary = The first case of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in December 2019. Bioinformatics analysis of the viral genome from one COVID-19 patient shared 89 and 82% sequence similarity with bat SARS-like-CoVZXC21 and human SARS-CoV, respectively [41] . In a recent report it was shown that SARS-CoV-2''s S-protein entry into 293/human ACE2 receptor cells is primarily mediated via endocytosis, and that PIKfyve, a TPC2 and cathepsin L are crucial for virus entry. Findings of an open-label nonrandomized clinical trial among 22 infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in COVID-19 cases and its effectiveness is promoted by azithromycin [99] . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response doi = 10.2217/fvl-2020-0129 id = cord-289892-yh1lioyz author = Bai, Bingke title = Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date = 2008-07-16 keywords = SARS summary = Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. In addition, because in vitro infection model of bat SL-CoV has not so far been established, we intended to use VLPs as an alternative to study the immune responses induced in DCs. Therefore, we compared the phenotypic and functional changes of immature DCs inoculated with BVLPs or with SARS CoV VLPs. The S-specific immune activation was further confirmed in mice using S DNA vaccines. Combining the flow cytometry results in Fig. 2 , it is reasonable to draw a conclusion that the structure of BVLPs, not LPS contamination, contributed to cytokine production in BVLPs-treated DCs. We previously constructed SARS CoV VLPs and investigated the humoral and cellular immune responses induced by SARS CoV VLPs in mice [29] . doi = 10.1371/journal.pone.0002685 id = cord-300423-q2i328sz author = Bai, Lei title = Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date = 2020-10-14 keywords = IAV; SARS summary = Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. The results demonstrate that the pre-infection of 57 IAV strongly enhances the infectivity of SARS-CoV-2 by boosting viral entry in the cells 58 and by elevating viral load plus more severe lung damage in infected mice. We 75 further tested more cell lines to show that the enhancement of the pSARS-CoV-2 infectivity 76 by IAV was a general effect although the increased folds were different (lower basal level 77 of infectivity, higher enhancement fold) (Fig.1D ). We found that the pre-infection of IAV 80 strongly increased the copy numbers of the SARS-CoV-2 genome (E and N genes) in both 81 cell lysates and supernatants of A549 (~15 folds) (Fig.1F) . The histological data in Fig. 2D further illustrated that IAV and 98 SARS-CoV-2 co-infection induced more severe lung pathologic changes with massive 99 infiltrating cells and obvious alveolar necrosis as compared to SARS-CoV-2 single 100 infection or mock infection. doi = 10.1101/2020.10.14.335893 id = cord-352886-6lzlt6ur author = Bai, Qifeng title = MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm date = 2020-08-11 keywords = GCGR; SARS summary = Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. To use the merit of deep learning, our designed soft tool employs the sequencebased generative model and graph neural networks (GNNs) generative model for producing the ligand set and small molecular fragments (see Figure 1 ). Figure 7B shows the drug virtual screening results of SARS-CoV-2 M pro from 2 million druglike ligands by deep learning generative model and molecular docking. doi = 10.1093/bib/bbaa161 id = cord-254162-tu81j66h author = Bai, Xiyuan title = Hypothesis: alpha-1-antitrypsin is a promising treatment option for COVID-19 date = 2020-11-12 keywords = AAT; ACE2; ADAM17; COVID-19; SARS summary = Sixth, AAT inhibition of elastase can antagonize the formation of neutrophil extracellular traps (NETs), a complex extracellular structure comprised of neutrophil-derived DNA, histones, and proteases, and implicated in the immunothrombosis of COVID-19; indeed, AAT has been shown to change the shape and adherence of non-COVID-19-related NETs. Seventh, AAT inhibition of endothelial cell apoptosis may limit the endothelial injury linked to severe COVID-19-associated acute lung injury, multi-organ dysfunction, and pre-eclampsia-like syndrome seen in gravid women. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. First, AAT is a serine protease inhibitor (SERPIN) shown to inhibit TMPRSS-2, the host serine protease that cleaves the spike protein of SARS-CoV-2, a necessary preparatory step for the virus to bind its cell surface receptor ACE2 to gain intracellular entry. doi = 10.1016/j.mehy.2020.110394 id = cord-269021-juh2qkm0 author = Bai, Zhihua title = The Rapid Assessment and Early Warning Models for COVID-19 date = 2020-04-01 keywords = China; SARS summary = Human beings have experienced a serious public health event as the new pneumonia (COVID-19), caused by the severe acute respiratory syndrome coronavirus has killed more than 3000 people in China, most of them elderly or people with underlying chronic diseases or immunosuppressed states. In the case of a gradually improved infectious disease surveillance system, the research on forecasting and early warning of epidemics based on models has become the focus of the public health system. In response to the current epidemic of SARS-CoV-2, many researchers have developed mathematical models with varying degrees of complexity, aiming to assess the capacity of pathogen transmission and which interventions are most likely to be effective (Fig. 2) . Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven Modelling analysis of the early outbreak doi = 10.1007/s12250-020-00219-0 id = cord-322811-6lebh7ca author = Baig, Mirza S. title = Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells date = 2020-06-26 keywords = ACE2; CoV-2; SARS summary = METHODS: Docking and Molecular Dynamics (MD) simulation studies revealed that designed peptide maintains their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. RESULTS: We have designed a novel peptide that could inhibit SARS-CoV-2 spike protein interaction with ACE2, thereby blocking the cellular entry of the virus. Currently, the computational analysis of structural differences in human ACE2 impact its binding to the SARS-CoV-2 spike protein, which thereby lays a foundation for the design and development of ACE2-based peptide inhibitors of SARS-CoV-2 [47] [48] [49] . After a detailed analysis of interface residues, a small stretch of the ACE2 PD N-terminal region (23-amino acids: Glu23 to Leu45) was found to be interacting majorly with the SARS-CoV-2 spike protein ( Fig. 2 and Table 1 ). Computational alanine (A) scanning was performed to identify the critically important amino acids of the 23aa peptide inhibitor involved in binding to the SARS-CoV-2 spike protein. doi = 10.1007/s40268-020-00312-5 id = cord-270550-if748w2n author = Bailey, Adam L. title = SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date = 2020-11-05 keywords = ACE2; CoV-2; Fig; RNA; SARS summary = To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. doi = 10.1101/2020.11.04.364315 id = cord-258873-l9oxmqdp author = Baker, D. title = COVID‐19 vaccine‐readiness for anti‐CD20‐depleting therapy in autoimmune diseases date = 2020-08-01 keywords = COVID-19; SARS summary = It appears that the innate immune response, and perhaps later anti-viral CD8 T cell responses, could eliminate the SARS-CoV2 before significant antibody responses have developed [20, 28, 33] (Fig. 1) , suggesting that most MS treatments that largely exhibit limited persistent effects on the innate immune and CD8 T cell responses would have limited influence on COVID-19. The suggestion that rituximab treatment may increase risk of infection should be considered in the context of possible sampling biases, although this Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells in the lung and the gut via the angiotensin-converting enzyme 2 (ACE2). If COVID-19-related vaccine responses become a key concern among people with MS or other autoimmune diseases choosing treatment options, the selection of B cell-depleting agents that allow quick repopulation of B cells may be relevant for optimum vaccine readiness. doi = 10.1111/cei.13495 id = cord-332271-slouuryl author = Baker, Jeremy D. title = A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date = 2020-08-27 keywords = Mpro; SARS; drug summary = title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing 27 as selective and potent inhibitors of SARS-CoV-2 Mpro. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Taken together this work suggests previous large-scale commercial 35 drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some 36 previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for 37 rapid repurposing. Before screening the Broad library, 100 we piloted our assay conditions against the NIH Clinical collections library (~650 compounds) and 101 calculated our Z''-factor for each plate at 0.780 and 0.784 (Fig 1C and D) . doi = 10.1101/2020.07.10.197889 id = cord-343043-piyt3i0h author = Baker, S. A. title = Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation. date = 2020-07-07 keywords = ACE2; SARS; at2; expression summary = In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly. Given that the mechanism of death in Covid-19 typically involves severe lower respiratory tract infection, a disease feature strongly correlated with age, previous studies have sought to connect lung ACE2 expression with aging 28, 29 . If lung ACE2 expression is triggered by mechanical ventilation itself via inflammatory cytokine production, then these factors may predispose older individuals to severe SARS-CoV-2 infection. In this small series of cases, we identified increased ACE2 RNA and ACE2 protein expression within the human lung associated with age, when controlling for ventilator status. doi = 10.1101/2020.07.05.20140467 id = cord-348823-u2gm3kyh author = Baksh, Mizba title = A Systematic Review of Cases of Acute Respiratory Distress Syndrome in the Coronavirus Disease 2019 Pandemic date = 2020-05-18 keywords = ARDS; COVID-19; SARS summary = About 80% of COVID-19 infections are mild or asymptomatic and never require hospitalization but about 5% of patients become critically ill and develop acute respiratory distress syndrome (ARDS). The widely used management for ARDS in COVID-19 has been in line with the standard approach, but the need to adjust the treatment protocols has been questioned based on the reports of higher mortality risk among those requiring mechanical ventilation. Although some antimalarial and antiviral drugs may prove effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), their safety and efficacy are still under clinical trials. We conducted a systematic review of case reports on ARDS in SARS-CoV-2 infection to summarize the clinical presentation, laboratory and chest imaging findings, management protocols, and outcome of ARDS in COVID-19-positive patients. Tissue plasminogen activator (tPA) treatment for COVID-19 associated acute respiratory distress syndrome (ARDS): a case series doi = 10.7759/cureus.8188 id = cord-009295-4c0zwhdh author = Bal, A. title = Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date = 2020-03-28 keywords = SARS; sample summary = title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) The phylogenetic analysis using the 571 WGS of SARS-CoV-2 publicly available (as of March 17th 2020) found that this sequence clustered with a sequence (EPI_-ISL_408488) collected in Jiangsu, China, on January 19th, suggesting a separate introduction from Asia (Fig. 1) . Compared to the reference SARS-CoV-2 sequence, a three-nucleotide deletion in open reading frame 1a (ORF1a) at positions 1607e1609 was identified. Letter to the Editor / Clinical Microbiology and Infection xxx (xxxx) xxx SARS-CoV-2 sequences were not further compared between the two patients due to largely incomplete coverage of the SARS-CoV-2 genome in sample #1. Despite low viral loads, the mNGS workflow used herein allowed us to characterize the wholegenome sequences of SARS-CoV-2 isolated from an asymptomatic patient in two clinical samples collected 1 day apart. doi = 10.1016/j.cmi.2020.03.020 id = cord-339711-f7xifne8 author = Bal, A. title = Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test date = 2020-09-30 keywords = SARS; Wantai summary = title: Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test The first study exploring the association of 75 commercial serological assays and VNT claimed that the Wantai Total Ab assay detecting 76 total antibodies directed against the SARS-CoV-2 receptor binding domain (RBD) had the 77 best characteristics to detect functional antibodies at different stages and severity of disease 78 [12] . In the first study comparing VNT with commercialized 215 tests, the authors found that the Wantai Total Ab assay had the best characteristics to detect 216 functional antibodies in different stages and severity of disease [12] . For evaluating protective immunity, the Wantai Total Ab assay 247 with an optimized cut-off or other tests targeting the S protein as Euroimmun, DiaSorin or 248 bioMérieux IgG could be more useful, notably to screen serum specimens candidate for the 249 presence of neutralizing antibodies. doi = 10.1101/2020.09.30.20194290 id = cord-283138-18q23z8l author = Balasubramanian, S. title = Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date = 2020-04-09 keywords = COVID-19; SARS; child; infection summary = Pediatric coronavirus disease-19 (COVID-19) infection is relatively mild when compared to adults, and children are reported to have a better prognosis. Clinical features of COVID-19 in children include fever and cough, but a large proportion of infected children appears to be asymptomatic and may contribute to transmission. It remains unclear why children and young adults are less severely affected than older individuals, but this might involve differences in immune system function in the elderly and/or differences in the expression/function of the cellular receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)Angiotensin converting enzyme 2 (ACE2). This review additionally considers COVID-19 in immunosuppressed children, and also suggests a management algorithm for the few children who appear to present with life threatening infection, including the potential use of antiviral and immunomodulatory treatment. Asymptomatic, mild and moderate infections comprise over 90% of all children who have tested positive for COVID-19 with fewer severe and critical cases (5.9%) compared to adults (18.5%) [13] . doi = 10.1007/s13312-020-1819-5 id = cord-352814-fcl2g5wr author = Balboni, Andrea title = A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date = 2011-11-22 keywords = PCR; RNA; SARS summary = In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The aim of this work was to develop a real-time PCR assay for diagnosing infection with SARS-related coronaviruses from bat guano in order to use it as a screening tool in epidemiological surveys for the detection of the viruses. The developed SYBR Green real-time PCR techniques were applied to an SARS-like coronavirus survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) which were sampled in Italy in 2009, resulting in a prevalence of coronavirus infection of 42%. After optimisation of the SYBR Green real-time PCR assay, for each run, duplicates of six 10-fold dilutions of the standard plasmid, triplicates of the viral reverse-transcribed RNA of the bat samples, and a no template control were simultaneously subjected to analysis. doi = 10.1100/2012/989514 id = cord-296128-kjoi54ea author = Balestri, Riccardo title = Do we have serological evidences that chilblain‐like lesions are related to SARS‐CoV‐2? A review of the literature date = 2020-08-26 keywords = CLL; SARS summary = Our review demonstrated a high prevalence of negative serological results in CLL: antibodies were observed only in a few patients, that are even less excluding those with positive IgA, not clearly involved in the pathogenesis of the disease. The outbreak of chilblain-like lesions (CLL) coincidentally to the COVID-19 pandemic is a topic of great concern 1 SARS-CoV-2 was hypothesized as the etiologic agent of CLL, initially on the basis of the temporal correlation between the "burst" of skin manifestations and the viral pandemic. However, it has been shown that CLL are not related to an acute infection, since real-time reverse transcription polymerase chain reaction (rt-PCR) tests from nasopharyngeal swabs seldom resulted positive 1-9Therefore, dermatologists'' attention shifted to the search for specific SARS-CoV-2 antibodies. The search was limited to articles published in English We included only case series, clearly declaring that a search for SARS-CoV-2 specific antibodies had been performed. Chilblain-like lesions during COVID-19 pandemic: a serological study on a case series doi = 10.1111/dth.14229 id = cord-319754-5isw53wl author = Balgoma, David title = Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date = 2020-08-31 keywords = HCV; SARS; cell; fusion; lipid; membrane; protein; virus summary = Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . doi = 10.3390/metabo10090356 id = cord-262192-w86qc3fq author = Balkhair, Abdullah A. title = COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases date = 2020-04-21 keywords = COVID-19; SARS summary = According to the World Health Organization (WHO), the world has witnessed the emergence of several disease outbreaks and epidemics caused by more than 20 infectious agents over the past decade. 3 Over the past two decades, the emergence of coronavirus-associated diseases (SARS and MERS) inflicted global challenges to public health systems. This is exemplified by the current COVID-19 pandemic where the appearance of a seemingly limited cluster of cases of pneumonia linked to a sea food market in Wuhan, China 7 has become one of the worst pandemics in human history with a staggering number of more than 1.4 million infections in 177 countries and more than 85 000 deaths globally as of 9 April 2020. The quest for a vaccine against SARS-CoV-2 is an urgent priority, and its development and global availability is a prerequisite for ending the COVID-19 pandemic. The current COVID-19 pandemic and its dreadful global impact is a reminder of the potential detriment of emerging infectious diseases. doi = 10.5001/omj.2020.41 id = cord-355528-y4a1g6km author = Balla, Mamtha title = COVID-19, Modern Pandemic: A Systematic Review From Front-Line Health Care Providers’ Perspective date = 2020-03-30 keywords = COVID-19; China; SARS; Wuhan; patient summary = The main aim of this systematic review is to provide a comprehensive clinical summary of all the available data from high-quality research articles relevant to the epidemiology, demographics, trends in hospitalization and outcomes, clinical signs and symptoms, diagnostic methods and treatment methods of COVID-19, thus increasing awareness in health care providers. Coronavirus disease 2019 (COVID19) infection, which is a global pandemic declared on March 11, 2020, by World Health Organization (WHO), was reported to have infected 168,000 cases worldwide in about 148 countries and territories and killed more than 6,610 people around the world as of March 16, 2020 [1]. According to the study by Xu et al, 60% of people diagnosed with COVID-19 had traveled to Wuhan or nearby regions (60%), 36% had close contact with novel coronavirus pneumonia (NCP) patients and 4% had no definite exposure [12] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.14740/jocmr4142 id = cord-265473-ju81kiyw author = Balmeh, Negar title = Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date = 2020-08-07 keywords = ACE2; GRP78; SARS summary = Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Approximately 377 predicted and valid targets of hsa-miR-1307 which were predicted The best herbal compounds for ACE2, TMPRSS2, GRP78, and AT1R receptors were identified based on their binding energy. The molecular docking results of the ACE2, TMPRSS2, GRP78, and AT1R receptors with medicinal herbal compounds are presented in Supplementary Table 2 . Increased expression of hsa-miR-1307-3p may lead to a reduction in SARS-CoV-2 replication through binding to the 3''UTR site of the virus genome. It has been confirmed that endocytosis and exocytosis are associated with virus entry and spread, therefore, controlling these pathways by hsa-miR-1307-3p could be an effective strategy for SARS-CoV-2 infection. doi = 10.1016/j.imu.2020.100407 id = cord-291577-nf80kih2 author = Baluku, Joseph Baruch title = HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date = 2020-05-21 keywords = HIV; SARS summary = From Wuhan, China, Zhu et al., reported a severe case of a newly diagnosed HIV/SARS-CoV-2 co-infected male with diabetes who presented with fever, hypoxemia, lymphopenia and chest computed tomography (CT) abnormalities, who was managed on oxygen therapy, the HIV antiviral agent lopinavir/ritonavir, moxifloxacin, gamma-globulin and methyl prednisone (5) . also reported 5 cases of HIV/SARS-CoV-2 co-infection -of whom 4 were virologically suppressed on antiretroviral therapy (ART) -from Spain, who invariably presented with cough and fever (6) . In a case series from Spain, all HIV/SARS-CoV-2 co-infected patients had cough and fever (6) . Also, similar to this patient, the HIV co-infected patient who had good adherence to ART and a suppressed viral load, presented with weakness and non-bloody diarrhoea with no significant clinical signs and laboratory abnormalities in a case series from Turkey (11) The presentation with chest pain, tachypnea, normal auscultation findings and tachycardia raises the possibility of alternative diagnoses that could mimic COVID -19. doi = 10.1002/jmv.26044 id = cord-342189-ya05m58o author = Banerjee, Abhik K. title = SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date = 2020-10-08 keywords = GFP; IFN; NSP1; RNA; SARS; SRP; figure; protein summary = Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. doi = 10.1016/j.cell.2020.10.004 id = cord-269537-h3lzl1un author = Banerjee, Aditi title = Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19 date = 2020-05-23 keywords = Andrographolide; COVID-19; SARS summary = Viral infections including SARS-CoV are associated with increased levels of reactive oxygen species, disturbances of Ca(++) caused by unfolded protein response (UPR) mediated by endoplasmic reticulum (ER) stress and is due to the exploitation of virus''s own protein i.e., viroporins into the host cells. Considering the properties of both compounds in terms of anti-inflammatory, antioxidant, anti-pyrogenic, anti-viral and ER stress modulation and computational approaches revealing andrographolide docks with the SARS-CoV2 binding site, we predict that this combination therapy may have potential utility against COVID-19. Accumulating evidence suggests that ER stress and sustained UPR signaling are major contributors to the pathogenesis of several diseases, including inflammatory disorders and viral infections [15] and can increase the severity of these events [16] . Endoplasmic reticulum stress and IRE-1 signaling cause apoptosis in colon cancer cells in response to andrographolide treatment doi = 10.1016/j.lfs.2020.117842 id = cord-295433-olmein3q author = Banerjee, Arinjay title = Bats and Coronaviruses date = 2019-01-09 keywords = MERS; SARS; bat; virus summary = Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . doi = 10.3390/v11010041 id = cord-284627-qvz63m93 author = Banerjee, Shuvam title = Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date = 2020-04-09 keywords = SARS summary = The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. 12, 14 In this study, we comprehensively analyzed the whole genome sequence homology from the available patient data uploaded by affected countries in NCBI Virus database, identified the mutations developed by different strains from the ancestor strain and studied the impact of those mutations at functional level. In summary, the present study reveals that the fatality rate increases with not only the number of mutations but also depending on its allelic rarity as well as functional alteration of protein. doi = 10.1101/2020.04.06.027854 id = cord-335075-6wo2o5pp author = Bangaru, Sandhya title = Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date = 2020-08-06 keywords = SARS; figure; spike summary = Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Site-specific glycosylation of the SARS-CoV-2 prefusion spike protein produced in SF9 insect cells was analyzed using our recently described mass spectrometry proteomics-based method, involving treatment with proteases followed by sequential treatment with the endoglycosidases (Endo H and PNGase F) to introduce mass signatures in peptides with N-linked sequons (Asn-X-Thr/Ser) to assess the extent of glycosylation and the degree of glycan processing from high mannose/hybrid type to complex type (24) . In this study, we performed structural analysis of the Novavax SARS-CoV We also observed two non-spike densities within the spike trimer that corresponded with linoleic acid and polysorbate 80 detergent. doi = 10.1101/2020.08.06.234674 id = cord-327601-4uqgwlnx author = Bangash, Mansoor N. title = SARS-CoV-2: is the liver merely a bystander to severe disease? date = 2020-06-02 keywords = SARS; liver summary = 1 Their study shows SARS-CoV-2 positive patients with ≥1 week history of increased aminotransferases have worse acute pulmonary disease (radiological and physiological) than those without. Considering that Interleukin (IL)-6 and C-reactive protein (CRP) are similar between patients with normal and prolonged abnormal liver aminotransferases, the authors speculate that liver injury is a direct effect of SARS-CoV-2 viral hepatitis rather than an indirect immune mediated injury. The fact that increases in liver aminotransferases occur and tend to parallel the severity of pulmonary disease remains unquestioned 2 , however, whether the liver injury is a true viral hepatitis rather than a bystander to the multi-organ pathophysiology of critical illness requires further discussion. Based on the above perspectives, we feel that raised liver aminotransferases associated with SARS-CoV-2 positivity are more likely attributable to illness severity, in which host response and iatrogenic harm (i.e. drugs, ventilation) drive bystander liver injury, thus explaining its association with mortality and in an analogous fashion to patterns seen in sepsis. doi = 10.1016/j.jhep.2020.05.035 id = cord-311445-b6bc6vwd author = Bansal, Kanika title = Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date = 2020-10-12 keywords = SARS; cup summary = Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. In the present study, we have focused on codon usage pattern (CUP) of SARS coronavirus from different hosts under debate (bat, pangolin, and dog) as a probable origin for SARS-CoV-2. However, another study comparing the codon usage pattern of SARS-CoV-2 with other betacoronaviruses suggested that current pandemic coronavirus is subjected to different evolutionary pressures (Gu et al., 2020) . The above analysis reveals single patterns for all five genes in different lineages of SARS-CoV-2 affirms a single event of host jump of codon-optimized SARS strain from its animal reservoir. doi = 10.1101/2020.10.12.335521 id = cord-012424-z3mkp9y9 author = Bansal, Poonam title = Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) date = 2020-08-13 keywords = SARS summary = title: Clinical Course of a Patient with Radiographically Described Acute Necrotizing Encephalopathy (ANE) We write in reference to a previously reported case of acute necrotizing encephalopathy (ANE) associated with acute SARS-COV-2 infection (1) . Repeat MRI brain without contrast showed residual T2 hyperintensities and hemosiderin deposition in the medial thalami; the former were significantly improved from previous. Several cases of COVID-19 associated ANE have now been reported (Table) . Immunotherapy has some role in the treatment of COVID-19 associated ANE, as described in the literature (1, 4, 5 COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia Acute necrotizing encephalopathy and myocarditis in a young patient with COVID-19 Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid COVID-19-associated acute necrotising encephalopathy successfully treated with steroids and polyvalent immunoglobulin with unusual IgG targeting the cerebral fibre network Does SARS-Cov-2 invade the brain? doi = 10.1148/radiol.2020203132 id = cord-343970-anocx4y1 author = Bansal, Rashika title = Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course date = 2020-06-30 keywords = ACE2; COVID-19; SARS; patient summary = ACE2 is expressed in pancreatic islets, vascular endothelium, and adipose tissue, and the SARS-CoV-2 -ACE2 interaction in these tissues, along with other factors, govern the spectrum and the severity of clinical manifestations among COVID-19 patients with metabolic syndrome. Moreover, the pro-inflammatory milieu observed in patients with metabolic syndrome may contribute towards COVID-19-mediated host immune dysregulation, including sub-optimal immune responses, hyper-inflammation, microvascular dysfunction, and thrombosis. SARS-CoV-2 virus attaches to the host cell membrane-bound angiotensin-converting enzyme 2 (ACE2) that is expressed in many cells, including the respiratory epithelial cells (type II alveolar A c c e p t e d M a n u s c r i p t epithelial cells), myocardium, Leydig cells and cells in seminiferous ducts in the testes, vascular endothelial cells, proximal renal tubular cells, gastrointestinal epithelial cells, urothelial cells lining the bladder, alveolar monocytes, macrophages, and in both exocrine pancreas and pancreatic islets (43, (46) (47) (48) . doi = 10.1210/endocr/bqaa112 id = cord-300866-cso6l6ze author = Bao, Yi title = Clinical Features of COVID-19 in a Young Man with Massive Cerebral Hemorrhage—Case Report date = 2020-05-23 keywords = COVID-19; SARS; patient summary = Both SARS-CoV-2 nucleic acid tests were negative (24 h interval), Fig. 2 The treatment of COVID-19 patients with intracerebral hemorrhage suggesting that antiviral treatment was effective. On February 29, the patient did not have high fever again, the results of the cerebrospinal fluid review showed that it was light red, no clot, protein decreased to 0.8 g/L, sugar increased to 4.45 mmol/L, and white blood cells decreased to 37 × 10 6 G/L, of which monocytes accounted for 74%. The patient''s cerebrospinal fluid showed improvement, and since the two re-examinations of SARS-CoV-2 nucleic acid test was negative, and the antiviral treatment with Abidol, Ribavirin, and Oseltamivir had reached the course of treatment, so it was discontinued. However, in combination with the patient''s high fever, lymphocytopenia, increased neutrophils, and poor antibacterial treatment effect, the clinical manifestations conform to the COVID-19 characteristics, and nucleic acid detection is required. doi = 10.1007/s42399-020-00315-y id = cord-340189-jo38hjqa author = Bar-On, Yinon M title = SARS-CoV-2 (COVID-19) by the numbers date = 2020-04-02 keywords = RNA; SARS summary = If you are infectious for 4 days, then you will infect four others on average, which is on the high end of the R 0 values for SARS-CoV-2 in the absence of physical distancing. Assuming entry of the virus to the cells is rapid (we estimate 10 min for SARS-CoV-2), the time it takes to produce progeny can be estimated by quantifying the lag between inoculation and the appearance of new intracellular virions, also known as the ''eclipse period''. While both the time to complete a replication cycle and the burst size may vary significantly in an animal host due to factors including the type of cell infected or the action of the immune system, these numbers provide us with an approximate quantitative view of the viral life-cycle at the cellular level. (Hirano et al., 1976) : "The average per-cell yield of active virus was estimated to be about 6-7  10 2 plaque-forming units." This data is for MHV, so more research is needed to verify these values for SARS-CoV-2. doi = 10.7554/elife.57309 id = cord-335784-v7nbck0n author = Barak, N. title = Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date = 2020-10-20 keywords = PCR; SARS summary = Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Major diagnostic challenges have emerged, mainly, the need for high throughput SARS-CoV-2 RT-PCR tests, aimed to detect not only symptomatic but also asymptomatic infectious viral carriers and to screen special or at-risk populations (such as health care personnel or nursing home tenants), in order to contain viral spread and guide control measures. To our knowledge, this is the most extensive analysis, addressing key considerations of efficiency, sensitivity and feasibility in the actual reality of routine, large-scale implementation of sample pooling for SARS-CoV-2 detection. doi = 10.1101/2020.10.16.20213405 id = cord-311843-un6urdb1 author = Baray, Juwel Chandra title = BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date = 2020-09-30 keywords = CD4; CD45; SARS summary = title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. The reactivity of the sera from each 221 group of mice immunized with BANCOVID was measured against SARS-CoV-2 S antigen 222 (SinoBiologicals, China). Analysis revealed IgG binding against SARS-CoV-2 S protein 223 antigens in the sera of the immunized mice. Flow cytometric analysis of total T cell (CD4 + ) populations producing TFN alpha on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. doi = 10.1101/2020.09.29.319061 id = cord-303017-4zx94rm6 author = Barbieri, Antonio title = Can Beta-2-Adrenergic Pathway Be a New Target to Combat SARS-CoV-2 Hyperinflammatory Syndrome?—Lessons Learned From Cancer date = 2020-09-30 keywords = IL-6; SARS; covid-19; patient summary = This hypothesis relies on different pieces of evidence: IL-6, TNFa, and IL-1b promote Th17 response and are associated with inflammatory symptoms including fever, and the two latter are also associated with vascular permeability and leakage; IL-17 has a broad inflammatory effect and together with GM-CSF is involved in inflammatory and autoimmune disease; Covid-19 patients have a significantly increased number of CCR6+ Th17 cells (4) ; elevated TH17 and IL-17 related pathways are increased in SARS-CoV, MERS-CoV, and H1N1 influenza virus patients (14) (15) (16) ; In MERS-CoV patients, IL-17 and low IFNg are associated with worse prognosis (14) . Targeting beta-2adrenergic pathway was shown to reduce inflammatory cytokine and Th17 response in different settings such as cancer and autoimmune diseases. Two different reports on cancer patients show that propranolol treatment reduces inflammatory cytokines including IL-6 and TNFa, inflammation-related transcription factors such as NFkB and STAT3 and reduces the activation of Treg lymphocytes (36, 37) . doi = 10.3389/fimmu.2020.588724 id = cord-260866-bzdd4f5h author = Barceló, Damià title = Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date = 2020-09-14 keywords = PCR; SARS; WBE; covid-19 summary = Paper-based devices would be certainly one of the best measurement solutions for the rapid and onsite detection of COVID-19 in sewage waters and humans as well [2, 16] and also the use of other biomarkers of exposure [1] . Detection of SARS-CoV-2 in sewage has been employed as a complementary method to clinical test .It is an early warning indicator of virus spreading in communities, covering both symptomatic and asymptomatic cases. Hopefully at certain moment applications to detect SARS-CoV-2 and other viruses in wastewater will be developed based on these LOC/POCT systems that will enable simple, fast and sensitive virus detection. PCR platforms like RT-qPCR are still the most widely used methods for SARS-Cov-2 detection in waste waters. Sewage sensors, such as paper-based and smartphones for SARS-CoV2 detection at the population level have as well a clear potential for early warning of COVID-19 pandemic. doi = 10.1016/j.cscee.2020.100042 id = cord-336000-v88bq4bx author = Barco, Stefano title = Enoxaparin for primary thromboprophylaxis in ambulatory patients with coronavirus disease-2019 (the OVID study): a structured summary of a study protocol for a randomized controlled trial date = 2020-09-09 keywords = COVID-19; LMWH; SARS; VTE; day; line; patient; study summary = OBJECTIVES: The OVID study will demonstrate whether prophylactic-dose enoxaparin improves survival and reduces hospitalizations in symptomatic ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. The OVID study will show whether prophylactic-dose enoxaparin improves survival and reduces any hospitalizations in ambulatory patients aged 50 or older diagnosed with COVID-19, a novel viral disease characterized by severe systemic, pulmonary, and vessel inflammation and coagulation activation. <30% of the expected number of patients six months after the enrolment of the first patient, also based on the course of SARS-CoV2 infections in Switzerland;  when the safety of the participants is doubtful or at risk, respectively, based on recommendations received from DSMB committee;  changes in accepted clinical practice that make the continuation of a clinical trial unwise, including the results of similar studies or the publication of international guidances. doi = 10.1186/s13063-020-04678-4 id = cord-257958-yehnlabq author = Barh, Debmalya title = Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19 date = 2020-10-10 keywords = COVID-19; CoV-2; SARS; Table; analysis summary = In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. In this paper, we have used an integrative omics approach considering the SARS-CoV-2 infected host interactome, proteome, transcriptome, and bibliome datasets and analysed the COVID-19 associated host genetic information to identify common host pathways that are deregulated during SARS-CoV-2 infection and potential drugs targeting those pathways. In our analysis, we observed SARS-CoV-2 infection shares other viral pathways such as To identify pathway specific drugs, we used the genes involved in the five most important common pathways (viral processes including all the individual virus pathways, mRNA splicing, ubiquitin mediated proteolysis, cytokine signaling in immune system, and protein processing in endoplasmic reticulum). doi = 10.1016/j.compbiomed.2020.104051 id = cord-302576-fv2ib5vc author = Barisione, Emanuela title = Fibrotic progression and radiologic correlation in matched lung samples from COVID-19 post-mortems date = 2020-09-28 keywords = COVID-19; DAD; SARS; patient summary = This study uses an innovative cryobiopsy approach for the post-mortem sampling of lung tissues from COVID-19 patients demonstrating the progression of fibrosis in time and correlation with computed tomography features. The main findings of this study include the following: (1) the identification of a chronological evolution of lesions from an early exudative phase with hyaline membranes to a mid-phase characterized by intra-alveolar fibrinous exudate and early fibroblastic interstitial fibrosis to a late phase with alveolar obliteration by fibrosis and possible micro-honeycombing; (2) mild degree of inflammatory infiltrates; and (3) correlation of histologic patterns with lung CT alterations. Immunohistochemistry for SARS-CoV-2 nucleocapsid protein also showed modification during disease progression as intense immunostaining was seen in early exudative phase Fig. 4 Histology and radiology of late/organizing phase of DAD pattern: aspects of progressive derangement/obliteration of alveolar structure by interstitial fibroblast proliferation. doi = 10.1007/s00428-020-02934-1 id = cord-314439-ufeiv47z author = Barkan, Elad title = Comparison of SARS-CoV-2 Exit Strategies Building Blocks date = 2020-04-28 keywords = April; SARS; release summary = For example, our simulations indicate that dividing the population into two groups completely released except for taking turns on a long weekend (Fri-Tue) self-isolation once every two weeks, while protecting the 5% most sensitive population would reduce R below 1 even if ten percent of the population does not follow it. 1. Quick and accurate measure of actual coronavirus spread -as on average symptoms onset about 5.2 days after infection 30 , and households enter immediate self-isolation, immediate testing gives an accurate and near real-time measure of virus spread in the community, and could prevent the need for population survey-testing for the virus. We compare the efficiency of several key exit strategies building blocks, comparing how much they are efficient in stopping the epidemic in terms of R, while in relation to how effective they are the amount of average released business days they allow for the population. doi = 10.1101/2020.04.23.20072850 id = cord-258172-p54j4zzo author = Barker, Harlan title = Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date = 2020-10-28 keywords = ACE2; RNA; SARS; cell; covid-19; expression summary = Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . doi = 10.1371/journal.pone.0240647 id = cord-323822-jtbfpx88 author = Barnett, Brad P. title = Potential of Ocular Transmission of SARS-CoV-2: A Review date = 2020-09-01 keywords = CD147; SARS; TMPRSS2 summary = Analysis of gene expression profiles from available datasets, published immunohistochemistry, as well as current literature was reviewed, to assess the likelihood that ocular inoculation of SARS-CoV-2 results in systemic infection. Recent findings: The ocular surface and retina have the necessary proteins, Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL) necessary to be infected with SARS-CoV-2. Summary: There is evidence that SARS-CoV-2 may either directly infect cells on the ocular surface, or virus can be carried by tears through the nasolacrimal duct to infect the nasal or gastrointestinal epithelium. From this literature search, four key proteins implicated in SARS-CoV-2 infection were identified: Transmembrane Serine Protease 2 (TMPRSS2), CD147, Angiotensin-Converting Enzyme 2 (ACE2) and Cathepsin L (CTSL), and datasets were utilized to analyze the expression of these proteins in ocular and non-ocular tissue. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection doi = 10.3390/vision4030040 id = cord-307303-9mzs5dl4 author = Barnett, Daniel J. title = The Application of the Haddon Matrix to Public Health Readiness and Response Planning date = 2005-02-02 keywords = Haddon; SARS; health; public summary = However, in practice, public health preparedness requires additional models and tools to provide a framework to better understand and prioritize emergency readiness and response needs, as well as to facilitate solutions; this is particularly true at the local health department level. By breaking a larger problem into smaller, more manageable components, the Haddon matrix provides a practical, efficient decisionmaking and planning tool that health department leaders can use to better understand current and emerging threats, perform vulnerability assessments, prioritize and allocate readiness and response resources, and maintain institutional agility in responding to an array of public health emergencies. Applying the Haddon matrix to the threat of a dirty bomb illustrates the value of this injury prevention model as a public health readiness and response tool, even when focusing exclusively on environmental issues. doi = 10.1289/ehp.7491 id = cord-344120-7t5ce2hb author = Baroutjian, Amanda title = SARS-CoV-2 pharmacologic therapies and their safety/effectiveness according to level of evidence date = 2020-09-01 keywords = COVID-19; HCQ; SARS; patient summary = CONCLUSION: According to level 1 evidence reviewed here, the most effective SARS-Co-V-2 pharmacologic treatments include remdesivir for mild to severe disease, and a triple regimen therapy consisting of lopinavir-ritonavir, ribavirin and interferon beta-1b for mild to moderate disease. 20 Another randomized controlled open-label trial in 199 hospitalized patients with confirmed SARS-CoV-2 with severe COVID-19 was done to compare the clinical effectiveness of lopinavir-ritonavir to standard care alone. According to the level 1 evidence reviewed here, the most effective treatments against SARS-CoV-2, measured by time to negative RT-PCR and time to clinical improvement, are remdesivir therapy and a triple medication regimen (lopinavir-ritonavir, ribavirin, and interferon beta-1b). First, in patients with severe COVID-19, treatment with lopinavir-ritonavir showed no significant difference in time to clinical improvement, mortality at day 28, or detectable viral load compared to standard care alone. doi = 10.1016/j.ajem.2020.08.091 id = cord-252019-tbalg6k5 author = Barra, Gustavo Barcelos title = Analytical Sensitivity and Specificity of Two RT-qPCR Protocols for SARS-CoV-2 Detection Performed in an Automated Workflow date = 2020-10-12 keywords = SARS summary = Here, the following analytical performance characteristics of Charité and CDC protocols for SARS-CoV-2 detection were evaluated: (a) analytical specificity, which refers to the qPCR assay detecting the appropriate target sequence rather than other nonspecific targets also present in a sample [17] ; (b) PCR amplification efficiency, which is the increase in amplicon per cycle, and is highly dependent on the primers used [17, 18] ; (c) analytical sensitivity or limit of detection, which refers to the minimum number of nucleic acid copies in a sample that can be detected with 95% probability [17] ; (d) cross-reactivity with other pathogens; (e) on-going accuracy in clinical specimens, which refers to agreement between the test method and another method during the daily routine. doi = 10.3390/genes11101183 id = cord-268211-egy8rgtl author = Barrasa, Helena title = SARS-Cov-2 in Spanish Intensive Care: Early Experience with 15-day Survival In Vitoria date = 2020-04-09 keywords = ICU; SARS; patient summary = Methods: We identified patients from the two public hospitals in Vitoria who were admitted to ICU with confirmed infection by SARS-CoV-2. Conclusion: This early experience with SARS-CoV-2 in Spain suggests that a strategy of right oxygenation avoiding non-invasive mechanical ventilation was life-saving. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring mechanical ventilation. Because of mortality reports in Wuhan [5] suggesting a close association, we assessed correlation between plasma procalcitonin at ICU admission and 7-day mortality. Our findings suggest that an oxygenation strategy emphasising optimisation of oxygenation, intubation based on clinical criteria of hyperventilation and avoiding ventilator-induced lung injury associated with non-invasive mechanical ventilation would be life-saving in a significant proportion of patients. Seven-day mortality in SARS-CoV-2 requiring intubation was lower than 15%, with 80% of patients still requiring prolonged mechanical ventilation. doi = 10.1016/j.accpm.2020.04.001 id = cord-350094-nkzbtcfw author = Barrett, Lisa F. title = Self-Limited Gastrointestinal Bleeding in COVID-19 date = 2020-07-15 keywords = SARS summary = Clinicians should be aware of a possible increased risk of GI bleeding and its complications when managing critically ill COVID-19 patients. SARS-CoV-2, a single-stranded RNA virus of the beta coronavirus genus, enters the body via the angiotensin converting enzyme 2 (ACE2) receptor [2] [3] . ACE2 is expressed in gastrointestinal (GI) epithelial cells suggesting that SARS-CoV-2 can infect and replicate in the GI tract [4] . We present a case series of six patients, most without a known source of GI bleeding, who tested positive for SARS-CoV-2 and concurrently suffered from hematochezia or melena. We recorded cases of SARS-CoV-2 infection and concurrent GI bleeding from March 1, 2020 to April 24, 2020. Coagulopathy is associated with SARS-CoV-2 infection. Given the possible increased risk of bleeding in COVID-19, therapeutic anticoagulation in infected patients should be used cautiously. This case series shows a possible increased risk of bleeding among patients with COVID-19. doi = 10.1016/j.clinre.2020.06.015 id = cord-309360-cpis1l4u author = Barrios-López, J. M. title = Ischaemic stroke and SARS-CoV-2 infection: A causal or incidental association? date = 2020-05-28 keywords = COVID-19; SARS; patient; stroke summary = Results: The association between COVID-19 and stroke was probably causal in 2 patients, who presented cortical infarcts and had no relevant arterial or cardioembolic disease, but did show signs of hypercoagulability and systemic inflammation in laboratory analyses. A recent study described the cases of 3 patients with COVID-19 who presented ischaemic stroke and antiphospholipid antibodies, in addition to elevated D-dimer levels and laboratory markers of systemic inflammation. 7 A recent study reported 3 cases of severe COVID-19 and ischaemic stroke; these patients presented antiphospholipid antibodies and laboratory findings compatible with systemic inflammation and coagulopathy. 19 In patients 1 and 2 of our series (Table 1) , the likelihood of a causal relationship between COVID-19 and stroke is high, as these patients presented laboratory markers of systemic inflammation and hypercoagulability and the aetiological study found no evident cause for ischaemic stroke. doi = 10.1016/j.nrleng.2020.05.008 id = cord-254630-ed5gawoj author = Barron, Sarah P. title = Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy? date = 2020-09-17 keywords = SARS; bronchoscope; cost; sufb summary = Additionally, RFBs pose a risk of nosocomial infection transmission between patients with the identification of human proteins, deoxyribonucleic acid (DNA) and pathogenic organisms on fully reprocessed bronchoscopes despite full adherence to the guidelines. Until now, disposable or single-use flexible bronchoscopes (SUFBs) have primarily been used by anaesthetists in an ICU or peri-operative setting where they perform to an acceptable level in comparison to RFBs [12, 13] combined with the distinct advantage of a reduced risk of infection owing to their sterility [14] . In this review, the risk of infection with standard RFBs will be outlined as will the advantages of SUFBs, with comment on their cost profile compared to RFBs and attempt to suggest a rationale for their use during the COVID-19 pandemic and in a respiratory setting. doi = 10.1007/s12325-020-01495-8 id = cord-266988-72uvawth author = Barth, Rolf F. title = The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 date = 2020-07-14 keywords = COVID-19; SARS; disease summary = title: The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 COVID-19 disease is caused by a novel coronavirus, which has been named "Severe Acute Respiratory Syndrome Corona virus-2 (SARS-CoV-2)" [2] . Our current understanding of the pathology and the pathogenesis of COVID-19 disease and SARS-CoV-2 transmission is at an early stage and much still remains to be learned [5, 6] . Therefore, the total number of autopsies performed is miniscule compared to the number of deaths, but nevertheless they are both very revealing and important in order to better understand the multi-organ involvement associated with COVID-19 infection and for the development of better treatment strategies [1, 3] . The autopsy reports that already have been published provide a solid base for a better understanding of the consequences of COVID-19 infection but much more remains to be learned about this complex disease in order to develop better treatment strategies. doi = 10.1186/s13000-020-00999-9 id = cord-256904-uq6gy24x author = Bartolini, A. title = Immunochromatographic assays for COVID-19 epidemiological screening: our experience date = 2020-06-02 keywords = SARS summary = We submitted to serological screening by two different immunochromatographic (IC) rapid testing for detection of IgG and IgM against SARS-CoV-2, 151 asymptomatic or minimally symptomatic healthcare workers previously tested positive for SARS-CoV-2 RT-PCR in order to evaluate the performance of rapid assays. Results showed discrepancies between molecular and IC results, and an inconsistency of immunoglobulins positivity patterns when compared to ELISA/CLIA results, highlighting the absolute necessity of assays performance validation before their marketing and use, in order to avoid errors in the results evaluation at both clinical and epidemiological level. Our aim was to evaluate the performances of two different IC assays, submitting to serological testing the 151 healthcare workers previously tested positive for SARS-CoV-2 RT-PCR and trying to find a correlation between the molecular method, that is considered the gold standard and rapid IC tests actually available. doi = 10.1101/2020.05.28.20116046 id = cord-284559-g9szoh3g author = Bartoloni, Elena title = Hypertension and SARS-Cov-2 infection: is inflammation the missing link? date = 2020-09-23 keywords = SARS summary = The dramatic emergence of the pandemic coronavirus disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised significant medical and public health concerns for the high disease mortality rate ranging from 1% to more than 5%. 2 In fact, pre-existing cardiovascular comorbidities, including hypertension (HTN), diabetes mellitus, cerebrovascular and coronary heart disease, enhance susceptibility to SARS-CoV-2 infection and are associated with increased risk of severe disease, myocardial injury and short-term mortality rate. 4 However, due to the high prevalence of hypertension in the general population, concerns raised as to whether hypertension represents merely a concomitant risk factor or a pivotal pathogenic trigger of cardiac injury in patients with SARS-CoV2 infection. In this setting, it may be hypothesized that COVID-19associated PAMPs may act as exogenous triggers of TLR4 signalling pathway leading to inflammasome activation and inflammatory cytokine release, including interleukin-1 (Figure) . doi = 10.1093/cvr/cvaa273 id = cord-274399-cd7cmpoj author = Barzin, Amir title = SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures date = 2020-09-29 keywords = CoV-2; SARS; UNC summary = This is one of the first published seroprevalence studies from North Carolina and included multicenter, primary care, and emergency care facilities serving a low-density, suburban and rural population since description of the North Carolina state index case introducing the SARS-CoV-2 respiratory pathogen to this population. Asymptomatic infection by SARS-CoV-2 (with no clinical symptoms) was examined using an Emergency Use Authorization (EUA)-approved antibody test (Abbott) for the presence of SARS-CoV-2 IgG. This study identifies a very limited seroprevalence of SARS-CoV-2 among asymptomatic individuals accessing the UNC Health system. This study employed an EUA assay performed in a CLIA-certified laboratory on a venous blood sample, with demonstrated specificity to detect antibodies only to SARS-CoV-2, not to seasonal coronaviruses. Upon arrival for SARS-CoV-2 Seroprevalence in North Carolina ® routine care or scheduled visits for enrollment into the study, patients performed a consent procedure that included reviewing recent COVID-19 clinical history using UNC IRB-approved questionnaires. doi = 10.1128/mbio.02426-20 id = cord-262730-1dxeg8ci author = Barón-Sánchez, J. title = Smell and taste disorders in Spanish patients with mild COVID-19 date = 2020-10-08 keywords = COVID-19; PCR; SARS summary = [12] [13] [14] The olfactory alterations associated with SARS-COV-2 infection present sudden onset, are generally not accompanied by rhinorrhoea or nasal obstruction with mucus, and are of variable intensity, although patients frequently report complete loss of the sense of smell. V a r i a b l e s Participants meeting the inclusion criteria were asked to complete a questionnaire, which gathered the following data: sex; age; medical history; characteristics of olfactory/gustatory alterations (complete loss of the sense of smell/taste [anosmia/ageusia], decreased sense of smell [hyposmia], altered sense of taste [dysgeusia]); date of onset and resolution of the alterations; symptom progression; associated symptoms; close contact with a patient with COVID-19 (confirmed by PCR testing); and PCR results for COVID-19, if the test was performed. In our study, only 8.4% of individuals with olfactory/gustatory alterations undergoing PCR testing were negative for SARS-CoV-2; this supports the hypothesis that these symptoms are highly prevalent in patients with mild COVID-19. doi = 10.1016/j.nrleng.2020.07.007 id = cord-303609-9217t0ui author = Baselga, María Trinidad title = Trombosis y COVID-19: revisión de alcance date = 2020-09-24 keywords = COVID-19; SARS summary = Esta revisión de alcance (scoping review) resume y evalúa críticamente la evidencia sobre la relación entre la trombosis y el COVID-19, y se basa en una búsqueda bibliográfica sistemática de todos los artículos publicados hasta el 5 de mayo de 2020 e incluidos en las bases de datos PubMed, Scopus, Cochrane y Clinicaltrials.gov. En otros estudios se estandarizó el uso de ecografía para la detección de las complicaciones J o u r n a l P r e -p r o o f DISCUSIÓN Esta es la primera scope review que revisa los artículos que relacionan la infección por SARS-CoV-2 y las alteraciones en la coagulación, incluyendo sus repercusiones clínicas y radiológicas; en orden cronológico desde el 1 de diciembre de 2019 hasta el 5 mayo de 2020. doi = 10.1016/j.acci.2020.09.002 id = cord-104501-e5e0xrou author = Bashash, Davood title = The Prognostic Value of Thrombocytopenia in COVID-19 Patients; a Systematic Review and Meta-Analysis date = 2020-09-19 keywords = COVID-19; SARS summary = To provide a well-conceptualized viewpoint demonstrating the prognostic value of platelet count in SARS-CoV-2 infection, we performed a meta-analysis of pertinent literature to evaluate whether the emergence of thrombocytopenia could discriminate between severe and non-severe cases. Even though the results of a recent study to establish a prediction model for the prognosis of SARS-CoV-2 infection (19) introduced C reactive protein, lactic dehydrogenase, and lymphocyte count as the most valuable laboratory parameters reflecting COVID-19 severity, articles continuously introducing novel biomarkers with the ability to predict disease outcome are published daily. To provide a clear viewpoint demonstrating the prognostic value of platelet count in this novel infection, we performed a meta-analysis of pertinent literature representing information on the indicated parameter in patients with a clinically validated definition of severe disease. doi = nan id = cord-341919-8gnthufw author = Basi, Saajan title = Clinical course of a 66-year-old man with an acute ischaemic stroke in the setting of a COVID-19 infection date = 2020-08-23 keywords = COVID-19; SARS; patient summary = 3 There appears to be a growing correlation between COVID-19 positive patients presenting to hospital with ischaemic stroke; however, studies investigating this are in progress, with new data emerging daily. 10 The patient, in this case, illustrates the clinical relevance of understanding COVID-19, as he presented with an ischaemic stroke underlined by minimal respiratory symptoms, which progressed expeditiously, resulting in acute respiratory distress syndrome and subsequent death. Our case is an example of a new and ever-evolving clinical correlation, between patients who present with a radiological confirmed ischaemic stroke and severe COVID-19 pneumonia. As of April 2020, no comprehensive data of the relationship between ischaemic stroke and COVID-19 has been published, however early retrospective case series from three hospitals in Wuhan, China have indicated that up to 36% of COVID-19 patients had neurological manifestations, including stroke. doi = 10.1136/bcr-2020-235920 id = cord-331856-j0gedx43 author = Basile, K. title = Accuracy amidst ambiguity: false positive SARS-CoV-2 nucleic acid tests when COVID-19 prevalence is low date = 2020-09-30 keywords = CoV-2; SARS summary = In countries with a low prevalence of COVID-19 and a low pre-test probability, confirmation of positive nucleic acid test (NAT) results for SARS-CoV-2 is recommended given the potential for false positive results. [2] [3] [4] Initially, the Public Health Laboratory Network (PHLN) Australia recommended that confirmatory testing be performed on samples where SARS-CoV-2 RNA had been detected to ensure that the result was a true positive. In the context of Australia''s low prevalence of COVID-19 and thus low pre-test probability for infection, we recommend that all positive SARS-CoV-2 NAT results be confirmed by supplementary testing on the original nucleic acid extract and/or re-extraction of nucleic acid from the original sample (if available) and tested using another assay(s) with different gene targets and/or lower limits of detection 10 (Fig. 1) . doi = 10.1016/j.pathol.2020.09.009 id = cord-262043-66qle52a author = Basit, Abdul title = Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent date = 2020-05-20 keywords = ACE2; RBD; SARS; protein summary = Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. We designed a truncated version (tACE2) of ACE2 receptor covering the binding residues and performed protein-protein docking and molecular dynamic simulations to analyze its binding affinity for RBD and complex stability. Based on the HADDOCK score and the docking RMSD value, the docked complexes of ACE2 and tACE2 with RBD were analyzed for binding affinity DG (kcal mol À1 ) and stability using protein binding energy prediction (PRODIGY) server (Xue et al., 2016) . doi = 10.1080/07391102.2020.1768150 id = cord-323807-e220ut9u author = Bassetti, Matteo title = The novel Chinese coronavirus (2019‐nCoV) infections: Challenges for fighting the storm date = 2020-02-05 keywords = China; SARS summary = Four (229E, NL63, OC43 and HKU1) are responsible for mild upper respiratory tract infections (common cold), whereas the severe acute respiratory syndrome coronavirus (SARS-CoV, which has been contained 4 ) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are able to cause atypical pneumonia. Worth noting is also that the case fatality rate of 2019-nCoV reported in the press news is lower than those previously described for SARS-CoV and MERS-CoV infections (9.5% and 40%, respectively 11 ). Lopinavir/ritonavir is available in several hospitals and has shown promising results in pre-clinical models and case series of SARS-CoV and MERS-CoV infections, 14, 15 although no high-level evidence of efficacy and safety is currently available for its use either as monotherapy or in combination with interferons or other drugs (a randomized controlled trial has been initiated in patients with 2019-nCoV pneumonia in China). doi = 10.1111/eci.13209 id = cord-269756-tid8a464 author = Basso, Luis G. M. title = SARS-CoV fusion peptides induce membrane surface ordering and curvature date = 2016-11-28 keywords = IFP; SARS; membrane; peptide summary = Although membrane fusion promoted by class I viral glycoproteins, such as SARS-CoV Spike, human immunodeficiency virus (HIV) gp160 or influenza virus hemagglutinin (HA), has been broadly studied in recent years [16] [17] [18] [19] , many aspects of the molecular mechanism behind the virus-host cell membrane fusion remain unknown, including conformational changes of the lipid bilayers during peptide-membrane interactions. In the present study, we investigated the effects of two putative fusion peptides from SARS-CoV S glycoprotein, corresponding to residues 770-788 (SARS FP ) and 873-888 (SARS IFP ) 13, 15, 22, 23 , on the structural dynamics, physicochemical properties, and thermotropic phase behavior of lipid model membranes by differential scanning calorimetry (DSC), continuous wave (CW) and pulsed electron spin resonance (ESR) along with nonlinear least-squares (NLLS) spectral fitting 24 . doi = 10.1038/srep37131 id = cord-257468-woyycghi author = Basso, Trude title = Transmission of infection from non-isolated patients with COVID-19 to health care workers date = 2020-08-20 keywords = COVID-19; SARS summary = This study evaluated transmission of infection from a symptomatic patient with COVID-19 to 60 HCWs exposed ≤2 m for ≥15 minutes, or during aerosol generating procedures. Following ≥106 unique high-risk contacts, none of the HCWs tested positive for SARS-CoV-2 RNA or had developed antibodies. These results were in accordance with other reports and should reassure HCWs and further stimulate a broader evaluation of the foundation for the current practice of home-quarantine of non-symptomatic HCWs. During the Coronavirus Disease-19 (COVID-19) pandemic, the proportion of health care workers (HCWs) amongst verified, infected individuals, has been reported somewhere between 10 and 20 % [1, 2] . In this study we found that ≥106 unique close contact exposures, including 12 contacts during AGPs with a nonisolated patient with COVID-19, resulted in no SARS-CoV-2 transmissions from patient to HCWs. With one exception, all included HCWs were certain or quite certain that their adherence to the hand hygiene procedure had been proper at the time of exposure. doi = 10.1016/j.jhin.2020.08.015 id = cord-330337-d41imvo7 author = Basu, Souradip title = Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date = 2020-10-20 keywords = SARS; mutation; protein summary = Our observations and analysis direct us to identify that all the major mutations have a negative impact in context of stability of the viral proteins under study and the mutant proteins suffer both structural and functional alterations as a result of the mutations. The secondary structure of the wild type and the mutant proteins along with their degree of disordered residues and accessible surface area was predicted using the primary sequence of the protein. Each of the seven proteins were assigned a score of either ''-1'' or ''0'', for each of the four computational tools used for epitope prediction, where ''-1'' corresponds to any change in number or binding efficacy of antigenic determinants, that may have surfaced because of mutation and ''0'' corresponds to no changes between wild type and mutant forms. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure doi = 10.1101/2020.10.20.347021 id = cord-296219-zzg9hds0 author = Battaglini, Denise title = Neurological Manifestations of Severe SARS-CoV-2 Infection: Potential Mechanisms and Implications of Individualized Mechanical Ventilation Settings date = 2020-08-12 keywords = COVID-19; CoV-2; SARS; brain; patient summary = Within this Abbreviations: ACE2, angiotensin-converting enzyme-2; ANE, acute necrotizing encephalopathy; ARDS, acute respiratory distress syndrome; BALF, bronchoalveolar lavage fluid; BBB, blood brain-barrier; CA, Ammon''s horn; CD, cluster of differentiation; CI, confidence interval; CNS, central nervous system; CoV, coronavirus; COVID-19, coronavirus disease 2019; CT, computed tomography; CXCR, chemokine receptor; DIC, disseminated intravascular coagulation; DO 2 , oxygen delivery; DPP4, dipeptidyl dipeptidase-4; ECMO, extracorporeal membrane oxygenation; FiO 2 fraction of inspired oxygen; FOX, forkhead box; HLH, hemophagocytic lymphohistiocytosis; ICAM, intracellular adhesion molecule; ICH, intracerebral hemorrhage; ICP, intracranial pressure; IFN, interferon; MERS, Middle East respiratory syndrome; MHV, mouse hepatitis virus; MRI, magnetic resonance images; nCoV, novel coronavirus; OR, odds ratio; PaCO 2 , partial pressure of carbon dioxide; PaO 2 partial pressure of oxygen; PbtO 2 brain tissue oxygenation tension; PCR, polymerase chain reaction; PEEP, positive end-expiratory pressure; PRES posterior reversible encephalopathy syndrome; RM, recruitment maneuvers; RNA, ribonucleic acid; SARS, severe acute respiratory syndrome; TLRs, toll-like receptor; TMPRSS2 transmembrane serine protease 2; TNF, tumor necrosis factor; WHO, World Health Organization. doi = 10.3389/fneur.2020.00845 id = cord-290443-naulq6q7 author = Battistoni, Allegra title = Might renin–angiotensin system blockers play a role in the COVID-19 pandemic? date = 2020-04-14 keywords = ACE2; SARS summary = 15, 16 Therefore, the higher ACE2 expression due to chronically medicating SARS-CoV-2-infected patients with ARB may protect them against acute lung injury by blocking the deleterious effect of angiotensin II, as well as by decreasing the production of angiotensin II by up-regulating ACE2, which in turn increases the production of angiotensin (1-7). 33-36 Moreover, even though ACEIs and ARBs might increase ACE2 levels in the lungs, this might not be relevant to SARS-CoV-2 infection. [38] [39] [40] [41] [42] [43] For the second aim, not only case series, but also autoptic exams should investigate the expression and activation of RAS components in different organs during COVID-19 infection in patients treated or not with an ACEI/ARB, also investigating ACE2 polymorphisms which could impact the affinity for the spike protein of SARS-CoV-2. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury doi = 10.1093/ehjcvp/pvaa030 id = cord-340563-hsj53inh author = Baud, David title = Using Probiotics to Flatten the Curve of Coronavirus Disease COVID-2019 Pandemic date = 2020-05-08 keywords = SARS; lactobacillus; probiotic summary = Clinical evidence shows that certain probiotic strains help to prevent bacterial and viral infections, including gastroenteritis, sepsis, and respiratory tract infections (RTIs). In one analysis of more than 8,000 preterm infants included in randomized control trials (RCTs), patients receiving enteral supplementation with probiotics showed a reduction in necrotizing enterocolitis, nosocomial sepsis, and all-cause mortality (14) . But low quality of evidence and conflicting results among different studies calls for additional well-conducted RCTs. It should be noted that not all probiotics, even those with gastrointestinal benefits, necessarily contribute in every way to reducing the risk of respiratory infection. Effects of consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114 001 on common respiratory and gastrointestinal infections in shift workers in a randomized controlled trial Lactobacillus plantarum DR7 improved upper respiratory tract infections via enhancing immune and inflammatory parameters: a randomized, double-blind, placebo-controlled study doi = 10.3389/fpubh.2020.00186 id = cord-257729-s0vo7dlk author = Bauer, Melissa title = Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date = 2020-04-20 keywords = SARS; covid-19; infection; patient summary = T he management of obstetric patients infected with Coronavirus Disease 2019 (COVID19) due to human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires quite unique considerations-from caring for critically ill pregnant and postpartum women to protecting health care workers from exposure during the delivery hospitalization (health care providers, personnel, family members, and beyond). 4 An additional manifestation noted among patients with COVID-19 infection is the sudden loss (or reduction) of the sense of smell and taste, which is currently recommended by the American Academy of Otolaryngology-Head With increasing numbers of Coronavirus Disease 2019 (COVID 19) cases due to efficient human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United States, preparation for the unpredictable setting of labor and delivery is paramount. doi = 10.1213/ane.0000000000004856 id = cord-274513-0biyfhab author = Baumgartner, M. T. title = Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19 date = 2020-07-22 keywords = COVID-19; SARS; model summary = In this study, we used an individual-based age-structured network model to assess the effective roles of different healthcare protocols such as the use of personal protection equipment and social distancing at neighborand city-level scales. Our results revealed that the model was more sensitive to changes in the parameter representing the rate of contact among people from different neighborhoods, which defends the social distancing at the city-level as the most effective protocol for the control of the disease outbreak. By varying model parameters related to these protocols, we were able to discuss better scenarios considering the delay in the infection peak and lower numbers of cases, as well as activities with a low potential to boost the outbreak. Given the specified model structure, those results forecasting early wave peaks emerged under moderate to high probabilities of the individual-level exposure to SARS-CoV-2 virus (high β), in combination with higher encountering rates among people (v and k) ( Figure 1 ; Table S1 ). doi = 10.1101/2020.07.20.20158576 id = cord-353996-slnyun4l author = Baumgartner, M. T. title = Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil date = 2020-05-08 keywords = Brazil; COVID-19; SARS; international summary = In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the cityand country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. We studied the exponential growth of time series data for over 460 cities with reported cases of infections by the new coronavirus, considering the effect of the environment, socioeconomic indicators, movement of people across the country, and social distancing. Our results show that the early spread of the new coronavirus in Brazil was mitigated by social distancing in some regions, but was also positively related to the size of the population of cities and how people moved across them. . https://doi.org/10.1101 In Great China, the ongoing COVID-19 outbreak expanded fast throughout the country and the majority of early cases reported outside of its origin had admitted recent travels to Wuhan, the core of the disease spread (Chinazzi et al., 2020) . doi = 10.1101/2020.05.02.20088013 id = cord-340537-pdvpmydk author = Bañon-Gonzalez, Rafael title = Autopsies of suspected SARS-CoV-2 cases date = 2020-07-15 keywords = COVID-19; SARS; virus summary = Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body''s tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. doi = 10.1016/j.remle.2020.05.002 id = cord-338647-dtuohsf5 author = Başcı, Semih title = Outcome of COVID-19 in patients with chronic myeloid leukemia receiving tyrosine kinase inhibitors date = 2020-08-27 keywords = CML; COVID-19; SARS summary = INTRODUCTION: In this study, we aim to report the outcome of COVID-19 in chronic myeloid leukemia (CML) patients receiving tyrosine kinase inhibitor (TKI). METHOD: The data of 16 laboratory-confirmed COVID-19 patients with CML receiving TKI and age, gender, and comorbid disease matched COVID-19 patients without cancer at a 3/1 ratio (n = 48), diagnosed between March 11, 2020 and May 22, 2020 and included in the Republic of Turkey, Ministry of Health database, were analyzed retrospectively. RESULTS: The rates of intensive care unit (ICU) admission, and mechanical ventilation (MV) support were lower in CML patients compared to the control group, however, these differences did not achieve statistical significance (p = 0.1, and p = 0.2, respectively). Moreover, the rates of ICU admission and MV support, CFR were lower and length of hospital stay was shorter in CML patients receiving TKI compared to the age, gender and comorbidity matched control group but these differences were not statistically significant. doi = 10.1177/1078155220953198 id = cord-332268-x30svp5y author = Bearden, Donna M. title = COVID-19: a primer for healthcare providers date = 2020-05-20 keywords = COVID-19; China; MERS; SARS summary = A viral genome sequence of a novel coronavirus, currently termed SARS-CoV‑2, with a disease process called COVID-19 was released 1 week later via online resources to obtain public health support in control of spread. Perhaps the most detailed study to date, shedding light on how patients may present and progress, is an analysis of the first 99 cases of confirmed novel corona pneumonia in Wuhan [12] . Nowak and Walkowiak, in a recently released review of five in vitro studies reporting on the effect of lithium in coronavirus infections, concluded that the drug does have antiviral activity and should be explored as a potential treatment or prophylaxis for COVID-19 [24] . The authors concluded "our work suggests that remdesivir may improve disease outcomes in coronavirus patients, serve to protect health care workers in area with endemic MERS-CoV and prove valuable in preventing future epidemics " [3] . doi = 10.1007/s00508-020-01678-x id = cord-348727-o38uplxe author = Beaudoin-Bussières, Guillaume title = Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date = 2020-07-09 keywords = SARS summary = Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. Neutralizing activity against pseudoparticles bearing the SARS-CoV S 120 glycoprotein was detected in only 25% of convalescent plasma and exhibited low potency, as 121 previously reported (Figure 2) (14) . Of note, while we observed enhanced infectivity for the 122 D614G variant compared to its WT SARS-CoV-2 S counterpart ( Figure S3A ), no major 123 differences in neutralization with convalescent plasma were detected at both time-points ( Figure 124 S3B), thus suggesting that the D614G change does not affect the overall conformation of the 125 Spike, in agreement with recent findings (18) . 126 127 The capacity to neutralize SARS-CoV-2 S WT or D614G-pseudotyped particles 128 significantly correlated with the presence of RBD-specific IgG, IgM and anti-S antibodies 129 ( Figure S4 ). Interestingly, we observed a pronounced decrease (20-30%) in the percentage of 130 patients able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 131 10 weeks after symptoms onset. doi = 10.1101/2020.07.09.194639 id = cord-356325-gk5jve0i author = Beaudoin-Bussières, Guillaume title = Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals date = 2020-10-16 keywords = Fig; SARS summary = Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. Of note, while we observed enhanced infectivity for the D614G variant compared to its WT SARS-CoV-2 S counterpart (see Fig. S2A in the supplemental material), no major differences in neutralization with convalescent plasma were detected at either time point (Fig. S2B) , thus suggesting that the D614G change does not affect the overall conformation of the Spike, in agreement with recent findings (17, 22) . The capacity to neutralize SARS-CoV-2 S WT-or D614G-pseudotyped particles significantly correlated with the presence of RBD-specific IgG, IgM, IgA, and anti-S antibodies (Fig. S3) . Interestingly, we observed a pronounced (20% to 30%) decrease in the proportion of convalescent individuals able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 10 weeks after the onset of symptoms. doi = 10.1128/mbio.02590-20 id = cord-317227-zb434ve3 author = Beck, Bo Ram title = Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model date = 2020-03-30 keywords = DTI; SARS summary = title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model In this study, we applied our pre-trained MT-DTI model to identify commercially available antiviral drugs that could potentially disrupt SARS-CoV-2''s viral components, such as proteinase, RNA-dependent RNA polymerase, and/or helicase. AutoDock Vina (version 1.1.2), which is a molecular docking and virtual screening application (17) , was used to predict binding affinities (kcal/mol) between 3C-like proteinase of SARS-CoV-2 and 3,410 FDA-approved drugs. To identify potent FDA-approved drugs that may inhibit the functions of SARS-CoV-2''s core proteins, we used the MT-DTI deep learning-based model, which can accurately predict binding affinities based on chemical sequences (SMILES) and amino acid sequences (FASTA) of a target protein, without their structural information (12) . Drug-target interaction (DTI) prediction results of antiviral drugs available on markets against a novel coronavirus (SARS-CoV-2, NCBI reference sequence NC_045512.2) RNA-dependent RNA polymerase (accession YP_009725307.1). doi = 10.1016/j.csbj.2020.03.025 id = cord-018265-twp33bb6 author = Becker, Pablo D. title = Community-acquired pneumonia: paving the way towards new vaccination concepts date = 2007 keywords = RSV; SARS; dna; protein; response; vaccine; virus summary = doi = 10.1007/978-3-7643-7563-8_10 id = cord-311730-189vax2m author = Becker, Richard C. title = Covid-19 treatment update: follow the scientific evidence date = 2020-04-27 keywords = SARS; chloroquine; covid-19; drug; patient summary = The SNS exists under the authority of the United States Department of Health and Human Services (HHS) and accepted 30 million doses of hydroxychloroquine sulfate donated by Sandoz™, the Novartis™ generics and biosimilars division, and one million doses of chloroquine phosphate donated by Bayer Pharmaceuticals™ for potential use in treating patients who were hospitalized with COVID-19 or for use in clinical trials. The adverse effects associated with taking hydroxychloroquine are similar to those observed with chloroquine and include nausea, vomiting, diarrhea, AV conduction defects, a prolonged QTc interval with torsades de pointe ventricular tachycardia, hypokalemia, hypotension and circulatory collapse. Similarly, patients with Covid-19 for whom a clinician believes that either chloroquine or hydroxychloroquine is indicated must receive information, preferably in the form of a fact sheet that clearly summarized the dose, duration of treatment, potential risks, side-effects and drug-drug interactions. doi = 10.1007/s11239-020-02120-9 id = cord-268098-71g1w1mc author = Beckman, M. F. title = Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date = 2020-09-15 keywords = SARS; September; VEP; gene summary = Visualization of protein-protein interaction networks was completed using STRINGv11.0 [31] program by testing different confidence levels to identify ontologies of biological significance for the significant pathways associated with comorbidities. Possible comorbidity significant associated gene sets/pathways were checked for quality control by generating Quantile-Quantile (Q-Q) plots using observed quantiles and residual Z-scores of genes within the gene set, based on the MAGMAv1.07b publicly available Rv3.6.2 script (posthoc_qc_107a.r) [32, 33] . . https://doi.org /10.1101 was used to test the top 250 human mRNA gene expressions for each comorbidity based on available human data using NCBI GEO[39] , by only including comorbidities that had significant pathways identified by MAGMAv1.07b and VEP STRING analyses. For each comorbidity, human mRNA gene expression data corresponding to average log-fold change (aLFC) were formatted for clustering of genes identified by MAGMAv1.07b and VEP and subsequently matched to STRING protein-protein interactions. doi = 10.1101/2020.09.14.20192609 id = cord-318499-uihof6k6 author = Beddingfield, Brandon title = The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date = 2020-06-16 keywords = ATN-161; SARS summary = Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5β1integrin-based mechanism, and indicates that inhibiting α5β1 integrin interaction with ACE2 and the spike protein using a novel molecule ATN-161 represents a promising approach to treat COVID-19. In order to assess disruption of binding of α5β1 to SARS-CoV-2 Spike protein, 96-well plates were coated as before, but incubation with ATN-161 was performed in conjunction with 1µg/mL spike (produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH: Spike Glycoprotein Receptor Binding Domain (RBD) from SARS-Related Coronavirus 2, Wuhan-Hu-1, Recombinant from HEK293 Cells, NR-52306) in the presence of 1mM MnCl2, followed by detection with an anti-spike antibody. Inhibition of SARS-CoV-2 spike protein binding to human ACE2 by ATN-161. doi = 10.1101/2020.06.15.153387 id = cord-310879-b8tdug93 author = Beddingfield, Brandon J. title = In the Age of CoVID: Genomic Changes Over the Lifespan Help Explain Severe SARS-CoV-2 Disease date = 2020-10-23 keywords = SARS summary = Because additional receptor interactions have been implicated in host cell invasion by previous coronaviruses, other receptors have been investigated for their potential role in SARS-CoV-2 infection. Previous studies have also The potential entry gene BSG was found to be in higher abundance in cardiorenal tissues than in the lung, though it was well expressed in all tissues examined. This is in contrast to ACE2, which was found to be expressed at low levels in lung, but higher levels in cardiorenal tissues (kidney, heart and blood vessels) across the individuals examined. Taken together, this could explain the higher levels of viral replication in lung tissue for SARS-CoV-2, even if the receptor itself is not highly expressed. Males also had an increased expression of BSG, PPIA, PPIB in endothelial cells, and higher levels of ACE2 and TMPRSS2 in the coronary artery. Airways Expression of SARS-CoV-2 Receptor, ACE2, and TMPRSS2 Is Lower in Children Than Adults and Increases with Smoking and COPD doi = 10.1016/j.jacbts.2020.10.004 id = cord-283196-laerx0n2 author = Bedford, Juliet title = Living with the COVID-19 pandemic: act now with the tools we have date = 2020-10-08 keywords = SARS; covid-19 summary = The Strategic and Technical Advisory Group for Infectious Hazards (STAG-IH), the independent advisory group to the WHO Health Emergencies Programme, has reviewed information from countries around the world and has concluded that the most sound approach on the basis of current understanding is to deploy long-term strategies with a focus on preventing amplification of transmission, protecting those most at risk of severe illness, and supporting research to better understand the virus, the disease, and people''s responses to them. 2 This approach is based on three principles: understanding, trust, and participation by all population groups; decreased transmission of SARS-CoV-2 using basic epidemiological and public health interventions; and acknowledging that any potential COVID-19 vaccines and treatments will only be part of the solution and that they will best perform in conjunction with a longterm overall public health strategy. With current knowledge, even in the absence of COVID-19 vaccines or treatments and comprehensive knowledge of the immune response to SARS-CoV-2, countries can navigate pathways to reduced transmission, decreased severe illness and mortality, and less economic disruption in the short and longer term. doi = 10.1016/s0140-6736(20)32117-6 id = cord-297202-oup8ptya author = Beer, Martin title = SARS‐CoV‐2 vaccination—A plea for fast and coordinated action date = 2020-07-01 keywords = SARS summary = If we assume that the level of herd immunity to halt the spread follows the 1 − 1/R 0 rule (Anderson, Heesterbeek, Klinkenberg, & Hollingsworth, 2020) and given conservative estimates for the basic reproduction number R 0 = 3 (Sanche et al., 2020) at least two-thirds of the world''s population must mount an effective immune response against the virus to prevent recurrent outbreaks. Yes, an R t < 0.2 would halt the spread of SARS-CoV-2 in a given population at time t, but any re-introduction of the virus could catapult us back to where we were. Unless serological surveys suggest a much higher-than-expected silent exposure of the human population to SARS-CoV-2, there is no reasonable scenario to reach the required level of herd immunity under the ''reduce spread'' paradigm that many countries have emulated. doi = 10.1111/zph.12740 id = cord-352230-8mazd3eu author = Beeraka, Narasimha M. title = Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date = 2020-09-18 keywords = ACE-2; CoV-2; Nrf-2; SARS; TMPRSS2; coronavirus; infection summary = Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. COVID-19 is a devastating disease caused by a coronavirus related to the one that caused outbreaks of Severe Acute Respiratory Syndrome (SARS) in the year 2002 (1, 2) . doi = 10.3389/fimmu.2020.552925 id = cord-319555-pccqo36g author = Beggs, Clive B. title = Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study date = 2020-10-13 keywords = SARS summary = Given that COVID-19 can be transmitted by the inhalation of aerosolised respiratory droplets containing the SARS-CoV-2 virus (Beggs, 2020; Miller et al., 2020; Morawska et al., 2020; Stadnytskyi et al., 2020) , and that several studies have recovered viral RNA from hospital air samples (Chia et al., 2020; Guo et al., 2020; Jiang et al., 2020; Santarpia et al., 2020) , there is reason to believe that upper-room UVGI might be effective at "killingx201D; (inactivating) SARS-CoV-2 virions in the air, thus reducing the transmission of COVID-19 in buildings and other enclosed spaces. Because no UV irradiation experiments have to date been performed on aerosols containing the SARS-CoV-2 virus, it was necessary when undertaking the feasibility study to make assumptions regarding an appropriate value of Z ur to use in the upper-room UVGI analysis. The results for the expected and worst-case scenarios in Table 7 , strongly suggest that upper-room UVGI, if applied correctly, should be effective at disinfecting SARS-CoV-2 virions suspended in respiratory droplets in the air. doi = 10.7717/peerj.10196 id = cord-262556-gpnp06je author = Behrens, Estuardo title = COVID-19: IFSO LAC Recommendations for the Resumption of Elective Bariatric Surgery date = 2020-08-22 keywords = COVID-19; SARS; surgery summary = RESULTS: The resumption of elective BMS must be a priority maybe similar to oncological surgery, when hospitals reach phase I or II, treating obesity patients in a NON-COVID area, avoiding inadvertent intrahospital contagion from healthcare provider, patients, and relatives. On December 2019, Wuhan, China, reported an outbreak of the coronavirus SARS-CoV-2 (COVID19) , an RNA virus that affects the respiratory system and has a high fatality rate especially in adults over the age of 60 and patients suffering obesity and its comorbidities [1] [2] [3] . Currently, the most effective treatment against obesity available is bariatric and metabolic surgery, which further resolves or improves the related comorbidities that are the same risk factors in developing a severe case of SARS-CoV-2. It is recommended that elective bariatric surgery be performed in medical facilities with the necessary infrastructure to treat obesity patients in a NON-COVID area. doi = 10.1007/s11695-020-04910-9 id = cord-300395-87bl6e38 author = Behrmann, Ole title = Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification date = 2020-10-14 keywords = RPA; SARS summary = As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplifi cation (RT-RPA) technology. DOI: 10.1007/s12268-020-1458-3 © Die Autoren 2020 ó Die derzeitigen Protokolle zur Diagnose von SARS-CoV-2-Infektionen beruhen auf der quantitativen reversen Transkriptions-PCR (RT-qPCR) für den Direktnachweis der viralen RNA [1] . Alternativ sind seit einigen Jahren isotherme Verfahren -wie die loop-mediated isothermal amplifi cation (LAMP) [2] oder die recombinase polymerase amplification (RPA) [3] -verfügbar, welche der PCR hinsichtlich Sensitivität und Spezifi tät gleichwertig sind. Aufbauend auf vorhergehenden Arbeiten, in welchen der Nachweis anderer Coronaviren wie MERS-CoV [4] und Bovines Coronavirus (BCoV) [5] mittels RPA demonstriert wurde, stellen wir in diesem Artikel die Entwicklung eines RPA-Assays für den Schnellnachweis von SARS-CoV-2 vor. doi = 10.1007/s12268-020-1458-3 id = cord-285315-7r44j3q9 author = Bein, Berthold title = SARS-CoV-2/COVID-19: Empfehlungen zu Diagnostik und Therapie date = 2020-04-09 keywords = COVID-19; China; Patienten; SARS; Wuhan summary = Die Case Fatality Rate (Zahl der Infizierten, die verstirbt; Letalität) von SARS-CoV-2 beträgt aktuellen Berechnungen nach nur 1,4 %, wobei das Risiko für eine symptomatische Infektion mit zunehmendem Alter ansteigt (ca. Die Surviving Sepsis Campaign (SSC) zitiert in ihren kürzlich publizierten Empfehlungen zur Behandlung von Patienten mit COVID-19 eine aktuelle Metaanalyse, in der keine Überlegenheit von speziellen "respiratory masks" (analog unseren FFP2/FFP3-Masken) gegenüber konventionellem Mund-Nasen-Schutz bezüglich einer Ansteckung von medizinischem Personal, das infektiöse Patienten betreut hatte, gefunden werden konnte [30] . Das bedeutet konkret, dass die Behandlung von Patienten mit COVID-19 zuallererst auf "Best Standard Care" beruht, also auf einer optimalen Anwendung evidenzbasierter Therapieempfehlungen, die für die Therapie des akuten Lungenversagens (Acute respiratory Distress Syndrome, ARDS) erarbeitet wurden [33] . doi = 10.1055/a-1146-8674 id = cord-022234-jjaqlyo5 author = Beirman, David title = A Comparative Assessment of Three Southeast Asian Tourism Recovery Campaigns: Singapore Roars: Post SARS 2003, Bali Post-the October 12, 2002 Bombing, and WOW Philippines 2003 date = 2009-11-16 keywords = Asia; Bali; Philippines; SARS; Singapore summary = doi = 10.1016/b978-0-7506-7898-8.50021-7 id = cord-300191-vpc7p0d6 author = Bektaş, Osman title = The relationship between severe acute respiratory syndrome coronavirus 2 (SARS - COV - 2) pandemic and fragmented QRS date = 2020-07-22 keywords = FQRS; SARS summary = OBJECTIVE: The aim of the study is to determine the frequency of fragmented QRS (FQRS) in patients with SARS COV 2. [7] In a study, evaluating patients with coronary artery disease (CAD), those with FQRS had significantly higher all cause mortality and higher frequency of adverse cardiovascular outcomes (myocardial infarction, sudden cardiac death, revascularization) [8] . The requirement for intensive care unit incresed with increasing levels of troponin in patients with SARS-COV-2 (p<0.000, Table 3 ). Moreover, a significant positive correlation was detected between serum CRP levels,heart rate and frequency of FQRS in patients with SARS-COV-2 (r=0.204, p=0.024, r=0.187 p=0.029) Lineer regression analyses revealed that serum CRP levels and heart rate were the independent predictors of presence of FQRS (Table 4 ). Fragmented QRS on a 12-lead ECG: a predictor of mortality and cardiac events in patients with coronary artery disease doi = 10.1016/j.jelectrocard.2020.07.009 id = cord-271495-5906wju4 author = Beldomenico, Pablo M. title = Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date = 2020-05-11 keywords = SARS; viral summary = Data and modelling supported the existence of ''superspreaders'' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. doi = 10.1016/j.ijid.2020.05.025 id = cord-304898-he57l0y7 author = Belghmaidi, Sarah title = Third Cranial Nerve Palsy Presenting with Unilateral Diplopia and Strabismus in a 24-Year-Old Woman with COVID-19 date = 2020-10-15 keywords = COVID-19; SARS summary = Patient: Female, 24-year-old Final Diagnosis: Third cranial nerve palsy in a women presenting COVID-19 Symptoms: Ophthalmoplegia Medication:— Clinical Procedure: — Specialty: Ophthalmology OBJECTIVE: Rare disease BACKGROUND: Coronavirus disease (COVID 19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is the causative agent of a serious disease that is of great global public health concern. We describe the case of a patient with an incomplete palsy of the left third cranial nerve sparing the pupils in the context of SARS-CoV-2 virus infection. CASE REPORT: We report the case of a 24-year-old woman with confirmed COVID-19, which presented with acute onset of diplopia and strabismus of the left eye that occurred 3 days after the start of general symptoms. A previously healthy 24-year-old woman, with no medical history (such as diabetes, high blood pressure, dyslipidemia, vasculitis, smoking, obesity, familial neurological disease, or other risk factors for ischemic ophthalmoplegia), presented to the Emergency Department for acute onset of strabismus and diplopia of the left eye, evolving for 3 days. doi = 10.12659/ajcr.925897 id = cord-253993-ynrthadj author = Belhassan, Assia title = Assessment of effective imidazole derivatives against SARS-CoV-2 main protease through computational approach date = 2020-09-18 keywords = COVID-19; SARS summary = The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Based on all these effects, the study of interactions between chloroquine, hydroxychloroquine and the eighteen imidazole derivatives against the SARS-CoV-2 main protease are recommended. In this paper, the modeling interaction of eighteen imidazole derivatives against novel Coronavirus are performed using the molecular docking method followed by comparison with chloroquine, hydroxychloroquine interactions formed in the same binding site of SARS-CoV-2 main protease. In this study, we have tried to carry out a docking study of chemical compounds reported as potent Antiplasmodial inhibitors of imidazole derivatives based on 7-chloro-4-aminoquinoline and analogues in the active site of SARS-Cov-2 main protease, flowed by comparison with two drugs; chloroquine and hydroxychloroquine. doi = 10.1016/j.lfs.2020.118469 id = cord-309394-vroscj3m author = Belingheri, Michael title = Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers date = 2020-04-07 keywords = SARS summary = title: Risk Exposure to Coronavirus Disease 2019 in Pregnant Healthcare Workers 3 As known, the risk of exposure to coronavirus is higher among healthcare workers than other workers, due to their role in assistance and care of COVID-19 patients. Some limited data are available about previous coronavirus infections, such as severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome (MERS-CoV). Unauthorized reproduction of this article is prohibited Since the structural analysis of novel coronavirus has suggested that it would use the same mechanism of SARS-CoV, it is fundamental to consider the potential role of SARS-CoV-2 during pregnancy. [9] [10] [11] Furthermore, there is no evidence for intrauterine infection due to a vertical transmission in pregnant women affected by COVID-19. Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes doi = 10.1097/jom.0000000000001881 id = cord-285787-xvi5miqw author = Bell, Jennifer AH title = SARS and hospital priority setting: a qualitative case study and evaluation date = 2004-12-19 keywords = SARS; priority summary = The purpose of this study is to describe and evaluate priority setting in a hospital in response to SARS using the ethical framework ''accountability for reasonableness''. CONCLUSIONS: ''Accountability for reasonableness'' is a framework that can be used to guide fair priority setting in health care organizations, such as hospitals. ''Accountability for reasonableness'' is an explicit ethical framework for legitimate and fair priority setting in health care [2] . The purpose of this study was to describe priority setting in a hospital in response to SARS and evaluate it using ''accountability for reasonableness''. In this section we describe one hospital''s priority setting in response to SARS by focusing on the types of decisions, the decision making process, and the supportive reasoning. ''Accountability for reasonableness'' is a framework that can be used to guide legitimate and fair priority setting in health care organizations, such as hospitals. Priority setting in a hospital critical care unit: qualitative case study doi = 10.1186/1472-6963-4-36 id = cord-314013-g091lv0s author = Belladonna, Maria Laura title = Potential Benefits of Tryptophan Metabolism to the Efficacy of Tocilizumab in COVID-19 date = 2020-06-19 keywords = COVID-19; IL-6; SARS summary = Here, we briefly discuss the potentially multiple, synergistic mechanisms whereby tocilizumab might exert therapeutic activity, mostly focusing on the production of tryptophan-derived catabolites that would result from blockade of IL-6 signaling, as contextualized to the cytokine storm occurring in COVID-19 patients. If a cytokine storm occurs, the ensuing cytokine release syndrome (CRS) is typically associated with severe, rather than moderate, COVID-19, with an immunopathology being characterized by high serum levels of cytokines, CD4 + and CD8 + T (but not B) cell lymphopenia, diffused alveolar damage, pulmonary hypertension, pneumonia, and acute RDS (Pedersen and Ho, 2020) . COVID-19 is associated to a CRS referred as "cytokine storm" (A), whose reduction at lung level (the main target organ of SARS-CoV2 viral infection) may be achieved by TCZ therapy inhibiting IL-6 proinflammatory effect (B). TCZ treatment might restore a proper IDO1 activity, providing immunoactive Kyn as a ligand for AhR-dependent immune regulation, including the fostering of T-regulatory cell responses. doi = 10.3389/fphar.2020.00959 id = cord-341883-eh0aw3re author = Bellanger, Anne-Pauline title = Studying smoking benefit in farmer’s lung to understand Covid-19 date = 2020-08-11 keywords = SARS summary = It was observed, first in China, and then in France, that the proportion of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients was significantly lower in active smokers compared to the proportion of active smokers in the general population. The protection conferred by smoking for a respiratory disease has so far only been described for hypersensitivity pneumonitis (HP), especially for farmer''s lung, and to a lesser degree, for bird fancier''s lung. The under-representation of active smokers in SARS-CoV-2 patients suggests a protective effect of smoking, similar to that in the farmer''s lung. We chose to highlight the most obvious similarities between SARS-CoV-2 and farmer''s lung but there are probably others, especially concerning the hyperactive immune response described as ''cytokine storm''. The lack of knowledge about the mode of action of smoking in farmer''s lung disease limits comparisons with SARS-CoV-2 and more research is required. doi = 10.1093/occmed/kqaa147 id = cord-260618-k0y0fz7k author = Belli, Simone title = Coronavirus mapping in scientific publications: When science advances rapidly and collectively, is access to this knowledge open to society? date = 2020-07-01 keywords = China; SARS; USA summary = Our main objectives are to identify the most productive countries in coronavirus publications, to analyse the international scientific collaboration on this topic, and to study the proportion and typology of open accessibility to these publications. (2004) , and collected 256 articles indexed in the Science Citation Index (SCI) in the period March-July 2003, analyzing traditional indicators (authorship, collaboration, journals, language, document type, organization, times cited, etc.). We offer a general search in all databases available at Web of Science (WoS) platform and a deeper bibliometric analysis of recent coronavirus scientific publications indexed in its Core Collection. For the 2001-2020 period (Table 1) , the value of the TLS in proportion to the number of documents provided is especially low in countries such as Japan, South Korea, Taiwan or Brazil, with 0.46, 0.35, 0.28 and 0.38 links per document and 35.87%, 25.81%, 19.89% and 31.79% of documents resulted from international collaboration respectively. doi = 10.1007/s11192-020-03590-7 id = cord-298920-1lc2xf7u author = Bello-Perez, Melissa title = Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date = 2020-07-05 keywords = IBV; SARS; autophagy; pathway summary = Along this line, the generation of these coronavirus-induced autophagosomes requires the PtdIns3P-enrichment of the ER membrane outer leaflet, and the recruitment of ZFYVE1/DFCP1 (a key protein in omegasome formation), WIPI1/2, ATG5 and LC3-II (all components of the autophagic machinery), and SQSTM1/p62 (a receptor protein for selective autophagy) [31, 50, 51] . Briefly, chloroquine, apart from disorganizing the Golgi, induces lysosomal alkalinization, which prevents amphisome/autophagosome-lysosome fusion and blocks the vesicle trafficking system [53] [54] [55] 93] , which potentially affects the replication cycle of coronavirus systemically, including their entry, which is mediated by pH-dependent endocytosis and requires a low pH for the S protein to trigger its membrane fusion activity [94, 95] . Nitazoxanide is another late-stage autophagy blocker [96] that shows high anti-SARS-CoV-2 activity in cell cultures (IC 50 : 2.12 µM) [97] , although it should be considered that its main metabolite, tizoxanide, induces autophagy by inhibiting the PI3K-AKT-MTOR pathway [98] . doi = 10.3390/cells9071619 id = cord-103545-2v89ku4o author = Bellos, Ioannis title = Maternal and perinatal outcomes in pregnant women infected by SARS-CoV-2: A meta-analysis date = 2020-11-13 keywords = COVID-19; SARS; case summary = The following data were planned to be extracted from each of the included studies: name of first author, country, maternal age, medical history (diabetes mellitus, hypothyroidism or polycystic ovary syndrome), symptoms (fever, cough, shortness of breath, diarrhea, nausea/vomiting, myalgia, fatigue, headache, sore throat, nasal congestion, abdominal pain, chest pain), radiological signs, presence of co-infection (bacterial or influenza), laboratory tests (lymphopenia, thrombocytopenia, increased Creactive protein, procalcitonin, ferritin, liver function tests and D-dimers), type of treatment, pregnancy outcomes (fetal distress, premature rupture of membranes-PROM, placenta previa, preeclampsia, preterm birth, cesarean section, stillbirth), maternal outcomes (admission to intensive care unit-ICU or death), neonatal outcomes (gender, gestational age, birthweight, 1-minute/5-minute Apgar score, horizontal/vertical transmission, admission to ICU, mechanical ventilation, sepsis and death). As a result, the present meta-analysis was based on 16 observational studies [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] and 44 case reports/series , including a total of 920 neonates born to women with SARS-CoV-2 infection. doi = 10.1016/j.ejogrb.2020.11.038 id = cord-318715-p6agoqu8 author = Belser, Jessica A title = Assessment of SARS-CoV-2 replication in the context of other respiratory viruses date = 2020-05-07 keywords = SARS summary = Hui and colleagues show the susceptibility of human conjunctival explant cultures to SARS-CoV-2 infection (with higher levels of virus replication than SARS-CoV), a notable finding considering reports of ocular manifestations in some patients with confirmed COVID-19 infection, and detection of viral RNA in ocular swabs. 6 Human colorectal carcinoma epithelial cells were also found to support virus replication with SARS-CoV-2, consistent with reports of detection of viral RNA in faecal samples and other tissues from the gastrointestinal tracts of patients with confirmed COVID-19, even in the absence of gastrointestinal symptoms. Tropism of the novel coronavirus SARS-CoV-2 in human respiratory tract: an analysis in ex vivo and in vitro cultures Tropism and innate host responses of a novel avian influenza A H7N9 virus: an analysis of ex-vivo and in-vitro cultures of the human respiratory tract doi = 10.1016/s2213-2600(20)30227-7 id = cord-325529-pid58g2r author = Ben-Ami, Roni title = Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date = 2020-06-23 keywords = PCR; RNA; SARS summary = METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. doi = 10.1016/j.cmi.2020.06.009 id = cord-351854-5s03f0pp author = Ben-Ami, Roni title = Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date = 2020-04-22 keywords = PCR; RNA; SARS summary = title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. doi = 10.1101/2020.04.17.20069062 id = cord-283411-40ojqv1y author = Ben-Shmuel, Amir title = Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date = 2020-09-10 keywords = RNA; SARS summary = title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. doi = 10.1016/j.cmi.2020.09.004 id = cord-266034-811lov8f author = Benameur, Karima title = Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020 date = 2020-09-17 keywords = CSF; SARS; level summary = CSF analysis also showed markedly increased levels of interleukin (IL)-6, IL-8, and IL-10, but severe acute respiratory syndrome coronavirus 2 was not identified in any CSF sample. Because MRI changes seen in these patients could be caused by hypercoagulability (15) or metabolic encephalopathy (16) , we propose that CSF investigation can improve the distinction between neurologic involvement of SARS-CoV-2 (or neuro-COVID) and neurologic symptoms caused by other COVID-related causes. The failure to detect CSF SARS-CoV-2 RNA does not diminish the likelihood of direct CNS infection because it is only recovered from blood in 1% of the actively infected cases (18) , and increased levels CSF IgM are also more commonly found as evidence for CNS infection than viral recovery in other encephalitides, including those for infection with Japanese encephalitis virus (19) , dengue virus (20) , human parvovirus 4 (21) , and rabies virus (22) . doi = 10.3201/eid2609.202122 id = cord-325019-hznnoxw6 author = Benavides-Cordoba, Vicente title = Drug Repositioning for COVID-19 date = 2020-06-30 keywords = COVID-19; SARS; drug summary = In this review, we present a selection of drugs, of different classes and with potential activity against COVID-19, whose trials are ongoing; and as proofs of concept, double blind, add-on event-driven, would allow proposing research that generates results in less time and preserving quality criteria for drug development and approval by regulatory agencies. Likewise, when researching new molecules in humans, it is necessary to ask several questions that could improve the designs, and avoid some failures, such as, for example, did the drug hit the target?, did the medication change the target?, what was the dose response?, and what are the characteristics of the study patients?. Hydroxychloroquine, a chloroquine analog, is a medicine widely used in the treatment of systemic autoimmune diseases 35 , being currently the most studied drug for treating COVID-19. In COVID 19, 133 clinical trials are registered, taking different degrees of severity, ranging from prophylactic use in the general population and in health workers 38 to patients with severe acute respiratory syndrome (SARS). doi = 10.25100/cm.v51i2.4279 id = cord-350451-lf27iuwk author = Benedetti, Francesca title = SARS‐CoV‐2: March toward adaptation date = 2020-07-11 keywords = CoV-2; SARS summary = A third factor still subject of debate is how and how much the mutations observed in SARS-CoV-2 provide an indication of viral fitness and adaptation, and their role first into the initial phases of transmission and now during the reduction of viral spreading. The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel human pathogen, first detected in China quickly became a global health emergency, culminating with the World Health Organization publicly proclaiming the SARS-CoV-2 outbreak as a pandemic (11 March 2020) . Several reports result show that SARS-CoV-2 is rapidly moving across countries, and new mutation hotspots are emerging in different parts of the genome. Although SARS-CoV-2 is less lethal than MERS-CoV, up to 20% of the infected people develop rapidly a severe disease characterized by interstitial pneumonia and acute respiratory distress syndrome that can ultimately lead to death. Davide Zella http://orcid.org/0000-0001-5576-5770 Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant doi = 10.1002/jmv.26233 id = cord-274366-t138l6px author = Benetti, Elisa title = ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population date = 2020-07-17 keywords = ACE2; SARS; italian; protein; variant summary = Taking advantage of the Network of Italian Genomes (NIG), a consortium established to generate a public database (NIG-db) containing aggregate variant frequencies data for the Italian population (http://www.nig.cineca.it/), here we describe the genetic variation of ACE2 in the Italian population, one of the newly affected countries by the SARS-CoV-2 outbreak causing COVID-19. In order to shed light on the role of ACE2 variants on interindividual variability and susceptibility to COVID-19 in Italian population we performed WES analysis on a cohort of 131 patients and 258 controls who agreed in participating to the study (see "Materials and methods"). These variants which surround residual essentials for the SARS-CoV-2 spike protein binding were predicted to likely affect the cleavage-dependent virion intake, such as the polymorphic c.2158A>G p.(Asn720Asp) (allele frequency 0.011) which lies four amino acids from the cleavage sequence of TMPRSS2 or to have a substantial impact on protein structure and spike protein interaction by MD simulation (Fig. 3a) . doi = 10.1038/s41431-020-0691-z id = cord-282750-d9sb7o63 author = Benhadou, F. title = Improvement of SARS‐CoV2 symptoms following Guselkumab injection in a psoriatic patient date = 2020-05-07 keywords = SARS summary = We read with great interest the publication of Messina et al (1) reporting the first case of SARS‐CoV2 infection in a young patient of 32‐year‐old suffering from psoriasis and psoriatic arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)‐23(2).The patient contracted the SARS‐CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. arthritis treated by Guselkumab, a monoclonal antibody that targets specifically the p19 subunit of Interleukin (IL)-23 2 .The patient contracted the SARS-CoV2 infection after a dinner with some friends but fortunately she developed very discrete symptoms including only mild fever and rhinorrhea. These findings support the potential role of IL-23p19 inhibitors to counteract the « cytokine storm » triggered by the SARS-CoV2 and which is potentially implicated in the severity of the symptoms 3 . doi = 10.1111/jdv.16590 id = cord-023888-w2sbyfy2 author = Beniac, Daniel R. title = Structural Molecular Insights into SARS Coronavirus Cellular Attachment, Entry and Morphogenesis date = 2009-07-22 keywords = ACE2; SARS; spike summary = Receptor binding results in structural changes that have been observed in the spike molecule, and these appear to be the initial step in viral membrane fusion. However, despite the size differences, the SARS-CoV spike performs the same fundamental task in viral entry to the host cell as other smaller type 1 viral fusion proteins, such as the influenza hemagglutinin (HA) (~220 kD per trimer). This structural data has been modeled into a scheme to propose a mechanism for SARS-CoV spike-mediated membrane fusion (Figs. Our cryo-EM results show that it is possible for the spike to attach to three ACE2 receptors at once; this may serve to hold on to the host membrane like a tripod so as to accurately orientate the fusion core ( Fig. 3.7) . doi = 10.1007/978-3-642-03683-5_3 id = cord-305274-mcsdem7y author = Beniac, Daniel R. title = Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date = 2007-10-24 keywords = ACE2; SARS; fusion; spike summary = We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. The structures of ACE2 bound to a fragment of the SARS spike containing the receptor-binding domain and the pre-and postfusion configurations of the fusion core heptad repeats of the spike have been solved to atomic resolution [2, 3, [24] [25] [26] . In addition, the atomic resolution structures of two neutralizing antibodies bound to the SARS spike receptor-binding domain have been solved [27, 28] showing that blocking of the receptor binding domain, preventing attachment of virions to cell-surface ACE2, is the likely mechanism of virus neutralization by these antibodies. doi = 10.1371/journal.pone.0001082 id = cord-342660-xigv4u3f author = Benotmane, I. title = In-depth virological assessment of kidney transplant recipients with COVID-19 date = 2020-06-19 keywords = SARS; viral summary = We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. We thus conducted a retrospective cohort study in kidney transplant recipients (KTR) in Alsace, Grand-Est France, to determine the dynamics of nasopharyngeal and plasma viral loads and SARS-CoV-2 serology and to study their association with mortality and severe forms of COVID-19. . https://doi.org/10.1101/2020.06.17.20132076 doi: medRxiv preprint positive viral load greater than 3 log10 copies/reaction after D10, and ten patients (24.4 %) In this retrospective study conducted in a sample of 40 immunocompromised KTR hospitalized for COVID-19, we precisely determined the temporal evolution of nasopharyngeal and plasma SARS-CoV-2 loads, as well as the serological response to the virus. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China doi = 10.1101/2020.06.17.20132076 id = cord-319351-hcxbkvgd author = Benrahma, H. title = Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS date = 2020-06-20 keywords = SARS summary = title: Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new infectious disease that first emerged in Hubei province, China, in December 2019. This study aims to analyze the epidemiological profile of the SARS-CoV-2 in Moroccan cases and to investigate the dynamic of RdRp gene, N gene, and E gene in patients from diagnosis until the recovery. To date, no studies exploring the variation of RdRp, N and E genes expression of SARS-CoV-94 2 in the patient''s specimen. In this study, in first time, we analyses the epidemiological profile The LNR provide a RT-PCR to clinically suspected COVID-19 patients when they were (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.06.18.20135137 id = cord-308912-2pd801t1 author = Bensimon, Cécile M. title = A qualitative study of the duty to care in communicable disease outbreaks date = 2007-12-31 keywords = SARS; care; duty; hcp summary = He continued, stating that on the whole, institutions have a responsibility to provide resources and set up mechanisms with respect to ''''anything that would impact on potentially impairing healthcare workers from carrying out their duties.'''' A nurse echoed this view, stating his expectation that, ''''if I''m going to be involved in dealing with patients with some type of infectious disease, I want to know that my employer has instituted policies and procedures that are protecting my rights.'''' Many other participants agreed that ''''HCPs have the right to adequate protection,'''' and if such is not the case, ''''they should have the right to opt out, legally and ethically.'''' While many participants shared this view, several participants added the qualifier that ''''in a situation where the institution fulfills its obligation to protect these individuals, yat that point [they] can no longer respect [providers''] voluntary decision to withdraw from work and stay home.'''' A nurse stated that if someone is protected with proper equipment, ''''I don''t think you should be given a choice of saying no,'''' thus suggesting, as many others did, that HCPs ought not be able to refuse to provide care if supports are in place. doi = 10.1016/j.socscimed.2007.07.017 id = cord-311545-3rll9mca author = Bentley, Gillian R title = Don''t blame the BAME: Ethnic and structural inequalities in susceptibilities to COVID‐19 date = 2020-07-16 keywords = BAME; COVID-19; SARS summary = However, more recently, insidious and potentially racist allusions are beginning to emerge appearing to blame African Americans as somehow responsible for the relatively large number of cases and deaths from COVID-19 in the USA, stoking age-old tropes, and attributing morbidity and mortality to the behaviors and predispositions of BAME groups (Guardian, 2020b; Strings, 2020) . In reality, structural or social inequalities that affect individual vulnerabilities to SARS-CoV-2 include exposures through types of employment, whether people are working in essential transport networks carrying large numbers of people, or in small grocery shops that place BAME communities at greater risk of contracting COVID-19 ( Figure 1 ). doi = 10.1002/ajhb.23478 id = cord-328962-1c4vqaqr author = Benítez-Cardoza, Claudia Guadalupe title = Potential inhibitors of the interaction between ACE2 and SARS-CoV-2 (RBD), to develop a drug date = 2020-06-15 keywords = ACE2; SARS; compound summary = KEY FINDINGS: 20 best compounds directed to interact in ACE2 with a high probability to be safe in humans, validated by web servers of prediction of ADME and toxicity (ProTox-II and PreADMET), to difficult the interaction between ACE2 and region binding domain (RBD) of SARS-CoV-2. We use the amino acids reported in the crystallographic structure of the interaction between the S-protein-RBD of SARS-CoV-2 and ACE2 (Gln24, Asp30, His34, Tyr41, Gln42, Met82, Lys353 and Arg357 in ACE2) [10] [22] , therefore, using the crystallographic structure of ACE2 (PDB 1R42), we carried out a Docking directed to these mentioned residues using a library of compounds (EXPRESS-pick Collection from Chembridge Corp.) to select the best compounds, and that these can affect the interaction between ACE2 and SARS-CoV-2, making these results an important contribution to establishing the foundations that allow the development of a drug that optimizes the resolution of this pandemic. doi = 10.1016/j.lfs.2020.117970 id = cord-347263-ci6mv72z author = Berekashvili, k. title = Etiologic Subtypes of Ischemic Stroke in SARS-COV-2 Virus patients date = 2020-05-08 keywords = COVID-19; SARS; patient summary = Methods: Over the last 6 weeks, data from four centers in New York City were collected to review the possible ischemic stroke types seen in COVID-19 positive patients. We also wanted to better describe the different ischemic stroke subtypes seen in patients with SARS-COV2 infection especially with the view to assess its unique features seen in the context of COVID-19. Two patients who presented with LVO had no prior complaints of viral illness but went on to develop a severe course of the disease. Only three patients had a severe course of the pulmonary disease prior to the neurological event requiring them to be hospitalized. The LVO cases were typically younger, had a worse neurological presentation, more severe form of viral disease and higher levels of hypercoagulability markers than the non-LVO patients. Ischemic stroke can be a presenting symptom of COVID-19 and may not always be associated with severe disease markers including in the young, minorities and healthcare workers. doi = 10.1101/2020.05.03.20077206 id = cord-314746-1o0rf0ii author = Bergasa-Caceres, Fernando title = Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2 date = 2020-08-10 keywords = Protein; SARS; SCM; contact summary = [Image: see text] In this article, we predict the folding initiation events of the ribose phosphatase domain of protein Nsp3 and the receptor binding domain of the spike protein from the severe acute respiratory syndrome (SARS) coronavirus-2. The identification of the primary contacts along the folding pathway of viral proteins constitutes an important result for at least two reasons: (a) the sequences of the specific segments involved in the primary contacts provide a template to specify candidate peptide drugs of inhibitory effect with the maximum possible contact affinity to compete with the natural folding mechanism; and (b) it provides insight for further investigation into the subsequent folding steps leading to a fully functional viral protein, potentially providing for additional FITRs. The fact that the primary contact is defined by the interaction between two well defined amino acid sequences suggests that a strategy to develop FITR-based therapeutic drugs could be one utilizing trial peptide drugs as suggested above. doi = 10.1021/acs.jpcb.0c03716 id = cord-277076-yvsyo4l9 author = Berger, A. title = SARS date = 2019-09-12 keywords = CoV; SARS; antibody; human summary = Measures including source isolation of patientswho only became infectious after onset of clinical symptomsstrict infection control in health care facilities, timely identification and quarantining of exposed contacts, and perhaps also measures to increase social distance, such as travel warnings and screening of travelers, had led to this remarkable and remarkably rapid success. A further, small SARS outbreak occurred again in Guangdong in late 2003/early 2004; molecular analysis of virus isolates from human cases and animals sampled at the same place and time confirmed that this was zoonotically acquired from Paguma larvata. The laboratory diagnosis of SARS remains a challenge; in fact, despite the rapid identification of SARS-CoV as the etiological agent, testing contributed little to the successful control of the 2003 outbreak. A negative antibody test result later than 21 days after the onset of illness is likely to indicate that no infection with SARS-CoV has taken place. doi = 10.1016/b978-0-444-63951-6.00624-0 id = cord-285557-my16g91c author = Berger, A. title = Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date = 2004-01-31 keywords = Health; SARS; acute; respiratory; severe summary = This strengthened the case for the novel coronavirus being the cause of SARS, but only after it had been shown to cause a similar illness in artificially infected macaques could it be regarded as fulfilling all four of Koch''s postulates ; World Health Organisation Multicentre Collaborative Networks for Severe Acute Respiratory Syndrome Diagnosis, 2003) . Nevertheless, and despite considerable progress in this field, much remains to be done until laboratory tests become a useful tool for the management of SARS cases (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003) . An enzyme-linked immunosorbent assay (ELISA) was developed that detects antibodies in the serum of SARS patients and reliably yields positive results at around day 21 after the onset of illness (World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome Diagnosis, 2003). doi = 10.1016/j.jcv.2003.09.011 id = cord-286923-o4fj8kx0 author = Berhan, Yifru title = What immunological and hormonal protective factors lower the risk of COVID-19 related deaths in pregnant women? date = 2020-07-18 keywords = COVID-19; SARS; vitamin summary = The immunological changes predominantly inclining to anti-inflammatory state, which is augmented by placental hormones'' immune modulating action, looks against with COVID-19 inflammatory reaction leading to cytokine storm and multiple organ failure. As discussed hereunder, accumulating evidence from other infections and autoimmune diseases shows that immune modulating hormones, cytokines and other anti-inflammatory endogenous ligands are determinant factors in reducing the severity of several diseases during pregnancy; which could also be the most plausible explanation for the less severity and mortality of Covid-19 in pregnant women. Despite serious concern for patients with autoimmune disease, taking their immune suppression and medications, at least 110 individuals (79% females) with rheumatoid arthritis and got infected with SARS CoV-2 (from six continents) were not as such at higher risk of mortality, probably as they were on anti-inflammatory medication; only 6(5%) persons died of COVID-19 [89] . doi = 10.1016/j.jri.2020.103180 id = cord-304282-om2xc4bs author = Berhan, Yifru title = Will Africa be Devastated by Covid-19 as Many Predicted? Perspective and Prospective date = 2020-05-17 keywords = Africa; Europe; SARS; covid-19 summary = Since the novel coronavirus disease 2019 (Covid-19 or SARS CoV-2 infection) has been declared as pandemic, several mathematicians and statisticians have developed different trajectory curves for Africa, with the assumption that the virus can have an exponential pattern of transmission. A very important argument is; had the Covid-19 transmission been as contagious as in Europe and USA, by this time, every health facility in Africa and other tropical countries could have been flooded with severely ill patients and deaths. The other side of the coin is; the overwhelming cases and deaths experienced in Europe and USA is despite the fact that they started to report Covid-19 confirmed cases almost same time or later than many of the countries in the tropical climate zone. An important observation was that, like the currently observed Covid-19 pandemic, the morbidity and mortality of the aforementioned influenza outbreaks were not that much spreading and killing outside the temperate zone, at least in Africa. doi = 10.4314/ejhs.v30i3.17 id = cord-335844-dybozins author = Berkowitz, Kathleen M. title = IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY date = 2020-07-11 keywords = SARS summary = key: cord-335844-dybozins title: IMPLEMENTATION OF UNIVERSAL TESTING FOR SARS-CoV-2 IN PREGNANT WOMEN WITH INTENDED ADMISSION FOR DELIVERY cord_uid: dybozins Cleveland Clinic Foundation recently implemented a policy OF SARS-CoV-2 testing for all 9 pregnant patients with planned delivery or admitted for labor at obstetric units in Ohio. In contrast to a recent report (1) on universal screening of pregnant women residing in an 12 area of high disease prevalence, our experience derives from a population experiencing a low 13 prevalence of active disease. 14 Patients with planned delivery were tested 3-5 days prior to admission using a CDC approved 15 RT-PCR testing platform. Patients presenting 16 in spontaneous labor were tested using a rapid platform (Xpert Xpress SARS-CoV-2 (Cepheid, Screening all pregnant women admitted to 40 labor and delivery for the virus responsible for coronavirus disease 2019 Universal Screening for SARS-CoV-2 in 46 Women Admitted for Delivery Women Admitted for Delivery doi = 10.1016/j.ajog.2020.07.011 id = cord-323024-blc3mnbj author = Bernard-Valnet, R. title = CSF of SARS-CoV-2 patients with neurological syndromes reveals hints to understand pathophysiology date = 2020-11-04 keywords = CSF; SARS; patient summary = Methods: We checked for SARS-CoV-2 RNA by RT-qPCR, SARS-CoV-2-specific antibodies and for 48 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluids (CSF) +/sera of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological control patients (inflammatory [IND], non inflammatory [NIND], multiple sclerosis [MS]). Methods: We checked for SARS-CoV-2 mRNA by qPCR, SARS-CoV-2-specific antibodies and for 49 cytokines/chemokines/growth factors (by Luminex) in the cerebrospinal fluid (CSF) +/serum of a cohort of 17 COVID-19 patients with neurological presentation and 55 neurological controls (inflammatory, non inflammatory, multiple sclerosis). Thus, the main hypotheses to explain neurological complications in COVID patients point at mechanisms either related to low grade presence of the virus in the CNS, to cytokine storm or to the presence of an auto-immune response, such as anti-neuronal antibodies by analogy to what occurs in autoimmune encephalitis. We found that SARS-CoV-2 patients tend to have signs of blood brain barrier opening and possible astrocytes activation, but no strong immune response in the CSF or obvious CNS infection by the virus. doi = 10.1101/2020.11.01.20217497 id = cord-288484-qy619tfg author = Bernard‐Valnet, R. title = Two patients with acute meningoencephalitis concomitant with SARS‐CoV‐2 infection date = 2020-05-30 keywords = CoV-2; SARS summary = We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. We report here two patients infected with SARS-CoV-2 who presented with neurological symptoms and signs. Patient 1 was a 64-year-old woman without psychiatric history, known to have had contact with SARS-CoV-2 (her husband tested positive 15 days before) and presenting for 5 days with flu-like symptoms (mild asthenia, myalgia, cough) without fever, acutely developed psychotic symptoms. Cerebral magnetic resonance imaging was normal, but her lumbar puncture was compatible with viral meningoencephalitis (Table 1) and SARS-CoV-2 was detected in her nasopharyngeal swab. A 67-year-old woman, already diagnosed with SARS-CoV-2 infection for 17 days with mild respiratory symptoms, presented an intense wake-up headache. However, CSF SARS-CoV-2 and viral/bacterial pathogen polymerase chain reaction tests were negative (Table 1 ). To conclude, we report the first temporal association between acute SARS-CoV-2 infection and aseptic encephalitis with focal neurological symptoms and signs. doi = 10.1111/ene.14298 id = cord-291156-zxg3dsm3 author = Bernasconi, Anna title = Empowering Virus Sequences Research through Conceptual Modeling date = 2020-05-01 keywords = SARS; VCM; sequence; virus summary = We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. doi = 10.1101/2020.04.29.067637 id = cord-299449-226dd23u author = Bernhardt, Denise title = Neuro-oncology Management During the COVID-19 Pandemic With a Focus on WHO Grade III and IV Gliomas date = 2020-05-05 keywords = HGG; SARS; TMZ; patient summary = It is acknowledged that the SARS-CoV-2 pandemic will require center specific discussions of appropriate resource allocation that considers patient and provider safety, resource constraints, and a realistic evaluation of the impact of therapy upon Incurable brain tumors. This international multidisciplinary group of experts in HGG provides a risk-adapted framework for decisions in both pandemic scenarios, considering both ethical issues and resource constraints, in order to minimize the irreparable damage associated with withholding necessary treatments. We recognize that during the pandemic the challenges of ICU capacity, conservation of PPE, availability of health care professional expertise and the risk for patients'' exposure to SARS-CoV-2 may reduce the ability to provide optimal surgical management. Patients and caregivers should be included in the decision-making process as much as possible, and this should include all relevant data on chemotherapy and radiotherapy, as well as the individual risk profile associated with a potential SARS-CoV-2 infection. doi = 10.1093/neuonc/noaa113 id = cord-355758-tk7eturq author = Berrio, Alejandro title = Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date = 2020-09-22 keywords = Coronavirus; RNA; SARS summary = Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. doi = 10.1101/2020.09.16.300038 id = cord-301974-4wn40ivq author = Berry, Jody D title = Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus date = 2004-09-01 keywords = CoV; ELISA; SARS; Spike; western summary = A total of 15 l of SARS-CoV antigen (infected Vero cell lysate) or 5 g of highly purified virus is coated (per spot) for 1 h at 37 • C. c Protein specificity tests shown here were determined by Western immunoblot with purified virus and infected cell lysate under denaturing conditions (Fig. 1) . The four Western immunoblot negative, virus-neutralising mAbs were tested for their ability to bind native SARS-CoV in infected cells by immunofluorescence assay. While purified virus is clearly the optimal antigen tested in this series of experiments, the lower quality SARS-CoV-infected Vero cell lysates are, however, much easier to prepare for diagnostic assays. This paper describes the development of murine mAbs which recognise SARS-CoV antigens in ELISA, immuno-dotblot, Western immunoblot, on the surface of infected cells, and in neutralisation assays. doi = 10.1016/j.jviromet.2004.04.009 id = cord-335567-ssnvr6nj author = Berry, Michael title = Identification of New Respiratory Viruses in the New Millennium date = 2015-03-06 keywords = MERS; NL63; SARS; human; respiratory summary = In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients doi = 10.3390/v7030996 id = cord-284191-05djnz4p author = Bert, Nina Le title = Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date = 2020-05-27 keywords = SARS summary = To study SARS-CoV-2 specific T cells associated with viral clearance, we collected peripheral blood of 24 individuals who recovered from mild to severe COVID-19 (demographic, clinical and virological information are summarized in Extended Data Table 1 ) and studied the T cell response against selected structural (nucleocapsid protein-NP) and non-structural proteins (NSP7 and NSP13 of ORF1) of the large SARS-CoV-2 proteome ( Figure 1A) . To confirm and further delineate the multispecificity of the NP-specific T cell response detected ex vivo in COVID-19 recovered patients, we defined in nine individuals, the distinctive sections of NP targeted by T cells. This is consistent with the findings of Grifoni et al 11 : using selected peptides, they detected ORF-1 specific T preferentially in some SARS-CoV-2 unexposed donors while T cells of COVID-19 recovered donors preferentially recognized structural proteins. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals doi = 10.1101/2020.05.26.115832 id = cord-262863-f07v5uk8 author = Bertocchi, Ilaria title = The hidden role of NLRP3 inflammasome in obesity‐related COVID‐19 exacerbations: lessons for drug repurposing date = 2020-08-09 keywords = COVID-19; NLRP3; SARS; inflammasome summary = We and others have demonstrated that NLRP3 inflammasome over-activation is involved not only in the pathogenesis of diabesity, but also in the exacerbation of related cardiovascular injuries, including myocardial infarction, and this process is associated to an increase in the local inflammatory response. Similarly, the diabesityrelated basal activation of the NLRP3 inflammasome cascade, leading to increase in either gastrointestinal or vascular permeability, may contribute to exacerbate SARS-CoV-2 systemic diffusion and enhance the intricate mechanisms of intracellular cross talk operational in the pathogenesis of COVID-19. Up to nowadays six clinical trials (NCT04347980, NCT04325061, NCT04395105, NCT04344730, NCT04360876, NCT04327401), reported on clinicaltrials.gov are recruiting patients to test the efficacy of the corticosteroid dexamethasone, whose beneficial effects in airway inflammation has been recently demonstrated to involve lung inhibition of the activity of NLRP3 inflammasome and the release of IL-1β and IL-18 (Guan, Ma, Fan, Chen, Miao & Wu, 2020) . doi = 10.1111/bph.15229 id = cord-280280-9jr7ekbu author = Bertoncelli, Deborah title = COVID19: potential cardiovascular issues in pediatric patients date = 2020-05-11 keywords = COVID-19; Kawasaki; SARS; patient summary = Ongoing studies and accumulated data are detailing the features and the effects of the new coronavirus disease 19 (COVID 19) in the adult population, and cardiovascular involvement is emerging as the most significant and life-threatening complication, with an increased risk of morbidity and mortality in patients with underlying cardiovascular disease. At present, though the limited data on the effects of COVID 19 in pediatric patients, children seem to count for a little proportion of SARS-COV 2 infection, and present with less severe disease and effects However infants and toddlers are at risk of developing critical course. Coronavirus disease 19 (COVID-19) is a severe acute respiratory syndrome for which the etiologic agent is the novel beta coronavirus SARS-CoV-2, first described in December 2019 in China in a cluster of patients presenting with pneumonia. The main presenting clinical feature of the disease is pneumonia, ranging from asymptomatic or mildly symptomatic to severe acute respiratory distress syndrome, but cardiovascular involvement is emerging as one of the most significant and life-threatening complications of SARS-CoV-2 infection (1, 2) . doi = 10.23750/abm.v91i2.9655 id = cord-298967-vjyh1xvh author = Bertossi, Dario title = Safety guidelines for non‐surgical facial procedures during covid‐19 outbreak date = 2020-06-07 keywords = SARS; covid-19; patient summary = METHODS: A virtual meeting was conducted with the members (n=12) of the European Academy of Facial Plastic Surgery Focus Group to outline the safety protocol for the non‐surgical facial aesthetic procedures for aesthetic practices in order to protect the clinic staff and the patients from SARS‐CoV‐2 infection. While many medical Accepted Article practices are being run with online consultations 10 , some countries have recently decided to allow the opening of practices requiring one-on-one contact like dental, physiotherapy, for emergencies provided they strictly follow the guidelines detailing the infection control measures [12] [13] . In our largely elective field, both staff and resources should ideally be allocated through careful protocols in order to prevent COVID-19 infection. In response to this pandemic, our focus group has developed a process to stratify procedures and clinical levels with protocols that aim to minimize the risk of contagion and the diffusion of COVID-19 infection. doi = 10.1111/jocd.13530 id = cord-333763-45dzsn2j author = Bestle, Dorothea title = TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells date = 2020-07-23 keywords = Calu-3; S29; SARS; TMPRSS2 summary = The data demonstrate that efficient inhibition of S cleavage by a combination of TMPRSS2 and furin inhibitors can dramatically block SARS-CoV-2 replication in human airway epithelial cells. In conclusion, our data demonstrate that both TMPRSS2 and furin cleave the SARS-CoV-2 S protein and are essential for efficient virus multicycle replication in Calu-3 human airway cells. Virus titers in supernatants were determined by TCID 50 multicycle replication of SARS-CoV-2 in Calu-3 human airway cells is strongly suppressed by inhibiting TMPRSS2 and furin activity, demonstrating that both proteases are crucial for S activation in these cells. Together, our data indicate that furin and TMPRSS2 cleave S at different sites and that cleavage by both proteases is crucial to render the S protein active for mediating virus entry and membrane fusion (Fig 6) . doi = 10.26508/lsa.202000786 id = cord-296440-18vpg419 author = Beurnier, Antoine title = Characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who require hospitalisation date = 2020-07-30 keywords = COVID-19; SARS; patient summary = The objective of this study was to investigate the characteristics and outcomes of asthmatic patients with COVID-19 pneumonia who required hospitalisation during the spring 2020 outbreak in Paris, France. As the world faces the coronavirus disease 2019 (COVID-19) pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, concerns have arisen about a possible increased risk of asthma exacerbations. In Wuhan, authors pointed out a rate of 0.9% [3] , markedly lower than that in the local population; in another study investigating the clinical characteristics and allergy status of 140 patients infected by SARS-CoV-2 in Wuhan, no patient were reported as being asthmatic [3] . All adult patients hospitalized from March 15, 2020 to April 15, 2020 with a diagnosis of SARS-CoV-2 infection and reporting a history of asthma were included. Moreover, obesity, hypertension and diabetes were the most common comorbidities observed in our cohort of hospitalized asthmatics with COVID-19, which is consistent with earlier research in other patient groups [4] [23] . doi = 10.1183/13993003.01875-2020 id = cord-285896-lb8toc1m author = Beurton, Alexandra title = Limiting positive end-expiratory pressure to protect renal function in SARS-CoV-2 critically ill patients date = 2020-07-10 keywords = SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related pneumonia is a risk factor for acute respiratory distress syndrome (ARDS) and acute kidney injury (AKI) [1, 2] . Herein, we report our experience in SARS-CoV-2 critically ill patients before and after having modified our practices in the view of the high occurrence of AKI that needed renal replacement therapy (RRT) in the first cases we managed. During "period 1" (between 04 and 15 March 2020), all mechanically ventilated patients with confirmed SARS-CoV-2 admitted to our intensive care unit received volume-controlled ventilation with a tidal volume of 6 ml/kg of ideal body weight and PEEP stepwise increased to reach a plateau pressure below 28 cmH 2 O. Our findings suggest that changing our practices was associated with a decreased need for RRT and a lower proportion of patients with AKI KDIGO 3. doi = 10.1016/j.jcrc.2020.07.008 id = cord-283310-5wam14aa author = Bevova, M. R. title = The New Coronavirus COVID-19 Infection date = 2020-09-09 keywords = COVID-19; China; SARS; disease summary = Later, the pneumonia was associated with a new coronavirus; in February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus causing it. In February 2020, the World Health Organization (WHO) gave the name COVID-19 to the new disease, while the International Committee on Taxonomy of Viruses (ICTV) gave the name SARS-CoV-2 to the virus. The estimation of the case-fatality rate (portion of deaths divided by the total number of cases) for the disease varies from 1 to 7% [24, 25] depending on the sex and age composition of the population; strategies of testing, diagnostics, and treatment; bureaucratic peculiarities of healthcare in a particular country; and congestion of healthcare systems. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.3103/s0891416820020044 id = cord-304660-w7rs2dvt author = Bharadwaj, Shiv title = SARS-CoV-2 M(pro) inhibitors: identification of anti-SARS-CoV-2 M(pro) compounds from FDA approved drugs date = 2020-11-05 keywords = SARS; figure summary = The top 10 screened potential compounds against SARS-CoV-2 M(pro) were then studied by re-docking, binding affinity, intermolecular interaction, and complex stability via 100 ns all atoms molecular dynamics (MD) simulation followed by post-simulation analysis, including end point binding free energy, essential dynamics, and residual correlation analysis against native crystal structure ligand N3 inhibitor. Hence, comparative molecular docking analysis of screened FDA approved drugs against N3 inhibitor suggested the potential of selected drugs to inhibit SARS-CoV-2 M pro by formation of hydrogen and non-covalent interaction with its catalytic dyad and substrate binding residues. Based on the combinatorial computational analysis, including structure-based virtual screening, molecular docking, binding free energy calculations, MD simulation and post-MD simulation analysis for the screened FDA drugs with viral protease, suggested the drugs, R428, Teniposide, VS-5584, and Setileuton with comparatively higher stability and affinity with SARS-CoV-2 M pro against N3 inhibitor via strong intermolecular interactions formation as well disturbing the conformation of viral protease active pocket. doi = 10.1080/07391102.2020.1842807 id = cord-256307-2b1vlda8 author = Bhardwaj, Vijay Kumar title = Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs date = 2020-11-12 keywords = DSPD; Mpro; SARS; Saquinavir summary = RESULTS: The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated deep inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). The selected DSPD molecules (DSPD-1 to 6) were compared on different computational parameters (Docking energy, RMSD, protein-ligand interactions, MM-PBSA binding energy, Contribution energy, and SASA) to repurposed FDA approved antiviral drugs. The inbuilt published tools (ADMET and Toxicity Prediction by Komputer Assisted Technology (TOPKAT) module) and models such as the CYP2D6 Prediction, Hepatotoxic Prediction, PPB Prediction, Solubility Level, Absorption Level, 2D Polar Surface Area, AlogP98, Rat Female NTP Prediction, Rat Male NTP Prediction, Carcinogenic Potency TD50 Rat, Rat Oral LD50, Ames Prediction, DTP Prediction, Skin Irritant, and Skin Sensitization in the discovery J o u r n a l P r e -p r o o f studio package were used to calculate and analyze the pharmacokinetic profiles of DSPD molecules along with the selected FDA approved drugs [31, 32] . doi = 10.1016/j.compbiomed.2020.104117 id = cord-353116-7t1prfkr author = Bhargava, Ashish title = Predictors for Severe COVID-19 Infection date = 2020-05-30 keywords = CRP; SARS; covid-19 summary = BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. doi = 10.1093/cid/ciaa674 id = cord-264653-ms6zrrnd author = Bhatnagar, Tarun title = Lopinavir/ritonavir combination therapy amongst symptomatic coronavirus disease 2019 patients in India: Protocol for restricted public health emergency use date = 2020-04-28 keywords = MERS; SARS; ritonavir summary = In view of the earlier evidence about effectiveness of repurposed lopinavir/ritonavir against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as preliminary docking studies conducted by the ICMR-National Institute of Virology, Pune, the Central Drugs Standard Control Organization approved the restricted public health use of lopinavir/ritonavir combination amongst symptomatic COVID-19 patients detected in the country. Hospitalized adult patients with laboratory-confirmed SARS-CoV-2 infection with any one of the following criteria will be eligible to receive lopinavir/ritonavir for 14 days after obtaining written informed consent: (i) respiratory distress with respiratory rate ≥22/min or SpO(2) of <94 per cent; (ii) lung parenchymal infiltrates on chest X-ray; (iii) hypotension defined as systolic blood pressure <90 mmHg or need for vasopressor/inotropic medication; (iv) new-onset organ dysfunction; and (v) high-risk groups age >60 yr, diabetes mellitus, renal failure, chronic lung disease and immunocompromised persons. doi = 10.4103/ijmr.ijmr_502_20 id = cord-345106-5szz1et3 author = Bhattacharya, D. D. title = Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2 date = 2020-09-11 keywords = SARS summary = Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Total RNA was isolated from the SARS-CoV-2-infected saliva samples using QIAamp Viral preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.09.11.20192591 doi: medRxiv preprint A total number of 53 subjects were tested positive both in NPS and saliva assay, whereas 5 samples were found only as NPS positive (Table 1) Statistically, we detected lower C T value for ORF1 gene in the saliva specimens (mean C T = 27.07; 95% confidence interval [CI], 25.62 to 28.52) than in the NPS specimens (mean C T = 28.24; 95% CI, 26.62 to 29.85) (Figure 2A) . doi = 10.1101/2020.09.11.20192591 id = cord-353748-y1a52z8e author = Bhattacharya, Rajarshi title = A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 date = 2021-01-02 keywords = RBD; SARS summary = title: A natural food preservative peptide nisin can interact with the SARS-CoV-2 spike protein receptor human ACE2 Nisin, a food-grade antimicrobial peptide produced by lactic acid bacteria has been examined for its probable interaction with the human ACE2 (hACE2) receptor, the site where spike protein of SARS-CoV-2 binds. Among the eight nisin variants examined, nisin H, nisin Z, nisin U and nisin A showed a significant binding affinity towards hACE2, higher than that of the RBD (receptor binding domain) of the SARS-CoV-2 spike protein. The present study attempts to investigate the ability of food-grade nisin A and its natural variants to block the interaction between hACE2 and the spike protein of SARS-CoV-2, a key step of COVID-19 disease initiation. The binding affinity of docked structures of all eight variants of nisin in complex with hACE2 was calculated as ΔG derived from analysis with Prodigy for each complex in comparison with the RBD of spike protein of SARS-CoV-2. doi = 10.1016/j.virol.2020.10.002 id = cord-193136-7g6qr73e author = Bhattacharya, Sujit title = Visible Insights of the Invisible Pandemic: A Scientometric, Altmetric and Topic Trend Analysis date = 2020-04-22 keywords = Google; SARS; paper; research summary = (2018) "Google Trends shows the changes in online interest for time series in any selected term in any country or region over a selected time period, for example, a specific year, several years, 3 weeks, 4 months, 30 days, 7 days, 4 hours, 1 hour, or a specified time-frame." They argue that as the internet penetration is increasing web based search activity has become a valid indicator of public behaviour. The paper positions itself in this direction; applying various tools and techniques of scientometrics, Altmetrics and Google Trends to draw meaning from the huge volume of research papers and online activity surrounding this pandemic. The trends observed in measures like lockdown, social distancing and quarantine at global and country level showed the societal increasing concern with these aspects.The findings of this study suggests how the research and public interest has been shaped around this disease. doi = nan id = cord-341246-fz66z2p2 author = Bhattacharyya, Pranab J title = Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection date = 2020-09-28 keywords = SARS; TTC summary = title: Takotsubo cardiomyopathy in early term pregnancy: a rare cardiac complication of SARS-CoV-2 infection A 32-year-old primigravida at a 38-week gestation was initially admitted in cardiology isolation ward on referral by her local obstetrician for inferolateral ST-segment elevation on ECG (figure 1A) which was obtained for complaints of New York Heart Association functional class II symptoms with palpitations of a 3-day duration. As typified by this index case, TTC can mimic acute ST-segment elevation myocardial infarction and is considered to be a reversible form of cardiomyopathy characterised by a complete recovery of RWMA and LV function within weeks of presentation. 2 This is the first reported case of TTC in pregnancy as a manifestation of SARS-CoV-2 infection during this ongoing pandemic. ► The presentation of takotsubo cardiomyopathy can mimic STsegment elevation myocardial infarction but in the absence of angiographic evidence of significant obstructive coronary artery disease. doi = 10.1136/bcr-2020-239104 id = cord-254419-qw83atrx author = Bhattacharyya, Rajat title = The Interplay Between Coagulation and Inflammation Pathways in COVID-19-Associated Respiratory Failure: A Narrative Review date = 2020-08-25 keywords = COVID-19; SARS; disease; patient; severe summary = This narrative review aims to summarize the current available evidence on the interplay between hypercoagulability, thrombo-inflammation, and pulmonary microvascular thrombosis in COVID-19 infection resulting in respiratory failure and how this information can be used to design clinical trials to optimize patient outcomes. ACE2 angiotensin-converting enzyme 2, CRP C-reactive protein, ESR erythrocyte sedimentation rate, LDH lactate dehydrogenase, NETS neutrophil extracellular traps, SARS-COV-2 severe acute respiratory syndrome coronavirus 2, TMPRSS2 transmembrane protease serine 2 shown to be at higher risk of worse outcomes [13] [14] [15] (Fig. 2) . CHD chronic heart disease, CLD chronic lung disease, CKD chronic kidney disease, DOACS direct oral anticoagulants, FDPs fibrinogen degradation products, HTN hypertension, IFN interferon, JAK Janus kinase, LDH lactate dehydrogenase, LMWH low molecular weight heparin, NSAIDS nonsteroidal anti-inflammatory drugs, PT prothrombin time, TNF tumor necrosis factor, VW Ag Von Willebrand antigen and microvascular thrombosis appears to be responsible for the clinical picture that leads to progressive multi-organ failure in a small percentage of patients, ultimately causing fatalities. doi = 10.1007/s41030-020-00126-5 id = cord-336563-hwemigk7 author = Bhimraj, Adarsh title = Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date = 2020-04-27 keywords = COVID-19; SARS; clinical; patient; treatment summary = Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . doi = 10.1093/cid/ciaa478 id = cord-268074-9mact9br author = Bi, Qifang title = Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study date = 2020-04-27 keywords = SARS; Shenzhen summary = We compared cases identified through symptomatic surveillance and contact tracing, and estimated the time from symptom onset to confirmation, isolation, and admission to hospital. We characterise differences in demographics and severity between cases identified through symptom-based surveillance and monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterise SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval, and observed reproductive number (R). This study is, to our knowledge, the first analysis of SARS-CoV-2 transmission and COVID-19 natural history based on a large primary dataset of cases and close contacts, for which the mode of surveillance (ie, symptom-based versus contact-based) was sufficiently documented and RT-PCR testing was nearly universal. Between Jan 14 and Feb 12, 2020, the Shenzhen CDC confirmed 391 cases of SARS-CoV-2 infection ( of 87) than were those detected through contact-based surveillance (tables 1, 2). doi = 10.1016/s1473-3099(20)30287-5 id = cord-297800-hnx213kp author = Bi, Qifang title = Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts date = 2020-03-04 keywords = SARS; Shenzhen summary = We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We characterize differences in demographics and severity between cases identified through symptom-based surveillance and the monitoring of close case contacts, and estimate the time to key events, such as confirmation, isolation, and recovery. Using data from contact tracing, we characterize SARS-CoV-2 transmission by estimating key values, such as the household secondary attack rate, serial interval and observed reproductive number. Based on 48 pairs of cases with a clear infector-infectee relationship and time of symptom onset, we estimate that the serial interval is gamma distributed with mean 6.3 days (95% CI 5.2,7.6) and a standard deviation of 4.2 days (95% CI, 3.1,5.3) ( Figure 2B , Table S2 ). This analysis of early SARS-CoV-2 cases and their close contacts in Shenzhen China, provides insights into the natural history, transmission and control of this disease. doi = 10.1101/2020.03.03.20028423 id = cord-263123-5y8cc5eb author = Bian, Jingwei title = Anti-RAS drugs and SARS-CoV-2 infection date = 2020-04-28 keywords = SARS summary = authors: Bian, Jingwei; Zhao, Rongsheng; Zhai, Suodi; Li, Zijian In addition, ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAS) and plays a key role in cardiovascular disease, especially Here, we present a completely different perspective on the relationship between SARS-CoV-2 infection and ACEI/ARB drugs. Firstly, there is no sufficient evidence to support that ACEIs and ARBs can upregulate the protein expression level of ACE2. Therefore, there is no adequate evidence to support that ACEIs/ARBs increase the risk of the SARS-CoV-2 infection by up-regulating ACE2 protein level. In addition, liver/lymph node-specific and dendritic In summary, there is currently no clear evidence indicating that anti-RAS drugs (ACEIs and ARBs) increase the risk of SARS-CoV-2 infection, as well as target organ injury. There is still no need to recommend the discontinuation of ACEIs/ARBs for hypertensive patients with or at high risk of SARS-CoV-2 infection, or the change to other antihypertensive drugs. Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19 doi = 10.1016/j.apsb.2020.04.013 id = cord-280662-gakayv6e author = Bian, Jingwei title = Angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 receptor and RAS modulator date = 2020-10-13 keywords = ACE2; CoV-2; RAS; SARS summary = Angiotensin-converting enzyme 2 (ACE2) was rapidly identified as the critical functional receptor for SARS-CoV-2. Given that ACE2 functions as both a SARS-CoV-2 receptor and a RAS modulator, the treatment for COVID-19 presents a dilemma of how to limit virus entry but protect ACE2 physiological functions. We propose five novel working modes for functional receptor for SARS-CoV-2 infection and the routes of ACE2-mediated virus entering host cells, as well as its regulatory mechanism. SARS-CoV-2 has been shown to share the same functional receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV) 4, 5 . SARS-CoV S-protein binding facilitates ADAM17-dependent ACE2 shedding and has been shown to induce viral entry into the cell 52 . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.1016/j.apsb.2020.10.006 id = cord-299552-rgrm8dil author = Bianchi, Martina title = Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? date = 2020-05-30 keywords = Sars summary = In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. In this report, a structural comparison between the Sars-CoV-2 surface proteins from different isolates with homologous proteins from closely related viruses such as those from Bat and Pangolin is described. Sars-CoV-2 E sequences differ from the homologous proteins also at positions 55-56, where the dyad Ser-Phe replaces Thr-Val (except in Bat coronavirus isolate BtKY72, accession code KY352407). In this paper, E and M proteins from 797 Sars-CoV-2 genomes have been compared to the counterparts taken from the most closely related virus also to evaluate the potential role of amino acid mutations in the epizootic origin of COVID-19. doi = 10.1155/2020/4389089 id = cord-259261-fmuozy3w author = Bickler, Stephen W. title = AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date = 2020-06-16 keywords = PRR; SARS summary = title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. We also asked the question if the differentially expressed genes between the oldest and youngest age groups encode proteins that interact with SARS-CoV-2 (see "Methods" section). Our analysis revealed eleven differentially expressed genes between the oldest and youngest age groups that encode proteins known to interact with SARS-CoV-2 (Fig. 3d) . Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts we show that expression of PRR genes and ACE2, the receptor for SARS-CoV-2 vary with age. doi = 10.1101/2020.06.15.134403 id = cord-354148-87tpjvs6 author = Bidra, Avinash S. title = Rapid In‐Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Using Povidone‐Iodine Oral Antiseptic Rinse date = 2020-06-16 keywords = SARS; oral; pvp summary = PURPOSE: To investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone‐iodine (PVP‐I) against SARS‐CoV‐2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. MATERIALS AND METHODS: The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) USA‐WA1/2020 strain, virus stock was tested against oral antiseptic solutions consisting of aqueous povidone‐iodine (PVP‐I) as the sole active ingredient. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. The purpose of this study was to investigate the optimal contact time and concentration for viricidal activity of oral preparation of povidone-iodine (PVP-I) against SARS-CoV-2 (''corona virus'') to mitigate the risk and transmission of the virus in the dental practice. doi = 10.1111/jopr.13209 id = cord-268809-plgip4h6 author = Bielecki, Michel title = Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date = 2020-06-29 keywords = COVID-19; SARS summary = We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. To our knowledge, it is unknown if lowering the viral inoculum during infection with SARS-CoV-2 or altering the mode of infection by physical means can affect the clinical course of the disease. Here, we present an outbreak at a Swiss Army Base with two very similar groups infected prior and after the implementation of stringent social distancing and hygiene A c c e p t e d M a n u s c r i p t measures (SDHMs). We describe an outbreak of SARS-CoV-2 infections in young, healthy soldiers in two spatially separated groups with almost identical baseline characteristics but different clinical courses. doi = 10.1093/cid/ciaa889 id = cord-317795-689at1qx author = Bielicki, Julia A title = Monitoring approaches for health-care workers during the COVID-19 pandemic date = 2020-07-23 keywords = COVID-19; SARS; care; health summary = One of the greatest risks to the health-care system is a high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health-care workers and the consequent lack of skilled staff to ensure a functioning local or regional response to the pandemic. 5 National and international recommendations for risk assessment and management of hospital health-care staff working with patients infected with SARS-CoV-2 are detailed and publicly available. Can rapidly deplete the workforce, particularly in cases of HCWs infected with SARS-CoV-2 exposing many colleagues or when there is uncontrolled community transmission, with HCWs exposed outside of the hospital; might not be relevant in settings where some level of PPE is universally recommended (eg, wearing surgical mask for all patient contacts) and there is high adherence to other IPC measures Specific recommendations for monitoring health-care workers for potential SARS-CoV-2 infection should be available for all staff who are expecting to see or currently managing patients with COVID-19. doi = 10.1016/s1473-3099(20)30458-8 id = cord-287448-hwsr1804 author = Bigaut, Kévin title = Guillain-Barré syndrome related to SARS-CoV-2 infection date = 2020-05-27 keywords = SARS summary = Twenty-one days after the beginning of respiratory symptoms, he presented with in a rapidly progressive manner paraesthesia, hypoesthesia, and distal weakness in the lower limbs. CSF results showed normal cell count (1 × 10 6 /L), increased protein level (0.94 g/L), and negative SARS-CoV-2 on RT-PCR assay. CSF results showed subnormal cell count (6 × 10 6 /L), increased protein level (1.06 g/L), and negative SARS-CoV-2 on RT-PCR assay. We reported here 2 cases of GBS related to SARS-CoV-2 infection with neurologic improvement on IVIg, adding to few cases of GBS, one case of Miller Fisher syndrome, and one case of polyneuritis cranialis already published. 3 However, previous reports and our cases suggest that GBS associated with SARS-CoV-2 infection could start between 5 and 21 days after the SARS-CoV-2 clinical symptoms. 4 It could follow a postinfectious profile as reported on Middle East respiratory syndrome coronavirus infection in 4 patients with Bickerstaff''s encephalitis overlapping with GBS. doi = 10.1212/nxi.0000000000000785 id = cord-353235-jiqhgf56 author = Bigliardi, Guido title = Middle cerebral artery ischemic stroke and COVID-19: a case report date = 2020-09-08 keywords = COVID-19; SARS summary = We present a clinical case of a patient with SARS-CoV-2 infection and respiratory symptoms, complicated with a pro-thrombotic state involving multiple vascular territories and concomitant interleukin-6 increase. Here, we report a case of a patient with SARS-CoV-2 infection that developed severe coagulopathy affecting both pulmonary and cerebral vessels. In the following days, the patient respiratory symptoms worsened with increasing need for oxygen therapy. Arterial and venous thrombotic events are recognized complications of SARS-CoV-2 infection (Klok et al. Of note, severe respiratory failure was heralded by a marked D-dimer increase 5 days earlier (Fig. 1) . This case underlines the importance of constant neurological monitoring in COVID-19 patients during ICU staying, especially in those with suspected thrombotic events, to detect possible neurological complications. High risk of thrombosis in patients with severe SARS-CoV-2 infection: a multicenter prospective cohort study Incidence of thrombotic complications in critically ill ICU patients with COVID-19 doi = 10.1007/s13365-020-00898-1 id = cord-350686-q2bu7o4i author = Bilder, Christopher R title = Pool size selection when testing for SARS-CoV-2 date = 2020-06-16 keywords = SARS summary = title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people doi = 10.1093/cid/ciaa774 id = cord-303384-bgvagdft author = Bilinska, Katarzyna title = Anosmia in COVID-19: A Bumpy Road to Establishing a Cellular Mechanism date = 2020-07-16 keywords = COVID-19; SARS summary = Several very recent papers contributed to explaining the key cellular steps occurring in the olfactory epithelium leading to anosmia/hyposmia (collectively known as dysosmia) initiated by SARS-CoV-2 infection. Initial hospital observations and early studies have suggested several possible mechanisms for the development of anosmia in COVID-19, including olfactory cleft syndrome, nasal obstruction and rhinorrhea, cytokine storm, direct damage to olfactory receptor neurons (ORNs), and impairment of the olfactory perception centers in the brain. The current model of olfactory dysfunction in COVID-19 is based on the already proven observation that SUS cells are the primary target of the virus and that SUSs infection initiates a series of events leading to dysosmia. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. doi = 10.1021/acschemneuro.0c00406 id = cord-313728-08kwkbmd author = Binda, Barbara title = Follow-up and Management of Kidney Transplant Recipients During the COVID-19 Lockdown: the experience of an Italian Transplant Center, Including Two Cases of COVID-19 Pneumonia date = 2020-06-28 keywords = COVID-19; SARS; patient summary = Conclusion In the context of a lockdown, such as that occurring in response to COVID-19, we suggest implementing remote surveillance programs in kidney transplant recipients, with the help of any available technology, and offering medical consulting and logistic support as needed. In this article, we report the strategy implemented by our KT transplant center in Central Italy to maintain follow-up of KT recipients during the lockdown response to COVID-19. Both of our COVID-19 patients had several risk factors for an unfavorable outcome of the infection: chronic immunosuppression, advanced age, cardiovascular chronic disease and, in one case, diabetes. Consistent with this, we suggest implementing remote surveillance programs in fragile populations, such as transplant recipients, with the help of any available technology (e-mail, phone calls, video calls) as soon as possible, and offering medical consulting and logistic support as needed during the COVID-19 pandemic. Case report of COVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? doi = 10.1016/j.transproceed.2020.06.026 id = cord-330387-7lci44w5 author = Bird, Paul title = High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads date = 2020-06-18 keywords = SARS summary = title: High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads Similarly, another study from Leicester, UK compared hospitalised and community patient SARS-CoV-2 PCR (polymerase chain reaction) positivity rates with that of staff, 2 but again, did not assess which staff groups or clinical specialties were at most risk of acquiring COVID-19. In addition, we compared the SARS-CoV-2 PCR positivity rate against ethnicity for both the HCW and household contacts combined (Fig. 1C) . 8 We then compared the SARS-CoV-2 PCR positivity rates against various demographic parameters, ethnicity and symptom patterns in both the HCWs and household contacts (n=47, Table 1 ). In summary, we have compared the SARS-CoV-2 PCR positivity rates in this HCW and household contact cohort, across different clinical roles and specialties, ethnic groups, and explored the correlation between their symptom patterns and swab viral loads. doi = 10.1016/j.jinf.2020.06.035 id = cord-282899-kp114q7n author = Biswas, Saurav title = Blood clots in COVID-19 patients: Simplifying the curious mystery date = 2020-11-06 keywords = ACE2; SARS; covid-19 summary = Considering the above facts and recent unusual reports, a hypothesis develops for the blood clots formation in the COVID-19 patients (Figure 1) , states that "Due to an internal injury in the endothelium of blood vessels, either directly by SARS-CoV-2 infection (coexpression and binding of the spike protein with the ACE2) or my virus-mediated inflammatory immune response, may result in vasoconstriction and the activation of coagulation and blood clotting pathways, resulting in the formation of blood clots". During COVID-19 infection, SARS-CoV-2 enters into the systemic circulation and binds with the ACE2 expressing endothelial cells (endothelium) lining the blood vessels. SO, in COVID-19 patients, the SARS-CoV-2 mediated endothelial inflammation, thrombin generation, platelet, and leukocyte recruitment, complement activation, and the initiation of innate and adaptive immune responses, forming clots, culminate in immunothrombosis, ultimately resulting in thrombotic complications, stroke, and finally death. doi = 10.1016/j.mehy.2020.110371 id = cord-344170-qrupbtem author = Biswas, Subrata K title = Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 date = 2020-05-24 keywords = SARS summary = Variations in the genomic sequences were also observed when sequencing data from viral isolates of patients from other European and North American countries were compared with each other and with reference sequence [1] . However, this recent study [2] did not explore the association between genetic variation in SARS-CoV-2 and the severity of COVID-19. Therefore, it is an urgent need to explore the association of the mutation pattern of SARS-CoV-2 genome with the severity and fatality of COVID-19. Based on the above discussion, we hypothesize that the genetic variation in SARS-CoV-2 may explain variable severity of COVID-19 in the population. Analysis of sequencing data of SARS-CoV-2 genome showed evidence of mutation at the beginning of the worldwide spread of COVID-19 [1] . This hypothesis can be tested by obtaining genetic sequences of SARS-CoV-2 from two groups of COVID-19 patients. doi = 10.1016/j.mehy.2020.109877 id = cord-318944-13zk6cco author = Bizzoca, Maria Eleonora title = Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date = 2020-05-27 keywords = COVID-19; PPE; SARS; dental; infection; patient; procedure summary = The authors performed a narrative review on Severe Acute Respiratory SyndromeCoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (prevs post-COVID19) for the most common dental procedures. After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The precautions for infection control require wearing gloves, aprons, as well as eye and mouth protection (goggles and mask, such as medical masks and Filtering Face Piece or FPP) for each procedure involving direct contact with the patient body fluids. doi = 10.3390/ijerph17113793 id = cord-293169-rd12xwvl author = Black, Margaret A. title = Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples date = 2020-11-07 keywords = LFI; SARS summary = OBJECTIVES: We validate the use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. Herein, we describe clinical validation of a new lateral flow immunoassay (LFI) test intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood. Plasma, serum, whole blood, and capillary blood (finger stick) samples from patients diagnosed with COVID-19 by PCR were tested with the 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) (Biolidics Ltd.), and the results were correlated with those obtained by enzyme-linked immunosorbent assay (ELISA), the gold standard for serologic detection of antibodies. Furthermore, we show J o u r n a l P r e -p r o o f that capillary whole blood obtained by finger stick shows comparable sensitivity for detecting anti-SARS-CoV-2 IgM and IgG antibodies as venous blood samples. doi = 10.1016/j.jim.2020.112909 id = cord-287644-ay0vv27m author = Blackall, Douglas title = Rapid Establishment of a COVID‐19 Convalescent Plasma Program in a Regional Healthcare Delivery Network date = 2020-08-04 keywords = CCP; COVID-19; SARS summary = Overall, 6 major implementation "themes" were addressed: (1) registration of individual hospitals and principle investigators with a national investigational new drug research protocol, (2) collaboration with a regional blood donor center, (3) targeted recruitment of convalesced donors, (4) information technology issues related to all aspects of CCP ordering, distribution, and transfusion, (5) prioritization of patients to receive CCP, and (6) evaluation of CCP products including antibody characteristics and patient response to therapy. The Mayo IND provides specific criteria for patient inclusion in the protocol; namely, that they have positive molecular testing for SARS-CoV-2, are an adult (≥ 18 years of age), and have met defined clinical criteria qualifying them as having severe or life-threatening COVID-19. randomized controlled study, this protocol provided the infrastructure to initiate a convalescent plasma transfusion program in the SSM-STL network, which is the basis for this report. doi = 10.1111/trf.16026 id = cord-252264-d9i19h8q author = Blackburn, Kyle M. title = Post-infectious neurological disorders date = 2020-08-30 keywords = Barre; GBS; Guillain; SARS; syndrome summary = In this review, we discuss the proposed mechanisms underlying pathogen-induced autoimmunity, and highlight the clinical presentation and treatment of several post-infectious autoimmune neurological disorders. 2 The role of infections in the pathogenesis of ''classic'' neuroimmunological disorders such as multiple sclerosis and Guillain-Barre syndrome (GBS) has been studied extensively. Here, we review the current landscape of post-infectious neurological autoimmunity, discuss proposed immunological mechanisms, highlight specific disorders strongly associated with pathogens, and review treatment considerations. Mimicry-induced autoimmunity may play an important role in GBS cases associated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. 168, 169 Furthermore, a recent systematic review determined that, among 43 post-HSE cases, no patients had experienced recurrence of herpes simplex following treatment for autoimmune encephalitis, despite the use of first and second-line immunotherapy. Guillain-Barre syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study Postinfectious Guillain-Barre syndrome related to SARS-CoV-2 infection: a case report Guillain Barre syndrome associated with COVID-19 infection: a case report doi = 10.1177/1756286420952901 id = cord-339128-npfoircv author = Blair, Robert V. title = Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques date = 2020-11-07 keywords = ARDS; COVID-19; SARS summary = Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. Here we report ARDS in two aged African green monkeys (AGMs) infected with SARS-CoV-2 that demonstrated pathological lesions and disease similar to severe COVID-19 in humans. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. We also report a comparatively mild COVID-19 phenotype characterized by minor clinical, radiographic and histopathologic changes in the two surviving, aged AGMs and four rhesus macaques (RMs) infected with SARS-CoV-2. This study demonstrates that following exposure to SARS-CoV-2 aged AGMs develop a spectrum of disease, from mild to severe COVID-19, which in some cases progress to ARDS. doi = 10.1016/j.ajpath.2020.10.016 id = cord-320826-o6ih2f23 author = Blairon, Laurent title = Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak date = 2020-07-31 keywords = SARS summary = title: Large-scale, molecular and serological SARS-CoV-2 screening of healthcare workers in a 4-site public hospital in Belgium after COVID-19 outbreak We read with great interest the study of Chen Y et al., who analyzed, during the Chinese epidemic peak, the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 105 healthcare workers (HCWs) exposed to COVID-19 patients [1] . Our purpose was to document at the end of the Belgium epidemic the seroprevalence of SARS-CoV-2 in HCWs exposed to COVID-19 at varying degrees and to compare these rates with those observed by other teams worldwide. On the same day, all asymptomatic HCWs who agreed to participate benefited from both serological and RT-qPCR SARS-CoV-2 tests. High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients COVID-19 study: 8,4% of Belgian health workers have antibodies to SARS-COV-2 n doi = 10.1016/j.jinf.2020.07.033 id = cord-310857-i9v9antx author = Blaisdell, Laura L. title = Preventing and Mitigating SARS-CoV-2 Transmission — Four Overnight Camps, Maine, June–August 2020 date = 2020-09-04 keywords = COVID-19; SARS summary = The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020.* Shortly thereafter, closures of 124,000 U.S. public and private schools affected at least 55.1 million students through the end of the 2019-20 school year.† During the summer of 2020, approximately 82% of 8,947 U.S. overnight camps did not operate.§ In Maine, only approximately 20% of 100 overnight camps opened.¶ An overnight camp in Georgia recently reported SARS-CoV-2, the virus that causes COVID-19, transmission among campers and staff members when nonpharmaceutical interventions (NPIs) were not strictly followed (1); however, NPIs have been successfully used to mitigate SARS-CoV-2 transmission among military basic trainees (2). During June-August 2020, four overnight camps in Maine implemented several NPIs to prevent and mitigate the transmission of SARS-CoV-2, including prearrival quarantine, preand postarrival testing and symptom screening, cohorting, use of face coverings, physical distancing, enhanced hygiene measures, cleaning and disinfecting, and maximal outdoor programming. To prevent, identify, and mitigate spread of COVID-19, four Maine overnight summer camps with similar size, session duration, and camper and staff member characteristics opened with uniform NPIs, including precamp quarantine, pre-and postarrival testing and symptom screening, cohorting, and physical distancing between cohorts. doi = 10.15585/mmwr.mm6935e1 id = cord-333122-xw8o189s author = Blasiak, A. title = IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-05-08 keywords = RDV; SARS; drug summary = IDentif.AI harnesses a quadratic relationship between therapeutic inputs (e.g. drug and dose) and biological outputs (e.g. quantifiable measurements of efficacy, safety) to experimentally pinpoint optimal combinations from large parameter spaces with a marked reduction in the number of required experiments (Fig. 1 ). The 12drug set included a broad spectrum of repurposed agents that are currently being evaluated in clinical studies for treatment of COVID-19 or being administered in conjunction with these therapies, including remdesivir (RDV), favipiravir (FPV), ritonavir (RTV), lopinavir (LPV), oseltamivir (OSV-P), dexamethasone (DEX), ribavirin (RBV), teicoplanin (TEC), losartan (LST), azithromycin (AZT), chloroquine (CQ), and hydroxychloroquine (HCQ). With a 3-order of magnitude reduction in required tests, we identified a clinically actionable list of 2-,3-, and 4-drug combinations ranked based on viral inhibition efficacy with accompanying safety data against kidney epithelial cells (Vero E6), liver epithelial cells (THLE-2) and cardiomyocytes (AC16). This study harnessed the IDentif.AI platform to interrogate a 12 drug-dose parameter space against the SARS-CoV-2 live virus to develop actionable and optimized combination therapy regimens. doi = 10.1101/2020.05.04.20088104 id = cord-347119-w780f0om author = Blitz, Matthew J. title = Race/ethnicity and spatiotemporal trends in SARS-CoV-2 prevalence on obstetrical units in New York date = 2020-08-17 keywords = SARS summary = We evaluated 7 temporal trends, regional geographic variation, and racial/ethnic disparity in SARS-CoV-8 2 prevalence among gravid women presenting to obstetrical units within a large health 9 system in New York during the COVID-19 outbreak. This retrospective study included all pregnant women who had SARS-CoV-2 testing 13 (both symptomatic and asymptomatic) at 7 hospitals within a 30-mile radius from April 14 1, 2020, before the peak of the outbreak in New York State, 4 to June 9, 2020. Of 4,811 pregnant women presenting to the 7 hospital sites after implementation of 38 universal SARS-CoV-2 testing, PCR results were obtained for 4,674 patients: 500 39 (11%) were positive. Non-Hispanic black women 50 constituted 12% (n=567) of the study population, had a test positivity rate of 14% 51 Considerable heterogeneity in SARS-CoV-2 prevalence was observed across hospitals 64 in the region (p<0.0001; Table 1 ). doi = 10.1016/j.ajogmf.2020.100212 id = cord-278249-vvhq9vgp author = Blot, Mathieu title = CXCL10 could drive longer duration of mechanical ventilation during COVID-19 ARDS date = 2020-11-02 keywords = ARDS; CXCL10; ELF; SARS; covid-19; dna summary = In addition, since most patients need to undergo mechanical ventilation in this context, ventilator-induced lung injury (VILI) could exacerbate tissue damage as well as local and systemic inflammation, thus acting as a "second hit." Our team has previously shown that mitochondrial alarmins (i.e., mitochondrial DNA) are released by human epithelial cells submitted to cyclic stretch, and these alarmins are also recovered from bronchoalveolar lavage (BAL) fluid obtained from either ventilated rabbits or ARDS patients. This comprehensive evaluation of systemic and pulmonary immune response showed that the higher CXCL10 concentrations in both the systemic and alveolar compartments of patients with COVID-19 ARDS were associated with a longer duration of mechanical ventilation. Finally, in both COVID-19 and non-COVID-19 patients, higher mitochondrial DNA concentrations in the plasma and ELF compartment were highly correlated with alveolar inflammation, as assessed by BALF cell count and ELF IL-8 and IL-1β concentrations. doi = 10.1186/s13054-020-03328-0 id = cord-336094-ssr5y4u3 author = Blumberg, Dean A. title = Vertical Transmission of SARS-CoV-2: What is the Optimal Definition? date = 2020-06-05 keywords = SARS summary = 11 We start with several underlying assumptions (►Fig. 1) as follows: (1) the incubation period is 1 to 14 days 12,13 ; (2) intrauterine infection may potentially occur transplacentally via blood, or via transmission through swallowed or aspirated amniotic fluid; (3) maternal viremia is unlikely during the incubation period >48 hours before symptom onset and the likelihood of positive SARS-CoV-2 through RT-PCR in blood samples is low (< 1%) in COVID-19 patients 9 ; (4) intrapartum transmission may potentially occur due to exposure to maternal blood, vaginal secretions, or feces; (5) early postnatal infection may occur via the respiratory route or due to direct contact with the infected mother or other caretakers, or potential transmission through breast milk (however, to date we are not aware of any reports of viral presence in breast milk); and (6) SARS-CoV-2 virus may be transiently detected for up to 24 hours after birth due to superficial contamination or transient viremia (similar to HIV). doi = 10.1055/s-0040-1712457 id = cord-276870-gxtvlji7 author = Bobrowski, Tesia title = Learning from history: do not flatten the curve of antiviral research! date = 2020-07-15 keywords = COVID-19; HIV; SARS; number summary = Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. However, despite many experimental and clinical studies, no effective drugs or treatments have emerged to treat the previous six epidemics of bird flu, SARS, swine flu, MERS, Ebola, and Zika as well as, thus far, COVID-19. We evaluated the number of publications (in both peer-reviewed journals and ArXiv preprint servers) and the number of clinical trials performed over the course of the epidemic to estimate the engagement and success of the scientific community in response to the seven major outbreaks of the past two decades: bird flu, SARS, swine flu, MERS, Ebola, Zika, and COVID-19. doi = 10.1016/j.drudis.2020.07.008 id = cord-315129-p31vm79o author = Bock, Jens-Ole title = Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response date = 2020-06-23 keywords = ACE2; COVID-19; SARS summary = title: Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. Here, we use the publicly available proteomics data from this study to re-analyze the in vitro cellular consequences of SARS-CoV-2 infection by impact pathways analysis and network analysis. Cellular factors exploited by SARS-CoV-2 to gain entry into cells have recently been studied, revealing that the virus uses the angiotensin-converting enzyme 2 (ACE2) host cell receptor, together with the serine protease TMPRSS2. Host cell proteomics studies that measure changes in protein abundance following viral entry and subsequent global pathway and network analysis can shed some light on the mechanisms that are used and/or altered by the virus and may reveal novel drug targets. doi = 10.18632/aging.103524 id = cord-275495-h60x89zi author = Bocksberger, S. title = Temporäre Hyposmie bei COVID-19-Patienten date = 2020-05-25 keywords = Patienten; SARS summary = CONCLUSION: The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1–3 weeks after the onset of COVID-19 symptoms. Die im Dezember 2019 erstmalig in Wuhan, China, aufgetretene Coronaviruserkrankung (COVID-19) wird durch die Infektion mit SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), einem neuartigen RNA-β-Coronavirus, hervorgerufen und verursacht in einer Vielzahl von Fällen eine akute Atemwegsinfektion [1] . The data imply that a) COVID-19 can lead to hyposmia in a relevant number of patients, the incidence was approximately 30% in this cohort; b) in most cases, the olfactory disturbance was not associated with nasal obstruction, thus indicating a possible neurogenic origin; and c) the olfactory disorder largely resolved within 1-3 weeks after the onset of COVID-19 symptoms. doi = 10.1007/s00106-020-00891-4 id = cord-354080-glcq4qp9 author = Bodro, Marta title = Increased CSF levels of IL-1β, IL-6, and ACE in SARS-CoV-2–associated encephalitis date = 2020-07-01 keywords = CSF; SARS summary = For the latest articles, invited commentaries, and blogs from physicians around the world NPub.org/COVID19 Clinical features, serum, and CSF characteristics including cytokines and angiotensin-converting enzyme (ACE) profile from both cases are shown in the table. Three previous case reports of CNS involvement in COVID-19 suggest different pathogenic mechanisms: direct CNS infection demonstrated by detection of SARS-CoV-2 RNA in CSF, 2 recrudescence of symptoms related to previous lesions (e.g., brain infarction) in the context of systemic infection, 3 and inflammatory-mediated mechanisms resulting in acute hemorrhagic necrotizing encephalopathy. Hence, in a study of children with acute encephalitis-like syndrome, serum anti-human coronavirus-OC43 immunoglobulin M antibodies were present in 12% of patients and levels of IL-6, IL-8, monocyte chemotactic protein-1, and Granulocyte Macrophage Colony-Stimulating Factor were increased in their CSF. The main implication of these 2 patients is that physicians should be aware of COVID-19 infections presenting or predominantly manifesting as encephalitis, likely resulting from activation of inflammatory pathways with increased ILs and ACE in CSF. doi = 10.1212/nxi.0000000000000821 id = cord-286029-rafcdzhm author = Bogaards, Johannes Antonie title = The potential of targeted antibody prophylaxis in SARS outbreak control: A mathematic analysis() date = 2006-05-05 keywords = SARS; outbreak summary = METHOD: We developed a mathematical model to investigate the effects of hospital admission and targeted antibody prophylaxis on the reproduction number R, defined as the number of secondary cases generated by an index case, during different SARS outbreak scenarios. RESULTS: Assuming a basic reproduction number R(0)=3, admission of patients to hospital within 4.3 days of symptom onset is necessary to achieve outbreak control without the need to further reduce community-based transmission. Based on our model, we derived an expression for the effective reproduction number of SARS to study conditions for containment and we explored how the size and duration of an outbreak depend on the efficacy of control. Given functions for the distribution of onset-to-admission time and transmission rate before the implementation of public health measures, we define the basic reproduction number R 0 as the average number of secondary cases before intervention is in place. doi = 10.1016/j.tmaid.2006.01.007 id = cord-259572-8n12n6ym author = Bogensperger, Christina title = Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report date = 2020-07-22 keywords = SARS summary = title: Dealing with liver transplantation in the SARS-CoV-2 pandemic: Normothermic machine perfusion enables for donor, organ and recipient assessment – A Case Report Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). Here we present the case of a 29-year-old liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine perfusion (NMP). NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. NMP offers to extend preservation times in liver transplantation while awaiting SARS-CoV-2 test results and availability of ICU capacity. Here we present the case of a liver transplant recipient, in whom prolonged liver preservation required for SARS-CoV-2 screening was accomplished through normothermic machine preservation (NMP), which we have recently established as a routine in liver transplantation (6). doi = 10.1016/j.transproceed.2020.07.011 id = cord-256224-qprj8vlc author = Boixeda, R. title = Is chronic obstructive pulmonary disease a protective factor in SARS-CoV-2 infection? The importance of bronchodilator treatment() date = 2020-09-26 keywords = COPD; SARS summary = In a systematic review of infections in patients with COPD that required hospital admission, it was observed that the rhinovirus, respiratory syncytial virus (RSV), and influenza virus were the most prevalent agents, followed by parainfluenza and coronavirus. We have analyzed the prevalence of COPD in patients treated for COVID-19 in our center, specifically evaluating their baseline treatment with inhalers as a potential protective factor against SARS-CoV-2 infection. However, the use of tiotropium was significantly lower in patients with COPD who had been hospitalized for COVID-19 in relation to other cohorts of patients with stable COPD and without SARS-CoV-2 infection and controlled in primary care (12% vs. Members of the COCOHMAT (COhorte COvid del Hospital de MATaró) Group Table 1 Treatment with inhaled corticosteroids and anticholinergics in patients with COPD in series of patients hospitalized due to SARS-CoV-2, severe exacerbation of COPD, and patients in the stable phase (primary care) doi = 10.1016/j.rceng.2020.07.004 id = cord-313910-bwe2f7xf author = Bojadzic, Damir title = Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date = 2020-10-22 keywords = DRI; PPI; SARS summary = Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. We were able to set up a cell-free ELISA-type assay to quantify the binding of SARS-CoV-2 S protein (as well as its SARS-CoV analog) to their cognate receptors (human ACE2) and used this to screen our existing in-house compound library containing a large variety of organic dyes and a set of colorless analogs prepared as potential SMIs for costimulatory PPIs. These maintain the main molecular framework of dyes but lack the aromatic azo chromophores responsible for the color as they are replaced with amide linkers (58, 59). doi = 10.1101/2020.10.22.351056 id = cord-297974-sduz0j35 author = Bokelmann, L. title = Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date = 2020-08-06 keywords = LAMP; RNA; SARS summary = Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp. doi = 10.1101/2020.08.04.20168617 id = cord-294501-1nf98mpb author = Bonafè, Massimiliano title = Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes date = 2020-05-03 keywords = ACE2; COVID-19; SARS; age summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by a high mortality of elderly men with age-related comorbidities. Consistent with this finding, the ability of DCs and macrophages to elicit CD8 + T cell response and proliferation and to release antiviral cytokines is impaired in elderly individuals [34] ; in parallel, these subjects are characterized by a reduced activity of plasmacytoid DCs, the main sources of type I IFNs, which underpin the antiviral response and provide the first-line sentinels in immune surveillance, also in the lung [35] . 4. In older men with age-related diseases, the aging-dependent reduction in ACE2 activity worsens SARS-CoV-2 infection outcomes Angiotensin-converting enzyme (ACE)2, the main SARS-CoV2 host cell receptor, plays a crucial role in virus entry into the cell, as previously demonstrated in SARS and NL63 human coronaviruses [41] . In these individuals, acute SARS-CoV-2 infection compounds their chronic, subclinical, aging-related proinflammatory state (inflamm-aging) which, together with immune senescence and the age-and gender-specific distribution of ACE2 in the airway epithelia, could blunt the antiviral response to inflammation. doi = 10.1016/j.cytogfr.2020.04.005 id = cord-331547-uqmjhhna author = Bonalumi, Giorgia title = A call to action becomes practice: cardiac and vascular surgery during the COVID-19 pandemic based on the Lombardy emergency guidelines date = 2020-06-25 keywords = COVID-19; SARS; patient summary = In Lombardy, the hub-and-spoke system was introduced to guarantee emergency and urgent cardiovascular surgery, whereas most hospitals were dedicated to patients with coronavirus disease 2019 (COVID-19). Daily morning briefings were held internally at the Monzino hospital to monitor every aspect of all in-patients (COVID-19 status, number of available beds) and to share news from the Health Care Lombardy Regional System and the national government. If the test results were positive (chest CT scan indicative of interstitial pneumonia and/or positive results from the nasal swab), the patient was transferred to a dedicated zone called the ''red area'', a separate zone with physical barriers and heavy use of personal protective equipment to protect working personnel, where only patients with COVID-19 were hospitalized. In cases of emergency surgery, the patient was considered and treated as positive for SARS-CoV-2 by the health care staff, who wore personal protective equipment, until screening results were available. doi = 10.1093/ejcts/ezaa204 id = cord-332480-3uodkrkp author = Bonam, Srinivasa Reddy title = Adjunct immunotherapies for the management of severely ill COVID-19 patients date = 2020-04-30 keywords = IVIG; SARS; covid-19; patient; severe summary = Current COVID-19 data clearly highlight that cytokine storm and activated immune cell migration to the lungs characterize the early immune response to COVID-19 that causes severe lung damage and development of acute respiratory distress syndrome. 13, 14, 16, 17 Of note, similar to severely ill COVID-19 cases, elevated serum levels of IL-6, TNF-α and IFN-γ have been consistently observed in cytokine release syndrome (CRS) that is common in the patients receiving T cell-engaging immunotherapies (bispecific antibody constructs or chimeric antigen receptor (CAR) T cell therapies). A randomized Phase 1b/2, double-blind, placebo-controlled clinical trial is currently recruiting patients to investigate the therapeutic efficacy of a humanized anti-GM-CSF IgG1 monoclonal antibody TJ003234 in severely ill COVID-19 patients (NCT04341116). 68 Similarly, treatment of ten severely ill COVID-19 patients with 200 mL of convalescent plasma containing viral neutralizing antibody titers more than 1:640 (A dilution of plasma that neutralized 100 TCID 50 (50% tissue-culture-infective dose) of SARS-CoV-2) led to reduced CRP levels, undetectable viremia and improved clinical symptoms. doi = 10.1016/j.xcrm.2020.100016 id = cord-220618-segffkbn author = Bonamassa, Ivan title = Geometric characterization of SARS-CoV-2 pandemic events date = 2020-07-20 keywords = Fig; SARS; epidemic summary = Disposing of a robust and comprehensive framework to classify the SARS-CoV-2 pandemic events reported across different countries not only can enhance early [19, 20] public and governmental responses in containing the spreading and/or better absorbing the impact of a rapidly emerging epidemic outbreak, but it can further provide new information to better understand real-world epidemics and to boost the forecasting power of existing models [21] [22] [23] [24] [25] [26] [27] [28] [29] . Moving to a polar representation, we classify the plumes'' form through a set of three geometric parameters yielding two complementary rating scales for the SARS-CoV-2 pandemic types: one according to their epidemic magnitude-labeled with roman numbers from I to X for increasing strengths-and measuring the "size" of a national outbreak, and a second one according to their intensity-labeled alphabetically from A to D for increasing speed-quantifying instead the damage inflicted on the population. doi = nan id = cord-302015-z2k6wuhm author = Bonardel, Claire title = Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case date = 2020-06-28 keywords = MRI; SARS summary = authors: Bonardel, Claire; Bonnerot, Mathieu; Ludwig, Marie; Vadot, Wilfried; Beaune, Gaspard; Chanzy, Bruno; Cornut, Lucie; Baysson, Hélène; Farines, Magali; Combes, Isabelle; Macheda, Gabriel; Bing, Fabrice title: Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by Covid-19. Bilateral posterior infarction in a SARS-Cov-2 infected patient: discussion about an unusual case Abstract In time of SARS-Cov2 pandemic, neurologists need to be vigilant for cerebrovascular complications of Covid-19. We present a case of bilateral occipito-temporal infarction revealed by a sudden cortical blindness with haemorrhagic transformation after intravenous thrombolysis in a diabetic patient infected by . A first brain MRI performed one hour after clinical onset showed bilateral and asymmetric acute occipito-temporal infarction without visibility of the P3 segments of the posterior cerebral arteries (PCA) (Figure 2A to C). doi = 10.1016/j.jstrokecerebrovasdis.2020.105095 id = cord-345879-nbfg47x5 author = Bonaz, Bruno title = Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? date = 2020-07-29 keywords = SARS; VNS; covid-19 summary = title: Targeting the cholinergic anti-inflammatory pathway with vagus nerve stimulation in patients with Covid-19? We hypothesize that this cytokine storm and the worsening of patients'' health status can be dampened or even prevented by specifically targeting the vagal-driven cholinergic anti-inflammatory pathway (CAP). Hence, targeting the α7nAChRs through vagus nerve stimulation (VNS) could be of interest in the management of patients with SARS-CoV-2 infection. Indeed, through the wide innervation of the organism by the vagus nerve, especially the lungs and gastrointestinal tract, VNS appears as a serious candidate for a few side effect treatment that could dampen or prevent the cytokine storm observed in COVID-19 patients with severe symptoms. Indeed, a septic shock-induced increase of TNF in the liver and the blood in mice was dampened by stimulation of the distal end cut of the vagus nerve thus arguing for an anti-inflammatory effect of vagal efferents which release acetylcholine (ACh) (Borovikova et al. doi = 10.1186/s42234-020-00051-7 id = cord-258905-0hgdtalg author = Bond, Katherine title = Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting date = 2020-08-06 keywords = SARS; covid-19 summary = METHODS: Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). A testing panel was specifically developed to test PoCT devices for this study (Supplementary Material), consisting of 3 patient populations: (1) sera from 91 patients with SARS-CoV-2 detected by RT-PCR from upper and/or lower respiratory tract specimens; (2) sera from 36 patients with seasonal coronavirus infections or other acute infections (eg, dengue, cytomegalovirus, Epstein-Barr virus); and (3) serum from a random cohort (56 patients) of the Australian population obtained in 2018. In this study, we assessed the performance characteristics of 5 serological PoCT, a commercial ELISA, and a commercial novel sVNT against a large serum panel from a cohort of over 100 patients with RT-PCR-confirmed SARS-CoV-2. doi = 10.1093/infdis/jiaa467 id = cord-336481-vrnxu217 author = Bonifácio, Lívia Pimenta title = Are SARS-CoV-2 reinfection and Covid-19 recurrence possible? a case report from Brazil date = 2020-09-18 keywords = SARS; covid-19 summary = Case reports have identified persistent or recurrent elimination of viral RNA in nasopharyngeal samples, raising the possibility of reinfection by SARS-CoV-2 [4] [5] [6] [7] . She also reported that the doctor who provided medical care for her on the second episode developed flu-like symptoms about a week after the contact, and Covid-19 was lately confirmed on him by means of nasopharyngeal RT-PCR. DISCUSSION Since the beginning of the Covid-19 pandemic, due to several reports of persistent detection of viral RNA by RT-PCR in a nasopharyngeal or oropharyngeal swab, but without recurrence of symptoms, the possibility of SARS-CoV-2 reinfection has been suggested and investigated by different researchers around the world 5,6,10,11 . In conclusion, this case report presents strong evidence that SARS-CoV-2 reinfection and Covid-19 recurrence, although rare, are possible. This possibility should be further investigated in patients presenting with recurrence of Covid-19 symptoms. doi = 10.1590/0037-8682-0619-2020 id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 keywords = SARS; bat; figure; human; virus summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . doi = 10.1016/j.ijid.2020.08.050 id = cord-301638-2f8r37ns author = Bonney, Glenn Kunnath title = SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? date = 2020-05-29 keywords = SARS summary = title: SARS-COV-2 associated acute pancreatitis: Cause, consequence or epiphenomenon? The rapid spread of a novel coronavirus disease (COVID-19) caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) has triggered a global pandemic. [2] The severity of AP observed varies from mild [1, 2] to severe,[43 but unfortunately accepted diagnostic criteria [4] was not used in these studies, raising the possibility that the elevated pancreatic enzymes may be due to other causes including increased gut permeability with SARS-CoV-2 infection. A study from 2010 using immunostaining found ACE2 to be highly expressed in islet cells and postulated that binding of SARS-CoV caused islet cell injury and hyperglycaemia in infected patients. [9] It is not known whether SARS-CoV-2 causes AP, whether the AP is a consequence of severe systemic inflammation and microvascular thrombosis from COVID-19 infection, or whether it is just an epiphenomenon. ACE2 Expression in Pancreas May Cause Pancreatic Damage After SARS-CoV-2 Infection Coronavirus Disease-19 (COVID-19) associated with severe acute pancreatitis: Case report on three family members doi = 10.1016/j.pan.2020.05.019 id = cord-334582-ccg27nmf author = Bonora, Benedetta Maria title = Glycaemic Control Among People with Type 1 Diabetes During Lockdown for the SARS-CoV-2 Outbreak in Italy date = 2020-05-11 keywords = SARS; diabetes; t1d summary = CONCLUSION: Despite the limited possibility to exercise and the incumbent psychologic stress, glycaemic control improved in patients with T1D who stopped working during the lockdown, suggesting that slowing down routine daily activities can have beneficial effects on T1D management, at least in the short term. Using data collected by remote monitoring of glucose sensors, we investigated whether glycaemic control in people with type 1 diabetes (T1D) during lockdown improved or worsened. None of the patients who continued to work showed improvement in any of the measures of glucose control during the lockdown period (period 2) compared to the 3 months or the week before the SARS-CoV-2 outbreak: average glucose, standard deviation, CV%, time in hypoglycaemia, time in range and time in hyperglycaemia remained unchanged (Table 2) , as did the number of scans per day. doi = 10.1007/s13300-020-00829-7 id = cord-346212-mcnr7bcp author = Bonzano, Chiara title = Doxycycline: From Ocular Rosacea to COVID-19 Anosmia. New Insight Into the Coronavirus Outbreak date = 2020-05-08 keywords = Dox; IFN; SARS summary = doi = 10.3389/fmed.2020.00200 id = cord-249166-0w0t631x author = Booss-Bavnbek, Bernhelm title = Dynamics and Control of Covid-19: Comments by Two Mathematicians date = 2020-08-17 keywords = Health; SARS; Sect; case; covid-19 summary = We give an overview of the main branches of mathematics that play a role and sketch the most frequent applications, emphasising mathematical pattern analysis in laboratory work and statistical-mathematical models in judging the quality of tests; demographic methods in the collection of data; different ways to model the evolution of the pandemic mathematically; and clinical epidemiology in attempts to develop a vaccine. A few physicians suggested that every epidemic ends because there are finally not enough people left to be infected, which is a naïve predecessor to the mathematical-epidemiologic concept of Herd Immunity (see Sect. Parallel to the entering the scene of these and other epidemics, and partly motivated by them, basically new mathematical tools of public health emerged in the first part of the 20 th Century, preceded by a few studies in the late 19 th . Dealing with large epidemics mathematically was no longer a matter of demography alone, although that continued to be the main tool for estimating number of cases and deaths. doi = nan id = cord-262499-68vmdqky author = Bordi, Licia title = Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay date = 2020-10-20 keywords = COVID-19; DSO; NPS; SARS summary = We evaluated the use of commercial Simplexa™ COVID-19 Direct assay on OF samples from hospitalized COVID-19 patients, for identification of SARS-CoV-2 RNA, duration of viral shedding, and determining the assay specificity and sensitivity on OF samples compared to NPS and BAL samples. The first performance evaluation on clinical specimen was done by testing 41 consecutive OF samples, including 9 samples from SARS-CoV-2-negative patients, with the Simplexa™ COVID-19 Direct assay and comparing results with that obtained using RT-PCR method established by Corman VM. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. The performance of Simplexa™ COVID-19 Direct assays on clinical specimens was further established by testing in parallel NPS and OF samples for the presence of SARS-CoV-2 RNA. Second, results from testing on paired OF, NPS and BAL samples by Simplexa™ COVID-19 Direct assay showed almost perfect concordance for virus detection, and high correlation of Ct values. doi = 10.3390/v12101184 id = cord-295957-s17z2ccf author = Bordi, Licia title = Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay date = 2020-05-04 keywords = COVID-19; SARS summary = BACKGROUND: So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. CONCLUSIONS: The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients. Moreover, to evaluate the performance of the test in a different clinical specimen, a total of 33 Broncho-Alveolar Lavage (BAL) collected for COVID-19 diagnosis between 20 March and 03 April 2020 were also analysed in parallel with the Simplexa™ COVID-19 Direct assay and the routine laboratory method, based on the WHO protocols (7, 8) , using the Abbot m2000 extraction platform. doi = 10.1016/j.jcv.2020.104416 id = cord-327095-y2zsm8sc author = Boretti, Alberto title = Favipiravir use for SARS CoV-2 infection date = 2020-10-27 keywords = Favipiravir; SARS summary = For the specific use against SARS CoV-2, [22] evaluated the in vitro efficacy of different drugs, from Remdesivir to Chloroquine, also including Favipiravir. Li and De Clercq [23] include Favipiravir together with Remdesivir, Galidesivir, and Ribavirin in between the existing antiviral agents'' RNA-dependent RNA polymerase inhibitors to repurpose to treat SARS CoV-2 infection. [24] also include Favipiravir, together with Chloroquine, Arbidol, and Remdesivir, all under clinical studies in China to test their efficacy and safety for SARS CoV-2 infection. Up to date, there is not enough information from specific trials to infer any conclusion on the use of Favipiravir for SARS CoV-2 infection. SARS-CoV-2: recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus Dose rationale for favipiravir use in patients infected with SARS-CoV-2 doi = 10.1007/s43440-020-00175-2 id = cord-292386-hfbgigj6 author = Borges, Lysandro Pinto title = Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil date = 2020-10-06 keywords = COVID-19; SARS; Santos; Sergipe summary = In order to support the ongoing public health response, all participants who tested positive for SARS-CoV-2 antibodies were contacted by phone by staff from the designated authorities to track the infection. The importance of NPIs on reducing the infection rate was observed in Vo, Italy, where prevalence estimates showed a significant decrease after a period of lockdown, suggesting that viral transmission could be effectively suppressed by combining the early isolation of detected cases with social distancing total assessed cases in that city [CI, 11.5% -21.4%]) and 12 (5.9% of the total assessed cases in that city [CI, 3.1% -10.1%]) cases; Itabaiana, that presented 55 (14.8% of the total assessed cases in that city [CI, 11.4 -18.9]) and 17 of the total assessed cases in that city (5.4% [CI, 3.1% -8.4%]) cases, being the three cities with the highest seroprevalence of SARS-CoV-2 in the state. doi = 10.26633/rpsp.2020.108 id = cord-353274-wozwpvpq author = Borremans, B. title = Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date = 2020-05-20 keywords = RNA; SARS; international summary = In this study we quantified IgG and IgM antibody kinetics and RNA shedding probability during SARS-CoV-2 infection (up to 60 days post symptom onset) by drawing on published data. This formal integration approach enabled us to leverage 3,214 data points from 516 individuals with symptoms ranging from asymptomatic to critical, published in 22 studies, resulting in a quantitative synthesis of diverse data on anti-SARS-CoV-2 antibody patterns and RNA shedding during the early phase of infection. One of the goals of this study is to estimate the means and variation of IgG and IgM seroconversion times (time between symptom onset and first antibody detection) for different assays, antigens, and disease severity. . https://doi.org/10.1101/2020.05.15.20103275 doi: medRxiv preprint weighted bootstrapping procedure integrates all types of data that contain useful information about the timing of seroconversion of different antibodies in day(s) post symptom onset (dpo). The probability of detecting SARS-CoV-2 specific IgG or IgM in plasma or serum samples was estimated by integrating data on whether an individual tested positive or negative on a given dpo. doi = 10.1101/2020.05.15.20103275 id = cord-314793-kb319t4c author = Borroni, Barbara title = Diaphragmatic myoclonus due to SARS-CoV-2 infection date = 2020-10-22 keywords = CoV-2; SARS summary = Neurological signs in patients with SARS-CoV-2 have been widely reported, suggesting a neuroinvasive nature of virus [2, 3] . With the present observation, we report two cases of diaphragmatic myoclonus as neurological subacute manifestation of SARS-CoV-2 infection. The Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10072-020-04766-y) contains supplementary material, which is available to authorized users. Electromyographic recording confirmed rhythmic and synchronous contractions of the diaphragm at 3-Hz frequency as the cause of her abdominal movements (see Fig. 1 ), thus making the diagnosis of diaphragmatic myoclonus or van Leeuwenhoek''s disease [5] . Here, we draw attention to two patients who developed focal diaphragmatic myoclonus after SARS-CoV-2 infection. Indeed, three cases of generalized myoclonus due to SARS-CoV-2 infection have been recently reported [10] . With the present report of two cases, we confirm and extend the neurotropic properties of SARS-CoV-2 virus and point out to a further neurological clinical manifestation of the infection. doi = 10.1007/s10072-020-04766-y id = cord-314948-7tnrfk24 author = Borrás, A title = Pandemia del SARS-CoV-2 y reproducción asistida date = 2020-06-19 keywords = ACE2; COVID-19; SARS summary = Estas medidas fueron cruciales no sólo para permitir hospitales e instalaciones médicas tratar el aumento explosivo de pacientes con la infección por SARS-CoV-2 (denominada COVID19) , sino también para reducir la transmisión de la enfermedad, mediante estrategias de mitigación, especialmente individuales (el aislamiento). Se sugiere que la presencia de ACE2 puede ser uno de los principales determinantes de la susceptibilidad de las células a la infección por SARS-CoV-2. Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida Recomendaciones para la seguridad y reducción de riesgos ante la infección por coronavirus ( SARS-CoV-2 ) en las unidades de reproducción asistida doi = 10.1016/j.gine.2020.06.004 id = cord-333391-6l0cpvgr author = Bortolotti, Daria title = SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date = 2020-08-26 keywords = HLA; SARS; figure summary = title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. doi = 10.3390/cells9091975 id = cord-326736-jd6fvaop author = Bosco-Lauth, Angela M. title = Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date = 2020-05-29 keywords = SARS summary = title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. The first report of reverse zoonosis, or transmission from human to animal, was reported 46 from Hong Kong, where a COVID patient''s dog tested PCR positive for SARS2 multiple times 47 (Sit et al. Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of 414 COVID-19 patients in a veterinary campus Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Transmission of 422 SARS-CoV-2 in Domestic Cats doi = 10.1101/2020.05.28.120998 id = cord-269946-zb7gcw0m author = Boscolo-Rizzo, Paolo title = New onset of loss of smell or taste in household contacts of home-isolated SARS-CoV-2-positive subjects date = 2020-05-24 keywords = SARS; smell summary = PURPOSE: To estimate the prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. To better estimate the burden of smell and taste impairment during COVID-19 pandemic, we searched for the prevalence of these symptoms in subjects at high risk for SARS-CoV-2 infection, i.e. household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. We previously reported the prevalence of loss of the sense of smell or taste as well as other COVID-19 symptoms in a case series of 202 home-isolated mildly symptomatic confirmed cases of SARS-CoV-2 infection [8] . The prevalence of smell or taste impairment in household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients was 1.5%, 22.3%, and 63.0% in subjects tested negative, non-tested, and tested positive for SARS-CoV-2 infection, respectively. However, this study showed that smell or taste impairment is quite common in not-tested household contacts of mildly symptomatic home-isolated SARS-CoV-2-positive patients. doi = 10.1007/s00405-020-06066-9 id = cord-273311-dl9u85nh author = Boscolo‐Rizzo, Paolo title = Challenges in interpreting the diagnostic performance of symptoms to predict COVID‐19 status: the case of anosmia date = 2020-06-25 keywords = SARS summary = Consequently, several studies have tried to estimate the sensitivity and specificity as well as the positive predictive value of self-reported new onset of smell and/or taste impairment for COVID-19 in populations of patients with flu-like symptoms. The first is that the standard diagnostic tool for diagnosis of SARS-CoV-2 infection, i.e. This article is protected by copyright. While the pooled sensitivity was 61% (95% CI, 55-68%), the pooled specificity reached 87% (95% CI, 80-92%); publication bias is possible (Figure 1b In conclusion, despite we believe that the new onset of smell and/or taste loss during COVID-19 pandemic should be considered a manifestation of SARS-CoV-2 infection until proven otherwise, sufficient to justify testing, self-isolation and the use of personal protective equipment by medical personnel interacting with these subjects, taken into account the above considerations, diagnostic performance of single symptoms should be fully understood and considered with caution when predicting SARS-CoV-2 infection in patients with flu-like symptoms. doi = 10.1002/alr.22650 id = cord-304139-ya3d7u9b author = Bosmann, Markus title = Complement Activation during Critical Illness: Current Findings and an Outlook in the Era of COVID-19 date = 2020-07-15 keywords = SARS; complement; pathway summary = 230-240) report on the association between alternative complement pathway activity and better survival in patients with critical illness (3). The alternative pathway hemolytic assay (AH50) and total complement activity (CH50) tests were retrospectively analyzed in a single-center heterogeneous cohort of n = 321 patients with acute respiratory distress syndrome (33%), with suspected sepsis (63%), and on mechanical ventilation (96%). Inappropriate complement activity may result in the unloading of harmful effector functions on host cells, with the consequence of disease-causing tissue injury and organ dysfunction during critical illness. Complement activation may occur early during SARS-CoV-2 infection by the direct interaction of viral proteins with the MBL (mannose-binding lectin) and ficolin pathway, rather than the alternative pathway. In another experimental study, the host transcriptional response in SARS-CoV-2-infected A549 human lung epithelial cells included the differential expression of C3, C1R, and other complement proteins (10) . Increased alternative complement pathway function and improved survival during critical illness doi = 10.1164/rccm.202005-1926ed id = cord-260673-gf028lf6 author = Bottemanne, Hugo title = Does the Coronavirus Epidemic Take Advantage of Human Optimism Bias? date = 2020-08-26 keywords = SARS; belief summary = Building on evidence from past epidemics and three decades of research in psychology suggesting that various cognitive biases influence beliefs about life hazards, we propose that such cognitive biases have contributed to the discrepancy between early warnings about the danger of SARS-CoV-2 and slow growth of consideration for these warnings. Importantly, data collected in Western countries during the peak of the COVID 19 pandemic provides direct evidence favoring the hypothesis that unrealistic optimism has played a role in the apparent discrepancy between official warnings and individual beliefs about the consequences of the pandemic for oneself: When getting infected and infecting others became frequent events as the number of cases and deaths sharply increased, citizens in the US, Europe and the United Kingdom estimated their probability of getting infected with the virus and of subsequently infecting others as lower for themselves than for someone else (Dolinski et al., 2020; Kuper-Smith et al., 2020) . doi = 10.3389/fpsyg.2020.02001 id = cord-252818-1gms4zw3 author = Bouayed, Jaouad title = Behavioural manipulation ‐ key to the successful global spread of the new Coronavirus SARS‐Cov‐2? date = 2020-08-19 keywords = COVID-19; SARS; spread summary = The very rapid global spread has raised the issue whether there are further multi‐dimensional consequences of SARS‐CoV‐2 infection on human behaviour, the key of its transmission. In this perspective, we highlight the possibility that COVID‐19 is facilitated by altered human social behaviour that benefits SARS‐CoV‐2 transmission, through showcasing similar virus‐induced changed behaviour by other pathogens and relating this to reports from the grey literature. Interestingly, it was also estimated that 10% of the cases are super-spreaders, resulting in 80% of viral spread, meaning that the majority of SARS-CoV-2 carriers do not appear to unaccountably transmit the virus. In this perspective, we highlighted the possibility that COVID-19 is facilitated by altered human social behaviour that benefits SARS-CoV-2 transmission (Figure 1 ). The scheme highlights the potential manipulative strategy of the novel coronavirus, resulting in viral spread, following an altered behavioural pattern in some COVID-19 patients, as a consequence of a direct impact on brain structure/function, owing to viral infiltration into the CNS, and/or via perturbation of the brain-immune axis or the gut-brain axis. doi = 10.1002/jmv.26446 id = cord-331055-5ni0jxij author = Bouche, Pierre-Alban title = Were protective procedures against SARS-CoV-2 effective in an orthopaedic and trauma centre during the lockdown period? A retrospective study date = 2020-07-16 keywords = SARS; covid summary = To take care of COVID-19 positive and negative patients, various procedures have been set up: reverse transcriptase polymerase chain reaction (RT-PCR) tests for all hospitalized patients, a specific unit for COVID-positive patients, a specific surgical room, and use of protective personal equipment. To allow the effectiveness of the procedures implemented, we evaluated the number of complications attributed to SARS-CoV-2 and the number of patients who became COVID positive during hospitalization. All elective surgery had to be stopped in order to decrease the influx of patients into hospitals and to redeploy medical and paramedical staff in different units to provide assistance in emergency departments, COVID-19 units, and intensive care units [6] . The purpose of this retrospective study was to assess the effectiveness of the guidelines implemented in our orthopaedic and trauma centre, Cochin Hospital, during the lockdown imposed in France period between March 15 and May 11, 2020. doi = 10.1007/s00264-020-04729-0 id = cord-290845-bf1q4k6t author = Bouchghoul, Hanane title = Do pregnant women have protective immunity against COVID‐19? date = 2020-06-24 keywords = SARS summary = Thornton, in which the author relates that coronavirus disease 2019 (COVID-19) is less severe in pregnancy than the two previous coronavirus infections, SARS and Middle East respiratory syndrome. Furthermore, as SARS-CoV-2 infection can activate innate and adaptive immune responses with severe consequences, pregnant women could be preserved by the state of immunomodulation during pregnancy. In the most severe SARS-CoV-2 infections we report uncontrolled inflammatory innate responses and impaired adaptive immune responses that may lead to harmful tissue damage, both locally and systemically. 3 A cytokine profile has been reported in most severe SARS-CoV-2 infections, characterised by increased levels of cytokines and chemokines. As in patients infected with SARS-CoV-2, the serious complication is acute respiratory distress syndrome and ventilation of the mother may be difficult in the third trimester of pregnancy; it is certainly possible that the decision to delivery by an elective caesarean section was influenced by the understandable anxiety towards the potential consequences. COVID19 during pregnancy: a systematic review of reported cases doi = 10.1111/1471-0528.16342 id = cord-336560-m5u6ryy9 author = Boudewijns, Robbert title = STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date = 2020-07-02 keywords = Fig; RNA; SARS; STAT2; lung summary = Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . doi = 10.1101/2020.04.23.056838 id = cord-324128-css42bsb author = Boukli, Narjis title = High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies date = 2020-10-21 keywords = SARS summary = title: High Incidence of False-Positive Results in Patients with Acute Infections Other than COVID-19 by the Liaison SARS-CoV-2 Commercial Chemiluminescent Microparticle Immunoassay for Detection of IgG Anti-SARS-CoV-2 Antibodies The median day of IgG seroconversion is around 14 days after symptom onset (2), but a high interindividual variation has been reported, as well as contrasting performances between commercial assays (3) (4) (5) (6) . Furthermore, the 100 samples in our specificity panel were negative with the Alinity I SARS-CoV-2 IgG assay, except for one serum sample from a patient with coronavirus 229E infection, which was weakly reactive (signal-to-cutoff index ϭ 1.93; cutoff is 1.4 index), which leads to a specificity of 99%. While the clinical significance of SARS-Cov-2 antibody detection remains to be determined, our results confirm that careful evaluation of the tests on appropriate samples is required before implementing assays for routine use. doi = 10.1128/jcm.01352-20 id = cord-317952-4oa9hfb4 author = Bourgonje, Arno R. title = Angiotensin‐converting enzyme‐2 (ACE2), SARS‐CoV‐2 and pathophysiology of coronavirus disease 2019 (COVID‐19) date = 2020-05-17 keywords = ACE2; COVID-19; CoV-2; SARS; clinical; disease; patient summary = ACE2 was highly expressed on lung alveolar epithelial cells and small intestinal epithelial cells, consistent with potential routes of viral transmission of SARS-CoV-2, as both respiratory and gastrointestinal systems share interfaces with the external environment. ACE2 expression in the lungs and SARS-CoV-2 viral load have been suggested to increase with age, which might provide an explanation to the higher disease severity observed in older patients with COVID-19 [35] . Both SARS-CoV-2 infection, directly mediated by ACE2 expression and activity, and superimposed disease triggers may be responsible for the observed pathological findings. Additionally, another study reported purpura and livedo racemosa in several severely affected COVID-19 patients with small vessel thrombosis with co-localization of complement and SARS-CoV-2 spike proteins on histopathology [148] .This indicates direct viral infection of the small skin vessels. Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone-inhibitors: Potential implications for coronavirus SARS-CoV-2 infected patients doi = 10.1002/path.5471 id = cord-268886-mpceglk1 author = Bourne, T. title = ISUOG Consensus Statement on rationalization of gynecological ultrasound services in context of SARS‐CoV‐2 date = 2020-04-08 keywords = SARS; patient; ultrasound summary = Given the challenges of the current coronavirus (SARS-CoV-2) pandemic and to protect both patients and ultrasound providers (physicians, sonographers, allied professionals), the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) has compiled the following expert-opinion-based guidance for the rationalization of ultrasound investigations for gynecological indications. While these are extremely troublesome conditions, patients and healthcare providers should consider delaying ultrasound evaluation until resolution of the COVID-19 pandemic. Although associated symptoms (mass effect leading to pressure, bladder/bowel symptoms) are not usually acute or life-threatening, they may signal advanced ovarian cancer, in which case, it may be reasonable to recommend that ultrasound assessment should be carried out by an expert soon and appropriate treatment commenced. • Abdominopelvic ''mass'' without associated symptoms (SOON or LATER): the healthcare provider may consider delaying the ultrasound evaluation until the resolution of the pandemic if there is a known history of pelvic pathology, such as leiomyoma. doi = 10.1002/uog.22047 id = cord-282576-mcx0xq0w author = Boutin, Catherine-Audrey title = Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument date = 2020-09-04 keywords = SARS summary = title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. We evaluated the concordance between the two-target cobas SARS-CoV-2 test (Roche Molecular Diagnostics, Laval, Canada) on the fully automated cobas 8800 platform authorized by Health Canada and a laboratory-developed (LD) standardized RT-PCR test using widely used primer set and probe (2, 3) in samples submitted at the diagnostic laboratory for patient care at the Centre Hospitalier de l''Université de Montréal. The correlation between Ct values obtained in the LD RT-PCR test and cobas SARS CoV-2 ORF-1 target for positive samples in both assays was good (r 2 = 0.82, data not shown). doi = 10.1016/j.jcv.2020.104615 id = cord-300707-k9uk14b3 author = Bouwman, Kim M. title = Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date = 2020-09-04 keywords = RBD; SARS summary = Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. Our results show that fully glycosylated trimeric RBD proteins are attractive to analyze receptor binding and explore ACE2 expression profiles in tissues. The results demonstrate 104 that fully glycosylated trimeric SARS-CoV-2 RBD proteins reveal the 105 differences in ACE2 expression between cell cultures and tissue sections. A similar trend of binding intensities was observed for 214 monomeric, trimeric, and different N-glycosylated SARS-CoV-RBD proteins 215 fused to mOrange2 ( Fig S3A) . 226 227 To confirm our observations of different binding on tissues, we quantified the 228 intensities of the ACE2 antibody and SARS-CoV-1 and -2 RBD proteins, except 229 for the monomeric GnTI derived proteins as these were almost at the 230 background ( Fig 4D) . doi = 10.1101/2020.09.04.282558 id = cord-276784-8lmg97zc author = Boziki, Marina Kleopatra title = COVID-19 Immunopathology and the Central Nervous System: Implication for Multiple Sclerosis and Other Autoimmune Diseases with Associated Demyelination date = 2020-06-04 keywords = COVID-19; SARS; patient summary = Moreover, the management of chronic neurological diseases, such as Multiple Sclerosis (MS), underwent guided modifications, such as an Extended Interval Dose (EID) of Disease-Modifying Treatment (DMT) administration, in order to minimize patients'' exposure to the health system, thus reducing the risk of SARS-CoV-2 infection. In this review, we summarize existing evidence of key immune pathways that the SARS-CoV-2 modifies during COVID-19 and the relevant implication for MS and other autoimmune diseases with associated demyelination (such as Systemic lupus erythematosus and Antiphospholipid syndrome), including the context of potential neuroinvasion by SARS-Cov-2 and the alterations that DMT induces to the immune system. In this respect, the clinical implication of SARS-CoV-2 infection in PwMS needs to be carefully evaluated in long-term prospective studies that assess not only physical disability measurements but also cognition, patient-reported outcomes, and quality of life, thus aiming to elucidate COVID-19-related long-term effects on MS-related neurological status and beyond. doi = 10.3390/brainsci10060345 id = cord-302806-1e99cygs author = Bozkurt, Banu title = The COVID-19 Pandemic: Clinical Information for Ophthalmologists date = 2020-04-29 keywords = COVID-19; January; SARS; patient summary = 27 published in the journal Ophthalmology last week, viral culture and RT-PCR analysis of 64 tear samples collected simultaneously with nasopharyngeal swabs from 17 COVID-19 patients between 3 and 20 days after initial symptom onset failed to demonstrate the presence of 2019-CoV. 34 The Turkish Ministry of Health, in a guidance report entitled "Evaluation of Healthcare Workers with Patient Contact" published on March 25, 2020, identified ophthalmologic examination as a procedure requiring intensive contact, and recommended prophylaxis with hydroxychloroquine for a total of 3 days (400 mg twice on day 1, 200 mg twice daily on days 2 and 3) and 5 days of home isolation followed by a PCR test in the event of high-risk contact with COVID-19 patients without the use of personal protective equipment. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Assessing Viral Shedding and Infectivity of Tears in Coronavirus Disease 2019 (COVID-19) Patients. doi = 10.4274/tjo.galenos.2020.29805 id = cord-279474-c5y2lygj author = Bozzo, Caterina Prelli title = IFITM proteins promote SARS-CoV-2 infection of human lung cells date = 2020-08-18 keywords = IFITM; SARS summary = Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) restrict numerous viral pathogens and are thought to prevent infection by severe acute respiratory syndrome coronaviruses (SARS-CoVs). In striking contrast, however, endogenous IFITM expression promoted genuine SARS-CoV-2 infection in human lung cells both in the presence and absence of interferon. Taken together, our results show that all three IFITMs prevent SARS-CoV-2 S/ACE2-mediated attachment and membrane fusion in single round pseudotype infection assays. Notably, titration experiments showed that IFITMs do not promote genuine SARS-CoV-2 247 infection in HEK239T cells over a broad range of expression levels ( Figure S4E ). (F) Quantification of the entry of VSV(luc)ΔG*-SARS-CoV-2-S by luciferase activity in HEK293T cells transiently expressing indicated proteins (IFITM mutants) and infected 24 h post-transfection with the VSVpp (MOI 0.025) for 16 h. (G) Quantification of the entry of HIV(Fluc)Δenv*-SARS-CoV-2-S by luciferase activity in HEK293T cells stably expressing indicated proteins (IFITM mutants) and ACE2 doi = 10.1101/2020.08.18.255935 id = cord-272654-hh29olk7 author = Bošnjak, Berislav title = Low serum neutralizing anti-SARS-CoV-2 S antibody levels in mildly affected COVID-19 convalescent patients revealed by two different detection methods date = 2020-11-02 keywords = CoV-2; Fig; SARS; covid-19 summary = We used a surrogate virus neutralization test (sVNT) and SARS-CoV-2 S protein-pseudotyped vesicular stomatitis virus (VSV) vector-based neutralization assay (pVNT) to assess the degree to which serum antibodies from coronavirus disease 2019 (COVID-19) convalescent patients interfere with the binding of SARS-CoV-2 S to ACE2. Similarly, anti-SARS-CoV-2 S IgA antibodies were present in 33/37 (89.2%) of the tested sera; two samples were diagnosed as borderline positive and two as negative Fig. 1 Qualitative analysis of serum total IgG (A) and IgA (B) antibodies against SARS-CoV-2 S1 in convalescent patients with mild or severe COVID-19 and healthy controls (HC) determined by ELISA. The median sVNT titer of the mildly affected convalescent cohort was 1:180, indicating that patients with mild COVID-19 produce relatively low amounts of SASRS-CoV-2 neutralizing antibodies (Fig. 2H ). This hypothesis is further supported by a positive correlation between the duration of symptoms and total anti-SARS-CoV-2 IgG, but not IgA, antibodies in convalescent patients with mild disease (Fig. 5A, B) . doi = 10.1038/s41423-020-00573-9 id = cord-256888-tdx12ccj author = Bradley, Benjamin T title = Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series date = 2020-07-16 keywords = COVID-19; CoV-2; SARS; USA; patient summary = To date, documentation of the histopathological features in fatal cases of the disease caused by SARS-CoV-2 (COVID-19) has been scarce due to sparse autopsy performance and incomplete organ sampling. 8 Post-mortem studies have shown pulmonary, renal, and small vessel injury, with particles resembling virus observed in the kidney by electron microscopy. By electron microscopy, aggregates of uniform, round enveloped particles ranging in size from around 70 nm to 100 nm with peripheral spike-like projections consistent with the morphology described for SARS-CoV-2 were observed in the lung, trachea, kidney, and large intestine of patient 8 and patient 13. [9] [10] [11] [12] We present a case series of autopsy findings in 14 patients who died after SARS-CoV-2 infection. The major histopathological observation in our series of patients who died with COVID-19 was diffuse alveolar damage-type lung injury in the acute or organising phases (12 [86%] of 14 patients). doi = 10.1016/s0140-6736(20)31305-2 id = cord-307148-k1uo3fxm author = Bradshaw, Patrick C. title = COVID-19: Proposing a Ketone-Based Metabolic Therapy as a Treatment to Blunt the Cytokine Storm date = 2020-09-09 keywords = BHB; COVID-19; IAV; NADPH; ROS; SARS; cell; increase summary = R-BHB activates anti-inflammatory GPR109A signaling and inhibits the NLRP3 inflammasome and histone deacetylases, while a ketogenic diet has been shown to protect mice from influenza virus infection through a protective γδ T cell response and by increasing electron transport chain gene expression to restore energy metabolism. Others have also suggested that increasing systemic ketone levels may aid host defenses against respiratory viral infection, in part, by decreasing inflammation [1, 2] , including a recent comprehensive review [3] , while a clinical trial of the effects of a ketogenic diet on intubated SARS-CoV-2 patients has recently been registered (NCT04358835). Coronaviruses have been shown to increase the oxidation of phospholipids, which stimulate toll-like receptor 4 (TLR4) signaling on macrophages, leading to cytokine production and acute lung injury [163] , so HDAC inhibition with R-BHB appears to be a viable treatment to decrease cytokine levels and inflammation. doi = 10.1155/2020/6401341 id = cord-258382-ep73us0e author = Braga, Cássia L. title = The renin–angiotensin–aldosterone system: Role in pathogenesis and potential therapeutic target in COVID‐19 date = 2020-07-13 keywords = ACE2; SARS summary = 8, 9 According to Zhou et al, SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor to invade and infect cells. These proteins bud into the endoplasmic reticulum-Golgi intermediate compartment (ERGIC); new viral particles are then assembled and released to infect new target cells comes from the observation that endosomal alkalization induced by ammonium chloride inhibited SARS-CoV-2 replication. Once a hypertensive patient is infected with SARS-CoV-2, sensitization of the immune system toward an overactivation of the inflammatory response could be associated with subsequent development of cytokine storm. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS doi = 10.1002/prp2.623 id = cord-307815-reg04lpt author = Brancatella, Alessandro title = Is subacute thyroiditis an underestimated manifestation of SARS-CoV-2 infection? Insights from a case series date = 2020-08-11 keywords = SARS; SAT summary = After our initial description of a patient experiencing subacute thyroiditis (SAT) associated with SARS-CoV-2 infection (1), three additional case have been reported (2) (3) (4) . On March 1 st , a 38 year-old-woman underwent oropharyngeal swab for SARS-CoV-2 because of symptoms suspected for COVID-19 (Table 1) . At last evaluation (on May 10 th ), while taking prednisone 15 mg/d, patient was asymptomatic and thyroid function tests and inflammatory markers were in the normal range (Table 1) . At last evaluation (on May 18 th ), while taking 15 mg/d of prednisone, patient was asymptomatic, inflammatory markers were in the normal range, whereas thyroid function tests was consistent with subclinical hypothyroidism (Table 1) . In the present series, as well as in our previous report (1), patients experienced SAT after the resolution of distinctive symptoms of SARS-CoV-2 infection. doi = 10.1210/clinem/dgaa537 id = cord-313371-fdyfg0kf author = Brancatella, Alessandro title = Subacute Thyroiditis After Sars-COV-2 Infection date = 2020-05-21 keywords = SARS; SAT summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that began in Wuhan, China, has spread rapidly worldwide and Italy has been severely affected by this outbreak. OBJECTIVES: The objective of this work is to report the first case of SAT related to SARS-CoV-2 infection. METHODS: We describe the clinical, laboratory, and imaging features of an 18-year-old woman who came to our attention for fever, neck pain radiated to the jaw, and palpitations occurring 15 days after a SARS-CoV-2–positive oropharyngeal swab. S ubacute thyroiditis (SAT) is a self-limited inflammatory thyroid disease characterized by neck pain, general symptoms, and thyroid dysfunction (1, 2) . Here, we report the first case of SAT in a patient affected by SARS-CoV-2. SAT is a self-limited, inflammatory disorder characterized by neck pain and general symptoms, often associated with thyroid dysfunction (1, 2) . SAT is usually preceded by an upper respiratory infection and usually presents in association with characteristic symptoms of viral disease. doi = 10.1210/clinem/dgaa276 id = cord-315058-t7bq4yqw author = Brand, Samuel P C title = Forecasting the scale of the COVID-19 epidemic in Kenya date = 2020-04-14 keywords = China; Kenya; SARS; covid-19 summary = Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. In the scenario with no transmission from asymptomatics the observed epidemic was dominated by cases among the working-age population (Figure 3 ), who we estimated as having high rates of assortative (i.e. within same age-group) mixing ( Figure 4 ) and a small but not negligible risk of developing symptoms of COVID-19 after infection. In this modelling study we have integrated existing data on the social structure, and mobility, of the Kenyan population with rapidly evolving estimates of the fundamental epidemiology of SARS-CoV-2 so as to make the best possible prediction of the scale of the epidemic risk that Kenya faces from the first coronavirus pandemic. doi = 10.1101/2020.04.09.20059865 id = cord-309540-4pk5tq5w author = Brandsma, E. title = Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date = 2020-07-29 keywords = DETECTR; PCR; SARS summary = Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) in combination with Cas12 detection does not need expensive specialised equipment, is highly sensitive and specific, has a short TAT and is easy to implement and therefore could be used as an alternative for qRT-PCR (5, 6) . Since DETECTR depends on both signal amplification by RT-LAMP and reporter degradation after Cas12-dependent amplicon recognition, the assay produces a binary readout and is potentially more sensitive and specific compared to qRT-PCR (5, 6) . In this manuscript we describe the development of an in-house SARS-CoV-2 DETECTR assay, compare its performance with routine diagnostic qRT-PCR on almost 400 patient samples of three Dutch hospitals, thereby providing a first field test of this novel Cas12-mediated SARS-CoV-2 detection tool. doi = 10.1101/2020.07.27.20147249 id = cord-260793-bb4h255w author = Brann, David H. title = Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date = 2020-05-18 keywords = ACE2; SARS; TMPRSS2; cell; figure; gene; olfactory; type summary = It has recently been demonstrated through single cell RNA sequencing analysis (referred to herein as scSeq) that cells from the human upper airway -including nasal RE goblet, basal and ciliated cells -express high levels of ACE2 and TMPRSS2, suggesting that these RE cell types may serve as a viral reservoir during CoV-2 infection (33) . The presence of Ace2 and Tmprss2 transcripts in mouse WOM and their (near total) absence in purified OSNs suggest that the molecular components that enable CoV-2 entry into cells are expressed in non-neuronal cell types in the mouse nasal epithelium. An independent mouse scSeq data set (obtained using the 10x Chromium platform, see Methods) revealed that olfactory sensory neurons did not express Ace2 (2 of 28769 mature OSNs were positive for Ace2), while expression was observed in a fraction of Bowman''s gland cells and HBCs ( Figure S4 , see methods). doi = 10.1101/2020.03.25.009084 id = cord-277239-cedoi5jr author = Bray, R. A. title = Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins date = 2020-09-03 keywords = SARS; Spike summary = This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. The data demonstrate that while most individuals have significant IgG responses to community coronaviruses, all pre-COVID-19 samples tested negative against the SARS-CoV-2 targets as well as to SARS and MERS S1 proteins. . https://doi.org/10.1101/2020.09.02.20185199 doi: medRxiv preprint multiplexed, solid phase assay compared to other platforms (e.g., ELISA) include the ability to assay multiple viral targets simultaneously (and thereby provide internal assay controls for coronavirus specificity), the capacity to incorporate additional SARS-CoV-2 proteins in the future, a relatively short assay time, high throughput and semiquantitative assessment of the antibody response. doi = 10.1101/2020.09.02.20185199 id = cord-294134-o9bx1gn7 author = Brecher, Stephen M. title = Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2 date = 2020-07-23 keywords = SARS summary = One early issue in the validation/ evaluation of antibody tests for evidence of SARS-CoV-2 infection is the possibility of cross-reacting antibodies from the plasma of patients who had been infected with one or more of the common cold coronaviruses (coronavirus 229E, HKU1, NL63, and OC43). It also ties in with issues outlined in the Infectious Diseases Society of America (IDSA) guidelines (4) and in a commentary in Lancet (5) on how to best utilize antibody test data, especially when there could be false-positive results, including cross-reacting antibodies to the four common cold coronaviruses. Although the sample size was minimal, these data are reassuring that at least for the Abbott Architect SARS-CoV-2 antibody test, plasma from patients with documented positive PCRs for these four common cold coronaviruses did not test positive for the SARS-CoV-2 IgG antibody. However, this multisite study, including data from 3 regional Veterans Affairs (VA) institutions (MA, CT, and VT) suggests that cross-reacting antibodies are not detected when testing for SARS-CoV-2 IgG antibody. doi = 10.1128/jcm.01029-20 id = cord-022316-mh4pslnv author = Breda, Zélia title = Safety and Security Issues Affecting Inbound Tourism in the People's Republic of China date = 2009-11-16 keywords = China; SARS; Square; Taiwan; Tiananmen; chinese; tourism summary = doi = 10.1016/b978-0-7506-7898-8.50017-5 id = cord-312743-9e4yufo5 author = Breiman, Adrien title = Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 date = 2020-05-21 keywords = SARS summary = These observations suggested that, when produced in cells that express the A or B blood group enzymes, infectious SARS virions are decorated by the corresponding glycan antigens and that the presence of anti-A and anti-B antibodies in blood group O individuals could prevent infection by blocking virus attachment and entry. We therefore hypothesize that as they are produced in cells coexpressing the ACE2 receptor and either the αGal, NeuGc, or A/B blood group antigens, both SARS-CoV and SARS-CoV2 harbor the corresponding glycan epitopes. Likewise, impairment of transmission by the anti-blood group antibodies may not work to its full potential because of their variable titers in the population and of the high affinity of the SARS-CoV2 for ACE2 [18] , rendering its neutralization more difficult. doi = 10.1371/journal.ppat.1008556 id = cord-266175-4jyltfus author = Brendish, Nathan J title = Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date = 2020-10-08 keywords = COVID-19; PCR; Panel; SARS summary = METHODS: We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. [5] [6] [7] [8] The aim of this trial was to assess the clinical impact and real-world diagnostic accuracy of point-of-care testing using the QIAstat-Dx Respiratory SARS-CoV-2 Panel (Qiagen, Hilden, Germany) in adults presenting with suspected COVID-19 during the first wave of the pandemic in the UK. This prospective, non-randomised, controlled trial of routine point-of-care testing for COVID-19 in hospital shows the feasibility of point-of-care testing with the QIAstat-Dx Respiratory SARS-CoV-2 Panel, and shows clinical benefits across a range of outcome measures including time to results, infection control measures, and recruitment into clinical trials compared with a control group tested by centralised laboratory PCR. doi = 10.1016/s2213-2600(20)30454-9 id = cord-261059-rcpx4god author = Brenner, Steven Robert title = Erythropoietin Induced Hemoglobin Sub‐Unit Beta may Stimulate Innate Immune RNA Virus Pattern Recognition, Suppress Reactive Oxygen Species, Reduce ACE2 Viral Doorway Opening and Neutrophil Extracellular Traps against Covid‐19 date = 2020-07-09 keywords = SARS summary = Erythropoietin may stimulate innate immunity against RNA viruses, such as Covid‐19, through hemoglobin sub‐unit Beta acting on the retinoic acid inducible gene I (RIG‐1) and melanoma differentiation associated gene 5 (MDA5) viral pattern recognition receptors, causing interferon production and also maintains the vascular endothelium, a major target of SARS‐CoV‐2, possibly reducing thrombotic events which are becoming increasingly recognized complications of COVID19. Possibly hemoglobin (HB), especially subunit beta also contributed to recovery, since HB participates in innate immunity through differentially regulating the retinoic acid inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5), which are involved in viral recognition and mobilizing an interferon response. (Assessment of Endothelial and Haemostatic Changes During Severe SARS-CoV-2 Infection (Covid-Thelium), including syndecan-1, a marker of degradation of glycocalyx, D-dimers plasma levels association with thrombotic events, and von Willibrandt Factor, Viscoelastic testing and Vascular endothelial Growth Factor Receptor type 1. doi = 10.1002/jmv.26284 id = cord-338097-kdrq81w5 author = Brescia, Marilia D''Elboux Guimarães title = “Green July” 2020 and Another Good Reason to Quit Smoking: Help to Stop Spreading SARS-COV-2 and Save Lives! date = 2020-10-20 keywords = COVID-19; SARS summary = In Brazil, the initiative has been a great success coordinated by the Brazilian Society of Head and Neck Surgery (BSHNS), and it was expanded to one entire month, named "Green July." All around the country, besides press and television interviews and social media posts, members of the BSHNS and its accredited training centers run talks, shows and physical activities with the population to encourage healthy habits and to avoid exposure to the major risk factors associated with head and neck cancer. 2 Fortunately, for the time being, we are unaware of any Brazilian head and neck surgeons dying of SARS-Cov-2, even though the risk of severe infection to this medical specialty is quite real. Besides their individual risk for head and neck cancer, smoking is now a major risk factor for transmitting SARS-Cov 2. Tobacco Smoking a Potential Risk Factor in Transmission of COVID-19 Infection doi = 10.1055/s-0040-1716571 id = cord-264477-2onwu92a author = Brida, Margarita title = The globe on the spotlight: Coronavirus disease 2019 (Covid-19) date = 2020-07-01 keywords = ACHD; SARS summary = Our world, however, failed to learn necessary lessons from the SARS-CoV and MERS-CoV outbreaks and to invest on essential global research on ways of preventing the spread of infectious disease. The paper by Tan and Aboulhosn published in the current issue of the Journal, summarizes current knowledge regarding Covid-19 disease pandemic and its potential cardiovascular involvement, with a reference to adult congenital heart disease (ACHD) [8] . However, we are currently lacking ACHD specific data and a strict policy of social distancing employed in other parts of the world, seems to have had a positive response during the first phase of this pandemic in reducing the spread of disease and allowing for health care systems to prepare and somewhat cope with the unprecedented need. There are emerging publications regarding models of care of cardiovascular patients with infectious disease, which however are short of specific ACHD experience at present [14, 15] . doi = 10.1016/j.ijcard.2020.04.006 id = cord-340960-abanr641 author = Brigger, D. title = Accuracy of serological testing for SARS‐CoV‐2 antibodies: first results of a large mixed‐method evaluation study date = 2020-09-30 keywords = ELISA; RBD; SARS summary = In a mixed‐design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS‐CoV‐2 proteins and assessed the neutralizing activity of antibodies in patient sera. A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay (all collected in April 2020). Recombinantly expressed RBD has been used to establish an in-house ELISA for the detection of IgM and IgG anti-SARS-CoV-2 antibodies in human serum samples (supplementary Fig. 1a,b) . A total of 54 randomly selected sera from individuals who were tested positive in either of the three ELISA immunoassays as well as 6 negative controls were assessed in a live SARS-CoV-2 neutralization assay using ACE2-expressing Vero-E6 cells (34 inpatient samples, and 26 samples of medical personnel). doi = 10.1111/all.14608 id = cord-300716-urmogf97 author = Briguglio, Matteo title = Disentangling the Hypothesis of Host Dysosmia and SARS-CoV-2: The Bait Symptom That Hides Neglected Neurophysiological Routes date = 2020-06-05 keywords = COVID-19; CoV-2; SARS; nervous; olfactory summary = The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. Keywords: smell, olfactory bulb, coronavirus, SARS-CoV-2, COVID-19, infections, virulence, host pathogen interactions THE SNIFFING OUT OF CORONAVIRUSES Named after their crown-like spikes, coronaviruses are large non-segmented single-stranded positive-sense enveloped RNA viruses that may spill out from animals to infect humans and cause respiratory diseases. It is urgent to discuss whether SARS-CoV-2 can gain access to the central nervous system through a nasal-nervous pathway or other routes and if the fatal respiratory failure may be associated with a neuronal injury in critical brain areas of the host. doi = 10.3389/fphys.2020.00671 id = cord-269143-8j3m03gc author = Brindisi, Giulia title = Pills to think about in allergic rhinitis children during COVID‐19 era date = 2020-07-05 keywords = SARS summary = Allergic rhinitis (AR) is a common pediatric disease, that involves up to the 25% of children worldwide. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection in children is uncommon and often asymptomatic or mild. As described previously in the literature, novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children is uncommon and often asymptomatic or mild 1 . So far, we do not have data demonstrating a higher risk in the development of Coronavirus disease-19 (COVID-19) in allergic children, except for those with uncontrolled symptoms. This could help to detect affected children even with mild symptoms and limit SARS-CoV2 transmission. Instead it can be continued, as usual, in allergic children without clinical symptoms of COVID-19 and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Intranasal corticosteroids in allergic rhinitis in COVID-19 infected patients: An ARIA-EAACI statement doi = 10.1111/apa.15462 id = cord-030420-pgdmz69j author = Brion, Luc P. title = Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date = 2020-08-13 keywords = SARS summary = key: cord-030420-pgdmz69j title: Comment on Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) cord_uid: pgdmz69j As consistent with Lamouroux''s statement that ACE2 is low in the first trimester, ACE2 37 RNA expression is developmentally regulated with extremely low expression at 6-14 weeks, 38 although there is high expression at 24 weeks of gestation. 3 ACE2 RNA is highly expressed in 39 human villous, extravillous and syncytiotrophoblast as well as in several fetal organ cells (heart, 40 liver, and lung but not kidney) at 24 weeks of gestation. Evidence for and 65 against vertical transmission for SARS-CoV-2 (COVID-19) Clinical features of patients infected 69 with 2019 novel coronavirus in Wuhan The SARS-CoV-2 receptor ACE2 expression of 71 maternal-fetal interface and fetal organs by single-cell transcriptome study The expression and localization of 74 the human placental prorenin/renin-angiotensin system throughout pregnancy: roles in 75 trophoblast invasion and angiogenesis? Miscarriage in a Pregnant Woman With SARS-CoV-2 Infection doi = 10.1016/j.ajog.2020.08.022 id = cord-316018-zrui9i5z author = Bristow, Michael R. title = Dynamic Regulation of SARS-CoV-2 Binding and Cell Entry Mechanisms in Remodeled Human Ventricular Myocardium date = 2020-06-24 keywords = ACE2; NDC; SARS summary = SUMMARY Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling down-regulates into the normal range. Using serial analysis of myocardial gene expression employing endomyocardial biopsy starting material in a dilated cardiomyopathy cohort, we show that the SARS-CoV-2 cardiac myocyte receptor ACE2 is upregulated with remodeling and with reverse remodeling downregulates into the normal range. In explanted human heart preparations from patients with end stage reduced ejection fraction heart failure (HFrEF), ACE2 enzyme activity (22) as well as gene expression at the mRNA (20,23) and protein (20,22) levels are upregulated compared to organ donor controls. F/NDC baseline data for 10 integrins previously reported to bind to ACE2 (18,19), facilitate viral internalization (17) or be associated with LV remodeling (36) or cardiac myocyte injury protection (37) . doi = 10.1016/j.jacbts.2020.06.007 id = cord-273828-557vlq9d author = Brito, Carlos Antunes title = Mechanisms and consequences of COVID-19 associated liver injury: What can we affirm? date = 2020-08-27 keywords = COVID-19; SARS summary = Since the first reports of coronavirus disease 2019 (COVID-19) cases in December 2019 in China, numerous papers have been published describing a high frequency of liver injury associated with severe acute respiratory syndrome coronavirus 2 infection, many of them proposing a link between these findings and patient outcomes. Recently, many papers have been published reporting gastrointestinal manifestations, including acute liver injury, with increased levels of aminotransferases, in COVID-19 patients; these manifestations have been reported more frequently in patients with severe forms of this disease. Liver injury related to SARS-CoV-2 disease has been defined by increased liver enzyme serum levels, mainly aminotransferases and bilirubin, during the infection course in patients with or without previous liver disease [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] . Wide variability in deviations of liver enzyme serum levels from normal values is observed in infected patients, with an elevation frequency ranging from 16% to 62% for aminotransferases and from 5% to 21% for bilirubin. doi = 10.4254/wjh.v12.i8.413 id = cord-315339-dcui85lw author = Broadbent, Andrew J. title = Respiratory Virus Vaccines date = 2015-03-13 keywords = CD8; RSV; SARS; cell; influenza; respiratory; vaccine; virus summary = Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . doi = 10.1016/b978-0-12-415847-4.00059-8 id = cord-350342-j4p8235a author = Brocato, Rebecca L. title = Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date = 2020-10-27 keywords = Fig; RAG2; RNA; SARS summary = All of the SARS-CoV-2-challenged hamsters had detectable viral RNA in pharyngeal swabs at the first time point assayed, 3 dpi, and remained consistent (10 3 to 10 5 molecules of nucleocapsid using a second primer set [N2] per 100 ng RNA) throughout the duration of CyP treatment (Fig. 1C) . Viral RNA and infectious virus were detected in lung tissue from a subset of hamsters collected 13 dpi, on the day of euthanasia of moribund animals (14 to 34 dpi), or after euthanasia at 35 dpi (end of study) ( Fig. 1E and F). Electron microscopy studies were performed on lung sections of SARS-CoV-2infected, CyP-treated hamsters with various lung viral loads (Fig. 1) . Similarly, lung tissue collected at 13 dpi (end of study) indicate comparable levels of viral RNA detected (Fig. 6D ) but significantly reduced infectious virus in Centi-F1 MAb-treated animals (P ϭ 0.0002; unpaired t test) (Fig. 6E) . doi = 10.1128/jvi.01683-20 id = cord-256699-d2tf2g7f author = Brochot, Etienne title = Comparison of different serological assays for SARS-CoV-2 in real life date = 2020-08-02 keywords = SARS summary = Using 168 samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections, we evaluated the clinical performance of 5 serological assays widely used worldwide (WANTAI®, BIORAD®, EUROIMMUN®, ABBOTT® and LIAISON®). Thus, we evaluated five commercial serological tests widely used worldwide on samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections. The assays were validated using serum samples from (i) patients hospitalized for COVID-19 (n=20), non-hospitalized patients but PCR confirmed with SARS-CoV-2 (n= 58), patients participating in screening campaigns (n= 62), and samples from patients with a history of other seasonal coronavirus infections (n= 28). For the first group, with 20 patients hospitalized for COVID-19 with a positive nasopharyngeal SARS-CoV-2 PCR, all samples were positive with these serological assays evaluated ( Figure 1A ). doi = 10.1016/j.jcv.2020.104569 id = cord-322311-cg5xwx5a author = Broder, Kari title = Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges date = 2020-07-23 keywords = SARS summary = title: Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges Our institution utilizes the Roche Cobas 6800 SARS-CoV-2 assay, the Cepheid GeneXpert Xpress SARS-CoV-2 assay, and a laboratory-developed test (LDT) based on a modified CDC protocol, but there is no gold standard for the diagnostic accuracy of these assays. We collected 35 positive (positivity determined per assay instructions) nasopharyngeal samples with an E target C T value of Ն30 on the Roche Cobas 6800 assay; those samples then underwent secondary testing on the Cepheid GeneXpert assay within 3 days of initial testing. One sample tested positive on the Cobas 6800 assay (C T ϭ 37.9) and negative by the GeneXpert assay and was confirmed to be negative on the LDT. Overall, the Cepheid GeneXpert Xpress SARS-CoV-2 assay and the Roche Cobas 6800 SARS-CoV-2 assay showed a high level of agreement among patients with high C T values. doi = 10.1128/jcm.01187-20 id = cord-254668-szxhlejx author = Brogna, Barbara title = Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. date = 2020-06-13 keywords = SARS; SPM summary = title: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. Spontaneous pneumomediastinum (SPM) and Loculated pneumothorax (LPNX) are both generally rare clinical and radiological conditions associated with Coronavirus Disease 2019 (COVID-19). We report for the first time clinical data and radiological chest CT imaging of two patients affected by COVID-pneumonia associated with early radiological findings of SPM and LPNX. It has been suggested that a dysregulation of the immune response related to SARS-CoV-2, SARS-coV or MERS-CoV infection could lead to lung injury and the clinical and radiological findings typical of ARDS 2, 20 Most of the cases of SPM and PNX described in patients with COVID-19 pneumonia and in those affected by SARS have some features in common, including the absence of smoking history 16, 19 . doi = 10.1016/j.hrtlng.2020.06.005 id = cord-350103-liwvhuzj author = Brooks, Nathan A. title = The role of the urologist, BCG vaccine administration, and SARS‐CoV‐2: An overview date = 2020-06-22 keywords = BCG; Calmette; SARS summary = OBJECTIVES: To summarize the available literature regarding bacillus Calmette‐Guerin (BCG) administration, severe acute respiratory syndrome conoravirus‐2 (SARS‐CoV‐2), and the resulting clinical condition coronavirus disease (COVID‐19) in light of recent epidemiologic work suggesting decreased infection severity in BCG immunized populations while highlighting the potential role of the urologist in clinical trials and ongoing research efforts. Specifically, the epidemiologic evidence for decreased COVID‐19 morbidity in countries with BCG vaccination programs, current clinical trials for BCG vaccination to protect against COVID‐19, potential mechanisms and rationale for this protection, and the role of the urologist and urology clinic in providing support and/or leading ongoing efforts. 18 In both animal and human studies, BCG vaccination provides a non-specific benefit to the immune system, relative protection against, and reduced mortality from infections by other microbes (bacteria and viruses) which may occur by epigenetic reprogramming and induction of trained immunity. doi = 10.1002/bco2.21 id = cord-349159-rndtf508 author = Brosseau, Lisa M title = Selecting Controls for Minimizing SARS-CoV-2 Aerosol Transmission in Workplaces and Conserving Respiratory Protective Equipment Supplies date = 2020-08-21 keywords = COVID-19; SARS; control; exposure summary = Built on the recognition that aerosol-transmissible organisms are likely to exhibit a dose–response function, such that higher exposures result from longer contact times or higher air concentrations, this control banding model offers a systematic method for identifying a set of source and pathway controls that could eliminate or reduce the need for receptor controls. From that perspective, occupational hygienists have an obligation Annals of Work Exposures and Health, 2020, 1-10 doi: 10.1093/annweh/wxaa083 Original Article to consider hazardous SARS-CoV-2 aerosols in workplace risk assessments and to encourage employers to utilize well-studied and proven source and pathway control strategies for minimizing aerosol exposures. (2019) proposed a control banding method for aerosol-transmissible diseases, such as COVID-19, for two reasons: (i) to identify those jobs at highest risk and (ii) encourage the use of source and pathway controls before resorting to personal protective equipment (PPE), for the ultimate goal of conserving PPE for those in the highest risk categories. doi = 10.1093/annweh/wxaa083 id = cord-272135-a09bf50o author = Brouqui, Philippe title = Infection control in the management of highly pathogenic infectious diseases: consensus of the European Network of Infectious Disease date = 2009-04-22 keywords = HID; HLIU; SARS; care; patient summary = However, because the modes of infectious agent transmission are often underestimated, as was recently reported for infl uenza and SARS, 55 and because tuberculosis cannot be identifi ed without biological testing, EUNID recommends that droplet precaution should be upgraded to airborne precaution each time Situations in which a patient would need to be admitted to an HLIU • Patients with an unknown human-to-human transmittable or a potentially transmittable epidemic febrile illness that is native or imported from abroad • Patients with a known infectious disease caused by a group 3 or 4 agent* At admission of patients with HID to an emergency department • Systematically apply standard precautions and cough and respiratory etiquette • Set up at least one single room with a dedicated route and direct access, or an isolation room as recommended by EUNID for a referral hospital, † if HLIU cannot be used for ruling out HID diagnoses • Off er special training to the emergency department team • Retain close relationships with the HLIU team of the referral hospital doi = 10.1016/s1473-3099(09)70070-2 id = cord-292015-pfvgpf7v author = Brouwer, A. F. title = SARS-CoV-2 surveillance in decedents in a large, urban medical examiner''s office date = 2020-08-07 keywords = COVID-19; SARS summary = We found large racial disparities in test results: despite no statistical difference in the racial distribution between those flagged and not, SARS-CoV-2 positive decedents were substantially more likely to be Black (89% vs 51%). Since mid-March (shortly after surveillance networks began detecting positive cases [7] ), WCME has been piloting daily SARS-CoV-2 surveillance by testing nasopharyngeal swabs of decedents, including both COVID-19 suspects and nonsuspects. In this analysis we compare percent positivity in WCME''s piloted SARS-Cov-2 surveillance among decedents-distinguishing between those flagged by a COVID-19 checklist and those that were not-to the percent positivity of tests among people in the surrounding catchment area. The percent positivity for SARS-CoV-2 infection among decedents flagged for testing by a COVID-19 checklist in large, urban medical examiner''s office closely mirrored percent positivity among tests in the catchment population. . https://doi.org/10.1101/2020.08.03.20162883 doi: medRxiv preprint CoV-2 test results among decedents not flagged by the COVID-19 checklist. doi = 10.1101/2020.08.03.20162883 id = cord-329041-coryaz2s author = Brown, Ariane J. title = Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date = 2019-09-30 keywords = OC43; RDV; RNA; SARS; Scientific summary = These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. We previously reported the antiviral activity of RDV against a genetically diverse panel of human endemic, emerging and zoonotic CoV including HCoV-NL63 (alpha 1b), mouse hepatitis virus (MHV, beta 2a), SARS-CoV and related Bat CoVs WIV1 and SHC014 (beta 2b), as well as MERS-CoV and related Bat CoV HKU5 (beta 2c) (Agostini et al., 2018; Sheahan et al., 2017) . Inhibition of viral protease has also been evaluated with lopinavir, a protease inhibitor designed for human immunodeficiency virus, which like chloroquine exerts a moderate antiviral effect on CoV replication (EC 50 values: MERS-CoV 8 μM, SARS-CoV 17.1 μM, HCoV-229E 6.6 μM) (de Wilde et al., 2014) . doi = 10.1016/j.antiviral.2019.104541 id = cord-354881-7o20cn1x author = Brown, Rebecca C H title = The scientific and ethical feasibility of immunity passports date = 2020-10-16 keywords = SARS; immunity; passport summary = Immunity passports could be implemented on the basis of either a laboratory test of immune response (a correlate of protection) or an immunising event (infection or vaccination), which would identify individuals less likely to get disease or transmit virus when exposed to SARS-CoV-2. 33, 34 Given the scale of the pandemic and the research into COVID-19, there is likely to be rapid progress in understanding the nature of infection and immunity such that clinical infection, with or without a measure ment of antibody response, might form the basis of a time-limited immunity passport. Evidence from previous work with seasonal coronaviruses and studies of SARS-CoV-2 vaccines in macaques suggests that previous infection or vaccination might protect from severe disease but an individual might nevertheless carry the virus at similar levels, and for a similar duration, to those previously uninfected, with an unchanged potential for transmission. doi = 10.1016/s1473-3099(20)30766-0 id = cord-288920-xkfcc2dx author = Broxmeyer, L title = SARS: Just another viral acronym? date = 2003-08-31 keywords = SARS; tuberculosis summary = Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. Outbreaks of multi-drug resistant (MDR) tuberculosis and the atypical mycobacteria simulate SARS on clinical, radiologic, epidemiologic, and diagnostic laboratory grounds and it is only logical then to include them in the differential to find a definitive cause and cure for SARS. CDC began supporting the World Health Organization (WHO) in the investigation of a multi-country outbreak of the atypical pneumonia of unknown etiology (1), referred to as severe acute respiratory syndrome (SARS). Although high fever, nonproductive cough, low blood oxygen saturation, and varying degrees of respiratory distress, all found in SARS, are nothing new to the clinical picture of tuberculosis (11) , the number of TB cases in which people in the Orient die of adult respiratory distress syndrome (ARDS) is definitely on the rise (12), the same ARDS that often provokes the ''crazypaving'' appearance at thin-section CT (13). doi = 10.1016/s0306-9877(03)00195-6 id = cord-255913-430lrbyx author = Brufsky, Adam title = DC/L‐SIGNs of Hope in the COVID‐19 Pandemic date = 2020-05-06 keywords = SARS summary = The current pandemic and its pleotropic effects can be explained in part by interaction between SARS‐CoV‐2 spike protein S, the ACE2/L‐SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC‐SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. The current pandemic and its pleotropic effects can be explained in part by interaction between SARS-CoV-2 spike protein S, the ACE2/L-SIGN/CD209 receptor on the type II alveolar cell of the lung, and the DC-SIGN receptor on the respiratory dendritic cell (DC) and associated endothelial cells. L-SIGN is expressed on human type II alveolar cells, is associated with ACE2 10 , and can enhance ACE2 mediated binding and cellular entry of viral pseudotypes expressing the spike protein S of SARS-CoV 9 . De-glycosylation reduces infectivity of viral pseudotypes expressing SARS-CoV spike protein 13 and specific asparagine glycosylation sites in three clusters within the SARS-CoV S protein appear critical for DC/L-SIGN mediated, but not ACE2 mediated, SARS Co-V pseudotype entry into cells 13 . doi = 10.1002/jmv.25980 id = cord-316374-mzomj1ab author = Brufsky, Adam title = Boning up: amino-bisphophonates as immunostimulants and endosomal disruptors of dendritic cell in SARS-CoV-2 infection date = 2020-06-29 keywords = SARS summary = Amino-bisphosphonates such as zoledronic acid (ZA) can possibly ameliorate or prevent severe COVID-19 disease by at least three distinct mechanisms: (1) as immunostimulants which could boost γδ T cell expansion, important in the acute response in the lung; (2) as DC modulators, limiting their ability to only partially activate T cells; and (3) as prenylation inhibitors of small GTPases in the endosomal pathway of the DC to prevent expulsion of lysosomes containing SARS-CoV-2 virions. Early and central infection of tissue resident dendritic cells (DC) by the SARS-CoV-2 coronavirus explain some of the immunopathology of the COVID-19 pandemic. Agents that alter endosomal pH such as hydroxychloroquine (HCQ) could be protective in SARS-CoV-2 infected DCs in maintaining the immune response as well as the lymphocyte count, as was observed in a recently reported randomized, parallel, open label, multicenter clinical trial of hydroxychloroquine (HCQ) and usual care versus usual care alone for the treatment of COVID infection [36] . doi = 10.1186/s12967-020-02433-6 id = cord-265595-55s19mr1 author = Brug, Johannes title = Risk Perceptions and Behaviour: Towards Pandemic Control of Emerging Infectious Diseases: International Research on Risk Perception in the Control of Emerging Infectious Diseases date = 2009-01-06 keywords = SARS; risk summary = Three papers [5] [6] [7] were the result of a European Commission funded project, called SARS-Control that was partly dedicated to exploring risk perceptions and risk communications related to SARS and other emerging infectious diseases. Effective management of new epidemic infectious disease risks in the phase that no treatment or vaccination is yet possible is largely dependent on precautionary behaviour of the population. Four of the papers present empirical mostly explorative original research on risk perceptions, knowledge, beliefs and other issues related to SARS during or after the SARS outbreak in 2003. Given the clear and present danger of newly emerging infectious disease outbreaks in the near future and the importance of the public response and precautionary actions to control the spread, additional research on risk perceptions and other behavioural determinants is warranted. Perceived threat, risk perception and efficacy beliefs related to SARS and other (emerging) infectious diseases: results of an international survey doi = 10.1007/s12529-008-9000-x id = cord-326568-twv2i3fb author = Bruminhent, Jackrapong title = Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date = 2020-09-15 keywords = COVID-19; SARS; Thailand summary = To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians'' diagnoses. Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. Apart from close contact with an infected case and visiting high-risk places, we found that having no medical coverage and presenting with productive cough were predictors of being diagnosed with COVID-19 among PUIs. SARS-CoV-2 is an emerging respiratory virus that commonly causes no or mild respiratory tract infection and is occasionally complicated by severe pneumonia [1] . doi = 10.1371/journal.pone.0239250 id = cord-350134-gl3qtoug author = Brun, Gilles title = COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? date = 2020-05-22 keywords = COVID-19; SARS summary = title: COVID-19—White matter and globus pallidum lesions: Demyelination or small-vessel vasculitis? Since December 2019, a novel coronavirus, also called severe acute respiratory syndrome CoV-2 (SARS-CoV-2), emerged in Wuhan, China, and caused a pandemic disease . Herein, we report a case of SARS-CoV-2 brain lesions suggesting an acute demyelination. At day 7, a brain MRI revealed lesions with restricted diffusion without any hemorrhage or enhancement after gadolinium injection (figure). 4 In our case, the distribution of bilateral but asymmetrical lesions with periventricular and deep white matter involvement is rather suggestive of an acute demyelination. Although mechanisms remain obscure, our case shows the importance of the MRI in the exploration of neurologic symptoms in COVID-19. Demyelination or small-vessel CNS vasculitis might be a rare but silent complication of sedated patients with COVID-19. COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection doi = 10.1212/nxi.0000000000000777 id = cord-004634-pkrxiipo author = Brun-Buisson, Christian title = SARS: The challenge of emerging pathogens to the intensivist date = 2003-05-08 keywords = SARS summary = In late February 2003, the WHO issued a worldwide public health alert on the emergence of a new epidemic of acute respiratory disease first identified in Asian countries since November 2002. In a few weeks, the new agent causing this "severe acute respiratory syndrome" (SARS), a coronavirus, has been identified, sequenced, and tests have been developed for diagnosis [1] . As of the end of April 2003, about 5,000 suspected or probable cases have been reported to the WHO from 27 countries [2] , with a vast majority from inland China (57% of reported cases), which appears to be at the origin of the epidemic, and Hong Kong (32%). In North America, however, an outbreak soon occurred in Toronto, Canada, following an household epidemic which appeared secondary to contamination of a Canadian resident of Asian origin who visited relatives in Hong Kong in February 2003 [3] . Affected areas-severe acute respiratory syndrome (SARS) A Major Outbreak of Severe Acute Respiratory Syndrome in Hong Kong doi = 10.1007/s00134-003-1823-y id = cord-312038-g76cpjp7 author = Brunaugh, Ashlee D. title = Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date = 2020-10-07 keywords = COVID-19; DPI; Fig; MERS; NIC; SARS; hlys summary = Utilizing repurposed NIC, and with the goal of developing a therapeutically effective, rapidly scalable and globally distributable antiviral therapy to reduce the spread of SARS-CoV-2, we describe an inhalable NIC formulation that can be administered using three major models or respiratory tract delivery systems: DPI, nasal spray and nebulizer. At the highest dose tested (0.125 µg/mL NIC), Vero cells with an established MERS-CoV infection exhibited an 82.2% ± 0.8% decrease in viral load compared to untreated controls after 24-hours of exposure to NIC-hLYS particles ( Fig 1D) . While brain viral titres did not exhibit further reduction from levels noted in the preliminary efficacy study, the inoculation of Vero E6 cells with viral particles obtained from lung and brain homogenates of surviving animals resulted in no observation of CPE at any of the inoculum concentrations tested, which indicates that remaining viral particles were not active. doi = 10.1101/2020.09.24.310490 id = cord-283034-ebely0rx author = Brunet, E title = Ileitis as the exclusive manifestation of covid-19. The first reported case date = 2020-10-19 keywords = SARS summary = The patient did not report any respiratory symptoms. Two nasopharyngeal and oropharyngeal swab specimens performed before admission had been negative for SARS-CoV-2. Respiratory auscultation was strictly normal, and pain was noted on the palpation of the right lower abdominal quadrant. The patient was admitted to the gastroenterology unit after a confirmatory negative SARS-CoV-2 NAAT The patient recovered completely, with normalization of the previous blood test abnormalities. A SARS-CoV-2 control NAAT in rectal swab was negative before discharge from hospital. To our knowledge, our report is the first well-documented case of SARS-CoV-2 intestinal infection without evidence of pulmonary involvement. The multiple negative nasopharyngeal swabs plus the normal chest X-ray and CT findings rule out pulmonary infection. We report a patient with SARS-CoV-2 infection apparently limited to the bowel. In conclusion, SARS-CoV-2 may occur with an exclusive intestinal symptoms. Abdominal Pain: A Real Challenge in Novel COVID-19 Infection doi = 10.1016/j.gastrohep.2020.10.001 id = cord-299783-8ti6r0eh author = Bruni, M. title = Persistence of anti-SARS-CoV-2 antibodies in non-hospitalized COVID-19 convalescent health care workers date = 2020-08-01 keywords = RBD; SARS; Spike summary = Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. The performances of these ELISA assays were assessed for the different viral antigens and classes of antibodies by determining ROC curves using i) a cohort of 56 sera from COVID-19 patients collected between April and June 2020 and tested positive for nasopharyngeal swabs, and ii) 436 pre-COVID-19 sera, collected between 2012 and 2015 (Supplementary Table 1 and Figure S1 ). Non-hospitalized COVID-19 subjects manifested a lower antibody titer as compared to severe ICU patients for all the tested antibody classes and viral antigens ( Figure 1B-D) . doi = 10.1101/2020.07.30.20164368 id = cord-318018-ybdkp398 author = Bruni, Margherita title = Persistence of Anti-SARS-CoV-2 Antibodies in Non-Hospitalized COVID-19 Convalescent Health Care Workers date = 2020-10-01 keywords = COVID-19; RBD; SARS; Spike summary = Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies as well as soluble pro-inflammatory mediators in the sera. Our data show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory cytokines. Here we show that humoral immune responses against SARS-CoV-2 correlated with disease severity in terms of both antibody titers, persistence over time and serum levels of pro-inflammatory mediators. Moreover, we showed that the vast majority of COVID-19 mildly symptomatic patients analyzed in the study halved their anti-RBD antibody titers after 4 weeks from viral negativization, thus confirming the short lifespan of humoral immune responses against SARS-CoV-2. doi = 10.3390/jcm9103188 id = cord-298716-pubhq564 author = Bryche, Bertrand title = Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date = 2020-06-16 keywords = Fig; SARS summary = title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. We measured the OE thickness, the OSN cilia quality (based on Golf staining) and the immune cell infiltration of the olfactory mucosa (based on the Iba1 staining) on 6 images per animal taken from 3 different slides spread along the nasal cavity. Two recent reports indicate that olfactory neurons in hamster (Sia et al., 2020) and respiratory cells in ferret (Ryan et al., 2020) may be the target of SARS-CoV-2 but these studies did not focus on the nasal cavity and they did not use double staining to clearly identify the infected cells in the OE. doi = 10.1101/2020.06.16.151704 id = cord-351314-atsuh8e2 author = Bryson-Cahn, Chloe title = A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date = 2020-03-12 keywords = SARS; hat summary = Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. doi = 10.1093/cid/ciaa256 id = cord-283491-y6t64pux author = Brzezinski, Dariusz title = Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date = 2020-09-27 keywords = PDB; SARS; structure summary = Understandably, firstline research findings, including molecular structure determinations, depositions in the Protein Data Bank (PDB), 1 and related results, are often made public on BioRxiv 2 or MedRxiv 3 before formal peer review. In this paper, we present covid-19.bioreproduciblity.org, a web resource that organizes SARS-CoV-2 related structural information in a way that should be understandable and useful for a wider scientific community, and not only for structural biologists. Finally, the structures are evaluated by a team of expert structural biologists who use a combination of the mined data, validation reports, and manual inspection of the protein models and associated electron density to examine potential problems. If raw diffraction data are available, the results of automatic processing of images by HKL-3000auto are examined to verify that the structure was determined in the correct space group and at optimal resolution. doi = 10.1002/pro.3959 id = cord-262104-oig3qrr7 author = Brüssow, Harald title = COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date = 2020-06-08 keywords = China; SARS; Wuhan; case; covid-19; infection summary = Very similar information was reported in data describing household transmission in Wuhan, where children showed a 4% infection rate compared with 17% in adults. 1.6 million tests were used to identify 1''400 SARS-CoV-2-positive cases; 1000 patients had had exposure to infected people from Hubei. In Wuhan, 105 index cases of patients suffering from moderate COVID-19 symptoms (fever, cough, fatigue) were investigated for secondary transmission to 392 household contacts. The control measures that stopped the epidemic locally have included: intense infection surveillance of incoming travelers; isolation of COVID-19 cases in hospitals; contact tracing and quarantine in holiday camps; and school closure but no lock-down, thus preventing the crisis from having a negative economic impact. Model calculations showed that the containment measures (the quarantine of exposed, and the isolation of infected persons) which depleted the number of susceptible individuals for the virus, reproduced the actually observed case development. doi = 10.1111/1462-2920.15118 id = cord-297168-t6zf5k99 author = Brüssow, Harald title = The Novel Coronavirus – A Snapshot of Current Knowledge date = 2020-03-06 keywords = China; SARS; Wuhan; coronavirus summary = While bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the Huanan food market in Wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. W. Tan and colleagues, who now constitute the China Novel Coronavirus Investigating and Research Team, described subsequently the isolation of further coronaviruses from three patients in Wuhan who tested negative for 18 viral and four bacterial respiratory pathogens. Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients Outside Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1111/1751-7915.13557 id = cord-302316-raf5rlkq author = Brüssow, Harald title = COVID‐19: From pathogenesis models to the first drug trials date = 2020-06-23 keywords = ACE-2; RNA; SARS; covid-19; patient summary = US researchers studied the viral and cellular transcriptional response upon infection of cell cultures and in animal models with different respiratory viruses including influenza A virus and SARS-CoV-2. A French study randomizing 181 COVID-19 patients with pneumonia on hydroxychloroquine or placebo, observed, however, no significant effect of treatment on transfer to ICU, mortality, or in the prevention of development of acute respiratory distress syndrome (Mah evas et al., 2020). A total of 86 COVID-19 cases of patients from China with mild/moderate disease were randomized on the antiviral lopinavir (an inhibitor of HIV protease combined with ritonavir, which prolongs the presence of drugs in the body) or the antiviral arbidol (an influenza virus fusion inhibitor only registered in Russia) or in a control group in a 2:2:1 ratio. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial doi = 10.1111/1751-7915.13611 id = cord-332820-6qx6svs5 author = Buck, M. D. title = Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay date = 2020-07-01 keywords = LAMP; SARS summary = The pipeline utilises a series of in-house buffers to first inactivate patient samples received from care homes and hospitals, and to then extract RNA before using a CE marked commercial kit to detect SARS-CoV-2 by RT-qPCR. Herein, we describe the use of loop mediated isothermal amplification PCR coupled with reverse transcription (RT-LAMP) as a robust method for SARS-CoV-2 detection in clinical specimens 6 . Our results demonstrate that within the CCC pipeline, RT-LAMP can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nosethroat swabs and endotracheal secretions/bronchoalveolar lavage fluid. The RT-LAMP assay reproducibility and precision were determined by extracting RNA 5 times from a confirmed COVID-19 positive patient sample through the CCC pipeline and assessing by N gene and 18S RT-LAMP in 5 independent experiments, performed by two different operators ( Figure 4D ). doi = 10.1101/2020.06.29.20142430 id = cord-311216-mfqlv3nh author = Buckley, Leo F. title = Cardiovascular Pharmacology in the Time of COVID-19: A Focus on Angiotensin-Converting Enzyme 2 date = 2020-04-13 keywords = ACE2; SARS summary = Severe acute respiratory syndrome coronavirus-2019 (SARS-CoV-2), the causative virus of COVID-19, infects host cells through angiotensin-converting enzyme 2 (ACE2). We review current knowledge of the role of ACE2 in cardiovascular physiology and SARS-CoV-2 virology, as well as clinical data to inform the management of patients with or at risk for COVID-19 who require renin–angiotensin–aldosterone system inhibitor therapy. [2] [3] [4] [5] [6] [7] [8] SARS-CoV-2 infects host cells by binding to human angiotensin-converting enzyme-2 (ACE2), [9] [10] [11] a membranebound enzyme expressed in the lungs, heart, and kidneys (among many other organs). 15 It has been proposed that renin-angiotensin-aldosterone system (RAAS) inhibitors predispose to SARS-CoV-19 infection and worsen outcomes after COVID-19 by upregulating ACE2 expression. Epidemiologic studies should be performed to estimate the association of RAAS inhibitor use to risk of COVID-19 in patients with hypertension, heart failure or chronic kidney disease. Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients doi = 10.1097/fjc.0000000000000840 id = cord-277611-3iynrfzq author = Buetti, Niccolò title = Risk factors for SARS-CoV-2 detection in blood of critically ill patients date = 2020-09-02 keywords = SARS summary = In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms'' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . doi = 10.1093/cid/ciaa1315 id = cord-337485-nqcnd9py author = Buetti, Niccolò title = SARS-CoV-2 detection in the lower respiratory tract of invasively ventilated ARDS patients date = 2020-10-16 keywords = LRT; SARS summary = Our objectives were to describe the viral shedding and the viral load in LRT and to determine their association with mortality in critically ill COVID-19 patients. Third, we assessed the association between viral presence in LRT and mortality using mixed-effect logistic models for clustered data adjusting for the time between symptoms'' onset and date of sampling. Our objectives were (1) to describe the viral shedding and the viral load in LRT and (2) to determine THE ASSOCIATION BETWEEN VIRAL PRESENCE AND MORTALITY in critically ill COVID-19 patients. The viral shedding in LRT lasted almost 30 days in median in critically ill patients, and the SARS-CoV-2 viral presence in the LRT was associated with the 6week mortality. Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients doi = 10.1186/s13054-020-03323-5 id = cord-307436-qcdlcxyb author = Bui, L. V. title = Estimation of the incubation period of SARS-CoV-2 in Vietnam date = 2020-05-15 keywords = SARS; Vietnam summary = Methods: Only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset and clearly defined window of possible SARS-CoV-2 exposure were included. To assure the reliability of analysis, we selected only confirmed COVID-19 cases who are Vietnamese and locally infected with available data on date of symptom onset (including fever, cough, and shortness of breath) and clearly defined window of possible SARS-CoV-2 exposure. We estimated the incubation period of Vietnamese confirmed COVID-19 cases from public reported data with three parametric models, including Weibull, Gamma and Lognornal . The estimated mean of incubation period for 19 Vietnamese confirmed COVID-19 cases using Weibull distribution model is higher than that of SARS in Hong Kong and Beijing [14] and in MERS [15, 16] . Our study has several strengths, including being the first effort to estimate SAR-CoV-2 incubation period using data from Vietnamese locally transmitted cases. doi = 10.1101/2020.05.09.20096800 id = cord-279131-1unb0z79 author = Buijsers, Baranca title = Beneficial non-anticoagulant mechanisms underlying heparin treatment of COVID-19 patients date = 2020-08-25 keywords = COVID-19; HPSE; LMWH; SARS summary = Here, we summarise potential beneficial, non-anticoagulant mechanisms underlying treatment of COVID-19 patients with heparin/LMWH, which include: (i) Inhibition of heparanase activity, responsible for endothelial leakage; (ii) Neutralisation of chemokines, and cytokines; (iii) Interference with leukocyte trafficking; (iv) Reducing viral cellular entry, and (v) Neutralisation of extracellular cytotoxic histones. In addition to functioning as anticoagulants, heparins have other therapeutic functions that are relevant for the treatment of COVID-19-associated clinical manifestations, i.e. neutralisation of inflammatory chemokines, and cytokines, such as CXCL-1, IL-6, and IL-8 that play a key role in ARDS; neutralisation of extracellular cytotoxic histones and by interfering with leukocyte trafficking [20] . Data for this review were identified by searches of PubMed, and preprint servers, and references from relevant articles using the search terms "COVID-19", "Heparin", "Non-anticoagulant functions of heparin", "Low molecular weight heparin", "ARDS", "Kidney dysfunction", "Endothelial barrier dysfunction", "Heparanase", "Heparan sulphate", "Viral entry", "Heparanase inhibition", "Inflammation", "Complement system", and "Neutrophil extracellular traps". doi = 10.1016/j.ebiom.2020.102969 id = cord-299116-1agfnjvq author = Bunders, Madeleine title = Implications of sex differences in immunity for SARS-CoV-2 pathogenesis and design of therapeutic interventions date = 2020-08-17 keywords = ACE2; COVID-19; SARS summary = Emerging knowledge on the basic biological pathways that underlie differences in immune responses between women and men needs to be incorporated into research efforts on SARS-CoV-2 pathogenesis and pathology to identify targets for therapeutic interventions aimed at enhancing antiviral immune function and lung airway resilience while reducing pathogenic inflammation in COVID-19. The current Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic highlights the clinical consequences of these sex differences in antiviral immunity and tissue resilience Scully et al., 2020) , with in particular older men suffering from severe Coronavirus disease 2019 (COVID-19) and experiencing higher case mortality rates (Docherty et al., 2020; Grasselli et al., 2020; Jin et al., 2020; Salje et al., 2020) . In the following, we will address the different stages of SARS-CoV-2 pathogenesis, including viral entry and sensing, induction of antiviral immune responses and inflammation, and immune-mediated tissue-repair, in the context of critical differences in immune responses that exist between the sexes and contribute to the male-bias in development of severe COVID-19. doi = 10.1016/j.immuni.2020.08.003 id = cord-325959-uqg2xkie author = Bundschuh, Christian title = Evaluation of the EDI enzyme linked immunosorbent assays for the detection of SARS-CoV-2 IgM and IgG antibodies in human plasma date = 2020-06-08 keywords = CoV-2; SARS summary = METHODS: Using EDI(TM) Novel Coronavirus COVID-19 Enzyme Linked Immunosorbent Assays (ELISAs), we measured SARS-CoV-2 IgM and IgG antibodies in 64 SARS-CoV-2 RT-PCR confirmed COVID-19 patients with serial blood samples (n=104) collected at different time points from symptom onset. low "false" positivity rates for the EDI(TM) SARS-CoV-2 IgM and IgG ELISAs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus that causes Coronavirus Disease 2019 (COVID-19), has recently emerged to cause a human pandemic. For the clinical evaluation we measured SARS-CoV-2 IgM and IgG antibodies in three different cohorts: First in a "positive cohort" of patients with SARS-CoV-2 RT-PCR confirmed 5 COVID-19 with serial blood samples at different time points from symptom onset. Furthermore, the clinical evaluation study demonstrated high "true" positivity rates in the SARS-CoV-2 RT-PCR confirmed COVID-19 patients with symptom onset after 15 days with 94.4% for IgM and 100% for IgG SARS-CoV-2 doi = 10.1016/j.cca.2020.05.047 id = cord-292673-00s3wgem author = Buonaguro, Luigi title = SARS-CoV-2 RNA polymerase as target for antiviral therapy date = 2020-05-05 keywords = RNA; SARS summary = In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. Journal of Translational Medicine *Correspondence: l.buonaguro@istitutotumori.na.it 1 Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy Full list of author information is available at the end of the article SARS-CoV-2 is a positive-sense RNA virus belonging to the Orthocoronavirinae (coronavirus, CoV) family and, in particular, to the genus beta (group 2) together with the other two new human coronaviruses SARS-CoV and MERS-CoV. However, all three of them have been developed for negative-sense RNA viruses which show a significant difference in the RdRp sequence and structure compared to the positive-sense SARS-CoV-2 RNA virus. In conclusion, as for all RNA viruses, the RdRp of the newly identified positive-sense human SARS-CoV-2 RNA virus represents the most optimal target for an antiviral drug. doi = 10.1186/s12967-020-02355-3 id = cord-327272-fspxett8 author = Buonaguro, Luigi title = Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date = 2020-05-12 keywords = RNA; SARS summary = The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. The only positive-sense RNA virus, for which a very effective drug targeting specifically the RdRp is available and approved world-wide for clinical use, is hepatitis C virus (HCV). All these sequence and structural modelling evidences strongly support the concept that the SARS-CoV-2 RdRp is much more similar to the one from HCV than the one from negative-sense Influenza and Ebola RNA viruses. Therefore, repositioning of Sofosbuvir (Sovaldi®; Epclusa® by Gilead), the inhibitor of the HCV NS5B RdRp protein, as antiviral in the treatment of the SARS-CoV-2 infection has an extremely high potentiality of success, as recently postulated by others [17] , and is suggested as a potential drug for the treatment of COVID-19 in the very recent EASL-ESCMID position paper [18] . doi = 10.1186/s13027-020-00302-x id = cord-293301-7bmj8qsv author = Buonanno, Giorgio title = Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment date = 2020-04-17 keywords = SARS; quanta; rate summary = The quanta emission rates of an asymptomatic SARS-CoV-2 infected subject, with a viral load in the mouth of 108 copies mL-1, were 10.5 quanta h-1 and 320 quanta h-1 for breathing and speaking respiratory activities, respectively, at rest. The findings in terms of quanta emission rates were then adopted in infection risk models to demonstrate its application by evaluating the number of people infected by an asymptomatic SARS-CoV-2 subject in Italian indoor microenvironments before and after the introduction of virus containment measures. In particular, airborne transmission of SARS-CoV-2 by an asymptomatic 76 subject within pharmacies, supermarkets, restaurants, banks, and post offices were simulated, and 77 the reduction in the average number of infected people from one contagious person, R0, was 78 estimated. The quanta emission rate used in the simulation of the scenario represents the average value 220 obtained from the four expiratory activities (whispered counting, voiced counting, speaking, and 221 breathing); the data are reported and discussed in the result sections. doi = 10.1101/2020.04.12.20062828 id = cord-281248-z2gisufl author = Buonsenso, Danilo title = A Pediatric Strategy for the Next Phase of the SARS–CoV-2 Pandemic date = 2020-10-09 keywords = COVID-19; SARS; child summary = Considering that most of these conditions present several overlaps with SARS-CoV-2 (Figure 1 ), this will pose challenges to pediatricians and health system to appropriately manage all these conditions and properly allocate resources, because COVID-19 will need to be considered until exclusion, in order to reduce nosocomial transmission and new outbreaks. In light of new evidences and the need to reduce as much as possible the diffusion of infectious diseases among children during the next season (because this would lead to include all cases in the differential diagnosis with COVID-19 because of similar symptoms), a reorganization of school environments should be a priority for policy makers. Therefore, even though the direct clinical impact of the SARS-COV-2 virus on children has been limited with a very low mortality rate, and the COVID-19-related pediatric inflammatory multisystem syndrome remains a relatively rare consequence of the disease, pediatricians will still need to include SARS-CoV-2 in the differential diagnosis. doi = 10.3389/fped.2020.582798 id = cord-289003-vov6o1jx author = Burdet, C. title = Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals date = 2018-02-28 keywords = Ebola; MERS; SARS; epidemic; human; risk summary = Abstract We present here the proceedings of the 5th seminar on emerging infectious diseases, held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows: encourage research on the prediction, screening and early detection of new risks of infection; develop research and surveillance concerning transmission of pathogens between animals and humans, with their reinforcement in particular in intertropical areas ("hot-spots") via public support; pursue aid development and support in these areas of prevention and training for local health personnel, and foster risk awareness in the population; ensure adapted patient care in order to promote adherence to treatment and to epidemic propagation reduction measures; develop greater awareness and better education among politicians and healthcare providers, in order to ensure more adapted response to new types of crises; modify the logic of governance, drawing from all available modes of communication and incorporating new information-sharing tools; develop economic research on the fight against emerging infectious diseases, taking into account specific driving factors in order to create a balance between preventive and curative approaches. doi = 10.1016/j.respe.2017.08.001 id = cord-297884-a6yrtuwf author = Burke, R. M. title = Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States date = 2020-05-03 keywords = COVID-19; SARS; case summary = To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with ≥ 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members. Among 49 HCP who provided care to or came into contact with the infectious fluids of travelassociated case patients and who had at least one set of respiratory samples collected and tested for SARS-CoV-2, the secondary attack rate was 0% (95% CI: 0 -7%). doi = 10.1101/2020.04.27.20081901 id = cord-324405-6uanhe2p author = Burke, Rachel M. title = Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date = 2020-09-02 keywords = COVID-19; SARS; case; travel summary = To interrupt transmission and facilitate early identification of secondary cases (i.e., transmissions of SARS-CoV-2 from the original travel-related case patient to a close contact), public health authorities at the state, county, and local levels, in consultation with subject-matter experts from the U.S. Centers for Disease Control and Prevention (CDC), mobilized rapidly to place the patients under appropriate isolation and identify contacts exposed to these patients. To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with � 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members and some healthcare personnel. doi = 10.1371/journal.pone.0238342 id = cord-260565-cdthfl5f author = Burkle, Frederick M. title = Declining Public Health Protections within Autocratic Regimes: Impact on Global Public Health Security, Infectious Disease Outbreaks, Epidemics, and Pandemics date = 2020-04-02 keywords = Africa; China; Health; Korea; SARS; chinese; public summary = While China is seeking to adhere as much as possible to the underlying norms and rules of global institutions," reemphasizing that China after SARS "perhaps [needs] to reframe health as a global public good that is available to each and every individual of the world, rather than merely as an issue of concern to nation-states." 37 In a rare openness, rarely seen before, the normally secretive Xi admitted at a meeting to coordinate the fight against the virus that China must learn from "obvious shortcomings exposed during its response." Yet given the second-guessing that always surfaces in these tragedies, "it cannot be denied that the Chinese government tried to control the narrative, another sign of irrational hubris, and as a result, the contagion was allowed to spread, contributing to equally irrational fear." A China researcher for Human Rights Watch (New York USA) noted: "authorities are as equally, if not more, concerned with silencing criticism as with containing the spread of the coronavirus. doi = 10.1017/s1049023x20000424 id = cord-281619-fhyamruq author = Burlacu, Alexandru title = Unpuzzling COVID-19 Prothrombotic State: Are Preexisting Thrombophilic Risk Profiles Responsible for Heterogenous Thrombotic Events? date = 2020-08-25 keywords = COVID-19; SARS summary = 1 The similarity between these 2 conditions is sustained by autopsy studies findings, documented immune pathogenesis, and microcirculation dysfunctions, the ability of SARS-CoV-2 to disseminate the infection in other organs and by the fact that many critically ill COVID-19 patients developed clinical symptoms of shock following a process called "viral sepsis." 2 A recent paper dealing with SARS-CoV-2 and "viral sepsis" raised alarm signals that despite the huge percentage of 71,4% of non-survivors of COVID-19 who matched the grade of overt disseminated intravascular coagulation, the concrete mechanisms of vascular thrombosis are not yet known. The hypercoagulation state consequent to SARS-COV-2 infection seems to manifest not only as pulmonary embolism, but also as other thrombotic events such as deep vein thrombosis, myocardial infarction, or ischemic stroke, 31 suggesting that the most plausible explanation has to be a pattern concerning either the patients or the virus. doi = 10.1177/1076029620952884 id = cord-328680-zdwep5b2 author = Burr, Tyler title = NMDA-receptor encephalitis associated with COVID-19 infection in a toddler date = 2020-10-09 keywords = SARS summary = Anti-NMDA receptor (NMDAR) encephalitis is characterized by mood and behavior changes, seizures, abnormal movements, autonomic instability, and encephalopathy. More recently, cases of anti-NMDAR encephalitis following viral infections have been reported, including herpes simplex virus (HSV), Japanese encephalitis virus (JEV), and now the 2019 novel coronavirus (SARS-CoV-2) 2-5 . We present the first pediatric case of SARS-CoV-2-associated anti-NMDAR Encephalitis. A post-infectious inflammatory condition following acute SARS-CoV-2, termed multisystem inflammatory syndrome in children (MIS-C), has been described. There have been two cases of anti-NMDAR encephalitis associated with SARS-CoV-2 in adults reported 5, 9 . At the time of publication, the authors are unaware of other cases of anti-NMDAR encephalitis with recent SARS-CoV-2 infection in pediatric populations. Herpes simplex virus-induced anti-N-methyl-d-aspartate receptor encephalitis: a systematic literature review with analysis of 43 cases Anti-N-methyl-D-aspartate receptor encephalitis associated with reactivated Epstein-Barr virus infection in pediatric patients: Three case reports Anti-NMDA receptor encephalitis in a psychiatric Covid-19 patient: A case report doi = 10.1016/j.pediatrneurol.2020.10.002 id = cord-347499-7q47jh14 author = Burrel, Sonia title = Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date = 2020-10-25 keywords = SARS summary = METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. In line with previous studies, different types of other respiratory viruses were detected together with SARS-CoV-2 among co-infected patients, including non-SARS-CoV-2 coronavirus, influenzavirus, adenovirus, rhinovirus/enterovirus, and parainfluenzavirus (Kim et al., 2020; Leuzinger et al., 2020; Lin et al., 2020a; Wee et al., 2020) . We evidenced the higher efficiency of LRT than URT samples for COVID-19 diagnosis, with a significantly higher rate of detection of SARS-CoV-2 and a 1 log-higher SARS-CoV-2 load for the majority of infected patients. In conclusion, the detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection, and LRT samples increases the accuracy of diagnosis of viral respiratory infections, including COVID-19. doi = 10.1016/j.ijid.2020.10.040 id = cord-305770-xygg4lxu author = Busetto, Gian Maria title = SARS-CoV-2 Infection and High-Risk Non-Muscle-Invasive Bladder Cancer: Are There Any Common Features? date = 2020-06-09 keywords = COVID-19; IL-6; NMIBC; SARS; cancer summary = Most severe cases of COVID-19 and high-risk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). Most severe cases of COVID-19 and highrisk NMIBC patients at higher recurrence and progression risk are characterized by innate and adaptive immune activation followed by inflammation and cytokine/chemokine storm (interleukin [IL]-2, IL-6, IL-8). When compared with COVID-19 patients without ARDS, patients with ARDS are generally older and have a higher proportion of comorbidities, and there are more observations of neutrophilia associated with lymphocytopenia, neutrophil-to-lymphocyte ratio (NLR) increase, increase in several inflammation indices (including interleukins, IL-2 and IL-6, tumor necrosis factor α, C-reactive protein and many other cytokines), elevated coagulation function and alteration of other organ dysfunction indices (liver, kidney, etc.) [4] . The following terms were the most commonly used: SARS-CoV-2, COVID-19, bladder cancer, risk factors, diabetes, obesity, aging, inflammation, cytokine, interleukin (IL), IL-6, smoking. doi = 10.1159/000509065 id = cord-297423-iefq0fh0 author = Bushman, Dena title = Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020 date = 2020-07-17 keywords = March; SARS summary = At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS) § who had negative test results for influenza and, in some instances, other respiratory pathogens. doi = 10.15585/mmwr.mm6928a5 id = cord-335172-5ig907on author = Busse, Laurence W. title = COVID-19 and the RAAS—a potential role for angiotensin II? date = 2020-04-07 keywords = ACE2; SARS summary = Likewise, patients on angiotensin-converting enzyme (ACE) inhibitors or angiotensin receptor blockers (ARB) could be at a greater risk due to the mechanism by which SARS-CoV-2 enters the cell. First, because it normally binds to ACE2 during its degradation and hydrolysis into angiotensin-(1-7) [11] , it may compete with the SARS-CoV-2 for the ACE2 receptor (Fig. 1) . Second, the binding of AngII to the AT1 receptor has been shown to cause internalization and downregulation of ACE2 through an ERK1/2 and p38 MAP kinase pathway in both in vitro animal and in vivo human models [12, 13] . However, to date, the link between ACE inhibitors and ARBs and severity of illness of SARS-CoV-2 infection is purely speculative. Ang-2, angiotensin II; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; ACE1, angiotensinconverting-enzyme 1; ACE2, angiotensin-converting-enzyme 2; H 2 O, water; Na + , sodium Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus doi = 10.1186/s13054-020-02862-1 id = cord-316658-zwxtbena author = Butler, S. E. title = Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals date = 2020-08-06 keywords = August; SARS summary = SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. In contrast to 168 observations in serum, nasal samples from subjects with severe disease showed little to no viral 169 neutralization, whereas subjects with elevated mucosal neutralization activity tended to have 170 experienced mild or moderate symptoms (Fig. 5b) . In contrast, the IgA-associated feature defined by nasal RBD-specific Abs binding to FcaR 226 ( Fig. 7C ) and its correlated function neutralization (Fig. 7D) were lowest in subjects with either mild or 227 severe disease, and elevated among those who recovered from moderate illness. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding 580 domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein 581 induces strong mucosal immune responses and provides long-term protection against 582 SARS-CoV infection doi = 10.1101/2020.08.05.20168971 id = cord-348384-8cvt1fo6 author = Butsashvili, M. title = Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population date = 2020-05-19 keywords = COV-2; SARS summary = This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus among Georgian population, including health care workers (HCWs). 20% of HCWs as well as other study subjects believe that SARS-COV-2 vaccine and medications do exist but are simply not available in Georgia. This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus and perceptions of preventive measures among the Georgian population, including health care workers (HCWs). We collected information on demographic data (age, gender, marital status, education, employment status), knowledge of symptoms and transmission modes of coronavirus, perceived differences between coronavirus and influenza, availability of antiviral medication and vaccination. In response to the question "Are you afraid of getting infected with SARS-COV-2?" almost half of study participants (46.3%) said "no." The majority of survey respondents correctly identified the transmission route and symptoms of the new coronavirus (96.9% and 98.0%, respectively). doi = 10.1101/2020.05.14.20101642 id = cord-296043-jc74soom author = Butterfield, T. R. title = Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica date = 2020-09-29 keywords = SARS summary = Serum samples collected [≥]14 days after onset of symptoms, or [≥]14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. For all assays examined, SARS-CoV-2 real-36 time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive 37 were significantly different for samples testing antibody positive versus negative. CoV-2 antibody assays: Roche Elecsys ® Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 53 preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. When moderate, severe and 109 critical disease was grouped, for each assay there was a significant association between this 110 group and testing antibody positive: Elecsys ® Anti-SARS-CoV-2 (χ 2 =19.03, p=0.001), Architect 111 SARS-CoV-2 IgG (χ 2 =15.72, p=0.003), Euroimmun SARS-CoV-2 IgA (χ 2 =21.11, p=0.007), 112 All rights reserved. doi = 10.1101/2020.09.27.20202655 id = cord-313275-znrvkmee author = Bwire, G. M. title = A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM date = 2020-06-12 keywords = COVID-19; SARS summary = title: A systematic review on the levels of antibodies in COVID-19 virus exposed but negative newborns: a possible vertical transmission of IgG/ IgM The research included studies on IgG/ IgM against SARS-CoV-2 among infants born to mother with COVID-19 published in English from December 1, 2019 onwards. On the other hand, natural passive immunity and detection of specific IgG and IgM antibodies to SARS-CoV-2 in infants born to COVID 19 confirmed mothers have been indicated in some studies where the newborns tested negative for the virus (8) . In this regard, a systematic review was conducted to determine the magnitude of IgG/ IgM in infants born to mothers with COVID-19 but tested negative for SARS-CoV-2. The median antibody levels detected in COVID-19 exposed newborns who tested negative for the virus after delivery but were born to mothers with COVID-19 were 75.49AU/mL (range: 7.25AU/mL-140.32AU/mL ) and for 3.79AU/mL (range: 0.16AU/mL-45.83AU/mL) (P = 0.0041) for anti-SARS-CoV-2 IgG and IgM, respectively. doi = 10.1101/2020.06.09.20127118 id = cord-343128-sh77c0af author = Bwire, G. M. title = Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis date = 2020-06-12 keywords = SARS summary = title: Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted. Recent study by Wang et al (6) using 1070 clinical specimens such as bronchoalveolar lavage fluid (BLF), fibrobronchoscope brush biopsy (FBB), sputum, nasal and pharyngeal swabs, urine, feces and blood collected from 205 patients revealed a dynamic profile with high detection rate of virus from lower respiratory tract (LRT) specimens, i.e., BLF and zero detection from urogenital tract specimen, i.e., urine. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2 from different types clinical specimens using a standard diagnostic test (qRT-PCR). A systematic review protocol was developed based on the question "What is the positivity rate for SARS-CoV-2 using qRT-PCR in different types of clinical specimens". doi = 10.1101/2020.06.11.20128389 id = cord-282817-vtzpf2wr author = Byrne, Hannah title = A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications date = 2013-10-02 keywords = CD3; SARS; antibody; bispecific; cell; figure summary = Despite significant positive clinical results, especially in the case of hematological malignancies, adverse clinical outcomes and animal studies have highlighted underlying limitations of mAbs. Accordingly, many strategies have been developed in order to improve the specificity and control the functions of antibodies. The BiTE format potentially overcomes several limiting factors relating to the biological activity of tumor-directed bsAbs. BiTEs combine the minimal binding domains (Fv fragments) of two different mAbs fused together by a short flexible linker that allows free rotation of the two arms, and thus facilitates optimal antibody:antigen interaction [28] . bsAbs are attractive in such assays because they simplify the detection steps and are currently used for the development of simple, rapid, and highly sensitive immunoassays for the detection of bacterial and viral infectious diseases and in cancer diagnostics. CD40-targeted adenoviral gene transfer to dendritic cells through the use of a novel bispecific single-chain Fv antibody enhances cytotoxic T cell activation doi = 10.1016/j.tibtech.2013.08.007 id = cord-318789-ylxh8vi2 author = Byrne, R. L. title = Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis. date = 2020-07-11 keywords = SARS summary = Samples were classified as RT-qPCR positive if both the internal extraction and the SARS-CoV-2 probes were detected at <40Ct. Virus copies/ml were quantified using the manufacturer''s positive control (1.67 Here we report for the first time the analytical sensitivity of saliva for the detection of SARS-CoV-2 compared to NT swab samples. In spiked saliva samples, SARS-CoV-2 can be detected with greater sensitivity in saliva compared to NT swabs by 100fold copies/ml, presumably due to the dilution factor of the amies transport medium. All saliva-positive, NT swab-negative samples in D2 (n=2) and D28 (n=1) reported low viral titre (<10 1 copies/ml) and are likely due to similar limitations outlined in the analytical sensitivity, a greater dilution factor of amies. This is in agreement with Wyllie et al., (2020) who reported that saliva had a greater sensitivity and was more likely to be constantly positive throughout the course of infection on a subset of COVID-19 hospitalised participants (n=29). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 participants than nasopharyngeal swabs doi = 10.1101/2020.07.09.20149534 id = cord-024649-y7nqz6vk author = Bösel, J. title = Neurologische Auswirkungen von COVID-19 date = 2020-05-11 keywords = COVID-19; Patienten; SARS; der; die; und; von summary = doi = 10.1007/s42451-020-00191-9 id = cord-258576-ywbyflas author = Bösmüller, Hans title = The evolution of pulmonary pathology in fatal COVID-19 disease: an autopsy study with clinical correlation date = 2020-06-30 keywords = COVID-19; IL-6; SARS; patient summary = We present the pulmonary findings in four cases of fatal COVID-19 with a spectrum of lung pathology reflecting disease course and duration, invasive therapies, and laboratory features. Based on conventional criteria, respiratory insufficiency therefore might be considered unlikely direct cause of death, but this case and recently published autopsy data indicate that pulmonary microvascular changes are an important and distinguishing feature of COVID-19 and may contribute to hypoxemia and acute cardiac insufficiency. Irrespective of the severity of pulmonary changes, however, all 4 patients showed SARS-CoV-2 RNA in lung tissues but failed to show detectable levels of viral RNA in other organs studied. The laboratory findings observed in patients 2 and 3 reflect common risk factors of fatal outcome, namely, lymphopenia; increased D-dimers; evidence of massive systemic inflammation including high levels of CRP, procalcitonin, and IL-6 during acute disease; and in the final stages massive ALT/AST elevation [1, 3, 4, 7, 11, 20] . doi = 10.1007/s00428-020-02881-x id = cord-287372-ya5uvoki author = Böszörményi, Kinga P. title = Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date = 2020-11-05 keywords = RNA; SARS; macaque summary = This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. doi = 10.1101/2020.11.05.369413 id = cord-304263-5kddk5fa author = C., Selvaa Kumar title = Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2 date = 2020-10-08 keywords = ACE2; CoV-2; SARS summary = In summary, nicotine showed a profound binding affinity for the sACE2-INS1 complex than the sACE2 alone paving for the clinical trials to validate its therapeutic efficacy as a bitter compound against the SARS-CoV-2 virulence. Research studies unveiled the interaction between the structural spike 1 (S1) protein of SARS-CoV-2 with the nicotinic acetylcholine receptors (nAChRs) that are likely to intervene with its biological function (20, 21) . Thus, the insilico study performed to unveil the nicotine''s urge for binding with the soluble ACE2 with or without SARS-CoV-2 in compliance with its interaction with the known human neuronal alpha4-beta2 nicotine-acetylcholine receptor (nN-AChR). We found the reported structural protein template of ACE2-SARS-CoV-2 complex with the enlisted PDB ID: 6VW1 (24) incomplete with numerous missing amino acid residues. Structural binding characteristics of nicotine with the soluble angiotensinconverting enzyme 2 (sACE2)-SARS-CoV-2 complex in the context of its interaction with the neuronal nicotinic acetylcholine receptor (nN-AChR). doi = 10.1016/j.toxrep.2020.10.002 id = cord-262428-erlmyzwn author = CABARKAPA, Sonja title = The psychological impact of COVID-19 and other viral epidemics on frontline healthcare workers and ways to address it: A rapid systematic review date = 2020-09-17 keywords = COVID-19; Health; SARS; psychological summary = The search strategy included terms for HCWs (e.g., nurse and doctor), mental health (e.g., wellbeing and psychological), and viral outbreaks (e.g., epidemic and pandemic). In terms of mental health impact of epidemics, HCWs represent a particularly vulnerable group due to the high risk of infection, increased work stress and fear of spreading to their families. The following search terms were used: ''health worker'', ''health care worker'', ''medical'', ''doctor'', ''nursing'', ''nurse'', ''allied health'', ''pandemic'', ''outbreak'', ''mental health'', ''mental illness'', ''psychiatric'', ''psychological'', ''coping'', ''psychosocial'', ''COVID-19'', ''coronavirus'', ''SARS'', ''MERS'' and ''Ebola''. 36, 51 At the early stages of the COVID-19 pandemic, a Wuhan study 28 found that 34.4% (342 of 994) of medical and nursing staff had mild mental health disturbances while 6.2% (62) had severe disturbances, while in another study 24 of 1,521 Chinese HCWs 14.1% had psychological abnormalities. Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 novel coronavirus disease outbreak: A cross-sectional study. doi = 10.1016/j.bbih.2020.100144 id = cord-326984-o27rp468 author = CHIEN, Jung‐Yien title = Temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome date = 2006-10-16 keywords = SARS; cap; patient summary = To improve understanding of the immuno‐pathological processes involved in lung injury associated with SARS, the temporal changes in cytokine/chemokine profiles in the sera of SARS patients were compared with those of patients with community‐acquired pneumonia (CAP), according to the degree of lung involvement. 5 In order to improve the understanding of the immuno-pathogenesis of SARS, an analysis of the dynamic changes in cytokine/chemokine profiles was undertaken in SARS patients who initially had a normal CXR, but who later progressed to typical manifestations of lung involvement. In this study, we investigated 14 SARS patients with initially normal CXR and 24 patients with non-SARS CAP, to clarify the association between temporal changes in cytokine/chemokine profiles and the severity of lung involvement during SARS. 15, 17, 18 Similar to the current study, many of the ''classic'' cytokines mediating inflammation in acute lung injury, 18 such as TNF-α and IFN-γ, were not reported to be significantly increased during SARS. doi = 10.1111/j.1440-1843.2006.00942.x id = cord-326169-delehk6x author = CJ Jorgensen, Sarah title = Baricitinib: A review of pharmacology, safety and emerging clinical experience in COVID‐19 date = 2020-06-15 keywords = JAK; SARS; covid-19 summary = The lack of reliable biomarkers to monitor patients'' immune status as illness evolves complicates deployment of immunosuppressive drugs like baricitinib. In this article we review available data on baricitinib with an emphasis on immunosuppressive and antiviral pharmacology, pharmacokinetics, safety and current progress in COVID‐19 clinical trials. In population PK analyses, body weight did not have a clinically meaningful 250 impact on baricitinib clearance, however obese RA patients have been reported to have lower 251 response rates. Thrombocytosis Accepted Article 499 treatment strategies aimed at attenuating both pathogen virulence and the pro-inflammatory 500 phenotype seen in the many critically ill patients with COVID-19. 5, 9, 12, 13, 20, 56 As detailed in this 501 review, baricitinib pairs immunosuppressive properties with antiviral activity making it a logical 502 candidate for further evaluation in COVID-19 clinical trials . Baricitinib therapy in 626 COVID-19: A pilot study on safety and clinical impact Impaired type I interferon activity and exacerbated 662 inflammatory responses in severe Covid-19 patients doi = 10.1002/phar.2438 id = cord-286341-16tghl48 author = CONCHA-MEJIA, A. title = CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia date = 2020-07-24 keywords = COVID-19; SARS summary = In Colombia, the first case was diagnosed on March 6, 2020 , with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Results: We included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). In this study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Bogota, Colombia, with special emphasis on the presence of gastrointestinal symptoms. doi = 10.1101/2020.07.24.20161604 id = cord-313829-pjscmen8 author = Caballero, A.E. title = COVID-19 in people living with diabetes: An international consensus date = 2020-07-06 keywords = COVID-19; PLWD; SARS; diabetes summary = The current clinical management of diabetes is a work in progress, requiring a shift in patient-provider interaction beyond the walls of clinics and hospitals: the use of tele-medicine when feasible, innovative patient education programs, strategies to ensure medication and glucose testing availability and affordability, as well as numerous ideas on how to improve meal plans and physical activity. It is difficult to predict but some indicators are available from the model of Harpreet In summary, while overall mortality due to COVID-19 is lower in India than in other countries, the elderly population, where most patients with diabetes, hypertension and CVD are concentrated, remains at high risk. Although it is clear that this option of care is not available to most people around the world, exploring how to improve the communication between providers and patients and families at home, in their own communities facing day to day challenges, may prove to be a more effective approach to managing the disease well beyond the COVID pandemic. doi = 10.1016/j.jdiacomp.2020.107671 id = cord-320331-wtxja5i9 author = Cabbab, Iris Louise N. title = Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection date = 2020-10-08 keywords = ACE2; Ang; COVID-19; RAAS; SARS summary = It is important to note that since the approach of this paper is to provide current knowledge on the anatomic, physiologic and molecular bases of anti-inflammatory drug and corticosteroid action on the RAAS, this paper will not demonstrate a systematic review or meta-analysis of current clinical evidence, but will only provide insight on the probable influences of the discussed pathways on early SARS-CoV-2 infection. A correspondence by Fang et al published at The Lancet this March discussed that hypertensives and diabetics taking ACE2 inhibitor (ACEi) and angiotensin receptor blocking (ARB) drugs may be at an increased risk of infection and severity by SARS-CoV-2 and COVID-19, respectively, citing three studies wherein diabetes and hypertension were major comorbidities of patients with severe COVID-19 and of non-survivors [20] . doi = 10.1016/j.virusres.2020.198190 id = cord-352668-qjlqsb2k author = Cabello, Francisco title = Consensus on Recommendations for Safe Sexual Activity during the COVID-19 Coronavirus Pandemic date = 2020-07-20 keywords = COVID-19; SARS; activity; sexual summary = Sexual activity offers numerous advantages for physical and mental health but maintains inherent risks in a pandemic situation, such as the current one caused by SARS-CoV-2. A group of experts from the Spanish Association of Sexuality and Mental Health (AESexSAME) has reached a consensus on recommendations to maintain lower-risk sexual activity, depending on one''s clinical and partner situations, based on the current knowledge of SARS-CoV-2. In all other cases (for those under quarantine, those with some clinical symptoms, health professionals in contact with COVID-19 patients, and during pregnancy), abstaining from coital/oral/anal sex, substituting it with masturbatory or virtual sexual activity to provide maximum protection from the contagion, and increasing the benefits inherent to sexual activity are recommended. Due to the ease of contagion and the lack of information about the possible transmission of SARS-CoV-2, a group of experts from the Spanish Association for Sexuality and Mental Health, covering the fields of sexology, psychiatry, psychology and medicine reached a consensus. doi = 10.3390/jcm9072297 id = cord-321235-h3w8827o author = Cabrera Alvargonzalez, Jorge Julio title = Pooling for SARS-CoV-2 control in care institutions date = 2020-10-12 keywords = Care; Homes; SARS summary = The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. The rationale in this study is to develop a new strategy based on initial individual identification of positive coronavirus cases in order to organize low prevalence clusters, followed by a serial pooling strategy testing of these clusters, in order to control areas free of virus circulation, allowing them to be fully operative. During the Coronavirus pandemic, SARS-CoV-2 prevalence was obtained by individually testing of 25, 386 people from 306 Galician Care Homes: 16,477 residents, 8599 workers and 310 not specified. A global SARS-CoV-2 seroprevalence of 5% in Spain [12] and a global viral prevalence around 3% at Care Homes reported in the present study, suggest that the number of people at risk of acquiring the infection continue to be very high. doi = 10.1186/s12879-020-05446-0 id = cord-256375-f4vrcjr1 author = Cabrera Muras, Antonio title = Bilateral Facial Nerve Palsy associated with COVID‐19 and Epstein‐Barr Virus co‐infection date = 2020-09-30 keywords = SARS summary = He was diagnosed with right peripheral facial palsy and was treated with prednisone 60 mg/24h with a tapering schedule. This patient presented with severe bilateral facial palsy, evidence of SARS-CoV-2 infection preceded by upper respiratory symptoms, and evidence of coinfection with EBV. EBV infection is responsible for 0.5%-7.5% of peripheral facial palsies, and up to 35% are bilateral [2, 3] . One of the reported patients had isolated bilateral facial palsy and was interpreted as a variant of GBS know as bifacial weakness with paresthesias [6] . SARS-CoV-2 infection should be suspected in patients with facial palsy or any suspicion of GBS in the times of COVID-19 pandemics since it may be the presenting feature in patients with mild respiratory symptoms. Bilateral facial nerve palsy associated with Epstein-Barr virus infection Bilateral facial nerve palsy associated with Epstein-Barr virus infection with a review of the literature Guillain-Barre Syndrome Associated with SARS-CoV-2 doi = 10.1111/ene.14561 id = cord-307208-tw6mwa5v author = Cabrera Villegas, Antonio title = [(18)F]-FDG PET/CT in oncologic patients with unsuspected asymptomatic infection with SARS-CoV-2 date = 2020-09-16 keywords = PET; SARS summary = The aim of this study was to retrospectively analyse the incidence of suspicious imaging findings of COVID-19 in PET/CT performed in asymptomatic patients referred to our Department with oncologic indications. Inclusion criteria were the following: (a) outpatients referred to Nuclear Medicine for whole-body PET/CT, (b) with [ 18 F]-FDG or [ 18 F]-fluorocholine, (c) referral was due only to oncologic indications, and (d) patients were asymptomatic for SARS-CoV-2 infection. The limitations in the diagnosis of COVID-19, together with the fact that most of the patients infected with SARS-CoV-2 are asymptomatic or present scarce symptoms, were the reason for initiating this retrospective study analysing patients scanned with PET/CT in which there were suspicious lung findings for SARS-CoV-2 infection. Our results confirm that the prevalence of SARS-CoV-2 infection is higher than the known figures, due to the relevant proportion of asymptomatic patients, some of them with lung disease, which can be diagnosed in a presymptomatic phase based on the incidental imaging findings in imaging procedures performed for completely different clinical indications. doi = 10.1007/s00259-020-04979-5 id = cord-316255-93srx4s7 author = Cacho, Pedro Muñoz title = Can climatic factors explain the differences in COVID-19 incidence and severity across the Spanish regions?: An ecological study date = 2020-10-13 keywords = SARS; UVR summary = Besides, temperature (February: rho = − 0.832; p < 0.001 and March: rho = − 0.904; p < 0.001), was the main climatic factor responsible for the infectivity of the coronavirus and directly contributed to a different spread of SARS-CoV-2 across the Spanish regions. To assess the possible influence on the infectivity of SARS-CoV-2 [9] [10] [11] , data on UVR (J/m 2 ), temperature (°C), and relative humidity (%) were also collected from the months with the highest infectivity (February and March 2020) to the peak of the pandemic in our country. Climatic parameters (temperature, UVR, and relative humidity) were considered as independent variables and epidemiological variables related to COVID-19 (cumulative incidence during the previous 14 days, total cases, newly diagnosed cases, hospital admissions, intensive care unit (ICU) admissions, and mortality, all referring to the period from 1 to 30 March 2020) were analyzed as dependent variables. doi = 10.1186/s12940-020-00660-4 id = cord-284873-m1ehdydr author = Cadegiani, Flavio A. title = Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 date = 2020-07-28 keywords = ACE2; COVID-19; SARS summary = title: Spironolactone: An Anti-androgenic and Anti-hypertensive Drug That May Provide Protection Against the Novel Coronavirus (SARS-CoV-2) Induced Acute Respiratory Distress Syndrome (ARDS) in COVID-19 At the onset of the COVID-19 pandemic, mortality following infection of severe acute respiratory coronavirus (SARS-CoV-2) was thought to be solely associated with aging and pre-existing conditions; however, as the pandemic ensued, several large scale epidemiological observations eluded to additional atypical risk factors, particularly hypertension, obesity, and male gender (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) . The Renin-Angiotensin-Aldosterone System (RAAS) has been shown to be central in COVID-19, since three of the key modulators of SARS-CoV-2 infectivity-angiotensin 1-7, ACE2, and AT1-belong to the RAAS, in addition to the TMPRSS2 expression (12) (13) (14) (15) (16) (17) (18) (19) . Abnormal ACE2 expression, angiotensin II and angiotensin 1-7 imbalance, and TMPRSS2 androgen-mediated overactivity seem to be key regulators of SARS-CoV-2 infectivity, in accordance with epidemiological observations of hypertension, obesity, and male sex as being major risk factors. doi = 10.3389/fmed.2020.00453 id = cord-284573-w0sk622m author = Caduff, Carlo title = What Went Wrong: Corona and the World after the Full Stop date = 2020-07-21 keywords = China; Italy; SARS; United; covid-19; health; pandemic summary = Published by a group of experts without peer review on an institutional website, the report compared Covid-19 with the great pandemic of 1918, which killed over 50 million people worldwide and suggested, without any evidence, that SARS-CoV-2 was "a virus with comparable lethality to H1N1 influenza in 1918." 1 Most frightening in all this was not so much the lethality of the SARS-CoV-2 virus but the license to rush forward with predictions, abandon basic standards of science, and make dramatic claims to scare people. This extreme and unprecedented blanket approach systematically imposed on entire populations was driven by a number of factors that variously prevailed in different countries across the world: a growing sense of panic, constant media sensationalism, deep authoritarian longings, increasing political pressure to contain the spread of the virus, disturbing accounts of overwhelmed hospitals unable to cope with the surge of patients, misleading mortality calculations, and, most importantly, a trust in the power of mathematical disease modeling. doi = 10.1111/maq.12599 id = cord-269563-2979u47a author = Caetano Silva-Filho, José title = The influence of ABO blood groups on COVID-19 susceptibility and severity: a molecular hypothesis based on carbohydrate-carbohydrate interactions date = 2020-08-02 keywords = ABO; ACE2; COVID-19; SARS; cell summary = Based on this survey, we hypothesize that the correlation between the ABO blood system and susceptibility to SARS-CoV-2 infection can be presumably explained by the modulation of sialic acid-containing receptors distribution on host cell surface induced by ABO antigens through carbohydrate-carbohydrate interactions, which could maximize or minimize the virus Spike protein binding to the host cell. to cell receptors, as well as (ii) the biochemical aspects of ABO blood group system and its association to infection and some circulatory conditions, we hypothesize that the influence of blood type on COVID-19 severity relies on the differential clustering of glycoproteins receptors to SARS-CoV-2 on host cell surface, induced by ABH antigens through carbohydrate-carbohydrate interactions with the glycan portions of these receptors, which could modulate virus binding to the target cell. doi = 10.1016/j.mehy.2020.110155 id = cord-354458-o2kcd085 author = Caffo, Orazio title = On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 date = 2020-06-18 keywords = SARS summary = title: On the relationship between androgen-deprivation therapy for prostate cancer and risk of infection by SARS-CoV-2 prostate cancer (PC) and risk of infection by SARSCoV-2 through a population-based study of patients with laboratory-confirmed SARS-CoV-2 infection from 68 hospitals in Veneto (1) . To further investigate this potential relationship, we identified all of the cases of COVID-19 that have occurred in metastatic castration-resistant PC (mCRPC) and metastatic castration-sensitive PC (mCSPC) patients treated in most of the high-volume referral medical oncology departments in northern Italy. The 19 high-volume medical oncology departments contributing to this study were treating a median of 80 metastatic PC patients each (range 48-230) for a total of 1,949. On the contrary, we identified a homogenous population of consecutive mCSPC/mCRPC patients treated in most of the high-volume referral medical oncology departments in northern Italy. Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (n=4532) doi = 10.1016/j.annonc.2020.06.005 id = cord-323940-ubazgvov author = Cafiero, Concetta title = Pharmacogenomics and Pharmacogenetics: In Silico Prediction of Drug Effects in Treatments for Novel Coronavirus SARS-CoV2 Disease date = 2020-10-13 keywords = SARS; clinical; covid-19; drug; genetic; patient; treatment summary = Recently, pharmacogenomics (the effects of a single genetic marker) and pharmacogenetics (the collective influence of variability across the genome to modulate an individual''s drug response) have received great attention for their abilities to provide a new way to select drugs for personalized therapy (optimal dosing for maximizing drug efficacy or minimizing the risk of toxicity). 35 Search terms were "Covid-19", "novel coronavirus", "SARS-CoV2", "pharmacogenetics", "treatment/s", "adverse side effects", "therapy", "lung", "ocular", "pulmonary infection", "drugs", "drug response", "virus", "candidate drugs", "potential inhibitors", "protease inhibitors", "personalized medicine", "individual therapy", "pneumonia", "ACE", "heparin", "vasculitis", "conjunctivitis", "rhinitis", "hematological complication" and "main metabolic routes", either alone or in combination. Drugs in use as routine therapy or in clinical trials for Covid-19 include steroids and antiviral and biological humanized neutralizing antibodies against some proinflammatory cytokines, such as IL1, IL6, IFN, and TNFα, in addition to supportive measures and symptomatic treatment, according to the severity of the disease. doi = 10.2147/pgpm.s270069 id = cord-291052-nstfe15a author = Cag, Yasemin title = A novel approach to managing COVID-19 patients; results of lopinavir plus doxycycline cohort date = 2020-08-27 keywords = SARS; patient summary = This manuscript aims to present a treatment algorithm we applied to manage COVID-19 patients admitted to our hospital. We administered hydroxychloroquine plus doxycycline to mild cases (isolated at home) for 3 days and lopinavir plus doxycycline to moderate and severe cases (hospitalized) for 5 days. Second, moderate to severe cases were hospitalized and prescribed with a regimen of lopinavir plus doxycycline plus ceftriaxone for 5 days. We hospitalized moderate to severe cases and administered lopinavir combined with doxycycline and ceftriaxone to 343 patients, among whom 161 had positive PCR test results (161/343, 46.9%). We administered hydroxychloroquine to mild cases isolated at home, lopinavir plus doxycycline to hospitalized moderate to severe cases, and favipiravir in the salvage treatment. We concluded that home isolation of mild cases is an effective means to manage the burden of disease, while lopinavir plus doxycycline is an alternative to current treatment regimens for COVID-19. doi = 10.1007/s10096-020-04016-1 id = cord-317246-8c7d5ynz author = Cagetti, Maria Grazia title = Could SARS‐CoV‐2 burst the use of Non‐Invasive and Minimally Invasive treatments in paediatric dentistry? date = 2020-08-03 keywords = SARS; treatment summary = The non-invasive treatment includes the non-restorative cavity control that manages non-cavitated and cavitated active caries lesions making them cleanable and promoting their arrest through the use fluoride vehicles only. Non-operative caries treatment is mostly recommended for decayed primary teeth, but may represent a suitable alternative also for permanent teeth of children with dental anxiety or disabilities, who offer insufficient collaboration for the traditional restorative treatment. 27 The non-invasive treatment and the minimally invasive treatment are often recommended in controlling and treating dental caries in children; however, even though dentists seem to know the advantages of these strategies, the traditional caries removal and restoration therapy are still preferred. 29 In conclusion, caries treatment using the non-invasive or the minimally invasive treatments is desirable, especially since the transmission risk of SARS-CoV-2 is potentially higher in the dental environment. doi = 10.1111/ipd.12679 id = cord-266888-ryvk6mte author = Cai, Guoshuai title = Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2 date = 2020-06-15 keywords = ACE2; SARS summary = In addition, we analyzed three microarray data sets of samples derived from healthy subjects and patients with chronic obstructive pulmonary disease (COPD), including small airway epithelium samples from current smokers (from GSE5058, n = 26 [7] ), bronchial airway epithelium samples from current and former smokers (GSE37147, n = 238 [9] ), and lung samples from white patients (n = 438) who underwent lung cancer surgery at the Institut Universitaire de Cardiologie et de Pneumologie de Québec (10). We identified upregulation of pulmonary ACE2 gene expression in ever-smokers compared with nonsmokers in all data sets, irrespective of tissue subset or COPD status (Figure 1) . The significant effect of smoking on ACE2 pulmonary expression identified in this study may suggest an increased risk for viral binding and entry of SARS-CoV and SARS-CoV-2 in lungs of smokers. We further evaluated the effect of smoking on ACE2 pulmonary expression in single bronchial epithelial cells from six never-smokers and six current smokers. doi = 10.1164/rccm.202003-0693le id = cord-312632-g4250q6l author = Cai, Xiaofang title = Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children date = 2020-05-12 keywords = COVID-19; SARS; patient summary = Five patients with non-respiratory symptoms as the first manifestation were hospitalized from the emergency department, and were later confirmed to have COVID-19, between 23 January and 20 February 2020, at the Wuhan Children''s Hospital. Severe COVID-19 was defined when the pediatric patients Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; WHO, World Health Organization; ICTV, the International Committee on Taxonomy of Viruses; MERS-CoV, Middle East respiratory syndrome coronavirus; CT, computed tomography; PICU, pediatric intensive care unit; NK, natural killer; CRRT, continuous renal replacement therapy; CRP, C-reactive protein; PCT, procalcitonin; PT, prothrombin time; APTT, activated partial thromboplastin time; IL, interleukin; EEG, electroencephalogram; ACE2, angiotensin converting enzyme 2. This might explain why case 3, who was admitted with head trauma but with no respiratory symptoms, tested positive for SARS-CoV-2 nucleic acid and his lung CT scan showed pneumonia. doi = 10.3389/fped.2020.00258 id = cord-330198-pwkxgbxk author = Cai, Xiaofang title = Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19 date = 2020-10-27 keywords = SARS; case; covid-19 summary = All febrile or suspected COVID-19 cases were referred to the fever clinic, and the others-including critically ill children-were received by the emergency department after pediatric 5-level triage. We retrospectively analyzed the clinical data of these children admitted from the emergency department to characterize thoroughly the features of COVID-19 that can be evaluated to distinguish this novel disease from pneumonia caused by other pathogens in pediatric patients. Owing to the parents'' fear that their children were infected with SARS-CoV-2, the median time from symptom onset to hospital admission was shorter for confirmed COVID-19 cases (2.0 days) than that for suspected COVID-19 cases (3.0 days) and non-COVID-19 cases (4.0 days) (P < 0.05). Moreover, serologic testing can serve as an important adjunctive method for COVID-19 diagnosis, especially when the patient is highly suspected of SARS-CoV-2 infection but is found to be negative by nucleic acid testing. doi = 10.1007/s11684-020-0820-7 id = cord-331897-4wnoa4l7 author = Cai, Yi title = Temporal event searches based on event maps and relationships() date = 2019-09-25 keywords = SARS; event; relationship; tem summary = Experiments conducted on a real data set show that our method outperforms the baseline method Event Evolution Graph (EEG), and it can help discover certain new relationships missed by previous methods and even by human annotators. Although some work has been done to find and link incidents in news stories [4, 5] or discover event evolution graphs [6, 7] , this scholarship has only focused on time sequences and content similarity between two component events to identify the dependence relationships. To the best of our knowledge, this is the first piece of work that (1) formalizes and handles the event search problem by analyzing all temporal, content dependence and event reference relationships between events to construct an overall picture of the event''s evolution; and (2) measures the importance of events based on the interrelationships of events. doi = 10.1016/j.asoc.2019.105750 id = cord-303517-8971aq02 author = Cajamarca-Baron, Jairo title = SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression date = 2020-10-16 keywords = COVID-19; China; CoV-2; Coronavirus; SARS; infection; patient summary = 27, 28 Among other comorbidities, chronic kidney disease is associated with in-hospital mortality, as are cancer and cerebrovascular disease, demonstrated through two meta-analyses that included over fifteen thousand patients ( Table 2) ; studies suggest that superficial fungal infections and psoriasis confer vulnerability to COVID-19; a body mass index (BMI) > 40 kg/m2 is an independent risk factor for complications from the infection; and there are discouraging results regarding underlying neurological disease and SARS-CoV-2. It is even possible that such disease-modifying therapies and their immunosuppressive effect may play a protective role during 19-COVID infection by preventing or dampening hyperimmune activity that, in some cases, could lead to clinical deterioration; there is even a report of a patient with primary progressive multiple sclerosis receiving treatment with ocrelizumab and becoming infected with SARS-CoV-2, in the context of lymphopenia and hypogammaglobulinema expected for this type of treatment, without generating major clinical complications, this hypothesis is obviously limited for now only to academic deductions and limited information. doi = 10.1016/j.reumae.2020.08.001 id = cord-295257-iguhy1z8 author = Calcagnile, Matteo title = ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date = 2020-04-24 keywords = ACE2; Fig; SARS; Spike summary = SARS-CoV-2 and respiratory syndrome corona virus (SARS-CoV) Spike proteins share very high phylogenetic similarities (99%), and, indeed, both viruses exploit the same human cell receptor namely angiotensin-converting enzyme 2 (ACE2), a transmembrane enzyme whose expression dominates on lung alveolar epithelial cells 6, 15, 16 . In this study we have used a combination of in silico tools to analyze the possible impact of ACE2 single-nucleotide polymorphisms (SNPs) on the interaction with SARS-CoV-2 Spike glycoprotein. Results indicate that some residues of the ACE2 interface, which are involved in the interaction with SARS-CoV-2 Spike glycoprotein can actually fluctuate (Fig. 5cd ). Indeed, in the rodent blockade of the renin-angiotensin-aldosterone system limits the acute lung injury induced by the SARS-CoV-1 spike protein 49 , suggesting that if ACE2 function is preserved (because of increased baseline expression, as especially seen in pre-menopausal women), clinical course of infection might be less severe. doi = 10.1101/2020.04.23.057042 id = cord-316930-0s7k9guq author = Caldas, Lucio Ayres title = Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy date = 2020-09-30 keywords = Fig; SARS; cell summary = title: Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2. At the same time, and with a MOI of 1, viruses that egressed from a previous cycle of infection were observed during the process of attachment to the cell plasma membrane ( Fig. 2A) . To approach SARS-CoV-2/cell interactions, we investigate several steps of virus infection in Vero cells at 2 and 48 hpi by SEM. These sites were appropriate to register the attachment of SARS-CoV-2 particles ( Fig. 2A ) similar to transmission electron microscopy images of the same early step of SARS-CoV infection of Vero cells 28 . Drastic vacuolization due to viral infection was previously described for other RNA viruses including SARS-CoV 20,32 . doi = 10.1038/s41598-020-73162-5 id = cord-272179-wvw5mmy3 author = Calderaro, Adriana title = Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date = 2020-10-02 keywords = SARS; respiratory summary = title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children doi = 10.1016/j.ijid.2020.09.1473 id = cord-277640-vy7ex5lv author = Calderaro, Adriana title = SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date = 2020-05-14 keywords = SARS summary = The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. doi = 10.1016/j.ijid.2020.05.035 id = cord-280671-0b1qcdwk author = Calderone, Alba title = Selective Estrogen Receptor Modulators in COVID-19: A Possible Therapeutic Option? date = 2020-07-15 keywords = IL-6; SARS summary = In particular, susceptibility to SARS-CoV-2 infection is almost similar in both genders, but higher severity and mortality are observed in male patients (Wenham et al., 2020) . The previous severe acute respiratory syndromes caused by SARS-CoV and MERS-CoV were often associated with rapid viral replication, huge infiltration of inflammatory cells, and excessive production of proinflammatory cytokines (cytokine storm syndrome), leading to lung injury and respiratory distress syndrome . Moreover, pro-inflammatory cytokines, including IL-1b and IL-6, are directly induced by SARS-CoV-2 by interaction between viral components (probably nucleocapsid proteins) and toll like receptors of the host cells. Besides their potential effects on proinflammatory cytokine expression (mediated by ERs), some SERMs seem to play broader roles in inhibiting viral replication by ER-independent mechanisms. Anti-inflammatory effect of selective estrogen receptor modulators (SERMs) in microglial cells doi = 10.3389/fphar.2020.01085 id = cord-320063-n9qzbnup author = Calender, Alain title = Modeling Potential Autophagy Pathways in COVID-19 and Sarcoidosis date = 2020-08-10 keywords = COVID-19; SARS summary = Of note, SARS-CoV2 protein has a high affinity for human ACE2, a membrane-bound peptidase highly expressed in the heart, lungs, digestive and renal tracts; this molecular interaction leads to a membrane fusion process and further formation of syncytia with multinucleated alveolar epithelial cells ( Figure 1 ) [7] . Different cellular receptors such as TLR3 (Toll Like Receptor 3) and RIG-1 (Retinoic Acid Inducible Gene 1) -closely related to autophagy activation in mammalian granulocyte and macrophage models -have been implicated in innate immunity response to RNA virus infections -e.g. Coronavirus, Measles, Hepatitis viruses, and Influenza virus [10] . These clinical observations raise the question of what the sensitivity of patients with sarcoidosis to respiratory viral disease is, such as that induced from SARS-CoV2 infection (COVID-19)presently being explored in several international projects [6] . doi = 10.1016/j.it.2020.08.001 id = cord-328064-7owd28rr author = Callahan, Cody J. title = Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck date = 2020-07-23 keywords = Fig; SARS; prototype; swab summary = We tested PCR compatibility by placing the swab head-downward after breaking it off at the break point, when present (as in a typical NP swab collection), in 3 ml of modified CDC VTM (Hanks'' balanced salt solution containing 2% heat-inactivated fetal bovine serum [FBS], 100 g/ml gentamicin, 0.5 g/ml amphotericin B [Fungizone], and 10 mg/liter phenol red [15] ) overnight to allow any PCR-inhibitory material to leach into the medium, spiking 1.5 ml with 200 copies/ml of control SARS-CoV-2 amplicon target (representing 2 times the limit of detection on our system), vortexing, and testing using the Abbott RealTime SARS-CoV-2 assay on an Abbott m2000 RealTime system platform (16) , following the same protocol as for clinical testing (37 cycles, with a cycle threshold [C T ] of Յ31.50 being reported as positive). Control and prototype swabs were placed in separate vials of VTM and transported to the BIDMC Clinical Microbiology Laboratories, where each sample was tested on the Abbott m2000 SARS-CoV-2 RT-PCR platform per the standard clinical protocol. doi = 10.1128/jcm.00876-20 id = cord-346389-gbmnoo84 author = Callender, Lauren A. title = The Impact of Pre-existing Comorbidities and Therapeutic Interventions on COVID-19 date = 2020-08-11 keywords = COVID-19; China; MERS; SARS; disease; patient summary = Here, we review immune dysfunction in response to SARS-CoV-2 infection and the impact of pre-existing comorbidities on the development of COVID-19. Furthermore, cardiovascular complications such as thromboembolic events, myocarditis, acute coronary syndrome, arrythmia, cardiogenic shock and heat failure, have been documented in COVID-19 patients without prior cardiovascular disease (71), demonstrating a significant impact of SARS-CoV-2 infection on the heart. As infection with SARS-CoV-2 results in an acute respiratory disease that can progress to ARDS, respiratory failure and potentially even death, it is reasonable to speculate that patients with pre-existing respiratory disease would be at increased risk of severe COVID-19. Consequently, it has been proposed that liver damage associated with severe COVID-19 patients is due to dysregulated innate immunity against SARS-CoV-2, or hepatoxicity in response to treatments, rather than pre-existing liver disease. Therefore, the underlying pathogenesis of chronic kidney disease may increase vulnerability to hyperinflammation and cytokine storm upon SARS-CoV-2 infection, resulting in severe COVID-19. doi = 10.3389/fimmu.2020.01991 id = cord-279346-7del8d2p author = Callendret, Benoît title = Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date = 2007-07-05 keywords = CTE; Fig; RNA; SARS; WPRE; dna summary = title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared. doi = 10.1016/j.virol.2007.01.012 id = cord-257600-0plhquk9 author = Calles, Antonio title = Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date = 2020-09-16 keywords = COVID-19; PCR; SARS; cancer; patient summary = Differences in health-care systems, in the incidence and prevalence of SARS-CoV-2 infection by geographic regions, and patient access to intensive support care -including MVand treatment with antivirals or anti-IL6/IL1 agents may ultimately influence outcomes in patients with lung cancer affected by COVID-19. We aimed to describe the clinical characteristics of lung cancer patients with COVID-19 attended in a tertiary hospital in Madrid, one of the most hit regions by coronavirus in the world so far, and analyze factors associated with worse outcome, including type of treatment receiving at the time of COVID-19 diagnosis. We performed SARS-CoV-2 RT-PCR to every suspicious case and included all lung cancer patients attended at our hospital (emergency room, hospitalization, ambulatory office, day care area). Data from Wuhan, in China, showed that active cancer treatment received in the 14 days before SARS-CoV-2 infection had an increase on the risk of severe outcomes of COVID-19 (HR 4.079, 95%CI, 1.086-15.322; p = 0.037) (9) . doi = 10.3389/fonc.2020.01777 id = cord-278678-ivye1qao author = Calvez, R. M. title = Molecular detection of SARS-CoV-2 using a reagent-free approach date = 2020-05-02 keywords = SARS summary = Optimisation of the heat-treatment method and inhibitory properties of UTM In a preliminary study to evaluate the best assay conditions, a range of SARS-CoV-2-positive and negative samples was selected and heat-treated at different temperatures and for different times. Each heat-treated sample was then subject to SARS-CoV-2 testing using our in-house assay derived from the CDC resource website (targeting the N-gene and using the TaqMan® Fast Virus 1-Step RT-qPCR kit from ABI). As shown in table 2 below, the ABI TaqMan® One-Step RT-qPCR mix systematically failed to detect SARS-CoV-2 in swab samples resuspended in UTM (COPAN swabs) even in the presence of viral loads greater than 1×10 6 copies/mL (003850 and 003862). Although heat-treatment of respiratory samples prior to RT-qPCR showed an attractive methodology compared to a conventional nucleic acid extraction method, the addition of an internal control is critical for quality control and successful detection of this virus if present in the patient samples. doi = 10.1101/2020.04.28.20083626 id = cord-354407-zzxjv666 author = Campanacci, Valérie title = Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date = 2004-06-07 keywords = Nsp9; RNA; SARS summary = title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. The crystal structure of the main (or 3CL) protease of transmissible gastroenteritis virus, a related coronavirus, has been determined and was used to construct a model of the SARS-CoV 3CL protease, facilitating future drug design against this important target (Anand et al., 2003) . In the related mouse hepatitis virus, which is a group 2 coronavirus, the SARS-CoV Nsp9 corresponds to a 12 kDa cleavage product (P1a-12) that is found preferentially in the perinuclear region of infected cells, where it co-localizes with other components of the viral replication complex (Bost et al., 2000) . doi = 10.1107/s0907444903016779 id = cord-270049-54t3w94z author = Campione, Elena title = Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date = 2020-08-17 keywords = MOI; SARS summary = We performed a randomized, prospective, interventional study assessing the role of oral and intra-nasal lactoferrin to treat mild-to-moderate and asymptomatic COVID-19 patients to prevent disease evolution. The antiviral activity of lactoferrin related to its binding to SARS-CoV-2 and cells and protein-protein docking methods, provided the direct recognition between lactoferrin and spike S, thus hindering the spike S attachment to the human ACE2 receptor and consequently virus entering into the cells. 222 We performed the same analysis over the evaluated human lactoferrin (hLF)-Spike complex, 223 obtaining a binding pose superimposable to that observed for the bovine protein (Fig. 5B) . Clinical trial 397 We performed a randomized, prospective, interventional study to assess the efficacy of a liposomal Blood parameters obtained at T0 in COVID-19 group and control group were compared using t-test. doi = 10.1101/2020.08.11.244996 id = cord-301590-70qmpccs author = Campos, António title = The Paradigm Shift of Ophthalmology in the COVID-19 Era date = 2020-09-14 keywords = COVID-19; SARS; patient summary = CONCLUSION: It was possible to keep the ophthalmological activity during the pandemic outbreak due to the existence of a pre-scheduled fixed regimen for IVI and to the availability of personal protective equipment. We are facing a different sort of challenge now: how to accommodate the usual huge number of patients previous to the COVID-19 outbreak in the waiting rooms, while respecting the new demands from the healthcare authorities to reduce the number of waiting patients to a half or one-third. 9 Issues such as the use of personal protective equipment, the size of waiting rooms, ventilation, adherence to disinfection protocols, choose of whom to treat based on the disease natural evolution and the need to prioritize treatment visits over monitoring visits, were addressed recently. Symptomatic patients, SARS-CoV-2 positive patients and contacts, were postponed until they were RT-PCR negative, except for emergency surgeries that were performed in a COVID-dedicated OR (one room with negative pressure and special requirements 12 doi = 10.2147/opth.s267427 id = cord-331465-humpwwk2 author = Canaday, David H title = On setting expectations for a SARS-CoV-2 Vaccine date = 2020-06-04 keywords = SARS summary = Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials doi = 10.1093/cid/ciaa726 id = cord-278106-ev1nx60h author = Cancarevic, Ivan title = Coronavirus Disease 2019 (COVID-19) in Cancer Patients date = 2020-04-26 keywords = SARS; patient summary = The Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the most talked-about clinical entity in early 2020. Management presents its own set of challenges, including but not limited to, deciding whether postponing cancer treatment until the infection resolves is going to benefit the patient and how to organize all aspects of patient care when social contact is as limited as it is for patients newly diagnosed with COVID-19. found that the prevalence of cancer among patients infected with SARS-CoV-2 (COVID-19) was higher than in the general population [12] . We would strongly encourage clinicians to keep reporting any cases of cancer patients infected with SARS-CoV-2, their management, and the outcome in order to further our understanding of this complex issue. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges The treatment and outcome of a lung cancer patient infected with SARS-CoV-2 doi = 10.7759/cureus.7835 id = cord-265262-r01u4jr6 author = Cannarella, Rossella title = Systemic effects of the hormonal treatment of male hypogonadism with preliminary indications for the management of COVID-19 patients date = 2020-10-13 keywords = SARS; TRT; man; patient; testosterone summary = Furthermore, recent findings on novel coronavirus disease (COVID-19) epidemiology have shown a greater mortality in male compared with female patients and a role of T in promoting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection of the host cells has been demonstrated. To accomplish the aims of the study, we performed a search on PubMed, Scopus, Ovid and Science Direct, and the following keywords were used: hypogonadism, TD, TRT, blood pressure, hypertension, ischemic heart disease, heart failure, stroke, obesity, insulin, diabetes, metabolic disorders, prostatic hyperplasia, prostate cancer, COVID-19, and SARS-CoV2. 45 In 2017, a meta-analysis including 39 randomized controlled trials (RCTs) and 10 observational studies with a total of about 5500 patients did not find any significant association between TRT and myocardial infarction, stroke, or mortality, even if the quality of the evidence was low. doi = 10.1177/2042018820966438 id = cord-203232-1nnqx1g9 author = Canturk, Semih title = Machine-Learning Driven Drug Repurposing for COVID-19 date = 2020-06-25 keywords = SARS; drug; sequence; virus summary = Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. doi = nan id = cord-309319-si5c14e8 author = Cao, Chunxiang title = Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China date = 2016-08-15 keywords = BME; China; SARS; TRF summary = Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The Bayesian Maximum Entropy (BME) approach of modern geostatistics incorporates higher-order statistical estimation for space-time epidemic phenomena and has shown more accurate mapping results than those derived from linear kriging geostatistics [19] . BME provides an effective stochastic method, based on a cogent theoretical and technological strategy, to analyze relationships of SARS outbreaks in the composite space-time domain. (2) BME considers spatial heterogeneity in SARS outbreaks, which broadens the traditional epidemic research field from the temporal to space-time domain. In the case of the SARS outbreaks, we used the observations to explore general structural characteristics of the SARS S/TRF, that is, the existence of mean (or surface) trends in the space-time domain, and to explore the underlying temporal and spatial structure of the S/TRF with suitable covariance functions. doi = 10.1155/2016/7247983 id = cord-326427-06djb0sd author = Cao, Dongmei title = Vaginal delivery in women with COVID-19: report of two cases date = 2020-10-02 keywords = COVID-19; SARS summary = Because of the positive result of the maternal swabs for SARS-CoV-2 obtained on the 2nd day after sampling, we transferred the mother to the designated hospital and followed up with her by telephone interviews. Although the nucleic acid test for SARS-CoV-2 of the second patient was negative on February 29, the result was positive Delayed cord clamping and skin-to-skin contact between the mother and infant were not permitted in either case. The pregnant woman in case 2 had the typical manifestations of COVID-19, including cough, lymphopenia, and abnormal chest CT images, and her infant''s nasopharyngeal swab tested negative for SARS-CoV-2. The two cases in our study showed that there is still insufficient evidence supporting maternal-fetal vertical transmission of COVID-19 in late pregnancy, and there is no evidence that vaginal delivery would increase the possibility of neonatal infection. In conclusion, there is still insufficient evidence supporting maternal-fetus vertical transmission of COVID-19 for pregnant women in late pregnancy, and vaginal delivery may not increase the possibility of neonatal infection. doi = 10.1186/s12884-020-03281-4 id = cord-273613-cpiveo7j author = Cao, Xia title = Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date = 2020-09-29 keywords = SARS; STI-1499; STI-2020; Spike summary = Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Affinity maturation of STI-1499 resulted in identification of STI-2020, an antibody with a 35-fold increased affinity for the SARS-CoV-2 Spike receptor-binding domain (RBD) leading to a greater than 50-fold increase in virus neutralization potency against live WA-1/2020 and 2020001 viruses in vitro. In this study, we detail the initial discovery and profiling of a SARS-CoV-2 nAb isolated from a phage display antibody library derived from the B-cell repertoire of over 600 healthy normal individuals. Candidate nAbs were characterized for binding of Spike S1 subunit and neutralization of related clinical SARS-CoV-2 isolates. doi = 10.1101/2020.09.27.316174 id = cord-347030-yx3j6373 author = Cao, Xuetao title = COVID-19: immunopathology and its implications for therapy date = 2020-04-09 keywords = COVID-19; SARS summary = Most patients with COVID-19 exhibit mild to moderate symptoms, but approximately 15% progress to severe pneumonia and about 5% eventually develop acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure 1, 2 . Convalescent plasma containing neutralizing antibodies has been used to treat a small number of patients with severe disease, and preliminary results show clinical improvement in 5 of 5 critically ill patients with COVID-19 who developed ARDS 8 . High levels of pro-inflammatory cytokines may lead to shock and tissue damage in the heart, liver and kidney, as well as respiratory failure COVID-19: immunopathology and its implications for therapy Xuetao Cao 1, 2 Severe coronavirus disease 2019 (COVID-19) is characterized by pneumonia, lymphopenia, exhausted lymphocytes and a cytokine storm. In addition to the cytokine-based pathology in patients with severe COVID-19, complement activation has also been observed, indicating that complement inhibitors, if used at an early stage of the infection, may attenuate the inflammatory damage. doi = 10.1038/s41577-020-0308-3 id = cord-348713-tucolje2 author = Cao, Yanan title = Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations date = 2020-02-24 keywords = ACE2; SARS summary = Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations Yanan Cao 1 , Lin Li 1 , Zhimin Feng 1 , Shengqing Wan 1 , Peide Huang 1 , Xiaohui Sun 1 , Fang Wen 1 , Xuanlin Huang 1 , Guang Ning 1 and Weiqing Wang 1 Therefore, genetic analysis of expression quantitative trait loci (eQTLs) 8 and potential functional coding variants in ACE2 among populations are required for further epidemiological investigations of 2019-nCoV/SARS-CoV-2 spreading in East Asian (EAS) and other populations. To systematically investigate the candidate functional coding variants in ACE2 and the allele frequency (AF) differences between populations, we analyzed all the 1700 variants (Supplementary Table S1) in ACE2 gene region from the ChinaMAP (China Metabolic Analytics Project, under reviewing) and 1KGP (1000 Genomes Project) 9 databases. doi = 10.1038/s41421-020-0147-1 id = cord-277491-q18b88lm author = Cao, Ying-Li title = Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date = 2011-02-11 keywords = SARS; gene summary = title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus Nucleocapsid (N) protein of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a major pathological determinant in the host that may cause host cell apoptosis, upregulate the proinflammatory cytokine production, and block innate immune responses. In the current study, we compared the N gene sequences derived from 16 different isolates of SARS-CoV and selected three novel siRNA targeting sites in the N gene, including one targeting the 3'' terminus of the gene. Overall, the above results provide strong evidence to show that all three novel siRNAs (si-N213, si-N863 and si-N1240) are specific and effective inhibitors to block the isolated SARS-CoV N gene expression. Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles Small interfering RNA effectively inhibits the expression of SARS coronavirus membrane gene at two novel targeting sites doi = 10.3390/molecules16021544 id = cord-272986-ebgusf3o author = Cao, Yipeng title = Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date = 2020-05-17 keywords = SARS; ion; protein summary = title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel. We tried to use potential mean force (PMF) to reveal the permeability of different physiological ions and water molecules in the pores of the E protein pentamer. Figure 3A shows the PMF of ions and water molecules permeating through the SARS-CoV-2 E protein pentamer pore. The free energy calculation of the ions permeating through the SARS-CoV-2 pentameric E protein channel strongly suggests that the pore has selection permeability for monovalent ions. doi = 10.1101/2020.05.17.099143 id = cord-266313-b518n9dx author = Cao, Yu-chen title = Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence date = 2020-04-02 keywords = COVID-19; Ebola; MERS; SARS summary = China has also taken immediate action to put remdesivir into clinical trials with the purpose of applying it into clinical therapeutics for Corona Virus Disease 2019 (COVID-19). When we set our sights on the broad-spectrum antiviral drugs, we found that a drug unlisted, remdesivir, has demonstrated strength in trials related to MERS-CoV and Ebola virus infection. This article starts from the structure, immunogenicity, and pathogenesis of infection of the SARS-CoV-2, and then analyzes the feasibility of conducting trials and putting into clinical use of COVID-19 from the pharmacological characteristics and successful cases of remdesivir. Remdesivir (GS-5734) is a nucleoside analogues drug (Fig. 3B ) with extensive antiviral activity and effective treatment of lethal Ebola and Nipah virus infections in nonhuman primates [21] . The need of treatment on COVID-19 is urgent, so if the results of clinical trials prove it has the potential to benefit the treatment, according to China''s "Compassionate Use", remdesivir will be more immediately used in patients with severe illness. doi = 10.1016/j.tmaid.2020.101647 id = cord-281393-96j70n2z author = Capai, L. title = Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020. date = 2020-09-30 keywords = ELISA; SARS; September summary = A minimum sample size of 1814 was calculated assuming an a priori 5% IgG anti-SARS-CoV-2 seroprevalence (Salje et al., 2020) , a confidence in the estimate of 95%, a maximum allowable error in the prevalence of 1%, and a Corsican population size of 344,679 habitants based on the latest French census data (INSEE, 2020). Residual sera obtained from persons of all ages were tested for the presence of anti-SARS-CoV-2 IgG using the EUROIMMUN enzyme immunoassay kit for semiquantitative detection of IgG antibodies against S1 domain of viral spike protein (ELISA-S) (reference: In all samples with a ratio ≥ 0.8, neutralizing antibodies were detected using a VNT as previously described (Gallian et al., 2020) . To the best of our knowledge this is the first study describing the prevalence of SARS-CoV-2 antibodies in a representative sample of Corsican patients having carried out a blood analysis in biological laboratories after the COVID19 epidemic period. doi = 10.1101/2020.09.29.20201368 id = cord-346197-7g5d9x57 author = Capecchi, E. title = Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? date = 2020-07-05 keywords = SARS summary = title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children? Since the use of nasopharyngeal aspirate (NPA) seemed to be better than nasopharyngeal swab (NS) to identify respiratory virus in paediatrics 4,5 we decided to compare these methods in detecting SARS-CoV-2 in children. . https://doi.org/10.1101/2020.07.02.20142521 doi: medRxiv preprint Considering NPA as the gold standard for detection of SARS-CoV-2, we calculated sensitivities and specificities of NS. The NS has in any case a low sensitivity in detecting SARS-CoV-2 in children when referred to NPA. Our results, the first we know are available, suggest to prefer the collection of NPA whenever possible for the detection of SARS-CoV-2 in children. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted July 5, 2020. doi = 10.1101/2020.07.02.20142521 id = cord-325559-di8lljoi author = Cappello, Francesco title = Does SARS-CoV-2 Trigger Stress-Induced Autoimmunity by Molecular Mimicry? A Hypothesis date = 2020-06-29 keywords = COVID-19; SARS; cell; clinical; protein summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced disease (COVID-19) is a planetary emergency that is urging many research groups to redirect their efforts and to channel their experience towards understanding its pathogenesis. These human epitopes, in turn, can be recognized by circulating antibodies made against crossreactive microbial antigens; these antibodies behave like autoantibodies, causing the destruction of the stressed cells, representing a typical example of pathology caused by molecular mimicry and manifested as autoimmunity [30] . We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. We hypothesize that, at the basis of the generalized activation of the immune system, there are molecular mimicry phenomena: the antibodies produced against the virus could turn into autoantibodies against crossreactive proteins expressed on human cells, causing autoimmunity with cell destruction. doi = 10.3390/jcm9072038 id = cord-256761-rjss51sq author = Caputo, Leonardo title = Repurposing therapeutic agents and herbal medicines to defeat viral nemesis date = 2020-03-30 keywords = Ebola; SARS summary = After a deep analysis and exhaustive illustration of both the rationale behind this tentative approach and related safety concern, Gurwitz suggested that data mining of clinical patient records survived to COVID-19 epidemic might be useful to assess the feasibility of sartans'' repurposing as therapeutic treatment to decrease acute respiratory distress syndrome (ARDS) and reduce the aggressiveness from severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. Obviously, repurposing old drugs for COVID-19 may start from therapeutic agents with proven efficacy against other lethal viral infections. On the other hand, the use of traditional Chinese remedies as a therapeutic approach for combating SARS-CoV has been well publicized (World Health Organization [WHO], 2003) and it was recently proposed for prevention of COVID-19 (Luo et al., 2020) . Whatever sources of drugs (natural, synthetic, or repurposed) are suggested to be used for COVID-19, their efficacy should be proven through a valid clinical trial. doi = 10.1002/ddr.21668 id = cord-262575-06i2nv0t author = Caracciolo, Massimo title = Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome date = 2020-08-25 keywords = COVID-19; IL-6; SARS summary = title: Case Report: Canakinumab for the Treatment of a Patient With COVID-19 Acute Respiratory Distress Syndrome Severe cases of COVID-19 present with serious lung inflammation, acute respiratory distress syndrome and multiorgan damage. SARS-CoV-2 infection is associated with high cytokine levels, including interleukin-6 and certain subsets of immune cells, in particular, NK, distinguished according to the cell surface density of CD56. Cytokine levels are inversely correlated with lymphocyte count, therefore cytokine release syndrome may be an impediment to the adaptive immune response against SARS-CoV-2 infection. An 85 year old male presenting in our hospital with COVID-19, whose condition was complicated by acute respiratory distress syndrome and cardiac and renal failure (with oliguria) after 25 days of hospitalization, was intubated and received canakinumab for compassionate use. The immune response, including the release of pro-inflammatory cytokines and activation of T cells, are essential for controlling the viral spread, inflammation, and tissue renewal (5, 6) . doi = 10.3389/fimmu.2020.01942 id = cord-257487-xanqvdhn author = Carbajo-Lozoya, Javier title = Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date = 2012-02-10 keywords = NL63; SARS; fk506 summary = Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. Knockdown of the cellular FK506binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. To examine whether FK506 exerts an inhibitory activity on other human coronaviruses, CaCo2 cells were infected with HCoV-NL63 at MOI = 0.004 (Herzog et al., 2008) in the presence of increasing inhibitor concentrations. In order to examine whether the cellular FK506-binding proteins FKBP1A and FKBP1B are required for virus replication, CaCo2 knockdown cell lines were established using lentiviral expression of shRNA (Sirion GmbH, Martinsried, Germany). doi = 10.1016/j.virusres.2012.02.002 id = cord-293890-thfros7x author = Carbo, Ellen C. title = Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness date = 2020-08-21 keywords = CoV-2; SARS summary = METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. Additionally, the efficacy of detection of novel coronaviruses using capture probes targeting vertebrate viruses [10] [11] known before the current pandemic was analyzed using a SARS-CoV-2 clinical sample. After extraction of human reads, FASTQ files generated for SARS-CoV-2 samples (with and without viral enrichment) were uploaded for classification and de novo assembly by the commercial webbased tool Genome Detective v1.120 (www.genomedetective.com, accessed 2020-05-11) [9] , using a reference database (generated 2019-09-21). In this study, we evaluated the performance of a metagenomic sequencing protocol for the identification of emerging viruses using clinical samples in combination with a simulated reference database. doi = 10.1016/j.jcv.2020.104594 id = cord-313537-920tgv1j author = Carbonell, Ana Piera title = Covid-19 y tromboprofilaxis: recomendaciones para nuestra práctica clínica en atención primaria date = 2020-09-18 keywords = COVID-19; SARS summary = Teniendo en cuenta que muchos de nuestros pacientes ya reciben terapia antitrombótica o anticoagulante, el hecho de que puedan desarrollar una infección por COVID-19 tendrá implicaciones para la elección, dosificación y control en associated with SARS-CoV-2 infection, increasing its severity and conferring a worse prognosis. La enfermedad producida por coronavirus SARS-CoV-2 (COVID19) , si bien en la mayoría de los pacientes infectados cursa con síntomas leves, en casos más severos puede progresar rápidamente y desarrollar un síndrome de dificultad respiratoria aguda, shock séptico, coagulopatía y disfunción endotelial, que son los determinantes principales de la afectación microvascular, al producir una mayor vasoconstricción, isquemia orgánica, inflamación con edema tisular asociado y un estado procoagulante que predispone a la enfermedad tromboembólica venosa (ETEV) y arterial. doi = 10.1016/j.semerg.2020.07.007 id = cord-308252-qwoo7b1l author = Cardinale, Vincenzo title = Intestinal permeability changes with bacterial translocation as key events modulating systemic host immune response to SARS-CoV-2: A working hypothesis date = 2020-09-16 keywords = CoV-2; SARS; covid-19; patient summary = During the course of severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and 2 (SARS-CoV-2) infection, this pathway is unbalanced due to intestinal involvement and systemic inflammatory response. This review provides evidence on gut-liver axis involvement in Covid-19 as well as insights into the hypothesis that intestinal endotheliitis and permeability changes with bacterial translocation are key pathophysiologic events modulating systemic inflammatory response. Since inflammation seems to upregulate ACE2 expression [17] , it is important to understand whether patients with inflammatory bowel disease (IBD) are more susceptible to Covid-19 and the cytokine release syndrome (CRS) associated with lung injury and fatal outcome [21] . While the risk of SARS-CoV-2 infection in IBD patients depends on several universal risk factors, including social distancing [22] , older age and comorbidities have been associated with a negative outcome in IBD, whereas IBD treatments have not, highlighting that acute IBD flare prevention and inflammation reduction may avoid severe Covid-19 [23] . doi = 10.1016/j.dld.2020.09.009 id = cord-331140-5b0y1xzb author = Cardona Maya, Walter D. title = SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health date = 2020-06-01 keywords = SARS summary = key: cord-331140-5b0y1xzb title: SARS-CoV-2 and Prostatitis: dangerous relationship for male sexual and reproductive health cord_uid: 5b0y1xzb . Recently, SARS-CoV-2 was detected in semen samples (5) . Therefore, it is not unreasonable to believe that the latest coronavirus could potentially be transmitted via semen (6) . It was also reported that angiotensin converting enzyme 2 (ACE2) is a functional receptor that mediates the entry of SARS-CoV-1 (7) and 2 (8) , and this receptor is expressed in the prostate. Perhaps in the coming years, the real effect of SARS-CoV-2 on prostatitis cases will be evaluated and scope for researching factors that cause the clinical syndrome will be expanded. Male infertility: a public health issue caused by sexually transmitted pathogens Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease SARS-CoV-2 and the Testis: similarity to other viruses and routes of infection Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus doi = 10.1016/j.mehy.2020.109914 id = cord-304791-wv4qu9xm author = Carfora, Vincenzo title = Anticoagulant treatment in COVID-19: a narrative review date = 2020-08-18 keywords = COVID-19; LMWH; SARS; patient summary = Besides the respiratory involvement, COVID 19 patients frequently develop a pro-coagulative state caused by virus-induced endothelial dysfunction, cytokine storm and complement cascade hyperactivation. [11] enrolled 183 consecutive COVID-19 patients and performed routine coagulation tests [PT, [8] In COVID-19-patients it is common to observe increased fibrinogen and D-Dimer levels Chen, 2020 [9] In COVID-19-patients it is common to observe variable levels of prothrombin time (PT), activated partial thromboplastin time (aPTT) and International standardized ratio (INR) Qin, 2020 [15] In COVID-19 the hyperinflammation mediated by IL-1, TNF-alfa and IL-6 leads to an increase of plasma concentrations of fibrinogen and plasminogen activator inhibitor-1 (PAI-1) Campbell, 2020 [19] In a murine model of MERS-CoV infection, increased concentrations of C5a and C5b-9 were found in sera and lung tissues. Moreover, patients with cardiovascular disease and dyslipidemia have high levels of circulating asymmetric di-methyl-arginine (ADMA) [28] , an analogue of L-arginine that inhibits NOS-3 activity [29] , and this leads to lower NO levels; this explains why endothelial dysfunction and the pro-coagulant state are more severe in this cohort of patients. doi = 10.1007/s11239-020-02242-0 id = cord-351100-llyl97ry author = Cariani, Lisa title = Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date = 2020-07-23 keywords = PCR; SARS summary = We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. We collected cycle threshold values of the first SARS-CoV-2-positive nasopharyngeal swabs (T0) for all 182 HCWs and CT values at one week before the two negative RT-PCR tests (T1) for the 58 subjects who healed by 30 April 2020 (Figure 2 ). In the present study, we analyzed 2443 nasopharyngeal swabs from 1683 HCWs by molecular laboratory testing for suspected SARS-CoV-2 infection in a large university hospital in Milan, showing 10.8% positive HCWs. Overall, the majority of HCWs with COVID-19 were physicians, and the main reported symptoms were fever, cough, and headache. doi = 10.3390/ijerph17155313 id = cord-285822-b5itedu3 author = Carlos Marín-Gabriel, José title = Documento de posicionamiento AEG-SEED para el reinicio de la actividad endoscópica tras la fase pico de la pandemia de COVID-19 date = 2020-05-27 keywords = CCR; SARS; los summary = Promover la participación de los residentes de Aparato Digestivo en los procedimientos endoscópicos en pacientes con bajo riesgo de infección por SARS-CoV-2, siempre y cuando se disponga de los recursos necesarios que garanticen la seguridad del procedimiento. En la situación actual de alto riesgo de transmisión de la infección por SARS-CoV-2 en el entorno hospitalario, es crítico revisar los protocolos de la UE en relación con la circulación de los pacientes y acompañantes, las estrategias de cribado de COVID-19, la disponibilidad de EPI y las medidas de desinfección de las salas y equipos de endoscopia. Las sociedades firmantes de este documento se posicionan a favor de que los residentes en Aparato Digestivo continúen realizando procedimientos bajo supervisión directa en pacientes de bajo riesgo de infección por SARS-CoV-2. Para los pacientes con alta sospecha o infección confirmada por SARS-CoV2, es recomendable una desinfección en profundidad de la sala después de cada endoscopia 6 , 27 . doi = 10.1016/j.gastrohep.2020.05.004 id = cord-339782-rybjc58j author = Carmo, Anália title = Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date = 2020-06-02 keywords = RNA; SARS summary = The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. In men, the first negative test took 24 ± 9 days (range: 7 -46) and in women it took 25 ± 9 days (range: 9 -44), P>0.05, In an attempt to understand why some patients maintained positive tests for longer, we correlated the detection of SARS-CoV-2 RNA with the host immune response to virus infection. The lack of information regarding persistence of virus RNA and infectivity, disease severity and immune response, supports the current guidance of viral clearance confirmation prior to patient transference out of dedicated COVID-19 wards and of ending isolation in mild illness patients. doi = 10.1002/jmv.26103 id = cord-321259-wio2b49i author = Carmona-Gutierrez, Didac title = Digesting the crisis: autophagy and coronaviruses date = 2020-05-04 keywords = COVID-19; Coronavirus; MERS; SARS; autophagy summary = Of note, cellular manipulation of autophagic levels during infection may also reflect desperate attempts of the cell to reestablish homeostasis, either through restriction of viral entry by actively shunting endocytosis/endosomal trafficking (possibly resulting in autophagy reduction as a sideeffect) [39] or to counteract virally induced cell death by increasing cytoprotective autophagy. Thus, the group-specific accessory proteins, which by definition are not essential for viral replication but are involved in the modulation of host cells and immune evasion [66, 67] , may represent targets for reducing the autophagy-inhibitory effects of CoVs. The FDA-approved anti-malarial drugs chloroquine and hydroxychloroquine have been suggested to be repurposed for the treatment of COVID-19 [68] [69] [70] , but this remains widely controversial [71] [72] [73] . Intriguingly, another recent preprint presents in vitro data showing that SARS-CoV-2 infection restricts autophagy and that, in turn, pro-autophagic compounds -including spermidine -may inhibit viral propagation [85] . doi = 10.15698/mic2020.05.715 id = cord-297418-36j840wm author = Carneiro Leão, Jair title = Coronaviridae ‐ old friends, new enemy! date = 2020-05-31 keywords = MERS; SARS summary = However, in recent years, coronaviruses have given rise to significant diseases such as severe acute respiratory syndrome (SARS-CoV) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) SARS-CoV infected 8,000 people, from 2002 to 2003 and had a mortality rate of approximately 10% (Marra et al., 2003) . On the other hand, evolutionary analysis based on the ORF1a / 1b, S and N genes suggests that SARS-CoV-2 is more likely to be a new coronavirus that has been introduced independently from animals to humans due to the inherent mutation property of coronaviruses in nature (Lam et al., 2020) . Severe acute respiratory syndrome (SARS) is a human disease associated with severe pneumonia and as noted above is caused by SARS-Coronavirus (SARS-CoV) (Drosten et al., 2003) . The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges doi = 10.1111/odi.13447 id = cord-324892-mg2dziuw author = Carneiro, João title = CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2 date = 2020-06-12 keywords = SARS summary = The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens doi = 10.1101/2020.04.19.048991 id = cord-354372-vfvnjmv1 author = Carpenito, L. title = The autopsy at the time of SARS-CoV-2: Protocol and lessons date = 2020-07-04 keywords = SARS; autopsy; death; patient; sample summary = In the current pandemic scenario of SARS-CoV-2, the autopsy appears to be a crucial tool to clarify the virus target cells in human, the frameworks of organ damage and the biological mechanisms that lead to death or allow the patient to heal. To minimize the dispersion of blood and biological fluids, it is essential to always operate in the area of the autopsy table: the viscera removed from the body must be placed either on the iron section table, placed above the patient''s thighs, or in a large tray with high steel edges resting on the patient''s legs, during weighing, macroscopic examination and sampling of the viscera. Given the multiple clinical findings of neurological symptoms in patients infected with SARS-CoV-2 [22, 23] , it appears indispensable to perform the evisceration and examination of the brain and brainstem, for the completeness of the autopsy and for the very few morphological data available today on the central nervous system. doi = 10.1016/j.anndiagpath.2020.151562 id = cord-271920-1dzkgt6w author = Carpenter, Christopher R. title = Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date = 2020-06-16 keywords = COVID-19; PCR; SARS; patient; test summary = 3 As waves of COVID-19 patients present to ED''s in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient''s exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. doi = 10.1111/acem.14048 id = cord-326013-5i35zdmv author = Carpinteiro, Alexander title = Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells date = 2020-10-29 keywords = CoV-2; SARS; VSV summary = The data justify clinical studies investigating whether amitriptyline, a safe drug used clinically for almost 60 years, or other antidepressants that functionally block acid sphingomyelinase prevent SARS-CoV-2 infection. Pretreatment of the cells with 5, 10, 20, or 25 µM amitriptyline prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike for 30 min (Fig. 3B, Fig. 4A ). Treating Vero cells with neutralizing antibodies to spike or with recombinant ACE2 protein prevented the activation of acid sphingomyelinase and the release of ceramide upon infection with pp-VSV-SARS-CoV-2 spike (Fig. 3B, Fig. 4A Amitriptyline and other drugs with similar structure and properties have been clinically used for many years (since 1962) to treat patients with depressive disorder. Best results were obtained with venlafaxin, fluoxetine, escitalopram and mirtazipine, drugs that were also shown in the present study to inhibit acid sphingomyelinase and ceramide release upon pp-VSV-SARS-CoV-2 spike infection. doi = 10.1016/j.xcrm.2020.100142 id = cord-326150-cf4rlqe5 author = Carrascosa, J M title = Manifestaciones cutáneas en el contexto de la infección por SARS-CoV-2 (COVID-19) date = 2020-08-31 keywords = COVID-19; SARS summary = Desde el punto de vista patogénico, la respuesta inmune desencadenada frente a la infección por SARS-CoV-2 puede resultar en efectos deletéreos, como la disfunción de las células endoteliales y la activación de las vías de la coagulación, que podrían explicar las complicaciones cardiovasculares y trombóticas que afectan a un subgrupo de pacientes. Desde el punto de vista histológico, en el conjunto de exantemas J o u r n a l P r e -p r o o f En el estudio histológico de lesiones purpúricas cutáneas se ha encontrado la presencia de una vasculopatía trombogénica pauciinflamatoria, con depósito de C5b-9 y C4d , con localización de partículas virales, lo que ha permitido proponer la existencia de un síndrome de lesión microvascular catastrófica mediada por la activación del complemento 6 . De este modo, no puede descartarse que las lesiones acrales, descritas como características por su coincidencia epidemiológica más que por pruebas microbiológicas en la mayoría de los casos, puedan no tener que ver directamente con la COVID-19. doi = 10.1016/j.ad.2020.08.002 id = cord-284042-awl5bb0j author = Carrascosa, J.M. title = Cutaneous Manifestations in the Context of SARS-CoV-2 Infection (COVID-19)() date = 2020-10-15 keywords = COVID-19; SARS; lesion; patient summary = From the pathogenic point of view, the immune response triggered by infection with SARS-CoV-2 may result in harmful effects, such as endothelial cell dysfunction and activation of J o u r n a l P r e -p r o o f coagulation pathways; this may explain the cardiovascular and thrombotic complications that affect a subgroup of patients. 19 Vesicular lesions, usually monomorphic, appear early on and may at times precede other symptoms (in 15% of patients), 11 although in most cases, up to 79.2% in a series of 24 patents reported by Fernandez-Nieto et al., 20 they occur at the onset of other symptoms. 21 reported the case of a female patient who developed an urticarial rash, accompanied by odynophagia and arthralgia, before developing the full clinical manifestations of COVID-19. doi = 10.1016/j.adengl.2020.10.001 id = cord-313193-q5zeoqlb author = Carrat, F. title = Seroprevalence of SARS-CoV-2 among adults in three regions of France following the lockdown and associated risk factors: a multicohort study. date = 2020-09-18 keywords = ELISA; SARS; September summary = Methods Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE), two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA), with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE) -two regions with high rate of COVID-19, or in the Nouvelle-Aquitaine (NA) -with a low rate, were asked to take a dried-blood spot (DBS) for anti-SARS-CoV-2 antibodies assessment. Participants with a positive ELISA-S had a higher rate of self-reported symptoms than those with negative tests except for skin lesions (table 2) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint doi = 10.1101/2020.09.16.20195693 id = cord-276895-p85obwp2 author = Carriazo, Sol title = Kidney disease and electrolytes in COVID-19: more than meets the eye date = 2020-07-16 keywords = AKI; SARS; covid-19; kidney summary = The current issue of Clinical Kidney Journal presents 15 articles on COVID-19 and kidney disease from three continents, providing a global perspective of the impact of severe acute respiratory syndrome coronavirus 2 on electrolytes and different kidney compartments (glomeruli, tubules and vascular compartments) and presenting clinically as a syndrome of inappropriate antidiuretic hormone secretion, acute kidney injury, acute kidney disease, collapsing glomerulopathy and thrombotic microangiopathy, among others, in the context of a brand-new cardiorenal syndrome. The present issue of Clinical Kidney Journal (ckj) contains reports from the most affected countries (Figure 1 ) that illustrate the impact of SARS-CoV-2 on electrolytes and the kidneys, the different possibilities for acute renal replacement therapy (RRT) and the impact of COVID-19 in patients with pre-existing chronic kidney disease (CKD) and on chronic RRT, with emphasis on preventive measures and providing insights into therapy. doi = 10.1093/ckj/sfaa112 id = cord-282530-55lhjfm8 author = Carsana, Luca title = Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study date = 2020-06-08 keywords = COVID-19; SARS; case summary = [6] [7] [8] [9] We describe the lung histopathological findings from a large series of patients who died from COVID-19 in northern Italy, with the aim of reporting the main micro scopic pulmonary lesions associated with SARS-CoV-2 infection and severe respiratory failure. To our knowledge, these data represent the first relevant provisional information regarding tissue damage specifically induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), besides the previously described diffuse alveolar damage, a feature that characterises interstitial pneumonia regardless of infectious agent. 3, 4, 11, 14 In two autopsy studies of patients who died from SARS (eight cases from Singapore 11 and 20 cases from Toronto), 3 the predominant pattern of lung injury was diffuse alveolar damage, including the exudative and proliferative phases. In a case report of a patient who died from COVID-19 in China, the histological findings in the lungs included desquamation of pneumocytes, diffuse alveolar damage, and oedema. doi = 10.1016/s1473-3099(20)30434-5 id = cord-292347-d7xq7x5g author = Carter, Linda J. title = Assay Techniques and Test Development for COVID-19 Diagnosis date = 2020-04-30 keywords = COVID-19; PCR; RNA; SARS summary = 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. doi = 10.1021/acscentsci.0c00501 id = cord-264261-98h1bmb2 author = Caruana, Giorgia title = Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date = 2020-06-25 keywords = PCR; SARS summary = It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients doi = 10.1016/j.cmi.2020.06.019 id = cord-354597-xubsodnk author = Carvalho, Alexandre title = SARS-CoV-2 Gastrointestinal Infection Causing Hemorrhagic Colitis: Implications for Detection and Transmission of COVID-19 Disease date = 2020-04-17 keywords = CoV-2; SARS; patient summary = Recent reports from China have described concomitant digestive symptoms, such as nausea, vomiting, diarrhea, and abdominal pain, in patients with confirmed SARS-CoV-2 pulmonary infection (5) (6) (7) (8) and the presence of SARS-CoV-2 RNA in fecal samples (8, 9) . We present a case of SARS-CoV-2 gastrointestinal infection causing acute hemorrhagic colitis and signaling COVID-19 disease which endoscopy confirmed colonic injury and helped exclude other etiologies of disease. On hospital day 4, 9 days after the onset of her digestive symptoms, the patient developed a cough; nasopharyngeal swabs were sent for comprehensive viral detection, including SARS-CoV-2 RNA (Quest Diagnostics). Given the patient''s elevated C-reactive protein and persistent abdominal pain and bloody diarrhea, a flexible sigmoidoscopy was performed on hospital day 4 to evaluate for evidence of inflammatory bowel disease or ischemic colitis. doi = 10.14309/ajg.0000000000000667 id = cord-282539-skzosh6u author = Casadevall, Arturo title = Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date = 2020-08-17 keywords = SARS; Wang summary = The article by Wang et al in this issue of Clinical Infectious Diseases reports that neutralizing antibody titers to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus peak 4-5 weeks after the onset of symptoms and decline by 3 months [1] . The decline in neutralizing antibody titers measured by Wang et al [1] in 93.5% of the patients studied is concerning for it raises the possibility that like other coronaviruses, COVID-19 may not result in the establishment of long lasting immunity. Whereas implications of the kinetics of the antibody response to SARS-CoV-2 for long-lasting and vaccine-mediated immunity are uncertain, the results of Wang et al [1] are important for the development and use of antibody therapies. The finding that SARS-CoV-2 neutralizing titers declined relatively quickly in the Wang et al study [1] means that efforts to collect convalescent plasma with high titers of neutralizing antibody for therapy and hyper-immune globulin preparation need to be highly organized such that potential donors are contacted early in the weeks following COVID-19. doi = 10.1093/cid/ciaa1213 id = cord-286390-ytgw3j4s author = Case, James Brett title = Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. date = 2020-07-03 keywords = SARS; VSV summary = An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, which engages with host ACE2 receptor for entry. Using an infectious molecular clone of vesicular stomatitis virus (VSV) expressing eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We engineered an infectious molecular clone of vesicular 83 stomatitis virus (VSV) to encode the SARS-CoV-2 S protein in place of the native envelope 84 glycoprotein (G) and rescued an autonomously replication-competent virus bearing the spike. Evaluation of a novel vesicular stomatitis virus pseudotype-based assay for detection of 641 neutralizing antibody responses to SARS-CoV Vesicular stomatitis virus pseudotyped with severe acute 645 respiratory syndrome coronavirus spike protein Retroviruses pseudotyped with the severe acute respiratory 722 syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting 723 enzyme 2 doi = 10.1016/j.chom.2020.06.021 id = cord-265233-v5sq5epy author = Cassorla, Lydia title = Decontamination and Reuse of N95 Filtering Facepiece Respirators: Where Do We Stand? date = 2020-10-15 keywords = FFR; N95; SARS; decontamination summary = P ersistent shortages of filtering facepiece respirators (FFR) to protect health care workers (HCW) 1 during the current coronavirus disease 2019 (COVID-19) pandemic 2,3 has driven interest in decontamination and reuse. 8 While FFR are not superior to surgical masks for protection of HCW from seasonal flu, [9] [10] [11] [12] [13] [14] retrospective studies showed increased protection from severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1). [28] [29] [30] [31] [32] [33] [34] In 2006, the Institute of Medicine, now the National Academy of Medicine, convened a "Committee on the Development of Reusable Facemasks for Use during an Influenza Pandemic." Highlighting unpreparedness, 2 reports recommended "expeditious research and policy action" to develop personal protective equipment (PPE) designed to withstand decontamination, evidence-based performance standards, and improved coordination among regulatory agencies. Best available evidence supports moist heat, low T autoclave, MWGS, and HP-based decontamination as effective methods for SARS-CoV-2 without causing significant damage to FFR for 2-5 cycles. doi = 10.1213/ane.0000000000005254 id = cord-245161-xbw72k4m author = Castano, Nicolas title = Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date = 2020-05-23 keywords = PCR; SARS; disinfectant; disinfection; fomite; surface; transmission; virus summary = Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. doi = nan id = cord-277760-i4xjk61t author = Castillo, Andrés E. title = Phylogenetic analysis of the first four SARS‐CoV‐2 cases in Chile date = 2020-04-08 keywords = SARS; chilean summary = To aboard this emergency, and like never before, scientific groups around the world have been working in a fast and coordinated way to get the maximum of information about this virus when it has been almost 3 months since the first cases were detected in Wuhan province in China. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this work, we studied the complete genome of the first four cases of the new coronavirus disease in Chile, from patients who traveled to Europe and Southeast Asia. In this report, we present the sequence analysis for the first four complete genomes for SARS-CoV-2 isolates on Chilean patients. Also, a phylogenetic study was performed with worldwide SARS-CoV-2 sequences and the full genomes from Chilean isolates, to identify their genetic similarity. doi = 10.1002/jmv.25797 id = cord-355672-egjdy7o0 author = Castillo, Edward M. title = Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date = 2020-07-02 keywords = SARS summary = Initial testing protocols from the US Centers for Disease Control and Prevention (CDC) for COVID-19 for detection in patients with possible infection recommend that samples also should be first sent for influenza viruses along with respiratory panels for detection of parainfluenza virus, adenovirus, human rhinovirus, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae. 1 The problem with testing for coinfections in suspected patients is that the presence of a positive upper respiratory pathogen nucleic acid detection (RPNA) test for viruses other than SARS-CoV-2 may suggest to the clinicians alternate explanations for the patients'' symptoms. This study is a retrospective analysis of data from an academic medical center with 2 hospitals and 2 urgent care centers in San Diego, California, during the initial 2 weeks of SARS-CoV-2 testing, March 10, 2020 Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID-19) doi = 10.1002/emp2.12172 id = cord-313305-tih33rys author = Castro, Rodolfo title = COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil date = 2020-04-18 keywords = SARS summary = We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se=82% [76-87]; Sp=97% [96-98]; DOR=168 [92-305] and SROC=0.98 [0.96-0.99]; (ii) for IgG antibodies Se=97% [90-99]; Sp=98% [97-99]; DOR=1994 [385-10334] and SROC=0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se=97% [85-99]; Sp=99% [77-100]; DOR=2649 [30-233056] and SROC=0.99 [0.98-1.00]. The aim of this study was to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. Our study reports that antigen testing and/or molecular assays using nasopharyngeal and oropharyngeal specimens had high accuracy for SARS-CoV-2 detection. doi = 10.1016/j.bjid.2020.04.003 id = cord-340583-kjrxrk50 author = Castro‐Rodriguez, Jose A. title = Asthma and COVID‐19 in children – a systematic review and call for data date = 2020-06-18 keywords = SARS; asthma; covid-19 summary = Importantly, none of the largest epidemiological studies including children with COVID-19 reported clinical findings or underlying characteristics to help assess whether asthma -or other chronic lung diseases-constitutes a risk factor for SARS-CoV-2 infection or COVID-19 severity. Rather than a risk factor, a recent review of data in adults reported that both asthma and COPD appear to be under-represented in the comorbidities reported for patients with COVID-19, compared with global estimates of prevalence for these conditions in the general population (63) . After an extensive review of the current literature, only two reports included information on asthma as a potential risk factor for COVID-19 infection -but not severity or mortality-in children. However, the largest studies to date have been limited to a description of the number of cases by age group, and so it remains unclear whether childhood asthma -or other pediatric respiratory diseases-are associated with COVID-19 risk or severity. doi = 10.1002/ppul.24909 id = cord-294028-pcc6mucj author = Caussy, Cyrielle title = Obesity is Associated with Severe Forms of COVID‐19 date = 2020-05-21 keywords = SARS summary = which reports a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2) requiring invasive mechanical ventilation. (1) , which reported a high prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation (IMV). The findings (1) reporting a higher IMV in severe obesity (BMI ≥ 35) versus lean patients (BMI < 25) from Lille University Center in France may not be generalizable to other centers in France or in other countries, depending on the criteria implemented for the indication of IMV in other centers (2) . However, our data tend to confirm the observation from Lille University Center of a higher requirement for IMV in severe obesity (BMI ≥ 35) compared with lean patients (81.8% vs. High prevalence of obesity in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requiring invasive mechanical ventilation doi = 10.1002/oby.22842 id = cord-336543-ydrmlujj author = Cavalli, Eugenio title = Entangling COVID-19 associated thrombosis into a secondary antiphospholipid antibody syndrome: Diagnostic and therapeutic perspectives (Review) date = 2020-06-25 keywords = APS; SARS; covid-19; patient summary = We propose here that the thromboembolic events and eventually the development of DIC provoked by SARS-CoV-2 infection may represent a secondary anti-phospholipid antibody syndrome (APS). On the basis of empirical observations and emerging laboratoristic findings, we will elaborate the hypothesis that several cases of thrombotic events during cOVId-19 infection represent the clinical epiphenomenon of a viral-induced secondary anti-phospholipid antibody syndrome (APS) that, in the most severe cases, may develop as catastrophic anti-phospholipid antibody syndrome (cAPS). clinical evidence and emerging data from pathological examinations indicate that a thrombotic diathesis, potentially leading to venous thromboembolism (VTE), and to dIc in some of the most severe cases, may occur in a substantial proportion of patients with cOVId-19 infection, also in a manner independent of long-term bed rest and eventual hormonal treatment. doi = 10.3892/ijmm.2020.4659 id = cord-260054-iihgc5nr author = Cavallo, Luigi title = D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date = 2020-06-08 keywords = HR1; SARS; fusion summary = 3D structures are now available from the Protein Data Bank (PDB) (21) for the SARS-CoV-2 S protein in the pre-fusion conformation, also bound to the ACE2 receptor (22) (23) (24) (25) (26) (27) (28) , and for the post-fusion core of its S2 subunit in the postfusion conformation (29) . We downloaded all the SARS-CoV-2 genomic sequences from the GISAID resource on April 21 st 2020, extracted from them 7,692 complete S protein sequences and identified all the point mutations occurring in at least two identical sequences (see Methods). When looking at the post-fusion conformation of the SARS-CoV-2 spike protein S2 subunit, these mutations appear more revealing. Based on a thorough analysis of the S protein sequences, that we extracted from the genomic sequences of SARS-CoV-2 reported in GISAID on April 21 st , we identified the fusion core of the HR1 as a mutational hotspot. doi = 10.1101/2020.06.08.140152 id = cord-306749-qetf3uur author = Caves, N.D. title = Attitudes to basic life support among medical students following the 2003 SARS outbreak in Hong Kong() date = 2005-10-10 keywords = BLS; SARS summary = This study seeks to explore whether this epidemic has altered the willingness of Hong Kong medical students to perform basic life support and mouth-to-mouth ventilation during an out-of-hospital cardiac arrest. The survey was conducted during July and August 2003, approximately two months after Hong Kong was removed from the World Health Organisation SARS Infected Areas list, and was designed to examine student confidence in BLS skills, their perceptions of the risks associated with performing BLS and their willingness to perform BLS in varying situations. Many of the previous studies investigating this issue have indicated that respondees are more reluctant to perform mouth-to-mouth ventilation than chest compressions, and have highlighted rescuers'' fears regarding transmission of the human immunodeficiency virus (HIV) in particular as a reason for not performing BLS. doi = 10.1016/j.resuscitation.2005.05.014 id = cord-273784-sr6afv60 author = Cazares, Lisa H. title = Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein date = 2020-09-23 keywords = PRM; SARS summary = The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. To determine the feasibility of targeted MS for SARS-CoV-2 diagnostics, we developed a method for the detection and quantitation of the S and NP, which employs parallel reaction monitoring (PRM) using a high-resolution Orbitrap instrument, thereby providing very high specificity. To test the ability of the PRM assay to detect S protein and NP in a relevant sample type, we spiked inactivated SARS CoV-2 virions into in vitro derived mucus. (B) PRM assay was then used to quantitate the SARS-CoV-2 protein levels in a mock sample that was created by adding an inactivated virus sample to in vitro derived mucus. Using the calibration curve from the best performing peptide for NP (DQVILLNK), the low and high SARS-CoV-2 mock samples contained on average 227 and 422 amol of NP, respectively, on column (see Figure 5A ). doi = 10.1021/acs.analchem.0c02288 id = cord-270035-1e1wzdri author = Cazzaniga, Marco title = SARS-COV-2 Infection and Kawasaki Disease: Case Report of a Hitherto Unrecognized Association date = 2020-07-03 keywords = Kawasaki; SARS summary = The association of Kawasaki disease and COVID-19 infection has to our knowledge been reported only once (5), we report a second case from Italy, currently the third most affected country in the world with regard to number of proven SARS-COV-2 infections. We were then contacted as reference Center for Kawasaki Disease (KD) in our Pediatric Immunology Unit: considering the clinical history (fever lasting more than 5 days, erythematous rash, labial, and conjunctival hyperemia) and the result of laboratory tests we confirmed the diagnostic suspicion of atypical/incomplete KD without coronary involvement, and started treatment with high dose intravenous immunoglobulins (IVIG) 2 g/kg and high dose acetylsalicylic acid (ASA 50 mg/kg/day). In the setting of COVID-19 there are several reports of using corticosteroids for Acute Respiratory Disease Syndrome (ARDS), but considering the not severe clinical course and presentation in our patient we did not start steroid therapy. doi = 10.3389/fped.2020.00398 id = cord-306034-1u29o2id author = Cazzolla, Angela P. title = Taste and Smell Disorders in COVID-19 Patients: Role of Interleukin-6 date = 2020-08-04 keywords = IL-6; SARS; covid-19; taste summary = [Image: see text] The rapid recovery of smell and taste functions in COVID-19 patients could be attributed to a decrease in interleukin-6 levels rather than central nervous system ischemic injury or viral damage to neuronal cells. To correlate interleukin-6 levels in COVID-19 patients with olfactory or gustatory dysfunctions and to investigate the role of IL-6 in the onset of these disorders, this observational study investigated 67 COVID-19 patients with taste or smell disorders or both, who did not require intensive care admission, admitted at COVID Hospital of Policlinico of Bari from March to May 2020. Interleukin-6 levels in COVID-19 patients in relation to olfactory or gustatory disorders were correlated from the time of their admission to the time of swab negativization. The aim was to monitor and to correlate IL-6 levels in laboratory-confirmed COVID-19 patients with olfactory or gustatory disorders from the time of their admission to the time of swab negativization. doi = 10.1021/acschemneuro.0c00447 id = cord-265170-yv04ijsm author = Ceccarelli, Giancarlo title = Probiotics and COVID-19 date = 2020-07-13 keywords = COVID-19; SARS summary = SARS-CoV-2 has been postulated to affect gut inflammation both directly and indirectly, infecting intestinal epithelial cells through the angiotensin-converting enzyme 2 (ACE2) receptor and transmembrane protease serine 2, and inducing proinflammatory chemokine and cytokine release. 7 Given this evidence, bacteriotherapy could represent a complementary resource for the prevention and restoration of SARS-CoV-2 intestinal mucosa damage through the modulation of gut microbiota and decreasing related inflammation. In other infections, such as HIV, in which intestinal inflammation and related microbiota impairment can affect gut epithelial barrier function, bacteriotherapy (through microbiota surface compounds and metabolites) to exist between different probiotic bacterial species and strains. 8, 9 We believe that studies of bacteriotherapy in SARS-CoV-2 are needed to evaluate the potential effects on intestinal mucosal inflammation and microbiome homoeostasis. In the absence of a vaccine or effective therapy for COVID-19, we agree that probiotics represent a complementary approach for the prevention and restoration of SARS-CoV-2-induced mucosal damage or inflammation through the modulation of gut microbiota. doi = 10.1016/s2468-1253(20)30196-5 id = cord-342084-fbtx7rwi author = Ceccarelli, Giancarlo title = IS TEICOPLANIN A COMPLEMENTARY TREATMENT OPTION FOR COVID-19? THE QUESTION REMAINS date = 2020-05-23 keywords = SARS summary = We read with great interest the editorial by Baron Coronavirus (MERS-CoV), but also Ebola virus, influenza A and B viruses, and feline infectious peritonitis virus (FIPV), were reported as potential targets of teicoplanin and its chemical derivatives. Based on the aforementioned, teicoplanin has been used either as a potential antiviral agent and treatment of possible Staphylococcus aureus superinfection in our critical patients with severe SARS-CoV-2 pneumonia, since this latter may represent a major complication of respiratory viral infections. Moreover, a recent study showed that teicoplanin potently prevents the entrance of SARS-CoV2 into the cytoplasm with an IC50 of only 1.66 μM which is much lower than the routine trough serum drug concentration (approximately 7-8 μM/L). Therefore, the routinely-used teicoplanin doses adopted in our series might be considered as potentially adequate for treatment of patients with SARS-CoV2 infection. Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) doi = 10.1016/j.ijantimicag.2020.106029 id = cord-279115-eyk8sxk7 author = Cecconi, Maurizio title = Ten things we learned about COVID-19 date = 2020-06-05 keywords = COVID-19; SARS summary = The infection starts with the competition between the SARS-CoV-2 virions arrived in the respiratory mucosa that express high levels of ACE2 receptors and the barrier made by mucus secreted by goblet cells and moved by hair-like cilia and innate immunity reactions. Evidence from SARS-CoV-1 suggests that these viruses may block interferon-mediated antiviral immunity (Fig. 1 ). Inflammation plays a key role in the development of COVID-19 from a SARS-CoV-2 infection. Unsurprisingly for a disease characterised by an inflammatory state in response to a viral infection, venous and arterial thromboembolic complications are common in hospitalised patients [6] . Given the timing and characteristics of the antibody response (see above), appropriately validated assays are instrumental for epidemiological studies, evaluation of plasma donations (see below), assessment of memory and response to vaccine, and as a companion diagnostic in RT-PCR-negative patients. Baseline characteristics and outcomes of 1591 patients infected with SARS-CoV-2 admitted to ICUs of the Lombardy Region doi = 10.1007/s00134-020-06140-0 id = cord-323666-t7cshj05 author = Cegolon, L. title = Nasal Disinfection for the Prevention and Control of COVID-19: A Scoping Review on Potential Chemo-preventive Agents. date = 2020-08-18 keywords = COVID-19; CoV-2; SARS summary = Figure 1 reports the corresponding changes as percentage or odds; the latter detects the improvement of the index score better than the former because it is able to overcome the ceiling effects J o u r n a l P r e -p r o o f Therefore, in addition to an effective treatment for symptomatic patients, there is an urgent need to abate the carriage of SARS-CoV-2 in the human nasal cavity of asymptomatic/pre-symptomatic individuals, in order to contain the transmission of the novel coronavirus within the community. The abstracts of the original articles were explored for the following terms: mechanism(s) of action, tolerability and any evidence of toxic effects or selection of resistant strains, whether the treatment was tested in vitro (in particular against SARS-CoV-2), or reached the clinical trials stage, or is currently marketed/promoted/sold. doi = 10.1016/j.ijheh.2020.113605 id = cord-275023-0z219rcy author = Cerofolini, Linda title = Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes date = 2020-07-29 keywords = SARS; orientation; protein; surface summary = title: Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. In this manuscript we apply a very simple method based on a unitedresidue modelling of protein-surface interactions, to specifically address the problem of determining the orientation of the SARS-CoV-2 Spike protein Receptor Binding Domain (RBD) on a few prototypical surfaces for biomedical use. In this work, we describe the use of united-residue modelling for the prediction of the orientation of the receptor binding domain of the spike protein of the novel coronavirus SARS-CoV-2, a protein of high immunological relevance at the most commonly used surfaces for the preparation of lateral-flow immunochemical devices. doi = 10.1016/j.bpc.2020.106441 id = cord-343800-nbydaoac author = Cerutti, Francesco title = Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2 date = 2020-09-29 keywords = SARS summary = We evaluated the recently CE-approved rapid POCT SD-Biosensor for SARS-CoV-2 nucleoprotein detection in nasopharyngeal secretions from 330 patients admitted to the Emergency Room for a suspect of COVID-19 and travelers returning home from high risk countries. Point-of-care diagnostic tests (POCTs) for detecting viral antigens in clinical samples would be very helpful for the diagnosis of COVID-19 [2] either as mass-screening or first aid tests at the emergency room. To evaluate a recently CE-approved POCT, the STANDARD Q COVID-19 Ag (SD-Biosensor, RELAB, I), for the detection of SARS CoV-2 nucleoprotein in NP swabs in comparison with the gold standard RT-PCR. POCTs for the detection of SARS-CoV-2 J o u r n a l P r e -p r o o f antigens are quite promising; however, the principal concerns are the false-negative rate due to low viral loads [3] [4] [5] [6] [7] [8] . Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples doi = 10.1016/j.jcv.2020.104654 id = cord-338140-p88fgojk author = Cervantes-Pérez, Enrique title = Medical Nutrition Therapy in Hospitalized Patients With SARS-CoV-2 (COVID-19) Infection in a Non-critical Care Setting: Knowledge in Progress date = 2020-10-30 keywords = COVID-19; Cervantes; SARS; vitamin summary = The purpose of this review is to provide concise guidance for the nutritional management of individuals with COVID-19 based on the current literature and focused on those in the non-ICU setting or with an older age and polymorbidity, which are independently associated with malnutrition and its negative impact on mortality. Numerous cases of pneumonia caused by a new virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were initially reported in Wuhan, China, at the end of December 2019. The purpose of this review is to summarize what is known about SARS-CoV-2 infection and provide possible and potential nutritional interventions on novel coronaviruses for clinicians. Older adults and polymorbid individuals suffering from chronic and acute disease conditions are at increased risk for poor outcomes and higher mortality following infection with the COVID-19-causing virus. doi = 10.1007/s13668-020-00337-x id = cord-297256-i9468t8v author = Cesari, Matteo title = Geriatric Medicine in Italy in the Time of Covid-19 date = 2020-04-03 keywords = Italy; SARS summary = In fact, although current data indicate that persons aged 70 years and older contribute to about the 85% of the death events in Italy, it cannot be overlooked the fact that Japan has substantially smaller figures despite being the oldest country in the world. To keep the healthcare machine running and support the colleagues overwhelmed in the management of COVID patients, there have been pediatricians working with older patients, or surgeons taking care of internal medicine issues... Geriatric medicine has produced substantial evidence showing that frail older persons require adaptations in the clinical approach, and that the environment plays a critical role for the wellbeing of the aging individual (5,6). Many older persons (with their chronic conditions and care needs) remained isolated after the SARS-CoV-2 outbreak. The same human interaction between the patient and his/her physician is lost behind the burdening personal protective equipment in COVID-19 facilities. doi = 10.1007/s12603-020-1354-z id = cord-269206-160ddfsc author = Ceylan, Rahmiye Figen title = Historical evidence for economic effects of COVID-19 date = 2020-06-04 keywords = SARS; covid-19; economic; effect summary = Yet, the contagious diseases having global effects had forgotten long time ago even if there appeared some recent encounters in the past 20 The differentiating features of COVID-19 or SARS-COV2 from the recent encounters are its geographical dispersion in terms of contagion and its causalities. In an earlier attempt to comment on prospective COVID-19 effects, Barro and his friends estimated growth of national income and consumption expenditures of 42 countries between 1901 and 1929 on human capital loss due to the WWI. Due to changing labour market composition and economic conditions during and after the influenza, both productivity and overall income had declined and savings and investment potential were affected negatively. Confirming previous research on SARS, Lionello [26] indicated that rising social fear and reduction in social contact resulted in reduced supplies and reduced labour demand specifically in the services sector between 20 and 70%. Especially, shrinking services and industries facing lower labour supplies and reducing demand are expected to downsize all economic structures. doi = 10.1007/s10198-020-01206-8 id = cord-257258-hu9oxea1 author = Chabner, Bruce A. title = Taking the Longer View of COVID‐19 date = 2020-04-27 keywords = SARS; covid-19 summary = In the absence of a vaccine or effective antivirals, social distancing is currently the primary public health strategy for containing the epidemic and has been successful in South Korea and China, where it was stringently employed. Regarding the chances of creating an effective vaccine against SARS-CoV-2 infection, in the U.S. the Biomedical Advanced Research and Development Authority (BARDA) of the Department of Health and Human Services is devoting significant support for two currently approved trials: a lipid nanoparticle vaccine that contains mRNAs directing the synthesis of the SARS-CoV-2 spike protein (Moderna) and an adenovirus construct of virus material co-supported by Johnson & Johnson [1] . However, vaccine development and its worldwide implementation, coupled with effective antiviral treatment, will be required to control COVID-19 and prevent another pandemic. In order to be ready for the next iteration of COVID-19, the worldwide medical community will need to cooperate in conducting extensive clinical trials of vaccines, antivirals, and immune therapies on an accelerated time scale. doi = 10.1634/theoncologist.2020-0313 id = cord-296556-fr8x8j3i author = Chaccour, Carlos title = Ivermectin and COVID-19: Keeping Rigor in Times of Urgency date = 2020-04-16 keywords = Ivermectin; SARS summary = 10 recently reported that ivermectin is a potent inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication in vitro. 13 However, even with this dose, which is 10-fold greater than those approved by the US Food and Drug Administration, the C max values reported were ∼250 ng/mL, 13 one order of magnitude lower than effective in vitro concentrations against SARS-CoV-2. Very recently, preliminary findings on a potential effect of hydroxychloroquine combined with azithromycin against SARS-CoV-2 were widely publicized, 15 leading to a surge in demand and self-medication, which resulted in serious harm in some cases and a stock shortage that jeopardized drug availability for other critical conditions for which hydroxychloroquine or chloroquine is the standard of care, that is, vivax malaria, rheumatoid arthritis, and systemic lupus erythematosus. 20, 21 Second, boosted antiretrovirals such as lopinavir/ritonavir and darunavir/cobicistat, which have been widely used against SARS-CoV-2 based on limited evidence, and a number of other drugs, are potent inhibitors of cytochrome P 450 3A4, the main metabolic pathway for ivermectin. doi = 10.4269/ajtmh.20-0271 id = cord-332178-0xyrmk5a author = Chadchan, Sangappa B. title = The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date = 2020-06-24 keywords = ACE2; Fig; SARS summary = title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization STUDY QUESTION Is SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization? The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. WIDER IMPLICATIONS OF THE FINDINGS Expression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. Given the important function of the uterine stroma and the possibility that SARS-CoV-2 could infect the uterus, our goal here was to 101 determine whether ACE2 is expressed in endometrial stromal cells, is regulated by progesterone, 102 and is required for decidualization. Given the high ACE2 expression in the human 143 endometrium, SARS-CoV-2 may be able to enter endometrial stromal cells and elicit pathological 144 manifestations in women with COVID-19. doi = 10.1101/2020.06.23.168252 id = cord-283193-8qj41kpp author = Chak-Yiu Lee, Andrew title = Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters date = 2020-09-22 keywords = SARS; figure; pfu summary = title: Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters Utilizing Syrian hamster model, we demonstrate that the severity of pneumonia induced by intranasal inhalation of SARS-CoV-2 increases with virus inoculum. By 4 dpi, the hamsters infected with 10 2 or 10 3 PFU of SARS-90 CoV-2 also developed lung parenchymal damage which were milder than those observed in the 91 hamsters infected with 10 4 or 10 5 PFU of virus ( Figure 1D including both arteries and veins. The 133 intranasally infected hamsters had significantly higher viral load in oesophagus and stomach, but 134 no detectable virus in small intestinal tissues (n=3, Figure 2C ). In order to quantitatively compare the severity of lung damage after oral and intranasal 196 inoculation, we performed semi-quantitative histopathological evaluation of the bronchioles, 197 alveoli and blood vessels using a method modified from our previous influenza infection mouse 198 model and a reported hamster infection model (Table S1 ). doi = 10.1016/j.xcrm.2020.100121 id = cord-264266-6xvj9zey author = Chakrabarti, Sankha Shubhra title = COVID-19 in India: Are Biological and Environmental Factors Helping to Stem the Incidence and Severity? date = 2020-05-09 keywords = COVID-19; India; SARS; case summary = Apart from SARS-CoV and MERS-CoV which caused severe respiratory diseases following outbreaks in 2003 and 2012, there are four endemic human corona viruses, HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1 in populations that are responsible for various types of respiratory illness which are generally self-limiting in young and immunecompetent persons [8] . It can be assumed that some degrees of sequence homology or conformational similarities among the structural proteins, especially the S protein, of SARS-CoV-2 and the endemic corona viruses (HCoV-229E, HCoV NL-63, HCoV-OC4, HCoV-HKU1) may result in cross-reactive immunity (circulating antibodies or primed T-cells) in persons with prior exposure to the latter viruses, and this may modulate the course and outcome of COVID-19. Thus, the possibility of a protective cross-immunity in the Indian population against COVID-19 cannot be ignored in explaining a rather mild effect of the current coronavirus pandemic in India in comparison to that in Europe and the USA. Therefore, cross-reactive antibodies generated as a result of infections from other human corona viruses may have a protective role in a population affected by COVID-19. doi = 10.14336/ad.2020.0402 id = cord-253366-03cg831z author = Chakraborty, Hirak title = Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics date = 2020-07-22 keywords = SARS; fusion; membrane summary = In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes doi = 10.1016/j.bpc.2020.106438 id = cord-322724-7l1668bf author = Challener, Douglas title = In Reply - Repeated testing in SARS-CoV-2 infection date = 2020-08-10 keywords = SARS summary = In general, we agree that repeat testing may be helpful in certain situations of ongoing high suspicion for active infection where alternative approaches are not feasible; however, we believe that testing should not be applied indiscriminately in a resource-constrained situation. Several studies have suggested that the number of unique patient specimens tested for SARS-CoV-2 is directly related to the positive identification of the virus and that there may be a high false-negative rate of molecular testing. 2, 3 The study by Zhang et al reported 41 hospitalized patients with an initial negative PCR test who had at least one positive result on subsequent testing. 4 We agree that there may be a role for repeat testing in patients with high clinical suspicion of Low Utility of Repeat Real-Time PCR Testing for SARS-CoV-2 in Clinical Specimens Distinct characteristics of COVID-19 patients with initial rRT-PCRpositive and rRT-PCR-negative results for SARS-CoV-2 doi = 10.1016/j.mayocp.2020.08.006 id = cord-283413-xapzer5s author = Chan, A. K. M. title = Social media for rapid knowledge dissemination: early experience from the COVID‐19 pandemic date = 2020-03-31 keywords = SARS; healthcare summary = During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2], while a recent study from Wuhan, China reported that 1716 healthcare workers were infected with COVID-19, representing 3.8% of confirmed cases [3]. During the Severe Acute Respiratory Syndrome (SARS) epidemic, 21% of the global cumulative case total were healthcare workers [2] . Known risks of non-peer-reviewed materials disseminated via social medial include the application of context-specific resources to unsuitable situations; engagement with biased knowledge within echo chambers'' (groups consisting of only like-minded individuals) and algorithm-driven filter bubbles that selectively display information based on user preferences [15] ; and insufficient source information available to Box 1 Criteria for the responsible use of social media disseminated information. In the current COVID-19 pandemic, social media has the potential, if responsibly and appropriately used, to provide rapid and effective dissemination routes for key information. doi = 10.1111/anae.15057 id = cord-325744-i3r3ff3t author = Chan, Angelina O. M. title = Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore date = 2004-05-17 keywords = SARS; care summary = title: Psychological impact of the 2003 severe acute respiratory syndrome outbreak on health care workers in a medium size regional general hospital in Singapore Aims To describe the psychological impact of severe acute respiratory syndrome (SARS) on health care workers in a regional general hospital 2 months post-outbreak. The questionnaires consisted of demographics, the General Health Questionnaire (GHQ) 28, the Impact of Events Scale (IES) and a set of questions enquiring about changes in life''s priorities and circumstances that helped them to cope with the SARS situation better. This questionnaire was developed specifically for this study, as there were no suitable scales available for measuring changes in life''s priorities and coping among health care workers as a result of SARS. From this survey, although it was perceived that the SARS situation had greatly impacted on the emotional state of health care workers, there was no significant change in the prevalence of psychiatric disorders among health care workers (35% of doctors and 25% of nurses) in this hospital who responded. doi = 10.1093/occmed/kqh027 id = cord-285849-jg43tcfh author = Chan, Ben Chong Pun title = Universal SARS preventive measures in an obstetrics unit: Experience of health care staff date = 2004-10-30 keywords = SARS summary = doi = 10.1016/j.ajic.2004.01.006 id = cord-306431-r83n27la author = Chan, Chak-Ming title = The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function date = 2009-05-04 keywords = Fig; SARS summary = title: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function Consistent with the Vero E6 cells data (Fig. 2) , our in vivo results further validate the importance of cysteine-rich, Yxx and diacidic domains of 3a (Fig. 1A) in 3a''s pro-apoptotic function. In this study, we generated mutant 3a constructs, 3a-CS, 3a-YA and 3a-DE (Fig. 1A) , and investigated the functional significance of the cysteine-rich, Yxx and diacidic domains on 3a''s pro-apoptotic activity. We previously reported caspase-8 activation in 3a-WTexpressing Vero E6 cells , and our in vivo data also showed that cytochrome c can modulate 3a-WT-induced apoptosis . Over-expression of severe acute respiratory syndrome coronavirus 3b protein induces both apoptosis and necrosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway doi = 10.1016/j.biocel.2009.04.019 id = cord-332680-zfn81hew author = Chan, Chieh-Kai title = Renin-Angiotensin-Aldosterone System Inhibitors and Risks of Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Systematic Review and Meta-Analysis date = 2020-09-10 keywords = COVID-19; SARS; ace summary = The following variables were extracted: author, journal, publication year, study design, geographic location, participants'' details (number, study population, age, sex, and comorbidities, including hypertension, diabetes mellitus, heart failure, and chronic kidney disease), use of antihypertensive drugs, such as ACE inhibitors, ARBs, calcium-channel blockers, beta-blockers, diuretics, outcomes (including positive SARS-CoV-2 test results and disease prognosis/severity, if available). The systematic review findings of the 7 high-quality studies (with comparative data on the controls) on SARS-COV-2 infection provide the best available evidence proving that therapy with ACE inhibitors or ARBs is not associated with an increase of positive SARS-CoV-2 test result and the severity of COVID-19 disease or overall population mortality as a whole in case-population and cohort studies. ACE indicates angiotensin-converting enzyme; ARBs, angiotensin receptor blockers; BMI, body mass index; CKD, chronic kidney disease; DM, diabetes mellitus; HTN, hypertension; ICU, intensive care unit; N/A, not applicable; OHA, oral hypoglycemic agents; RAASi, renin-angiotensin-aldosterone system inhibitors; and SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. doi = 10.1161/hypertensionaha.120.15989 id = cord-280350-ay4cnzn5 author = Chan, Jasper F.W. title = Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus date = 2013-10-03 keywords = East; MERS; SARS summary = We then assessed the anti-MERS-CoV activities of the identified compounds and of interferons, nelfinavir, and lopinavir because of their reported anti-coronavirus activities in terms of cytopathic effect inhibition, viral yield reduction, and plaque reduction assays in Biosafety Level-3 laboratory. Given the limited time available to develop novel anti-MERS-CoV agents in this evolving epidemic, we attempted to provide an alternative solution by identifying potential broad-spectrum antiviral agents against MERS-CoV and influenza A viruses by a small compound-based forward chemical genetics approach using chemical libraries consisting of 1280 drug compounds already marketed or having reached clinical trials in the United States, Europe, or Asia (Microsource Discovery Systems, USA). 25 We then assessed the anti-MERS-CoV activities of the identified drug compounds in cell culture by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction assay (PRA) assays, as well as drug cytotoxicity. doi = 10.1016/j.jinf.2013.09.029 id = cord-263508-row2mn17 author = Chan, Jasper Fuk-Woo title = The emerging novel Middle East respiratory syndrome coronavirus: The “knowns” and “unknowns” date = 2013-07-21 keywords = East; MERS; SARS; case summary = Ten years after the devastating epidemic of severe acute respiratory syndrome (SARS) caused by SARS coronavirus (SARS-CoV), which resulted in a total of 774 deaths among more than 8000 confirmed cases in over 30 countries, the world is facing a new challenge posted by a "SARS-like" infection caused by another novel coronavirus emerging from the Middle East, which was originally named human coronavirus EMC/2012 (HCoV-EMC) and recently renamed by the Coronavirus Study Group of the International Committee for Taxonomy of Viruses as Middle East respiratory syndrome coronavirus (MERS-CoV). 6,7,10e14 Although the number of laboratory-confirmed cases remains limited, the severe clinical manifestations with an unusually high mortality rate of over 50%, the spread of the infection beyond the geographical confinement in the Middle East, and the epidemiological evidence of human-to-human transmission arising from the recent clusters of cases in a family in the United Kingdom (Cases 10 to 12), and in hospitals in KSA (Cases 18 to 30, 32 and 33) and France (Cases 31 and 34), have raised significant concerns on the possible emergence of another SARS-like epidemic in the near future. doi = 10.1016/j.jfma.2013.05.010 id = cord-291847-x3b6j5d0 author = Chan, K. H. title = The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus date = 2011-10-01 keywords = SARS; humidity summary = The dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22–25°C and relative humidity of 40–50%, that is, typical air-conditioned environments. The better stability of SARS coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as Hong Kong) during the spring and in air-conditioned environments. Thus, information on the survival of the SARS coronavirus (SCoV) in the environment at different temperature and humidity conditions is of significant interest to understanding virus transmission. A recent study using surrogate coronaviruses (transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHC)) has investigated the effect of air 2 Advances in Virology (21) temperature and relative humidity on coronavirus survival on surface [18] . SARS CoV can retain its infectivity up to 2 weeks at low temperature and low humidity environment, which might facilitate the virus transmission in community as in Hong Kong which locates in subtropical area (Table 2(e)). doi = 10.1155/2011/734690 id = cord-315866-6vcts4w3 author = Chan, KC Allen title = Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study date = 2005-04-09 keywords = ARDS; SARS summary = title: Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Therefore, in this study, we investigated the association of the ACE insertion/deletion (I/D) polymorphism of the 287 bp Alu repeat to the susceptibility to SARS and the development of adult respiratory distress syndrome (ARDS) with a larger population. The genotypic distributions and allelic frequencies of ACE I/D polymorphism in the SARS patients and control subjects are shown in table 2. doi = 10.1186/1471-2334-5-26 id = cord-326337-s0fp5z1q author = Chan, Kui K. title = An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date = 2020-10-19 keywords = ACE2; RBD; SARS; figure summary = Deep mutagenesis of the isolated receptor-binding domain (RBD) by yeast surface display 44 has easily identified mutations in S that retain high expression and ACE2 affinity, yet are no longer bound 45 by monoclonal antibodies and confer resistance (19) . An alternative protein-based antiviral to monoclonal antibodies is to use soluble ACE2 (sACE2) as a 56 decoy to compete for receptor-binding sites on the viral spike (6, (22) (23) (24) (25) of diverse SARS-associated betacoronaviruses that use ACE2 for entry. The sequence 162 diversity observed among natural betacoronaviruses, which display high diversity at the ACE2 binding 163 site, is therefore replicated in the deep mutational scan, which predicts the SARS-CoV-2 spike tolerates 164 substantial genetic diversity at the receptor-binding site for function. From this accessible sequence 165 diversity SARS-CoV-2 might feasibly mutate to acquire resistance to monoclonal antibodies or 166 engineered decoy receptors targeting the ACE2-binding site. doi = 10.1101/2020.10.18.344622 id = cord-285179-26ey3fm8 author = Chan, Kwok-Hung title = Cross-reactive antibodies in convalescent SARS patients'' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests date = 2013-04-10 keywords = EMC; HCoV; OC43; SARS summary = title: Cross-reactive antibodies in convalescent SARS patients'' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests We conducted a seroprevalence study on archived sera from 94 game-food animal handlers at a wild life market, 28 SARS patients, and 152 healthy blood donors in Southern China to assess the zoonotic potential and evidence for intrusion of HCoV-EMC and related viruses into humans. 12 In order to further substantiate the hypothesis of HCoV-EMC being a zoonotic agent and elicit evidence for intrusion of HCoV-EMC and its related viruses into humans, we studied the antibody titers using immunofluorescence (IF) as screening and neutralization as confirmatory tests in at-risk groups working in a wild life market in Guangzhou of Southern China who were constantly exposed to a wide range of game food animals, SARS patients who might have acquired their infection directly from wild animals, and healthy blood donors. doi = 10.1016/j.jinf.2013.03.015 id = cord-341069-kngf6qpe author = Chan, Kwok-Hung title = Factors affecting stability and infectivity of SARS-CoV-2 date = 2020-07-09 keywords = SARS summary = AIM: The aim of this study was to investigate the infectivity of SARS-CoV-2 under various environmental factors, disinfectants and different pH conditions. The viability of virus was determined after treatment with different disinfectants and pH solutions at room temperature (20∼25(o)C). SARS-CoV-2 could be detected under a wide range of pH conditions from pH4 to pH11 for several days and 1 to 2 days in stool at room temperature but lost 5 logs of infectivity. One hundred microliters of SARS-CoV-2 with 114 10 6.5 TCID 50 /ml was added into each bottles of 0.9 ml VTM and incubated at room temperature 115 (20-25 o C). When SARS-CoV-2 was added in VTM with pH ranging from 2 to 13, the virus remained 163 viable up to 6 days but lost between 2.9 and 5.33 logs of infectivity from pH5 to pH9 and up 164 to 1~2 days in pH4 and pH11 ( Table 2) . doi = 10.1016/j.jhin.2020.07.009 id = cord-351354-10rusr6j author = Chan, Louis Y. title = Diagnostic Criteria during SARS Outbreak in Hong Kong date = 2004-06-17 keywords = DDT; SARS summary = Before the etiologic agent was identified, the diagnosis of SARS was made according to a set of clinical-epidemiologic criteria as suggested by the Centers for Disease Control and Prevention (CDC) (1-3). These criteria remained important in the initial diagnosis and prompt isolation of patients because the overall sensitivity of initial reverse transcriptase-polymerase chain reaction (RT-PCR) testing for SARSassociated coronavirus (SARS CoV) RNA on upper respiratory specimens ranged from approximately 60% to 70% (though sensitivity improved with a second test) (4, 5) . By using paired serologic testing to determine SARS-CoV infection (3), we evaluated the relative importance of the clinical-epidemiologic diagnostic criteria during an outbreak. Probable SARS case-patients were those who met the CDC clinical criteria for severe respiratory illness of unknown etiology (3), and met the epidemiologic criterion for exposure in either a close or a possible contact. Our findings showed that 5.9% of cases defined as probable SARS on the basis of clinical-epidemiologic criteria had no serologic evidence of coronavirus infection. doi = 10.3201/eid1006.030618 id = cord-309588-kw4d32dt author = Chan, Michael H.M. title = Steroid-induced osteonecrosis in severe acute respiratory syndrome: a retrospective analysis of biochemical markers of bone metabolism and corticosteroid therapy date = 2006-06-30 keywords = BALP; Day; SARS summary = Summary Aim We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. Biochemical markers of bone metabolism were analysed retrospectively using serial clotted blood samples collected from each patient during the course of hospital admission to discharge and subsequent follow-up at out-patient clinic using the arbitrary time periods: (i) Day <10; (ii) Day 28-44; (iii) Day 51-84; and (iv) Day >90 after the onset of fever. Aim: We investigated the effect of massive doses of corticosteroid therapy on bone metabolism using specific biochemical markers of bone metabolism, and the prevalence of osteonecrosis in severe acute respiratory syndrome (SARS) patients at a university teaching hospital in Hong Kong. 9, 10 In this study, biochemical markers of bone metabolism were used retrospectively to investigate the effect of massive doses of pulse and maintenance corticosteroid therapies on patients with SARS. doi = 10.1080/00313020600696231 id = cord-310687-qw164eyl author = Chan, Ming-Chin title = Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 date = 2020-09-01 keywords = SARS summary = title: Surveillance for Coronavirus Diseases 2019 (COVID-19) among Health Care Workers at a Medical Center in Taiwan, March to August 2020 Healthcare workers (HCWs) have been singled out, by mass screening supporters, as a high-risk group which are particularly in need to be mass-screened for the presence of SARS-CoV-2 virus or anti-SARS-CoV-2 antibodies, despite the fact that all Taiwanese If HCWs are indeed at high risk of contracting and carrying SARS-CoV-2 virus, then the current HCWs virological surveillance for COVID-19 should be able to detect SARS-CoV-2-positive cases among HCWs. Therefore, we reviewed the HCWs surveillance results at our hospital. 5 Since March 31, 2020, in consistent with Taiwan Central Epidemic Command Center''s HCWs surveillance policy, 5 all HCWs who developed fever or any respiratory symptoms were required to be tested for SARS-CoV-2 regardless of the presence of occupational exposure history or not . Taiwan Centers for Disease Control: COVID-19 statistics Taiwan Centers for Disease Control. doi = 10.1016/j.jfma.2020.08.037 id = cord-335375-n6q70o35 author = Chan, Paul K. S. title = Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date = 2005-07-01 keywords = SARS; sample summary = Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. doi = 10.1086/430615 id = cord-307490-b4un4703 author = Chan, Sophia S.C. title = Improving older adults’ knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study date = 2007-09-30 keywords = Hong; Kong; SARS summary = title: Improving older adults'' knowledge and practice of preventive measures through a telephone health education during the SARS epidemic in Hong Kong: A pilot study Objectives To assess the effectiveness of delivering a telephone health education programme dealing with anxiety levels, and knowledge and practice of measures to prevent transmission of SARS among a group of older adults with low SES. This is the first systematic study to assess the effectiveness of delivering telephone health education to older adults during the outbreak of SARS in Hong Kong. Results of the study supported that telephone health education was effective in relieving anxiety and improving knowledge of the main transmission routes of SARS in older adults, but not fostering practice of preventing SARS. This is the first systematic study to assess the effectiveness of telephone health education in improving older adults'' knowledge and practice of preventive measures during the SARS epidemic. doi = 10.1016/j.ijnurstu.2006.04.019 id = cord-310438-744r7gc3 author = Chan, Ta-Chien title = The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date = 2010-06-25 keywords = H3N2; P&I; SARS; Taiwan summary = This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan''s influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. The aims of this study were: (1) to evaluate the effectiveness of matching or mismatching influenza vaccine strains on influenzaassociated mortality, (2) to assess whether public health improvements during the post-SARS period might have decreased elderly mortality, and (3) to investigate molecular variation among vaccine-mismatched influenza viruses that may be associated with increased excess influenza-associated mortality. Explanatory variables for the above three outcome measures include monthly meteorological parameters (monthly means of temperature and humidity), annual periodic cycle (i.e., sine/cosine function of seasonal periodicity), monthly virus isolation rates for different subtypes/types of influenza viruses [A (H3N2) or A (H1N1) or B], matching status of different vaccine strains for each subtype/type in each of the studied years, post-SARS effect, and linear temporal monthly trends. doi = 10.1371/journal.pone.0011317 id = cord-347462-yz67t10x author = Chan, Tak Yeung title = A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date = 2004-07-19 keywords = PCR; SARS summary = title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). A retrospective study was undertaken in the department of medicine and geriatrics of the hospital to evaluate the clinical course of young and elderly SARS patients. Single or paired serum samples were tested for SARS-CoV antibody in 96% (50/52) of young and 76% (19/25) of older patients. Because the proportion of patients with positive RT-PCR in stool samples was similar in two groups, fewer older patients with diarrhea probably represents a generalized paucity of symptoms rather than a different site of involvement by SARS-CoV. In the current study, similar proportions of young and older patients with SARS had RT-PCR performed, and comparable positivity rates were achieved. doi = 10.1111/j.1532-5415.2004.52362.x id = cord-298281-wkje5jyt author = Chan, Vinson Wai-Shun title = A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date = 2020-05-27 keywords = COVID-19; RNA; SARS summary = Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Primary outcomes of our study included urological manifestations of COVID-19, detection rates of SARS-CoV-2 viral RNA in urine and stool samples, and special considerations in urological conditions. For the urological manifestations and viral RNA detection rates, data were pool analysed using MetaXL and Microsoft Excel when there are two or more studies with at least four patients reporting the same outcome under the same definition. There were a total of 11 studies that reported the number of patients who had their urine tested for SARS-CoV-2 viral RNA. Our meta-analysis included 12 studies that reported the number of patients with stools tested for SARS-CoV-2 viral RNA. Our study showed that 5.74% of the COVID-19 patients had positive viral RNA in urine samples. doi = 10.1007/s00345-020-03246-4 id = cord-278682-s4gfbsqy author = Chan, W-M title = Precautions in ophthalmic practice in a hospital with a major acute SARS outbreak: an experience from Hong Kong date = 2005-04-29 keywords = SARS; infection; patient summary = The ultimate infectivity of the tears secretion and ocular discharge from SARS patients may bring impacts on not only the daily ophthalmic practice but also the universal infection control measures practiced by general public and health-care workers. Discard gloves, wash or alcohol-rub the hands and then put on new gloves in-between case Wear glove in high-risk procedure General categories: for all patients attending the ophthalmic outpatients in which the SARS status is not certain. In a case-control study among 254 Hong Kong health-care workers with documented exposure to SARS patients, none of the 69 staff reporting use of four infection control measures, namely mask, gloves, gowns, and hand washing, was infected. Hospital Authority guideline on infection control of Severe Acute Respiratory Syndrome (SARS) doi = 10.1038/sj.eye.6701885 id = cord-324325-rmlrhyf2 author = Chan, Wai S title = Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) date = 2005-05-13 keywords = SARS; protein summary = Immunohistochemical studies on different human tissues, including a cohort of nine autopsies, two liver biopsies and intestinal biopsies of SARS patients, further confirmed the existence of coronaviral hypothetical and structural proteins in the cytoplasm of pneumocytes and small intestinal surface enterocytes in SARS patients. In those tissue sections showing positive signals for immunohistochemical staining, we further performed immunohistochemical studies using all other antibodies tested positive in SARS-CoV-infected Vero E6 cells. The cellular distribution of SARS-CoV protein and viral genome in immunohistochemical-positive lung and small intestine sections was further evaluated by immunofluorescence-fluorescence in situ hybridization analysis (Figure 4) . 3 In Vero E6 cells, positive cytoplasmic immunohistochemical signals were detected by Figure 3 Immunohistochemical studies of antipeptide antibody SARS-AbS13a against the nucleocapsid protein on small intestine sections. In addition, in the study of tissue sections, only those cells with viral genome detected by fluorescence in situ hybridization were positive for immunohistochemical stainings for the antipeptide antibodies. doi = 10.1038/modpathol.3800439 id = cord-320619-r466dc5t author = Chand Dakal, Tikam title = SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 date = 2020-11-05 keywords = ACE2; CoV-2; RGD; SARS summary = title: SARS-CoV-2 Attachment to Host Cells is Possibly Mediated via RGD-Integrin Interaction in a Calcium-dependent Manner and Suggests Pulmonary EDTA Chelation Therapy as a Novel Treatment for COVID 19 The higher expression of integrins in lungs along with their previously known high binding affinity (∼K(D) = 4.0nM) for virus RGD motif could serve as a possible explanation for high infectivity of SARS-CoV-2. This study is the first study to present striking evidence (substantiated by existing facts in literature) favoring the role of calcium and other divalent ions (magnesium, manganese etc.) in RGD-integrins mediated virus attachment with the host cells for and that lowering the concentration of calcium and other divalent ions in lungs could be a possible mechanism to avert SARs-CoV-2 infection and invasion. A number of motifs were predicted in the spike protein sequence such as RGD (from 403-405 aa in receptor binding domain of SARS-CoV-2) ( Table 2 ). doi = 10.1016/j.imbio.2020.152021 id = cord-301535-eui41zyg author = Chandler-Brown, Devon title = A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date = 2020-04-10 keywords = GCE; RNA; SARS summary = This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). doi = 10.1101/2020.04.07.029199 id = cord-308715-uo6h1h2e author = Chandra, Aman title = Personal protective equipment (PPE) for vitreoretinal surgery during COVID-19 date = 2020-05-12 keywords = COVID-19; SARS summary = SARS-CoV-2 is the recently discovered virus which has resulted in the pandemic illness known as coronavirus disease 2019 (COVID-19) [1] . Estimates for the proportion of asymptomatic patients infected with SARS-CoV-2 in different populations range between 7 and 80% [10] [11] [12] , with a substantial proportion of transmission occurring prior to illness onset [13, 14] . Gloves, disposable aprons, eye protection, fluid resistant type IIR surgical masks and slit lamp guards are recommended as personal protective equipment (PPE) for ophthalmic clinic assessment by the Royal College of Ophthalmologists [17] . Symptomatic patients with SARS tend to develop lower respiratory tract infections, suggesting aerosol transmission is important [25] . Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed Coronavirus Disease 2019 (COVID-19) in Healthcare Settings Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review doi = 10.1038/s41433-020-0948-3 id = cord-310221-car394ou author = Chandrashekar, Abishek title = SARS-CoV-2 infection protects against rechallenge in rhesus macaques date = 2020-05-20 keywords = CoV-2; Fig; SARS summary = We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. On day 2 following challenge, both necropsied animals demonstrated multifocal regions of inflammation and evidence of viral pneumonia, including expansion of alveolar septae with mononuclear cell infiltrates, consolidation, and edema (Fig. 3, A and B) . SARS-CoV-2 infection in rhesus macaques led to humoral and cellular immune responses (Fig. 2) and provided protection against rechallenge (Fig. 5) . In summary, SARS-CoV-2 infection in rhesus macaques induced humoral and cellular immune responses and provided protective efficacy against SARS-CoV-2 rechallenge. doi = 10.1126/science.abc4776 id = cord-343365-4y9fedcr author = Chang, Christopher title = Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date = 2013-11-30 keywords = RSV; SARS; disease; respiratory; vaccine summary = The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] . doi = 10.1007/s12016-013-8399-2 id = cord-314833-6fue84x6 author = Chang, Chung-ke title = The SARS coronavirus nucleocapsid protein – Forms and functions date = 2014-01-11 keywords = CTD; NTD; RNA; RNP; SARS summary = The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. proposed a structure-based domain arrangement for SARS-CoV N protein where the NTD and CTD are sandwiched between three IDRs. Sequence alignments suggested that other coronavirus N proteins might share the same structural organization based on intrinsic disorder predictor profiles and secondary structure predictions (Fig. 2) . noticed that effective binding to RNA by MHV N protein in host cells required the presence of both the NTD and CTD (Hurst et al., 2009) , suggesting that the NTD and CTD formed a single bipartite RNA interaction site, a feature to be reiterated in the final SARS-CoV RNP model. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA doi = 10.1016/j.antiviral.2013.12.009 id = cord-342639-vf9n2vf9 author = Chang, Chung-ke title = Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date = 2013-05-23 keywords = CTD; SARS; protein summary = For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA doi = 10.1371/journal.pone.0065045 id = cord-347460-9vechh4x author = Chang, Feng-Yee title = Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date = 2020-06-04 keywords = COVID-19; CoV; IFN; MERS; SARS; infection summary = Three components are crucial for SARS-CoV induced diseases: 1) the role of CD8+ T cells in defense against the virus, which causes apoptosis in the infected cells, 2) interactions of the virus with macrophages and dendritic cells, which initiate the early innate and subsequent adaptive immune responses, and 3) type I interferon (IFN) system, an innate response against viral infections, which can inhibit virus replication in the early phase. Existing information suggests that the SARS-CoV-infected airways and alveolar epithelial cells secrete abundant chemokines to attract immune cell infiltrations to the lungs, including macrophages and neutrophils, thereby causing damage due to high levels of proinflammatory cytokines and other mediators secreted by these cell types. After a decade of research on coronavirus, unfortunately, still there are no licensed vaccines, effective specific antivirals, nor drug combinations supported by high-level evidence to treat the infection, especially for newly emerging strains such as SARS-COV-2 [59] . doi = 10.1186/s12929-020-00663-w id = cord-337304-2ad2m317 author = Chang, Le title = Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations date = 2020-07-17 keywords = SARS summary = Because of high rates of 2019 novel coronavirus disease in Wuhan, China, Wuhan Blood Center began screening for severe acute respiratory syndrome coronavirus 2 RNA on January 25, 2020. We screened donations in real-time and retrospectively and found plasma samples positive for viral RNA from 4 asymptomatic donors. Lei Zhao, 1 1) and detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in plasma (2, 3) , the safety of China''s blood supply became a major concern (4). By March 4, we identified 4 blood donors in Wuhan whose plasma samples tested positive for SARS-CoV-2 RNA (Figure; Appendix Table) . We tested the 4 donors multiple times, using different sample sources, including sample tubes, retained nucleic acid templates, or blood products, indicating the accuracy and validity of our results (Appendix Table) . We extracted total nucleic acids from samples on an Most reverse transcription PCR protocols for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include 2-3 targets for detection. doi = 10.3201/eid2607.200839 id = cord-261297-kbcsa9zj author = Chang, Shan-Chwen title = Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) date = 2005-03-31 keywords = SARS summary = title: Clinical Findings, Treatment and Prognosis in Patients with Severe Acute Respiratory Syndrome (SARS) Severe acute respiratory syndrome (SARS) is a new infectious disease in humans caused by SARS-associated coronavirus (SARS-CoV). Liu et al reported clinical characteristics, management, and analysis of prognostic factors in patients with probable SARS who were treated at a specially designated hospital in Taipei City during the SARS epidemic from late April to July 2003. A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Clinical characteristics, management and prognostic factors in patients with probable severe acute respiratory syndrome (SARS) in a SARS center in Taiwan Temporal relationship of viral load, ribavirin, interleukin (IL)-6, IL-8, and clinical progression in patients with severe acute respiratory syndrome doi = 10.1016/s1726-4901(09)70229-1 id = cord-285907-xoiju5ub author = Chang, Shang-Miao title = Comparative study of patients with and without SARS WHO fulfilled the WHO SARS case definition date = 2005-05-31 keywords = SARS; non; patient summary = Abstract To differentiate severe acute respiratory syndrome (SARS) from non-SARS illness, we retrospectively compared 53 patients with probable SARS and 31 patients with non-SARS who were admitted to Mackay Memorial Hospital from April 27 to June 16, 2003. SARS patients with an initially normal chest X-ray study developed infiltrates at a mean of 5 ± 3.44 days after onset of fever (21/22 SARS vs. Severe acute respiratory syndrome (SARS) is a rapidly progressive disease caused by a novel coronavirus. Initial chest X-ray studies were normal in 22 of 53 SARS patients (41%) and 5 of 31 non-SARS patients (16%) ( Table 4 ). All except 1 of the 22 SARS patients with an initially normal chest X-ray study eventually developed abnormalities (mean FD 5 Ϯ 3.44). No non-SARS patient with an initially negative chest X-ray developed abnormalities on follow-up films. doi = 10.1016/j.jemermed.2004.11.022 id = cord-292580-caxb9ob9 author = Chang, Z title = RNAi therapeutics: Can siRNAs conquer SARS? date = 2005-11-10 keywords = SARS summary = The epidemic of the severe acute respiratory syndrome (SARS) [1] [2] [3] in 2003 heightened the necessity for us to develop strategies to cope with emerging infectious diseases. Recent work has also shown that selected siRNAs can effectively inhibit SARS-CoV replication in cultured cells. This new study provided, for the first time, the evidence that siRNAs have a significant effect on suppression of SARS-like symptoms in a macaque model. The authors'' results indicated that the SARS-CoV-infected monkeys had attenuated SARS-like symptoms when the animals were treated with siRNA duplexes. Rhesus macaque is a good model for studying human SARS-CoV infections. Although this approach is obviously not a cure for SARS since the treated animals also developed SARS symptoms, it can be used as a complementary strategy to reduce the severity of the disease and to low the viral load in patients. doi = 10.1038/sj.gt.3302682 id = cord-281254-x7ivjvti author = Chang, Zhijie title = Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date = 2012-08-16 keywords = RNA; SARS; siRNA summary = The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. Since SARS-CoV rep-To address the issue related to delivery of siRNAs into cells or lication also requires certain host proteins, genes from host cells living organisms, researchers have used several approaches, ininvolved in viral replication can also be selected as targets. Therefore, RNA interference this coronavirus family), siRNAs targeting different genes of can be a tool for down-regulation of gene expression in cultured SARS-CoV were used by various groups to inhibit virus gene cells as well as in living organisms. doi = 10.2165/00063030-200721010-00002 id = cord-327685-fymfqvp3 author = Channappanavar, Rudragouda title = Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date = 2017-05-02 keywords = IFN; MERS; SARS; respiratory summary = In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice doi = 10.1007/s00281-017-0629-x id = cord-299470-sqqer16k author = Chappell, J. G. title = Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom date = 2020-08-21 keywords = March; SARS summary = In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. Initial SARS-CoV-2 RT-PCR testing in the UK was offered via referral to Public Health England (PHE) national and regional diagnostic laboratories, and required strict epidemiological and clinical criteria to be met, specifically a recent travel history to Hubei province or contact with a known case and 1 or more of fever, shortness of breath or new and persistent dry cough. We describe the detection of SARS-CoV-2 from 8 patients admitted to hospital with severe respiratory distress who were not tested at the time because they had no travel history or contact with someone infected and therefore did not meet the case definition applied at the time. doi = 10.1101/2020.08.18.20174623 id = cord-351864-zozrj7w5 author = Chappleboim, A. title = ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date = 2020-08-13 keywords = PCR; RNA; SARS; figure summary = Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Briefly, we show ( Figure 1 ) that we can introduce barcoded and target-specific reverse transcription primers to the samples, allowing them to hybridize to target RNA molecules already in the lysis buffer, or after a brief RNA cleanup step. Observing the target sequence directly allowed us to identify viral sequence variations in some cases ( Figure 2D ).Cross-Sample Contamination is minimal When pooling samples early on in the protocol, the main concern is that RNA molecules will be erroneously tagged due to residual free primers, or due to other artifacts during RT, PCR, or sequencing. doi = 10.1101/2020.08.08.20170746 id = cord-268324-86a0n0dc author = Charitos, Ioannis A title = Special features of SARS-CoV-2 in daily practice date = 2020-09-26 keywords = COVID-19; Health; SARS; disease; patient; respiratory summary = The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia. doi = 10.12998/wjcc.v8.i18.3920 id = cord-351218-ei8dyxfg author = Charles Bronson, Stephen title = Letter to the Editor in response to the article “Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? date = 2020-07-03 keywords = SARS summary = title: Letter to the Editor in response to the article "Lack of type 1 diabetes involvement in the SARS-CoV-2 population: Only a particular coincidence? Dear Sir, I read with great interest the article by Pitocco et al titled "Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence?". The authors have pointed towards an apparent lack of involvement of type 1 diabetes patients in the COVID-19 patients'' population in the data from three studies. Also, I have come across another COVID-19 patient who was detected to have increased blood glucose levels along with ketosis for the very first-time during his admission for COVID-19. This is in line with reports where newly detected diabetes presented with ketoacidosis in COVID-19 patients. Lack of type 1 diabetes (T1D) involvement in the SARS-CoV-2 population: Only a particular coincidence? Association of Blood Glucose Control and Outcomes in Patients with COVID-19 and Pre-existing Type 2 Diabetes doi = 10.1016/j.diabres.2020.108306 id = cord-312027-5tntdjp9 author = Charlton, Carmen L. title = Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies date = 2020-09-22 keywords = Affinity; SARS; assay summary = We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. To develop a panel of positive sera from patients with COVID-19, serum samples were collected from hospitalized patients confirmed to be positive for SARS-CoV-2 upon nasopharyngeal swab or endotracheal aspirate testing by rRT-PCR. Performance characteristics of EIAs. In total, 46 samples from 28 different patients testing positive for SARS-CoV-2 by rRT-PCR and 50 negative samples from serum samples stored prior to 1 November 2019 were run on each assay. Interestingly, despite four different samples collected from patient 6 (ranging from 18 to 29 days after symptom onset), antibodies were never detected by the Roche assay. doi = 10.1128/jcm.01361-20 id = cord-322473-fmob6k0q author = Charpiat, Bruno title = Proton Pump Inhibitors are Risk Factors for Viral Infections: Even for COVID-19? date = 2020-08-10 keywords = PPI; SARS summary = During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more attention should be paid to the balance of risks and benefits associated with proton pump inhibitors for the following reasons. Studies have documented that proton pump inhibitors are a risk factor for rotavirus, influenza virus, norovirus, and Middle East respiratory syndrome coronavirus infections, and are associated with an increased risk of acute gastroenteritis during periods of highest circulation of enteric viruses. Given the magnitude of the SARS-CoV-2/COVID-19 pandemic, associated with the widespread misuse of PPIs, this suggests that we cannot/should not rule out the hypothesis that patients treated with PPIs may be more at risk of being infected by COVID-19. They, therefore, hypothesized that PPI treatment may also be a potential risk factor for the development of secondary infections and of acute respiratory distress syndrome in hospitalized patients with COVID-19 [12] . doi = 10.1007/s40261-020-00963-x id = cord-335137-5qt286kc author = Chatterjee, Swapan K. title = Molecular Pathogenesis, Immunopathogenesis and Novel Therapeutic Strategy Against COVID-19 date = 2020-08-11 keywords = ACE2; COVID-19; CoV-2; SARS; cell summary = It is believed that interaction between angiotensin converting enzyme 2 (ACE2) cell receptor and viral Spike protein mediates the coronavirus entry into human respiratory epithelial cells and establishes the host tropism. The most significant surface protein is spike glycoprotein which interferes in establishing the association between the human respiratory epithelial cells to the virus via cell surface membrane receptor angiotensin-converting enzyme 2 (ACE2) and finally establishes the host tropism (Li et al., 2003) . A recent study suggests that prediction of SARS-CoV-2 spike glycoprotein structure, glycan shield pattern and pattern of glycosylation has great inference on understanding the viral camouflage as well as the outline of cell entry, and also facilitate the development of new small-molecule drugs, vaccines, antibodies, and screening of the human host targets (Song et al., 2018) . Various studies have proved that SARS-CoV-2 infection initiation and spread of disease into the host cells mainly depends upon S protein priming by TMPRSS2 (Transmembrane protease serine type 2), the serine protease. doi = 10.3389/fmolb.2020.00196 id = cord-274156-c0c4rjfa author = Chau, J.P.C. title = Infection control practices among hospital health and support workers in Hong Kong date = 2010-08-31 keywords = Kong; SARS summary = We examined compliance with isolation precautions and infection control guidelines, including proper wearing of a mask, goggles/face shield, or gown; handling patient care equipment, linen, and laundry; routine and terminal cleaning; and terminal cleaning of an isolation room. Activities were recorded using an observation checklist for two patient care activities: direct (physical examination, basic and technical nursing care) and indirect (computer data entry and disinfection of equipment); and for compliance with isolation precautions and infection control guidelines laid down by the Centers for Disease Control and Prevention (CDC) and the Hong Kong Hospital Authority (HKHA). The support workers who performed this work demonstrated good compliance, though one was found not to wear a gown during the terminal cleaning of bedside equipment of a patient requiring contact precaution, and some failed to clean and disinfect environmental surfaces such as doorknobs, faucet handles and floors. doi = 10.1016/j.jhin.2009.10.014 id = cord-270776-oulnk1b3 author = Chau, Tai-nin title = Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome date = 2004-08-15 keywords = SARS; acute; patient summary = title: Value of initial chest radiographs for predicting clinical outcomes in patients with severe acute respiratory syndrome Purpose To determine whether the initial chest radiograph is helpful in predicting the clinical outcome of patients with severe acute respiratory syndrome (SARS). Results Bilateral disease and involvement of more than two zones on the initial chest radiograph were associated with a higher risk of liver impairment and poor clinical outcome. Together with the clinical characteristics of SARS, such as fever and chest symptoms, and a recent history of contact with a suspected or confirmed SARS patient, radiographic evidence of infiltrates consistent with pneumonia or acute respiratory distress syndrome is important in establishing the diagnosis (5) . Studies involving patients with community-acquired pneumonia (10) , acute interstitial pneumonia (11) , or idiopathic pulmonary fibrosis (12) have shown that quantitative and qualitative changes on chest radiographs might predict clinical outcome. doi = 10.1016/j.amjmed.2004.03.020 id = cord-340042-intxyu46 author = Chaudhry, Sundas Nasir title = New insight on possible vaccine development against SARS-CoV-2 date = 2020-09-11 keywords = COVID-19; CoV-2; SARS; vaccine; virus summary = In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . doi = 10.1016/j.lfs.2020.118421 id = cord-335768-ry5boej6 author = Chauhan, Shaylika title = Comprehensive review of coronavirus disease 2019 (COVID-19) date = 2020-06-01 keywords = April; COVID-19; China; SARS summary = Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, the capital of China''s Hubei province and has rapidly spread all over the world. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 12, 2020, as shown in Fig. 1 , this has evolved into a pandemic affecting 187 countries/regions with 1, 484, 811 cases in the world with maximum being in USA(1, 347,936) followed by 227,436 in Spain and 224, 422 in United Kingdom at the time of writing .6 It is an un-precedented global health crisis with 286,355 deaths since the virus was first reported. Severe outcomes among patients with coronavirus disease 2019 (COVID-19) d United States doi = 10.1016/j.bj.2020.05.023 id = cord-327799-ngzvdd8c author = Chaumont, Claire title = The SARS-CoV-2 crisis and its impact on neglected tropical diseases: Threat or opportunity? date = 2020-09-21 keywords = NTD; SARS summary = The current global priority is to protect people from attaining the COVID-19 infection and to attend to those infected, resulting in the disruption of other activities of the health sector, such as neglected tropical disease (NTD) control and elimination programs, which, across the globe, have postponed mass drug administration (MDA) campaigns. The most obvious impact of the crisis on NTD programs relates to its effect on infection prevalence due to delayed mass drug administration campaigns. Shifts in human capital availability and transmission dynamics of SARS-CoV-2 will require national NTD programs to adopt different implementation approaches to ensure availability and use of appropriate personnel, as well as preventive measures, including social distancing, safe hygiene practices, and face masks and/or coverings. This approach could better mitigate the risk of SARS-CoV-2 transmission, but community acceptance and costs would need to be carefully considered, as well as its potential impact on coverage. doi = 10.1371/journal.pntd.0008680 id = cord-346530-o65m0whe author = Chaumont, H. title = Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection date = 2020-06-12 keywords = SARS summary = title: Mixed central and peripheral nervous system disorders in severe SARS-CoV-2 infection We report four cases of severe COVID-19 in male patients aged 50-70 with the combination of central and peripheral nervous system disorders occurring unexpectedly late after the first symptoms. Several acute neurological syndromes have been associated with SARS-CoV-2 infection, including anosmia and ageusia [1, 2] , meningoencephalitis [3, 4] , acute hemorrhagic necrotizing encephalopathy [5] , axonal or demyelinating polyradiculoneuropathy [6] [7] [8] , polyneuritis cranialis [8] . They consisted of miscellaneous symptoms such as confusion, cognitive dysfunction (memory deficit, frontal syndrome), psychiatric disorders (paranoid delusion, hallucinations), weakness, pyramidal signs, dysautonomia, swallowing dysfunction, vertical supranuclear eye palsy, upper limbs myoclonus, fasciculation and focal muscle atrophy (Table 1) . COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurologic features in severe SARS-CoV-2 infection doi = 10.1007/s00415-020-09986-y id = cord-308831-u5bj1sod author = Chaung, Jenna title = Coinfection with COVID‐19 and Coronavirus HKU1 – the critical need for repeat testing if clinically indicated date = 2020-04-15 keywords = SARS summary = COVID-19 is the latest global pandemic caused by the severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2). We describe a case of endemic HCoV co-infection with SARS-CoV-2 in a patient with COVID-19. Nasopharyngeal swabs were sent on day 1 of admission, one was positive for HCoV-HKU1 on the FilmArray Respiratory Panel (RP) (BioFire Diagnostics, bioMerieux) but another was negative for SARS-CoV-2 by RT-PCR (in-house-laboratorydeveloped test detecting the N and ORF1ab genes by primers, with LightCycler 2.0 instrument from Roche, RotKreuz, Switzerland a ) 6 . Hence, we believe that our patient experienced co-infection with both endemic HCoV-HKU1 and pandemic SARS-CoV-2. Our case illustrates the importance of maintaining a high degree of suspicion and to note that positivity for a known virus on any respiratory multiplex assay does not exclude the possibility of co-infection with SARS-CoV-2 in a patient with a compatible clinical presentation and epidemiological history. doi = 10.1002/jmv.25890 id = cord-256688-yy7abob9 author = Chavez, Summer title = Coronavirus Disease (COVID-19): A primer for emergency physicians date = 2020-03-24 keywords = COVID-19; China; Coronavirus; Disease; SARS; patient summary = DISCUSSION: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing COVID-19, is primarily transmitted from person-to-person through close contact (approximately 6 ft) by respiratory droplets. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), previously referred to as 2019-nCoV, is the virus responsible for causing Coronavirus Disease 2019 (COVID-19) [3] [4] [5] [6] [7] . An emergency medicine approach to COVID-19 should focus on identifying and isolating patients at risk for infection, informing hospital infection prevention and local public health authorities, and engaging infectious disease and other specialists early in care. Emergency physicians should obtain a detailed travel history from all patients and suspect COVID-19 in patients presenting with symptoms of an acute upper respiratory illness and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Home care for patients with suspected novel coronavirus (nCoV) infection presenting with mild symptoms and management of contacts doi = 10.1016/j.ajem.2020.03.036 id = cord-321819-lqyo9px1 author = Chaw, Liling title = Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei date = 2020-11-17 keywords = Brunei; SARS; case summary = We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. Brunei''s thorough contact tracing provides a rare opportunity to study the epidemiologic and transmission characteristics of SARS-CoV-2 in different community settings. Among 1,755 close contacts of the COVID-19 cluster among Tablighi members in Brunei, 52 local transmissions were detected, giving an overall nonprimary attack rate of 2.9% (95% CI 2.2%-3.8%). We could not calculate the attack rate for attendees of the local religious gathering because the 3 primary cases at the event had different symptom statuses and we could not ascertain how transmission occurred. In the household setting, symptomatic casepatients had 2.7 times the risk of transmitting SARS-CoV-2 to their close contacts, compared with asymptomatic and presymptomatic case-patients (crude risk ratio 2.66 [95% CI 1.12-6.34]; Table 3 ). doi = 10.3201/eid2611.202263 id = cord-291726-8670s4st author = Che, Xiao-yan title = A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date = 2006-07-01 keywords = SARS; case summary = Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. doi = 10.1086/504943 id = cord-293579-w5sub348 author = Che, Xiao-yan title = Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome—Associated Coronavirus and Human Coronaviruses 229E and OC43 date = 2005-06-15 keywords = OC43; SARS summary = By use of Western blot analysis, indirect immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA), antigenic cross-reactivity between severe acute respiratory syndrome (SARS)—associated coronavirus (SARS-CoV) and 2 HCoVs (229E and OC43) was demonstrated in immunized animals and human serum. In the present study, we cloned the nucleocapsid genes of SARS-CoV, HCoV-229E, and HCoV-OC43 and produced specific animal antisera to determine if the nucleocapsid protein is responsible for the observed antigenic cross-reactivity. The serum samples from patients with SARS had antibody responses to SARS-CoV as well as to HCoV-229E and HCoV-OC43 when nucleocapsid proteins were used in the Western blot analysis and when CoV-infected cells were used in the IFA. Furthermore, antibodies to SARS-CoV could be detected in only 1 serum sample from a healthy donor by either IFA or nucleocapsid protein-based Western blot analysis, even though patients with SARS had antibodies to HCoV-229E and HCoV-OC43. doi = 10.1086/430355 id = cord-350990-tywbe4o2 author = Checchi, Vittorio title = COVID‐19 dentistry‐related aspects: a literature overview date = 2020-07-05 keywords = COVID-19; Sars; dental; patient summary = The terms used for the identification of keywords were: COVID-19, 2019-nCov, Sars-CoV-2, COVID-19 transmission, Coronavirus pneumonia, Coronavirus infection, Severe acute respiratory syndrome, Atmospheric contamination, Droplets, Aerosol, PPE/DPI, COVID-19 guidelines, Airborne contamination, Masks and respirators, and COVID-19 dental-related aspects. Therefore, dental procedures can be considered as one of the most probable causes of Sars-CoV-2 infection because such procedures require close proximity to the patient''s mouth, possess a risk of contact with saliva, blood and other biological fluids and involve the use of instrumentation that creates large aerosols 4, 19, 20 . Moreover Sars-CoV-2 demonstrates persistent adherence, for a maximum of 9 days, to various surfaces 1, 21 ; therefore, all surfaces and instruments in a dental clinic should be considered as potential sources of virus transmission because infected droplets from saliva or aerosols could land on any exposed surface 16, 19, 22 . doi = 10.1111/idj.12601 id = cord-331066-ediowz4s author = Chechetkin, Vladimir R. title = Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date = 2020-09-09 keywords = DDFT; RNA; SARS summary = Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Therefore, the putative weakly specific assembly/packaging signals in the genomic RNA of coronaviruses should be coordinated with the parameters of the helical nucleocapsid (such as the helix pitch, inner and outer diameters) which are established by cryoelectron microscopy (cryo-EM) and other structural methods. In this article, we provide methods for the detection and comparative analysis of assembly/packaging signals in the genomic RNA of the coronaviruses SARS-CoV and SARS-CoV-2 and describe main results of our study. The abundance of quasi-periodic patterns in the genomic DNA/RNA sequences can be assessed by the spectral entropy (Balakirev et al., 2003 (Balakirev et al., , 2005 (Balakirev et al., , 2014 Chechetkin, 2011; Chechetkin & Lobzin, 1996; Chechetkin & Turygin, 1994) . doi = 10.1080/07391102.2020.1815581 id = cord-189561-jhvwozsn author = Chechetkin, Vladimr R. title = Combining Detection and Reconstruction of Periodic Motifs in Genomic Sequences with Transitional Genome Mapping date = 2020-10-14 keywords = SARS; TAMGI; dna summary = A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences. f The distribution of k-mer lengths after TAMGI for the steps within interval 1-500 for the genome of SARS-CoV-2 (shown by crosses) and its comparison with the counterpart distribution for a random reshuffled sequence (shown by circles). The correspondence should be searched between the (generally multiple) elements of icosahedral symmetry and the character of large-scale quasi-periodic segmentation induced by weakly specific cooperative interactions between genomic RNA/DNA and capsid proteins. To sum up, TAMGI method developed in this article is quite general and can be applied to the combined detection/reconstruction of quasi-periodic motifs in the genomic RNA/DNA sequences. doi = nan id = cord-301251-6f2nzvhz author = Cheemarla, N. R. title = Host response-based screening to identify undiagnosed cases of COVID-19and expand testing capacity date = 2020-06-05 keywords = SARS summary = Based 25 on previous work, we hypothesized that an elevated level of the interferon inducible protein 26 CXCL10 in the nasopharynx could serve as a sensitive screen for patients with an active 27 respiratory virus infection including SARS-CoV2 2 . Protein measurements lend themselves to 30 rapid, high throughput, and point-of care diagnostic methodologies 3,4 , so this combined strategy 31 offers the potential to have a first step which is sensitive and convenient (CXCL10 assay) 32 followed by a more specific test (PCR) for a subset of screen-positive patients. . https://doi.org/10.1101/2020.06.04.20109306 doi: medRxiv preprint Previously, we found that the CXCL10 level in the NP swab viral transport medium was a useful 45 indicator of infection with many common respiratory viruses 2 , suggesting that this measurement 46 could be used to indicate which of these 376 samples were most likely to contain a virus not 47 detected by the RVP. doi = 10.1101/2020.06.04.20109306 id = cord-255752-ofph98ac author = Chegondi, Madhuradhar title = Coronavirus Disease 2019 (COVID-19) Associated With Febrile Status Epilepticus in a Child date = 2020-08-18 keywords = SARS; covid-19 summary = Infection associated with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been named coronavirus disease 2019 (COVID-19). We report the case of a two-year-old child who presented to our pediatric intensive care unit with febrile status epilepticus and was diagnosed to have COVID-19 infection. The emerging literature suggests that the SARS-CoV-2 infection can affect children, including all age groups, predominantly males, and cause milder disease compared to adult patients [2, 3] . We report the case of a two-year-old child who presented to our pediatric intensive care unit (PICU) with febrile status epilepticus and was diagnosed to have COVID-19 infection. A retrospective study from China reported that common neurological symptoms in adult patients with COVID-19 include headache, dizziness, and rarely seizures [12] . Our index case illustrates that SARS-CoV-2 associated COVID-19 can present with febrile seizure and febrile status epilepticus in children. doi = 10.7759/cureus.9840 id = cord-337825-ujq9mxk7 author = Chen, Bin title = Overview of lethal human coronaviruses date = 2020-06-10 keywords = ACE2; CoV; CoV-2; East; MERS; Middle; SARS; coronavirus; protein summary = Coronaviruses are the largest +ssRNA viruses and contain at least 14 ORFs, 16 protein combines with viral RNA to form a nucleocapsid, which is involved in the replication of SARS-CoV and is the most abundant protein in virus-infected cells. MERS-CoV can infect T-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, Nanopore Targeted Sequencing, also has the potential for efficiently detecting viruses in a reasonable time. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein Identification of a receptor-binding domain in the S protein of the novel human coronavirus Middle East respiratory syndrome coronavirus as an essential target for vaccine development Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.1038/s41392-020-0190-2 id = cord-271339-wt5o9sgm author = Chen, Chao-Ju title = Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date = 2020-05-21 keywords = PCR; SARS summary = The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To ensure the whole process of the COVID-19 diagnostic testing took place without a problem, we simultaneously added primers and a probe of human RNase P gene (RP gene) as an internal control in the same well with the RdRp gene assay according to the protocol from the U.S. CDC [6] (Figure 3 ). In the present report, we demonstrated our experience of relying on a protocol template from the Taiwan CDC to establish an optimized COVID-19 molecular diagnostic test within our routine services in a public health emergency. doi = 10.3390/diagnostics10050333 id = cord-343034-dzvo9v01 author = Chen, Chun-Fan title = Role of dipeptidyl peptidase-4 inhibitors in patients with diabetes infected with coronavirus-19 date = 2020-04-29 keywords = SARS summary = The pandemic infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is widely increasing the patients affiliated with coronavirus disease 2019 (COVID-19) from last December of 2019. Notably, whether the ACE-related inhibitors or drugs modulated ACE2 activity in affecting the viral activity and disease severity of SARS-CoV-2 is still an open question. In this article, we are focusing on the impact of ACE inhibitors (ACEI) and DPP4 inhibitors used on SARS-CoV-2 activity and discussions about those drugs that may be related to infectious condition of COVID-19 diseases. Severe acute respiratory syndrome coronavirus (SARS-CoV-1) was the first epidemic coronavirus threat infected more than 8000 people with case-fatality rate (CFR) about 11%. Previous experiments had confirmed that angiotensin-converting enzyme 2 (ACE2) is the entry receptor in SARS-CoV-1 and dipeptidyl peptidase-4 (DPP4, also known as CD26) is the entry receptor in MERS-CoV. Among numerous anti-diabetic drugs, DPP4 inhibitors might play an important role during coronavirus infection, including pandemic COVID-19. doi = 10.1097/jcma.0000000000000338 id = cord-296195-m2wwlvgx author = Chen, Chung-Jen title = Toona sinensis Roem tender leaf extract inhibits SARS coronavirus replication date = 2008-10-30 keywords = SARS; TCM; Toona summary = RESULTS: Only TSL-1, the extract from tender leaf of Toona sinensis Roem was found to have an evident effect against SARS-CoV with selectivity index 12∼17. In the third study, five TCM formulae included Yin-Chiau-San, Pu-Zhi-Siau-Du-Yien, Ger-Gern-Hwang-Lein, Sang-Zhiu-Yien and Huang-Lein-Zhei-Du-Tang as well as Toona sinensis Roem tender leaf extract TSL-1 and TSL-1nm were tested against SARS-CoV. Much different from a lot of previously identified components or drugs against SARS-CoV, the tender leaf of Toona sinensis Roem has been used as a popular vegetable by Chinese people in both mainland China and Taiwan with high level of safety. To our knowledge, this is the first report to show extract from the tender leaf of Toona sinensis Roem against SARS-CoV. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. In conclusion, this paper reports for the first time that extract from a vegetable, the tender leaf of Toona sinensis Roem, can inhibit SARS-CoV in vitro. doi = 10.1016/j.jep.2008.07.048 id = cord-283590-xvnv17zy author = Chen, Dabiao title = Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date = 2020-03-05 keywords = RNA; SARS summary = Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People''s Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). doi = 10.1016/j.ijid.2020.03.003 id = cord-276017-2375ipkk author = Chen, Dongsheng title = Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date = 2020-06-14 keywords = ACE2; SARS summary = Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Previous studies have proposed that animal tissues show high heterogeneity in terms of cellular composition and gene expression profiles 15 , and ACE2 is only expressed in a small proportion of specific cell populations 16 , making single cell analysis of SARS-CoV-2 target cells an attracting field to investigate. Here, we constructed the single cell atlas for livestock, poultry, pets and wildlife, then screened putative SARS-CoV-2 target cells (indicated by the co-expression patterns of SARS-CoV-2 entry receptor ACE2 and SARS-CoV-2 entry activator TMPRSS2) and systematically evaluated their susceptibility, with the aim to understand the virus transmission routes and provide clues to fight against COVID-19. doi = 10.1101/2020.06.13.149690 id = cord-312899-ot5pvtbl author = Chen, F title = In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds date = 2004-09-30 keywords = SARS; Vero; interferon summary = Commercial antiviral agents and pure chemical compounds extracted from traditional Chinese medicinal herbs were screened against 10 clinical isolates of SARS coronavirus by neutralisation tests with confirmation by plaque reduction assays. Interferon-beta-1a, leukocytic interferon-alpha, ribavirin, lopinavir, rimantadine, baicalin and glycyrrhizin showed antiviral activity. We report in this study on the in vitro antiviral susceptibility of 10 isolates of SARS coronavirus to commercially available antiviral agents and pure chemical compounds including baicalin, glycyrrhizin, and chlorogenic acid extracted from traditional Chinese herbs. Further testing by neutralization tests Table 3 Comparison of antiviral activity of 10 compounds against 10 strains of SARS-CoV in fRhK4 cell line, against the prototype strains (39849) with the other 9 isolates of SARS coronavirus against the active compounds confirmed detectable inhibitory activities for leukocytic interferon-alpha, interferon-beta-1a, ribavirin, lopinavir, rimantadine, and baicalin. doi = 10.1016/j.jcv.2004.03.003 id = cord-299354-rmjohbse author = Chen, Fu-Lun title = Co-infection with an atypical pathogen of COVID-19 in a young date = 2020-05-21 keywords = SARS summary = key: cord-299354-rmjohbse authors: Chen, Fu-Lun; Wang, Cheng-Hui; Hung, Ching-Sheng; Su, Ying-Shih; Lee, Wen-Sen title: Co-infection with an atypical pathogen of COVID-19 in a young date: 2020-05-21 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.05.007 sha: doc_id: 299354 cord_uid: rmjohbse nan Dear Editor: The article by Jean et al. Treatment options for COVID-19: The reality and challenges Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV Recommendations and guidelines for the treatment of pneumonia in Taiwan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical characteristics of coronavirus disease 2019 in China doi = 10.1016/j.jmii.2020.05.007 id = cord-289332-hvakv08t author = Chen, Guoqian title = Pathogenic role of HMGB1 in SARS? date = 2004-04-30 keywords = HMGB1; SARS summary = High mobility group box 1 protein (HMGB1) is released by necrotic cells or activated macrophages/monocytes, and functions as a late mediator of lethal systemic and local pulmonary inflammation. In light of observations that three Chinese herbal formulations recommended for treatment of severe acute respiratory syndrome (SARS) specifically inhibited the release of HMGB1 from innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. High mobility group box 1 protein (HMGB1, formerly known as HMG-1 or amphoterin) has recently been identified as a new proinflammatory cytokine and a late mediator of inflammation, sepsis, and acute lung injury. In light of observations that several Chinese herbal remedies recommended for treatment of SARS specifically inhibited the release of HMGB1 from activated innate immune cells, we hypothesize that HMGB1 might occupy a pathogenic role in SARS by mediating an injurious pulmonary inflammatory response. doi = 10.1016/j.mehy.2004.01.037 id = cord-352509-qrzt4zva author = Chen, Haohui title = Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak date = 2020-03-16 keywords = SARS; Wuhan; awareness summary = This study examines publicly available online search data in China to investigate the spread of public awareness of the 2019 novel coronavirus (COVID-19) outbreak. We use the continuing Wuhan coronavirus outbreak as our case study to estimate the effects of social distance and SARS memory on the spread of public awareness. The effects of social distance and SARS memory on the lead-time advantage are estimated according to Eq. 4, controlled by Euclidean distances, GDP per capita and the city''s administrative level (Table 1) . That means cities of strong SARS memory and which are closer to Wuhan in terms of Social distances develop early awareness. Through controlling for development, administrative levels, and Euclidean distances, we observe cities that were struck by SARS and have more migration to the epicentre, Wuhan, showed earlier, stronger and more durable public awareness of the outbreak. doi = 10.1101/2020.03.11.20033688 id = cord-282045-pf08iakf author = Chen, Haoyan title = Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production date = 2020-07-08 keywords = Fig; SARS summary = title: Single cell transcriptome revealed SARS-CoV-2 entry genes enriched in colon tissues and associated with coronavirus infection and cytokine production The percentage of these five SARS-CoV-2 entry genes was similar as ACE2, which is gradually increased in epithelial cells from normal control, CRA to CRC samples (Supplementary Fig. S3d ). Strikingly, pathways associated with virus infection, inflammation and cytokine signaling were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) . Given that IL-6 and TNF pathways were upregulated in six potential SARS-CoV-2 entry genes enriched cells (Fig. 1a) , we compared the IL-6 and TNF-alpha levels in peripheral blood from mild (n = 102) and severe (n = 50) COVID-19 pneumonia patients Table S3 ). Here, we first proved that the six SARS-CoV-2 entry genes, including ACE2 and TMPRSS2, are expressed in the colon epithelial cells of Chinese adults. In a word, the expression of additional five SARS-CoV-2 entry genes, virus infection, and inflammatory pathways are significantly enriched in colon epithelia cells with ACE2-positive expression. doi = 10.1038/s41392-020-00237-0 id = cord-288197-drto66xt author = Chen, Huijun title = Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records date = 2020-02-12 keywords = SARS; covid-19; patient summary = METHODS: Clinical records, laboratory results, and chest CT scans were retrospectively reviewed for nine pregnant women with laboratory-confirmed COVID-19 pneumonia (ie, with maternal throat swab samples that were positive for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) who were admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from Jan 20 to Jan 31, 2020. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy. Evidence of vertical transmission was assessed by testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in amniotic fluid, cord blood, breastmilk, and neonatal throat swab samples from six of nine patients. Based on data from this small group of patients, there is currently no evidence of vertical transmission in pregnant women who develop COVID-19 pneumonia in the third trimester. doi = 10.1016/s0140-6736(20)30360-3 id = cord-278540-gy65bvot author = Chen, I-Yin title = Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date = 2019-01-29 keywords = NLRP3; SARS summary = A recent study shows that the SARS-CoV E protein, which comprise only 76 amino acids, forms Ca 2+ -permeable ion channels and activates the NLRP3 inflammasome (Nieto-Torres et al., 2015) . To this end, we substituted amino acids Cys-127, Cys-130, and Cys-133 within the cysteine-rich domain of the SARS-CoV 3a protein with serine to generate a lentivirus expressing the ion channel activity-loss mutant, 3a-CS (Chan et al., 2009; Figure 2A) . Together, these data provide evidence that the ion channel activity of the SARS-CoV 3a protein is essential for triggering the NLRP3 inflammasome. Since mitochondrial ROS are important for NLRP3 inflammasome activation (Nakahira et al., 2011; Zhou et al., 2011) , we next stimulated BMMs with extracellular ATP or lentiviruses expressing the SARS-CoV E or 3a proteins in the presence or absence of the antioxidant, Mito-TEMPO, a scavenger that is specific for mitochondrial ROS Trnka et al., 2009) . doi = 10.3389/fmicb.2019.00050 id = cord-287349-1zcq7kzx author = Chen, James title = Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date = 2020-07-28 keywords = RNA; SARS; figure; structural summary = title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. The analogous structural 234 arrangement leads us to propose that the SARS-CoV-2 RdRp may backtrack, generating a single-235 stranded RNA segment at the 3''-end that would extrude out the RdRp secondary channel 236 Table S1 ; Video S1). This aspect of helicase function could provide the NTP-296 dependent motor activity necessary to backtrack the RdRp. In cellular organisms, DdRp 297 backtracking plays important roles in many processes, including the control of pausing during 298 transcription elongation, termination, DNA repair, and fidelity (Nudler, 2012) . Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase doi = 10.1016/j.cell.2020.07.033 id = cord-133453-23rfdkuw author = Chen, Jiahui title = Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies date = 2020-10-13 keywords = ACE2; BFE; RBD; SARS; antibody summary = By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. The vaccination mechanism is to stimulate the primary immune response of the human body, which will activate T cells and B cells to generate the antibodies and long-lived memory cells that prevent infectious diseases, which is one of the most effective and economical means for combating with COVID-19 at this stage. Notably, understanding how mutations have changed the SARS-CoV-2 structure, function, infectivity, activity, and virulence is of great importance for coming up with life-saving strategies in virus control, containment, prevention, and medication, especially in the antibodies and vaccines development. Next, we study the BFE changes ∆∆G induced by 39 mutations on the SARS-CoV-2 S protein RBD for the antibody Fab 2-4 (PDB: 6XEY) in Figure 6 . doi = nan id = cord-167889-um3djluz author = Chen, Jianguo title = A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19 date = 2020-07-04 keywords = COVID-19; CXR; SARS; image; model summary = The progress of CT image inspection based on AI usually includes the following steps: Region Of Interest (ROI) segmentation, lung tissue feature extraction, candidate infection region detection, and COVID-19 classification. Data sources Methods Country/region Huang [82] Yang [231] , WHO [216] CNN, LSTM, MLP, GRU China Hu [80, 81] The Paper [148] , WHO [216] MAE, clustering China Yang [233] Baidu [16] SEIR, LSTM China Fong [51, 52] NHC [139] SVM, PNN China Ai [3] WHO [54, 216] ANFIS, FPA China, USA Rizk [168] WHO [216] ISACL-MFNN USA, Italy, Spain Giuliani [62] Italy [144] EMTMGL Italy Ayyoubzadeh [14] Worldometer [218] , Google [201] LR, LSTM Iran Marini [129, 130] Swiss population Enerpol Switzerland Lai [110] IATA [126] , Worldpop [219] ML Global Punn [155] JHU CSSE [49] SVR, PR, DNN, LSTM, RNN Predicting commercially available antiviral drugs that may act on the novel coronavirus (sars-cov-2) through a drug-target interaction deep learning model doi = nan id = cord-328479-1tzysg7u author = Chen, Jianjun title = Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Pets in Wuhan, China date = 2020-06-21 keywords = SARS summary = In this study, we collected swab and blood samples from pet cats and dogs in Wuhan whose owners were confirmed to have COVID-19. Swab and whole blood samples were collected from 10 cats (four female, six male) and 9 dogs (four female, five male) (Supplementary Table 1 We then conducted telephone questionnaires with the owners of the three pets. In this study, we conducted a survey for SARS-CoV-2 in pets whose owners were diagnosed with COVID-19, in 15 communities in Wuhan. Prior to our study, a preprint of a research article posted online at bioRxiv indicated that SARS-CoV-2-specific antibodies were detected in cats in Wuhan at the time of the COVID-19 epidemic (7) . In addition, pet dogs and cats in Hong Kong (8), whose owners had been diagnosed with COVID-19, tested positive for SARS-CoV-2 RNA. Collectively, these results indicate the SARS-CoV-2 can be transmitted to companion animals, possible through contact with owners carrying COVID-19. doi = 10.1016/j.jinf.2020.06.045 id = cord-318342-eipscagh author = Chen, Juan title = The Impact of COVID-19 on Blood Glucose: A Systematic Review and Meta-Analysis date = 2020-10-05 keywords = COVID-19; SARS; study summary = Results: Three studies reported blood glucose and HbA1c according to the severity of COVID-19 and were included in this meta-analysis. It remains unclear regarding the effect of severity of COVID-19 infection on glycemic parameters, including blood glucose and glycated haemoglobinA1c (HbA1c). Finally, three papers were included in the meta-analysis that evaluated blood glucose and/or HbA1c levels according to the severity of COVID-19 (17) (18) (19) . The z-test result for overall effects was statistically significant (P < 0.001), indicating a significantly greater elevation in blood glucose in patients with severe COVID-19 infection than those in the mild group. In the present meta-analysis, we found that blood glucose was significantly higher in patients with severe COVID-19 than those with mild COVID-19 (WMD 2.21, 95% CI: 1.30-3.13, P < 0.001, I 2 = 0%). doi = 10.3389/fendo.2020.574541 id = cord-262467-epqqd8n8 author = Chen, Jun title = COVID-19 infection: the China and Italy perspectives date = 2020-06-08 keywords = COVID-19; China; HCQ; PCR; SARS; patient summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 disease as originally shown in Wuhan, China, as early as documented from 1 December 2019 (ref. A recent prospective study failed to find antiviral activity or clinical benefit of this combination for the treatment of our hospitalized patients with severe COVID-19 (ref. More recently, a randomized, controlled study conducted in Wuhan, China also failed to identify beneficial effect of LPV/r beyond standard therapy in hospitalized patients with severe Covid-19 (ref. Clinical trials also showed that in patients with severe H1N1 influenza A, in the 2009 pandemic, therapy with convalescent plasma from patients who recovered, especially within 5 days of symptom onset, resulted in a lower viral load and lower mortality 66, 67 . The duration from onset of symptoms to viral clearance is significantly longer in severe and critical ill SARS-CoV-2infected patients compared with that in the mild cases 48 . doi = 10.1038/s41419-020-2603-0 id = cord-031079-9lxhvyyb author = Chen, Li title = The effects of chloroquine and hydroxychloroquine on ACE2 related coronavirus pathology and the cardiovascular system: An evidence based review date = 2020-07-27 keywords = ACE2; CoV-2; HCQ; SARS summary = CQ and HCQ may be potential inhibitors of SARS-CoV-2 entry into host cells, which is mediated via the angiotensin-converting enzyme 2 (ACE2), and may also inhibit subsequent intracellular processes which lead to COVID-19, including damage to the cardiovascular system. CQ and HCQ could potentially be useful drugs in the treatment of COVID-19 and other ACE2 involved virus infections, but the antiviral effects of CQ and HCQ need to be tested in more well-designed clinical randomized studies and their actions on the cardiovascular system need to be further elucidated. CQ and its more soluble and less toxic metabolite HCQ are primarily used for prophylaxis and treatment of malaria, but they have also been reported to effectively inhibit the effects of certain viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza A H5N. 40, 41 Several studies have reported that 3% to 29% of COVID-19 patients develop acute respiratory distress syndrome (ARDS) which is a common complication and cause of death as a result of SARS-CoV-2 infection. doi = 10.1093/function/zqaa012 id = cord-348723-sf073cmj author = Chen, Liang title = The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 date = 2020-03-30 keywords = ACE2; SARS summary = title: The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Angiotensin-converting enzyme 2 (ACE2), the key host cellular receptor of SARS-CoV-2, has been identified in multiple organs, but its cellular distribution in human heart is not illuminated clearly. This study performed the first state-of-art single cell atlas of adult human heart, and revealed that pericytes with high expression of ACE2 might act as the target cardiac cell of SARS-CoV-2. The finding of this study explains the high rate of severe cases among COVID-19 patients with basic cardiovascular disease; and these results also perhaps provide important reference to clinical treatment of cardiac injury among severe patients infected by SARS-CoV-2. In the present study, we investigated ACE2 expression in the adult human hearts from healthy and diseased individuals, to illuminate the potential capacity of heart infection by SARS-CoV-2. This result suggested that pericyte was a potential SARS-CoV-2 virus targeted host cell type in the human heart. doi = 10.1093/cvr/cvaa078 id = cord-350393-j80k2v21 author = Chen, Liping title = Clinical characteristics in patients with SARS‐CoV‐2/HBV co‐infection date = 2020-07-15 keywords = HBV; SARS summary = In our previous study 7 (138 cases), there were only 9 (6.1%) cases (too small) with underlying liver diseases, so no further analysis was made Accepted Article over the clinical features of COVID-19 patients with HBV infection. In this retrospective study, we expanded the sample size and aimed to evaluate the influence of SARS-CoV-2/HBV co-infection on the clinical characteristics including liver function and disease outcome. Taken into consideration that viral co-infection can exacerbate liver injury thus have a big impact on disease progression and outcome 11, 12 , we investigated the prevalence of HBV infection in COVID-19 patients and found that there was a comparable rate of SARS-CoV-2/HBV co-infection to that of general population (6.1% vs 6%). Taken together, our study is the first to elaborate on the clinical characteristics of SARS-CoV-2/HBV co-infection patients and demonstrate that the coinfection with HBV slightly affect liver function, showing no impact on the COVID-19 outcome. doi = 10.1111/jvh.13362 id = cord-268653-mje0rysp author = Chen, Miaomiao title = Changes in physiology and immune system during pregnancy and coronavirus infection: a review date = 2020-10-16 keywords = SARS; pregnancy; pregnant summary = We explained why pregnant women are susceptible to coronavirus in terms of their adaptive changes in physiology and immune system during pregnancy, and described the associations between maternal clinical symptoms, perinatal outcomes and coronavirus infections. Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been labeled as a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) on January 30, 2020 [1] [2] . Pregnant women are suspected to aspiration pneumonia because of the decreased sphincter tone in the lower esophagus, which is thought to be associated with high levels of progesterone [30] , which can reduce both pro-inflammatory and cytotoxic T cell responses. As mentioned earlier, pregnant women in their first and third trimester of pregnancy are both at the pro-inflammatory state, and the cytokine storm induced by SARS-CoV-2 in these periods may exacerbate the severity of inflammatory J o u r n a l P r e -p r o o f state, following the obstetric adverse outcomes. doi = 10.1016/j.ejogrb.2020.10.035 id = cord-350513-ho32ajsx author = Chen, Paul Chih‐Hsueh title = Re: To KF, Tong JH, Chan PK, et al. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. J Pathol 2004; 202: 157–163 date = 2004-05-07 keywords = SARS summary = Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in‐situ hybridization study of fatal cases. Using in situ hybridization (ISH), To et al demonstrated the presence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) in pneumocytes and in the surface enterocytes of the small intestine. Supplementing their findings, we report here our recent study, which suggests that the SARS-CoV may not be exclusively located in pneumocytes, but also in pulmonary macrophages. Under low magnification, scattered cells containing dark bluish signals, which represented the SARS-CoV, were visualized ( Figure 1A , nuclear fast red counterstain) within the damaged alveolar spaces, small bronchioles, and even the vascular lumina. Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Chen and Hsiao make an interesting observation on the pathology of severe acute respiratory syndrome (SARS). doi = 10.1002/path.1575 id = cord-320333-audnwp8t author = Chen, Qi-Lin title = Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis date = 2020-05-19 keywords = ACE2; SARS; TMPRSS2 summary = BACKGROUND: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. METHODS: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. The GSE121862 database is a combination of data from different experiments and institutions, and studies have suggested that single-nuclear transcriptome sequencing technology is more suitable in the kidney than other methods of gene expression analysis [25] . To compare cell receptor-related genes of SARS-CoV-2 in different tissues, high-quality single-cell transcriptome databases of the lung and small intestine were used for further analysis. For the first time from the single-cell level analysis, our results demonstrate that cell receptor-related genes of SARS-CoV-2 are differentially expressed in cell subgroups of different tissues. doi = 10.1159/000508162 id = cord-319236-gxcs77pl author = Chen, Qingyan title = Can we migrate COVID-19 spreading risk? date = 2020-08-28 keywords = SARS summary = However, we may have under-estimated the disease transmission by small droplets or aerosols that contain SARS-CoV-2 virus. This paper recommended wearing masks in airplanes and use partition screens in the middle of a table in a restaurant to reduce the infectioncausedbySARS-CoV-2virus. Experts so far cannot agree if SARS-CoV-2 transmission could be airborne (Lewis, 2020) , via small droplets or aerosols, although research has shown the risk. Figure 1 shows the droplet cloud that may contain SARS-CoV-2 virus with and without a screen in the middle of a table in a restaurant. The air with displacement ventilation does not mix so that the risk of inhaling airborne infectious disease virus from a neighboring student can be greatly reduced. for a long time, everyone should wear a mask to reduce infection risk although the SARS-CoV-2 virus concentration in indoor air may not be very high. Wearing mask would help as it can reduce the exposure to SARS-CoV-2 virus in air. doi = 10.1007/s11783-020-1328-8 id = cord-343143-tzuhig3f author = Chen, Rong-chang title = Treatment of Severe Acute Respiratory Syndrome With Glucosteroids The Guangzhou Experience date = 2006-06-30 keywords = Guangzhou; SARS; steroid summary = Conclusion This Guangzhou retrospective study revealed that proper use of corticosteroid in confirmed critical SARS resulted in lowered mortality and shorter hospitalization stay, and was not associated with significant secondary lower respiratory infection and other complications. However, the result of a logistic regression based on the data of 152 critical SARS cases showed that steroid therapy significantly reduced the case fatality among critical SARS patients after the death-related variables were adjusted, such as age, rigor at onset, secondary lower respiratory infection, pulmonary rales, and OI grading (1, Ͻ 100; 2, Ն 100 and Ͻ 200; 3, Ն 200 and Ͻ 300; and 4, Ն 300). doi = 10.1378/chest.129.6.1441 id = cord-257206-av2k44ig author = Chen, Ruey title = Effects of a SARS prevention programme in Taiwan on nursing staff''s anxiety, depression and sleep quality: A longitudinal survey date = 2006-02-28 keywords = SARS; care; patient summary = Abstract The aim of this research is to determine the levels of anxiety, depression, and sleep quality a severe acute respiratory syndrome (SARS) nursing staff experienced before and after a SARS prevention program. Using general estimating equations (GEE) statistical analysis to control possible for affecting factors, we found that the nursing staff''s anxiety and depression along with sleep quality started to improve 2 weeks after the initiation of SARS prevention controls. This research is to describe the anxiety level, depression level, and sleep quality of nursing staff who cared for SARS patients during a sweeping epidemic and the effects of a SARS prevention program. Tables 2 and 3 show the effects of the SARS prevention program on nursing staff through their self-reported levels of anxiety and depression as well as sleep quality. doi = 10.1016/j.ijnurstu.2005.03.006 id = cord-314321-klb8oe9q author = Chen, Serena H. title = Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date = 2020-04-18 keywords = SARS; protein; structure summary = Recent experimental structures of the SARS-CoV-2 S protein receptor binding domain (RBD) in complex with ACE2 provide detailed interface information [4] , [6] ; targeting this interface represents an active area of research for therapeutic development [11] . By first comparing the S protein protomer structure of SARS-CoV-2 to those from previous human coronaviruses, we identified distinct clusters for each virus in the 3-D latent space, where representative structures from these clusters highlight their differences in domain flexibility. To further understand the molecular structures of different human coronavirus S proteins and the oligomeric state of SARS-CoV-2 S protein, we deployed a custom-built deep learning architecture, a convolutional variational autoencoder (CVAE), to encode the high dimensional protein structures from the MD simulations into lower dimensional latent spaces. The size of each resulting matrix was also 191 ⇥ 191, and we merged a total of 10,000 distance matrices of the protomer and trimer of SARS-CoV-2 S protein. doi = 10.1101/2020.04.17.047548 id = cord-300041-1d9xu4ts author = Chen, Sharon C-A title = Focus on SARS-CoV-2 and COVID-19 date = 2020-10-08 keywords = CoV-2; SARS summary = In contrast, more recent pandemics have been dominated by viruses such as influenza H1N1 and H3N2, localised epidemics by Ebola virus, severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1), MERS-CoV, and now, SARS-CoV-2, the causative agent of COVID-19. However, by having a single edition, with broad focus on human pathology of SARS-CoV-2 infection, we aim to provide the readers of Pathology with insights from different areas of COVID-19 diagnosis. 2 Substantive progress continues to be made in the arena of diagnostic tests for SARS-CoV-2 infection with improvements in molecular diagnostics, rapid antigen detection tests and serological assays. We continue to be faced by the risk of pandemics and we must learn from our observations at present with SARS-CoV-2 infection, and resulting COVID-19 disease. Virus isolation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnostic and research purposes Rapid deployment of pathology services to a remote Australian quarantine setting during the COVID-19 pandemic doi = 10.1016/j.pathol.2020.09.010 id = cord-349031-tbof9yqi author = Chen, Shiu-Jau title = Novel Antiviral Strategies in the Treatment of COVID-19: A Review date = 2020-08-20 keywords = COVID-19; MSC; SARS; patient; plasma summary = Fortunately, some novel antiviral strategies, such as convalescent plasma, clustered regularly interspaced short palindromic repeats (CRISPR), and mesenchymal stem cell (MSC) therapy, potentially offer an additional or alternative option or compassionate use for the people suffering from COVID-19, especially for critically ill patients, although their safety and efficacy are also under study. In this review, we explore the applications, possible mechanisms, and efficacy in successful cases using convalescent plasma, CRISPR, and MSC therapy for COVID-19 treatment, respectively. In this case series study of five critically ill patients with COVID-19 and ARDS, the administration of convalescent plasma containing neutralizing antibodies significantly improved their clinical status [53] . Under the condition that traditional drugs cannot assure their safety and efficacy for COVID-19 treatment, novel antiviral strategies, including convalescent plasma, CRISPR, and cell therapy, may be able to provide an additional or alternative option or compassionate use for the treatment of COVID-19, particular for critically ill patients. doi = 10.3390/microorganisms8091259 id = cord-271259-6kkzh1tp author = Chen, Shuai title = Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode date = 2010-01-01 keywords = Fig; SARS summary = Therefore, the N-terminal auto-processing of M(pro) appears to require only two "immature" monomers approaching one another to form an "intermediate" dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. These results indicate that N-terminal autocleavage of SARS-CoV M pro from the polyproteins only requires two "immature" proteases approaching one another to form an "intermediate" dimer structure and does not depend on the active dimer conformation existing in the mature protease. Since mutation of either of these two residues were reported to completely abolish the dimer of mature M pro , our finding raises the intriguing question of how the E290R and R298E mutants can auto-process their N-terminal GST tags when they are unable to form the active dimer structure. doi = 10.1007/s13238-010-0011-4 id = cord-343192-fkc7af9y author = Chen, Siyang title = Comment on “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ‐2 (SARS‐CoV‐2)” date = 2020-05-08 keywords = SARS summary = We read the article "Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)" with great interest. Although there have been several reports previously suggesting that the similar SARS-CoV-2 virus could infect neuronal cells and cause central and peripheral neurological morbidities in COVID-19 patients (3) (4) (5) , few direct detection of virus by RT-PCR in cerebrospinal fluid (CSF) has casted earlier doubt whether there is indeed a direct infection of central nervous system (CNS). It is not clear whether SARS-CoV-2 viruses can be similarly detected in endothelial cells from other severe COVID-19 patients with central neurological involvement (3). It is worthy to point out that one very recent report from a Chinese case demonstrating the presence of SARS-CoV-2 virus sequence in the CSF fluid of a COVID-19 patient presenting viral encephalitis (7) . Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) doi = 10.1002/jmv.25991 id = cord-300697-p96i25uc author = Chen, Taojiang title = A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report date = 2020-09-29 keywords = GIB; SARS; patient summary = title: A severe coronavirus disease 2019 patient with high-risk predisposing factors died from massive gastrointestinal bleeding: a case report CASE PRESENTATION: We herein described a case of severe SARS-CoV-2 infected patient with several risk factors for poor prognosis, including male, hypertension, old age, mixed bacterial infection and multilobular infiltration on radiological imaging. After improvement of respiratory status, the onset of gastrointestinal bleeding occurred, probably resulting from direct viral invasion as evidenced by the positive findings for SARS-CoV-2 in the repeat stool specimens. Additionally, despite the clinical manifestations of coronavirus disease 2019 (COVID-19) are dominated by respiratory symptoms, evidences from recent studies have suggested that SARS-CoV-2 has the ability to actively infect and replicate in the gastrointestinal tract [3] . Herein, we described an old-aged COVID-19 patient with multiple risk factors for severe disease and ultimately died from massive GIB at Wuhan Union Hospital. doi = 10.1186/s12876-020-01458-x id = cord-351770-cirq6pfx author = Chen, Wei title = SARS-CoV-2 neutralizing antibody levels are correlated with severity of COVID-19 pneumonia date = 2020-08-13 keywords = COVID-19; SARS summary = In this study, we analyzed the SARS-CoV-2 NAb titers in patients recently recovered from COVID-19 using a novel SARS-CoV-2 surrogate virus neutralization test (sVNT) [12] . The distribution of NAb titers in patients with COVID-19 were then plotted based on the variables of age, sex, symptom, laboratory parameters and chest CT findings at the time of admission, treatment during hospitalization and the time of blood collection for antibody analysis (Figure 1 ). Independent variables included in the OLS model included age, sex, CT score, comorbidity, laboratory parameters that associated with disease severity (CRP level and lymphocyte counts), treatment that may influence immune response to pathogen (corticosteroids and intravenous immunoglobulin) and time of blood collection for NAb analysis. In multivariate analyses, after adjustment for age, sex, comorbidity, corticosteroid treatment, CRP level, lymphocyte count and time of NAb analysis, baseline chest CT scores still strongly correlated with NAb titers in patients recovered from COVID-19 (Table 2 , p=0.02). doi = 10.1016/j.biopha.2020.110629 id = cord-350737-nrtrhq1f author = Chen, Xinchun title = Serology of Severe Acute Respiratory Syndrome: Implications for Surveillance and Outcome date = 2004-04-01 keywords = CoV; SARS; patient summary = A virus from the family Coronaviridae, termed "SARS coronavirus" (SARS CoV), has been identified as the cause [2] [3] [4] [5] [6] [7] , and criteria for laboratory confirmation of SARS CoV infection have been provided by WHO, on the basis of the following methods: (1) detection of SARS CoV RNA by reversetranscription polymerase chain reaction (RT-PCR); (2) serological detection of SARS CoV-related antibody; and (3) isolation of SARS CoV by cell culture [4] . Using an indirect immunofluorescence assay and parallel acute and convalescent serum samples obtained from patients with SARS, tested for IgG antibody to SARS CoV, Peiris et al. In addition, our results indicated that 9 (25.0%) of 36 patients with probable SARS CoV infection had not produced detectable anti-SARS CoV antibody by day 21 after the onset of fever; this implies that 25.0% of patients with SARS might be misdiagnosed by the laboratory confirmation guidelines that WHO currently recommends [5] . doi = 10.1086/380397 id = cord-017942-og0b2l6b author = Chen, Yi-Da title = Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data date = 2007 keywords = SARS; SNA summary = title: Incorporating Geographical Contacts into Social Network Analysis for Contact Tracing in Epidemiology: A Study on Taiwan SARS Data In this research, we use Taiwan SARS data to investigate the differences in connectivity between personal and geographical contacts in the construction of social networks for these diseases. In 1985, Klovdahl [6] used AIDS as an example to illustrate the usefulness of Social Network Analysis (SNA) in studying the transmission of an infectious disease. However, from these two studies, we can see that incorporating geographical contacts into SNA provides us a good way to find potential connections among patients and to see the role that those geographical locations play in disease outbreaks. The studies of SNA in epidemiology primarily use personal contacts to construct social networks and model the transmission of diseases. In this research, by using Taiwan SARS data as the test dataset, we further investigate the differences in connectivity between personal and geographical contacts in the network construction for these diseases. doi = 10.1007/978-3-540-72608-1_3 id = cord-340205-cwn0gx7h author = Chen, Yih-Ting title = Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis date = 2020-07-16 keywords = SARS summary = title: Mortality rate of acute kidney injury in SARS, MERS, and COVID-19 infection: a systematic review and meta-analysis There was no evidence of statistical heterogeneity among studies reporting AKI mortality in SARS (I2: 0.0%, p = 0.589) and MERS (I2: 0.0%, p =v0.758), but there was for COVID-19 infection (I2: 97.0%, p < 0.001) (Fig. 1 ). Possible mechanisms of higher AKI mortality following coronavirus infections are multifactorial (e.g., severe sepsis-related multiorgan failure, direct kidney involvement, and acute respiratory distress syndrome) [26] [27] [28] , although comparative pathogenesis of kidney involvement among the three infections remains unclear. A single center observational study of the clinical characteristics and short-term outcome of 20 kidney transplant patients admitted for SARS-CoV2 pneumonia Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.1186/s13054-020-03134-8 id = cord-350015-mg5wiihj author = Chen, Yiyin title = Aging in COVID-19: Vulnerability, immunity and intervention date = 2020-10-31 keywords = China; CoV-2; SARS; covid-19 summary = The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic was first reported in Wuhan, China in December 2019, moved across the globe at an unprecedented speed, and has caused a profound and yet still unfolding health and socioeconomic impacts. We hypothesize that age-related decline and dysregulation of immune function, i.e., immunosenescence and inflammaging play a major role in contributing to heightened vulnerability to severe COVID-19 outcomes in older adults. Therefore, age-associated reduction in type 1 IFN response coupled with direct viral suppression could serve as a critical innate immune mechanism that leads to poor cell mediated immunity and increased vulnerability of older adults against SARS-CoV-2 infection with therapeutic implication (Sallard et al., 2020) . On the other hand, children with COVID-19 manifested lower levels of T cell activation than adult COVID-19 patients (Moratto et al., 2020) , suggesting better immune system control and regulation in response to SARS-CoV-2 infection in children. doi = 10.1016/j.arr.2020.101205 id = cord-277342-40d24mvm author = Chen, Yu title = SARS-CoV-2: virus dynamics and host response date = 2020-03-23 keywords = SARS summary = In The Lancet Infectious Diseases, Kelvin To and colleagues 4 report the viral load and antibody profiles of a cohort of 23 patients admitted to hospital with COVID-19. First, the high viral load during the early phase of illness suggests that patients could be most infectious during this period, and it might account for the high transmissibility of SARS-CoV-2. Second, age was associated with viral load in this study, which could explain the high degree of severe disease in older patients with SARS-CoV-2. 5, 6 The high viral load in elderly patients is associated not only with low immunity but also with high expression of the ACE2 receptor (the cellentry receptor for SARS-CoV-2) in older adults. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore doi = 10.1016/s1473-3099(20)30235-8 id = cord-311762-f6muhf3d author = Chen, Yu Wai title = Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates date = 2020-02-21 keywords = 3CL; CoV-2; SARS summary = title: Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates Therefore, we are confident to prepare a structural model of the SARS-CoV-2 3CL pro by molecular modelling (Extended data 7 , Figure S1 ), which will be immediately useful for in silico development of targeted treatment. After we submitted the first draft of this study, the crystal structure of SARS-CoV-2 3CL pro was solved and released (PDB ID 6LU7), which confirms that the predicted model is good within experimental errors (Extended data 7 , Figure S2 ). By analogy, these compounds were speculated to act on SARS-CoV 3CL pro specifically, but there is as yet no crystal structure to support that, although docking studies were carried out to propose various binding modes 20-23 . • Tab S2.docx (The results of virtual screening of drugs on the active site of SARS-CoV-2 3CL pro crystal structure). doi = 10.12688/f1000research.22457.1 id = cord-252919-647zcjgu author = Chen, Yun title = Structure analysis of the receptor binding of 2019-nCoV date = 2020-02-17 keywords = ACE2; RBD; SARS summary = We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. In this study, we analyzed the structure of spike glycoprotein RBD of 2019-nCoV and identified a unique feature that potentially allows a high affinity binding to ACE2 in human cells. There are 16 amino acid residues in SARS-CoV RBD that are directly in contact with ACE2, of which 8 are conserved in 2019-nCoV (see Fig. 1B ). Among the 16 amino acid residues in RBD of SARS that are in contact with ACE2, 14, 14, 7, and 8 are shared by SARSv, civet, bat, and 2019-nCoV, respectively (Fig. 1B) . Our study suggests unique structural features of the spike glycoprotein RBD of 2019-nCoV that confers potentially higher affinity binding for its receptor than found with SARS-CoV. doi = 10.1016/j.bbrc.2020.02.071 id = cord-297702-vxcj25sn author = Chen, Yuxin title = A comprehensive, longitudinal analysis of humoral responses specific to four recombinant antigens of SARS-CoV-2 in severe and non-severe COVID-19 patients date = 2020-09-10 keywords = SARS; covid-19 summary = We continuously monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the nucleoprotein (NP), receptor binding domain (RBD), S1 protein, and ectodomain (ECD) of the spike protein among non-severe and severe COVID-19 patients for seven weeks since disease onset. In this retrospective study, we successively monitored the serum IgM and IgG responses specific to four SARS-CoV-2 related antigens, including the NP protein, RBD protein, S1 protein, and ECD protein in 19 non-severe and 7 severe COVID-19 patients during the disease progression. The severe patients and non-severe patients had comparable reduced fold of IgM, IgG, and IgA binding titer specific to RBD, ECD, S1, and NP protein and neutralization activities. Furthermore, 80.7% of the convalescent sea from COVID-19 patients displayed varying levels of neutralization activities against SARS-CoV-2, which correlated with S1-specific and ECD-specific IgA responses in non-severe patients. doi = 10.1371/journal.ppat.1008796 id = cord-298639-v9yg80jw author = Chen, Yuxin title = High SARS-CoV-2 Antibody Prevalence among Healthcare Workers Exposed to COVID-19 Patients date = 2020-06-04 keywords = China; SARS; covid-19 summary = Risk analysis revealed that wearing face mask could reduce the infection risk (odds ratio [OR], 0.127, 95% confidence interval [CI] 0.017, 0.968), while when exposed to COVID-19 patients, doctors might have higher risk of seroconversion (OR, 346.837, 95% CI 8.924, 13479.434), compared with HCWs exposed to colleagues as well as nurses and general service assistants who exposed to patients. Our study revealed that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. Briefly, 96-well plates were coated with 500 ng/mL of recombinant RBD or NP protein overnight, incubating with diluted were also collected and the nasopharyngeal swab samples from these patients have been repeatedly tested as negative for SARS-CoV-2 RNA at least twice at a two-day apart. Our study proved that the serological testing is useful for the identification of asymptomatic or subclinical infection of SARS-CoV-2 among close contacts with COVID-19 patients. doi = 10.1016/j.jinf.2020.05.067 id = cord-306332-ug6pare2 author = Chen, Ze-Liang title = From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends date = 2020-05-05 keywords = SARS; outbreak summary = title: From severe acute respiratory syndrome-associated coronavirus to 2019 novel coronavirus outbreak: similarities in the early epidemics and prediction of future trends [1, 2] The 2019 novel coronavirus (2019-nCoV) caused a pneumonia outbreak, which is spreading around the country and has affected 32 provinces and regions of China as of January 27, 2020. [14, 15] Subsequent case investigations also showed that SARS-CoV had the capability to multiply and continuously undergo human-to-human transmission [Supplementary Figure 2C , http://links.lww.com/CM9/ A209]; at least four generations of cases were identified from one original patient. [18] On January 19, 2020, a cluster of cases, including 15 healthcare workers, were confirmed to have been infected via patients, confirming that 2019-nCoV also has humanto-human transmission capability. Transmission and epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected pneumonia (COVID-19): preliminary evidence obtained in comparison with 2003-SARS doi = 10.1097/cm9.0000000000000776 id = cord-343502-1n0o4akm author = Chen, Zhang-Ren title = Pharmacotherapics Advice in Guidelines for COVID-19 date = 2020-06-24 keywords = COVID-19; China; SARS summary = SARS-CoV-2 (previously termed 2019 novel coronavirus, 2019-nCoV), a virus that causes COVID-19, likely initially transmitted from bat to human (Gorbalenya et al., 2020) , infected over 6 million people worldwide from its outbreak in December 2019 to May 2020 (China CDC, 2020; WHO, 2020a) . China, Italy, Germany, the ATS (American Thoracic Society), the SSC (Surviving Sepsis Campaign), the NIH (National Institutes of Health), the IDSA (Infectious Diseases Society of America), and the FDA (Food and Drug Administration) released guidelines and recommended several medicines for the treatment of COVID-19 (Table 1) . The majority of anti-SARS-CoV-2 virus drugs are adopted from the treatment of severe acute respiratory syndrome (SARS) or Middle East respiratory syndrome (MERS): alpha-interferon, lopinavir/ritonavir, and ribavirin. The guideline from Italy recommended remdesivir (Italian Society of Infectious and Tropical Diseases SECTION, 2020), and the FDA approved emergency use authorization (EUA) of remdesivir for the treatment of COVID-19 (FDA, 2020). doi = 10.3389/fphar.2020.00950 id = cord-026528-1ozgabwk author = Chen, Zhe title = Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination date = 2020-06-09 keywords = SARS summary = key: cord-026528-1ozgabwk title: Delivery method choice for COVID-19 pregnant women: stick to obstetric indications and avert anorectum contamination cord_uid: 1ozgabwk We appreciate that Dr. Carosso brought up several important points about our paper, 16 which are worth discussing and clarifying. 17 We stated that we did not find SARS-CoV-2 in lower female genital tract and our 18 results may provide evidence to guide the choice of delivery method for COVID-19 19 pregnant women. However, a high incidence of cesarean sections was mentioned 22 by Dr. Carosso. It might result from concerns that SARS-CoV-2 exists in vagina. It 23 was a reasonable suspicion since SARS-CoV-2 had been identified in anal swabs, 24 urine, and tears in an early time. Review of the 2019 novel coronavirus 53 (SARS-CoV-2) based on current evidence Severe 58 COVID-19 during Pregnancy and Possible Vertical Transmission Severe Acute Respiratory Syndrome Coronavirus 2 63 (SARS-CoV-2) Vertical Transmission in Neonates Born to Mothers With 64 doi = 10.1016/j.ajog.2020.06.013 id = cord-282990-qb4wk4yb author = Chen, Zhuo title = Safety considerations in the bioanalytical laboratories handling specimens from coronavirus disease 2019 patients date = 2020-08-21 keywords = SARS; covid-19 summary = Since blood specimen is one of the most commonly analyzed sample types, viral load of SARS-CoV-2 in blood is a key issue for laboratory biosafety. Besides the above three studies, other recently published papers also demonstrated that the detection rates of SARS-CoV-2 RNA in blood from COVID-19 patients were generally low as: five of 48 (10%) [1] , two of 9 (22%) [2] and six of 41 (15%) [3] . Despite the relatively low SARS-CoV-2 viral load detected in the blood and urine of COVID-19 patients, scientists have yet to draw conclusions about the infectivity of these specimens. The Centers for Disease Control and Prevention (CDC) has issued the interim laboratory biosafety guidelines for handling COVID-19 specimens, which recommends virus inactivation prior to sample processing to reduce the risk of infection [10] . Nevertheless, only the protocol of heating at 92 • C for 15 min completely inactivated SARS-CoV-2 in respiratory specimens with much higher viral load. doi = 10.4155/bio-2020-0185 id = cord-314381-ltil9hwl author = Cheng, Cecilia title = The psychology behind the masks: Psychological responses to the severe acute respiratory syndrome outbreak in different regions date = 2004-03-11 keywords = Hong; SARS summary = The present paper proposes the influence of psychological factors on people''s cognitive, affective, and behavioral responses during the SARS outbreak. Because SARS affected a number of regions, including people from both Asian and Western cultures, did individuals from different cultures perceive and cope with the crisis in distinct manners? These results suggest a link between general coping strategies and specific health behavior to avoid contracting SARS, which applies to people in areas that were and were not affected by SARS. This commentary, together with the five articles, provides valuable information on the ways in which people from different regions of the world responded affectively, cognitively, and behaviorally to the SARS outbreak. In conclusion, this special issue highlights the role of psychological factors in people''s cognitive and behavioral responses to the SARS outbreak. doi = 10.1111/j.1467-839x.2004.00130.x id = cord-277796-9ddi0mm9 author = Cheng, Hao title = Organ‐protective effect of angiotensin‐converting enzyme 2 and its effect on the prognosis of COVID‐19 date = 2020-04-05 keywords = ACE2; SARS summary = doi = 10.1002/jmv.25785 id = cord-275946-ofd2ipvs author = Cheng, Matthew P. title = Serodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review date = 2020-06-04 keywords = COVID-19; CoV-2; SARS; antibody summary = Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation. Appropriately designed seroepidemiologic studies will play an essential part in the public health response to the COVID-19 pandemic by characterizing transmission dynamics, refining disease burden estimates, and providing insight into the kinetics of humoral immunity to SARS-CoV-2. Serologic surveillance studies can also assess the accumulation of persons with antibody responses over time to estimate incidence of SARS-CoV-2 infection (57, 58) and can track age-and jurisdiction-specific disease susceptibility and identify at-risk populations (59) . doi = 10.7326/m20-2854 id = cord-259347-3acsko74 author = Cheng, Qi title = Infectivity of human coronavirus in the brain date = 2020-05-28 keywords = CNS; MERS; OC43; SARS summary = A new strain of human coronaviruses (hCoVs), Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has been identified to be responsible for the current outbreak of the coronavirus disease 2019 (COVID-19). Data from multiple hACE2 transgenic mouse models has revealed that SARS-CoV detection in the brain is significantly delayed compared to that within the lung, consistent with the initial establishment of infection within the respiratory system before dissemination to the CNS [21À23]. In addition, the detection of SARS-CoV in CSF of patients with neurological manifestation has also provided direct evidence for the neuroinvasion and neurovirulence of hCoVs. However, the role of the virus in the process of the disease in acute phase as well as in the long term still remains elusive. Severe acute respiratory syndrome coronavirus infection of mice transgenic for the human Angiotensin-converting enzyme 2 virus receptor doi = 10.1016/j.ebiom.2020.102799 id = cord-288558-rthnj6wd author = Cheng, V. C. C. title = Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date = 2004-02-15 keywords = SARS; diarrhea; patient summary = The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log 10 vs. In this retrospective study, we attempt to correlate the virus load of SARS coronavirus shedding from the nasopharynx, the upper end of the aerodigestive tract, with the presence of diarrhea in a cohort of patients with SARS. doi = 10.1086/382681 id = cord-270909-wb7mwklo author = Cheng, Vincent C.C. title = Absence of nosocomial transmission of coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in the pre-pandemic phase in Hong Kong date = 2020-05-24 keywords = Hong; SARS summary = BACKGROUND: To describe the infection control strategy to achieve zero nosocomial transmission of symptomatic coronavirus disease (COVID-19) due to SARS-CoV-2 during the pre-pandemic phase (the first 72 days after announcement of pneumonia cases in Wuhan) in Hong Kong. Pandemic infection of a coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) was declared by World Health Organization (WHO) on 11 March 2020, which is 72 days after announcement of a cluster of patients with community acquired pneumonia in Wuhan, Hubei Province by National Health Commission of the People''s Republic of China (NHCPRC), on 31 December 2019 (day 1) [1] . Up to 11 March 2020 (day 72 after the official announcement of a cluster of pneumonia of unknown etiology in Wuhan, Hubei Province, a total of 130 cases of SARS-CoV-2 infection were confirmed in Hong Kong, while the first 42 patients were reported previously [9] . doi = 10.1016/j.ajic.2020.05.018 id = cord-255697-trig04hd author = Cheng, Vincent Chi-Chung title = Viral Infections, an Overview with a Focus on Prevention of Transmission date = 2016-10-24 keywords = HBV; HIV; SARS; virus summary = Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. doi = 10.1016/b978-0-12-803678-5.00514-2 id = cord-299105-3ivzmiqn author = Cheng, Yi‐Qiang title = Deciphering the Biosynthetic Codes for the Potent Anti‐SARS‐CoV Cyclodepsipeptide Valinomycin in Streptomyces tsusimaensis ATCC 15141 date = 2006-03-01 keywords = NRPS; SARS; VLM summary = Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors d‐α‐hydroxyisovaleric acid and l‐lactic acid. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Aimed at generating analogues by metabolic engineering, the valinomycin biosynthetic gene cluster has been cloned from Streptomyces tsusimaensis ATCC 15141. Sequence analysis of the NRPS system reveals four distinctive modules, two of which contain unusual domain organizations that are presumably involved in the generation of biosynthetic precursors D-a-hydroxyisovaleric acid and L-lactic acid. The respective adenylation domains in these two modules contain novel substrate-specificity-conferring codes that might specify for a class of hydroxyl acids for the biosynthesis of the depsipeptide natural products. The key element of this approach is to sequence a certain number of random genomic clones and to identify candidate gene(s) involved in natural product biosynthesis. doi = 10.1002/cbic.200500425 id = cord-285748-us5do6c2 author = Cheng, Yongqian title = SARS-CoV-2-Related Kidney Injury: Current Concern and Challenges date = 2020-09-23 keywords = ACE2; CKD; SARS; covid-19 summary = Currently, the diagnosis and treatment of SARS-CoV-2 infection in patients with chronic kidney disease (CKD) are still unclear. Here, we review the recent findings of characteristics of COVID-19 in CKD patients and highlight the possible mechanisms of kidney injury caused by SARS-CoV-2 infection. Controversial results also exist like another study [18] indicating that SARS-CoV-2 infection was not found significantly correlated with incremental acute renal injury or aggravate chronic kidney failure in the COVID-19 patients. Therefore, SARS-CoV-2 infection in kidney transplant patients from this study showed that such cases may be severe enough requiring intensive care admission and these patients are in high risk of disease progression and death. Another study based on single-cell analysis by Lin and colleagues [28] also found that ACE2 was enriched in proximal tubular cells which may indicate that the kidney is more susceptible to SARS-CoV-2 infection. doi = 10.1007/s42399-020-00529-0 id = cord-338684-po3hfibp author = Cheong, Kai Xiong title = Systematic Review of Ocular Involvement of SARS-CoV-2 in Coronavirus Disease 2019 date = 2020-09-26 keywords = COVID-19; SARS; ocular summary = PURPOSE OF REVIEW: Studies have reported ocular involvement in the coronavirus disease 2019 (COVID-19), with SARS-CoV-2 having been detected in ocular swab samples. Observational studies which both described ocular involvement among patients with COVID-19 and attempted to detect SARS-CoV-2 in ocular samples via RT-PCR and/or viral cultures were included. In contrast, other studies have reported the detection of SARS-CoV-2 in ocular samples from patients who did not experience ocular symptoms and signs [5, 9, 10] . reported in a retrospective case series that SARS-CoV-2 was detected in conjunctival swab samples from both eyes of two patients (6.06%) in a population of 33 patients. Seah et al., in a prospective case series of 17 patients, reported that SARS-CoV-2 could not be detected in RT-PCR of tear samples. In the studies that took serial samples, SARS-CoV-2 was reported to remain detectable up to 27 days after the onset of ocular and respiratory symptoms [16, 18] . doi = 10.1007/s40135-020-00257-7 id = cord-310790-3ikgmiof author = Cherrak, Sabri Ahmed title = Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date = 2020-10-15 keywords = Fig; Mpro; SARS summary = title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. The three compounds with highest affinity (Fig 2) for the active site are quercetin 3-rhamonoside, myricetin 3-rutinoside and rutin with binding energies of -9.7, -9,3 and -9.2 kcal.mol -1 respectively. Thirty eight flavonoids have been tested in this study by molecular docking against the active site of the SARS-CoV-2Mpro. Glycosylated flavonoids as SARS-CoV-2 Inhibitors: A molecular docking and simulation studies Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies doi = 10.1371/journal.pone.0240653 id = cord-294237-6hovffso author = Cherry, James D title = SARS: The First Pandemic of the 21(st) Century date = 2004 keywords = Hong; Kong; SARS summary = SARS (severe acute respiratory syndrome) was a new disease in the fall of 2002, which first occurred in Guangdong Province, China and spread to 29 countries with 8422 cases and 916 fatalities (1) (2) (3) . Moreover, cataloging the genome from human cases assisted in the search for the origin of this disease, when viruses related to the SARS-CoV were identified in animals [Himalayan palm civets (Paguma larvata) and raccoon dogs (Nyctereutes procyonoides)] in a live animal market in Shenzhen, China (12) . On the one hand, in the initial phases of the spread of SARS in Hong Kong, Singapore, and Toronto, a disproportionate number of health care workers became ill and apparent "superspreader" cases were noted (2-4, 6, 11, 14 -18) . Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens, Kowloon Bay, Hong Kong, main findings of the investigation Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong doi = 10.1203/01.pdr.0000129184.87042.fc id = cord-282338-u01qv3uc author = Cherry, James. D. title = The chronology of the 2002–2003 SARS mini pandemic date = 2004-11-05 keywords = CoV; SARS; case summary = SARS-CoV disease should be considered at a minimum in the differential diagnoses for persons requiring hospitalisation for pneumonia confirmed radiographically or acute respiratory distress syndrome without identifiable aetiology and who have one of the following risk factors in the 10 days before the onset of illness: (1) Travel to mainland China, Hong Kong, or Taiwan, or close contact with an ill person with a history of recent travel to one of these areas, or; (2) Employment in an occupation associated with a risk for SARS-CoV exposure (e.g. healthcare worker with direct patient contact or worker in a laboratory that contains live SARS-CoV) or; (3) Part of a cluster of cases of atypical pneumonia without an alternative diagnosis. doi = 10.1016/j.prrv.2004.07.009 id = cord-016451-k8m2xz0e author = Chertow, Daniel S. title = Influenza, Measles, SARS, MERS, and Smallpox date = 2020-01-03 keywords = East; MERS; Middle; SARS; respiratory; virus summary = Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection doi = 10.1007/978-3-030-33803-9_5 id = cord-262180-t4akem15 author = Cheruiyot, Isaac title = Comment on “Encephalopathy in patients with COVID‐19: A review” date = 2020-07-11 keywords = SARS summary = key: cord-262180-t4akem15 title: Comment on "Encephalopathy in patients with COVID‐19: A review" cord_uid: t4akem15 I read with great interest the article by Garg and colleagues on "Encephalopathy in patients with COVID-19: A review". The authors performed a review of published reports on COVID-19-associated encephalitis and encephalopathy. Encephalopathy in patients with COVID-19: a review Status of SARS-CoV-2 in cerebrospinal fluid of patients with COVID-19 and stroke Facial diplegia, a possible atypical variant of Guillain-Barré Syndrome as a rare neurological complication of SARS-CoV-2 Guillain-Barré syndrome after SARS-CoV-2 infection Guillain-Barré syndrome associated with leptomeningeal enhancement following SARS-CoV-2 infection A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 Sars-Cov-2: underestimated damage to nervous system COVID-19 encephalopathy: detection of antibodies against SARS-CoV-2 in CSF Encephalopathy and encephalitis associated with cerebrospinal fluid cytokine alterations and coronavirus disease How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis? doi = 10.1002/jmv.26238 id = cord-278325-ykcd7d59 author = Cheung, Carmen Ka Man title = Coronavirus Disease 2019 (COVID-19): A Haematologist''s Perspective date = 2020-07-28 keywords = COVID-19; Coronavirus; ICU; SARS; Wuhan; patient summary = Two meta-analyses showed that a lower platelet count is associated with an increased risk of severe disease and mortality in patients with COVID-19 and may serve as a marker for progression of illness [53, 54] . Experience from previous SARS patients, caused by SARS-CoV-1, suggested that coronavirus could cause thrombocytopenia by direct viral infection of bone marrow haematopoietic stem cells via CD13 or CD66a, formation of auto-antibodies and immune complexes, disseminated intravascular coagulopathy (DIC), and consumption of platelet in lung epithelium [61, 62] . The International Society on Thrombosis and Haemostasis (ISTH) suggested all patients (including non-critically ill) who require hospital admission for COVID-19 infection should receive a prophylactic dose of LMWH unless contraindicated (Table 2 ) [102] . Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 doi = 10.1159/000510178 id = cord-269771-hffxb7bm author = Cheung, Ka Shing title = Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date = 2020-04-03 keywords = COVID-19; China; RNA; SARS summary = title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. The proportion of patients with detectable stool viral RNA was higher among those with diarrhea than those without diarrhea Table 2 including the hospital admission period, places in which the patients were recruited, sample size, age, sex, disease severity, non-gastrointestinal symptoms (fever and respiratory symptoms) on presentation, and gastrointestinal symptoms (anorexia, nausea/vomiting, diarrhea and abdominal pain/discomfort). In this meta-analysis of 4,243 COVID-19 patients from six countries, the pooled prevalence of all gastrointestinal symptoms (including anorexia, nausea/vomiting, diarrhea or abdominal pain) was 17.6%. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1053/j.gastro.2020.03.065 id = cord-267388-jz5mm91w author = Cheung, Szeya title = Recurrent Acute Pancreatitis in a Patient with COVID-19 Infection date = 2020-08-24 keywords = SARS; pancreatitis summary = Patient: Male, 38-year-old Final Diagnosis: Recurrent idiopathic acute pancreatitis with COVID-19 Symptoms: Nausea • severe abdominal pain • fever • vomiting Medication:— Clinical Procedure: — Specialty: Gastroenterology and Hepatology • Infectious Diseases • General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: The novel COVID-19 disease has infected more than 2 million people worldwide, causing more than 120 000 deaths. CONCLUSIONS: The temporal relationship between clinical presentation of acute pancreatitis and SARS-CoV-2 infection in this patient with no precipitating risk factors for pancreatitis suggests COVID-19-associated acute pancreatitis. Our review of the literature showed a few case studies that described the presentation of idiopathic acute pancreatitis in patients with concurrent SARS-CoV-2 infection [5] [6] [7] [8] [9] [10] . It is also important to note that while respiratory symptoms improve in patients with COVID-19 infection, these patients can still test positive for SARS-CoV-2 and are at risk for developing acute pancreatitis. doi = 10.12659/ajcr.927076 id = cord-346032-188gnf8j author = Cheung, Ying-Kit title = Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date = 2007-08-10 keywords = HLA; MHC; SARS summary = title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. doi = 10.1016/j.vaccine.2007.05.025 id = cord-298156-d0pb1kik author = Cheval, Sorin title = Observed and Potential Impacts of the COVID-19 Pandemic on the Environment date = 2020-06-10 keywords = April; COVID-19; Coronavirus; March; SARS; impact; pandemic summary = Consequently, by the end of April 2020, the COVID-19 pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. The concept of disaster has evolved over time, and here we use an adapted Intergovernmental Panel on Climate Change (IPCC) definition: a disaster is an event, which severely alters the functioning of a community due to hazardous physical, biological or human related impacts leading to widespread adverse effects on multiple scales and systems (environment, economic, social). While negative impacts on the economy and society in general are probably huge, it is very likely that the global-scale reduction of economic activities due to the COVID-19 crisis triggers a lot of sensible improvements in environmental quality and climatic systems. doi = 10.3390/ijerph17114140 id = cord-318262-w8oixzdg author = Chevance, A title = Ensuring mental health care during the SARS-CoV-2 epidemic in France: a narrative review date = 2020-04-22 keywords = SARS; care; covid-19; disorder; patient; psychiatric summary = Results: We identified four types of major vulnerabilities among patients with mental disorders during this pandemic: 1) medical comorbidities that are more frequently found among patients with mental disorders (cardiovascular and pulmonary pathologies, diabetes, obesity, etc.) which are risk factors for severe covid-19 infection; 2) age (the elderly form the population most vulnerable to the coronavirus); 3) cognitive and behavioural disorders, which can hamper compliance with confinement and hygiene measures and finally and 4) psychosocial vulnerability as a result of stigmatization and/or socio-economic difficulties. At the end of hospitalization, in particular for the population of patients in compulsory ambulatory care situations, specific case-management are organized with the possibility of home visits, in order to support patients when they get back home and to help them cope with the experience of confinement, which is liable to induce recurrences of mental disorders. doi = 10.1016/j.encep.2020.04.005 id = cord-354373-lldfoptb author = Chi, Jeffrey title = COVID-19 Clinical Research date = 2020-05-05 keywords = SARS; covid-19; patient summary = They can be categorized into four groups: drugs that combat SARS-CoV-2, immunomodulatory agents to counteract cytokine storm, convalescence plasma therapies and vaccines trials. They can be categorized into 1) drugs that combat SARS-CoV-2, 2) immunomodulatory agents to counteract cytokine storm, 3) convalescent plasma therapies and 4) vaccines trials (Table 1) . In vitro studies of these agents showed antiviral activities against SARS-VoV-2 and they are now repurposed for treating COVID-19 in clinical trials (Table 1) . Currently there are many ongoing clinical trials (e.g. NCT04292899, NCT04292730) to evaluate the efficacy of remdesivir in patients with mild to moderate or severe COVID-19. Sarilumab, another IL-6 receptor antagonist approved for RA, is also being studied in clinical trials (e.g. NCT04288713) in hospitalized patients with severe COVID-19 (Table 1) . As of April 19, 2020, there were 5 registered convalescent plasma therapy clinical trials in the United States for the treatment of severe and critically ill COVID-19 patients (Table 1) . doi = 10.33696/signaling.1.006 id = cord-330607-zn4urrxc author = Chi, Qiong title = Differential diagnosis for suspected cases of coronavirus disease 2019: a retrospective study date = 2020-09-18 keywords = COVID-19; SARS summary = METHODS: Sixty-eight cases of suspected COVID-19 treated in Wenzhou Central Hospital from January 21 to February 20, 2020 were divided into confirmed and COVID-19-negative groups based on the results of real-time reverse transcriptase polymerase chain reaction (RT-PCR) nucleic acid testing of the novel coronavirus in throat swab specimens to compare the clinical symptoms and laboratory and imaging results between the groups. More common chest imaging characteristics of the confirmed COVID-19 cases by high-resolution computed tomography (HRCT) included ground-glass opacities (GGOs), multiple patchy shadows, and consolidation with bilateral involvement than COVID-19-negative group (82.4% vs 31.4%, P = 0.0002; 41.2% vs 17.6% vs P = 0.048; 76.5% vs 43.1%, P = 0.017; respectively). CONCLUSIONS: WBC count inversely correlated with the severity of fever, GGOs, multiple patchy shadows, and consolidation in chest HRCT and clustered infection are common but not specific features in the confirmed COVID-19 group. doi = 10.1186/s12879-020-05383-y id = cord-327654-9g8zcxaa author = Chi, Xiaojing title = Humanized single domain antibodies neutralize SARS-CoV-2 by targeting the spike receptor binding domain date = 2020-09-10 keywords = CoV-2; Fig; RBD; SARS summary = Here, using SARS-CoV-2 spike receptor-binding domain (RBD) as a bait, we generate a panel of humanized single domain antibodies (sdAbs) from a synthetic library. Competitive ligand-binding experiments suggest that the sdAbs either completely block or significantly inhibit the association between SARS-CoV-2 RBD and viral entry receptor ACE2. To determine whether sdAbs targeted different antigenic regions on the SARS-CoV-2 RBD surface, we performed a competition-binding assay using a real-time biosensor (Fig. 3) . Fc fusion sdAbs in culture supernatants were affinity purified with HiTrap Protein A HP antibody purification columns ( Supplementary Fig. 2 ) and analyzed in both reducing and non-reducing conditions in Western blot using an anti-human IgG to detect Fc. As shown in Fig. 4c , the size of the constructed intact sdAb-Fc is around 80 KDa in the non-reducing condition, but a 40 KDa monomer was observed by prior treatment in reducing condition to break disulfide bonds. doi = 10.1038/s41467-020-18387-8 id = cord-304201-fziv9a9k author = Chiang, Chi-Huei title = Eight-Month Prospective Study of 14 Patients With Hospital-Acquired Severe Acute Respiratory Syndrome date = 2004-11-30 keywords = ARDS; LDH; SARS summary = CONCLUSION The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The need for mechanical ventilation was associated with bilateral lung involvement on the initial chest radiograph and higher peak levels of LDH and CRP. The clinical picture of our patients presenting with hospital-acquired SARS revealed atypical pneumonia associated with lymphopenia, elevated serum levels of LDH, rapid clinical deterioration, and lack of response to empirical antibiotic therapy. Although several case series of SARS have been reported, 7-9 to our knowledge, a prospective clinical study including long-term follow-up assessment by chest radiography, chest high-resolution computed tomography (HRCT), and pulmonary function testing has not been reported, particularly for hospital-acquired cases. doi = 10.4065/79.11.1372 id = cord-308451-pmwmfl3w author = Chiang, Shu-Fen title = SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells date = 2010-07-27 keywords = Fig; SARS; SSDRB summary = In this report, we showed that spike protein of SARS virus could induce phenotypic conversion of human B cells, either from peripheral blood or B lymphoma cells, to macrophage-like cells that were steadily losing the B-cell marker CD19 and in turn expressing the macrophage-specific marker Mac-1. In conclusion, our results suggest that conversion of B cells to macrophage-like cells, similar to a pathophysiological response, could be mediated by a devastating viral ligand, in particular spike protein of SARS virus, or in combination with severe local hypoxia, which is a condition often observed in afflicted lungs of SARS patients. Our results show that spike protein of SARS displayed on recombinant baculovirus or prolonged exposure to hypoxia can trigger the conversion of peripheral B cells and B lymphoma cells into Mac-1 positive macrophage-like cells. As determined by microarray analysis, expression of CD86 (B7-2) gene was rapidly induced in B lymphoma cells within 12 h of SSDRB treatment (Fig. 4B) . doi = 10.1016/j.molimm.2010.06.014 id = cord-255782-w6nfkdok author = Chikhale, Rupesh V. title = Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach date = 2020-06-22 keywords = QGRG; RMSD; SARS; Tyr summary = somnifera in comparison to reference drugs (hydroxychloroquine, lopinavir and remdesivir) against two different protein targets, that is, NSP15 endoribonuclease and prefusion spike RBD from SARS-CoV-2 using in-silico docking simulation and molecular dynamics (MD) study. The top three binding energy scorer ligand to each protein, that is, QGRG, Withanoside X and Ashwagandhanolide for spike RBD and QGRG, Dihydrowithaferin A and Withanolide N for NSP15 Endoribonuclease were selected for further MD study. Therefore, in the present study 100 ns of MD simulations were performed for all selected best six docked complexes to observe how the interaction pattern of the binding site of NSP15 endoribonuclease and spike RBD from SARS CoV-2 adapts to the docked bioactive. The phytochemicals Ashwagandhanolide, QGRG and Withanoside X in complex with the SARS-CoV-2 spike protein (PDB: 6M0J) were selected for the MDS based on molecular docking study results. doi = 10.1080/07391102.2020.1778539 id = cord-308066-lrbi5198 author = Childs, James E. title = Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date = 2007 keywords = Disease; H5N1; SARS; States; United; surveillance; virus summary = The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). doi = 10.1007/978-3-540-70962-6_16 id = cord-324953-3sacf4wu author = Childs, James E. title = Introduction: Conceptualizing and Partitioning the Emergence Process of Zoonotic Viruses from Wildlife to Humans date = 2007 keywords = SARS; human summary = The process of zoonotic disease emergence can be understood by coupling knowledge of how zoonotic viruses have evolved and are maintained among their wildlife hosts, transmitted across a species barrier to cause productive infection in a taxonomically distinct secondary host, initiate a pathologic process causing disease, and, by repetitive infection within the secondary host species, result in incident morbidity or mortality of sufficient magnitude to be detected and characterized as a novel health concern of local, regional, or global significance (see the chapter by Childs, this volume). The ecologic process of zoonotic disease emergence can be schematized by four transition stages (Fig. 1 ) , of which only the first two are prerequisites for emergence: (1) contact between infectious propagules originating from the wildlife H R with individuals of a susceptible H S and (2) cross-species transmission, a transition subsuming the complex interactions of the virus infectious cycle within the H S (Nayak 2000; Childs 2004 ). doi = 10.1007/978-3-540-70962-6_1 id = cord-308231-1t70vkxm author = Childs, S. J. title = Could Deficiencies in South African Data Be the Explanation for Its Early SARS-CoV-2 Peak? date = 2020-09-02 keywords = July; SARS summary = It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, while the second is that of an imperceptible, pre-existing, immune fraction of the population. This fact, alone, is nonetheless unable to reasonably explain the SARS-CoV-2 threshold observed in the South African data, without contemplating improbably-high, though not impossible, values. It contemplates the effect of two, different, hypothetical errors in the data: The first is that the true level of infection has been underestimated by a multiplicative factor, denoted a, while the second is that of an imperceptible, pre-existing, immune fraction of the population, denoted b. The phenomenon of infections having been underestimated by a multiplicative factor, alone, is unable to comprehensively explain the SARS-CoV-2 peak observed in the South African data, without contemplating improbably-high values. doi = 10.1101/2020.08.31.20185108 id = cord-337700-2n9tswr8 author = Chilimuri, Sridhar title = Predictors of Mortality in Adults Admitted with COVID-19: Retrospective Cohort Study from New York City date = 2020-07-08 keywords = COVID-19; SARS summary = On multiple regression analysis, increasing odds of mortality during hospitalization was associated with older age (odds ratio [OR] 1.04; 95% confidence interval [CI], 1.01–1.06 per year increase; p < 0.0001), admission D-dimer more than 1000 nanograms per milliliter (ng/mL) (OR 3.16; 95% CI, 1.75–5.73; p<0.0001), admission C-reactive protein (CRP) levels of more than 200 milligrams per liter (mg/L) (OR 2.43; 95% CI, 1.36–4.34; p = 0.0028), and admission lymphopenia (OR 2.63; CI, 1.47–4.69; p 0.0010). CONCLUSION: In this retrospective cohort study originating in NYC, older age, admission levels of D-dimer of more than 1000 ng/mL, CRP of more than 200 mg/L and lymphopenia were associated with mortality in individuals hospitalized for COVID-19. In the final analysis, we excluded the following patients: those whose SARS-Cov-2 results were pending or whose definitive outcomes were not available at the time of the study as they were still hospitalized; and those with incomplete information. doi = 10.5811/westjem.2020.6.47919 id = cord-264042-4hc2i25r author = Chim, Harvey title = Severe Acute Respiratory Syndrome in a Naval Diver date = 2006-06-17 keywords = SARS; patient summary = In the early recovery period, potential problems during diving are caused by inadequate lung ventilation in relation to exercise level and increased breathing resistance attributable to weak respiratory muscles, with corresponding risk of hypoxia and hypercapnia, as well as decreased ability to respond to nonrespiratory problems during diving. From our experience, we suggest that computed tomographic scans of the thorax, lung function tests, and careful follow-up monitoring should play a vital role in the assessment of patients during the convalescent period, before certification of fitness to dive. S evere acute respiratory syndrome (SARS) is an emerging infectious disease that was first reported in Guangdong Province in southern China in November 2002 and subsequently caused outbreaks in Singapore, Hong Kong, Southeast Asia, and Canada. In the week following diagnosis of SARS in this patient, only essential personnel in the diving unit were required to report to work to prevent the possible spread of SARS. doi = 10.7205/milmed.171.6.491 id = cord-016160-ugc7ce21 author = Ching, Frank title = Bird Flu, SARS and Beyond date = 2018-03-15 keywords = China; Guangdong; H7N9; Health; Hong; Kong; SARS; University; Yuen summary = At the end of 2002, unknown to anyone in Hong Kong, another deadly virus was circulating in neighboring Guangdong Province, propagating a disease that had no name but which was preliminarily dubbed atypical pneumonia in China and later renamed Severe Acute Respiratory Syndrome, or SARS, by the World Health Organization. And now it''s been identified by all the other laboratories." 76 Also, just as Hong Kong University publicized its breakthrough before the CDC''s announcement, so the university was able to get its scientific discovery into print first, with the publication of a paper in the online Lancet on April 8, 2003, "Coronavirus as a possible cause of severe acute respiratory syndrome." The success was very much the result of a group effort, as the list of authors shows, with Malik Peiris as the lead writer, K.Y. Yuen as the last writer and others, including Guan Yi, Leo Poon, John Nicholls and K.H. Chan, in between. doi = 10.1007/978-981-10-6316-9_14 id = cord-274141-vujx538o author = Chinsembu, Kazhila C. title = Coronaviruses and Nature’s Pharmacy for the Relief of Coronavirus Disease 2019 date = 2020-10-06 keywords = COVID-19; CoV; SARS; TCM summary = De Clercq (2005 suggested that it was feasible to develop SARS-CoV fusion inhibitors analogous to enfuvirtide, a linear 36-amino acid synthetic peptide marketed under the trade name Fuzeon, an approved anti-HIV drug that inhibits the entry of the virus into cells. It was hypothesized that specific flavonoids, such as quercetin, hesperetin, and myricetin (7) and their glycosylated derivatives, may play an effective role in inhibiting SARS-CoV entry into host cells, specifically by binding with high affinity to the spike protein, helicase, and protease sites on the ACE receptor (Ngwa et al. Although the ongoing SARS-CoV-2 global pandemic should remind scientists that current options for treating life-threatening zoonotic coronavirus infections are very limited , medicinal plants offer a strong pipeline for the discovery of novel lead compounds that can be converted into new drugs to treat COVID-19. doi = 10.1007/s43450-020-00104-7 id = cord-272414-oo8kcuf3 author = Chiocchetti, Roberto title = ACE2 Expression in the Cat and the Tiger Gastrointestinal Tracts date = 2020-08-13 keywords = ACE2; ACE2-IR; SARS summary = Although the evidence of ACE2-IR in the feline GIT does not necessarily indicate the possibility of viral replication and SARS-CoV-2 spread with stool, the findings in the present study could serve as an anatomical basis for additional studies considering the risk of the SARS-CoV-2 fecal-oral transmission between cats/felids, and between cats/felids and humans. Since the necessary condition for the enteric multiplication of SARS-CoV-2 is represented by the expression of its election receptor on the host cells, the present study immunohistochemically investigated the localization of ACE2 in the GIT of feline domestic (cat) and wild (tiger) species. The present study described the expression of the ACE2 receptor in the stomach and intestine of the cat and tiger for the first time and highlighted the GIT as a potential site of SARS-CoV-2 replication. doi = 10.3389/fvets.2020.00514 id = cord-264333-mgeicojq author = Chiotos, Kathleen title = Multisystem Inflammatory Syndrome in Children During the Coronavirus 2019 Pandemic: A Case Series date = 2020-05-28 keywords = SARS summary = On 6 May 2020, authors from London, England, reported clinical and laboratory features of a cluster of 8 children with hyperinflammatory shock, all of whom tested positive for SARS-CoV-2 antibodies [1] . To evaluate for incomplete Kawasaki disease/Kawasaki disease shock syndrome, an echocardiogram was performed on HD 6 that demonstrated normal biventricular systolic function (shortening fraction [SF], 38%; normal, 28%-45%) but identified right coronary artery dilation (Boston z score, 3.15). A 12-year-old male with no chronic medical conditions presented to an outside facility with a 6-day history of fever, Nasopharyngeal SARS-CoV-2 PCR was negative. Her lowest documented blood pressure within 24 hours of her PICU admission was 92/50 mm Hg. A repeat SARS-CoV-2 nasopharyngeal PCR was positive with a high cycle threshold (37.54). Further, for some patients, fever and gastrointestinal symptoms preceded the development of other "classic" clinical features of Kawasaki disease, including rash, conjunctivitis, mucous membrane changes, and extremity edema, which were variably present in our cohort. doi = 10.1093/jpids/piaa069 id = cord-344486-iu5flbcl author = Chiotos, Kathleen title = Multicenter interim guidance on use of antivirals for children with COVID-19/SARS-CoV-2 date = 2020-09-12 keywords = COVID-19; Coronavirus; Disease; SARS; child; patient summary = In the few months since this initial publication, new evidence has emerged demonstrating the efficacy of the antiviral medication remdesivir in shortening time to clinical recovery in adults with COVID-19, while several other studies have shown ineffectiveness of hydroxychloroquine and lopinavir-ritonavir (4) (5) (6) (7) (8) . Further, additional observational studies have provided insight into the clinical epidemiology of COVID-19 in children, demonstrating that while most young patients experience mild illness, a small proportion develop severe illness associated with adverse clinical outcomes, including need for pediatric intensive care unit (PICU) admission and mortality (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) . Nevertheless, the panel recognizes that pediatric clinicians are likely to consider comorbidities when weighing the risks and benefits of antiviral therapy on a case-bycase basis, and in making these decisions may consider: 1) the available, albeit limited, pediatric COVID-19 literature; 2) risk factors associated with severe COVID-19 in adults; and 3) pre-existing medical conditions in children associated with worse clinical outcomes for other viral infections. doi = 10.1093/jpids/piaa115 id = cord-341620-nmrkhx5t author = Chirico, Francesco title = Can Air-Conditioning Systems Contribute to the Spread of SARS/MERS/COVID-19 Infection? Insights from a Rapid Review of the Literature date = 2020-08-20 keywords = COVID-19; HVAC; MERS; SARS summary = Therefore, to evaluate the COVID-19 risk associated with the presence of air-conditioning systems, we conducted a rapid review of the literature concerning outbreaks of coronaviruses (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) in indoor environments. We utilized the participants-exposure-comparisons-outcome (PECOS) criteria, and we defined them according to evidence-based practice [32] -P (participants) is human subjects residing in indoor environments, E (exposure) is exposed to air-conditioning systems (HVAC), C (comparisons) is any comparison between the pathogens under study, and O (outcome) is respiratory infection outbreaks caused by SARS-CoV-1, MERS-CoV, or SARS CoV-2. A retrospective study of on outbreak involving 74 patients in the same hospital indicated that the rapid evaporation of the droplets produced by coughing in a relatively dry, air-conditioned environment, could also induce virus-laden aerosol, which was probably responsible for spreading the infection to patients who were not in the same room [35] . doi = 10.3390/ijerph17176052 id = cord-276969-mdry8qzv author = Chirumbolo, Salvatore title = Might the many positive COVID19 subjects in Italy have been caused by resident bat‐derived zoonotic β‐coronaviruses instead of the Wuhan (China) outbreak? date = 2020-03-27 keywords = SARS summary = Might the many positive COVID19 subjects in Italy have been caused by resident bat-derived zoonotic β-coronaviruses instead of the Wuhan (China) outbreak? The same authors concluded that the SARS-CoV2 in Italy might be present at least since September and October 2019, much before the claimed Wuhan outbreak. Questions may be raised, therefore, if, taking into account the genomic distance (or similarity) and the RNA-virus mutation rate, the "Italian" SARS-CoV2 might be the evolutionary balanced genotype (or strain) from a resident zoonotic spillover. 3 This should suggest that the cross-talk between evolution and epidemiology is closely intertwined, causing that the maintenance of an onward transmission might be crucially asThe issue of human coronaviruses virulence was recently addressed for SARS-CoV and MERS-CoV and some reports have outlined the role of coronavirus E protein in triggering an inflammatory response, cytokine storm, and/or inhibition of the innate immunity with dampening Th1 interferon-γ signaling. doi = 10.1002/jmv.25777 id = cord-333498-d25qfq0f author = Chitranshi, Nitin title = Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL(pro) targeting repurposed drug candidates date = 2020-07-09 keywords = 3CL; CoV-2; Fig; Pangolin; SARS; pro summary = Recent release of the high-resolution crystal structure for the main proteinase 3CL pro (Protein Data Bank, PDB ID: 6Y2G), describing an additional amide bond with the α-ketoamide inhibitor pyridone ring to enhance the half-life of the compound in plasma [16] is suggested to accelerate the targeted drug discovery efforts. Since the initial stages of the SARS-CoV-2 outbreak, laboratories and hospitals around the world have sequenced viral genome data with unprecedented speed, enabling real-time understanding of this novel disease process, which will hopefully contribute to the development of novel candidate drugs. In contrast, our docking studies revealed that bilobetin, predicted almost comparable binding energy with that of amentaflavone (− 8.29 kcal/mol) suggesting that mutation in SARS-CoV-2 3CL pro could potentially disrupt hydrogen bonding or induce some conformational change that could result in alterations in the binding site thus affecting inhibitor interactions with the enzyme active site residues. doi = 10.1186/s12967-020-02448-z id = cord-217961-2rczhxp2 author = Chitsaz, Mohsen title = A small molecule drug candidate targeting SARS-CoV-2 main protease date = 2020-06-16 keywords = Fig; SARS summary = We aligned the inhibitor on the protein and on the initial conformation of the ligand and computed structural deviations RMSDs. To observe the interaction of the inhibitor with the active site and confirming that the inhibitor stays in the active site of SARS-CoV-2 protease, we ran a simulation of 250ns that was 10 times longer than two previous MD simulations. For each of the two complexes, we analyzed the active-site by investigating all hydrophobic, H-bond, ionic and water bridge interactions of the inhibitor with SARS-Cov-2 protease and SARS-CoV protease (see Fig. 5 and Fig. 6 respectively) . We observed that the inhibitor remains in the active site for the entire duration of the simulation and maintains H-bond and water bridge contacts with GLU166 and hydrophobic Pi-Pi stacking contact with HIS41 (see Fig. 13 ). Our primary observation was that the molecule remained in the active site of SARS-CoV-2 protease for the entire duration of the simulation. doi = nan id = cord-290333-996tmrgo author = Chiu, Cheng-Hsun title = Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic date = 2020-07-23 keywords = SARS summary = title: Fecal microbiota transplantation and donor screening for Clostridioides difficile infection during COVID-19 pandemic 7 Soon on March 23, the US Food and Drug Administration (FDA) responded that the following actions be taken: donor screening with questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2 and testing donors and/ or donor stool for SARS-CoV-2, to ensure the safety of FMT. 8e12 In addition to the recommended testing procedures, all the screening protocols include questions directed at identifying donors who may be currently or recently infected with SARS-CoV-2. Safety alert regarding use of fecal microbiota for transplantation and additional safety protections pertaining to SARS-CoV-2 and COVID-19 Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward Additional safety protections relating to COVID-19 for faecal microbiota transplant (FMT) products Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification doi = 10.1016/j.jfma.2020.07.028 id = cord-312170-p2yrbosz author = Chiu, Man-Chun title = Suggested management of immunocompromized kidney patients suffering from SARS date = 2003-10-24 keywords = SARS summary = The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial. The treatment of severe acute respiratory syndrome (SARS) is still empirical and controversial, and little is known worldwide about the treatment for SARS kidney transplant patients. It seems children suffered much less from the infection than adults, although some adolescents could have severe lung involvement [3, 4, 5] . In Hong Kong, 7 of 19 adult ESRD patients on haemodialysis or peritoneal dialysis infected with SARS died (C.B. Leung et al., pers. Paediatric nephrologists should be on the alert for SARS, because we have to care for a group of immunocompromised patients including those transplant children. Cumulative number of reported probable cases of severe acute respiratory syndrome (SARS) www Clinical presentations and outcome of severe acute respiratory syndrome in children Severe acute respiratory syndrome in children: experience in a regional hospital in Hong Kong Treatment of severe acute respiratory syndrome with convalescent plasma doi = 10.1007/s00467-003-1325-8 id = cord-324638-gwd8qin6 author = Chiu, Rossa WK title = Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date = 2006-02-09 keywords = RNA; SARS summary = We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. doi = 10.1186/1471-2334-6-20 id = cord-350212-448mv4lt author = Chiuppesi, Flavia title = Development of a Multi-Antigenic SARS-CoV-2 Vaccine Using a Synthetic Poxvirus Platform date = 2020-07-17 keywords = MVA; SARS; dna; smva summary = We demonstrate that these sMVA vectors stimulate robust SARS-CoV-2 antigen-speci c humoral and cellular immunity in mice, including potent NAb. These results emphasize the value of a novel vaccine platform based on synthetic DNA to e ciently produce recombinant poxvirus vectors and warrant further pre-clinical and clinical testing of a multiantigenic sMVA vaccine candidate to control the ongoing SARS-CoV-2 pandemic and its devastating consequences. In response to the ongoing global SARS-CoV-2 pandemic, we used this novel vaccine platform to rapidly produce sMVA vectors co-expressing SARS-CoV-2 S and N antigens and show that these vectors can induce potent SARS-CoV-2 antigen-speci c humoral and cellular immune responses in mice, including potent NAb. These results highlight the feasibility to e ciently produce recombinant MVA vectors from chemically synthesized DNA and to rapidly develop a synthetic poxvirusbased vaccine candidate to prevent SARS-CoV-2 infection. doi = 10.21203/rs.3.rs-40198/v1 id = cord-326045-x8xntne7 author = Chng, Shu-Sin title = Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate date = 2004-12-20 keywords = SARS summary = title: Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate Synthesis of intermediate 1 and analogues proceeded via a highly diastereoselective indium-mediated allylation of α-aminoaldehydes. Based on these findings, it was suggested that the HRV 3C pro inhibitor, AG7088, could serve as a good starting point for modifications leading to an efficient and bio-available inhibitor for the SARS-CoV M pro and other coronavirus main proteinases. The synthesis of 1 in our group has proceeded via the highly stereoselective indium-mediated allylation reaction of N-protected valinal as illustrated in Scheme 2. 8 In addition, when we performed the same indium-mediated allylation reaction on N-t-butyloxycarbonyl-L L-valinal, we obtained the homoallylic alcohol as an 87:13 mixture of syn/anti isomers (Scheme 4). The critical step in the synthesis involved a highly diastereoselective indium-mediated allylation reaction. doi = 10.1016/j.tetlet.2004.10.146 id = cord-304321-y177sqee author = Cho, Ryan H. W. title = Pearls of experience for safe and efficient hospital practices in otorhinolaryngology—head and neck surgery in Hong Kong during the 2019 novel coronavirus disease (COVID-19) pandemic date = 2020-05-15 keywords = COVID-19; China; SARS; patient summary = We hope that our experiences will serve as pearls for otolaryngologists and other healthcare personnel working in institutes that serve large numbers of patients every day, particularly with regard to the sharing of clinical and administrative tasks during the COVID-19 pandemic. In 2003 outbreak of SARS in Hong Kong, the initial phase of outbreak began in Prince of Wales Hospital with a carrier of coronavirus in a medical ward causing widespread infection to patients and medical staff through the use of nebulizer for bronchodilators which facilitated the transmission of the virus through aerosol spread. Health seminars on COVID-19, which were organized by the infection control team to all hospital staff on daily basis across the whole month, provided a direct platform from which to educate healthcare personnel about the virus, its mode of transmission, the course of the disease, management and the mortality rate. doi = 10.1186/s40463-020-00427-4 id = cord-017668-my2l85bn author = Cho, Yeon-Jin title = Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction date = 2005 keywords = SARS summary = title: Rule Generation Using NN and GA for SARS-CoV Cleavage Site Prediction We present a new method that generates prediction rules for SARS-CoV protease cleavage sites. Experimental results show that the method could generate new rules for cleavage site prediction, which are more general and accurate than consensus patterns. In this paper, we present new approaches to rule generation for the cleavage site prediction, and the rule is represented in an explicit form such as "if L@p2 and R@p3, then cleavage". We used the methods of rule extraction from neural networks and knowledge-based genetic algorithms in this paper. used feed-forward neural networks for SARS-CoV cleavage site analysis [11] . Domain knowledge was obtained by extracting rules from consensus patterns, decision tree and neural networks. Finally, we compare the rule performances between decision tree, neural network and knowledge-based genetic algorithm (KBGA). We presented a new method that generates rules and improves quality of the rules with the subject of SARS-CoV protease cleav-age site prediction. doi = 10.1007/11553939_111 id = cord-262338-ipvzugo8 author = Choi, Jun-Yong title = The pathogenesis and alternative treatment of SARS-CoV2 date = 2020-05-03 keywords = SARS summary = The scientific community has identified the culprit of the shock wave as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) (1). Since 2002, however, newly merged hCoV causes fever, dyspnea, and often organ failure, which bestow SARS (severe acute respiratory syndrome) to otherwise benign hCoV (5) . During the MERS-CoV and SARS-CoV outbreaks, most patients died of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS), a severe case of ALI (11) . Fortunately, the mortality of SARS-CoV2 infection, which is related to ALI or ARDS, is lower than those of the other two outbreaks (13) . As yet, however, no evidence is available that, if administered to patients on the principles of traditional Asian medicine, the medicinal herbs show effectiveness against ALI caused by SARS-CoV2 infection. The time comes to examine whether antiinflammatory medicinal herbs give a medical benefit to patients infected by SARS-CoV2. doi = 10.1016/j.imr.2020.100421 id = cord-332716-1d89j7jh author = Choi, Marcelo title = El SRAA y el SARS-CoV-2: el acertijo a resolver date = 2020-05-27 keywords = Ang; COVID-19; ECA2; SARS summary = Uno de los temas que ha generado debate se vincula con la asociación entre la terapia antihipertensiva con inhibidores del sistema renina-angiotensina-aldosterona (SRAA) y la infección por el virus SARS-CoV-2. Para ingresar a las células el coronavirus interactúa, utilizando como receptor, con la ECA2 y serina-proteasas transmembrana de tipo II (TMPRSS2) ubicadas en la superficie celular del huésped (7) . Los estudios clínicos llevados a cabo hasta el día de hoy no han demostrado que existen diferencias entre ambos tratamientos en términos de aumento del riesgo de infección por SARS-CoV-2 o de desarrollo de resultados graves en pacientes con COVID-19 (27) (28) (29) (30) (31) . Si bien existe evidencia in vitro de que el SARS-CoV-2 se une a los receptores ECA2 y que éstos se encuentran aumentados en presencia de IECA o ARA-II, no hay evidencia al momento de que la exposición a estos fármacos facilite la entrada del coronavirus ni que produzcan un mayor riesgo de COVID-19. doi = 10.1016/j.hipert.2020.05.005 id = cord-270278-d61n3v90 author = Choi, S.M.Y. title = Enhancing legal preparedness for the prevention and control of infectious diseases: Experience from severe acute respiratory syndrome in Hong Kong date = 2009-03-31 keywords = Kong; QPDO; SARS summary = This article shares Hong Kong''s experience in reforming its public health legislation to: (1) update terminology and re-organize provisions in accordance with modern public health disease control principles and control mechanisms for disease; (2) enhance responsiveness for better preparedness and flexibility in handling emergent infections; (3) ensure appropriate checks and balances to coercive powers; and (4) introduce emergency powers for the handling of public health emergencies. During the outbreak of SARS in 2003, the Quarantine and Prevention of Disease Ordinance 2 (QPDO) of the laws of Hong Kong was the legal tool that provided the legal framework for the prevention and control of infectious diseases of public health importance in Hong Kong. This article shares Hong Kong''s experience in reforming its public health legislation, leading to the passing of the Prevention and Control of Disease Ordinance 4 in order to strengthen the capacity of law to support strategy in the control of infectious diseases. doi = 10.1016/j.puhe.2009.01.004 id = cord-345854-f0dq94j1 author = Chong, Wai Po title = The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome date = 2006-05-04 keywords = IFN; SARS summary = We examined whether polymorphisms of IFN-γ,TNF-α and IL-10 affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). In this study, we hypothesized that the polymorphisms of the cytokine genes, i.e. IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C, might be associated with SARS. We tested our hypotheses in 476 SARS patients and 449 healthy controls and found that polymorphism of IFN-γ +874A allele was associated with susceptibility to SARS in a dose-dependent manner. The frequencies of genotypes and alleles of the 4 single nucleotide polymorphisms (SNPs) were compared between the SARS patients and healthy controls by 3 × 2 and 2 × 2 chi square test respectively. Our case-control study genotyped the 4 SNPs IFN-γ +874A/T, TNF-α -308G/A, IL-10 -1082G/A and -592A/C in 476 Chinese patients with SARS and 449 healthy controls. Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection doi = 10.1186/1471-2334-6-82 id = cord-296271-85io9yvy author = Chong, Woon H. title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) date = 2020-07-28 keywords = SARS summary = title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Rhabdomyolysis and Acute Kidney Injury (AKI) 1 A study of 701 SARS-CoV-2 patients by Cheng and colleagues demonstrated that in-hospital mortality increased by almost three-fold in those who had AKI. 2 We report a patient with SARS-CoV-2 who developed AKI likely secondary to rhabdomyolysis and discuss the possible association between cytokine storm as the etiology. A case series of SARS-CoV-related rhabdomyolysis showed the development of AKI with peak CK levels ranging from 7,500 to 340,000 IU/L. 3 Jin and colleagues were the first to describe a 60-year-old man who was admitted with RT-PCR confirmed SARS-CoV-2 pneumonia and developed rhabdomyolysis on day 9 th of hospital admission. A retrospective study of 171 SARS-CoV-2 patients showed that CK of more than 185 IU/L, AKI, and requirement of RRT was associated with an increase in mortality. doi = 10.1016/j.amjms.2020.07.032 id = cord-270788-w0pewq52 author = Chou, Chih-Fong title = A novel cell-based binding assay system reconstituting interaction between SARS-CoV S protein and its cellular receptor date = 2004-11-05 keywords = CHO; SARS summary = A binding epitope with lesser degree of glycosylation and native conformation was localized by using rabbit anti-sera raised against five denatured recombinant S protein fragments expressed in Escherichia coli. Cells were washed once with PBS and three times with PBS containing 500 mM NaCl. To test whether the anti-sera from SARS patients or raised against S protein fragments can block the binding between CHO-SG and Vero E6, dislodged CHO-SG cells were preincubated with the anti-serum to be tested at 4 • C for 1 h. The CHO-G cells resisted the PBS wash but were detached by the solutions containing supplemented NaCl. In contrast, the binding between CHO-SG and Vero E6 could resist up to 1M NaCl. We sought to investigate the binding specificity of this interaction by testing whether the serum from a recovered SARS patient (P8 in Tan et al., 2004a ) and a goat anti-ACE2 antibody could block the interaction. doi = 10.1016/j.jviromet.2004.09.008 id = cord-309650-6xz9gjq0 author = Chou, Roger title = Update Alert 4: Epidemiology of and Risk Factors for Coronavirus Infection in Health Care Workers date = 2020-09-11 keywords = COVID-19; SARS summary = Specific risk factors for SARS-CoV-2 transmission among health care workers in a university hospital Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers Prevalence of SARS-CoV-2 infection among health care workers in a tertiary community hospital Asymptomatic infection by SARS-CoV-2 in healthcare workers: a study in a large teaching hospital in Wuhan, China Dynamic of SARS-CoV-2 RT-PCR positivity and seroprevalence among high-risk health care workers and hospital staff Risk factors of healthcare workers with Corona Virus Disease 2019: a retrospective cohort study in a designated hospital of Wuhan in China Impact on mental health and perceptions of psychological care among medical and nursing staff in Wuhan during the 2019 Novel Coronavirus Disease outbreak: a cross-sectional study Analysis of the infection status of the health care workers in Wuhan during the COVID-19 outbreak: A cross-sectional study SARS-CoV-2 infection among healthcare workers in a hospital in doi = 10.7326/l20-1134 id = cord-313345-zwe3tmq0 author = Chou, Roger title = Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings date = 2020-07-20 keywords = SARS summary = title: Update Alert: Masks for Prevention of Respiratory Virus Infections, Including SARS-CoV-2, in Health Care and Community Settings Masks for prevention of respiratory virus infections, including SARS-CoV-2, in health care and community settings: a living rapid review Facemasks and hand hygiene to prevent influenza transmission in households: a cluster randomized trial Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study A case-control study on the risk factors of severe acute respiratory syndromes among health care workers Factors associated with transmission of severe acute respiratory syndrome among health-care workers in Singapore Surgical mask vs N95 respirator for preventing influenza among health care workers: a randomized trial A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. N95 Respirators vs medical masks for preventing influenza among health care personnel: a randomized clinical trial doi = 10.7326/l20-0948 id = cord-326320-flfrdrbi author = Choudhary, Shalki title = Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date = 2020-08-29 keywords = ACE2; SARS summary = title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 The multi-targeting potential of generated analogues was explored against various targets involved in the pathogenesis of COVID-19 including SARS-CoV-2 SP, ACE2, furin, TMPRSS2 (in viral attachment) and 3CLPro (in viral replication). A cutoff value of 3 was used for the screening of compounds based on synthetic possibility and topranked molecules were submitted to structure-guided drug binding analysis such as molecular docking studies. All these molecules were docked against SARS-CoV-2 SP-ACE2 complex, furin, TMPRSS2 and main protease (3CLPro) and the binding affinity of their docked complexes was also calculated in terms of MM-GBSA score. J o u r n a l P r e -p r o o f 44 A combination of scaffold morphing and a structure-based drug designing approach was successfully utilized to identify putative multi-targeting analogues of arbidol against COVID-19. doi = 10.1016/j.virusres.2020.198146 id = cord-334891-4jgtxg07 author = Choudhury, Abhigyan title = In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date = 2020-11-11 keywords = RNA; SARS; figure summary = This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. doi = 10.1101/2020.11.11.377713 id = cord-356021-lr3wj8we author = Choudhury, Chinmayee title = Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease date = 2020-06-01 keywords = SARS; fragment; pro summary = With the arrival of the very first structure (6LU7) of this protein in PDB (Jin et al., 2020) , several groups have come up with interesting strategies such as artificial intelligence based de novo design (Bung et al., 2020) , repurposing existing drugs that can bind this protein or virtually screening large chemical databases to identify peptide like small molecules (Pant et al., 2020) , natural products such as Moroccan medicinal plants products (Aanouz et al., 2020) , against this protein (Islam et al., 2020; Sarma et al., 2020) , identification of Andrographolide as a potential inhibitor of SARS-CoV-2 main protease through in silico screening (Enmozhi et al., 2020) using molecular docking, molecular dynamics simulations and PCA based quantitative structureactivity relationship (QSAR) for pattern recognition of the best ligands (Islam et al., 2020) , to mention a few. doi = 10.1080/07391102.2020.1771424 id = cord-323643-lu3ngt6r author = Chow, C.B. title = Post-SARS infection control in the hospital and clinic date = 2004-11-05 keywords = Hong; Kong; SARS; infection summary = The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. PAEDIATRIC Summary The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. 17 Despite great concerns, compliance to infection control precautions by community general practitioners in Hong Kong lagged behind their hospital counterparts -97.7% had not worn masks at all times, a third did not wash their hands after seeing/examining a patient and half did not wear gowns. In a study looking into factors affecting nosocomial infection in Hong Kong, it was found that all HCWs consistently used N95s or surgical masks and perceived that the inadequacy of personal protective equipment (PPE) supply, infection control training <2 h and inconsistent use of goggles, gowns, gloves and caps were significant independent risk factors for SARS infection. doi = 10.1016/j.prrv.2004.07.006 id = cord-258223-8dhtwf03 author = Chow, Cristelle title = The Next Pandemic: Supporting COVID-19 Frontline Doctors Through Film Discussion date = 2020-09-05 keywords = SARS; film; participant; public summary = Themes derived from the film included preparedness, blame, and the impact on healthcare workers and public, which were further discussed to include concerns regarding current local readiness levels given global connectivity, the need for international cooperation, and the effects of blame such as racism and prejudice. These rich discussions demonstrate the pivotal role health humanities has in times of uncertainty such as an emerging infectious disease outbreak by providing timely pandemic education and supporting reflective learning. Hence, as the world experiences the current COVID-19 pandemic situation, this study aims to describe the use of a short film and post-film discussion to educate and support frontline doctorsin-training during an acute emerging infectious disease outbreak. While the focus of this study was on the implementation of a timely film screening and discussion, the themes that emerged from the guided reflections were insightful and can inform future pandemic-preparedness efforts for frontline healthcare staff. doi = 10.1007/s10912-020-09662-2 id = cord-289038-15yp9uqy author = Chow, Jonathan Tak-Sum title = Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date = 2020-08-26 keywords = RNA; SARS; hsa; miRNA summary = The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. Another recent study used a high-throughput reporter screen of miRNA from human and mouse respiratory epithelial cells to identify hsa-miR-127-3p, hsa-miR-486-5p, and hsa-miR-593-5p as contributors to the antiviral defence against influenza A virus by targeting the genomes of the H3N2 and attenuated PR8 (H1N1) viral strains [16] . Given the wealth of evidence supporting a role for miRNA in host cell antiviral defence mechanisms, we sought to identify human miRNA that have the potential to target the SARS-CoV-2 genome. DEA of Calu3 cells infected with SARS-CoV revealed that only hsa-miR-155-3p (upregulated) and hsa-let-7a-3p (downregulated) out of the 128 miRNA we identified in this study, were differentially expressed ( Figure 4B ). doi = 10.3390/genes11091002 id = cord-326273-6rp12py3 author = Chow, Kuan-Chih title = Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date = 2004-04-01 keywords = SARS; cell; viral summary = Previous reports have indicated that patients with severe acute respiratory syndrome (SARS)–associated coronavirus infection could develop atypical pneumonia with fulminant pulmonary edema. Severe acute respiratory syndrome (SARS) is an acute infectious disease that affects primarily the lower respiratory tract, with clinical manifestations of atypical pneumonia with dry cough, persistent fever, progressive dyspnea, and, sometimes, the abrupt deterioration of lung function [1] [2] [3] [4] [5] and the ensuing oxygen deprivation-associated systemic organ failures. Nevertheless, when antisense oligonucleotide probes specific to the replicase-encoding (REP) region of the SARS viral genome were used to determine the presence of virus, the intensity of the in situ hybridization signal decreased substantially compared with that detected by probes to the N and M regions ❚Image 2D❚ ❚Table 3❚. B, By using in situ hybridization and antisense oligonucleotide probes specific to the nucleic acid binding protein-encoding (N) and membrane protein-encoding (M) regions of the severe acute respiratory syndrome (SARS) viral genome, the SARS viral signal was detected in the enlarged and multinucleated cell (arrow, purple blue precipitates). doi = 10.1309/c0edu0raqbtxbhce id = cord-309556-xv3413k1 author = Chow, Ryan D. title = The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date = 2020-04-15 keywords = SARS; age; cluster; figure; gene summary = In aggregate, these analyses showed that the age-associated genes with functional roles in SARS-CoV are expressed in specific cell types of the human lung. Of note, the overlap between lung ageassociated genes and SARS-CoV-2 regulated genes was statistically significant across all 3 cell lines (Figure 6d-f) , suggesting a degree of similarity between the transcriptional changes associated with aging and with SARS-CoV-2 infection. Among the age-associated genes that were induced by SARS-CoV-2 infection, the majority of these genes increase in expression with age (Cluster 1) (Figure 6g-i) . To identify a consensus set of age-associated genes that are regulated by SARS-CoV-2 infection, we integrated the analyses from all 3 cell lines. By integrating these data with single cell transcriptomes of human lung tissue, we further pinpointed the specific cell types that normally express the age-associated genes. doi = 10.1101/2020.04.07.030684 id = cord-342557-a7q8vp8m author = Chowdhury, Surid Mohammad title = Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 date = 2020-10-23 keywords = RBD; SARS; figure summary = [Image: see text] Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Peptides that showed higher S protein-binding affinity compared to the α-helix (AH) of the ACE2 peptidase were further analyzed with molecular dynamics (MD) simulation and the structure− activity relationship (SAR) in order to achieve a high-affinity binder for the S protein. 30 Initially, stepwise multiple linear regression (MLR) was performed considering these properties as variables to predict the calculated binding affinity of the test peptides with the RBD of the SARS CoV-2 spike protein. All 51 peptides were docked to the RBD of the SARS CoV-2 spike protein using PatchDock. Various residues including Glu484, Tyr449, and Tyr505 present in the ACE2 binding site of the RBD were involved in noncovalent interaction with the antiviral peptides ( Figure 1a) . doi = 10.1021/acs.jpcb.0c05621 id = cord-256270-7e8zlt3t author = Choy, Ka-Tim title = Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro date = 2020-04-03 keywords = SARS summary = We evaluated the in vitro antiviral effect of compounds that were previously reported to inhibit coronavirus replication and compounds that are currently under evaluation in clinical trials for SARS-CoV-2 patients. We report the antiviral effect of remdesivir, lopinavir, homorringtonine, and emetine against SARS-CoV-2 virus in Vero E6 cells with the estimated 50% effective concentration at 23.15 μM, 26.63 μM, 2.55 μM and 0.46 μM, respectively. Among the 16 compounds we tested, remdesivir, lopinavir, homoharringtonine, and emetine dihydrochloride were found to inhibit SARS-CoV-2 replication in Vero E6 cells with EC 50 under 100 μM (Table 1) . Importantly, we observed that some of the compounds currently undergoing clinical trials such as ribavirin, favipiravir, oseltamivir, or baloxavir showed no apparent antiviral effect against the SARS-CoV-2 virus in vitro at concentrations under 100 μM (Table 1) . doi = 10.1016/j.antiviral.2020.104786 id = cord-340970-389t032s author = Choy, Wai-Yan title = Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development date = 2004-06-01 keywords = SARS; peptide summary = Background: The S (spike) protein of the etiologic coronavirus (CoV) agent of severe acute respiratory syndrome (SARS) plays a central role in mediating viral infection via receptor binding and membrane fusion between the virion and the host cell. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. The rabbit and monkey antisera against the synthetic peptides were diluted to 1:40-fold with PBS, and 10 L of each diluted serum was added to a well of the slide that was coated with SARS-CoV-infected African green monkey kidney Vero cells and incubated at 37°C for 1 h. The first batch of the rabbit and monkey antisera against the six synthetic peptides was collected 1 week after the second immunization and was tested for antibody specificity against the corresponding antigen (either conjugatefree or KLH-conjugated peptide) by ELISA analysis. doi = 10.1373/clinchem.2003.029801 id = cord-325421-1ysn0kyr author = Christensen, Johanna title = Covid-19 Viremia, Serologies and Clinical Course in a Case Series of Transplant Recipients date = 2020-09-03 keywords = COVID-19; SARS; patient summary = In this preliminary report, we find that immunocompromised transplant patients had higher rates of RNAemia (67%) than reported in the general population (15%), seeming absence of allo-immune injury despite systemic inflammation and formation of IgG overtime after recovery from infection. 8, 9 J o u r n a l P r e -p r o o f In this first case series, we report the characteristics, inflammatory immune response, biomarkers of graft injury along with SARS-CoV-2 RNAemia and serological response in a small cohort of kidney/liver transplant patients. Between, March 2020 and May 2020, six symptomatic kidney transplant recipients presented to the Virginia Commonwealth University hospital and tested positive for SARS-CoV-2. While it is not yet established if J o u r n a l P r e -p r o o f seroconversion confers immunity in the general population, 8, 9 the low re-infection rates and early reports of favorable efficacy of convalescent plasma in patients with severe COVID-19 manifestations [15] [16] [17] [18] suggest that this may be true. doi = 10.1016/j.transproceed.2020.08.042 id = cord-279520-zccd1mq5 author = Christian, Michael D. title = Possible SARS Coronavirus Transmission during Cardiopulmonary Resuscitation date = 2004-02-17 keywords = ICU; SARS; transmission summary = Infection of healthcare workers with the severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to occur primarily by either contact or large respiratory droplet transmission. We investigated a possible cluster of SARS-CoV infections in healthcare workers who used contact and droplet precautions during attempted cardiopulmonary resuscitation of a SARS patient. On the basis of the results of this investigation and previous reports of SARS transmission during aerosol-generating procedures, a systematic approach to the problem is outlined, including the use of the following: 1) administrative controls, 2) environmental engineering controls, 3) personal protective equipment, and 4) quality control. However, despite the use of infection control precautions and personal protective equipment designed to prevent contact and droplet transmission, episodes of SARS-CoV transmission to health-care workers have continued to occur under certain circumstances. We present the results of an investigation of the first reported transmission of SARS-CoV to healthcare workers that occurred during attempted cardiopulmonary resuscitation of a completely unresponsive SARS patient. doi = 10.3201/eid1002.030700 id = cord-327263-d5mmeu96 author = Christoff, A. P. title = Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2 date = 2020-09-05 keywords = SARS; September summary = Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint detect clear differences due to dilution alone, with point estimates from 0.43 to 0.61 Cq. In practice, observational data from 246 positive patients generated point estimates of mean Cq differences between individual tests and their corresponding pools ranging from 0.1 to 2.09 Cq. While such values are hardly significant in terms of analytical sensitivity, the expected counterparts for traditional pooling would range from 3.3 to 5 Cq under optimal amplification conditions. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint of diagnostic samples for SARS-CoV-2 can also perform swab pool analysis using the same detection methods and infrastructure already in use. . https://doi.org/10.1101/2020.09.03.20187732 doi: medRxiv preprint CONCLUSION Pool testing is a major alternative for large-scale screening of SARS-CoV-2 in low prevalence populations. doi = 10.1101/2020.09.03.20187732 id = cord-302442-jhio7mrl author = Chrzanowski, Wojciech title = Can Stem Cells Beat COVID-19: Advancing Stem Cells and Extracellular Vesicles Toward Mainstream Medicine for Lung Injuries Associated With SARS-CoV-2 Infections date = 2020-05-26 keywords = COVID-19; SARS; cell summary = Stem cell therapies and, more recently, their secreted extracellular vesicles (EVs), are emerging as new promising treatments, which could attenuate inflammation but also regenerate the lung damage caused by COVID-19. In this review article, we outline the mechanisms of cytokine storm and lung damage caused by SARS-CoV-2 virus leading to COVID-19 disease and how mesenchymal stem cells (MSCs) and their secreted EVs can be utilized to tackle this damage by harnessing their regenerative properties, which gives them potential enhanced clinical utility compared to other investigated pharmacological treatments. The safety profile and efficacy of MSCs are well-established based on the results from a number of completed clinical studies investigating the therapeutic potential of these therapies in lung diseases such as ARDS (Matthay et al., 2019; and bronchopulmonary dysplasia (Namba, 2019) , cardiovascular diseases (Kim et al., 2015; Suvakov et al., 2020) , diabetes (Thakkar et al., 2015; Cho et al., 2018) , and spinal cord injury (Xu and Yang, 2019) . doi = 10.3389/fbioe.2020.00554 id = cord-261279-6mef38eo author = Chu, Daniel K W title = Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date = 2020-01-31 keywords = PCR; RNA; SARS summary = RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. doi = 10.1093/clinchem/hvaa029 id = cord-336517-v7z62tld author = Chu, Hsu-Feng title = Porcine epidemic diarrhea virus papain-like protease 2 can be noncompetitively inhibited by 6-thioguanine date = 2018-08-20 keywords = PEDV; PL2; SARS summary = Further studies suggest that PEDV PL2 pro exhibits much higher DUB activity than that of SARS-and MERS-CoV PL pro s and can be inhibited by the anti-leukemia drug 6-thioguanine (6TG). Previous studies suggested that the Ubl domain was not involved in the catalytic activity of SARS-and MERS-CoV PL pro s (Chou et al., 2012; Clasman et al., 2017) . Overall, the secondary, tertiary and quaternary structures of the PEDV PL2 pro catalytic core are similar to those of SARS-and MERS-CoV PL pro s, even though their sequence identity is only 22-25% (Fig. S1 ). In contrast, previous studies suggested that the binding site of 6TG for SARS-and MERS-CoV PL pro s may be near the catalytic triad''s cysteine residue due to its competitive pattern of inhibition Chou et al., 2008) . Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin doi = 10.1016/j.antiviral.2018.08.011 id = cord-337812-arivkkj0 author = Chu, Ling-Hon Matthew title = Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry date = 2006-03-07 keywords = 3CL; CoV; SARS; peptide summary = To screen the substrate specificity of SARS-CoV 3CL pro in a rapid and highthroughput manner in contrast to the traditional tedious procedures, we applied the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis in combination with the novel "cartridge replacement" solid-phase peptide synthesis approach to investigate the biological significance of amino acid residues in the P2, P3, P4, P1¢, P2¢, and P3¢ positions that are flanking the conserved Gln residue in the P1 position at the SARS-CoV 3CL pro cleavage site (Schechter and Berger 1967; Fan et al. In this study, we used MALDI-TOF MS analysis in combination with the solid-phase peptide synthesis approach to examine the biological significance of amino acid residues in a total of six target positions at the SARS-CoV 3CL pro cleavage sites, including the P2, P3, and P4 positions at the amino side of the P1 position; and the P1¢, P2¢, and P3¢ positions at the carboxyl side of the P1 position (Table 1) . doi = 10.1110/ps.052007306 id = cord-277498-hdhq99k2 author = Chua, Melvin L.K. title = Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic date = 2020-05-15 keywords = SARS; cancer; patient summary = title: Follow-up and management of head and neck cancer patients during the 2019 novel coronavirus (SARS-CoV-2) disease pandemic These scenarios would be considered high-risk for SARS-CoV-2 transmission, and the HCW consulting the patient would require full personal protection equipment (PPE) consisting of N95 mask, surgical gowns, gloves, and goggles/face shields 16 . Following the completion of treatment any patient with direct contact with a SARS-CoV-2 infected individual or who has personally tested positive or has symptoms of COVID-19 should not be seen in an oncology clinic for a follow-up visit. When it is challenging to distinguish between post-treatment edema and residual tumor on imaging, a detailed physical exam including endoscopy may be required, and as aforementioned, full PPE is required to protect the HCW from transmission of SARS-CoV-2 through aerosolization during NPL. Herein, we focused on the impact of this pandemic on the management of head and neck cancer patients who are undergoing or have completed radiation treatment. doi = 10.1016/j.adro.2020.04.031 id = cord-290414-8i8g0xdc author = Chuan, Ong Sze title = Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? date = 2020-06-21 keywords = SARS summary = title: Do slit lamp shields and face masks protect ophthalmologists amidst COVID-19? Unlike face masks which provided some protection against both aerosols and droplets, slit lamp shields conferred protection only against direct large droplet transmission, with a limited role in reducing aerosol transmission risk. The SARS-CoV-2 is primarily transmitted via respiratory droplets, contact with 1 contaminated surfaces, or free-floating aerosols. We attempted to replicate the 5 spread of infected aerosols and large droplets in the clinical setting of a slit lamp 6 examination, to evaluate the efficacy of protective equipment in reducing the risk of viral 7 4 The experimental setup ( Figure S1 , available online at 12 www.aaojournal.org) consisted of a slit lamp (B900 Slit Lamp, Haag-Streit Holding AG, 13 Switzerland), a mannequin face which represented the ophthalmologist, and a spray bottle at 14 the chin rest which represented respiratory particle production from the patient. doi = 10.1016/j.ophtha.2020.06.031 id = cord-353479-kwi8zxo6 author = Chuang, H.-L. title = Impact of enhanced infection control procedures on clinical outcome following resuscitation attempts date = 2007-11-30 keywords = SARS; resuscitation summary = Other strict hospital ICMs in period 2 included the following: (i) all new admissions were required to be examined by our emergency department''s SARS screening team; (ii) all febrile patients were required to be admitted to the fever screening ward regardless of their diagnoses; (iii) unnecessary contact between HCWs was restricted and regular meetings and conferences were cancelled; (iv) each step of the standard operating procedure was strictly audited during resuscitation. There were also more emergency resuscitations performed without intubation and a higher number of ''do not resuscitate'' orders signed during resuscitation in the period of strict implementation of ICMs. These changes resulted in an abnormal situation in which the hospital''s facilities were adversely affected and the ability of the hospital to provide patients with medical care during the SARS outbreak was reduced. doi = 10.1016/j.jhin.2007.08.015 id = cord-331563-4yvfdqbq author = Chughtai, Abrar Ahmad title = Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis date = 2013-05-31 keywords = CDC; Health; SARS summary = title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis BACKGROUND: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). RESULTS: Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). This study aimed to examine available policies and guidelines around the use of masks and respirator for HCWs, for the prevention of influenza, SARS and TB; and to describe areas of consistency and inconsistency between guidelines, as well as gaps, with reference to the WHO and the CDC guidelines. Health care organizations and countries have different policies and guidelines around mask and respirator use for influenza, SARS and TB. doi = 10.1186/1756-0500-6-216 id = cord-276857-i948aq4b author = Chung, Grace TY title = A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study date = 2005-10-18 keywords = SARS summary = We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination. Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing. In-depth analysis of the available sequence data on SARS-CoV also revealed that the viral isolates could be readily subclassified into several major genotypes based on nucleotide variations at specific genomic positions [8, 12] . In this study, we demonstrate the feasibility of the adoption of allelic discrimination assays based on the use of fluorogenic oligonucleotide probes for the genotyping of SARS-CoV isolates. Our study has clearly demonstrated the feasibility of using allelic discrimination assays as a method for genetic characterization of SARS-CoV genotypes in patients. Genotype of SARS-CoV culture isolates from 30 patients determined by Taqman Allelic Discrimination assays Petric M, Skowronski DM doi = 10.1186/1471-2334-5-87 id = cord-334717-zg9f19p8 author = Chung, Mina K. title = SARS-CoV-2 and ACE2: The biology and clinical data settling the ARB and ACEI controversy date = 2020-08-06 keywords = ACE2; ARB; Ang; SARS summary = Angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) have been reported to increase ACE2 expression in animal models, and worse outcomes are reported in patients with co-morbidities commonly treated with these agents, leading to controversy during the COVID-19 pandemic over whether these drugs might be helpful or harmful. Recently there has been controversy over whether use of angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) might be harmful in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with cardiovascular disease, hypertension, or diabetes mellitus under treatment with these agents. SARS-CoV-2, the coronavirus causing COVID-19, enters host cells via binding of the virus spike protein to angiotensin-converting enzyme 2 (ACE2). In a study of 2877 hospitalized patients with COVID-19, 850 had hypertension of which 183 were treated with renin-angiotensin-aldosterone system inhibitors (RAASi) and 527 were not; RAASi use was not associated with severity of disease or mortality [66] . doi = 10.1016/j.ebiom.2020.102907 id = cord-023510-gd4phncm author = Chuo, Hsin-You title = Theme Park Visitors’ Responses to the SARS Outbreak in Taiwan date = 2007-05-02 keywords = SARS; Taiwan; outbreak; park summary = 1. Can a significant discriminant function be developed to interpret the differences between respondents who did and did not visit theme parks during the SARS outbreak period in Taiwan on the basis of their personal characteristics? In addition to the information of respondents'' general demographics, their patronage frequency in the last year and whether they visited theme parks in the period of the SARS outbreak, the question content also consisted of scale items to measure ''''benefit sought,'''' ''''product involvement,'''' and ''''risk perception.'''' Ten individual benefit scale items were derived from Pearce''s (1993) Leisure Ladder Model for theme park visitors. Thus, on the one hand, whether or not the respondents visited theme parks during the SARS outbreak was adopted to be the dependant (criterion) variable; on the other, respondents'' age, their patronage frequency in the last year, and the factors condensed from scale items of respondents'' risk perception, benefit sought, and product involvement were adopted to be the independent variables (predictors) in the developing discriminant function. doi = 10.1016/s1745-3542(06)03006-2 id = cord-322913-sq9mq6f1 author = Ciabattini, Annalisa title = Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date = 2020-11-06 keywords = COVID-19; CoV-2; SARS; age; response; vaccine summary = The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of innate and adaptive immune responses, and the lack of a clear correlate of protection, make the design of vaccination strategies for older people extremely challenging (Fig. 3 ). doi = 10.1007/s00281-020-00821-0 id = cord-342396-n3txsvf7 author = Ciaglia, Elena title = COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children date = 2020-04-23 keywords = ACE2; SARS summary = title: COVID-19 Infection and Circulating ACE2 Levels: Protective Role in Women and Children In another case control study conducted in the north eastern Chinese Han population, the serum ACE2 activity negatively correlated with body mass index (BMI), pulse pressure, and estrogen levels in female EH (essential hypertension) patients (14) . Cases of coronavirus disease 2019 (COVID-19) among children in China have been less severe than those in adults, according to a new study. Now, circulating level of ACE2 may have prognostic effect in monitoring COVID-infection, and the genetic analysis of ACE2 polymorphisms might be a key element of individualized care for its prevention, diagnosis, and treatment. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury doi = 10.3389/fped.2020.00206 id = cord-017903-92hnaiyc author = Cieslak, Theodore J. title = Communicable Diseases and Emerging Pathogens: The Past, Present, and Future of High-Level Containment Care date = 2018-07-07 keywords = EVD; Ebola; HLCC; Lassa; PTP; SARS summary = These two facilities cared for seven Ebola virus disease (EVD) patients during the 2014-2016 outbreak, while another two were cared for at the National Institutes of Health''s Special Clinical Studies Unit, which had also developed HLCC capability. First, patients harboring diseases caused by pathogens that require handling under BSL-4 conditions in the laboratory would seem to be obvious candidates for clinical management under HLCC conditions. Lujo virus, an Old World arenavirus closely related to Lassa, was first described in 2008 as the cause of a single outbreak of viral hemorrhagic fever involving five patients in Lusaka, Zambia, and Johannesburg, South Africa (the name, Lujo, derives from the two cities) [20] . It would seem prudent to manage patients potentially harboring such diseases under HLCC conditions when feasible and to handle their causative viruses in a BSL-4 laboratory. doi = 10.1007/978-3-319-77032-1_1 id = cord-340305-jtvn9tlm author = Cimolai, Nevio title = A Minimalist Strategy Towards Temporarily Defining Protection for COVID-19 date = 2020-09-19 keywords = COVID-19; CoV-2; SARS; antibody summary = At this time, the best correlates with protection from natural coronavirus infections are systemic neutralizing antibody and mucosal IgA. Others have found strong correlations between neutralizing antibodies and EIA-detected antibodies to various SARS-CoV-2 antigens [41, 42] .Some have found diversity in immune responses contingent on the nature of presenting disease [38, 43] . With the availability of viral antigen, most scientists in the know-how would be able to fashion a test for antibody determination in short order and most would likely choose an enzyme immunoassay (EIA) (or nearly equivalent non-enzymebased assay) for its potential of automation and widespread use. Sensitive and specific detection of low-level antibody responses in mild Middle East Respiratory Syndrome coronavirus infections A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients doi = 10.1007/s42399-020-00533-4 id = cord-352146-i4ezsclf author = Cimolai, Nevio title = Efficacy of povidone‐iodine to reduce viral load date = 2020-07-31 keywords = SARS summary = (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. (2020) provide some preliminary findings on the potential use of povidone-iodine for reducing oropharyngeal viral load of SARS-CoV-2. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. The use of RT-PCR as the tool to assess viral load nevertheless has some potential limitations. While povidone-iodine may be the main ingredient in the specific mouthwash preparation, there are often a number of unlisted ingredients (e.g., alcohol) which can potentially provide both antisepsis and RT-PCR inhibition. As another form of control, however, it would be of relevance to see what the lavage properties of gargling in itself have for reducing viral load in those samples assessed. COVID-19, povidone-iodine, quantitation, respiratory, SARS-CoV-2 Is povidone-iodine mouthwash effective against SARS-CoV-2? doi = 10.1111/odi.13557 id = cord-300319-9k8zseao author = Cinatl Jr., J. title = Infection of cultured intestinal epithelial cells with severe acute respiratory syndrome coronavirus date = 2004 keywords = IFN; SARS; cell summary = To identify a model for the study of intestinal pathogenesis of severe acute respiratory syndrome (SARS) we tested the sensitivity of six human intestinal epithelial cell lines to infection with SARS coronavirus (SARS-CoV). In both cell lines, SARS-CoV infection deregulated expression of cellular genes which may be important for the intestinal pathogenesis of SARS. To investigate whether ACE2 is a functional receptor for SARS-CoV in intestinal epithelial cell cultures, the cells were pre-treated for 60 min at 37°C with goat antibody directed against the human ACE2 ectodomain (R&D Systems; Wiesbaden-Nordenstadt, Germany). SARS-CoV infection of Caco-2 cells up-regulated OAS2 and MXA but not PKR genes. The discrepancy between transcriptional activation of IFN-induced genes and the ability of SARS-CoV to replicate in Caco-2 cells could be explained by the existence of a specific viral mechanism for escaping IFNinduced anti-viral effects common to most viruses [28] . This justifies the use of intestinal cell lines as a model to study the direct effects of SARS-CoV infection on gene expression in permissive human cells. doi = 10.1007/s00018-004-4222-9 id = cord-294933-oc2glu4a author = Cinesi Gómez, César title = Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date = 2020-06-19 keywords = COVID-19; NIMV; SARS; patient; respiratory summary = The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations. doi = 10.1016/j.medine.2020.03.002 id = cord-262159-8y0q45gr author = Ciorba, Andrea title = Don’t forget ototoxicity during the SARS-CoV-2 (Covid-19) pandemic! date = 2020-07-10 keywords = SARS summary = Aim of this communication is to remind clinical professionals to be aware of ototoxic side effects of several specific drugs proposed for the treatment of the new virus SARS-CoV-2 (Covid-19). In particular, chloroquine and hydroxychloroquine have been widely promoted and used during the pandemic; 2,3 however, in the past, data in the literature have suggested that in many treated cases side effects such as sensorineural hearing loss, tinnitus, and/or persistent imbalance were common. However, ototoxicity has been reported among the possible side effects of the adenosine nucleotide analogues; 5, 6 specifically, data in the literature report that patients may develop irreversible unilateral or bilateral hearing loss and tinnitus due to the use of these drugs, usually after a few weeks of administration. 7, 8 Lopinavir, a nucleoside reverse-transcriptase inhibitor, proposed in the treatment of SARS-CoV-2 infections, has been related to the onset of sensorineural hearing loss, 9 after several weeks of administration. doi = 10.1177/2058738420941754 id = cord-338798-xsun927w author = Ciorba, Andrea title = Ototoxicity prevention during the SARS-CoV-2 (Covid-19) emergency date = 2020-10-17 keywords = SARS summary = • To remind the risk of ototoxicity when using chloroquine and hydroxychloroquine, in particular as prophylactic agents against SARS-CoV-2, during the pandemic. • Healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. eventually adequate treatment is established (3) (4) (5) . Pure tone audiometry represents the main instrument for the identification and classification of hearing impairment; however, Otoacoustic Emissions (OAEs) are reported to be very sensitive in evaluating early manifestations of cochlear damages (6), as ototoxic drugs typically affect primarily outer hair cells (1, (3) (4) (5) . Therefore, healthy subjects taking chloroquine and hydroxychloroquine as prophylactic agent against SARS-CoV-2, during the pandemic, should be screened periodically, at least by OAEs. Clearly, even without a fatal condition, it is important to avoid the onset of ototoxic manifestations, especially when chloroquine and hydroxychloroquine are administered with a prophylaxis intent. doi = 10.1016/j.jgar.2020.09.030 id = cord-252804-u7tz6xzz author = Ciotti, Marco title = COVID-19 Outbreak: An Overview date = 2020-04-07 keywords = COVID-19; SARS; Wuhan summary = Inoculation of bronchoalveolar lavage fluid obtained from patients with pneumonia of unknown origin into human airway epithelial cells and Vero E6 and Huh7 cell lines led to the isolation of a novel coronavirus, SARS-CoV-2, previously named 2019-nCov [1] . As soon as on January 7, 2020, the Chinese health authorities had declared that a novel coronavirus was responsible for this outbreak of pneumonia in Wuhan, a European network of academic and public laboratories designed an rRT-PCR protocol based on the comparison and alignment of previously available SARS-CoV and bat-related coronavirus genome sequences as well as five sequences derived from the novel coronavirus SARS-CoV-2 made available by the Chinese authorities [23] . Regarding the sites under positive selective pressure found on the Spike glycoprotein, the results have shown that amino acid position 536 in COVID-19 has an Asn residue, while the Bat SARS-like coronavirus has a Gln 4 DOI: 10.1159/000507423 residue; the SARS virus, instead, has an Asp residue. Phylogenetic analysis of the SARS-CoV-2 genomes showed that the novel coronavirus responsible for the pneumonia outbreak in Wuhan, China, belongs to the Betacoronavirus genus, subgenus Sarbecovirus [37] . doi = 10.1159/000507423 id = cord-283440-8du0s33p author = Ciuca, Ioana M title = COVID-19 in Children: An Ample Review date = 2020-06-25 keywords = COVID-19; China; SARS; child summary = The aim of this review was to describe the current knowledge about coronavirus disease 2019 (COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) in children, from epidemiological, clinical, and laboratory perspectives, including knowledge on the disease course, treatment, and prognosis. This review highlights that COVID-19 in children is similar to the disease in the adult population, but with particularities regarding clinical manifestations, laboratory test results, chest imaging, and treatment. It started at the end of 2019, when many adult patients with a new form of pneumonia that was frequently fatal were admitted to Chinese hospitals; this illness was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [11] [12] [13] This study aimed to review the current data on SARS-CoV-2 infection in children, from epidemiological, clinical, and laboratory perspectives, including data on the disease course, treatment, and prognosis. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.2147/rmhp.s257180 id = cord-275454-an8xvow3 author = Clark, Andrew E title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date = 2020-09-28 keywords = CoV-2; SARS summary = We read with interest the study appearing in this issue by Li et al, who utilized a pooled sample strategy and a point-of-care (POC) reverse transcriptase-polymerase chain reaction (RT-PCR) assay for screening asymptomatic airline passengers arriving from areas of high SARS-CoV-2 prevalence. At the time of this writing, 2 reference laboratories in the United States (Quest Diagnostics and LabCorp) have received emergency use authorizations from the US Food and Drug Administration to use pooled specimens for SARS-CoV-2 detection [2] . In this work, pooling was performed in a 10:1 ratio, meaning 10 patient specimens were combined and tested using a single SARS-CoV-2 assay. At our institution, we are aware of patients who underwent preprocedure SARS-CoV2 screening utilizing the same assay deployed in this work, only to be diagnosed with active, symptomatic COVID-19 within 5 days of testing. doi = 10.1093/cid/ciaa1145 id = cord-256156-mywhe6w9 author = Clausen, Thomas Mandel title = SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 date = 2020-09-14 keywords = ACE2; Fig; RBD; SARS; cell; protein summary = We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain (RBD). Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. In this report, we show that the ectodomain of the SARS-CoV-2 spike (S) protein interacts with cell surface HS through the Receptor Binding Domain (RBD) in the S1 subunit. Adjacent to the ACE2 binding site and exposed in the RBD lies a group of positively-charged amino acid residues that represents a potential site that could interact with heparin or heparan sulfate ( Fig. 1A and Suppl. The SARS-CoV-2 spike protein depends on cellular heparan sulfate for cell binding. Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin doi = 10.1016/j.cell.2020.09.033 id = cord-311758-wof4yi39 author = Clauw, Daniel J. title = Considering the potential for an increase in chronic pain after the COVID-19 pandemic date = 2020-06-03 keywords = COVID-19; SARS summary = The experience of living within this pandemic has disrupted daily life across all sectors, including those living with chronic pain (CP), those infected with the coronavirus Severe Acute Respiratory Syndrome (SARS)-CoV2, healthcare providers and essential workers, as well as those who remained physically healthy. Specific possibilities might include: (1) CP as part of a postviral syndrome or the result of viral-associated organ damage; (2) worsening of CP due to exacerbation of preexisting pain physical or mental complaints; and (3) CP newly triggered in individuals not infected with COVID by exacerbation of risk factors (poor sleep, inactivity, fear, anxiety, and depression). In a small study of 22 subjects (21 of whom were healthcare workers) infected during the SARS epidemic, a chronic post-SARS syndrome consisting of fatigue, diffuse myalgia, depression, and nonrestorative sleep persisted for almost 2 years. doi = 10.1097/j.pain.0000000000001950 id = cord-341453-9yrvjlpx author = Clay, Candice C title = Severe acute respiratory syndrome-coronavirus infection in aged nonhuman primates is associated with modulated pulmonary and systemic immune responses date = 2014-03-19 keywords = CD8; CoV; SARS; aged; figure summary = The aim of this study was to determine how the peripheral and mucosal immune responses to SARS-CoV infection compare in the aged and juvenile nonhuman primate host and to determine how this may impact viral replication levels. No virus was detected in any sample collected from either age group at 10 d.p.i. To determine if advanced age correlated with increased severity of lung pathology, a comprehensive histological analysis of the respiratory tract following SARS-CoV infection was conducted in aged and juvenile animals. To determine how mucosal cytokines in SARS-CoV infection compared to systemic responses and how age may impact mucosal cytokine expression; the inflammatory protein profile was evaluated by bead-based arrays in standardized-collected lung tissue from the proximal portion of the right caudal lobe. Although no age-dependent differences were observed in the frequency of naïve (CD45RA + CCR7+) CD8 T cells in peripheral blood, there were significantly lower levels of these cells in the lung and lymph node of aged animals during SARS-CoV infection ( Figure 6A -C; unpaired student T-tests). doi = 10.1186/1742-4933-11-4 id = cord-325261-bdumhy5b author = Clemente, Valentino title = Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19 date = 2020-05-15 keywords = IRF3; MERS; PLP; SARS; dub summary = Since viral PLPs are used by coronaviruses to both replicate and to antagonize the innate immune response, they are considered important therapeutic targets for coronavirus infections and thus may be of interest for future COVID-19 treatment strategies. The multifunctional activities of PLPs, namely as cysteine proteases, DUBs and deISGylating enzymes, play two important roles in coronavirus pathogenesis: the first involves the production of non-structural proteins (nsp) required for the replication process and the second consists of blocking the innate immune system of the infected host cell. Since it is known that cellular antiviral pathways include (de)ubiquitination within their regulatory mechanisms [14, 15] , PLPs are believed to contribute to infection pathogenesis by using their intrinsic DUB and deISGylating activities to antagonize the activation of the host cell innate immune response [5] . Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression doi = 10.3390/ijms21103492 id = cord-315328-8g40ukml author = Clementi, Nicola title = Interferon-β-1a Inhibition of Severe Acute Respiratory Syndrome–Coronavirus 2 In Vitro When Administered After Virus Infection date = 2020-06-19 keywords = IFN; SARS summary = In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In this report, we demonstrate that IFN-β-1a was highly effective in inhibiting in vitro SARS-CoV-2 replication at clinically achievable concentration when administered after virus infection. In the current study, we assessed its anti-SARS-CoV-2 activity in vitro to give a preclinical background to clinical trials evaluating the possible therapeutic role of IFN-β-1a in patients with coronavirus disease 2019 (COVID-19). Vero E6 cells were treated with concentrations ranging from 5000 to 0.01 IU/mL of IFN-β-1a 1 hour after inoculation with SARS-CoV-2 and monitored for cytopathic effect and real-time-PCR quantitative evaluation at 48, 72, and 96 hours after infection. Our in vitro observations shed light for the first time on that antiviral activity of IFN-β-1a against SARS-CoV-2 when administered after the infection of cells, highlighting its possible efficacy in an early therapeutic setting. doi = 10.1093/infdis/jiaa350 id = cord-320401-itltvh3f author = Clementi, Nicola title = NARINGENIN IS A POWERFUL INHIBITOR OF SARS-CoV-2 INFECTION IN VITRO date = 2020-10-20 keywords = Nar; SARS summary = In the present insight, we highlight novel experimental evidence that the flavanone Naringenin, targeting the endo-lysosomal Two-Pore Channels (TPCs), could be added to the list of potential weapons against SARS-CoV-2 infection and COVID-19 disease. Noteworthy, our recent evidence has shown that the activity of human TPC channels can be inhibited by the natural flavonoid compound Naringenin (Nar) [4] , one of the main flavonoids present in the human diet. Images showed that Nar treatment did not cause toxicity on uninfected cells at any of the tested concentrations and DMSO (vehicle) did not significantly affect SARS-CoV-2 replication (Fig.1D-E) . Of note, results indicated a strong decrease of CPE (>90%) at 48hpi when Vero E6 cells were treated with 250 and 62.5 μM Nar (Fig.1E) . Differences between treated samples (n=4, n=3 at 72hpi) and controls (untreated infected cells, n=4, not shown) were significant Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? doi = 10.1016/j.phrs.2020.105255 id = cord-337198-4sors3bg author = Clementi, Nicola title = Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date = 2020-07-10 keywords = CPE; HCQ; PCR; SARS summary = In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . doi = 10.3389/fmicb.2020.01704 id = cord-308760-xonuu04p author = Clerici, Bianca title = A case of newly diagnosed immune thrombocytopenia in the COVID-19 era date = 2020-11-12 keywords = ITP; SARS summary = First-line treatment options for ITP include corticosteroids and intravenous immunoglobulin (IvIg); of the two, corticosteroids induce a more persistent increase in platelet count, and appear more suitable in this case. In this patient, the benefits of a rapid increase in platelet count must be weighed against the risk of deterioration of the ongoing viral infection, of superimposed hospital-acquired infections, of liver impairment, and of venous thromboembolic events, which might be favored by ITP itself [6, 7] , the treatment with a TPO-RA [8] , the suspected presence of a neoplasm, the length of hospitalization and SARS-CoV-2 infection [9, 10] . The impact of the anti-CD20 activity of Rituximab on the course of SARS-CoV-2 infection in a patient on steroid treatment was unknown and particularly worrisome given the crucial role of humoral immunity in infection contrast [11, 12] . doi = 10.1007/s11739-020-02553-3 id = cord-274945-6p5de7o2 author = Clevers, Hans title = COVID-19: organoids go viral date = 2020-06-01 keywords = SARS; organoid summary = Indeed, enterocytes generated in ASC derived, small intestinal organoid cultures allowed cultivation of multiple human norovirus strains. There is no robust in vitro model beyond the use of ex vivo bronchus explant cultures for assessing the infectivity of emerging flu viruses in humans. Penninger and colleagues 7 demonstrated that SARS CoV2 could directly infect capillary organoids and kidney organoids, both established from human iPSCs. These observations may explain the spread of the virus through the body and the loss of kidney function in severely ill individuals. All three studies reported that the most common cell type of the intestinal epithelium, the enterocyte, is readily infected, suggesting that the intestine is a poten tial site of SARS CoV2 replication. Differentiated human airway organoids to assess infectivity of emerging influenza virus TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes Infection of bat and human intestinal organoids by SARS-CoV-2 doi = 10.1038/s41580-020-0258-4 id = cord-222664-4qyrtzhu author = Coban, Mathew title = Attacking COVID-19 Progression using Multi-Drug Therapy for Synergetic Target Engagement date = 2020-07-06 keywords = Ace2; COVID-19; Caulfield; Fig; SARS; Tmprss2; protein summary = We have therefore initiated a computational dynamics drug pipeline using molecular modeling, structure simulation, docking and machine learning models to predict the inhibitory activity of several million compounds against two essential SARS-CoV-2 viral proteins and their host protein interactors; S/Ace2, Tmprss2, Cathepsins L and K, and Mpro to prevent binding, membrane fusion and replication of the virus, respectively. Using a computational pipeline that aimed to expeditiously identify lead compounds against COVID-19, we combined compound library preparation, molecular modeling, and structure simulations to generate an ensemble of conformations and increase high quality docking outcomes against two essential SARS-CoV-2 viral proteins and their host protein interactions; S/Ace2, Tmprss2, Cathepsin L and K, and M pro that are known to control both viral binding, entry and virus replication (Fig. 1A) . doi = nan id = cord-031289-uxoz0xhk author = Coccolini, Federico title = SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients date = 2020-05-18 keywords = CoV-2; SARS summary = title: SARS-CoV-2 Is Present in Peritoneal Fluid in COVID-19 Patients The present article represents the very first positive result describing the presence of the virus in peritoneal fluid during an emergency surgical procedure in a COVID-19 sick patient. Interestingly, the nasal swab contained less SARS-CoV-2 RNA virus compared to the viral fluid that scored positive in 2 targets out of 3. This indicates that the viral load in the peritoneal fluid was higher compared to the upper respiratory material and suggests that the surgical operation was indeed a procedure at risk of infection. As no information exist about the virus passage to peritoneal cavity and fluids, present data may suggest that potentially all people even those with mild to moderate respiratory symptoms by SARS-CoV-2 could present viral load in peritoneal fluid, thus increasing the exposure and contagion risks for the entire surgical staff.Peritoneal fluid contamination with blood of feces may interfere with the virus detection. doi = 10.1097/sla.0000000000004030 id = cord-328000-i9tzr13z author = Cockrell, Adam S. title = Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice date = 2018-07-24 keywords = CoV; DPP4; MERS; SARS summary = Three different strategies were employed for development of SARS-CoV mouse models: (i) different mouse species (or subspecies) were challenged with wildtype human SARS-CoV isolates in order to find a model that allows for replication and reflects severe respiratory disease symptoms observed in infected human patients; (ii) mice were genetically engineered to modify the host receptor, which facilitated productive SARS-CoV replication and pathogenesis; and (iii) adaptive evolution of wild-type SARS-CoV to a chosen mouse species was done to enhance pathogenesis, and associated clinical phenotypes in vivo. To adapt SARS-CoV to cause severe acute respiratory disease in mouse lungs, 6-week-old female BALB/c mice were intra-nasally infected with the clinical Urbani isolate (Roberts et al. Virus infection studies in CC mouse lines, including SARS-CoV, have led to mapping of high and low host response alleles as they relate to development of clinical signs of disease following viral pathogenesis (Bottomly et al. doi = 10.1007/s00335-018-9760-9 id = cord-312367-24huwt3y author = Coelho, Camila title = Biochemical screening for SARS-CoV-2 main protease inhibitors date = 2020-10-06 keywords = SARS; pro summary = As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). As viral proteases, following polymerases, are the most prominent targets for antiviral drug design [9] , here we describe initial biochemical screenings with recombinant purified SARS-CoV-2 M pro performed in order to define possible candidates which could serve as lead compounds for the design of future COVID-19 therapies. In order to contribute to the ongoing worldwide research and development efforts to contain COVID-19, we cloned, expressed recombinantly in E.coli BL21(DE3) and purified an important drug target of SARS-CoV-2, its main protease (M pro ). From these obtained compounds, esculetin-4-carboxylic acid ethyl ester (IC 50 = 46 μM in M pro inhibition assays), a coumarin derivative and natural product, demonstrated an EC 50 of 112 μM (median toxic concentration TC 50 >800μM) in Vero-cell SARS-CoV assays [13] and MP576 (IC 50 = 2.5 μM), a quinolinecarboxylate, demonstrated an EC 50 of 7 μM (TC 50 >50μM) [15, 17] , thus validating the M pro biochemical screening approach for the development of SARS-CoV drugs. doi = 10.1371/journal.pone.0240079 id = cord-260854-v7wgb6mr author = Colafrancesco, Serena title = COVID-19 gone bad: A new character in the spectrum of the hyperferritinemic syndrome? date = 2020-05-05 keywords = COVID-19; MAS; SARS; patient summary = The severe form of COVID-19 share several clinical and laboratory features with four entities gathered under the term "hyperferritinemic syndrome" and including macrophage activation syndrome (MAS), adult-onset Still''s disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS) and septic shock. COVID-19 systemic inflammatory reaction and "hyperferritinemic syndromes" are all characterized by high serum ferritin and a life-threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi-organ failure. In this review, we analyze the possible epidemiological and molecular mechanisms responsible for hyper-inflammation in patients with severe COVID-19 and we underline the similarities between this condition and "hyperferritinemic syndromes" which would allow considering this entity as the fifth member of the spectrum of inflammatory conditions. The umbrella term "hyperferritinemic syndrome" encompasses four clinical conditions, macrophage activation syndrome (MAS), adult-onset Still''s disease (AOSD), catastrophic anti-phospholipid syndrome (CAPS), and septic shock, all characterized by high serum ferritin and a life -threatening hyper-inflammation sustained by a cytokines storm which eventually leads to multi -organ failure [1] . doi = 10.1016/j.autrev.2020.102573 id = cord-288553-fez60jyn author = Colaneri, Marta title = Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. date = 2020-03-19 keywords = SARS summary = title: Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy. Health care workers are at increased risk of acquiring COVID-19 infection, possibly due to direct contact with the patients. In this regard, studies suggest that surfaces and suspensions can carry HCoVs, increasing the risk of contact transmission that could lead to hospital acquired HCoVs infections [4, 5] Since February 21, 2020, when the first autochthonous case in Italy was confirmed, an overwhelming number of SARS-CoV-2 infections is continuously being detected, exceeding 8,000 cases at the time of writing. Fondazione IRCCS Policlinico San Matteo, Pavia, is a 1,300-bed tertiary teaching hospital in Northern Italy and a national SARS-CoV-2 referral center. Survival of human coronaviruses 229E and OC43 in suspension and after drying on surfaces: A possible source of hospital-acquired infections Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination doi = 10.1016/j.jhin.2020.03.018 id = cord-353615-9aj5yxkd author = Colaneri, Marta title = Running out of bullets: the challenging management of acute hepatitis and SARS‐COV‐2 from the SMatteo COvid19 Registry (SMACORE) date = 2020-07-17 keywords = COVID-19; SARS summary = Since several of the currently administered drugs against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are possibly hepatotoxic, the management of patients with COVID‐19 and liver failure is still an almost unexplored field. Beyond the well-known catastrophic pulmonary effects of coronavirus disease 2019 , the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has also been associated with a significant damage to other organ systems, including kidney, heart, vessels and liver (1) (2) (3) (4) (5) . et al (12) , patients with SARS-CoV-2 and chronic HBV co-infection with liver injury and coagulation dysfunction were more likely to develop severe illness and had higher mortality. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: A retrospective study Clinical Characteristics of Hospitalized Patients with SARS-CoV-2 and Hepatitis B virus Co-infection Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection doi = 10.1111/liv.14609 id = cord-288998-0by0bkgs author = Colarusso, Chiara title = A lesson from a saboteur: high molecular weight kininogen (HMWK) impact in COVID‐19 date = 2020-06-04 keywords = ACE2; SARS; covid-19 summary = In the attempt to understand how the virus spreads and how to pharmacologically abolish it, it was highlighted that SARS‐CoV‐2 infects human cells by means of angiotensin converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2) and SARS‐CoV‐2 main protease (M(pro)). Our attention has been focused on the role of ACE2 in that its blockade by the virus increases Bradykinin and its metabolites, well known to facilitate inflammation in the lung (responsible for cough and fever), facilitate both the coagulation and complement system, three mechanisms that are typical of angioedema, cardiovascular dysfunction and sepsis, pathologies which symptoms occur in COVID‐19 patients. Once SARS-CoV-2 binds to ACE2 , the enzyme is blocked, therefore, leading to what we are actually assisting in terms of high blood pressure in COVID-19 patients and pulmonary edema up to angioedema, which underlies the fact that physiologically ACE2 cleaves several bioactive peptides, among which [des-Arg 9 ]bradykinin ([des-Arg 9 ]BK) (Vickers et al. doi = 10.1111/bph.15154 id = cord-323831-1qadv7r1 author = Coleman, H title = Severe acute respiratory syndrome coronavirus-2 in post-laryngectomy patients: case series of four patients date = 2020-06-23 keywords = SARS; patient summary = OBJECTIVE: To report our experience of diagnosis, investigation and management in patients who had undergone laryngectomy secondary to previous squamous cell carcinoma, who were subsequently infected with severe acute respiratory syndrome coronavirus-2 during the coronavirus disease 2019 pandemic. CASE REPORTS: Four post-laryngectomy patients with laboratory-proven severe acute respiratory syndrome coronavirus-2 infection were admitted to our institution from 1 March to 1 May 2020. 2 There is no published evidence to date on the post-operative and ward management of this group of patients with laboratory-proven SARS-CoV-2 infection. 3 Here, we present our experience of the diagnosis, investigation and management of SARS-CoV-2 positive, post-laryngectomy patients, who attended our institution between 1 March and 1 May 2020, during the Covid-19 pandemic. Patient one, a 50-year-old female, was an in-patient on the ENT ward, who was progressing well 2 weeks following total laryngectomy, bilateral neck dissection and pectoralis major flap reconstruction for a tumour-node staged T 3 N 2c moderately differentiated supraglottic SCC. doi = 10.1017/s0022215120001310 id = cord-293315-kx4x2g24 author = Colmenero, I. title = SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases date = 2020-06-20 keywords = COVID-19; SARS; case summary = title: SARS‐CoV‐2 endothelial infection causes COVID‐19 chilblains: histopathological, immunohistochemical and ultraestructural study of 7 paediatric cases CONCLUSIONS: Although the clinical and histopathological features were similar to other forms of chilblains, the presence of viral particles in the endothelium and the histological evidence of vascular damage, support a causal relation of the lesions with SARS‐CoV‐2. 4 Most patients have been negative for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) when tested by PCR of nasopharyngeal and oropharyngeal swabs, and less than 50% have a history of exposure to positive household contacts or previous history of mild upper respiratory or gastrointestinal symptoms. Lymphocytic vascular damage was the hallmark feature in biopsies from our 7 patients with COVID-19 related chilblains. 25 We have demonstrated the presence of viral particles within endothelial cells in lesional skin biopsies from patients presenting with chilblains during the COVID-19 pandemic. Chilblain-like lesions: a case series of 41 patients during the COVID-19 pandemic doi = 10.1111/bjd.19327 id = cord-307113-mu3ow7m4 author = Colmenero, I. title = SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors date = 2020-09-30 keywords = SARS summary = title: SARS‐CoV‐2 Has Not Been Detected Directly by Electron Microscopy in the Endothelium of Chilblain Lesions: reply from authors The size and shape of the particle shown in our paper fit with other descriptions of SARS‐CoV‐2, but there may be a bias in interpretation. The size and shape of the particle shown in our paper fit with other descriptions of SARS-CoV-2, but there may be a bias in interpretation. After the publication of our series, new evidence is rising favouring a causal role for SARS-CoV-2 in COVID chilblains. Positive immunohistochemistry for SARS-CoV has been reported by different authors in cutaneous biopsies of COVID chilblains using antibodies directed against different parts of the virus, 3, 4 and SARS-CoV-2 RNA-positive cells have been demonstrated by RNAscope. SARS-CoV-2 endothelial infection causes COVID-19 chilblains: histopathological, immunohistochemical and ultrastructural study of seven paediatric cases Chilblains and COVID-19: why SARS-CoV-2 endothelial infection is questioned. doi = 10.1111/bjd.19579 id = cord-355283-ny1ju7vc author = Colombo, L. title = How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism date = 2020-08-12 keywords = COVID-19; SARS summary = title: How to manage thromboembolic risk in patient with SARS-CoV-2-related disease in the Emergency Department: a case report of cardiogenic shock due to massive pulmonary embolism Although the most known feature of SARS-CoV-2 associated infection is a mild to severe pneumonia, increasing evidence suggests the existence of an infection-associated risk of both arterial and venous thromboembolism (VTE), but the exact magnitude of this phenomenon is still unknown. Only a few months have passed since the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19) , have spread all over the world, resulting in more than 17 million cases, more than 670,000 infection-related deaths [1] and a global health threat that has no comparison in the last decades. High incidence of venous thromboembolic events in anticoagulated severe COVID-19 patients doi = 10.1016/j.rmcr.2020.101185 id = cord-266480-u8o4eitu author = Colubri, Andrés title = Preventing outbreaks through interactive, experiential real-life simulations date = 2020-09-02 keywords = SARS; outbreak summary = Operation Outbreak (OO) is an educational curriculum and simulation platform that uses Bluetooth to spread a virtual "pathogen" in real-time across smartphones in close proximity. The app-generated data from these simulations represented the "ground truth" of the mock outbreaks, captured several essential features of SARS-CoV-2, and allowed us to observe behavioral changes among participants--many of which are now being mirrored in real life. Our 2018 SMA Ebola simulation first showed how student social-distancing could affect an "outbreak''s" trajectory ( Figure 2A More detailed data from the 2019 simulation allowed us to reconstruct transmission chains over time and identify important features of the outbreak, such as the existence of two super-spreaders causing 4 and 5 secondary infections early in the game ( Figure 2C ). We envision OO as playing two key roles: (1) as a pedagogical platform for teaching fundamentals of pandemic response that are vital for the public to understand and (2) as a novel system for simulating outbreaks and evaluating real-world mitigation strategies, including those needed to restart in-person education. doi = 10.1016/j.cell.2020.08.042 id = cord-328644-odtue60a author = Comandatore, Francesco title = Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date = 2020-05-28 keywords = Coronavirus; SARS; sequence; variant summary = These variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded RNA viruses -as in the case of SARS-CoV-2 (Sanjuán and Domingo-Calap 2016) , which has a single, positive-strand RNA genome. To have a better insight on the history and spread of the COVID-19 pandemic in Italy and thanks to the sequences deposited in the Gisaid database, we identified 7 non synonymous mutations that are differentially frequent in Italian SARS-CoV-2 strains respect to strains circulating globally. Our analysis allowed us to identify 7 positions in four proteins that present drastic changes in amino acid frequencies when comparing Italian sequences with worldwide sequences available on Gisaid.org on April, 10, 2020 ( Figure 1 ). doi = 10.1101/2020.04.30.071027 id = cord-316345-a1cirnya author = Comas, Carmina title = COVID‐19 and pregnancy: An opportunity to correct an historic gender bias date = 2020-08-02 keywords = COVID-19; SARS summary = Unfortunately, this bias seems to be maintained in the COVID‐19 epidemic: most current guidelines for diagnosing SARS‐CoV‐2 infection during pregnancy apply the same standard criteria as for the general population. Unfortunately, this bias seems to be maintained in the COVID-19 epidemic: most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population. This pandemic is an opportunity to begin redressing this historic gender bias against pregnant women, and to achieve this, we recommend two actions that are easy to implement, and would have a large impact. Indeed, despite significant variation in protocols between hospitals, most current guidelines for diagnosing SARS-CoV-2 infection during pregnancy apply the same standard criteria as for the general population, namely performing one of the available molecular tests, such as quantitative reverse transcription polymerase chain reaction. doi = 10.1002/jmv.26350 id = cord-279940-i2rgjpxf author = Comentale, Giuseppe title = Sars-Cov-2 interference in HEME production: is it the time for an early predictive biomarker? date = 2020-06-29 keywords = Cov-2; Sars summary = In particular, thrombosis seems to drive the entire disease course: Sars-Cov-2 infection triggers a large thrombophilic response that results in diffuse occlusion of the smaller vessels, especially in the lungs where the result is a wide thrombotic microangiopathy [5] explaining the radiologic "ground glass" pattern. Furthermore, as IL-1 was shown to be a major culprit in the development of many cardiovascular diseases [11] , its involvement in the Sars-Cov-2 infection could explain the high mortality and morbidity rate among cardiopathic patients. Identifying the mechanisms by which Sars-Cov-2 damages the human body, focusing on the structural proteins, could be a possible strategy to finding an effective solution. From this point of view, Sars-Cov-2 seems to be very similar to malaria: many clinical and scientific reports have shown that Covid-19, not only can be successfully treated with chloroquine but also, like malaria, appears to be diagnosed much more frequently in blood group A patients [14] . doi = 10.1007/s00109-020-01945-4 id = cord-285960-1zuhilmu author = Conly, John title = Use of medical face masks versus particulate respirators as a component of personal protective equipment for health care workers in the context of the COVID-19 pandemic date = 2020-08-06 keywords = COVID-19; PPE; SARS; transmission summary = The report by the World Health Organization (WHO) Joint Mission on Coronavirus Disease 2019 (COVID-19) in China supports person-to-person droplet and fomite transmission during close unprotected contact with the vast majority of the investigated infection clusters occurring within families, with a household secondary attack rate varying between 3 and 10%, a finding that is not consistent with airborne transmission. Based on the scientific evidence accumulated to date, our view is that SARS-CoV-2 is not spread by the airborne route to any significant extent and the use of particulate respirators offers no advantage over medical masks as a component of personal protective equipment for the routine care of patients with COVID-19 in the health care setting. The findings from multiple systematic reviews and meta analyses over the last decade have not demonstrated any significant difference in the clinical effectiveness of particulate respirators compared to the use of medical masks when used by HCWs in multiple health care settings for the prevention of respiratory virus infections, including influenza [57] [58] [59] . doi = 10.1186/s13756-020-00779-6 id = cord-280147-xvzi1i0v author = Consoli, Letizia title = 2019 novel coronavirus (COVID-19) pneumonia complications: the importance of lung ultrasound date = 2020-06-19 keywords = COVID-19; SARS summary = Herein, we report a case of a patient affected by COVID-19 pneumonia referred in the emergency department of our institution on April 4, 2020, with peculiar lung ultrasound findings. In January 2020, Chinese scientists isolated a novel coronavirus from patients affected by viral pneumonia, denominated severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), and in February 2020, the World Health Organization designated as COVID-19 the coronavirus disease caused by SARS-COV-2. As indicated in a report from the Chinese Center for Disease Control and Prevention on 44,500 SARS-COV-2 patients, severe respiratory symptoms were found in 14% of cases, characterized by dyspnea, hypoxia, or > 50% lung involvement on imaging. On the other hand, ultrasound may produce a real-time and dynamic evaluation, even in Convex array probe showed the absence pleural sliding at the left lung with a "barcode sign" at the M-mode evaluation cases with critical complications of severe COVID-19 pneumonia, such as pneumothorax. doi = 10.1007/s40477-020-00494-3 id = cord-351555-hsgsuor2 author = Constantinou, Constantina title = Developing a holistic contingency plan: Challenges and dilemmas for cancer patients during the COVID‐19 date = 2020-07-20 keywords = COVID-19; SARS; cancer; patient; treatment summary = Zhang et al, 21 reported that patients who had their last anti-tumor treatment (including chemotherapy, immunotherapy, and radiation) within 14 days prior to infection with SARS-CoV-2 had a significantly increased risk of developing severe events (HR = 4.079, 95% CI 1.086-15.322, P = .037). 37, 38 In order to achieve this, in the most affected areas medical specialists, including oncologists, were asked to provide their assistance in managing patients suffering from COVID-19 requiring hospitalization in ICUs or in the departments of infectious or respiratory diseases or general internal medicine. 40 Currently, there are no official reports of how the treatment of cancer patients has been affected by the lack of resources and limited access to healthcare due to the COVID-19 pandemic in most afflicted countries. The decision should be based on the cancer type and stage, the clinical condition of the patient, the treatment indicated for the condition, the patient''s response to anticancer therapy, and the potential risks for an infection with SARS-CoV-2. doi = 10.1002/cam4.3271 id = cord-305270-vos341i1 author = Conte, Luana title = Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection date = 2020-06-29 keywords = SARS; covid-19; probiotic summary = title: Targeting the gut–lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection 16 Targeting the gut-lung microbiota axis by means of a high-fibre diet and probiotics may have anti-inflammatory effects in COVID-19 infection keywords: anti-inflammatory effects, COVID-19 infection, gut-lung microbiota aixs, high-fibre diet, probiotics, SARS-CoV-2 Among dietary supplements, potential new treatments against COVID-19 infection could be based on probiotics, 17, 22 which might not only reduce colonisation by pathogenic species but also increase commensal bacterial growth in the respiratory tract. Although there is no clinical evidence that targeting the gut-lung microbiota axis would play a therapeutic role in COVID-19 infection, we believe that the manipulation of microbial patterns through the use of probiotics, prebiotics and a high-fibre diet may help to reduce cell inflammation, maintain a healthy gut microbial diversity and strengthen the immune system. doi = 10.1177/1753466620937170 id = cord-313265-lff5cajm author = Conway, Michael J. title = Identification of coronavirus sequences in carp cDNA from Wuhan, China date = 2020-03-16 keywords = SARS summary = Severe acute respiratory syndrome (SARS)‐like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. SARS-like virus sequences that were highly homologous to SARS-CoV-2 were identified in two separate complementary DNA (cDNA) pools. Tblastn analysis using this sequence identified two cDNA clones that were highly homologous to SARS-like coronaviruses. The first cDNA pool was made from Carassius auratus (crucian carp) blastulae embryonic cell line and contained a sequence of 152 amino acids that covered 2% of the SARS-CoV-2 genome and was 93.42% The second cDNA pool was made from Ctenopharyngodon idella (grass carp) head kidney and contained a sequence of 88 amino acids that covered 1% of the SARS-CoV-2 genome and was 93.18% identical. Protein and nucleic acid alignments of each cDNA clone were performed to compare with the most related coronavirus sequences (Figures 1 and 2) . doi = 10.1002/jmv.25751 id = cord-263538-0wozg085 author = Cooch, P. B. title = Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date = 2020-10-23 keywords = PCR; SARS summary = Conclusions: Supervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, paired with infection mitigation strategies (e.g., masking, physical distancing, stable cohorts, and hand hygiene), comprise a comprehensive strategy for safe school reopening. We hypothesized that supervised self-collection of anterior nares and saliva samples for the purpose of SARS-CoV-2 surveillance would be acceptable and feasible for kindergarten through 8 th grade children, their household contacts, and camp staff, and that camp staff could assist with collection supervision. 17 To our knowledge, this is the first study to describe self-collected anterior nares SARS-CoV-2 testing among children, or any participants in a school-like setting. In conclusion, we demonstrated excellent feasibility and acceptability of a serial surveillance SARS-CoV-2 testing approach with supervised anterior nares self-collection in 5-14 year-old children, their household contacts, and staff, during indoor summer camp. doi = 10.1101/2020.10.21.20214338 id = cord-259863-ndclxrm7 author = Cooke, William R. title = SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases date = 2020-05-15 keywords = SARS summary = title: SARS-CoV-2 infection in very preterm pregnancy: experiences from two cases We present our experience of managing two cases of SARS-CoV-2 infection in very preterm pregnancy. SARS-CoV-2 infection causing type 1 respiratory failure was presumed. A multidisciplinary (obstetric, anaesthetic and intensivist) decision was made for delivery by caesarean section, to facilitate invasive ventilation of the woman. SARS-CoV-2 RNA swab from the patient was positive, and from the baby was negative. SARS-CoV-2 RNA swab from the mother was positive, and from the baby was negative. To date 3 cases of severe SARS-CoV-2 infection in very preterm pregnancy (<32 weeks) have been published; all underwent caesarean section for maternal resuscitation; one woman died [1] [2] [3] . 1. Both women deteriorated within 24 hours of presentation: we recommend early administration of corticosteroids for fetal maturation. A case of 2019 Novel Coronavirus in a pregnant woman with preterm delivery doi = 10.1016/j.ejogrb.2020.05.025 id = cord-311125-v9ddes3c author = Cooper, Keiland W. title = COVID-19 and the chemical senses: supporting players take center stage date = 2020-07-01 keywords = ACE2; COVID-19; CoV-2; SARS; cell; olfactory summary = Given data suggesting that ACE2 is necessary for SARS-CoV2 to infect host cells, researchers have used a variety of approaches to discern the pattern of expression of ACE2 and other viral entry proteins across the tissue landscape, with the goal of inferring possible target cells and disease mechanisms. It remains unclear whether SARS-CoV-2 (given that it likely does not directly infect OSNs, and thus cannot pass directly through the olfactory nerve, see However, scSeq and immunostaining of the mouse OB has revealed -as in the nose -that bulb neurons do not express detectable levels of ACE2 ( Figure 2 ) . This model suggests that neural function is altered indirectly due to sequelae of SARS-CoV-2 infection of peripheral support cells, including (but not limited to) local inflammation and changes in OSN gene expression and ciliary structure. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia doi = 10.1016/j.neuron.2020.06.032 id = cord-347356-uc9dqhyq author = Cooper, TJ title = Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date = 2020-07-15 keywords = COVID-19; HIV; SARS summary = OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The aim of this systematic review was to identify studies that discuss PLHIV who have been infected with SARS-CoV-2 and that report whether coinfection results in a greater risk of adverse outcomes and, furthermore, whether controlled HIV infection vs. A comprehensive literature search was carried out in Global Health, SCOPUS, Medline and EMBASE to identify articles that discussed HIV-positive patients and the clinical implications of HIV infection in COVID-19 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines [13] . [21] , also highlighted a case study of a HIV patient with SARS-CoV2 co-infection, diagnosis of viral pneumonia was made on clinical examination and chest CT findings. doi = 10.1111/hiv.12911 id = cord-309089-ex9nh1yi author = Coperchini, Francesca title = The Cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system date = 2020-05-11 keywords = ARDS; COVID-19; CXCL10; MERS; SARS summary = Since the first reports on COVID-19 disease, it appeared clear that Acute respiratory distress syndrome (ARDS) accounted for a significant number of deaths among infected patients and that ARDS should be regarded as the hallmark immune-mediated clinical consequence in SARS-CoV-2, similarly to what described for SARS-CoV and MERS-CoV infections [11] . As shown by previous data in the literature, increased circulating levels of pro-inflammatory cytokines (eg, Interferon γ, interleukin (IL-) 1B, IL-6, IL-12) and chemokines (CXCL10, and CCL2) are associated with pulmonary inflammation and extensive lung involvement in SARS patients, similarly to what happens in MERS-CoV infection [13] . In mice infected with SARS-CoV, the clinical features of the syndrome showed an age-dependent increase in severity (similarly to what observed in humans), which was related to an increased level of pro-inflammatory cytokines and chemokines, paralleled by a reduction in T-cell responses [78] . doi = 10.1016/j.cytogfr.2020.05.003 id = cord-344842-9cfbb7p6 author = Coppola, Maurizio title = Potential Unconventional Medicines for the Treatment of SARS-CoV-2 date = 2020-05-19 keywords = SARS summary = Adem and colleagues in their virtual screening based molecular docking study reported a potential binding affinity exerted by various bioflavonoids at the active site of the MPro, the main protease of the SARS-CoV-2 [1] . Potential inhibition properties were studied using the Molegro Virtual Docker Program and some flavonoids, in particular hesperidin, rutin, and diosmin showed a better affinity for the MPro than nelfinavir [1] . Rutin showed the second strongest binding energy at the active site of the MPro with a MoLDock score of −176.2740 and a HBond of −21.2402. Recently, Caly and colleagues reported a potential antiretroviral activity of the anti-parasitic agent ivermectin against SARS-CoV-2 virus. Despite the absence of clinical evidences regarding some potential anti-SARS-CoV-2 drugs, preliminar information reported by researchers suggest anyhow further studies in order to evaluate the clinical effects as well as the possibility to synthesize derivatives with stronger antiretroviral properties. doi = 10.1055/a-1170-4624 id = cord-312670-hi3fjne4 author = Corman, V. M. title = Coronaviren als Ursache respiratorischer Infektionen date = 2019-08-27 keywords = CoV; Infektionen; MERS; SARS summary = Zusätzlich zu diesen ständig im Menschen zirkulierenden Varianten wurden in den vergangenen Jahren zwei CoV im Menschen gefunden, nämlich SARS-CoV und MERS-CoV, die aus dem Tierreservoir auf den Menschen übergegangen sind und bei einem deutlich größeren Anteil der Infizierten schwere virale Pneumonien mit tödlichem Verlauf auslösen [25, 28] . Obwohl die Mehrzahl der Infektionen mit den vier endemischen CoV nur leichte Atemwegserkrankungen verursacht, können alle HCoV auch schwere Hier steht eine Anzeige. Inwiefern diese sekundären Infektionen auf die intensivmedizinische Behandlung und Beatmung zurückzuführen sind oder ein spezifisches grundsätzliches Risiko einer CoV-Infektion darstellen, ist noch nicht verstanden. Jedoch ist eine spezifische Labordiagnostik bei Verdacht auf eine Infektion mit endemi-schen CoV bei harmlosem Verlauf und Patienten ohne besonderes Risiko für die Entstehung von Komplikationen auch nicht indiziert. Bei der typischerweise unspezifischen Klinik von MERS-CoV-Infektionen sollte auch die Möglichkeit einer Infektion mit anderen Pathogenen in Betracht gezogen werden [26] . RKI (2015) Schwere respiratorische Erkrankungen in Verbindung mit Middle East Respiratory Syndrome Coronavirus (MERS-CoV). doi = 10.1007/s00108-019-00671-5 id = cord-317608-otd81rvy author = Corman, Victor M. title = SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission date = 2020-05-27 keywords = SARS summary = Oral swabs, sputum, and blood samples from 18 asymptomatic and symptomatic patients with SARS‐CoV‐2 infection were examined using RT‐PCR testing in order to assess the risk of transfusion‐related transmission. In asymptomatic patients as well as patients with flu‐like symptoms and fever, no SARS‐CoV‐2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • In asymptomatic patients as well as patients with flulike symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. • As patients with symptoms of infectious disease will not be admitted to blood donation, the risk for transfusion transmission of SARS-CoV-2 seems to be negligible. In asymptomatic patients who are eligible for blood donation as well as patients with flu-like symptoms and fever, no SARS-CoV-2 RNA could be detected in the blood or serum despite a clearly positive result in all throat swabs. doi = 10.1111/trf.15841 id = cord-353342-2n6kqyeo author = Corman, Victor M. title = Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date = 2016-02-15 keywords = MERS; RNA; SARS summary = title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays doi = 10.1093/cid/civ951 id = cord-327259-7o7fs4yb author = Correa, I. A. title = Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date = 2020-08-19 keywords = PCR; RNA; SARS summary = We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . doi = 10.1101/2020.08.16.20167536 id = cord-264976-6n9cdex6 author = Corse, Tanner title = Clinical Outcomes of COVID-19 Patients with Pre-existing, Compromised Immune Systems: A Review of Case Reports date = 2020-10-18 keywords = SARS; covid-19; table summary = The high rate of positive outcomes suggests that heart transplant recipients with COVID-19 on immunosuppressants are not at an increased risk of mortality unless the patient develops complications such as ARDS and/or requires ICU care and ventilation. Since the overall 16.9% mortality rate of the SARS-CoV-2-infected kidney transplant recipient on immunosuppressants is attributed to death of older (>50 years) patients with comorbidities and/or secondary complications (Table 3) , the 16.9% mortality rate does not seem to be abnormally high because it is in line with the rates reported by others for different COVID-19 patients populations. In another report [72] , Katz-Greenberg et al., described the clinical outcomes of 20 kidney-transplant recipients (ages 30 to 73 years) who were infected by SARS-CoV-2, and showed that only 3 patients (2 males aged 72 and 73 and 1 female aged 63) died, suggesting a 15% mortality that is related to advancing age [72] , which agrees with our review of the published case reports. doi = 10.7150/ijms.50537 id = cord-270919-0hldozml author = Cortey, Martí title = SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date = 2020-05-17 keywords = SARS summary = title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%. 54 The aim of the present study was to determine the amino acid substitutions in viral 55 proteins that were widely present in available sequences of SARS-CoV-2, relating them 56 to the known chronology of the pandemic. doi = 10.1101/2020.05.16.099499 id = cord-314694-g0pes5o3 author = Cortiula, F. title = Managing COVID-19 in the oncology clinic and avoiding the distraction effect date = 2020-03-19 keywords = SARS; patient summary = The safety and management of cancer patients in the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is urgent and most cancer clinics need to establish a contingency plan. The authors suggest that postponing adjuvant chemotherapy or elective surgery for less aggressive cancers should be considered and that the increased risk for personal protection provisions should be emphasized for patients with cancer or cancer survivors. Furthermore, more intensive surveillance or treatment should be considered for those patients with cancer who are infected with SARS-CoV-2. Re-allocating an excessive amount of health care personnel, both nurses and doctors, to the COVID-19 triage and management may stretch an already fragile system and potentially leave uncovered some vital activities, such as treatment administration, surgeries and inpatient assistance. 5 Patients with advanced disease, and no suggestive symptoms of COVID-19, should keep receiving planned chemotherapy or radiotherapy treatment, without unnecessary delays. Risk of COVID-19 for patients with cancer doi = 10.1016/j.annonc.2020.03.286 id = cord-310692-8fuj9td2 author = Coste, A. T. title = Indication for SARS-CoV-2 serology: first month follow-up date = 2020-07-03 keywords = SARS summary = Our laboratory performed a prospective surveillance of the SARS-CoV-2 serologic test requested during the first 5 weeks, by specifically looking at rate of the different accepted indications. For the 303 serologies requested by hospital-based physicians working in tertiary hospitals or clinics, 94 were positive (31%), 205 were negative (68%), and four were undetermined (13%). They had specific directives in their hospital to systematically perform a SARS-CoV-2 RT-PCR screening and serology to any patient arriving at the hospital. The residuals symptoms with no documented or negative RT-PCR (indication N°6.4) appeared to be very important for patient care but was totally unexpected, since on 14 th April, when we started the SARS-CoV-2 serology, the occurrence of such post-infectious complications were not yet reported [5] . This work may serve as a seed for international guidelines regarding the indications of SARS-CoV-2 serology for patients care. doi = 10.1101/2020.06.30.20140715 id = cord-277889-8u685f45 author = Costela-Ruiz, Víctor J. title = SARS-CoV-2 infection: the role of cytokines in COVID-19 disease date = 2020-06-02 keywords = COVID-19; CSF; IL-10; IL-6; SARS; patient summary = The majority of patients infected with COVID-19 have normal or reduced white cell counts and lymphocytopenia, and those with severe disease have shown significantly elevated levels of neutrophils, dimer-D, and urea in blood, with a continuing decrease in lymphocytes. detected elevated levels of the antagonistic receptor of IL-1 (IL-1Ra) in 14 severe cases of COVID-19, and this marker has been associated with increased viral load, loss of pulmonary function, lung damage, and mortality risk [55] . observed that its expression during infection with an influenza virus had negative effects on CD8 + memory T cells [71] .Various studies of COVID-19 patients have detected elevated IL-4 levels as part of the cytokine storm associated with severe respiratory symptoms [16, 17, 43, 72] . Elevated IL-17 levels have been reported in patients with SARS-CoV-2 as part of the cytokine storm [17] , and they have been associated with the viral load and disease severity [56] . doi = 10.1016/j.cytogfr.2020.06.001 id = cord-312633-cks6aij2 author = Cotten, Matthew title = Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus date = 2013-05-17 keywords = EMC/2012; England; Qatar/2012; SARS summary = Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events. We describe a strategy for rapidly designing the primers necessary for reverse transcription and cDNA amplification of such diverse RNA viruses and report the full-genome determination of the novel CoV directly from patient sputum using next-generation short-read sequencing. A map of the primer mapping positions Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus and the predicted PCR products using EMC/2012 as the target is shown in Figure 1 , panel A. A ML phylogenetic tree inferred from the whole genome alignment indicated that the 3 novel human beta-CoVs sequences (England1, England/Qatar/2012, and EMC/2012) clustered closely, forming a monophyletic lineage that falls into group 2c (Figure 3 , panel A, Appendix, wwwnc.cdc.gov/EID/article/19/5/13-0057-F3.htm). doi = 10.3201/eid1905.130057 id = cord-300117-rlpzejjt author = Coutard, B. title = The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade date = 2020-02-10 keywords = SARS; site summary = In the case of human-infecting coronaviruses such as HCoV-OC43 (Le Coupanec et al., 2015) , MERS-CoV (Millet and Whittaker, 2014) , and HKU1 (Chan et al., 2008) the spike protein has been demonstrated to be cleaved at an S1/S2 cleavage site (Fig. 2) generating the S1 and S2 subunits. The furin-like S2′ cleavage site at KR↓SF with P1 and P2 basic residues and a P2′ hydrophobic Phe (Seidah and Prat, 2012) , downstream of the IFP is identical between the 2019-nCoV and SARS-CoV (Fig. 2) . However, in the other less pathogenic circulating human CoV, the S2′ cleavage site only exhibits a monobasic R↓S sequence (Fig. 2) with no basic residues at either P2 and/or P4 needed to allow furin cleavage, suggesting a less efficient cleavage or higher restriction at the entry step depending on the cognate proteases expressed by target cells. doi = 10.1016/j.antiviral.2020.104742 id = cord-268169-xry3nhzt author = Couturier, Aymeric title = Indirect effects of severe acute respiratory syndrome coronavirus 2 on the kidney in coronavirus disease patients date = 2020-05-22 keywords = FSGS; SARS summary = Among patients hospitalized for novel coronavirus disease (COVID-19), between 10 and 14% develop an acute kidney injury and around half display marked proteinuria and haematuria. Collapsing glomerulopathy is a peculiar form of focal segmental glomerulosclerosis (FSGS) [6] that has been well characterized in patients infected by human immunodeficiency virus (HIV) type 1 [7] . In order to better characterize the relationship between SARS-CoV-2 infection and collapsing FSGS, we performed an RT-PCR assay on the renal tissue specimen from Patient 1. Our results are in line with a recent inpress report that describes the presence of collapsing glomerulopathy and tubulointerstitial lesions in living COVID-19 patients of African origin, homozygous for APOL1 risk allele G1 and evidence of chronicity on kidney biopsy [12] . Although our findings do not definitely rule out a direct infection of kidney cells by SARS-CoV-2, COVID-19-related collapsing FSGS appears to be related to a viral-induced inflammatory response against a peculiar genetic background. doi = 10.1093/ckj/sfaa088 id = cord-311066-62edsbfc author = Cox, Brian J. title = Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date = 2020-06-24 keywords = SARS; TRS summary = Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5''-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. Some RNAs, especially non-coding RNAs, generally lack a poly-A tail, which could explain poor detection of TRS independent sgmRNAs. Using published sequencing data of ribosome depleted total RNA from SARS-CoV-2 infected cells and animals (Blanco-Melo et al., 2020) , I aligned these against the viral genome (Figure 2) . Using the aligned reads, I generated transcript models using stringtie, which identified multiple spliced species that aligned with the TRS-L templated events (Figure 2) . Split reads also identified TRS-independent sgmRNAs. In support of my observations on SARS-CoV-2, I also assessed SARS-CoV and MERs transcriptional data, two other human pathogenic CoV. I also identified the TIR motif, a novel sequence element (ATTGGC) flanking the spliced regions of TRS independent sgmRNAs in both SARS-CoV-2 and SARS-CoV. doi = 10.1101/2020.06.24.169144 id = cord-278542-vqp6ec6e author = Coyne, Carolyn title = Recommendations for future university pandemic responses: What the first COVID-19 shutdown taught us date = 2020-08-27 keywords = SARS; faculty; university summary = Successes and failures along the way highlighted how the autonomous nature of the American academic research enterprise and skillsets normally required of university leaders were ill-suited to mounting an emergency response. Here, as faculty from medical centers in the United States, we draw lessons from these experiences and apply them as we plan for the next possible COVID-19-induced shutdown as well as other large-scale pandemics and emergencies at universities in the United States and throughout the world. In addition, students (and faculty) with children or other dependents required homeschooling and alternative care plans that conflicted with classes they either were enrolled in or taught. Other swiftly implemented decisions included accommodating research groups who possessed expertise to work on SARS-CoV-2 while creating protocols such as social distancing and PPE use for their safety. In addition, institutions need to consider the needs of laboratory staff and trainees and include them in the decision-making process. doi = 10.1371/journal.pbio.3000889 id = cord-270880-azslipmp author = Cozzupoli, Grazia Maria title = Possible Retinal Impairment Secondary to Ritonavir Use in SARS-CoV-2 Patients: A Narrative Systematic Review date = 2020-08-22 keywords = SARS; retinal; rpe summary = Seven single cases and one case series, reporting a total of 10 patients affected by retinal changes secondary to long-term ritonavir treatment, were included in the review. Although a recent randomized trial [3] involving hospitalized adult patients with confirmed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection has not shown significant benefits with lopinavir/ritonavir treatment beyond standard care, this protease inhibitor association is used in worldwide hospitals [4] . us, we conducted a narrative systematic review of the published reports describing the clinical features and imaging signs associated with ritonavirinduced retinal toxicity. Anyway, it is not illogical to hypothesize that the retinal toxic effects of both long-term hydroxychloroquine [32] and ritonavir therapies might appear also after short-term treatments, as in the case of SARS-CoV-2 patients, enhanced by the deterioration of renal and hepatic clearance function, respectively. e authors report a case of bull''s eye maculopathy pattern in an HIV-positive patient, being treated with ritonavir for 13 years. doi = 10.1155/2020/5350494 id = cord-275420-zkxyxiv5 author = Crabtree, Scott J. title = The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States date = 2020-07-23 keywords = SARS; United summary = title: The role of multidisciplinary infection prevention teams in identifying community transmission of SARS-CoV-2 in the United States This case study highlights the role of a multidisciplinary Infection Prevention team in the identification of the first community-transmitted SARS-CoV-2 case at a large, tertiary referral center in the United States. By rounding on the hospital units such teams can serve vital infection prevention, antibiotic stewardship, and disease surveillance functions. Through the coordinated efforts of UCD''s multidisciplinary infection prevention (IP) program, the patient was identified as a possible COVID-19 case and obtained SARS-CoV-2 testing. During rounds, each patient is reviewed through the electronic medical record and via discussion with the bedside nurse to evaluate for possible infection prevention and antimicrobial stewardship interventions. The patient''s case was discussed with her bedside nurse, who confirmed that SARS-CoV-2 was considered by her primary team, but given the absence of exposures, testing for this agent was not pursued. doi = 10.1017/ice.2020.360 id = cord-263456-lqe1yckv author = Craney, Arryn R. title = Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-07-23 keywords = Fusion; SARS summary = We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. On 4 February 2020, the Centers for Disease Control and Prevention (CDC) received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for an RT-PCR assay to detect SARS-CoV-2 in a range of respiratory specimens (5) . In this study, we compared the diagnostic performances of the cobas 6800 and Panther Fusion high-throughput RT-PCR systems for the detection of SARS-CoV-2 RNA in 389 NP swab specimens, the predominant specimen type employed for SARS-CoV-2 RT-PCR (4). However, to the best of our knowledge, no study has evaluated the performance characteristics of the Panther Fusion SARS-CoV-2 RT-PCR assay or directly compared two high-throughput systems. In conclusion, the cobas 6800 and Panther Fusion systems and their associated SARS-CoV-2 tests are comparable in terms of their performance characteristics in the clinical setting. doi = 10.1128/jcm.00890-20 id = cord-334309-rddznfax author = Craver, Randall title = Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) date = 2020-05-13 keywords = COVID-19; SARS summary = title: Fatal Eosinophilic Myocarditis in a Healthy 17-Year-Old Male with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2c) Postmortem nasopharyngeal swabs detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) known to cause coronavirus disease 2019 (COVID-19). Myocardial damage, myocarditis, and cardiomyopathy is often referred to in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] [2] [3] [4] [5] [6] . There is little information regarding cardiac complications in children [11] [12] [13] We present a previously healthy 17 year male old dying suddenly with an eosinophilic myocarditis (EM) in which a nasopharyngeal swab detected SARS-CoV-2 at autopsy (Figs. The question of whether this is a direct complication of SARS-CoV-2 infection, or if this is an idiopathic eosinophilic myocarditis in which the stress of the COVID-19 contributed to the cardiac decompensation cannot be answered definitively at this time. doi = 10.1080/15513815.2020.1761491 id = cord-315448-bosazmlm author = Crawford, Katharine H D title = Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection date = 2020-09-30 keywords = SARS summary = Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post symptom onset from a prospective cohort of 32 recovered individuals with asymptomatic, mild, or moderate-severe disease. Most of these studies have reported that over the first three months, antibodies targeting spike decline several fold from a peak reached a few weeks post symptom onset [5, 7, 19] , suggesting that the early dynamics of the antibody response to SARS-CoV-2 are similar to those for other acute viral infections. A c c e p t e d M a n u s c r i p t 5 Here we build on these studies by measuring both the neutralizing and binding antibody levels in serial plasma samples from 32 SARS-CoV-2-infected individuals across a range of disease severity with follow-up as long as 152 days post symptom onset. doi = 10.1093/infdis/jiaa618 id = cord-332723-rz1iilsv author = Creager, Hannah M. title = Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date = 2020-07-06 keywords = CoV-2; SARS summary = Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10-7 dilution. Ten-fold serial dilutions of a natural nasopharyngeal swab specimen with known high positivity for SARS-CoV-2 RNA (E gene detected at a cycle threshold (Ct) of 16.6 by the cobas SARS-CoV-2 assay) were prepared with a diluent of pooled NPS. Comparison of SARS-CoV-2 Detection from Nasopharyngeal Swab Samples by the Roche cobas(R) 6800 SARS-CoV-2 Test and a Laboratory-Developed Real-Time RT-PCR test doi = 10.1016/j.jcv.2020.104538 id = cord-326406-n0qi6gs8 author = Creed, Marina title = Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. date = 2020-05-19 keywords = COVID-19; SARS summary = title: Mild COVID-19 infection despite chronic B cell depletion in a patient with aquaporin-4-positive neuromyelitis Optica spectrum disorder. Here, we report a 59-year-old woman with aquaporin-4-positive (AQPR4+) neuromyelitis Optica treated with rituximab who developed mild respiratory symptoms with COVID-19, despite B cell depletion at the time of infection. To infect the host, SARS-CoV-2 uses the viral receptors ACE2 and TMPRSS2, which are membrane associated proteins expressed in many cells throughout the body, particularly the respiratory system 2 . Most cases are mild, but in a number of patients, the disease evolves into an acute respiratory distress syndrome (ARDS) 3 or a dysregulated immune system state leading to cytokine storm, most often in older adults, requiring intensive care and resulting in increased mortality 4 . Here, we describe an AQPR4+ NMOSD patient treated with rituximab who developed mild COVID-19 infection despite B cell depletion. doi = 10.1016/j.msard.2020.102199 id = cord-344266-ug2uew71 author = Crema, E. title = The SARS-COV-2 outbreak around the Amazon rainforest: the relevance of the airborne transmission date = 2020-08-07 keywords = COV-2; SARS; air summary = Currently, this phenomenon has gained tragic relevance due to the uncontrolled dispersion of the Covid-19 throughout the planet, since airborne transmission is one of the forms of viral contamination, as well as the direct reception of drops exhaled by a contaminated person and the contact with infected surfaces. A relevant study issued in the journal Nature revealed the existence of the RNA of the SARS-COV-2 in aerosols collected from the air of several closed environments and open places of two hospitals in Wuhan dedicated only to patients infected with Covid-19 (12) . This indication is based only on old studies about the direct transmission by larger drops, dangerously ignoring the contamination by the virus airborne in droplets that remain suspended in the air for several hours, and even days after the environment has been visited by an infected person. doi = 10.1101/2020.08.06.20169433 id = cord-306675-kwrm8whn author = Crespo Sabarís, R title = “SARS-CoV-2: una presentación peculiar” date = 2020-05-08 keywords = SARS summary = El 27 de marzo se contacta con el paciente que refiere seguir con algunas lesiones y prurito, pero no se modifica tratamiento, aunque el día 30 acude muy nervioso y desde la consulta de enfermería se envían las fotografías 1 y 2 (figuras 1 y 2) al médico titular, que está haciendo teletrabajo, y al apreciar en las mismas componente inflamatorio y lesiones de rascado, se indica administrar metilprednisolona y dexcloreniramina parenterales, con mejoría en menos de una hora, y se pautan 5 días de tratamiento con prednisona de 30 mg, se aumenta la hidroxicina cambiándose cetirizina por rupatadina. Se sabe que estas lesiones, además de por la propia infección vírica, se pueden observar tras los tratamientos para la COVID19, pero esto no se cumple en el caso que nos ocuoa, por lo que hay una relación directa entre la propia infección y las lesiones, como en diversas infecciones víricas 6 , aunque todavía no se conoce su patogenia exacta. doi = 10.1016/j.semerg.2020.05.001 id = cord-322957-clf8f90t author = Crespo, Javier title = Resumption of activity in gastroenterology departments. Recommendations by SEPD, AEEH, GETECCU and AEG date = 2020-04-28 keywords = COVID-19; CoV-2; IBD; SARS; patient summary = The general objectives of these recommendations include: • To protect our patients against the risks of infection with SARS-CoV-2 and to provide them with high-quality care. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. doi = 10.1016/j.gastre.2020.04.001 id = cord-279363-4almssg6 author = Crespo, Roland Mojica title = Pandemia COVID-19, la nueva emergencia sanitaria de preocupación internacional: una revisión date = 2020-05-16 keywords = COVID-19; China; Coronavirus; SARS; que summary = En ese momento, a este nuevo coronavirus se le llamó 2019-nCoV (del inglés: 2019-novel coronavirus) y fue identificado por las autoridades sanitarias chinas como el agente causal de estos casos de neumonía atípica 1,3,4 . Hacia final de mes, el día 30 de enero la OMS declaró la enfermedad causada por el nuevo coronavirus como una emergencia de salud pública de preocupación internacional, ya que para aquel momento se habían reportado casos en todas las regiones de la OMS en solo un mes 9,11 . Concretamente la RNVE en su informe n°29 del día 7 de mayo enumera los principales síntomas presentados por el conjunto de la población española, hasta la fecha y a base de una muestra de 217,543 casos, de la siguiente manera: Entre estos hallazgos, es comúnmente observar la leucopenia y linfopenia, siendo esta última característica de COVID-19. doi = 10.1016/j.semerg.2020.05.010 id = cord-265813-2onv9mvl author = Criado, Paulo Ricardo title = Are the cutaneous manifestations during or due to SARS-CoV-2 infection/COVID-19 frequent or not? Revision of possible pathophysiologic mechanisms date = 2020-06-02 keywords = ACE2; COVID-19; SARS; TMPRSS2; cutaneous summary = RESULTS: The pathophysiology of the disease is multifactorial: association with innate immune response, hypercoagulability state, lung tissue damage, neurological and/or gastrointestinal tract involvement, monocytic/macrophage activation syndrome, culminating in exaggerated cytokine secretion, called "cytokine storm", which leads to worsening and death. Until the present day, the cardinal points in severe COVID-19 are upregulated innate immune human response; hypercoagulable state; polymorphous clinical manifestations, due to pulmonary tissue damage, neurological and/ or gastrointestinal tract involvement; and fatal outcome in severe cases of macrophage activation syndrome-like (MAS) [102] . Excessive activation of inflammatory mediators creating a "cytokine storm", leading to damage to the endothelium; formation of multiple thromboses in the microvasculature of the skin; changes in the cellular component of immunity with activation of the complement system, as well as, the possibility of direct entry of SARS-CoV-2 entry via receptor ACE2 and protease TMPRSS2 in the human endothelial cell in dermal blood vessels cannot be excluded such as possible mechanisms if the possibility of virus circulation in the blood is proved. doi = 10.1007/s00011-020-01370-w id = cord-347553-d7q6u7vj author = Criado, Paulo Ricardo title = Lessons from dermatology about inflammatory responses in Covid‐19 date = 2020-07-12 keywords = ACE2; MAS; SARS; TMPRSS2; cell; covid-19 summary = The antithrombotic effect of chloroquine analogues has been attributed to a range of mechanisms, including reduction in red blood cell aggregation, inhibition of platelet aggregation and adhesion, reduction in blood viscosity and enhancement of antiplatelet activity 86 Hydroxychloroquine and chloroquine were indicated for treat patients with COVID-19, under in vitro effects due to capacity as 87 : (a) an inhibitor of endocytic pathways through an elevation of endosomal pH, and (b) these drugs shown to interfere with the terminal glycosylation of angiotensin-converting enzyme-2 (ACE2), which acts as a plasma membrane receptor for both SARS-CoV and SARS-CoV-2. 61 99 Procoagulant factors, such F I G U R E 5 Clinical outcomes in SARS-CoV-2 infected patients/Covid-19, immune system responses, systemic and possible cutaneous manifestations.① The outcome spectrum is probably related to intrinsic host factors. ③ In a selected group of patients, with moderate and severe Covid-19, some authors proposed that a genetic background in these subjects might determinate one new immune response as ④ ''second wave'' of cytokines production, the ''CSS'' in response to the SARS-CoV-2 infection, similar to Macrophage Activation Syndrome (MAS-like/sHLH). doi = 10.1002/rmv.2130 id = cord-325197-j1uo8qmf author = Crimi, Ettore title = Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date = 2020-08-20 keywords = COVID-19; RNA; SARS; epigenetic; influenza summary = Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. The goal of the review was to provide an appropriate pathogenic scenario in which epigenetic-sensitive mechanisms and epidrugs may be clinically useful to stratify risk and treatment of patients in ICU affected by severe viral respiratory infections. Here, we give an update on clinical evidence about the usefulness of novel and FDA-approved drugs interfering with epigenetic pathways, which were applied to ICU patients affected by highly pathogenic strains of influenza virus and CoV, with a particular interest about the novel SARS-CoV-2 (Table 4 ). doi = 10.1016/j.bja.2020.06.060 id = cord-266702-6oxtlzqo author = Cristelo, Cecília title = SARS-CoV-2 and Diabetes: New Challenges for the Disease date = 2020-05-22 keywords = ACE2; Angiotensin; SARS; diabetes summary = Emerging evidence demonstrates that the correct management of diabetes in those patients infected with SARS-CoV-2 is of utmost importance for the viral disease progression, therefore, the importance of blood glucose control will also be addressed. In vitro and in vivo studies showed that angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for SARS-CoV virus [7, 8] . It has been confirmed in some clinical studies that the long-term use of ACEIs or ARBs by patients is not associated with an increased risk of SARS-CoV-2 infection, neither of developing severe COVID-19 or even with a higher risk of in-hospital death [40] [41] [42] . In the case of SARS-CoV-2 the same transient damage in the pancreas has already been documented [44] , and given its higher infectivity and affinity for the ACE2 receptor, there is increased concern relative to the complications caused by hyperglycemia, as well as the long-term effects of the infection on recovered patients. doi = 10.1016/j.diabres.2020.108228 id = cord-329504-91te3nu8 author = Croll, Tristan title = Making the invisible enemy visible date = 2020-10-07 keywords = PDB; RNA; SARS; structure summary = A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. doi = 10.1101/2020.10.07.307546 id = cord-265277-ymvrserl author = Crooke, Stephen N. title = Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date = 2020-05-14 keywords = HLA; SARS summary = A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. doi = 10.1101/2020.05.14.093757 id = cord-323092-j2u0ny2u author = Crosby, James C. title = COVID‐19: A review of therapeutics under investigation date = 2020-04-19 keywords = COVID-19; LPV; SARS; patient summary = The World Health Organization (WHO) has released general guidelines for managing the illness caused by the virus (COVID-19), which includes supportive care similar to other viral pneumonias: airway and respiratory support, empiric antibiotics for secondary bacterial infection, and acute respiratory distress syndrome (ARDS) management. 2 While these treatments are thought to offer the best chance of survival for the approximately 20% of COVID-19 cases that progress to severe disease, limited health care resources and the speed at which the pandemic has developed are pressuring clinicians and scientists to provide therapeutics that specifically target SARS-CoV-2 and improve mortality. 32, 33 There are a number of promising studies that have demonstrated shorter hospital stays, lower mortality rates, and reduced viral loads in SARS-CoV-1 and H1N1 influenza infected patients treated with convalescent plasma. There is another single ongoing observational trial examining the efficacy of anti-SARS-CoV-2 inactivated convalescent plasma in COVID-19 patients, the results of which remain to be seen. doi = 10.1002/emp2.12081 id = cord-344909-0o55l4iy author = Cross, Robert W. title = Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date = 2020-10-14 keywords = COVID-19; SARS summary = However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Differences in clinical parameters of the LD-treated group with untreated control animals from this study or historical control animals were minimal; however, the lack of infectious SARS-CoV-2 in the BAL samples from all of the LD-treated animals and reduced lung pathology suggest that an antiviral effect was present despite the lower concentration of neutralizing antibodies in the dose of convalescent sera administered. PRNT50 assays were performed on pooled convalescent sera from AGMs challenged with the homologous isolate of SARS-CoV-2 in previous studies (Cross et al., 2020; Woolsey et al., 2020) compared with control animals on day 2 post infection (d) and doi = 10.1101/2020.10.14.340091 id = cord-302146-51hof7it author = Cross, Thomas J. title = Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date = 2020-05-15 keywords = SARS; pro summary = Here we report sequence analysis, structure predictions, and molecular modeling for seventy-nine Mpro variants, constituting all clinically observed mutations in this protein as of April 29, 2020. Modeling and protein structure network analysis suggest differences in cohesion and active site flexibility, revealing patterns in viral evolution that have relevance for drug discovery. Molecular modeling is an important tool for guiding inhibitor discovery, making it possible to evaluate large numbers of candidate drugs in silico to select experimental targets; however, standard approaches screen against only one version of the protein, typically the reference or wild-type (WT) sequence. Here we characterize all 79 known variants of M pro as of 29 April, 2020, and analyze trends in amino acid substitutions and the resulting structural changes using network analysis and molecular modeling. Analysis of active site networks (ASN) from M pro variants suggests differences in active site flexibility and cohesion that may serve to guide the design of robust, mutation-resistant inhibitors. doi = 10.1101/2020.05.15.097493 id = cord-267308-rgqjolue author = Crovetto, F. title = SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY date = 2020-06-19 keywords = SARS summary = Introduction: Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. Case registries of pregnant women diagnosed with coronavirus disease (COVID-19) by polymerase chain reaction (PCR) have reported that the majority experienced mild infection, but up to 9% may require critical care. We evaluated the seroprevalence and clinical presentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pregnant women in the first and third trimester. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. In this study, none of the 125 pregnant women with SARS-CoV-2 infection required critical care as compared to 9% reported in cases diagnosed with PCR. doi = 10.1101/2020.06.17.20134098 id = cord-331060-b3z1zb4t author = Cruickshank, Marilyn title = COVID‐19: Lessons to be learnt from a once‐in‐a‐century global pandemic date = 2020-06-04 keywords = COVID-19; SARS; outbreak summary = Some of this includes the extent to which humans develop a protective immune response to COVID-19 via antibodies (The World Health Organization, 2020), the extent to which asymptomatic people can spread the infection (Bai et al., 2020; Kimball et al., 2020) , whether the use of face masks by asymptomatic members of the community can affect transmission (Feng et al., 2020) , the significance of the loss of smell as an early predictive or differential symptom of disease, the role of herd immunity and whether infection confers immunity, and if so, for how long. Once the number of new cases have stabilised, there can be a move to mitigation strategies which might not necessarily stop the spread, but can help to protect those most at risk of severe disease by isolating suspected cases and their households, while continuing to implement social distancing measures for older people and others at high risk. doi = 10.1111/jocn.15365 id = cord-352123-0bflqj1c author = Csiszar, Anna title = Companion animals likely do not spread COVID-19 but may get infected themselves date = 2020-08-07 keywords = COVID-19; CoV-2; SARS; animal summary = Recent evidence suggests that SARS-CoV-2, similar to other coronaviruses, can infect several species of animals, including companion animals such as dogs, cats, and ferrets although their viral loads remain low. In late March 2020, the Federal Agency for the Safety of the Food Chain (FASFC) in Belgium reported that a pet cat was diagnosed to be infected with SARS-CoV-2 [21, 22] , showing that felines living in the household of people with COVID-19 are at risk of contracting the disease and may potentially spread the virus. On April 23, it was reported that two pet cats in New York state have tested positive for the SARS-CoV-2, which are the first confirmed COVID-19 cases in companion animals in the USA [22] . In the current SARS-CoV-2 pandemic, the situation is rapidly evolving and in the light of the recent evidence, we should be aware of the possibility that humans can be potentially infected with COVID-19 by animals, including by pet cats, dogs, or other domesticated species. doi = 10.1007/s11357-020-00248-3 id = cord-317628-1inxq7t5 author = Cuccarese, Michael F. title = Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date = 2020-08-14 keywords = COVID-19; Fig; SARS; TGF; TNF; Thermo; cell; compound summary = We deploy the platform to develop phenotypic models of active SARS-CoV-2 infection and of COVID-19-associated cytokine storm, surfacing compounds with demonstrated clinical benefit and identifying several new candidates for drug repurposing. We used these capabilities to rapidly develop high-throughput-ready disease models for both SARS-CoV-2 viral infection and the resulting cytokine storm, and immediately launched large-scale drug screens that recapitulated known effective and ineffective therapies and, more importantly, identified several new potential treatments for both SARS-CoV-2 infection and COVID-19-associated cytokine storm. To define the model, we evaluated the effect of SARS-CoV-2 infection in multiple cell types, of which three resulted in robust phenoprints as compared to either mock infected or inactivated virus control populations: Calu3 (a lung adenocarcinoma line), Vero (an immortalized interferondeficient African green monkey kidney line 55 ), and primary Human Renal Cortical Epithelium (HRCE) (Fig. 5C, Fig. S6D ). doi = 10.1101/2020.08.02.233064 id = cord-013269-u1e0kzmm author = Cucinotta, Domenico title = Primum non nocere (first do no harm). The SARS-CoV-2 pandemic course in oldest in Italy date = 2020-05-11 keywords = COVID-19; SARS summary = Maybe a bad strategy and lack of timely intervention togheter with concurrent social events, comorbidities of oldest persons, bed rest, inadequate nutritional support and drugs'' side effects and infection of health professionals proved fatal for many. Different opinions among scientists, as occurred recently in COVID-19 pandemia in Italy, combined with the difficulties due to comorbidities and dependency of oldest persons have resulted in strategic errors, a significant part of which proved fatal for the patient and catastrofic for the society. On January 18 the Medical Literature Guide Amedeo (1) drowes the attention to a study of the Imperial College of London on the real high number of cases in Wuhan and on 23 the Chinese government put millions of people in quarantine, with severe travel restriction starting from 25. bas a consequence of the lack of a timely intervention with no appropriate prevention methodologies, virus entered into hospitals, nursing homes, day centers and doctor''s offices. et al Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China doi = 10.23750/abm.v91i2.9624 id = cord-272009-yxjhfg7m author = Cui, Jie title = Evolutionary Relationships between Bat Coronaviruses and Their Hosts date = 2007-10-17 keywords = SARS; bat summary = Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. doi = 10.3201/eid1310.070448 id = cord-265242-y8t37p0b author = Cui, Wei title = Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date = 2003-09-15 keywords = SARS summary = title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS. means ‫ע‬ SD The differences in the mean values between patients with SARS and healthy control subjects were estimated with Student''s t test, with a limit of significance of 0.05. The mean lymphocyte count of patients with SARS was significantly lower than that of healthy control subjects ( ; table 1) . The results of lymphocyte immunophenotyping demonstrated that the absolute counts of all lymphocyte subsets declined in patients with SARS (table 2) . Our study shows that the absolute counts of CD4 + T cells and CD8 + T cells have clinical significance in patients with SARS and that surveillance of lymphocytes and lymphocyte subsets is helpful in the diagnosis and treatment of SARS. doi = 10.1086/378587 id = cord-291113-iizj932l author = Cumbo, Enzo title = Alternative Methods of Sterilization in Dental Practices Against COVID-19 date = 2020-08-08 keywords = SARS; air; virus summary = It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. doi = 10.3390/ijerph17165736 id = cord-352737-3ttrx3lf author = Cunha, Lucas Leite title = Remodeling of the Immune Response With Aging: Immunosenescence and Its Potential Impact on COVID-19 Immune Response date = 2020-08-07 keywords = COVID-19; SARS; age; cell summary = Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Enhancing the efficacy of the adaptive immune response may be an important issue both for infection resolution as well as for the appropriate generation of immunity upon vaccination, while inhibiting inflamm-aging will likely emerge as a potential complementary therapeutic approach in the management of patients with severe COVID-19. Interestingly, polymorphonuclear leucocytes from the elderly are less capable of modulating the triggering receptor expressed on myeloid cell-1 (TREM-1)-induced oxidative bursts, suggesting that TREM-1 signal transduction altered with aging may be one of the mediators of the decrease in microbicidal potential of innate immune cells in older adults (41) . doi = 10.3389/fimmu.2020.01748 id = cord-265260-n6wm54wz author = Cuong, Hoang Quoc title = Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-09-25 keywords = SARS summary = RESULTS: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. CONCLUSIONS: Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. In this study, the assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master showed positive results from a single reaction of triplicate in the three days of 4.8 copies/reaction ( Table 3) . In this study, we reported the comparative analysis of laboratory screening for SARS-CoV-2 among three primer-probe sets in two different master mixes (Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master). doi = 10.1155/2020/7610678 id = cord-291194-cl3nu5cm author = DURDAĞI, Serdar title = Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target date = 2020-06-21 keywords = SARS; TMPRSS2 summary = One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC''s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. The small molecules from NCGC-NIH Chemical Genomics Center Pharmaceutical Collection (i.e. NPC library) were used in virtual screening studies at the active site of developed TMPRSS2 model target protein. Interestingly, benzquercin was also found as potent hit compounds in our previous virtual screening study using same protocol against another important cellentry target of SARS-CoV-2 Spike/ACE2 (Durdagi et al., 2020) . In this study, a virtual drug repurposing study was performed to identify new compounds against TMPRSS2 which is an important target for the entry of the SARS-CoV-2 to the host cell. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike Receptor-Binding Domain Bound with ACE2 COVID19 Target Proteins: A Virtual Drug Repurposing Study doi = 10.3906/biy-2005-112 id = cord-302527-n53d5en0 author = Dadlani, Shashi title = SARS-CoV-2 Transmission in a Dental Practice in Spain: After the Outbreak date = 2020-06-29 keywords = SARS; dental summary = SARS-CoV-2 is a human-to-human viral infection [4, 5] transmitted through airborne droplets from talking, coughing, or sneezing [6] or by touching or coming into contact with contaminated surfaces that are then transmitted to oral, nasal, and mucosal membranes [7] . During the coronavirus outbreak, dentists in Spain and other countries were recommended to only attend dental emergencies under strict measures wearing specific professional protection equipment to minimize the risk and maintain social distancing [12] . SARS-CoV-2 has been identified in the saliva of infected patients [14] , suggesting that the aerosols generated during dental procedures from an infected person can be extremely contagious. ese droplets can remain in the area even after the patient has left the clinic, leading to infection of dental professionals via contaminated surfaces [15] . e inhalation of airborne particles and aerosol particles during dental treatments on patients with SARS-CoV-2 is a very high-risk procedure where dentists can be exposed to the virus. doi = 10.1155/2020/8828616 id = cord-325419-15vm22d8 author = Dai, C. L. title = Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity date = 2020-10-15 keywords = SARS; hispanic; white summary = All multivariate models included race/ethnicity as an independent variable, with demographic factors (age; age-squared; sex), socioeconomic factors (insurance; neighborhood rates of poverty, crowded housing, limited English proficiency, and minority), and comorbidities (Charlson Comorbidity Index score; hypertension; and obesity) as covariates. Minority populations including Hispanic, Black, Asian, NH/PI and AI/AN had increased odds of SARS-CoV-2 infection compared to Whites in unadjusted and adjusted analysis ( race/ethnicity with White patients as the reference category. Minority races/ethnicities were not consistently associated with increased odds for COVID-19 hospitalization, until adjusting for demographics, comorbidities, insurance status and neighborhood characteristics. Race/ethnicity was associated with SARS-CoV-2 infection and COVID-19 hospitalization, with adjusted odds of both outcomes highest among Hispanics and NH/PI patients. The significant associations of minority races/ethnicities with SARS-CoV-2 infection and COVID-19-related hospitalization builds on previous analyses of Black and Hispanic patients(24-27). doi = 10.1101/2020.10.14.20212803 id = cord-303832-1kcqhgjw author = Dai, Manman title = Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date = 2020-09-06 keywords = SARS summary = Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. ABSTRACT 21 Several outbreaks of COVID-19 were associated with seafood markets, raising concerns that 22 fish-attached SARS-CoV-2 may exhibit prolonged survival in low-temperature environments. In this study, we detected the titer (50% tissue culture infectious dose/mL, TCID 50 /mL) of 35 viable SARS-CoV-2 attached on salmon or untreated SARS-CoV-2 in culture medium stored at 36 4°C, the temperature in refrigerators or cold rooms for the temporary storage of fish, or 25°C, the 37 regular room temperature, respectively, using end-point titration assay on Vero E6 cells as 38 described previously (8). As shown in Figure A and B, salmon-attached SARS-CoV-2 remained 39 viable at 4°C and 25°C for 8 and 2 days, respectively, while the untreated SARS-CoV-2 in 40 culture medium remained infectious at 4°C and 25°C for more than 8 days. doi = 10.1101/2020.09.06.284695 id = cord-281686-edpyn8fd author = Dalamaga, Maria title = 19 treatment regimens? date = 2020-05-08 keywords = COVID-19; SARS summary = These agents could attenuate ARDS and help control SARS-CoV-2 via multiple mechanisms including: 1) inhibition of viral replication; 2) decrease of iron availability; 3) upregulation of B cells; 4) improvement of the neutralizing anti-viral antibody titer; 5) inhibition of endothelial inflammation and 6) prevention of pulmonary fibrosis and lung decline via reduction of pulmonary iron accumulation. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. Interestingly, iron chelation has been shown in vitro to suppress endothelial inflammation in viral infection, which is the main pathophysiologic mechanism behind systemic organ involvement induced by SARS-CoV-2, by inhibiting IL-6 synthesis through decreasing NF-kB. It could also be reasonable to speculate that iron chelators may prevent the development of pulmonary fibrosis and lung function decline following COVID-19 infection. doi = 10.1016/j.metabol.2020.154260 id = cord-259933-ggx4v0bz author = Dalan, Rinkoo title = The ACE-2 in COVID-19: Foe or Friend? date = 2020-04-27 keywords = ACE-2; Ang; SARS summary = The SARS-CoV-2, a positive strand RNA virus, has been seen to infect humans through the angiotensin converting enzyme -2 (ACE-2) receptor [9] . In individuals with hypertension, diabetes, and other cardiovascular disorders with vascular complications, the renin angiotensin system (RAS) is known to be activated with an increase in ACE activity and a downregulation of ACE-2. Therefore, it may be assumed that the inherent downregulation of the ACE-2-Ang-(1-7)-Mas axis (as seen in metabolic conditions) is exacerbated in the COVID-19 state because (i) the virus uses the peptidase domain of the enzyme for entry into the cells and (ii) there is a decrease in ACE-2 with an increase in ACE [9] . Individuals with underlying hypertension, type 2 diabetes, or cardiovascular disease are at higher risk for respiratory failure and mortality in COVID-19. doi = 10.1055/a-1155-0501 id = cord-299520-2khjhows author = Dalla Volta, Alberto title = The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures date = 2020-08-18 keywords = Oncology; SARS summary = title: The Spread of SARS-CoV-2 Infection Among the Medical Oncology Staff of ASST Spedali Civili of Brescia: Efficacy of Preventive Measures We conducted a surveillance for SARS-CoV-2 infection among the staff members of the Medical Oncology Unit of ASST Spedali Civili in Brescia, one of the Italian areas most affected by the SARS-CoV-2 pandemic. Since last February 24, 2020, the Medical Oncology Unit of ASST Spedali Civili in Brescia put in place most of the protective measures that were subsequently acknowledged to be effective in preventing viral infection among healthcare professionals (HCPs) and patients (3) (4) (5) . The Medical Oncology Unit of ASST Spedali Civili of Brescia is located in one of the Italian areas that were most affected by the SARS-CoV-2 infection, and the hospital had to allocate the majority of its beds to patients with severe virus-related diseases. doi = 10.3389/fonc.2020.01574 id = cord-315756-g6g34uvh author = Danchin, A. title = Immunity after COVID-19: protection or sensitization ? date = 2020-05-23 keywords = COVID-19; SARS summary = Then we use a compartmental epidemic model structured by immunity level (taken here as age classes) that we fit on available data; this allows to derive quantitative insights into the future number of severe cases and deaths. Note that in both cases the results depend on the total epidemic infection rate, which is between α t = 5.7% (present) and the group immunity rate 1 − 1/R 0 (i.e., 70% for R 0 = 3.3). Note first that the relatively controlled nature of the 2003 SARS epidemic did not allow us to draw conclusions on how the 2003 epidemic influenced the infected (too few cases); by contrast, if a sensitizing process in the immune response triggered by SARS-CoV-2 exists, the pandemic nature of the 2019/20 COVID-19 outbreak will likely have noticeable effects on the overall population health state. doi = 10.1101/2020.05.21.20108860 id = cord-330131-yfhrmbvx author = Danchin, Antoine title = Cytosine drives evolution of SARS‐CoV‐2 date = 2020-04-27 keywords = CTP; RNA; SARS; virus summary = In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. doi = 10.1111/1462-2920.15025 id = cord-317333-unrd76bo author = Danesh, Ali title = Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation date = 2011-01-05 keywords = IFN; MX1; SARS; stat1; α2b summary = Evaluation of gene expression patterns in PBMCs and lung necropsies of SARS-CoV-infected ferrets led us to the identification of 7 upregulated IRGs that also were upregulated in response to IFN-α2b injection. Since STAT1 was phosphorylated following SARS-CoV infection and IFN-α2b injection, we investigated select IRG expression by qRT-PCR following in vitro stimulation of ferret peripheral whole blood with IFN-α2b. These gene expression and STAT1 phosphorylation findings suggested that robust IFN responses were activated following SARS-CoV infection 2 days post-infection. The comparison of microarray results between the lung tissue of IFN-α2b and SARS-CoV ferrets at day 1 revealed commonalities in the expression patterns of most IRGs. STAT1, MX1, OAS1, OAS2, ISG15, IFI44, IFI44L and EIF2AK2 were among the overlapping genes (Fig. 3B ). Analysis of the IFN signaling canonical pathway showed the upregulation of STAT1, MX1, OAS1, OAS2, ISG15 and IFI44 in lung necropsies of IFN-α2b injected and SARS-CoV infected ferrets (Fig. 4) . doi = 10.1016/j.virol.2010.10.002 id = cord-316946-bxfdq8e1 author = Danion, François title = The Good, the Bad, and the Hoax: When Publication Instantaneously Impacts Treatment Strategies for COVID-19 date = 2020-07-22 keywords = SARS summary = In Strasbourg University Hospital, France, which was severely affected by the SARS-CoV-2 epidemic at the beginning of March 2020, we analyzed the consumption of antiviral agents according to the emergence of relevant scientific data. The treatment strategies in our center, outside clinical trials, included standard of care alone or in combination with lopinavir-ritonavir or hydroxychloroquine (HCQ) in off-label utilization and without grading of the recommendations. Despite the major limitations of this study-including no outcome data on clinical efficacy or safety, the small number of patients enrolled, and the absence of randomization-we experienced a dramatic increase in our HCQ prescriptions following this publication (Fig. 1) . Following the publication of a large observational study on 22 May showing no beneficial effect of HCQ, this treatment regimen is not authorized anymore in France outside clinical trials (6) . Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial doi = 10.1128/aac.01127-20 id = cord-342145-cq6xe5r7 author = Dao Thi, Viet Loan title = A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date = 2020-08-12 keywords = Fig; LAMP; RNA; SARS summary = The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital''s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ). doi = 10.1126/scitranslmed.abc7075 id = cord-307285-bxy0zsc7 author = Dar Odeh, Najla title = COVID-19: Present and Future Challenges for Dental Practice date = 2020-04-30 keywords = COVID-19; SARS; dental; patient summary = Realizing the severity of outcomes associated with this disease and its high rate of transmission, dentists were instructed by regulatory authorities, such as the American Dental Association, to stop providing treatment to dental patients except those who have emergency complaints. In vitro studies have shown that azithromycin is active against Zika and Ebola viruses, [18] [19] [20] and is able to prevent severe respiratory tract infections when administrated to patients suffering viral infection [12] However, the efficacy of azithromycin in combination with hydroxychloroquine in the treatment of COVID-19 patients has not been confirmed yet [21, 22] , and more studies are needed to further investigate its clinical effects. Following the recommended cross-infection control procedures, spreading awareness based on evidence and not misconceptions, identifying emergency cases indicated for dental treatment, and practicing effective tele-dentistry when needed can all be helpful for dental patients and community as a whole. doi = 10.3390/ijerph17093151 id = cord-000333-4prvgmvt author = Darbyshire, Philip title = Nursing heroism in the 21(st )Century'' date = 2011-02-16 keywords = AIDS; SARS; care; nurse; nursing summary = Gary Carr, who was a Nurse Practitioner at the AIDS Clinic at San Francisco General Hospital, described the perverse ambivalence of a wider community that lauds and praises nurses for their ''heroic efforts'' in the face of such public health crises. When, two decades later, SARS emerged as a potentially lethal viral infection, nurses and health care staff again faced considerable dangers as they strove to treat patients and protect their communities. In addition, Hall and colleagues in the US reported that: "Nursing assistants working in long-term care facilities have the highest incidence of workplace violence of any American worker". Perhaps if we return to the definition of heroism as ''providing service in the face of extreme personal danger'', then our Emergency Department nurses should allow themselves to feel, at least somewhat heroic. So too, the health, wellbeing, safety and experiences of patients, clients and families are dependent upon the often invisible and overlooked caring practices of nurses. doi = 10.1186/1472-6955-10-4 id = cord-302111-kg0dmgq0 author = Darden, Dijoia B. title = The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date = 2020-04-29 keywords = SARS; pneumonia; respiratory; viral; virus summary = Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. doi = 10.1097/cce.0000000000000109 id = cord-314171-431buxxr author = Dariya, Begum title = Understanding novel COVID-19: its impact on organ failure and risk assessment for diabetic and cancer patients date = 2020-05-06 keywords = ACE2; CoV-2; SARS; covid-19; patient summary = In this review article, we have presented the effect of SARS-CoV-2 infection in comorbid patients and discussed organ failure caused by this virus. The mRNA and protein ACE2 expression levels are higher in these patients with cardiac disease, creating an increased risk for severe COVID-19 complications, including heart failure. After SARS-CoV-2 binds with ACE2, the virus degrades it, and thus the free angiotensin II induces acute lung injury [58] . Thus, targeting the binding site of the ACE2 receptor and SARS-CoV-2 with antibodies or therapeutic drugs might provide a successful treatment strategy. Moreover, this also increases the level of soluble ACE2 that competitively binds with SARS-CoV-2, causing delayed entry of the virus into cells and protecting against lung injury. The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 doi = 10.1016/j.cytogfr.2020.05.001 id = cord-022003-cvawdes6 author = Darling, Robert G. title = Future Biological and Chemical Weapons date = 2015-10-23 keywords = Biological; SARS; United; War; Weapons; World; agent; chemical summary = doi = 10.1016/b978-0-323-28665-7.00080-7 id = cord-303216-1pbuywz6 author = Das, Gaurav title = Neurological Insights of COVID-19 Pandemic date = 2020-04-22 keywords = COVID-19; CoV-2; SARS summary = If scientific reports relevant to the SARS-CoV-2 virus are noted, it can be seen that the virus owes much of its killer properties to its unique structure that has a stronger binding affinity with the human angiotensin-converting enzyme 2 (hACE2) protein, which the viruses utilize as an entry point to gain accesses to its hosts. The intriguing part though is that recently reported studies have noted altered mental health in some COVID-19 patients showing symptoms like anosmia and ageusia thereby indicating a neuroinvasive nature of the virus. The neurological manifestations of SARS-CoV-2 have been recently recognized from CT scan images and MRI scan of the brain of a patient who contracted COVID-19 and showed symptoms of necrotizing hemorrhagic encephalopathy. The brain reportedly, like most other organs, expresses the hACE2 considered to be the entry point of the SARS-CoV-2 viruses in humans and is therefore not immune to viral infection. doi = 10.1021/acschemneuro.0c00201 id = cord-292657-gq3965se author = Das, Piyanki title = Decoding the global outbreak of COVID-19: the nature is behind the scene date = 2020-06-22 keywords = SARS; host; virus summary = The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. doi = 10.1007/s13337-020-00605-y id = cord-259340-1ir19s25 author = Das, Rohit Pritam title = Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date = 2020-07-01 keywords = SARS summary = Here the authors have attempted to design epitope based potential peptide as a vaccine candidate using immunoinformatics approach. As of evidence from literatures, SARS-CoV-2 Spike protein is a key protein to initiate the viral infection within a host cell thus used here as a reasonable vaccine target. To its support, strong molecular interaction of the predicted peptide was also observed with MHC molecules and Toll Like receptors. The B-cell epitopic regions present in SARS-CoV-2 S protein were identified using BcePred prediction server (https://webs.iiitd.edu.in/cgibin/bcepred/) [17] . Molecular docking was performed between the predicted peptides and MHC representative structures using PatchDock web server [22, 23, 24] . Interaction of both TLR2 and TLR4 structures with the predicted peptides were performed using PatchDock web server [22, 23, 24] . This study is focused on the prediction of effective epitopes from Spike protein of SARS-CoV-2. doi = 10.1101/2020.07.01.150805 id = cord-301026-spgidqh3 author = Das, Shaoli title = In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data date = 2020-06-30 keywords = COVID-19; SARS; drug summary = Next, using the available drug perturbational data sets from the Broad Institute Connectivity map (CMAP project 14 , we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. To get a pathway-based estimation instead of individual genes, we calculated ssGSEA scores for the differentially enriched pathways in COVID-19 or SARS infection for all drug-treated cell lines at different dose/time points. Thereafter, combining the potential human interactome of SARS-CoV-2 from a recently published study 9 and SARS-CoV-1-interacting proteins curated in another publication 8 with drug target databases 10, 11 , drug perturbational data sets 14 , and drug sensitivity screening data sets 15 , we propose a map of the drugs that can be effective in COVID-19 treatment. Next, using the available drug perturbational data sets from the Broad Institute CMAP project, we assessed how the candidate drugs targeting SARS-CoV-2-interacting proteins affect the pathways that are altered after COVID-19 or SARS infection in a time-dependent manner. doi = 10.21203/rs.3.rs-39128/v1 id = cord-263576-pn2zieek author = Das, Sourav title = An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study date = 2020-05-13 keywords = CYS145; SARS; figure summary = Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. Hydroxychloroquine, a promising candidate for the treatment of the current pandemic due to SARS-CoV-2 (Gautret et al., 2020) , has been found to bind within the active site of the protease through p-sulphur interaction with MET165, p-sigma with GLN189, alkyl hydrophobic with LEU167 and PRO168, and van der Waals interactions with other residues as shown in Figure 2c . Curcumin, a potent bioactive molecule binds in the active site of SARS-CoV-2 M pro (Figure 3a ) through hydrogen bonding with GLY143 and GLN192, p-sulphur, p-sigma interactions with CYS145 and PRO168, respectively, along with other non-covalent interactions such as van der Waals interactions with other residues as shown in the 2 D plot (Figure Table 1 . doi = 10.1080/07391102.2020.1763201 id = cord-266113-3fp46sov author = Dashti‐Khavidaki, Simin title = Considerations for Statin Therapy in Patients with COVID‐19 date = 2020-05-04 keywords = COVID-19; SARS summary = Current coronavirus pandemic named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third coronavirus outbreak during the current century after severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses.1 Acute respiratory distress syndrome (ARDS) is an immunopathologic event and main cause of death following COVID-19. The main mechanism of ARDS is uncontrolled systemic inflammatory response and cytokine storm following release of proinflammatory cytokines (such as interferons (IFN), interleukines (IL), tumor necrosis factor (TNF)-α) and chemokines.2-3 So, some Chinese researchers proposed or used anti-inflammatory agents in the treatment regimen of patients with COVID-19.3-4. The current coronavirus pandemic is an outbreak of coronavirus disease 2019 (COVID19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2, 23 Thus, initiating statins in patients with COVID-19 may increase the risk and severity of myopathies and acute kidney injury. doi = 10.1002/phar.2397 id = cord-224516-t5zubl1p author = Daubenschuetz, Tim title = SARS-CoV-2, a Threat to Privacy? date = 2020-04-21 keywords = SARS; datum; information; privacy summary = We furthermore discuss the issues with privacy that can occur during a crisis such as this global pandemic and what can be done to ensure information security and hence appropriate data protection. When we are considering the example of doctors treating their patients, we can use the framework of contextual integrity to reason about the appropriate information flow as follows: the patient is both the sender and the subject of the data exchange, the doctor is the receiver, the information type is the patient''s medical information, the transmission principle includes, most importantly, doctor-patient confidentiality aside from public health issues. In Germany, the authority for disease control and prevention, the Robert Koch Institute (RKI), made headlines on March 18, 2020, as it became public that telecommunication provider Telekom had shared an anonymized set of mobile phone movement data to monitor citizens'' mobility in the fight against SARS-CoV-2. doi = nan id = cord-287682-97fquq16 author = Daubin, Cédric title = Is a COPD patient protected against SARS-CoV-2 virus? date = 2020-10-03 keywords = SARS summary = In addition, cigarette smoke and COPD were reported to up-regulate Angiotensin-converting enzyme 2 (ACE-2) expression, which plays a key role in the pathogenesis of SARS-CoV-2 in lower airways [2] . Considering a significant inverse relationship between ACE-2 gene expression and the severity of COPD [2] , one hypothesis could be that COPD protects against SARS-CoV-2 through a TMPRSS2 inhibitor activity or by an a downregulation of the inflammatory pathway limiting severe forms of infection. Interestingly, as reported by Halpin et al., inhaled corticosteroids, used by COPD patients can reduce the risk of viral infection. Therefore, inhaled corticosteroids in combination with bronchodilators could limit expression or activity of transmenbrane serine protease TMPRSS2 which facilitates SARS-CoV-2 entry in cells. Surprisingly current smokers (i.e., a large part of COPD patients) could be protected against SARS-CoV-2 infection [4] . Sin DD (2020) ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19 doi = 10.1016/j.medmal.2020.09.015 id = cord-321267-ihd30qi0 author = Daughton, Christian G. title = Natural experiment concept to accelerate the Re-purposing of existing therapeutics for Covid-19 date = 2020-05-15 keywords = SARS; covid-19; drug; nerd summary = Proposed here is a new but simple concept that would capitalize on the opportunity presented by the on-going natural experiment involving the collection of data from epidemiological surveillance screening and diagnostic testing for clinical treatment. These drug usage data would be collected for several major test groups those who test positive for active SARS-CoV-2 infection (using molecular methods) and those who test negative for current infection but also test positive for past infection (using serologic antibody tests). (1) As Covid-19 epidemiological surveillance screening and diagnostic testing proceeds, a national database would be continually populated with drug usage data collected from each case among three different combinations of sub-groups based upon whether they tested positive or negative for active SARS-CoV-2 infection or tested positive for past SARS-CoV-2 infection (see Table 1 ). doi = 10.1016/j.gloepi.2020.100026 id = cord-255101-l5ssz750 author = Daval, Mary title = Efficacy of local budesonide therapy in the management of persistent hyposmia in COVID-19 patients without signs of severity: A structured summary of a study protocol for a randomised controlled trial date = 2020-07-20 keywords = COVID-19; SARS; des; les summary = Objectif principal: Evaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. L''objectif de cet essai randomisé contrôlé, bicentrique, est d''évaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. Evaluer l''efficacité du budésonide en traitement local intranasal (lavage de nez), en complément de la rééducation olfactive, dans la prise en charge de la perte d''odorat de patients COVID-19 sans signes de gravité et présentant une persistance de l''hyposmie 30 jours après le début des symptômes. doi = 10.1186/s13063-020-04585-8 id = cord-346403-fuxs1axy author = Davanzo, G. G. title = SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes date = 2020-09-28 keywords = CD4; SARS summary = We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARSCoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. Since CD4 + T lymphocytes orchestrate innate and adaptive immune responses 19, 20 , infection of CD4 + T cells by SARS-CoV-2 might explain lymphocytopenia and dysregulated inflammatory response in severe COVID-19 patients. doi = 10.1101/2020.09.25.20200329 id = cord-268484-hf4zflsy author = Davanzo, Riccardo title = Breast feeding at the time of COVID-19: do not forget expressed mother’s milk, please date = 2020-04-06 keywords = SARS summary = In the context of the coronavirus disease (COVID-19) prevention and cure, a remarkable issue, particularly in maternity hospitals, is represented by the risk of mother to child transmission by a breastfeeding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive woman. Moreover, Chinese colleagues who have recently coped with COVID-19 just do not consider the breast feeding option, nor the use of expressed breast milk for newborn infants. Thus, the author seems to implicitly endorse the use of expressed mother''s milk, although in the flow chart contained in the online supplementary appendix, he contradictorily warns just against breast feeding for all SARS-CoV-2-positive mothers at delivery. In conclusion, protocols applied in maternity hospitals to prevent COVID-2 should consider, as far as possible, the promotion of breast feeding, without disregarding the feasible option of expressing mother''s milk. doi = 10.1136/archdischild-2020-319149 id = cord-285111-qjclp51i author = Davanzo, Riccardo title = Breastfeeding and coronavirus disease‐2019: Ad interim indications of the Italian Society of Neonatology endorsed by the Union of European Neonatal & Perinatal Societies date = 2020-04-26 keywords = COVID-19; SARS; mother summary = The Italian Society on Neonatology (SIN) after reviewing the limited scientific knowledge on the compatibility of breastfeeding in the COVID‐19 mother and the available statements from Health Care Organizations has issued the following indications that have been endorsed by the Union of European Neonatal & Perinatal Societies (UENPS). • If a breastfeeding mother and her newborn infant are managed jointly, measures aimed at preventing the transmission of the viral infection should be put in place: avoid kissing the neonate, protect him from adult coughing and respiratory secretions (wear a mask during feeding and intimate contact with the baby), wash hands, in particular, before feeding, suspend visits. We recognize that this guidance might be subject to change in the future when further knowledge will be acquired about the COVID-19 pandemic, its perinatal transmission, and clinical characteristics of cases of neonatal SARS-CoV-2 infection. doi = 10.1111/mcn.13010 id = cord-262485-sx2q5ol4 author = Davda, Jayeshkumar Narsibhai title = An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date = 2020-06-08 keywords = PCR; SARS summary = The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. doi = 10.1101/2020.06.08.139477 id = cord-305511-gdpxvqkk author = Dave, Gaurav S. title = High affinity interaction of Solanum tuberosum and Brassica juncea residue smoke water compounds with proteins involved in coronavirus infection date = 2020-08-11 keywords = ACE2; SARS summary = Phytoconstituents that possess remarkable pharmacological activity were selected as reported from Solanum tuberosum and Brassica juncea residue smoke water (Dave et al., 2018) and Ligand library was prepared of potential molecules to be used for the docking study with human, SARS-CoV and SARS-CoV-2 proteins as given in Table 1 (Sakai et al., 2014) , SARS-CoV-S in complex with ACE2 (PDB: 2AJF) (Li et al., 2005; Micholas & Jeremy, 2020) , PLpro (PDB: 3E9S) , SARS-CoV-2 3CLpro (PDB: 6LU7) , SARS-CoVRdRp (PDB: 6NUR) (Elfiky, 2020) , SARS-CoV-2 spike glycoprotein structure (SARS-CoV-2-S) (PDB: 6VSB) (Grifoni et al., 2020) , binding complex of human ACE2 and RBD (PDB: 6VW1) (Qiu et al., 2020) , SARS-CoV-2-S (closed) (PDB: 6VXX) (Walls et al., 2020) , SARS-CoV-2-S with one S B (open) (PDB: 6VYB) (Walls et al., 2020) and Human angiotensin-converting enzyme 2 (ACE2) (PDB: 1R42) (Jia et al., 2009) are selected for the present study as target proteins ( Figure 1 ). doi = 10.1002/ptr.6796 id = cord-295034-em6z8mlu author = Daverey, Achlesh title = COVID-19: Eco-friendly hand hygiene for human and environmental safety date = 2020-11-11 keywords = SARS; hand; sanitizer summary = Frequent handwashing with soap and the use of alcohol-based hand sanitizers is recommended by WHO for hand hygiene and to prevent the spread of COVID-19. However, there are safety concerns associated with the use of soaps and alcohol-based hand sanitizers. Therefore, the review aims to highlight the health and environmental concerns associated with the frequent use of soaps/detergents and alcohol-based hand sanitizers amid COVID-19. The potential of some of the natural detergents and sanitizing agents as eco-friendly alternatives to petrochemical-based soaps and alcohol-based hand rubs for hand hygiene are discussed. Overall, all these properties of plant-derived natural soaps and detergents have the potential to replace the synthetic detergents and alcohol-based sanitizers. Economical production of biosurfactants and extraction of bioactive antimicrobial agents from the plants will play a crucial role in their commercial application and sustainability as eco-friendly soaps and hand sanitizers and therefore further research is needed in this direction. doi = 10.1016/j.jece.2020.104754 id = cord-275108-snqbrxgr author = Daverio, Marco title = Testing for Novel Coronavirus Antibodies: A Necessary Adjunct date = 2020-05-22 keywords = SARS summary = We read with interest the article by Cowling and Aiello [1] about the use of proactive public health measures to help slow the spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over the world. Furthermore, the numbers of individuals infected are difficult to estimate, owing to the presence of both SARS-CoV-2-positive asymptomatic individuals and symptomatic, self-isolating individuals in whom nasopharyngeal swab samples were not obtained. It may seem a waste of resources but knowing people''s serological status regarding SARS-CoV-2 could allow those who were previously infected to return to work and restart the world economy before the entire pandemic is over. We therefore suggest, along with all the necessary public preventive measures, performing target testing for SARS-CoV-2 antibodies in particular subpopulations, for example, young and healthy persons who can actively work. doi = 10.1093/infdis/jiaa283 id = cord-253933-29tedkf8 author = David, Abel P. title = Tracheostomy guidelines developed at a large academic medical center during the COVID‐19 pandemic date = 2020-04-27 keywords = COVID-19; PPE; SARS summary = 1 As an aerosol-generating procedure (AGP), tracheostomy is associated with high droplet and particle generation, placing health care providers at increased risk for transmission of respiratory viral infections. Factors relevant to our review included optimal timing of tracheostomy, duration of viral shedding in patients with COVID-19, risk to procedural teams from aerosol generation during tracheostomy, ICU capacity, and availability of PPE. In the context of the current pandemic, Tay et al conducted a literature review of tracheostomies performed during the SARS epidemic and concluded the following: (a) proper PPE (N95 mask, surgical cap, gown, goggles, and gloves) is of utmost importance; (b) surgical tracheostomy is preferably performed in a negative pressure ICU room by experienced providers with meticulous planning and seamless communication; (c) aerosol generation should be minimized through patient paralysis, ventilation hold during creation of tracheal window, and utilization of HEPA-filtered suction systems. doi = 10.1002/hed.26191 id = cord-257105-vrwuaknf author = Davies, Julie title = Neuropilin-1 as a new potential SARS-CoV-2 infection mediator implicated in the neurologic features and central nervous system involvement of COVID-19 date = 2020-09-15 keywords = SarS; coV-2; olfactory summary = Preclinical studies have suggested that neuropilin-1 (NRP1), which is a transmembrane receptor that lacks a cytosolic protein kinase domain and exhibits high expression in the respiratory and olfactory epithelium, may also be implicated in COVID-19 by enhancing the entry of SARS-CoV-2 into the brain through the olfactory epithelium. This study presents a detailed in silico analysis of the expression of nrP1 in the human brain, highlighting the potential role of nrP1 as an additional SarS-coV-2 infection mediator in the CNS via NRP1-expressing cells. Given this newly identified role of nrP1 in enhancing SarS-coV-2 entry into the cnS, characterizing the precise expression of nrP1 in the human brain becomes important in the context of the neurologic involvement of coVid-19. Finally, the parolfactory gyri which receive inputs from the olfactory bulb and provide input to the limbic system, also exhibit nrP1 expression, and so their potential involvement in the SarS-coV-2 infection of the cnS merits further research. doi = 10.3892/mmr.2020.11510 id = cord-283253-qdq4mfz3 author = Davlantes, Elizabeth title = Notes from the Field: COVID-19 Prevention Practices in State Prisons — Puerto Rico, 2020 date = 2020-08-21 keywords = SARS summary = These results followed implementation in mid-March of a protocol (2) for the diagnosis, management, and prevention of COVID-19 in all Puerto Rico Department of Correction and Rehabilitation prisons based on CDC''s interim guidance on management of COVID-19 in correctional and detention facilities (3) . To minimize SARS-CoV-2 transmission from newly incarcerated persons, all state prison intakes in Puerto Rico now occur at a single location, in the municipality of Bayamon. During March 16-July 31, 2020, 1,340 persons entered Puerto Rico Department of Correction and Rehabilitation prisons, and two (0.1%) had positive SARS-CoV-2 RT-PCR test results. If any group member exhibits COVID-19 symptoms, which are defined according to CDC guidelines (4), the symptomatic person is isolated in the prison''s medical facility, and the entire group is quarantined until the symptomatic person receives a negative SARS-CoV-2 RT-PCR result. doi = 10.15585/mmwr.mm6933a4 id = cord-305959-x061q8t7 author = Davoudi-Monfared, Effat title = A Randomized Clinical Trial of the Efficacy and Safety of Interferon β-1a in Treatment of Severe COVID-19 date = 2020-08-20 keywords = COVID-19; IFN; SARS; patient summary = As the primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 ± 5.8 versus 8.3 ± 4.9 days, respectively, P = 0.95). The vital signs at the time of hospital admission were not statistically different, except respiratory rate was significantly higher in the IFN group (22 versus 20, respectively, P ϭ 0.009). As a primary outcome, the time to clinical response was not significantly different between the IFN and control groups (9.7 Ϯ 5.8 versus 8.3 Ϯ 4.9 days, respectively, P ϭ 0.95), which is shown in the Kaplan-Meier plot (Fig. 2) . On day 0, there was no significant difference between the groups in terms of the components Interferon ␤-1a in Treatment of Severe COVID19 Antimicrobial Agents and Chemotherapy of this scale. The present study was the first randomized, open-label, controlled trial that assessed the efficacy and safety of IFN ␤-1a in the treatment of patients diagnosed with severe COVID-19. doi = 10.1128/aac.01061-20 id = cord-258152-3udtsvga author = Dawood, Ali Adel title = Tunicamycin, an anticancer drug and inhibitor of N- linked glycosylation proteins is reliable to treat COVID-19 date = 2020-10-20 keywords = SARS summary = The glycans in some proteins play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. SARS-CoV is one of the viruses contain N-linked glycoproteins which are glycosylated by the transfer of core oligosaccharides from a dolichol pyrophosphate carrier to asparagine residues on the polypeptide [2] . Furthermore, HE protein of MHV was found to be modified by N-linked glycosylation and was inhibited by tunicamycin but not monensin. The inhibition Nlinked glycosylation of SARS-CoV 8ab protein by tunicamycin is not completely understood [33, 34] . HE and 8ab proteins of SARS-CoV glycosylation are inhibited by tunicamycin. Since tunicamycin has long been used as an anti-cancer and can inhibit glycoproteins of coronaviruses, we recommend using this drug to treat the SARS-CoV-2. doi = 10.1016/j.micpath.2020.104586 id = cord-355899-wd00f8cw author = Dawson, E. D. title = Multiplexed, Microscale, Microarray-based Serological Assay for Antibodies Against All Human-Relevant Coronaviruses date = 2020-09-04 keywords = SARS; September summary = This study reports on the VaxArray CoV SeroAssay linear dynamic range, limit of detection, specificity, reproducibility, accuracy, and investigates assay performance on a retrospective set of 263 blinded, de-identified human serum and plasma specimens to demonstrate positive and negative percent agreement to a mixed reference method of RT-PCR on a patient-matched specimen and collection date prior to the COVID-19 outbreak. A total of 132 serum samples known to be negative for the presence of antibodies to SARS-CoV-2 based on date of collection prior to December 2019, including 33 specimens from pediatric donors age 2-16, were analyzed via the standard VaxArray CoV SeroAssay procedure at a 1:100 dilution in PBB. To assess reproducibility and accuracy, a pooled human serum sample positive for antibodies to SARS-CoV-2, and also known to be reactive to the SARS antigen and the 4 endemic Table 3 shows the % CV in the back-calculated concentration value obtained on each relevant capture antigen for all 216 replicate measurements over all 3 days and all three lots of slides, with values ranging from 7 to 19 %CV for the 9 antigens. doi = 10.1101/2020.09.03.20179598 id = cord-325609-n6dpac6i author = Dawson, Kathryn L. title = Acute increase in deaths among adult congenital heart disease patients during COVID-19 - single center experience. date = 2020-06-13 keywords = ACHD; SARS summary = title: Acute increase in deaths among adult congenital heart disease patients during COVID-19 single center experience. Over the 12-month period preceding the SARS-CoV-2 related stay-at-home order, a total of 4 patients followed by the ACHD service at the University of Washington Medical Center with defects of various severities died in an acute setting. We believe that this change in emergency department volume, combined with the acute increase in mortality reported in this case series, emphasizes the potential adverse outcomes of delayed presentations in medically complex patients. These cases highlight the need for public education regarding the imperative to present for medical care when symptoms would have merited emergency treatment prior to the pandemic, particularly amongst our most vulnerable populations. It also highlights the need for routine follow-up care for patients with congenital heart disease, even in the presence of clinical stability, to assess for subclinical symptom burdens that may herald future acute presentations. doi = 10.1016/j.jaccas.2020.06.013 id = cord-266695-ktbgm0p9 author = Dawson, Liza title = SARS-CoV-2 Human Challenge Trials: Too Risky, Too Soon date = 2020-06-04 keywords = SARS; challenge summary = have recently argued that researchers should consider conducting SARS-CoV-2 human challenge studies to hasten vaccine development [1] . However, we disagree that SARS-CoV-2 challenge studies are ethically appropriate at this time, for three reasons: 1) current scientific knowledge of SARS-CoV-2 infection is insufficient to manage risks; 2) autonomous decision-making, while necessary, does not override concerns about risk; and 3) undertaking challenge studies now would imperil confidence in the research enterprise, potentially undermining the global response to the COVID-19 pandemic. Current scientific knowledge is insufficient to manage the risks of severe disease or death of volunteers in SARS-CoV-2 human challenge studies, especially in terms of selecting low risk volunteers [2] . It is not obvious that the possible benefits of developing a successful vaccine in less time justify the risks SARS-CoV-2 challenge studies, as Eyal and colleagues suggest. However, conducting SARS-CoV-2 human challenge trials now unjustifiably threatens both the well-being of volunteers and confidence in the research enterprise. doi = 10.1093/infdis/jiaa314 id = cord-020769-elzkwyz0 author = Day, Brennan title = The new normal: lessons learned from SARS for corporations operating in emerging markets date = 2004-07-01 keywords = China; Hong; Kong; SARS; disease summary = This paper uses the recent SARS epidemic as a background to highlight the importance of crisis planning, particularly in emerging economies, and suggests how organizations can address these concerns. This paper will start by presenting background information on the SARS epidemic and the impact on organizations, especially those operating in emerging markets. Since emerging markets are increasingly important to the world economy and are at the same time susceptible to outbreaks of infectious diseases, we need to understand how we are linked together on an interdependent global level. If just three of the Asian emerging economies -China, India, and Indonesia -are able to maintain this growth rate of 6 percent per year, the Organisation for Economic Co-operation and Development (OECD) has estimated that by 2010 approximately 700 million people in those countries will have an average income equivalent to that of Spain today. doi = 10.1108/00251740410542357 id = cord-291393-iht5zndl author = De Angelis, Giulia title = Confirmed or unconfirmed cases of 2019 novel coronavirus pneumonia in Italian patients: a retrospective analysis of clinical features date = 2020-10-19 keywords = COVID-19; SARS summary = METHODS: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Because of substantial pneumonia-related morbidity and mortality [3] , testing for SARS-CoV-2 infection of patients who meet the suspected-case definition for COVID-19 [4] is central for their management. We comparatively explored the clinical features of 165 patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia admitted to COVID-19 wards of the Fondazione Policlinico A. We tested the hypothesis that negative patients did not differ from SARS-CoV-2 RNA positive patients by comparing features of 165 cases with clinically diagnosed 2019-nCoV pneumonia in our hospital. doi = 10.1186/s12879-020-05504-7 id = cord-344382-vge4ho2v author = De Flora, Silvio title = Rationale for the use of N‐acetylcysteine in both prevention and adjuvant therapy of COVID‐19 date = 2020-08-11 keywords = COVID-19; GSH; NAC; SARS summary = 5 Elderly individuals maintain a chronic low level of inflammation that is associated with oxidative stress and inflammatory cytokine production, a condition that increases the severity of viral infections in this population and that could be attenuated by administration of antioxidants. 36 A randomized, double-blind, placebo-controlled, prospective clinical trial in 5 ICUs in the USA and Canada showed that the intravenous administration of NAC (70 mg/ kg body weight), every 8 hours for 10 days, effectively repleted GSH in red blood cells, decreased the number of days of acute lung injury, and significantly increased the cardiac index. 50 NAC inhibited the pulmonary inflammation and edema as well as myeloperoxidase (MPO) activity, total cells, neutrophils, macrophages, TNF-α, IL-6, IL-1β, and chemokine (C-X-C motif) ligand-10 (CXCL-10) in the bronchoalveolar lavage fluid and reduced the levels of toll-like receptor 4 (TLR4) protein and mRNA in the lungs of BALB/c mice inoculated intranasally with A/swine/HeBei/012/2008/ H9N2 influenza virus. doi = 10.1096/fj.202001807 id = cord-351092-b01o6f69 author = De Francesco, Maria A. title = Pneumocystis jirevocii and SARS-CoV-2 Co-Infection: A Common Feature in Transplant Recipients? date = 2020-09-18 keywords = COVID-19; Pneumocystis; SARS summary = Here we describe, for the first time in Europe, a fatal case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii in a kidney transplant recipient. Pneumocystis jirevocii pneumonia is an opportunistic infection affecting patients with cellular immunity defects due to human immunodeficiency virus (HIV) infections or iatrogenic immunosuppression [15, 16] . Here, we report the fatal case of a SARS-CoV-2 and Pneumocystis jirevocii co-infection in a kidney transplant recipient. This is, to the best of our knowledge, the first case of co-infection between SARS-CoV-2 and Pneumocystis jirevocii reported in Europe in a kidney transplant recipient. Pneumocystis jirevocii pneumonia in immunocompromised patients: Delayed diagnosis and poor outcomes in non-HIV infected individuals Acute respiratory failure due to Pneumocystis pneumonia in patients without human immunodeficiency virus infection: Outcome and associated features Critical care management and outcome of severe Pneumocystis pneumonia in patients with and without HIV infection doi = 10.3390/vaccines8030544 id = cord-278129-bpuyrsza author = De Haan, Cornelis A. M. title = Hosting the severe acute respiratory syndrome coronavirus: specific cell factors required for infection date = 2006-06-27 keywords = SARS summary = As with all viruses, the severe acute respiratory syndrome coronavirus (SARS‐CoV) utilizes specific host cell factors during its infection cycle. In this short review we focus on the severe acute respiratory syndrome coronavirus (SARS-CoV) describing what is currently known of the cell''s contributions during the successive phases of the infection cycle, i.e. entry, replication and assembly (Fig. 1) . Amino acids 270-510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensinconverting enzyme 2 Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry doi = 10.1111/j.1462-5822.2006.00744.x id = cord-353237-rob4ems7 author = De Maio, Antonio title = COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? date = 2020-05-18 keywords = HBOT; SARS summary = title: COVID-19, acute respiratory distress syndrome (ARDS), and hyperbaric oxygen therapy (HBOT): what is the link? The virus has been detected in the lungs and immune cells of patients who have succumbed to the infection, consistent with direct injury to the pulmonary tissue and activation of the immune response. Experimental animal studies about the response to sepsis have suggested that early interventions are critical to ameliorate the condition, such as source control of the infection or injury (Cauvi et al. In this regard, hyperbaric oxygen therapy (HBOT) that consists of exposure to 100% oxygen under increased atmospheric pressure up to 2.4 atm could be a great resource to improve the outcome from the infection when it is administered at early stages as soon as a reduction of arterial oxygen concentration is detected. Indeed, experimental animal studies have shown that an initial HBOT improved dramatically the outcome from sepsis, which was correlated with a reduction of the inflammatory response triggered by the initial insult (Halbach et al. doi = 10.1007/s12192-020-01121-0 id = cord-298482-r7lallv0 author = De Maio, Flavio title = Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis date = 2020-09-04 keywords = SARS summary = title: Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. The amino acid sequence of the SARS-CoV-2 Envelope protein was extracted, and the NMR structure of the 119 homologous protein of SARS-CoV (PDB code: 2MM4) was used as a template. In Figure 1B and 1C, the two predicted monomeric E full length protein structure models have been 159 constructed and show N-terminal (blue), transmembrane (green), C-terminal domains (red) as well as the 160 amino acid variants (yellow). In order to verify the potential implications of the altered amino acid sequence, the binding pose of the two 174 C-terminus octapeptides belonging to SARS-CoV and SARS-CoV-2 were determined and compared with 175 the crystallographic structure of the complex PALS1-CRB1[31]. doi = 10.1016/j.micinf.2020.08.006 id = cord-349311-yo4up42r author = De Maria, Andrea title = High prevalence of olfactory and taste disorder during SARS‐CoV‐2 infection in outpatients date = 2020-05-17 keywords = SARS summary = Here we comment on Sun and coll Metaanlysis with particular nuance to olfactory and taste disorders that very often herald SARS-CoV-2 in our country, particularly in outpatients, and are not reported so far in the medical literature from China. Limited or no information has been so far gathered on the majority of milder cases of SARS-CoV-2-disease that are cared for at home since they are not progressing to respiratory insufficiency and hospitalization/ventilation. In addition, profound olfactory and taste disorder (OTD), that has been reported to be frequent in hospitalized patients in Italy, 7 is not reported in China or other areas, 2,3,5 and correspondingly fails to be reported in the meta-analysis. Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: a single arm metaanalysis Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study doi = 10.1002/jmv.25995 id = cord-338225-8dlxnpcn author = De Meyer, Sandra title = Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date = 2020-05-29 keywords = SARS summary = Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. doi = 10.1016/j.ijid.2020.05.085 id = cord-332150-j76726no author = De Stefano, Ludovico title = A “Window of Therapeutic Opportunity” for Anti-Cytokine Therapy in Patients With Coronavirus Disease 2019 date = 2020-10-06 keywords = COVID-19; SARS; cytokine; patient summary = The main challenge for effective administration of anti-cytokine therapy in COVID-19 will be therefore to better define a precise "window of therapeutic opportunity." Only considering a more specific set of criteria able to integrate information on direct viral damage, the cytokine burden, and the patient''s immune vulnerability, it will be possible to decide, carefully balancing both benefits and risks, the appropriateness of using immunosuppressive drugs even in patients affected primarily by an infectious disease. Discovery of virus and host genomic factors will undoubtedly support risk stratification and targeted treatment; however, as genomic studies require long times before entering clinical practice, it is urgent to integrate easily accessible information on the dynamics and pathogenicity of the immune response during the different phases of SARS-CoV-2 infection. Accordingly, longitudinal immune profiling of hospitalized COVID-19 cases with different outcomes has recently shown that, despite similar levels of inflammatory cytokines in the first 10 days from symptom onset, patients with less severe disease evolution also express mediators of wound healing and tissue repair (41) . doi = 10.3389/fimmu.2020.572635 id = cord-290677-3gdcyrrz author = De Virgiliis, Francesco title = Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19 date = 2020-08-25 keywords = COVID-19; SARS; cell; lung summary = In line with these findings, virus-induced airway hyperresponsiveness in humans seems to be mediated by the vagus nerve 53 , raising the possibility that the dyspnoea and respiratory failure observed in patients with severe COVID-19 is exacerbated by neuroimmune crosstalk in the lungs. A plausible hypothesis is that these NAMs act in concert with neuronal cells to control inflammation, and that malfunctioning of this system in older or immunocompromised people could contribute to the cytokine storm and ARDS in patients with severe COVID-19 or other respiratory virus infections. In the context of SARS-CoV-2 infection, specific tissueresident macrophages that are involved in modulating inflammation following viral infection are in close contact with vagal fibres innervating the lungs, and this ''neuroimmune synapse'' could be one of the keys to controlling aberrant inflammation in patients with severe COVID-19. doi = 10.1038/s41582-020-0402-y id = cord-313756-2pqpk3v7 author = De Vriese, An S. title = In Reply to ‘Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?’ date = 2020-06-27 keywords = SARS summary = key: cord-313756-2pqpk3v7 title: In Reply to ''Is SARS-CoV-2 Serology Relevant for Hemodialysis Patients With COVID-19?'' cord_uid: 2pqpk3v7 In a small group of hemodialysis patients with confirmed SARS-CoV-2 infection, we reported that the presence of anti-SARS-CoV-2 IgG overlaps by several weeks with detectable viral RNA in the upper airways (1) . Viral load was highest during the first week of illness, suggesting that patients are most infectious during this period. It remains unclear whether the lower viral loads during the following weeks associate with a clinically relevant transmissibility of SARS-CoV-2 requiring further quarantining. We measured anti-SARS-CoV-2 IgG with a N protein-based ELISA (NovaLisa, NovaTec). Dudreuilh and Moutzouris suggest that the combination with a S protein-based assay may provide additional information. IgG Antibody Response to SARS-CoV-2 Infection and Viral RNA Persistence in Patients on Maintenance Hemodialysis Clinical performance of different SARS-CoV-2 IgG antibody tests doi = 10.1053/j.ajkd.2020.06.005 id = cord-305564-dj3vj4tk author = DeDiego, Marta L. title = PATHOGENICITY OF SEVERE ACUTE RESPIRATORY CORONAVIRUS DELETION MUTANTS IN hACE-2 TRANSGENIC MICE date = 2008-07-01 keywords = SARS; δ[6 summary = All these viruses were rescued in monkey (Vero E6) cells and were also infectious for human (Huh-7, Huh7.5.1 and CaCo-2) cell lines and for transgenic (Tg) mice expressing the SARS-CoV receptor human angiotensin converting enzyme-2 (hACE-2), indicating that none of these proteins is essential for the viral cycle. These data indicate that E gene might be a virulence factor influencing replication level, tissue tropism and pathogenicity of SARS-CoV, suggesting that ΔE attenuated viruses are promising vaccine candidates. In contrast, rSARS-CoV-Δ[6-9b] virus was detected at high titers in the brains of infected hACE2 Tg mice suggesting that the E protein is important for virus replication and dissemination within this tissue. Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR doi = 10.1016/j.virol.2008.03.005 id = cord-342220-lrqt2gcw author = Dearlove, Bethany title = A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants date = 2020-09-22 keywords = CoV-2; Fig; SARS; d614 summary = Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute While the evolutionary rate is likely to decrease over time (18) , it is important to monitor the introduction of any mutation that may compromise the potential efficacy of vaccine candidates derived from the first available SARS-CoV-2 sequences. In S, only site 614 was estimated to be under diversifying selection in a majority of subsampled alignments (58%); evidence of diversifying selection indicates that genetic diversity increases in the viral population (i.e., there was a higher proportion of mutations causing an amino acid change than not at site 614, or, the nonsynonymous/synonymous substitution rates ratio, dN/dS, was over 1, P < 0.1) (SI Appendix, Fig. S4 ). doi = 10.1073/pnas.2008281117 id = cord-261110-cnj0e0s9 author = Debarnot, Claire title = Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date = 2011-02-25 keywords = RNA; SARS; complex summary = This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. We present X-ray diffraction data from these SARS-CoV nsp10-nsp16 crystals. The purified SARS-CoV nsp10-nsp16 complex was analyzed by 12% SDS-PAGE and stained using Coomassie Blue. Lane MK, molecular-weight markers; lane 1, 2 mg nsp10-nsp16 protein complex eluted from the Strep-Tactin column. The nsp10-nsp16 complex eluted from the Strep-Tactin column was analyzed on a 16/60 S200 gel-filtration column and the elution of protein and nucleic acid was followed by measuring the absorption at 280 nm (blue) and 260 nm (orange), respectively. The purified SARS-CoV nsp10-nsp16 complex was loaded onto a 4-12% NuPAGE gel and stained using Coomassie Blue. We have crystallized a complex of the SARS-CoV nsp10 and nsp16 proteins. doi = 10.1107/s1744309111002867 id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 keywords = China; East; IBV; MERS; RNA; SARS; bat; coronavirus summary = In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. doi = 10.1016/j.vetmic.2020.108693 id = cord-312036-5867bc6i author = Decker, Annegrit title = Prolonged SARS‐CoV‐2 shedding and mild course of COVID‐19 in a patient after recent heart transplantation date = 2020-06-09 keywords = COVID-19; SARS summary = Here, we present a 62‐year old male COVID‐19 patient with recent heart transplantation who developed only mild symptoms, but had prolonged virus shedding, and summarize the available data on COVID‐19 in cardiac allograft recipients. [5] [6] [7] Here, we report a mild course of SARS-CoV-2 infection with prolonged virus persistence in a patient only five months after heart transplantation. In fact, in 71.8 % of patients with COVID-19 after heart transplant, immunosuppressive agents have been (partially) discontinued or reduced in dose (Table 1) , thus potentially increasing the risk of organ rejection. 19 In our case, continuation of the immunosuppressant regime was associated with a mild course of COVID-19, though we observed a transient increase in CRP and IL-6. Although the cardiovascular system seems to be a critical target site of SARS-CoV-2 infection, a mild course of COVID-19 is possible even in a high-risk patient after recent heart transplantation. doi = 10.1111/ajt.16133 id = cord-280958-36ytqapi author = Decker, Summer J title = 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date = 2020-09-10 keywords = FLNP; SARS summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. doi = 10.1093/cid/ciaa1366 id = cord-269526-3npk3u5t author = Dehghanbanadaki, Hojat title = Bibliometric analysis of global scientific research on Coronavirus (COVID-19) date = 2020-05-23 keywords = COVID-19; SARS summary = Methods: We extracted all COVID-19 documents indexed in the Scopus from December 1, 2019, to April 1, 2020, without any language limitation and determined their bibliometric characteristics, including document type, open accessibility status, citation counting, H-index, top cited documents, the most productive countries, institutions and journals, international collaboration, the most frequent terms and keywords, journal bibliographic coupling and cocitations. The most frequent terms were COVID (n = 983 repeats), patient (n = 741 repeats), SARS-CoV (n = 593 repeats), China (n = 497 repeats), case (n = 464 repeats), nCoV (n = 417 repeats), outbreak (n = 355 repeats), infection (n = 344 repeats), novel coronavirus (n = 324 repeats), Wuhan (n = 269 repeats), Coronavirus (n =243 repeats), virus (n = 204 repeats), pneumonia (n = 195 repeats), Coronavirus disease (n = 170 repeats), treatment (n = 162 repeats), transmission (n = 158 repeats), study (n = 156 repeats), data (n = 151 repeats), country (n = 137 repeats), and epidemic (n = 136 repeats). doi = 10.34171/mjiri.34.51 id = cord-343415-lj2trn85 author = Del Barba, Paolo title = COVID‐19 cardiac involvement in a 38‐day old infant date = 2020-06-18 keywords = COVID-19; SARS summary = We report the case of an infant who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and developed mild cardiovascular inflammation, a novelty for patients of very young age, that contributes to defining the puzzling nature of this disease in pediatric patients. 1 COVID-19 may indeed have cardiac complications, including myocarditis, 2 and up to 31% of children have myocardial enzyme elevation, mainly creatine kinase MB, despite no specific sign or symptom of clinical cardiac disease. For the first time, we report the case of an infant affected by COVID-19 with documented mild cardiac involvement. The chest computed tomograpghy scan was not performed, thus avoiding the exposure to Abbreviations: ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. We suggest that SARS-CoV-2 cardiac involvement should always be taken into account also in children; while our case was mild, it might be of concern especially in patients with other underlying conditions. doi = 10.1002/ppul.24895 id = cord-274028-dvsvtsn0 author = Del Brutto, Oscar H. title = SARS-CoV-2-related mortality in a rural Latin American population date = 2020-08-08 keywords = SARS summary = Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . doi = 10.1016/j.ijid.2020.08.003 id = cord-325498-4yciuh1n author = Del Brutto, Oscar H. title = Incident SARS-CoV-2 Infection and a Shared Latrine date = 2020-07-22 keywords = SARS summary = title: Incident SARS-CoV-2 Infection and a Shared Latrine Incident SARS-CoV-2 Infection and a Shared Latrine. In a recent serosurvey, we found that the use of open latrines (instead of flushing toilet systems) was significantly associated with seropositivity to SARS-CoV-2 on lateral flowbased antibody testing (BIOHIT Health Care Ltd., Cheshire, United Kingdom), suggesting a contributory role for fecal-oral transmission of the disease, as previously proposed by others. Here, we present a cluster of incident cases of SARS-CoV-2 involving a woman who lived alone (house A), and a five-member family (house B) who were seronegative during the first survey. Two weeks after our baseline serosurvey, a 22-year-old grandson of the old woman moved into Atahualpa from Guayaquil (a heavily infected urban center), staying at her house and using the shared latrine. There were no other incident cases in the entire block, where only one person in a distant house had tested positive at baseline, and several other inhabitants of other houses remained seronegative (Figure 2, left) . doi = 10.4269/ajtmh.20-0793 id = cord-285168-qkadqohe author = Delatorre, Edson title = Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries date = 2020-04-23 keywords = CoV-2; SARS summary = Here, we estimate the probable onset date of the community spread of SARS-CoV-2 from the cumulative number of deaths reported during the early stage of the epidemic in Western Europe and the Americas. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analyzed between the middle of January and early February 2020, thus long before community transmission was officially recognized and control measures were implemented. In some countries (Italy and Netherlands) community transmission was traced long before (2-4 weeks) the first confirmed SARS-CoV-2 infection case; while in others (Spain, France, United Kingdom, Germany, and Belgium) the onset date roughly coincides with the time of detection of the first imported cases (Figure 1 ). That quite long period of cryptic community transmission (> 4 weeks) in all analyzed countries draws attention to the great challenge of tracking the early global spread of SARS-CoV-2 and supports that control measures should be adopted at least as soon as first imported cases are detected in a new geographic region. doi = 10.1101/2020.04.20.20073007 id = cord-290056-x74cq2k5 author = Delgado-Roche, Livan title = Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection date = 2020-04-30 keywords = CoV; SARS summary = title: Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) infection Some authors suggest that the onset of severe lung injury in SARS-CoV infected patients depends on activation of the oxidative stress machinery that is coupled with innate immunity and activates transcription factors, such as NF-κB, resulting in an exacerbated proinflammatory host response (14) . Activation of the PI3K/Akt signaling pathway may lead to a delay in Oxidative stress -NF-kB -toll-like receptor (mainly TL4) signaling pathways, triggered by viral pathogens like SARS-CoV, may further amplify the host inflammatory response, ultimately leading to acute lung injury. In conclusion, literature evidence suggests that oxidative stress and chronic low-grade inflammation in the lungs are associated with aging and may contribute to age-related immune dysfunction and mortality risk in aged patients affected by respiratory virus infections, such as SARS-CoV-2. doi = 10.1016/j.arcmed.2020.04.019 id = cord-302733-rfuyd041 author = Dellicour, Simon title = A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date = 2020-10-21 keywords = Belgium; SARS; belgian summary = At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. We generated a time-scaled phylogenetic tree using a rapid maximum likelihood approach 16 and subsequently ran a preliminary discrete phylogeographic analysis along this tree to identify internal nodes and descending clades that likely correspond to distinct introductions into the Belgian territory ( Fig. 1, S2 ). We used the continuous diffusion model 13 available in BEAST 1.10 14 to perform a spatially-explicit (or "continuous") phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. doi = 10.1101/2020.05.05.078758 id = cord-262911-e9z00y3b author = Delpino, M. Victoria title = SARS-CoV-2 Pathogenesis: Imbalance in the Renin-Angiotensin System Favors Lung Fibrosis date = 2020-06-12 keywords = ACE2; SARS; TGF summary = In addition to its functions in regulating blood pressure, AngII plays a pivotal role in signaling cellular and molecular events that are considered critical in the pathogenesis of pulmonary fibrosis, such as: (i) inflammation (promoting production of proinflammatory cytokines such as IL-6, and IL-8 by macrophages), (ii) the production of reactive oxygen species (ROS) among infected-alveolar epithelial cells followed by its apoptosis, and (iii) the proliferation, migration, and differentiation of fibroblasts to myofibroblasts capable of synthesize smooth muscle alpha-actin (α-SMA) and produce extracellular matrix (collagen and fibronectin) through a mechanism mediated by autocratic trans-activation of TGF-β in the fibroblast itself (Wolf et al., 1992; Kagami et al., 1994; Jia, 2016) . In contrast, the Ang1-7 peptide, after interacting with its cellular receptor Mas, exhibits the ability to inhibit proapoptotic signaling in alveolar epithelial cells, promote autophagy, andtogether with the ACE2 receptor-counteract the profibrotic effects, reducing both TGF-β mediated collagen expression, as well as the transition from fibroblasts to myofibroblasts (Iwata et al., 2005; Zeng et al., 2009; Zhou et al., 2016) . doi = 10.3389/fcimb.2020.00340 id = cord-337220-yv7qdvzi author = Demeke, Addis title = Biosensor and molecular-based methods for the detection of human coronaviruses: A review date = 2020-09-08 keywords = COVID-19; SARS; detection summary = This assay involves simultaneous 130 reverse transcription and isothermal amplification using loop-mediated amplification (RT-131 LAMP) for RNA, followed by Cas12 detection of predefined coronavirus sequences, after which 132 cleavage of a reporter molecule confirms detection of the E and N genes of SARS-CoV-2. Rapid lateral flow-based assays for anti-COVID-19 antibodies (IgM and IgG) are under 147 development which will play an important role in the epidemiological investigation of the 148 disease [9] . Therefore, the convalescent plasma has been used as 155 therapy for the treatment of critically ill COVID-19 patients [26, 27] The biosensor was developed by using a spike protein of SARS-CoV-2 immobilized onto the 237 FET graphene sheet (a two-dimensional sheet of hexagonal oriented carbon atom) with 1-pyrene 238 butyric acid N-hydroxy succinimide ester (PBASE) (Figure 1) . Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription 473 loop-mediated isothermal amplification assay doi = 10.1016/j.mcp.2020.101662 id = cord-196129-3zfeamgs author = Demertzis, Konstantinos title = Flattening the COVID-19 Curve: The"Greek"case in the Global Pandemic date = 2020-10-09 keywords = COVID-19; Greece; SARS summary = Focusing on the peculiarities of the disease spreading in Greece, both in epidemiological and in implementation terms, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. Within this context, this paper applies an exploratory analysis of COVID-19 temporal spread in Greece and proposes a methodological approach for the modeling and prediction of the disease based on the Regression Splines algorithm and the change rate of the total infections. This paper studied the COVID-19 temporal spread in Greece and proposed an innovative, realistic, and highly reliable methodology for forecasting the flattening of the curve, based on the spline and logistic regression algorithm, along with the complex network analysis. doi = nan id = cord-311766-m9yv4qkm author = Demey, Baptiste title = Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date = 2020-05-07 keywords = SARS; test summary = Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection. doi = 10.1016/j.jinf.2020.04.033 id = cord-326718-jboiufoq author = Deming, Meagan E. title = COVID-19 and Lessons to Be Learned from Prior Coronavirus Outbreaks date = 2020-07-17 keywords = COVID-19; MERS; SARS summary = In addition, three novel CoVs have emerged as zoonotic human infections in the past 17 years; SARS-CoV, Middle East respiratory syndrome CoV (MERS-CoV), and the 2019 novel CoV (SARS-CoV-2) (2) have each been associated with lower respiratory symptoms, progressing in a subset of individuals to acute respiratory distress syndrome (ARDS) and death. Interestingly NL63, an hCoV that also uses angiotensin converting enzyme 2 as the host receptor, but typically causes mild upper respiratory disease, was the cause of a cluster of severe pediatric pneumonias in China in 2018, during which half of the patients were identified with viruses containing a specific substitution in the spike glycoprotein that enhanced binding to and entry via angiotensin converting enzyme 2 (4). It can be hypothesized that the spike glycoprotein of SARS-CoV-2, with its PERSPECTIVE structural similarity and higher affinity binding to angiotensin converting enzyme 2, provokes a similar mechanism of lung pathology leading to ARDS with severe COVID-19. doi = 10.1513/annalsats.202002-149ps id = cord-336742-42ebj3gi author = Demmler, Gail J title = Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future date = 2003-07-31 keywords = Hong; Kong; SARS summary = The disease, severe acute respiratory syndrome (SARS), spread quickly and caused numerous deaths, as well as public panic. The first report of the new disease, given the name "severe acute respiratory syndrome" (SARS), was received by WHO on February 11 from the Chinese Ministry of Health, which documented that 305 cases and 5 deaths had occurred in the Guangdon Province. 2, 5 By March 5, secondary probable SARS cases were identified among healthcare workers in Hanoi, and at the urging of Dr. Urbani and his colleagues, Vietnam closed the hospital to new patients and visitors on March 11. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: Clinical features of index patient and initial contacts Identification of a novel coronavirus in patients with severe acute respiratory syndrome doi = 10.1016/s1045-1870(03)00056-6 id = cord-354950-kmpbdvof author = Demurtas, Olivia C. title = Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS date = 2016-02-05 keywords = SARS; figure; plant; protein summary = Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. In addition, the WHO guidelines for SARS diagnosis, developed during the outbreak in 2003, suggested the use of N-based ELISA for specific IgG detection as confirmatory test of SARS-CoV infection (World Health Organization [WHO] , 2003 SARS: Laboratory diagnostic tests) due to the ability of the host to mount an early antibody response against the N protein (Che et al., 2004) . As the plant-derived recombinant M protein, the M RLV was also specifically recognized by the mouse anti-M pAb ( Figure 6C ) that had previously validated by Immunofluorescence Antibody Assay (IFA) in SARS CoV infected Vero cells (Carattoli et al., 2005) . doi = 10.3389/fpls.2016.00054 id = cord-270515-bfjdvfuq author = Deng, Chu-Xia title = The global battle against SARS-CoV-2 and COVID-19 date = 2020-03-15 keywords = SARS summary = Compared with its close related coronavirus family member SARS-CoV and MERS-CoV, which infected 8096 and 2494 people in year 2003 and year 2012, respectively, the outbreak of COVID-19 is much more serious with its high virulence. Zheng indicated that SARS-CoV-2 is an emerging new coronavirus that causes a global threat, and summarized the key events occurred during the early outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients, the possible transmission pathways of the virus, the Zhou and Zhao pointed out the great importance of using therapeutic neutralizing antibodies (NAbs) to control the spread and re-emergence of SARS-CoV-2 and assert that the development of NAbs therefore should be a high priority in near future [5] . Understanding the knowledge, attitudes and behaviors of residents towards COVID-19 during the early stage of disease outbreak could help the authority effectively implement preventive and control measures. Traditional Chinese Medicine in the Treatment of Patients Infected with 2019-New Coronavirus (SARS-CoV-2): A Review and Perspective doi = 10.7150/ijbs.45587 id = cord-262936-yo6jf3ng author = Deng, Jia-gang title = Carry forward advantages of traditional medicines in prevention and control of outbreak of COVID-19 pandemic date = 2020-06-02 keywords = COVID-19; SARS; chinese; medicine summary = This paper manly reviews the achievements of the implementation of the epidemic prevention and control plan, advances of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. After the outbreak of COVID-19, the research team of GXUCM responded actively, and the application for two special science and technology projects to prevent and control pneumonia caused by SARS-CoV-2 in Guangxi in 2020 was approved, including Sino-Singapore cooperation for evaluating the effectiveness and application of Guangxi Zhuang/Yao medicines against In summary, this paper manly contents achievements of the implementation of the epidemic prevention and control plan, advance of scientific basic studies on SARS-CoV-2, analysis and screening of potential targets and pathways of antiviral compounds based on network pharmacology and development of antiviral food dual-use products. doi = 10.1016/j.chmed.2020.05.003 id = cord-281081-rifr5uub author = Deng, Junhua title = Serological survey of SARS‐CoV‐2 for experimental, domestic, companion and wild animals excludes intermediate hosts of 35 different species of animals date = 2020-05-07 keywords = ELISA; SARS summary = In this study, 1,914 serum samples from 35 animal species were used for detection of SARS‐CoV‐2‐specific antibodies using double‐antigen sandwich ELISA after validating its specificity and sensitivity. The results showed that no SARS‐CoV‐2‐specific antibodies were detected in above samples which excluded the possibility of 35 animal species as intermediate host for SARS‐CoV‐2. The results showed that no SARS-CoV-2-specific antibodies were detected in above species of animals including pangolin which has been reported as an intermediate host of SARS-CoV-2 (Kangpeng Xiao, 2020) . After confirming the specificity, sensitivity and suitability of SARS-CoV-2 ELISA kit for different species of experimental animals, clinical serum samples from domestic livestock (pig, cow, sheep, horse), poultry (chicken, duck, goose), experimental animal (mice, rat and rhesus monkey), companion animal (dog and cat) and wild animals (camel, fox, mink, alpaca, ferret, bamboo rat, peacock, eagle, tiger rhinoceros, pangolin, leopard cat, jackal, giant panda, masked civet, porcupine, bear, yellow-throated marten, weasel, red pandas and wild boar) were used for antibody detection. doi = 10.1111/tbed.13577 id = cord-271813-nroflfmc author = Deng, Wang title = Positive results for patients with COVID-19 discharged form hospital in Chongqing, China date = 2020-06-19 keywords = COVID-19; SARS summary = METHODS: In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) to determine if they could be released from quarantine. CONCLUSIONS: Multi-site screening of SARS-CoV-2 including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. Among them, 61 patients had positive results of SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (RT-PCR) test, which provided the important information and clinical evidence for the improved management of patients recovered from COVID-19. The study revealed the clinical features of recovered patients with the recurrence of positive results of SARS-CoV-2.Multi-site screening including nasal and pharyngeal swabs, stool and sputum specimens could be considered to improve the diagnosis, treatment and infection control in patients with COVID-19. doi = 10.1186/s12879-020-05151-y id = cord-300174-5pt9jmyz author = Deng, Wei title = Therapeutic efficacy of Pudilan Xiaoyan Oral Liquid (PDL) for COVID-19 in vitro and in vivo date = 2020-05-08 keywords = PDL; SARS summary = 4 Twelve SARS-CoV-2infected hACE2 mice were randomly assigned to the two groups, PDL-treated group and model control group. Next, the viral RNA copies of lung were significantly reduced in SARS-CoV-2-infected hACE2 mice with PDL treatment compared with model control group at 3 dpi (****p < 0.0001, t = 27.94, df = 4) and 5 dpi (p = 0.0021) (Fig. 1c) . These data indicated that PDL had a potent inhibitory effect against SARS-CoV-2 in vitro and in vivo, as well as improved the weight loss caused by the viral replication. To evaluate the efficacy of PDL against pneumonia caused by SARS-CoV-2 infection, the histopathological changes were observed in PDL-treated mice and control mice. These data indicated that the pneumonia in SARS-CoV-2-infected hACE2 mice was relieved after PDL treatment. doi = 10.1038/s41392-020-0176-0 id = cord-312434-yx24golq author = Deng, Ziqin title = Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research date = 2020-09-23 keywords = COVID-19; MERS; SARS; coronavirus; human summary = Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. Therefore, in order to accurately, effectively and systematically reveal connections within the human coronavirus field, our study applied bibliometrics and visualization methods to analyze human coronaviruses-related publications and citations, countries and affiliations, as well as journal performance, author impact and keyword cooccurrence cluster. According to these keywords, human coronavirus diseases like "SARS, " "MERS" and COVID-19 may have something worthwhile for comparison with other "infectious diseases" like "influenza" in their epidemiological characteristics; "healthcare workers, " "transmission, " "surveillance, " "quarantine, " or "isolation" may be the focuses of these studies, which can help to promote current disease control and prevention measures. doi = 10.3389/fcimb.2020.581404 id = cord-304498-ty41xob0 author = Denison, Mark R title = Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date = 2011-03-01 keywords = ExoN; RNA; SARS; genome; virus summary = Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. doi = 10.4161/rna.8.2.15013 id = cord-258844-b4d79m1f author = Denning, M. title = DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY date = 2020-07-18 keywords = SARS; covid-19 summary = Methods From 22nd March 2020 to 18th June 2020, healthcare workers from the United Kingdom, Poland, and Singapore were invited to participate using a self-administered questionnaire comprising the Safety Attitudes Questionnaire (SAQ), Oldenburg Burnout Inventory (OLBI) and Hospital Anxiety and Depression Scale (HADS) to evaluate safety culture, burnout and anxiety/depression. Significant predictors of burnout included patient-facing roles: doctor (OR 2.10; 95% CI 1.49-2.95), nurse (OR 1.38; 95% CI 1.04-1.84), and other clinical staff (OR 2.02; 95% CI 1.45-2.82); being redeployed (OR 1.27; 95% CI 1.02-1.58), bottom quartile SAQ score (OR 2.43; 95% CI 1.98-2.99), anxiety (OR 4.87; 95% CI 3.92-6.06) and depression (OR 4.06; 95% CI 3.04-5.42). This study aims to describe the prevalence and predictors of burnout, anxiety and depression in healthcare workers during the Covid-19 pandemic. The survey consisted of four parts; demographic questions followed by 3 validated psychometric instruments; the Safety Attitudes Questionnaire, Oldenburg Burnout Inventory and Hospital Anxiety and Depression Scale. doi = 10.1101/2020.07.16.20155622 id = cord-258011-19yfwvki author = Deprest, Jan title = SARS‐CoV2 (COVID‐19) infection: is fetal surgery in times of national disasters reasonable? date = 2020-04-22 keywords = COVID-19; SARS summary = 10 From a fetal intervention perspective, we need to appreciate that doing an invasive procedure in a SARS-CoV2 positive woman potentially increases the risk of vertical transmission, similar to what was observed in HIV positive women prior to the introduction of antiviral therapies. With open fetal surgery, the risk of mother-child transmission is likely higher than with needle and fetoscopic procedures as the fetus is exposed to more maternal blood and the fetal skin integrity is usually breached in these interventions. SARS-CoV2 negative patients planned to undergo fetal intervention should be informed that exposure to healthcare professionals, other patients or hospital staff increases their risk of contracting the virus. 5 The risk for an asymptomatic SARS-CoV2-positive pregnant mother to progress to overt COVID-19 disease is unknown, though most sources quote it as ''low'' and not higher than health-and age-equivalent women. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes doi = 10.1002/pd.5702 id = cord-319022-1twsxzcd author = Desai, Antonio title = The role of anti-hypertensive treatment, comorbidities and early introduction of LMWH in the setting of COVID-19: A retrospective, observational study in Northern Italy() date = 2020-09-25 keywords = COVID-19; SARS; ace summary = BACKGROUND: There is a great deal of debate about the role of cardiovascular comorbidities and the chronic use of antihypertensive agents (such as ACE-I and ARBs) on mortality on COVID-19 patients. The aim of the study was to evaluate the role of chronic treatment with ACE-I or ARBs and other clinical predictors on in-hospital mortality in a cohort of COVID-19 patients. As for today, there are discordant results regarding the use of either angiotensin converting enzyme inhibitors (ACE-I) or angiotensin II receptor blockers (ARBs) as for their possible impact on COVID-19 mortality. We found that ACE-I, which acts by inhibiting the conversion from angiotensin I to angiotensin II, showed a trend in protecting from mortality from COVID-19 and was significant in delaying mortality as shown by multivariate Cox regression analysis unlike ARBs, which antagonize the effects of angiotensin II on its receptors 2,3 . Association of Inpatient Use of Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers with Mortality Among Patients With Hypertension Hospitalized With COVID-19 doi = 10.1016/j.ijcard.2020.09.062 id = cord-271919-pbs95hy0 author = Desenclos, Jean-Claude title = Introduction of SARS in France, March–April, 2003 date = 2004-02-17 keywords = PCR; SARS summary = For patients who fulfilled the definition of a probable case, respiratory secretion specimens were taken from the nose, throat, or sputum to detect for SARS-associated coronovirus (CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (7) at the National Reference Center for Influenza (Northern France), Institut Pasteur, Paris. As recommended by WHO, this follow-up included the passengers who sat within two rows of a SARS case-patient on the Air France Hanoi-Paris flight of March 22 and 23, 2003 (14) . Passengers on a flight in which a person with a symptomatic probable case had traveled were informed publicly through the media and mail of the potential exposure and advised to call the emergency service phone number to be evaluated and admitted to the closest university-affiliated infectious disease ward if a fever of >38°C developed within 10 days of the flight. doi = 10.3201/eid1002.030351 id = cord-294812-nnlzwaf1 author = Desforges, Marc title = Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date = 2014-03-12 keywords = CNS; OC43; SARS; human; virus summary = However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . doi = 10.1007/978-81-322-1777-0_6 id = cord-266511-g5h4tazp author = Deslandes, A title = SARS-COV-2 was already spreading in France in late December 2019 date = 2020-05-03 keywords = COV-2; SARS summary = We report here a case of a patient hospitalized in December 2019 in our intensive care, of our hospital in the north of Paris, for hemoptysis with no etiological diagnosis and for which RT-PCR was performed retrospectively on the stored respiratory sample which confirmed the diagnosis of COVID-19 infection. After its onset in December 2019 in China, the new coronavirus (SARS-COV-2) spreads widely in several countries, causing COVID-19 illness. 8 Clinical symptomatology between COVID-19 and ILIis similar,we therefore decided retrospectively to look for SARS-COV2 in respiratory samples collected in the intensive care units (ICUs) of our hospital near Paris. We reviewed medical record of ICUs patients admitted for ILI between December 2, 2019 and January 16, 2020, with a negative RT-PCR performed at admission. Samples taken from patients with both ILI symptoms (fever higher than 38.5°C, cough, rhinitis, sore throat or myalgia) and ground glass opacity according to their medical record underwent SARS-COV-2 RT-PCR. doi = 10.1016/j.ijantimicag.2020.106006 id = cord-280423-v3r7vo0o author = Desmazes‐Dufeu, Nadine title = Discordant courses of COVID‐19 in a cohabiting couple of lung transplant recipients date = 2020-07-31 keywords = SARS; covid-19 summary = Solid organ transplant recipients are perceived to be at increased risk of severe COVID‐19 due to their chronic use of immunosuppressive drugs (ISDs) and to their associated conditions. We report here two cases of COVID‐19 in a cohabiting couple of lung transplant recipients for cystic fibrosis, who had different ISDs management and who developed discordant courses of their disease. We report here two cases of synchronic COVID-19 in a cohabiting couple of lung transplant recipients for cystic fibrosis but who had discordant courses of their disease. 13 While lymphopenia and lower CD4 + and CD8 + lymphocytes count have been associated with worst outcome and prolonged viral shedding in the general population of COVID-19 patients, 14 other reports suggested that ISDs per se might diminish the "cytokine storm" underlying the development of acute respiratory distress syndrome (ARDS) and subsequent mortality. doi = 10.1111/tid.13410 id = cord-355122-x3v80bdp author = Desterke, Christophe title = PPARγ cistrome repression during activation of lung monocyte-macrophages in severe COVID-19 date = 2020-09-25 keywords = SARS; Supplemental; cell; covid-19; figure; lung summary = Overall, these results demonstrate for the first time, the involvement of the PPARγ complex in severe COVID-19 lung disease and suggest strongly its role in the major monocyte / macrophage-mediated inflammatory storm. A differentially expressed gene (DEG) analysis was performed on lung biopsies from COVID-19 patients and healthy donors; this revealed widespread repression of many gene pathways in COVID-19 lungs (Supplemental Figures 4A-4B) , which could affect major functionalities of the cells in this organ. Specifically, the gene-set enrichment analysis (performed using the ''hallmarks'' gene set of the MsigDB database) highlighted repression of the mitosis spindle and p53 pathway (cell cycle gatekeeper) in samples of COVID-19 lungs compared to those of healthy donors (NES = -3.45 and -2.77, respectively, with p-value<0.001, Supplemental Figure 5A ). Mononuclear cells, monocytes, and macrophages were found in positions similar to the COVID-19 lung samples, suggesting major infiltrations in this tissue (Supplemental Figure 4E ) and confirming the results of the ''xcell'' immune score analysis (Supplemental Figure 4C ). doi = 10.1016/j.isci.2020.101611 id = cord-311264-zn7ydrvh author = Deurenberg-Yap, M. title = The Singaporean response to the SARS outbreak: knowledge sufficiency versus public trust date = 2005-06-17 keywords = SARS; knowledge; measure summary = In this paper, the informing seeking and processing mindset of Singaporeans during a severe outbreak situation is assessed by testing the level of knowledge on SARS and its preventive/ control measures following the earlier communication efforts and subsequent public education campaign. More than nine out of 10 respondents thought that infection control measures undertaken at hospitals were Overall, the public trust index was high at 11.4 out of a maximum score of 14, with no significant difference between gender, age groups and educational levels. First, while knowledge about infection control measures undertaken at TTSH was low (mean per cent score of 20 ± 16%), the level of confidence was high, with 82% of the respondents expressing confidence in the hospital''s ability to deal with SARS. doi = 10.1093/heapro/dai010 id = cord-287410-boxxlopy author = Devi, Arpita title = In silico designing of multi-epitope vaccine construct against human coronavirus infections date = 2020-08-10 keywords = SARS; construct; protein; vaccine summary = Band T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. To predict the probable immune response of the designed multi-epitope vaccine construct in human immune system, in silico immune simulations were conducted using the C-ImmSim server (http://150.146.2.1/C-IMMSIM/index.php) (Rapin et al., 2010) . C-ImmSim is a novel in silico approach for the study of the mammalian immune system The tool is a combination of a mesoscopic scale simulator of the immune system with machine learning techniques for molecular-level predictions of major histocompatibility complex (MHC)-peptide-binding interactions, linear B-cell epitope discovery, and protein-protein potential estimation. The antigenicity of the vaccine construct including the adjuvant sequence and His-tag was predicted by the VaxiJen 2.0 server to be 0.6452 with a bacteria model at a threshold of 0.4. doi = 10.1080/07391102.2020.1804460 id = cord-325377-g68onkjt author = Dey, Anusree title = COVID-19: Scientific Overview of the global Pandemic date = 2020-10-28 keywords = Coronavirus; SARS summary = COVID-19 (Coronavirus Disease 2019) is the disease caused by the novel Coronavirus, SARS-CoV-2. This review gives a broad insight into different aspects of the COVID-19 disease, introduction to SARS-CoV-2, mitigation strategies, present status of diagnostics and therapeutics. According to the global data as well as the early estimates from China, both old 69 J o u r n a l P r e -p r o o f age and comorbidities may render the patients at higher risk of developing severe disease or 70 death due to COVID-19 infection, perhaps due to a weaker immune functioning [8, 10] . Interestingly, in an independent study, researchers have found 124 three blood based biomarkers which can predict disease severity at least ten days in advance 125 with more than 90% accuracy, based on a database of 485 infected patients from Wuhan, 126 doi = 10.1016/j.nmni.2020.100800 id = cord-298301-p1zj6jg9 author = Dey, Lopamudra title = Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins date = 2020-09-03 keywords = COVID-19; PPI; SARS; human; protein summary = title: Machine Learning Techniques for Sequence-based Prediction of Viral-Host Interactions between SARS-CoV-2 and Human Proteins A total of 1326 potential human target proteins of SARS-CoV-2 have been predicted by the proposed ensemble model and validated using gene ontology and KEGG pathway enrichment analysis. In this article, we have tried to predict the target human proteins of the SARS-CoV-2 virus based on their protein sequences combining amino acid composition, pseudo amino acid composition, and conjoint triad features using machine learning techniques. Subsequently, after feature reduction, we have used some popular supervised learning algorithms such as Support Vector Machine (SVM), Naive Bayes (NB), Random Forest (RF) and K-Nearest Neighbor (KNN) along with a deep multi-layer perceptron model and ensemble techniques (Voting classifier, XGBoost, AdaBoost) for classification and prediction. A total of 3 sets of sequence-based features, namely, amino acid composition, conjoint triad, and pseudo amino acid composition of the human proteins are considered to train the machine learning models. doi = 10.1016/j.bj.2020.08.003 id = cord-279255-v861kk0i author = Dhama, Kuldeep title = Coronavirus Disease 2019–COVID-19 date = 2020-06-24 keywords = COVID-19; China; CoV-2; MERS; SARS; Wuhan; clinical; coronavirus; human; infection; novel; outbreak summary = Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . Health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel CoV (originally named 2019-nCoV), which was first identified in Wuhan City, Hubei Province, China, on 12 December 2019. doi = 10.1128/cmr.00028-20 id = cord-327063-ea7a1xfl author = Dhama, Kuldeep title = SARS-CoV-2 jumping the species barrier: zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus date = 2020-08-02 keywords = COVID-19; China; CoV-2; Coronavirus; Health; MERS; SARS; human summary = The present review presents a comprehensive overview of COVID-19 and SARS-CoV-2, with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from SARSand MERS-CoVs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease. Further research exploring the SARS-CoV-2 associated zoonosis and mechanisms accounting for its initial transmission from animals to humans, will lead to sort out the spread of this virus as well as design and develop appropriate prevention and control strategies to counter COVID-19. The present comprehensive manuscript presents an overview on COVID-19, an emerging SARS-CoV-2 infectious disease while focusing mainly on the events and circumstantial evidences with regards to this virus jumping the species barriers, sharing a few lessons learned from SARS-and MERS-CoVs, zoonotic spillover events (zoonosis), acquiring transmission ability to infect humans, and adopting appropriate preventive and control measures [42] . doi = 10.1016/j.tmaid.2020.101830 id = cord-253124-s3pa4n8a author = Dhamad, Ahmed E. title = COVID-19: molecular and serological detection methods date = 2020-10-07 keywords = COVID-19; SARS; method summary = Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. And the top keywords that searched were: COVID-19, SARS-CoV-2, coronavirus, genomic RNA, protein structure, ACE2, transmission, symptoms, molecular detection methods, serological detection methods, rRT-PCR, ID NOW COVID-19, isothermal amplification, CRISPR, SARS-CoV-2 DETECTR, LAMP, recombinase polymerase amplification (RPA), Lateral flow assay (LFA) and Enzyme-linked immunosorbent assay (ELISA). In this method (e.g., SARS-CoV-2 DETECTR), the RNA virus is extracted from a specimen and designated regions of N2, E, RP genes are amplified at 62 C for 20 min by specific primes through Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) approach Lamb et al., 2020; Hong et al., 2004) . Unlike molecular methods, serological methods (also called antibody tests) can be applied to detect past and current SARS-CoV-2 infection and monitor the progress of the disease periods and immune response. doi = 10.7717/peerj.10180 id = cord-333200-yka7wfbi author = Dhampalwar, Swapnil title = Treatment armamentarium of COVID-19: Evolving strategies & evidence so far date = 2020-07-16 keywords = SARS; covid-19 summary = Keeping up with this current pace of information, we review the clinical studies of different therapeutic options available to treat SARS-CoV-2. (20) Since, these studies with CQ & HCQ have different therapeutic regimens, heterogenous study population, unequal arms to compare, ill-defined outcomes, and non-reproducible results; further randomized trials are needed before recommending the routine use of HCQ in mild COVID-19. Since Favipiravir and Lopinavir-ritonavir did not provide significant benefits in viral clearance or clinical improvement in severe disease, further randomized trials are necessary before recommending these drugs in clinical practice. A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an openlabel non-randomized clinical trial No Evidence of Rapid Antiviral Clearance or Clinical Benefit with the Combination of Hydroxychloroquine and Azithromycin in Patients with Severe COVID-19 Infection doi = 10.1016/j.jceh.2020.07.001 id = cord-024080-eh3ztsv5 author = Dheda, Keertan title = Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date = 2020-04-17 keywords = PCR; SARS; covid-19 summary = Recent data from infections in special contexts such as cruise liners (9) and in close contacts of COVID-19 patients (10) have demonstrated that SARS-CoV-2-specific RT-PCR may be positive in the early phase of the disease, and that viral shedding in the asymptomatic phase and in the early prodromal phase can be considerable. (19) This false negativity phenomenon may be due to several factors, including a low viral load below the detection limit of the assay, low sample volume or cellular mass during acquisition, sampling location (upper versus lower respiratory tract), sample degradation during transport or storage, sample processing methodology and the timing of sampling in relation to the stage of the disease (RT-PCR positivity may progressively increase during the course of the disease). In patients with more severe diseases, including those with lower respiratory tract infection, but also in individuals with mild disease, high viral loads can be detected often for several days after the resolution of symptoms. doi = 10.18772/26180197.2020.v2nsia1 id = cord-320149-3q4q98a6 author = Di Carlo, Davide Tiziano title = Exploring the clinical association between neurological symptoms and COVID-19 pandemic outbreak: a systematic review of current literature date = 2020-08-01 keywords = SARS; covid-19; patient summary = An increasing body of evidence suggests that patients with the coronavirus disease (COVID-19) might have a heterogeneous spectrum of neurological symptoms METHODS: A systematic search of two databases was performed for studies published up to May 29th, 2020. The pathophysiology of this association is under investigation and warrants additional studies, Physicians should be aware of this possible association because during the epidemic period of COVID-19, early recognition of neurologic manifestations otherwise not explained would raise the suspect of acute respiratory syndrome coronavirus 2 infection. Our systematic review of 2499 patients reported the occurrence of a wide spectrum of neurologic complications in hospitalized patients with laboratory-confirmed COVID-19 infection, supporting the possible neuroinvasive potential of SARS-CoV-2. Recently, several case reports described the occurrence of ischemic and hemorrhagic stroke (see supplementary material 1), confirming the association of cerebrovascular complications with severe COVID-19 infection, older age, and the presence of multiple comorbidity [46, 47] . doi = 10.1007/s00415-020-09978-y id = cord-315970-m5o962yw author = Di Ciaula, Agostino title = COVID‐19, internists and resilience: the north‐south Italy outbreak. date = 2020-06-01 keywords = Italy; SARS; covid-19; patient summary = The rates of infected subjects and deaths in Italy (whole country and regional level) per 100,000 residents were calculated considering the official number of residents derived from the National Institute of Statistics (ISTAT). Figure 1 summarizes the daily progression in the cumulative number of COVID-19 positive subjects and in the incidence of deaths related to COVID-19 in southern and northern Italy, since the start of the outbreak. On the national "lockdown" day (March 12), in northern Italy there was a total of 14,335 infected patients and 997 COVID-19 related deaths. Following the COVID-19 outbreak, the local Apulian government firstly increased the number of available beds in the units of intensive care, pneumology, and infectious diseases across the Region. In the most affected regions (northern Italy, mainly Lombardy) serious concerns existed about the effective capacity of the national health system to adequately face the burden of disease. doi = 10.1111/eci.13299 id = cord-268224-5tbb8df1 author = Di Gioacchino, Andrea title = The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date = 2020-08-27 keywords = Fig; ORF; SARS summary = Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven, in the N protein coding region, both by the viral codon bias and by the high value of the CpG content, leading to a loss in CpG. Finally we use a model of the viral gene evolution under human host pressure, characterized by the CpG force, to study synonymous mutations, and in particular those which change CpG content, observed since the SARS-CoV-2 entered the human population (Sec. 2.3). We first compute the global force on CpG dinucleotides for SARS-Cov-2 and a variety of other viruses from the Coronaviridae family affecting humans or other mammals (bat, pangolin), see Fig. 1a , using as null model the nucleotide usage calculated from human genome [22] (see Methods Sec. 4.2) 1 . doi = 10.1101/2020.05.06.074039 id = cord-256351-q8lkhklw author = Di Giorgio, Angelo title = Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy date = 2020-05-12 keywords = COVID-19; SARS summary = title: Health status of patients with Autoimmune Liver Disease during SARS-CoV-2 outbreak in northern Italy Twenty-six per cent (n= 39) developed mild/moderate respiratory symptoms likely due to an underlying SARS-CoV-2 infection; however, since the NPS was not carried out, they were classified as suspected cases of COVID-19. cases; the majority of them (3/4 patients, 75%) presented with a mild or moderate clinical phenotype (1 was asymptomatic) whilst 1 patient died ; this patient had risk factors for complicated COVID-19 described in the general population, including old age and associated comorbidities. We previously reported our review of past outbreaks of coronavirus infections and our preliminary experience with these patients followed in our center, and we suggested that immunocompromised patients (adults and children) are not at increased risk of COVID-19 complicated course compared to the general population (3). However we recently reported the uneventful course of patients with inflammatory bowel disease who were under IS or immunomodulating drugs, including antimetabolites, during the SARS-CoV-2 epidemic (4). doi = 10.1016/j.jhep.2020.05.008 id = cord-258067-par61wwh author = Di Martino, Marcello title = Elective Surgery During the SARS-CoV-2 Pandemic (COVID-19): A Morbimortality Analysis and Recommendations on Patient Prioritisation and Security Measures date = 2020-06-20 keywords = COVID-19; SARS; patient summary = Conclusions The patients undergoing the surgical procedures showed high rates of COVID-19 infection and postoperative complications, especially the patients with oncological diseases. The following variables were analysed: age; sex; functional status (defined according to the ECOG scale) (21); personal background; diagnosis; type of surgical intervention; the timing of SARS-CoV-2 infection; the treatment required (Table 1) ; the severity of the respiratory infection (according to the BRCSS) (20) ; and postoperative complications (according to the Dindo-Clavien classification) (19) . Ten (16.9%) of the oncological patients, one (1%) of those operated on electively for benign diseases and four (7%) of the urgent surgery group presented with a SARS-CoV-2 infection, with statistically significant differences in the infection rate of the three groups (p = 0.004) ( Table 2) . Patients undergoing elective surgery before and during the peak of the COVID-19 pandemic showed a high rate of postoperative complications, with a SARS-CoV-2 infection rate of up to 16% in patients undergoing oncologic surgical procedures. doi = 10.1016/j.cireng.2020.06.005 id = cord-281528-xy8j5jiv author = Di Paola, Luisa title = The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach date = 2020-06-17 keywords = ACE2; AMR; SARS; figure; protein summary = All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein. We also provided biophysical evidence based on the elastic network modeling (ENM) approach, combined with perturbation-response scanning (PRS) 36 that AMRs in both viruses acted as a mediator of intermolecular allostery between the S protein and ACE2. The map of the participation coefficient projected onto the ribbon structure of the SARS-CoV/ACE2 complex ( Figure 1C ) shows an active region (P > 0) in the junction between the fusion peptide and the trimeric bulk phase of the spike protein. doi = 10.1021/acs.jproteome.0c00273 id = cord-268425-xg8xnjf9 author = DiNicolantonio, James J. title = Harnessing Adenosine A2A Receptors as a Strategy for Suppressing the Lung Inflammation and Thrombotic Complications of COVID-19: Potential of Pentoxifylline and Dipyridamole date = 2020-07-02 keywords = COVID-19; HCQ; PTX; SARS summary = 5 Importantly, neutrophils, whose activation and transit into lung interstitial tissue and alveolar space is a key mediator of the respiratory distress syndrome associated with COVID-19, are highly responsive to the functionally suppressive effects of A2AR, as are the endothelial cells whose activation attracts and enables transendothelial passage of activated neutrophils. Most studies with DIP have focused on its platelet-stabilizing effects -which presumably could provide some protection from SARS-CoV-2''s pro-thrombotic effects -but experimental studies also show that DIP can act on neutrophils to suppress superoxide production, adhesion to endothelial cells, and, in a mouse model of anti-phospholipid syndrome (a sometime feature of COVID-19), NETosis formation. 79 Supplemental glucosamine may likewise up-regulate the type 1 interferon responses to viruses, while exerting anti-inflammatory effects that render it protective in rodent models of sepsis and lung inflammation induced by LPS or cigarette smoke. doi = 10.1016/j.mehy.2020.110051 id = cord-262726-lfuxhlki author = Diallo, Aïssatou Bailo title = Daytime variation in SARS-CoV-2 infection and cytokine production date = 2020-09-11 keywords = SARS summary = Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). We analyzed circadian rhythm implication in SARS-CoV-2 virus infection of isolated human monocytes, key actor cells in Covid-19 disease, from healthy subjects. Importance The implication of circadian rhythm (CR) in pathogenesis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been recently anticipated. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. Our results suggest that time day of SARS-CoV-2 infection affects viral infection and host immune response. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. In this study, we wondered 76 if SARS-CoV-2 infection and cytokine production by human monocytes, innate immune cells 77 affected by Covid-19, were regulated by CR. doi = 10.1101/2020.09.09.290718 id = cord-257789-pdybfft6 author = Diamond, Betty title = SARS-CoV-2 and interferon blockade date = 2020-11-09 keywords = ACE2; SARS; covid-19 summary = We propose that SARS-CoV-2 activates the innate immune system through the renin-angiotensin and kallikrein-bradykinin pathways, blocks interferon production and reduces an effective adaptive immune response. Here we propose that the systemic inflammation seen in Covid-19 patients results from the activation of two intersecting systems, the renin-angiotensin system (RAS) and the kallikrein-bradykinin system (Diamond 2020) . The engagement of these pathways helps explain how severe Covid-19 infection is characterized by massive inflammation in multiple target organs, a poor anti-viral response with little production of interferon, and little participation of the adaptive immune system. As we have hypothesized that some of the inflammation induced in severe, and perhaps even moderate, Covid-19 is the result of dysregulation of the RAS and kallikrein-bradykinin pathways, the associated players serve as potential therapeutic targets ( Fig. 1 ) As mentioned above, ACE inhibitors and AT1 blockers (ARBs) are approved and safe drugs. doi = 10.1186/s10020-020-00231-w id = cord-331786-wgt7kg6f author = Diego-Martin, Borja title = Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date = 2020-10-13 keywords = Fig; RBD; SARS; antibody summary = For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Finally, we performed sandwich ELISA tests of sybody17 and nanobody72 ( Fig 5E and Fig 5F, respectively) using the total and concentrated apoplastic fluid as detection reagent against serial dilutions of crude plant extracts from RBD-producing plants, showing that this simple antibody preparation can be directly employed in detection procedures without the need of additional purification steps. doi = 10.1101/2020.10.13.331306 id = cord-335347-vxl2flbn author = Diercks, Gillian R. title = Asymptomatic COVID-19 Infection in a Child with Nasal Foreign Body date = 2020-05-08 keywords = COVID-19; SARS summary = Aerosolized SARS-CoV-2 viral particles have been shown to remain viable for up to 3 hours 10 , raising concern about risk of exposure for healthcare workers during aerosol generating procedures (APGs), including endoscopy, in the nasal cavity, nasopharynx and upper airway. Prior to bringing the patient to the operating room, COVID-19 testing was pursued given concerns about the potential for asymptomatic infection in the pediatric population, and generation of aerosolized respiratory secretions during nasal endoscopy, suctioning and foreign body removal, in order to optimize protection of the perioperative care team and surgical staff. Preoperative planning and SARS-CoV2 testing is of particular importance for the pediatric population given the high proportion of SARS-CoV-2 infected children who are asymptomatic or exhibit minimal symptoms of COVID-19, but who may harbor significant viral loads in the nasopharynx and upper airway, placing healthcare workers at particular risk. doi = 10.1016/j.ijporl.2020.110092 id = cord-282771-iwpx02v3 author = Dietzel, Steffen title = A joint action in times of pandemic: the German BioImaging recommendations for operating imaging core facilities during the SARS‐Cov‐2 emergency date = 2020-06-24 keywords = SARS; SRL; german summary = To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS‐CoV‐2 between users and staff. The outcome of this workshop, the first version of the "German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic" was published on the GerBI-GMB website a few days after the meeting. The aim of these recommendations is to help protecting users and staff working in a low-safety environment (mostly biosafety level 1) from accidental contagion by yet unidentified, asymptomatic SARS-CoV-2 carriers, and are based on our current still fragmentary knowledge of this virus. Thus, all surfaces that might get touched by different users during operating a microscope are to be disinfected before and after each usage to avoid potential spread of SARS-CoV-2 via this route. German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic doi = 10.1002/cyto.a.24178 id = cord-281717-kzd9vvci author = Digard, Paul title = Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date = 2020-05-08 keywords = Fig; ORF; RNA; SARS summary = CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . doi = 10.1101/2020.05.08.083816 id = cord-300696-alpztpzw author = Dilek, Tugce Damla title = THE IMPACT OF SARS-COV 2 ON THE ANXIETY LEVELS OF SUBJECTS AND ON THE ANXIETY AND DEPRESSION LEVELS OF THEIR PARENTS date = 2020-10-26 keywords = SARS; STAI summary = This study was conducted to evaluate the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety depression status of their parents. In this study, we aimed to evaluate the the impact of SARS-CoV2 pandemic on daily lives of children with MS, and the anxiety status of these patients and anxiety -depression status of their parents. Disease flares, problems about reaching the hospitals, and medication, any history of contact with confirmed SARS-CoV2 infections of self or family members, encounters with digital screen, workout program, caring about diet, use of vitamins, direct exposure to sunlight, obeying the 14 rules recommended by the Ministry of Health and similar issues were questioned in the survey. The patient and control groups were compared according to STAI scores to investigate the anxiety status during SARS-CoV2 pandemic. doi = 10.1016/j.msard.2020.102595 id = cord-334584-xh41koro author = Dilucca, Maddalena title = Temporal evolution and adaptation of SARS-COV 2 codon usage date = 2020-05-29 keywords = CAI; SARS; codon summary = Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), non-structural 3C-like proteinase (3CLpro), ssRNA-binding protein (RBP), 2''-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase, RNA-dependent RNA polymerase (RdRp), Nsp7, Nsp8, and exonuclease ExoN. An EN C plot analysis was performed to estimate the relative contributions of mutational bias and natural selection in shaping CUB of 13 genes encoding proteins that are crucial for SARS-CoV-2. For the funtionally important genes in each genome, we calculated the average values of CAI and ENC over time, as compared to the reference SARS-CoV-2 sequence (WSM). Based on the SiD combined with the CAI results ( Figure 5 ), we suggest that SARS-CoV-2, over time, has preferentially accumulated mutations in its genome which correspond to codons that adapt better to the human host. doi = 10.1101/2020.05.29.123976 id = cord-333453-v3gap8kj author = Dima, Mirabela title = First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date = 2020-08-14 keywords = PCR; SARS; patient summary = The novel coronavirus officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Virus generated a pandemic, which erupted in Hubei, Wuhan, China and quickly spread throughout the world, [1, 2] has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. The clinic where the patient was born discharged her and the mother on April 6, 2020 both being negative for SARS-CoV-2 (RT-PCR test). On April 15, after 3 days of observing cough, lethargy, loss of appetite, jaundice, and constant fever, the mother presented in emergency room with the newborn, both being tested positive for SARS-CoV-2. [10] We believe it is important in the current epidemiologic context to mention that all 3 patients were discharged from the clinic where they were born with SARS-CoV-2 negative tests (RT-PCR), which were taken in conformity with our national protocol regarding COVID-19. doi = 10.1097/md.0000000000021284 id = cord-256633-vls23fu5 author = Dimeglio, Chloé title = The SARS-CoV-2 seroprevalence is the key factor for deconfinement in France date = 2020-04-29 keywords = SARS summary = We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. We have designed a model for predicting the evolution of the SARS-CoV-2 epidemic in France, which is based on seroprevalence and makes it possible to anticipate the deconfinement strategy. Our statistical model for predicting the spread of SARS-CoV-2 in France is based on a diffusion and transmission coefficient that varies with an individual''s age, the likelihood of contagion, and two administration parameters (confinement and quarantine). Figures 1.b, 1 .c, 1.d, 1.e showed predictions of new cases per day depending on the SARS-CoV-2 seroprevalence before and after the containment phase. Our data indicate that seroprevalence must reach approximately 50% after total deconfinement on May 11 or a gradual exit phase over several months starting on May 11 if an infection rebound is to be avoided (Figure 1 .d, 1.e and Figure 2 .b). doi = 10.1016/j.jinf.2020.04.031 id = cord-268335-mfcjldu3 author = Dimeglio, Chloé title = Children are protected against SARS-CoV-2 infection date = 2020-05-20 keywords = SARS summary = Chloé Dimeglio 1,2* , Jean-Michel Mansuy 2 , Sandrine Charpentier 3,4 , Isabelle Claudet 4,5 , and Jacques Izopet 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. As infants and young children infected with respiratory tract viruses are particularly at risk of hospitalization (3) the paucity of pediatric patients with COVID-19 has raised many questions for clinicians, epidemiologists and scientists. The study previously published by Lancet Infectious Disease has important implications for the clinical management of these patients and the social distancing needed to prevent virus transmission (4). The abovementioned study has found that children are susceptible to SARS-CoV-2 infection, but rarely display any physical signs of the disease. The most important finding emerging from this analysis is the clear evidence that children are less susceptible to SARS-CoV-2 infection than adults. While children have been regarded as facilitators of virus transmission, we now need to identify the mechanism which protects them, at least partially, against SARS-CoV-2 infection. doi = 10.1016/j.jcv.2020.104451 id = cord-017070-05vlz5dn author = Dimitrov, Dimiter S. title = Human Monoclonal Antibodies Against HIV and Emerging Viruses date = 2008 keywords = HIV; SARS; antibody; virus summary = These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1007/978-1-59745-569-5_34 id = cord-303377-lkewcf8a author = Dimke, H. title = Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date = 2020-05-27 keywords = AGPC; RNA; SARS summary = Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. A total of 87 clinical sample specimens were chosen based on SARS-CoV-2 status from the Cobas ® 6800 system and used to evaluate the analytical sensitivity, specificity and accuracy of our in-house SARS-CoV-2 RT-qPCR assay after RNA purification using the Maxwell ® RSC 48 and AGPC methods. The AGPC method delivers high analytical sensitivity, specificity and accuracy for SARS-CoV-2 testing To evaluate whether conventional AGPC based extraction of RNA could serve as a viable alternative to automated systems with respect to reliability and accuracy, we isolated RNA using the AGPC method from 87 clinical specimens (oropharyngeal or nasopharyngeal swabs) with known SARS-CoV-2 status (57 positive and 30 negative), and performed a side-by-side comparison with the identical samples extracted on a Maxwell ® RSC 48 instrument. doi = 10.1101/2020.05.26.20099440 id = cord-284829-dge21g0g author = Dinakaran, Damodharan title = Neuropsychiatric aspects of COVID-19 Pandemic: A Selective Review date = 2020-05-30 keywords = Barre; COVID-19; SARS summary = In this selective review, the authors present the neuropsychiatric manifestations and postulated mechanisms of COVID-19. Though the most common presentation is a self limiting viral illness with fever and dry cough, severe infection is reported in 15-20% of the affected population (26) . In about 5% of the severely ill patients, Acute Respiratory Distress Syndrome (ARDS), Multi organ involvement and septic shock leads to further clinical deterioration. Acute polyradiculopathy (Guillain Barre Syndrome -GBS) has been reported related to SARS-CoV-2 infection (41) (42) (43) (44) (45) (46) . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain Barre syndrome associated with COVID-19 infection: A case report doi = 10.1016/j.ajp.2020.102188 id = cord-348777-pk9y6vfp author = Ding, Cheng title = Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date = 2020-09-28 keywords = COVID-19; RNA; SARS summary = title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Our observational results revealed that corticosteroid therapy had no positive effect on the durations of SARS-CoV-2 RNA clearance among patients with mild COVID-19. Results from this study suggested that patients with mild COVID-19 may not benefit from corticosteroid therapy in terms of the duration of SARS-CoV-2 clearance. doi = 10.1007/s40121-020-00337-y id = cord-346263-8znpqcth author = Ding, Huiling title = Transnational Quarantine Rhetorics: Public Mobilization in SARS and in H1N1 Flu date = 2014-04-13 keywords = April; Beijing; China; H1N1; SARS; asian; quarantine summary = This essay examines how Chinese governments, local communities, and overseas Chinese in North America responded to the perceived health risks of Severe Acute Respiratory Syndrome (SARS) and H1N1 flu through the use of public and participatory rhetoric about risk and quarantines. One instance of mandatory quarantine is the widespread use of community entry surveillance tools such as temperature monitoring and health registration forms to identify floating people returning from severely SARS affected regions such as Guangdong or Beijing. As a sharp contrast to Asian American and Asian Canadian''s use of coerced quarantines as responses to racial targeting in SARS, overseas Chinese from H1N1 epicenters implemented voluntary quarantines when travelling back to China to reduce potential health risks they might have posed to local communities and the nation. doi = 10.1007/s10912-014-9282-8 id = cord-319519-mb9ofh12 author = Ding, J. title = A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes'' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date = 2020-07-02 keywords = COVID-19; HLH; SARS; gene summary = The algorithm establishes the shortest path between 118 the candidate genes and the known host interacting proteins with SARS-CoV-2 and calculates an 119 overall connectivity score for the network (a smaller value represents a greater connectivity) ( Fig 120 1 and Supplementary Table S1 ). The network-informed analysis presented in this paper, 262 revealed that 1) the top GO biological function associated with HLH genes is neutrophil 263 degranulation, consistent with a recent report highlighting the undervalued role of neutrophils in 264 HLH 36 ; 2) HLH genes are significantly enriched with the SARS-CoV-2 human interactome; 3) the 265 top-ranked HLH gene, AP3B1, has roles in cargo loading of type II pneumocytes, where it may 266 interact with SARS-CoV-2 to disturb surfactant physiological functions to promote 267 inflammation/pro-coagulation activities; 4) diseases/syndromes-associated with increased release 268 of Neutrophil Extracellular Traps (NETs) may predict vulnerable populations, including those 269 affecting children. doi = 10.1101/2020.07.01.20144121 id = cord-334833-7gv1c7we author = Ding, Yanqing title = The clinical pathology of severe acute respiratory syndrome (SARS): a report from China date = 2003-07-01 keywords = SARS; cell; figure summary = The pulmonary lesions included bilateral extensive consolidation, localized haemorrhage and necrosis, desquamative pulmonary alveolitis and bronchitis, proliferation and desquamation of alveolar epithelial cells, exudation of protein and monocytes, lymphocytes and plasma cells in alveoli, hyaline membrane formation, and viral inclusion bodies in alveolar epithelial cells. Systemic vasculitis included oedema, localized fibrinoid necrosis, and infiltration of monocytes, lymphocytes, and plasma cells into vessel walls in the heart, lung, liver, kidney, adrenal gland, and the stroma of striated muscles. With regard to the aetiology and pathogenesis of SARS, this study has demonstrated extensive pulmonary consolidation; significant pulmonary oedema; localized haemorrhage and necrosis; widespread hyaline membrane formation; a local inflammatory reaction consisting mostly of monocytes, lymphocytes, and plasma cells; desquamation of bronchial and alveolar epithelial cells; numerous multinucleate and mononuclear giant cells in pulmonary alveoli in two cases; and typical viral inclusion bodies in epithelial cells in alveoli in all the three cases. doi = 10.1002/path.1440 id = cord-023862-fakapdcc author = Dinman, Jonathan D. title = Programmed –1 Ribosomal Frameshifting in SARS Coronavirus date = 2009-07-22 keywords = PRF; SARS summary = doi = 10.1007/978-3-642-03683-5_5 id = cord-344246-sf9cymhc author = Diriba, Kuma title = The effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and the possibility of vertical maternal–fetal transmission: a systematic review and meta-analysis date = 2020-09-04 keywords = COVID-19; MERS; SARS; pregnant summary = Previous outbreaks of coronaviruses include the severe acute respiratory syndrome (SARS)-CoV epidemic in 2003 [2] and the Middle East respiratory syndrome (MERS)-CoV in 2012 [3] , while the newly emergent coronavirus, initially referred to as 2019-nCoV and subsequently termed SARS-CoV-2, the disease it produces has been termed COVID-19, which causes respiratory infection and can progress to severe pneumonia and, in a small number of cases, death [4] . A systematic review and meta-analysis was aimed to assess the effect of coronavirus infection (SARS-CoV-2, MERS-CoV, and SARS-CoV) during pregnancy and its possibility of vertical maternal-fetal transmission following the methodological framework suggested by Arksey and O''Malley [15] . The primary outcome variable of this study was the pregnancy outcomes observed, listed as follows: preterm birth (PTB; either before 37 or 34 weeks of gestation), preeclampsia, preterm prelabor rupture of membranes, (pPROM), fetal growth restriction (FGR), miscarriage, maternal death, mode of delivery and other clinical feature, laboratory findings and coexisting disease. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes doi = 10.1186/s40001-020-00439-w id = cord-267613-hsc2x36j author = Dittmar, Mark title = Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date = 2020-06-19 keywords = Calu-3; Fig; Huh7.5; SARS; Vero; cell summary = Moreover, we found 9 drugs are antiviral in lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity. Previous studies found that the antiviral drug remdesivir, which was developed against the RNA-dependent RNA polymerase of Ebola virus, was also active against SARS-CoV-2 in vitro, with promising results in clinical trials (5) (6) (7) . Both cepharanthine and tetrandrine were previously shown to have antiviral activity against the human coronavirus OC43 and in recent studies on SARS-CoV-2 in Vero cell screens (13, 62, 63) . Strikingly, the activities of all of these drugs is similar in the two cell lines suggesting the same target and mechanism-of-action and that Cyclosporine would block SARS-CoV-2 in diverse infected tissues in vivo. doi = 10.1101/2020.06.19.161042 id = cord-286084-2275xvxb author = Dixit, Alok title = Ivermectin: Potential Role as Repurposed Drug for COVID-19 date = 2020-08-19 keywords = COVID-19; IVM; SARS summary = Currently there is no effective treatment for coronavirus infection; major effort is to develop vaccine against the virus and development of therapeutic drugs for the disease. IVM is shown to be effective in vitro against RNA and deoxyribonucleic acid (DNA) viruses, including human immunodeficiency virus-1 (HIV-1), dengue virus (DENV), influenza, Venezuelan equine encephalitis virus (VEEV) and Zika virus (14) . Currently, remdesivir is a promising potential therapy for COVID-19 due to its broad-spectrum and potent in vitro activity against several novel coronavirus (nCoVs), including SARS-CoV-2 with EC 50 (half maximal effective concentration) and EC 90 (concentration to induce 90% maximal response) values of 0.77 μM and 1.76 μM, respectively (8). IVM which is a widely used as antiparasitic drug has shown to have antiviral activity in in vitro studies against HIV, dengue, influenza, VEEV and Zika virus. Studies are available for its use against RNA virus and have also been tested for its effectiveness against SARS-CoV-2 in vitro. doi = 10.21315/mjms2020.27.4.15 id = cord-291517-ifei60ly author = Dixon, Luke title = COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia date = 2020-05-26 keywords = ANE; SARS; acute summary = title: COVID-19-related acute necrotizing encephalopathy with brain stem involvement in a patient with aplastic anemia OBJECTIVE: To describe a novel case of coronavirus disease 2019 (COVID-19)-associated acute necrotizing encephalopathy (ANE) in a patient with aplastic anemia where there was early brain stem-predominant involvement. Nasopharyngeal swab testing for severe acute respiratory syndrome coronavirus (SARS-CoV-2) was positive, and CT during admission demonstrated diffuse swelling of the brain stem. 2 Here, we report a further case of possible COVID-19-related necrotizing hemorrhagic encephalopathy associated with early brain stem involvement. Extensive abnormal signal and microhemorrhage were found in a symmetrical distribution within the dorsolateral putamina, ventrolateral thalamic nuclei, subinsular regions, splenium of the corpus callosum, cingulate gyri, and subcortical Glossary ANE = acute necrotizing encephalopathy; COVID-19 = coronavirus disease 2019; GCS = Glasgow Coma Score; GTCS = generalized tonic-clonic seizure; SARS-CoV-2 = severe acute respiratory syndrome coronavirus 2. doi = 10.1212/nxi.0000000000000789 id = cord-343966-bfon094h author = Djaparidze, L. title = SARS-CoV-2 waves in Europe: A 2-stratum SEIRS model solution date = 2020-10-13 keywords = IFR; October; SARS; preprint summary = Almost every other finding in this paper also came from this tool: Immune level estimation sensitivity analysis (e.g. change Ro and fit); Estimating the spreading day if only one non-communitarian spreader is assumed (i.e. change initial spreading day until fitted initial spreaders is 1); Finding that Do=2 coupled with Eo=5 can explain the multiple valleys after lockdowns observed in the 1-day moving average daily death curves (i.e. fitting a dozen of different pairs of Do and Eo); Include lack of IgG in asymptomatic when predicting reported serology ratio (i.e. add TAK variable and equation); Estimate the proportion of asymptomatic for <60 and >60 (i.e. change proportions and fit until predicted asymptomatic to symptomatic ratio in Spain matches the reported = 1); Estimate that the proportion of SARS-CoV-2 positive reported deaths that are "with" the virus is 15% (i.e. add testing positive period parameter and yearly probability of dying for other causes to the predicted sars-cov2 positive deaths and lower IFR_vul until predicted serology ratio matches again); Estimate the minimum value of IFR_vul to have another wave in Brussels or the maximum that avoids the low one in Stockholm (i.e. change IFR_vul and fit until the second wave appears or disappears); Hypothesize that an early wave of a D614 like variant can be the cause of low mortality in most locations in Asia (i.e. fit with an hypothetical lower IFR_vul competing strain and then simulate setting the dominant spreading event 60 days earlier). doi = 10.1101/2020.10.09.20210146 id = cord-266885-a5fdeuvv author = Dlotko, P. title = Covid-19 clinical data analysis using Ball Mapper date = 2020-04-15 keywords = Cov-2; SARS summary = In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. Our target will be to locate any clusters of patients with particularly high value of variable 2 (positively of SARS-Cov-2 result), patients that have been admitted to a regular ward, semi intensive or intensive care unit. Our task is to present how the predictive variables 2, 3, 4 and 5 (SARS-Cov-2 result, standard ward, semi intensive care and intensive care admission) changes over P by examining how they change over the obtained Ball Mapper graph. The obtained Ball Mapper graph suggest that the patients, which are likely to have positive result for SARS-Cov2, have quite similar values coming from the blood tests. . Figure 6 : Ball Mapper graph for normalized data colored by the patients who required Intensive Care Unit. doi = 10.1101/2020.04.10.20061374 id = cord-305234-nclk7bbo author = Do, Mytrang H. title = Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date = 2020-06-27 keywords = SARS summary = key: cord-305234-nclk7bbo authors: Do, Mytrang H.; Minkis, Kira; Petukhova, Tatyana A.; Lipner, Shari R. title: Strategies to prevent SARS-CoV-2 transmission during dermatologic head and neck surgery date: 2020-06-27 journal: J Am Acad Dermatol DOI: 10.1016/j.jaad.2020.06.983 sha: doc_id: 305234 cord_uid: nclk7bbo nan . Furthermore, the patient''s mouth and nose are often exposed We hope that these suggestions provide the best possible protection for dermatologic efficiency particle air, RT-PCR, reverse transcription-polymerase chain reaction, SARS-CoV-2, 81 severe acute respiratory syndrome coronavirus 2 Head and neck surgery is a high-risk procedure for COVID-19 87 transmission and there is a need for a preventive strategy to protect professionals Detection of SARS-CoV-2 in Different Types of Clinical 4. American College of Surgeons. COVID-19: Considerations for Optimum Surgeon 19/clinical-guidance/surgeon-protection American Academy of Dermatology. Reopening the dermatologic surgery office in the doi = 10.1016/j.jaad.2020.06.983 id = cord-294304-9w6zt778 author = Doanvo, Anhvinh title = Machine Learning Maps Research Needs in COVID-19 Literature date = 2020-09-16 keywords = COVID-19; PCA; SARS summary = The projection values of COVID-19 abstracts on PC2 were lower and associated with 11 emergent COVID-19 clinical-, modeling-or field-based (CMF) research -such as observational, 12 clinical, and epidemiological studies -exemplified by stem terms "patient", "pandem", "estim", 13 and "case". 14 Furthermore, we developed a framework that improves upon existing bibliometric studies 15 in three key ways; namely, our approach (1) maps connections between publications by relying 16 directly on the abstracts instead of the narrow information gained from metadata as in other 17 bibliometric analyses, including those from other fields 9,10 ; (2) uses ML to explore latent 18 semantic information of vast scale and complexity to identify hidden trends; and (3) does not 19 rely on any a priori knowledge of what topics we expect coronavirus literature to cover but 20 rather highlights them without any preconceived assumptions. doi = 10.1016/j.patter.2020.100123 id = cord-297684-9q3oopaz author = Dobaño, Carlota title = Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date = 2020-06-12 keywords = ELISA; SARS; antibody; figure summary = The Receptor-Binding Domain (RBD) of the spike (S) glycoprotein of SARS-CoV-2, the leading vaccine candidate target, was selected as the primary antigen to develop the initial qSAT assay because (i) S is one of the most immunogenic surface proteins together with the nucleocapsid protein (N) (20) (ii) RBD is the fragment of the virus that mediates binding to the host receptor ACE2 in the lung cells (21) (iii) antibodies to RBD correlate with neutralizing antibodies (20)(22) that could be associated with protection based on studies of other coronaviruses and animal models (23) (24) (25) (26) , and (iv) an ELISA based on this same protein has received FDA approval for COVID-19 serology (11) . We developed three novel multiplex immunoassays for quantifying IgM, IgA and IgG to eight SARS-CoV-2 protein constructs and evaluated by machine learning classification algorithms the performance of several isotype/antigen combinations to detect any positive antibody response to infection, obtaining specificities of 100% and sensitivities of 94.94% (≥14 days since symptoms onset) or 96.08% (≥21 days since symptoms onset), and very high predictability (AUC ≥0.99). doi = 10.1101/2020.06.11.147363 id = cord-311477-gm0vg53l author = Doboszewska, Urszula title = Targeting zinc metalloenzymes in COVID‐19 date = 2020-07-15 keywords = COVID-19; SARS; zinc summary = We attempt to integrate data on the effects of agents targeting zinc fingers in viral metalloenzymes (zinc fingers targeting agents), which cause removal of zinc from the proteins, thus destabilizing the proteins and leading to increased intracellular concentration of zinc ions, and other agents which induce changes in intracellular levels of zinc (zinc ionophores), with data on consequences of altered level of intracellular zinc, with a focus on SARS-CoV-2 and related pathogens. Chloroquine, an old antimalarial drug (Blount, 1967) , was demonstrated to block virus infection at low micromolar concentration in Vero E6 cells infected with SARS-CoV-2 , thus suggesting the possible use of chloroquine in patients with COVID-19. With regard to COVID-19, a novel drug would target labile zinc fingers in SARS-CoV-2 proteins, thus destroying the proteins and producing an increase in intracellular concentration of zinc ions. doi = 10.1111/bph.15199 id = cord-349029-zyfop43z author = Dobrovolny, Hana M. title = Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date = 2020-08-10 keywords = SARS; asymptomatic summary = In order to estimate how effective these strategies will be, we will need a better understanding of the role of asymptomatic individuals in SARS-CoV-2 spread and the effect the proportion and relative infectiousness of asymptomatics have on the time course of the epidemic. In this paper, we study a compartmental epidemic model that includes asymptomatic infections to determine the role that asymptomatic individuals might play in the spread of SARS-CoV-2. We apply our model to data from SARS-CoV-2 epidemics in California, Florida, New York, and Texas, finding that a large number of infections in these states are unreported and that relaxing social distancing measures too early will cause a rapid spike in infections driven in part by these hidden infections. For the SARS-CoV epidemics examined here, the model predicts that there are far more asymptomatic or unreported cases at the peak of the infection, suggesting that there might be widespread community transmission if stay-at-home orders are relaxed too early. doi = 10.1371/journal.pone.0236976 id = cord-293615-f1e6hs11 author = Dockery, Dominique M. title = The Ocular Manifestations and Transmission of COVID-19; Recommendations for Prevention date = 2020-05-08 keywords = SARS summary = Abstract Background Coronavirus disease-2019 (COVID-19), caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been linked to ocular signs and symptoms in several case reports. Research has demonstrated that SARS-CoV-2 is spread primarily through close contact via respiratory droplets, but there is the possibility for ocular transmission with the conjunctiva as a conduit as well as a source of infection. Discussion Ocular manifestations of SARS-CoV-2 include follicular conjunctivitis and have been repeatedly noted as an initial or subsequent symptom of COVID-19 positive patients. Particularly in patients with ocular manifestations, there is evidence that the virus may present in tears based on the detection of SARS-CoV-2 in conjunctival swab samples via reverse transcription polymerase chain reaction (RT-PCR). The conjunctivitis was noted to resolve at day 20 and the patient continued to have daily viral 109 SARS-CoV-2 RNA detection in ocular samples until day 21. doi = 10.1016/j.jemermed.2020.04.060 id = cord-337444-pqoq8aew author = Doi, Kent title = Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series date = 2020-07-03 keywords = SARS summary = title: Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: a case series Through high-throughput screening of 1017 existing drugs, a clinically available serine protease inhibitor nafamostat mesylate was identified as a potent inhibitor of Middle East respiratory syndrome coronavirus entry into human epithelial cells [2] . Eleven adults with reverse transcriptase polymerase chain reaction-confirmed SARS-CoV-2 infection were admitted to the intensive care unit (ICU) at The University of Tokyo Hospital between April 6 and April 21, 2020, and treated with nafamostat mesylate in combination with favipiravir. Although the number of patients in this case series was very small, this low mortality rate suggests that combination treatment of favipiravir and nafamostat mesylate may be effective for critically ill Covid-19 patients. A clinical trial for the combination treatment of nafamostat mesylate and favipiravir against Covid-19 will be initiated in Japan (jRCTs031200026). Nafamostat mesylate blocks activation of SARS-CoV-2: new treatment option for COVID-19 doi = 10.1186/s13054-020-03078-z id = cord-255458-81ugj38k author = Doll, Michelle E. title = Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests date = 2020-05-11 keywords = SARS summary = title: Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: Impact of the interval between tests Infectious disease physicians designated each patient with high or low probability based on the following clinical criteria consistent with reported literature 7 : (1) exposure to SARS-CoV-2; (2) symptoms of COVID-19, including hypoxia, respiratory or gastrointestinal symptoms, or fever; (3) leukopenia; (4) chest imaging; (5) lack of other explanatory diagnosis. Overall, 70 inpatients with initially negative SARS-CoV-2 testing underwent repeat testing for ongoing clinical concerns between March 2 and April 4, 2020. Early interval retesting of patients with a high pretest probability for SARS-CoV-2 as part of a formal protocol was performed from March 31, 2020, through April 7, 2020. The patient who tested positive 6 days after a negative result was deemed "low probability" when re-evaluated for that repeat test. 3, 4 However, cases of high probability symptomatic patients with false-negative testing early in the course of illness have been reported. doi = 10.1017/ice.2020.224 id = cord-309619-glb2y82u author = Domingo, Pere title = The four horsemen of a viral Apocalypse: The pathogenesis of SARS-CoV-2 infection (COVID-19) date = 2020-07-29 keywords = ACE2; Ang; COVID-19; IFN; SARS; TNF summary = Severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 lights the wick by infecting alveolar epithelial cells (AECs) and downregulating the angiotensin converting enzyme-2 (ACE2)/angiotensin (Ang-1–7)/Mas1R axis. SARS-CoV induces the signal transducer and activator of transcription 1 TACE TNF-a converting enzyme TBK1 TANK-binding kinase 1 TLR toll-like receptor TMPRSS2 type II transmembrane serine protease TNF-a tumor necrosis alpha TRAF3 TNF receptor-associated factor 3 XCR1 XCL1 (Chemokine [C motif] ligand 1) and XCL3 (Chemokine [C motif] ligand 3) receptor production of double-membrane vesicles that lack PRRs and can then replicate in these vesicles [18] . COVID-19 patients have high serum levels of inflammatory cytokines, including interleukin (IL)-2, IL-7, IL-10, granulocyte-colony stimulating factor (G-CSF), interferon gamma-induced protein (IP)-10, monocyte chemoattractant protein (MCP)-1, macrophage SARS-CoV-2 infects primarily type II pneumocytes through binding to the ACE2 receptor. ACE2 = Angiotensin-converting enzyme 2; SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2; Ang II = Angiotensin II; ROS = Reactive oxygen species; AT1R = Angiotensin 1 receptor; ADAM17 = A disintegrin and metalloproteinase domain 17; TNF-a = Tumor necrosis factor alpha; TMPRSS2 = transmembrane protease serine 2. doi = 10.1016/j.ebiom.2020.102887 id = cord-308288-3ewdy5l3 author = Domingues, Renan Barros title = First case of SARS-COV-2 sequencing in cerebrospinal fluid of a patient with suspected demyelinating disease date = 2020-06-20 keywords = SARS summary = However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with clinically isolated syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74–100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS-COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs. The viral genome was demonstrated by RT-PCR technique in cerebrospinal fluid sample (CSF), suggesting that the virus has the ability to infect central nervous system (CNS) [1] . However, no case has been described of an association between SARS-COV-2 and CNS demyelinating disease so far. This case report suggests a possible association between CNS focal symptoms compatible with demyelinating disease and SARS-COV-2 infection. doi = 10.1007/s00415-020-09996-w id = cord-266444-rw94yls8 author = Dominguez Andres, Ana title = SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date = 2020-08-19 keywords = CoV-2; Fig; ORF9c; SARS; protein summary = The interactome and proteome studies identified cellular processes affected by SARS-CoV-2 infection or specific viral proteins, notably innate immune signaling (19, 20, 23, (28) (29) (30) , ubiquitin ligase activities (19, 20, 23, (28) (29) (30) , p38 mitogenactivated protein kinase (MAPK) signaling (19, 20, 23, (28) (29) (30) . To assess if there were notable differences in the intensity of the changes in protein abundance in response to proteasome inhibition, we calculated relative changes in protein abundance between control and ORF9c-expressing cells from both the DMSO and MG132 conditions for proteins associated with IFN signaling or the ubiquitin proteasome (UBP) system and antigen presentation (Fig. 2D ). In contrast to the proteomic results that revealed predominant downregulation of proteins following ORF9c expression, RNA-seq analysis showed a similar number of transcripts were increased or decreased in the presence or absence of MG132 (Fig. 3A, table S2 ). doi = 10.1101/2020.08.18.256776 id = cord-315415-3aotsb2g author = Dong, Jianbo title = Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2 date = 2020-10-20 keywords = RBD; SARS; VHH summary = In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19. (c) The binding of VHH-Fcs and ACE2 to Expi293 cells expressing SARS-CoV-2 S1 wild type (WT) or mutant proteins (del1-del5) were assessed by flow cytometry following FITC-conjugated secondary antibody treatment. Based on the binding and epitope binning data, we constructed 3D docking models that predicted the interactions between SARS-CoV-2 S1 RBD, ACE2 and lead VHH-Fcs (Fig. 2e) . Next, we tested whether the combination of individual VHHs binding to different S1 RBD epitopes into bi-specific antibody molecules would yield synergistic effects in SARS-CoV-2 binding and S/ACE2 blocking. doi = 10.1038/s41598-020-74761-y id = cord-354030-8tfg881h author = Dong, Rong title = Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date = 2020-07-28 keywords = MHC; SARS; epitope; figure; protein; vaccine summary = The realm of immunoinformatics tools considers the mechanism of the host immune response to yield additional methodologies in the design of vaccine against diseases are cost-effective and convenient, as in silico predictions can reduce the number of experiments needed (13, 14) . In this present, we employed immunoinformatics to predict multiple immunogenic proteins from the SARS-CoV-2 proteome and thereby design a multi-epitope vaccine. developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . developed a multi-epitope vaccine that was designed using immunoinformatics tools that potentially trigger both CD4+ and CD8+ T-cell immune responses (16) . A vaccine based on the spike protein could induce antibodies to block SARS-COV-2 binding and fusion or neutralize virus infection (18) , as well as induce harmful immune responses that cause liver damage (19) . To design an effective vaccine, we selected the SARS-CoV-2 protein through the above-mentioned methods for epitope prediction. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach doi = 10.3389/fimmu.2020.01784 id = cord-333682-ktbnrkwh author = Dong, Yunzhu title = Antibodies in the breast milk of a maternal woman with COVID-19 date = 2020-07-03 keywords = CoV-2; SARS summary = A maternal woman was positive for SARS-CoV-2 tested in throat swabs but negative tested in other body fluids, and she had IgG and IgA detected in breast milk. Although clinical and laboratory characteristics, and outcomes of pregnant women with COVID-19 have been reported [4], there are no continuously monitored data about the viral loads in several body fluids of the maternal women that would bring potential risks of SARS-CoV-2 infection to neonates [8] . The titers of IgG antibody in breast milk were 2.34, 3.02, 2.84, 2.79, and 3.35, respectively, when three SARS-CoV-2 negative maternal woman''s breast milk were tested as control (mean titer 0.98) (Figure 1, panel D) . (D) Titers of IgG antibody to SARS-CoV-2 in maternal woman''s breast milk determined using ELISA. doi = 10.1080/22221751.2020.1780952 id = cord-342731-rilr45yb author = Donia, Ahmed title = RNA interference as a promising treatment against SARS-CoV-2 date = 2020-09-01 keywords = SARS summary = Previous study also reported the production of plasmid-mediated small interfering RNAs (siRNAs) to target the viral RNA polymerase, which successfully inhibited the cytopathic effects of SARS-CoV on Vero cells (Wang et al. The genomic and the subgenomic mRNAs of coronaviruses have an identical 5′ leader sequence (via a unique mechanism called discontinuous transcription) and common 3′-ends, a unique feature in coronavirus replication. The siRNA targeting the leader sequence reduced the abundance of mRNA and protein expression levels of the reporter genes in 293 T cell line. They also found that the siRNA targeting the leader sequence could inhibit the replication of SARS-CoV via silencing gene expression in Vero E6 cells. Additionally, siRNA targeting the leader sequence exhibited a much potent inhibitory effect on the replication of SARS-CoV than the siRNAs targeting the spike gene made (Enjuanes et al. ) siRNA targeting the leader sequence of SARS-CoV inhibits virus replication doi = 10.1007/s10123-020-00146-w id = cord-330868-7ocseuz3 author = Donnelly, Christl A title = Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong date = 2003-05-24 keywords = Hong; Kong; SARS summary = Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Public-health interventions included encouragement to report to hospital rapidly after the onset of clinical symptoms, contact tracing for confirmed and suspected cases, and quarantining, monitoring, and restricting the travel of contacts. Key epidemiological determinants of the magnitude and timescale of the epidemic (figure 1) include the interval between infection and onset of symptoms and between onset and hospital admission, the degree and duration of the infectiousness of the agent, and the extent of contact and mixing between infectious and susceptible people enabling transmission of the virus. If ␥ distribution is assumed, the estimated distributions and case fatality rate varied as a function of patients'' age, but not the time from onset to admission (figure 2). doi = 10.1016/s0140-6736(03)13410-1 id = cord-311926-n7co0jtu author = Donà, Daniele title = COVID-19 Pandemic: Perspective of an Italian Tertiary Care Pediatric Center date = 2020-09-01 keywords = SARS; covid-19 summary = Predicting a rapid spread of the SARS-CoV-2 virus within our region, the Department for Women''s and Children''s Health promptly decided (i) to revise the distribution of the clinical areas in order to create both designated COVID-19 and COVID-19-free areas with their own access, (ii) to reinforce infection prevention control (IPC) measures for all healthcare workers and administrative staff and (iii) to adopt the new "double-gate approach": a phone call pre-triage and nasopharyngeal swab for SARS-CoV-2 detection before the admission of all patients and caregivers. • to ensure the protection of the healthcare workers, as the top priority; • to rigorously implement all the conventional rules emanated by the WHO for preventing the infection • to minimize the risk of admitting into hospital asymptomatic COVID-19 positive patients; • to adapt/transform some hospital areas in order to be able to admit and treat suspected/confirmed; COVID-19 pediatric patients Predicting a rapid spread of the SARS-CoV-2 virus within our region, in the afternoon of February 24th the Chief Executive Officer (CEO) of Padua University Hospital called for an emergency meeting with all the department chairmen and the mandates received were: doi = 10.3390/healthcare8030311 id = cord-327933-u0fcs3yg author = Doná, Daniele title = Pediatric transplantation in Europe during the COVID‐19 pandemic: early impact on activity and healthcare date = 2020-08-12 keywords = COVID-19; SARS; pediatric summary = Indeed, although severe outcomes (including deaths) have been reported in the pediatric population 6 , relatively fewer children with COVID-19 require hospitalization or admission to the intensive care unit (ICU) 7 . The survey included relevant questions to: i) assess pediatric transplantation activity, including living-donation issues; ii) identify the protocols adopted to prevent and manage SARS-CoV-2 infection at the hospital level; iii) evaluate the impact of these practices on the healthcare of transplanted children; and iv), describe the management of confirmed COVID-19 cases among the special population of pediatric transplant recipients and candidates. In eight centers (44%) outpatient visits were performed only after a telephone pretriage excluding epidemiological (e.g., close contact with a known COVID-19 case) and clinical risk factors (e.g., ongoing fever or respiratory symptoms in the patient or in the caregiver) for SARS-CoV-2 infection. Due to lack of experience in treating affected pediatric transplant patients, hospital admission criteria for suspected and confirmed COVID-19 cases varied between ERN-TransplantChild centers. doi = 10.1111/ctr.14063 id = cord-291588-tp89j1kk author = Dorche, Maryam Sharifian title = Neurological complications of coronavirus infection; a comparative review and lessons learned during the COVID-19 pandemic date = 2020-08-07 keywords = Barré; COVID-19; Guillain; SARS; patient summary = During the current pandemic, 370 patients with SARS-CoV-2 infection out of 37 studies (Table 3) were reported to suffer from AIS or transient ischemic attack (TIA). (145) Acute Necrotizing Encephalopathy(ANE) which was reported in 8 patients (Table 3) with COVID-19 is a distinct entity defined as rapid onset of neurological symptoms often secondary to a viral infection such as herpes viruses and influenza. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series Evolution and resolution of brain involvement associated with SARS-CoV2 infection: A close Clinical -Paraclinical follow up study of a case EEG Findings in Acutely Ill Patients Investigated for SARS-CoV-2/COVID-19: A Small Case Series Preliminary Report. Guillain-Barré syndrome in a patient infected with SARS-CoV-2, a case report Guillain-Barré Syndrome as a Neurological Complication of Novel COVID-19 Infection: A Case Report and Review of the Literature doi = 10.1016/j.jns.2020.117085 id = cord-310605-r63sg73c author = Dorward, D. A. title = Tissue-specific tolerance in fatal Covid-19 date = 2020-07-04 keywords = RNA; SARS; cell; covid-19 summary = Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. As analysis of SARS-CoV-2 RNA confirmed presence in numerous organs, detailed histological analysis of multiple tissues was undertaken on every patient to determine the associated pathological consequences and inflammatory responses. The present study shows that fatal Covid-19 is associated with variable but widespread distribution of viral RNA and protein but with a discordant inflammatory response to local viral presence, both between and within tissues, demonstrating tissue-specific tolerance of SARS-CoV-2. doi = 10.1101/2020.07.02.20145003 id = cord-346546-yffwd0dc author = Douangamath, Alice title = Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date = 2020-05-27 keywords = SARS; figure; fragment; structure summary = To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. For 113 another series of hit compounds, containing a N-chloroacetyl piperidinyl-4-carboxamide 114 motif (Table S2 ) which displays lower reactivity and were not frequent hitters in previous 115 screens, we attempted crystallization despite their absence of labelling in the stringent 116 The bound fragments comprehensively sample all subsites of the active 287 site revealing diverse expansion vectors, and the electrophiles provide extensive, systematic 288 as well as serendipitous, data for designing covalent compounds. Crystal structure of SARS-CoV-2 main protease 763 provides a basis for design of improved alpha-ketoamide inhibitors doi = 10.1101/2020.05.27.118117 id = cord-315968-q2rxj90s author = Douglas, Jennifer E. title = Management of a Unique Sinonasal Undifferentiated Carcinoma Subtype in the Era of SARS-CoV-2 date = 2020-10-05 keywords = SARS; SMARCB summary = Sinonasal undifferentiated carcinoma (SNUC) represents a rare malignancy of the sinonasal tract, a unique subset of which has never been previously reported in the otolaryngology literature and is characterized by inactivation of the SMARCB (INI-1) tumor suppressor gene. Here we present the case of an individual who was diagnosed with a sinonasal mass during the SARS-CoV-2 pandemic, which was ultimately found to be SMARCB (INI-1)-deficient sinonasal carcinoma. While SNUC has itself a poor prognosis, a subset of sinonasal neoplasms with inactivation of the SMARCB (INI-1) tumor suppressor gene exhibits particularly treatment-recalcitrant disease. Here we present the case of an individual with a sinonasal mass who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma and the unique management required during the SARS-CoV-2 pandemic. Here we present the case of an individual initially diagnosed with nasal polyps who was ultimately diagnosed with SMARCB (INI-1)-deficient sinonasal carcinoma during the SARS-CoV-2 pandemic and the unique management required. doi = 10.1159/000511713 id = cord-350959-bsbz3a1l author = Dovey, Zachary title = Impact of COVID-19 on Prostate Cancer Management: Guidelines for Urologists date = 2020-06-16 keywords = China; CoV-2; SARS; patient; risk summary = There is also epidemiological evidence that PCa patients have increased incidence and mortality from SARS-CoV-2 infection due to gender differences, age, and higher propensity for risk factors (eg, respiratory disease, obesity, hypertension, and smoking status). Patient summary Prostate cancer patients can be followed up remotely until the severe acute respiratory syndrome coronavirus 2 pandemic resolves, but higher-risk cases may have treatment expedited to limit any negative impact on prostate cancer outcomes. As shown in Table 2 , PCa patients with either diabetes or hypertension should seek advice from their physicians to optimize their treatment, especially if this includes ACE inhibitors or ARBs [32] , to reduce their risk of SARS-CoV-2 infection and morbidity. Tewari Prostate cancer (PCa) patients may have an increased risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. doi = 10.1016/j.euros.2020.05.005 id = cord-256023-21b5hanj author = Dowdell, A. K. title = Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon date = 2020-08-04 keywords = August; SARS; international summary = We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Genomic sequencing is rapidly emerging as an orthogonal strategy to RT-PCR for outbreak monitoring as the sequence specificity uncovered in individual SARS-CoV-2 isolates has shown significant utility for the epidemiological investigation of outbreak origins as well as the early identification of possible functional changes to the virus that may affect transmission rates or associated clinical outcomes. In order to assess the heterogeneity of SARS-CoV-2 genomes across OR, a total of 204 nasopharyngeal swab patient specimens (representing 188 unique patients) were sequenced from diverse clinical sites across OR. Next, we sought to determine whether sequence variants in the isolated SARS-CoV-2 genomes were associated with differential clinical manifestation of COVID-19 in the patients. doi = 10.1101/2020.07.30.20160069 id = cord-350935-p6euuop3 author = Doğan, Tunca title = CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date = 2020-09-15 keywords = COVID-19; SARS; protein summary = We aimed to address this issue by constructing a new biological and biomedical data resource, CROssBAR, a comprehensive system that integrates large-scale biomedical data from various resources and store them in a new NoSQL database, enrich these data with deep-learning-based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to users via easy-to-interpret, interactive and heterogenous knowledge graph (KG) representations within an open access, user-friendly and online web-service at https://crossbar.kansil.org. In this project, we aimed to address the current shortcomings by developing a comprehensive open access biomedical system entitled CROssBAR via integrating various biological databases to each other, inferring the missing relations between existing data points, and constructing informative knowledge graphs based on specific biomedical components/terms such as a disease/phenotype, biological process, gene/protein and drug/compound, or specific combinations of them. doi = 10.1101/2020.09.14.296889 id = cord-348202-6we8e60b author = Drake, Daniel H. title = Echo in Pandemic: Front Line Perspective, Expanding Role of Ultrasound and Ethics of Resource Allocation date = 2020-04-10 keywords = COVID-19; SARS; care; patient summary = During a declared health care crisis, providers must be familiar with the ethical principles, organizational structure, practical application, and gravity of limited resource allocation. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) associated acute cardiomyopathy is common in critical care patients and is associated with a high mortality. Echocardiography has been most useful for 1) initial assessment of patients with respiratory complaints who are seen in the COVID-19 evaluation pathway but may have another etiology for their symptoms, 2) assessment of cardiac function in critical care patients, where SARS-CoV-2 associated cardiomyopathy is prevalent and 3) volume assessment of patients with acute respiratory distress syndrome (ARDS), where sparing unnecessary fluids is mandatory. Ethical Considerations for Decision Making Regarding Allocation of Mechanical Ventilators During a Severe Influenza Pandemic or Other Public Health Emergency doi = 10.1016/j.echo.2020.04.007 id = cord-354763-odzrco6q author = Drake, John M. title = Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date = 2006-12-20 keywords = SARS; learning; outbreak summary = We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. We also retrospectively explore the effect of societal learning during the 2003 outbreak of SARS in Singapore, using weekly data on the time between onset of symptoms and removal of infectious individuals. Finally, we discuss societal and epidemiological factors that might affect societal learning, we observe that a difficult task during the early stages of an outbreak is to estimate the learning rate and suggest that the rate estimated here might be used as prior information in future outbreaks, and we conclude by recommending rapid investment in research at the time of initial detection when actions taken to reduce disease spread can be most efficient and cost effective. doi = 10.1371/journal.pone.0000020 id = cord-345992-3ij1vbqp author = Drosten, Christian title = SARS Molecular Detection External Quality Assurance date = 2004-12-17 keywords = SARS; sample summary = Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Inactivated severe acute respiratory syndrome-associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Highly sensitive methods for virus detection, such as reverse transcription-polymerase chain reaction (RT-PCR) are required to confirm SARS in the acute phase and prevent transmission. First, laboratories had to correctly detect the four samples containing >9,400 copies of viral RNA per milliliter, a concentration well above the detection limit of published and commercial nucleic acid amplification tests (NAT) for SARS-CoV, (6, 7, (10) (11) (12) . Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays doi = 10.3201/eid1012.040416 id = cord-297327-19dfgfz6 author = Drożdżal, Sylwester title = COVID-19: Pain Management in Patients with SARS-CoV-2 Infection—Molecular Mechanisms, Challenges, and Perspectives date = 2020-07-20 keywords = COVID-19; ICU; SARS; pain; patient summary = Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, nonPutative mechanisms of myalgia and headache during viral infection. Many patients with SARS-CoV-2 infection will suffer from severe pain and require reliable pain assessment to provide adequate analgesia, often with multiple drugs, including opioids, non-steroidal inflammatory drugs or analgosedation [52] . Recently, concerns about the possible higher frequency of adverse effects and exacerbation of symptoms of viral respiratory tract infections, such as COVID-19, in patients treated with NSAIDs have been raised [67] . There are reports of a significantly higher use of opioids because of sedation requirements during respiratory failure caused by SARS-CoV-2, which highlights the importance of undertaking a study aiming to determine efficacious and safe procedures of pain management in patients with COVID-19. doi = 10.3390/brainsci10070465 id = cord-252528-rgnhfcbx author = Du, Fenghe title = COVID-19: the role of excessive cytokine release and potential ACE2 down-regulation in promoting hypercoagulable state associated with severe illness date = 2020-07-16 keywords = ACE2; IFN; IL-6; SARS; covid-19 summary = • Anti-inflammatory therapies, including tocilizumab, chloroquine, and hydroxychloroquine, which can be promising treatment to control excessive cytokine release in severe COVID-19, have the potential to reduce the risk of vascular thrombotic events, but more clinical data are needed for optimum instruction of drug use and drug selection. By interpreting the pathological mechanisms, we aim to illustrate that excessive pro-inflammatory cytokine release and potential ACE2 down-regulation can promote the hypercoagulable state in severe COVID19 , and propose that the anti-inflammatory medications, as well as ACEI/ARB, can benefit severe COVID-19 patients by reducing the risk of vascular thrombotic events. doi = 10.1007/s11239-020-02224-2 id = cord-332555-jfqlkd72 author = Du, Hengzhi title = The potential effects of DPP‐4 inhibitors on cardiovascular system in COVID‐19 patients date = 2020-07-26 keywords = DPP-4; SARS summary = similar outer membrane spike glycoproteins among the coronavirus, it is possible that DPP-4 might also be a functional receptor of SARS-CoV-2. It has been reported that membrane-associated human DPP-4, as a functional MERS-CoV receptor, interacted with MERS-CoV through the spike glycoprotein S1b domain to facilitate the entry of MERS-CoV. Evidence from severely ill patients with COVID-19 suggested that the release of cytokines and chemokines was delayed in respiratory epithelial cells, dendritic cells (DCs) and macrophages at the early stage of SARS-CoV-2 infection. 17 Similar findings were also observed in SARS-CoV and MERS-CoV infected human airway epithelial cells, THP-1 cells, human peripheral blood monocyte-derived macrophages and DCs. 18 Although inflammation initially only damages limited organs, such as the lungs, an over-activated inflammatory response will spread all over the body rapidly, including the heart. Meanwhile, DPP-4 inhibitors could inhibit the over-activated inflammatory caused by SARS-CoV-2 and thus improve cardiovascular function. The potential effects of DPP-4 inhibitors on cardiovascular system in COVID-19 patients doi = 10.1111/jcmm.15674 id = cord-319089-hxpoy4gd author = Du, Li title = Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews date = 2020-09-18 keywords = COVID-19; SARS summary = title: Prevalence of depression during the SARS, MERS, and COVID-19 pandemics: A protocol for overview of systematic reviews BACKGROUND: The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has emerged to be the biggest global health threat worldwide. METHODS: Two independent reviewers will conduct comprehensively searches in PubMed, EMBASE.com, Web of Science, the Cochrane Library, Chinese biomedical literature database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wan fang Database, Chongqing VIP (CQVIP). Prevalence of stress, anxiety, depression among the general population during the COVID-19 pandemic: a systematic review and meta-analysis The psychological and mental impact of coronavirus disease 2019 (COVID-19) on medical staff and general public: a systematic review and meta-analysis Prevalence of depression, anxiety, and insomnia among healthcare workers during the COVID-19 pandemic: a systematic review and meta-analysis Psychological effects caused by the COVID-19 pandemic in health professionals: a systematic review with meta-analysis doi = 10.1097/md.0000000000022235 id = cord-308583-vtmwv8zl author = Du, Qishi title = Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase date = 2005-02-15 keywords = CoV; SARS summary = In this research we study the cleavage mechanism, the properties of the relevant chemical bonds, and the catalytic interactions between the octapeptides and the SARS CoV M pro using molecular mechanical and quantum chemical simulations to provide useful insights for the chemical modification. The docking calculation between SARS CoV M pro and the octapeptide AVLQSGFR was performed using the molecular although still bound to the active site, the peptide has lost its cleavability after its scissile bond was modified from a hybrid peptide bond to a strong bond. Fig. 5B is the contour map of differential electronic density of the peptide bond Gln-Ser in the octapeptide AVLQSGFR, obtained by subtracting the electron density in the gaseous phase from the electron density in the background [23] of SARS CoV M pro and solvent water molecules. For the peptide inhibitor of proteinase, the chemical modification to cleavable octapeptide should focus on the scissile peptide bond between R 1 and R 1 0 to be cleaved by SARS CoV M pro . doi = 10.1016/j.ab.2004.10.003 id = cord-337962-9le56say author = Duan, Fuyu title = Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2 date = 2020-08-20 keywords = SARS; cell; figure; macrophage summary = Here, we used directed differentiation of human pluripotent stem cells (hPSCs) to establish a lung and macrophage co-culture system and model the host-pathogen interaction and immune response caused by SARS-CoV-2 infection. Recent studies (Liao et al., 2020; Xu et al., 2020) on immunity of COVID-19 patients indicate that the cells damaged by SARS-CoV-2 infection induced innate in ammation in the lungs that is largely mediated by pro-in ammatory macrophages and granulocytes. To further characterize at the transcriptomic level the response of iLung and iMφ following viral infection, scRNA-seq was performed on the co-cultures with SARS-CoV-2 pseudo virus infection and the analysis revealed that a set of anti-in ammatory factors and anti-viral activity related genes, such as CCL26, CCL13, ISG15, IFITM2 and IFITM3, were clearly upregulated when cultures contained M2-iMφ ( Figure 4A and C, Figures S8A) . doi = 10.21203/rs.3.rs-62758/v1 id = cord-328003-yovp8squ author = Duan, Liangwei title = The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens date = 2020-10-07 keywords = ACE2; CoV-2; RBD; SARS; protein summary = Here, we provide a comprehensive overview of the wealth of research related to the SARS-CoV-2 S glycoprotein biosynthesis, structure, function, and antigenicity, aiming to provide useful insights into the design and development of the S protein-based vaccines as well as therapeutics to prevent or treat the ongoing global spread of SARS-CoV-2/COVID-19. Prefusion structures of human coronavirus HKU1 (HCoV-HKU1) and mouse hepatitis virus S protein ectodomains without two consecutive proline mutations reveal only fully closed conformation (37, 42) , similar to that observed for a full-length, wild-type prefusion form of the SARS-CoV-2 S glycoprotein (41) . Therefore, SARS-CoV-2 evades immune surveillance also through conformational masking, which is well-documented for HIV-1 (43, 44) ; while at the same time, the S protein could transiently sample the functional state to engage ACE2, consistent with the notion that the fusion glycoprotein of highly pathogenic viruses have evolved to perform its functions while evading host neutralizing antibody responses. doi = 10.3389/fimmu.2020.576622 id = cord-268895-m97zsodx author = Duan, Ping title = Safety considerations during return to work in the context of stable COVID-19 epidemic control: an analysis of health screening results of all returned staff from a hospital date = 2020-09-18 keywords = SARS summary = In total, 4729 returned staff from Zhongnan Hospital of Wuhan University, Wuhan, China were examined for COVID-19, and the basic information, radiology and laboratory test results were obtained and systematically analysed. The 4729 returned staff, all from Zhongnan Hospital of Wuhan University, underwent comprehensive SARS-CoV-2 screening, including SARS-CoV-2 nucleic acid test, antibody detection, chest CT scan, body temperature measurement and recording of infection characteristics. Among 172 people with abnormal first physical examination results, we observed that 170 cases (98.84%) were negative in the first SARS-CoV-2 nucleic acid test, but one of which was positive by RT-PCR at the time of reexamination. In summary, we efficiently identified asymptomatic infections through extensive health screening of all returned staff from a hospital in a short period of time, combined with a variety of inspection methods (including nucleic acid test for SARS-CoV-2, antibody detection and chest CT scan), and emphasising the presence of asymptomatic infections in the general population. doi = 10.1017/s0950268820002150 id = cord-342221-xvrpx9p8 author = Duan, Qing title = Reovirus, isolated from SARS patients date = 2003 keywords = Beijing; SARS summary = In this report, reovirus was isolated from throat swabs of SARS patients, including the first case in Beijing and her mother. SCV was isolated in lung tissue collected at autopsy from her father, and the first isolate in Beijing was named the BJO 1 strain of SARS-associated coronavirus, whose genome sequence has been determined [4] . Isolation of reovirus: To isolate viruses associated with SARS, we inoculated the clinical specimen (material from throat swabs) obtained from the first patient with SARS admitted to hospital in Beijing onto Hep-2 cells. We isolated the virus in throat swab specimen from the first case in Beijing and her mother, and initially considered it as a possible variant of SCv, but the PCR test failed to amplify DNA from it. Electron microscopy (EM) examination of Hep-2 cells and Vero-E6 cells infected with the virus isolated from throat swab specimens of the first case in Beijing revealed characteristic reovirus particles with a size of about 60-80 urn in diameter. doi = 10.1007/bf03184165 id = cord-343317-97n1j0jj author = Duan, Xiaohua title = Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date = 2020-05-02 keywords = CoV-2; Fig; SARS; cell summary = Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. The organoids infected with SARS-CoV-2 pseudo-entry virus at MOI=0.01 showed a strong signal at 24 hpi (Fig. 2a) . The mRNAs of SARS-CoV-2 pseudo-entry virus, including VSV-NS, VSV-N, and VSV-M, were detected in all five cell populations (Fig. 2f) , but not in the uninfected COs (Extended Data Fig. 2f) . Immunohistochemistry detected luciferase in ACE2 + and Villin + cells, suggesting these are permissive to SARS-CoV-2 pseudo-entry virus infection in vivo (Fig. 2k) . Next, we adapted hPSC-COs to a high throughput screening platform and probed the Prestwick FDA-approved drug library to identify drug candidates capable of blocking SARS-CoV-2 pseudo-virus infection. doi = 10.1101/2020.05.02.073320 id = cord-284625-to6w5hm2 author = Duan, Xiaopei title = A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date = 2020-05-26 keywords = PCR; SARS summary = Given the concept of the early diagnosis and treatment of SARS-CoV-2, this article mainly focused on the 25 initial laboratory-confirmed patients in the Luoyang area, discussing their imaging features and clinical characteristics. From January 10 to February 8, 2020, 25 patients with laboratory-confirmed SARS-CoV-2 infection in the area of Luoyang, Henan Province, China, were enrolled in the study. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. A woman who is the wife of the patient 3 and mother of patient 22 had two negative PCR results, but the lesions in her lung had the same progression, and the blood test also confirmed the SARS-CoV-2 infection. doi = 10.1007/s11604-020-00988-4 id = cord-321768-oevswvvd author = Duan, Ya-qi title = Deficiency of Tfh Cells and Germinal Center in Deceased COVID-19 Patients date = 2020-08-07 keywords = COVID-19; SARS; patient summary = In this study, we examined the immune cell compositions in the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients and 4 focal organizing pneumonia (FOP) patients who underwent lung surgery and served as controls. In contrast to the FOP patients, Tfh cells and germinal center formation were largely absent in the draining hilar lymph nodes in the deceased COVID-19 patients. Characterization of compositions of the immune cells within the lung tissues and draining hilar lymph nodes from the postmortem specimens might provide valuable insights on how the immune responses in the deceased patients were dysregulated and offer new strategies for treatment. To gain insight into the human immune responses during a fatal SARS-CoV2 infection, we performed postmortem autopsy studies of the immune cell compositions within the lung tissues and hilar lymph nodes using immunohistochemistry on 6 deceased COVID-19 patients, and 4 FOP patients who underwent lung surgery served as controls. doi = 10.1007/s11596-020-2225-x id = cord-284091-1dj4yxkz author = Duart, Gerard title = SARS-CoV-2 envelope protein topology in eukaryotic membranes date = 2020-09-09 keywords = SARS summary = In this report, we studied the E protein topology from the new SARS-CoV-2 virus both in microsomal membranes and in mammalian cells. Computer-assisted analysis of the SARS-CoV-2 E protein amino acid sequence using seven popular prediction methods showed that all membrane protein prediction algorithms except MEMSAT-SVM suggested the presence of one transmembrane (TM) segment located roughly around amino acids 12 to 39 (table 1) , which is not predicted as a cleavable signal sequence according to SignalP-5.0 [7] . Since multiple topologies have been reported for previous coronavirus E proteins [13] [14] [15] [16] [17] , SARS-CoV-2 E protein insertion into the microsomal membranes in two opposite orientations cannot be discounted, but according to our data being dominant an Nt lum /Ct cyt orientation. As shown in figure 2c, E protein (NST) was efficiently glycosylated when microsomal membranes were added to the translation mixture cotranslationally (lane 4). Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells doi = 10.1098/rsob.200209 id = cord-263365-ymnbktm5 author = Dube, Geoffrey K. title = COVID‐19 infection in pancreas transplant recipients date = 2020-06-09 keywords = COVID-19; SARS summary = 1 Clinical manifestations of COVID-19, the disease caused by SARS-CoV-2, range from asymptomatic infection to mild upper respiratory tract symptoms or viral pneumonia. We present here the first four cases of COVID-19 disease reported in PT recipients, with one case being a presumptive diagnosis based on suggestive symptoms and known nosocomial exposure in the absence of confirmatory PCR testing for SARS-CoV-2. First, the main presenting symptoms in our PT recipients (fever in 100%, cough in 75%) were similar to what is reported in the non-transplant population. The clinical deterioration of patient 3 after 10 days highlights the importance of close monitoring of suspected or confirmed COVID-19 in PT recipients followed in the outpatient setting until complete symptom resolution. When our patients informed us of symptoms consistent with COVID-19 infection, we held mycophenolate in 3 of our patients and temporarily held tacrolimus in 1 patient on monotherapy, a strategy similar to that employed in other solid organ transplant recipients at our center. doi = 10.1111/tid.13359 id = cord-294108-uvnh0s9r author = Dube, Taru title = Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date = 2020-10-25 keywords = COVID-19; CoV-2; FDA; Phase; RNA; SARS; patient; vaccine; virus summary = [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. doi = 10.1002/adtp.202000172 id = cord-356174-40k6m7l0 author = Ducloyer, Mathilde title = Complete post-mortem data in a fatal case of COVID-19: clinical, radiological and pathological correlations date = 2020-08-06 keywords = COVID-19; PMCT; SARS; lung summary = A reverse-transcription polymerase chain reaction test was positive for severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) using a nasopharyngeal swab sample. Post-mortem virology studies detected the presence of SARS-CoV-2 (B.1 lineage) in the nasopharynx, plasma, lung biopsies, pleural effusion and faeces confirming the persistence of viral ribonucleic acid 48 h after death. This case is one of the first to describe complete post-mortem data for a COVID-19 death and highlights the ability of PMCT to detect severe involvement of the lungs before autopsy in an apparently natural death. The present pathology results are concordant with previously reported findings and reinforce the disease pathogenesis hypothesis of combined viral replication with an inappropriate immune response. Concerning the post-mortem virology data, this case demonstrated that RNA from SARS-CoV-2 was still detectable in blood, faeces, the lungs and the upper airways more than 48 h after death. doi = 10.1007/s00414-020-02390-1 id = cord-333239-nj5dma98 author = Ducrest, P. J. title = Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2 date = 2020-10-13 keywords = RDT; SARS summary = Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). The aim of this study is to develop and evaluate the performance of a new IgM/IgG rapid diagnostic test (RDT) based on lateral flow assay (LFA) technology, in a high COVID-19 prevalence setting using gold standard RT-PCR as well as an Electro-chemiluminescence immunoassay (ECLIA) Elecsys® Anti-SARS-CoV-2 total Ig (Roche, Switzerland). The key finding of the present evaluation study, using an unmatched case-control design including 73.5% of negative control samples, is that the diagnostic accuracy of IgG/IgM RDT on plasma samples when compared to RT-PCR or ECLIA is the same and displayed a SE of 100%, a SP of 93% and a NPV of 100%. doi = 10.1101/2020.10.09.20209866 id = cord-340579-cvze15cj author = Dudley, Joseph P title = Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date = 2020-03-31 keywords = China; SARS summary = There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 doi = 10.1093/cid/ciaa354 id = cord-294700-pb5k21da author = Dulek, Daniel E title = Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute COVID-19 in Pediatric Patients date = 2020-08-18 keywords = COVID-19; IL-6; IVIG; SARS; css; patient; severe summary = Although the majority of SARS-CoV-2 infections in pediatric populations result in minimal or mild COVID-19 in the acute phase of infection, a small subset of children develop severe and even critical disease in this phase with concomitant inflammation that may benefit from immunomodulation. The framework presented herein offers an approach to decision-making regarding immunomodulatory therapy for severe or critical pediatric COVID-19 and is informed by currently available data, while awaiting results of placebo-controlled randomized clinical trials. Given the lack of available results from randomized-controlled trials of immunomodulatory therapy in children with COVID-19, the risk-benefit ratio for most pediatric patients points toward supportive care as the key management strategy. In the absence of such opportunity, and recognizing that definitive evidence is lacking, consideration for use of immunomodulatory agents in cases of SARS-CoV-2 infection with clinical and biochemical evidence of cytokine storm physiology (e.g., features of secondary HLH) should be limited to patients with clear evidence of critical COVID-19 disease and risk for multi-organ failure. doi = 10.1093/jpids/piaa098 id = cord-270935-t9pym9k0 author = Dumyati, Ghinwa title = Does Universal Testing for COVID-19 Work for Everyone? date = 2020-08-15 keywords = COVID-19; SARS; test summary = Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. Dr. Jump reports support for this work in part through the Cleveland Geriatric Research 50 While there is general agreement that increased access to testing is important for personal and 23 public health, the selection and use of diagnostic tests to mitigate COVID-19 infections in post-24 acute and long-term care settings is complex and should be tailored to individual sites. Because he met the nursing 36 home''s enhanced screening criteria for COVID-19 (Table 1) , 1 he was placed on transmission-37 based precautions and a laboratory test for SARS-CoV-2 was ordered. doi = 10.1016/j.jamda.2020.08.013 id = cord-317355-z5tk3v3b author = Dunker, Susanne title = No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread date = 2020-10-13 keywords = CoV-2; SARS summary = title: No SARS-CoV-2 detected in air samples (pollen and particulate matter) in Leipzig during the first spread Air samples collected at our measuring station in Leipzig and purified pollen were analyzed for SARS-CoV-2 typical signals or for virus-induced cytopathic effects, to test if the virus could bind to bioaerosols and if so, whether these complexes are infectious. We therefore aimed at investigating whether SARS-CoV-2 can bind to pollen or other kind of particulate matter within bioaerosols sampled at our station in Leipzig and if so, whether these complexes are infectious. In none of these samples SARS-CoV-2 typical For a detailed analysis of a possible correlation between concentrations of the most abundant pollen, particulate matter and registered Covid-19 cases, a correlation matrix was created with R (package "PerformanceAnalytics") (Fig. 2) . doi = 10.1016/j.scitotenv.2020.142881 id = cord-307702-n74wvika author = Durant, Thomas J S title = Impact of COVID-19 Pandemic on Laboratory Utilization date = 2020-07-14 keywords = COVID-19; PCR; SARS summary = METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. doi = 10.1093/jalm/jfaa121 id = cord-322885-ob5euspo author = Durdagi, Serdar title = Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date = 2020-09-09 keywords = 7CWB; 7cwc; Fig; Mpro; SARS; drug; structure summary = One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. Radiation-damage-free SFX method which enables obtaining the novel high-resolution ambient-temperature structures of the binding pocket of Mpro provides an unprecedented opportunity for identification of highly effective inhibitors for drug repurposing by using a hybrid approach that combines structural and in silico methods. We determined two radiation-damage-free SFX crystal structures of SARS-CoV-2 Mpro in two crystal forms at 1.9 Å and 2.1 Å resolutions with the following PDB IDs: 7CWB and 7CWC, respectively (Fig. 1A, B) (Supplementary Table 1&2 The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al., They reveal novel active site residue conformations and dynamics at atomic level, revealing several differences compared to the prior ambient-temperature structure of SARS-CoV-2 Mpro that was obtained at a home X-ray source (Fig. 1A, B ). doi = 10.1101/2020.09.09.287987 id = cord-291281-ygrh8ces author = Durner, J. title = Critical Questions when Interpreting Coronavirus PCR Diagnostics date = 2020-06-14 keywords = PCR; SARS summary = In contrast to other PCR examinations, or laboratory medical analyses, currently SARS-CoV-2 diagnostic information about the device or the detection limit / sensitivity is not usually provided by the laboratory. Using a protocol without purification of viral RNA, i.e. the Munich Extraction Protocol (MEP) [2] , we could show that the type of transport medium had little influence on the detection sensitivity of SARS-CoV-2 in the PCR (Table 1) . By using this system, the sensitivity could be increased by at least one more dilution step compared to the use of commercial purification methods in PCR (Table 3) . . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 1 Comparison of different types of transport media for their influence on the detectability of SARS-CoV-2. . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 2 Comparison of different purification systems for their influence on the detectability of SARS-CoV-2 (Cp = crossing point). doi = 10.1101/2020.06.11.20127241 id = cord-033010-o5kiadfm author = Durojaye, Olanrewaju Ayodeji title = Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date = 2020-10-02 keywords = Fig; SARS; model; protein; sequence; structure summary = RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Our current study took advantage of the availability of the SARS CoV main proteinase amino acid sequence to map out the nucleotide coding region for the same protein in the 2019-nCoV. The predicted secondary structure composition shows a high degree of alpha helix and beta sheets, respectively, occupying 45 and 47% of the total residues with the percentage loop occupancy at 8% regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology. doi = 10.1186/s43042-020-00081-5 id = cord-265191-unk6rt7u author = Durrani, Muhammad title = Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report date = 2020-06-22 keywords = ATM; SARS summary = title: Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report Among the respiratory viral pathogens, the Coronaviridae family and its genera coronaviruses have been implicated as having neurotropic and neuroinvasive capabilities in human hosts.1 Despite previous strains of coronaviruses exhibiting neurotropic and neuroinvasive capabilities, little is known about the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its involvement with the central nervous system (CNS). CONCLUSION: The patient underwent further workup and treatment with intravenous corticosteroids with improvement of symptoms and a discharge diagnosis of ATM secondary to SARS-CoV-2. 11 Additionally, the first case report of acute infectious myelitis associated with concurrent SARS-CoV-2 was only recently described. Our patient met the inclusion criteria for diagnosis of ATM based on bilateral motor symptoms and autonomic dysfunction with bladder incontinence along with evidence of CSF lymphocytic pleocytosis and characteristic MRI findings while ruling out other infectious, autoimmune, and connective tissue etiologies. doi = 10.5811/cpcem.2020.6.48462 id = cord-269766-arjoemla author = Dutescu, R. Michael title = Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date = 2020-09-08 keywords = RNA; SARS summary = title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. To clarify this, we tested the tear fluid of confirmed hospitalized SARS-CoV-2 patients by PCR using a method not previously used for the collection of tear samples. In this study, we could confirm SARS-CoV-2 RNA positive tear samples by PCR in as many as 28% of determined SARS-CoV-2 patients by oropharyngeal swabs. 13 In a more recent cross-sectional study, only 1 (1.38%) conjunctival swab of 72 confirmed SARS-CoV-2 cases was tested positive. doi = 10.1097/ico.0000000000002562 id = cord-300040-rvrp5zvv author = Dutta, Noton Kumar title = Search for potential target site of nucleocapsid gene for the design of an epitope-based SARS DNA vaccine date = 2008-06-15 keywords = SARS; dna summary = We constructed eukaryotic expression plasmid encoding N [(N1 (nucleotide: 1-1269), N2 (nucleotide: 1-327), and N3 (nucleotide: 328-1296)) gene fragments of the SARS-CoV and compared their individual potential immune responses in BALB/c mice for use in the development of SARS vaccine candidates. In this report, we detected SARS-Cov N1 and N3 protein-specific immune response induced by pVAX-N1 and N3 DNA vaccination, respectively, and found significantly high titres of specific antibody and specific cell mediated immunity compared to control. These results indicate that N protein, which naturally exists in virus particles after binding of viral RNA, was able to induce strong humoral and cellular immune responses when induced by DNA vaccine, and it might be a prospective candidate gene for development of SARS-CoV vaccine. showed that expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization. The expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization doi = 10.1016/j.imlet.2008.03.003 id = cord-352720-z1cvjc2y author = Díaz-Corvillón, Pilar title = Routine screening for SARS CoV-2 in unselected pregnant women at delivery date = 2020-09-29 keywords = COVID-19; PCR; SARS summary = While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. doi = 10.1371/journal.pone.0239887 id = cord-264614-2x7cdul3 author = Díaz-Guio, Diego Andrés title = COVID-19: Biosafety in the Intensive Care Unit date = 2020-08-27 keywords = COVID-19; ICU; PPE; SARS summary = PURPOSE OF REVIEW: COVID-19 is a new, highly transmissible disease to which healthcare workers (HCWs) are exposed, especially in the intensive care unit (ICU). This article aims to show the different strategies to prevent the widespread of the disease to critical care healthcare workers based on the review of the recent literature and the author''s experience with the personal protective equipment (PPE) in the care of patients with COVID-19 and work on human factors in crisis management. Nonetheless, to date, there is no robust evidence that medical masks are inferior to N95/FFP2 respirators for protecting healthcare workers against laboratory-confirmed COVID-19 during patients care and non-AGPs [31] . While personal protective equipment is an essential part of safety to prevent SARS-CoV-2 transmission, it must be employed appropriately, together with frequent hand hygiene, and mastering specific techniques and non-technical skills like awareness, closed-loop communication, leadership, team working, appropriate resource management, and cognitive aids [14, 34] . doi = 10.1007/s40475-020-00208-z id = cord-273182-djb0ozrt author = Díez, José María title = Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date = 2020-09-09 keywords = CoV; IVIG; MERS; SARS summary = Recently, we reported cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2 and MERS-CoV with Flebogamma R DIF 5 and 10% and Gamunex R -C, two currently available intravenous IGs (IVIG) [23] . Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2 and MERS-CoV by: ELISA techniques; and well-established neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT 50 titers ranging from 4.5 to >5 (Figure 2 ). This neutralizing activity correlates with the cross-reactivity to different coronavirus antigens observed in ELISA-binding assays with IVIG, as shown in a previous study [23] . • Intravenous immunoglobulin products were tested against severe acute respiratory syndrome coronavirus 2 in cell culture neutralization assays. doi = 10.2217/imt-2020-0220 id = cord-254318-w8wrn9lx author = Díez, José-María title = Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens date = 2020-05-13 keywords = ELISA; IVIG; SARS summary = MATERIAL & METHODS: Gamunex(®)-C and Flebogamma(®) DIF (Grifols) intravenous immunoglobulin (IVIG) products were tested using ELISA techniques for antibodies against several antigens of human common betacoronaviruses that may crossreact with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Gamunex R -C (Grifols Therapeutics, Inc., NC, USA) and Flebogamma R DIF (Instituto Grifols S.A., Barcelona, Spain) IVIGs were tested for crossreactivity against several betacoronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2 antigens, using ELISA techniques. Even with this uncertainty, in the context of the current health emergency (pandemic), the potential of IVIG as a therapy for COVID-19 is already being evaluated in a number of studies involving patients with severe SARS-CoV-2 viral infections including pneumonia [28] [29] [30] . • This is the first time that currently available intravenous immunoglobulins have been reported to contain antibodies that crossreact against antigens of SARS-CoV-2 and other coronaviruses. doi = 10.2217/imt-2020-0095 id = cord-296237-i9cti2ok author = Díez, José-María title = Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date = 2020-06-19 keywords = CoV-2; IVIG; MERS; SARS summary = Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. Recently, cross-reactivity in ELISA binding assays against antigens of SARS-CoV, SARS-CoV-2, and MERS-CoV has been reported with currently available intravenous immunoglobulins (IVIG) such as Gamunex-C and Flebogamma DIF 19 . In this study, the neutralization capacity of the IVIG products Gamunex-C and Flebogamma DIF against these epidemic human coronaviruses -SARS-CoV, SARS-CoV-2, and MERS-CoV-was evaluated. Six different lots of Flebogamma DIF and Gamunex-C were tested at several dilutions for cross-reactivity against SARS-CoV, SARS-CoV-2, and MERS-CoV by: i) ELISA techniques; and ii) well-stablished neutralization assays in cell cultures. For SARS-CoV-2 MAD6 isolate, all IVIG lots, except F1 (inconclusive results) showed a significant neutralizing activity and reached PRNT50 titers ranging from 4.5 to >5 (Figure 2 ). doi = 10.1101/2020.06.19.160879 id = cord-281241-k1adcls8 author = Döhla, M. title = Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date = 2020-04-18 keywords = SARS; test summary = Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. We therefore evaluated a rapid antibody IgG/IgMebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. Thirty-nine randomly selected individuals at the centre were tested simultaneously using the SARS-CoV-2 rapid test and the gold standard RT-qPCR method (Altona Diagnostics). The rapid test used for evaluation is a qualitative IgG/IgM detection system to test for a current or past infection of SARS-CoV-2. doi = 10.1016/j.puhe.2020.04.009 id = cord-353524-3w970ycx author = Dömling, Alexander title = Chemistry and Biology of SARS-CoV-2 date = 2020-05-22 keywords = CoV-2; RNA; SARS; drug summary = Given that SARS-CoV-2 and SARS-CoV share very high identical sequence in their 3CLpro, these HIV protease inhibitors are currently again repurposed for the treatment of COVID-19 (Chinese Clinical Trial Registry: ChiCTR2000029539). 30, 31 The interplay of the ACE receptor in cardiovascular diseases (with the well-known drug class of ACE inhibitors) and as the docking point for SARS-CoV-2 cellular infection is a current point of intense debate and research. For example, the crystal structure of SARS-CoV-2 N protein RNA-binding domain was just published and will give structural insight as a potential drug target. Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure-based drug design study Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites doi = 10.1016/j.chempr.2020.04.023 id = cord-312697-ffxcze6c author = Dübel, Stefan title = Rekombinante, vollständig humane Antikörper zur Behandlung akuter COVID-19 date = 2020-06-26 keywords = Antikörper; Impfstoff; SARS summary = COVID-19 (coronavirus disease 2019) ist eine akute schwere virale Erkrankung der oberen Atemwege und Lungen, die vom neuartigen SARS-CoV-2-Virus hervorgerufen wird und zum ersten Mal in Wuhan (China) Ende 2019 beschrieben wurde. Solche Antikörper sind eine komplementäre Ergänzung zu den derzeit laufenden Virus-Impfstoff-Entwicklungen, da sie mit sehr hoher Wahrscheinlichkeit auch den bereits an COVID-19 erkrankten Patienten helfen können. Dies könnte sehr schnell gehen: Aufgrund der großen Erfolge rekombinanter Antikörperwirkstoffe (fast 100 zugelassene Medikamente) stehen dafür zudem bereits heute umfangreiche Produktionskapazitäten und defi nierte Produktionsprozesse zur Verfügung, während diese bei einem neuartigen Impfstoff aus Viruskomponenten erst noch zeitaufwendig entwickelt, skaliert und zugelassen werden müssen. Auf Basis dieser Erfahrungen begannen wir im Februar dieses Jahres in Braunschweig an der TU und parallel an deren Ausgründung YUMAB GmbH mit Arbeiten zu dem Ziel, vollständig menschliche Antikörper zu entwickeln, welche die SARS-CoV-2-Infektion verhindern können. So konnte bisher ein sehr großer Satz von mehr als 750 komplett menschlichen monoklonalen Antikörpern gegen das SARS-CoV-2-Spike(S)-Protein gefunden und sequenziert werden. doi = 10.1007/s12268-020-1404-4 id = cord-328113-eczjjc2v author = D’Alessandro, Angelo title = Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level date = 2020-07-30 keywords = COVID-19; IL-6; SARS; figure; patient summary = Subjects seen at Columbia University Irving Medical Center/New York−Presbyterian Hospital included 33 COVID-19-positive patients, as determined by SARS-CoV-2 nucleic acid testing of nasopharyngeal swabs; in this group, the severity of the disease was inferred from serum levels of IL-6, which were determined by CLIAcertified ELISA-based measurements. Sera of COVID-19 patients, especially those with IL-6 levels >10 pg/mL, contained increased levels of multiple proteins in the acute phase response that is initiated by IL-6specifically components of the coagulation and complement cascades (top enriched pathway, p-value: 1.6 × 10 −31 ; Figure 2 ). Other RBC-derived proteins (i.e., band 3, anion exchanger 1 (AE1; the most abundant RBC membrane protein), peroxiredoxins 2 and 6, catalase, and Journal of Proteome Research pubs.acs.org/jpr Article biliverdin reductase B) correlated significantly with HBA and HBB levels, despite not reaching significance when compared to COVID-19-negative subjects, suggesting that minimal hemolysis was present in a subset of the most severely ill patients in our study ( Figure 4A ), perhaps due to mechanical ventilation or other iatrogenic interventions−including the sample collection protocol adopted in this study. doi = 10.1021/acs.jproteome.0c00365 id = cord-340908-8q7i5ds3 author = D’Ambrosi, Riccardo title = Guidelines for Resuming Elective Hip and Knee Surgical Activity Following the COVID-19 Pandemic: An Italian Perspective date = 2020-10-13 keywords = SARS; patient summary = 1. Facility requirement: All diagnosis and treatment activities related to surgery for patients not infected with SARS-CoV-2 must be performed in a COVID-19-free environment. 3. Patient selection: Patient selection must take into account age, urgency of treatment, risk of exposure to SARS-CoV-2, American Society of Anesthesiologists (ASA) classification, comorbidity, socio-professional situation, and the possibility of performing post-operative physiotherapy [7, 13] . (However, if these patients did have surgery, the procedure must take place in a separate environment within the hospital and with adequate assessment of the risk to healthcare staff and planning to optimize their ability to avoid infection.) Also, patients classified as ASA I or ASA II had priority for intervention regardless of the urgency of the treatment. The complete program including surgical treatment, post-operative physiotherapy management, and follow-up must be discussed and planned with the patient before surgery. doi = 10.1007/s11420-020-09809-w id = cord-265111-d44ireu5 author = D’Ardes, Damiano title = Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids date = 2020-08-31 keywords = SARS; covid-19; patient summary = A longer duration of COVID-19 with delayed clinical healing (symptom-free) occurred in patients presenting at admission a lower PaO(2)/FiO(2) ratio (p < 0.001), a more severe clinical presentation (p = 0.001) and a lower lymphocyte count (p = 0.035). All adult patients were diagnosed with COVID-19 according to World Health Organization (WHO) interim guidance: they had clinical symptoms of COVID-19 and confirmation of SARS-CoV-2 infection through instrumental signs and a positive result on RT-PCR assays of nasopharyngeal swab specimens. The specific inclusive criteria were as follows: (1) patients confirmed by positive detection of SARS-CoV-2 RNA from nasopharyngeal/throat swabs by RT-PCR with clinical data suggesting for COVID-19, (2) patients aged more than 18 years old and (3) patients with a known date of performing different RT-PCR assays. Disease severity and lower lymphocyte levels at admission also predict longer SARS-CoV-2 viral shedding. doi = 10.3390/microorganisms8091327 id = cord-313460-oao2zppd author = D’Ardes, Damiano title = Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection date = 2020-05-11 keywords = SARS summary = title: Long-term Positivity to SARS-CoV-2: A Clinical Case of COVID-19 with Persistent Evidence of Infection We describe the case of a 65-year-old woman who clinically recovered from COVID-19 but showed persistent infection with SARS-CoV-2 for 51 days. Although the patient had clinically recovered and had been transferred from our acute department to a unit for clinically stable patients, the nasopharyngeal swabs for SARS-CoV-2 continued to be positive until the end of April (swabs taken in mid-April, 22 April and 30 April), an interval of around 51 days from the onset of symptoms on 10 March. In contrast to the 15-20 days usually described as the average duration of mild COVID-19 disease, in this case we demonstrated SARS-CoV-2 positivity which lasted for over 50 days even though the patient was clinically well 2 weeks after the onset of symptoms. Positive RT-PCR test results in patients recovered from COVID-19 doi = 10.12890/2020_001707 id = cord-004204-cpub9oah author = D’Cunha, Colin title = SARS: Lessons Learned from a Provincial Perspective date = 2004-01-01 keywords = SARS; health summary = T o say that SARS was a unique threat, and one that challenged public health and the entire health system in Ontario could be viewed as somewhat of an understatement. Never had the modern public health or the health care system been put to such a test or been put under such pressure to respond as during the two phases of SARS outbreaks earlier this year. The very uniqueness and stress that the SARS outbreaks placed on our system inevitably revealed the weaknesses and the areas where change or fortification in our public health defenses was needed in order for us to meet successfully future challenges. Funding for public health services in Ontario is based on a mixed model with municipal and provincial partners contributing to the funding. Other public health professionals should be cross-trained in communicable disease management to create additional surge capacity. A Report of the National Advisory Committee on SARS and Public Health doi = 10.1007/bf03403629 id = cord-269009-0i2bvt77 author = D’Souza, Rohan title = A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID‐19 date = 2020-08-05 keywords = COVID-19; SARS; patient summary = Should patients develop coronavirus disease (COVID‐19) pneumonia requiring hospital admission for treatment of hypoxia, the risk for thromboembolic complications increases greatly. 2 As pregnancy is a prothrombotic state, the possibility of an increased risk of thrombosis in pregnant women with COVID-19 has become an area of concern, and a number of international organiPatients with severe COVID-19 may be at risk for pulmonary thromboembolic complications through at least two distinct mechanisms -immunothrombosis and hospital-associated venous thromboembolism (VTE). 12 A recent study of patients with severe COVID-19 demonstrated a correlation between IL-6 and fibrinogen levels, 3 further supporting the theory that massive activation of the acute phase response, with increased production of coagulation factors, appears to be the predominant prothrombotic mechanism in COVID-19. A critical review of the pathophysiology of thrombotic complications and clinical practice recommendations for thromboprophylaxis in pregnant patients with COVID-19 doi = 10.1111/aogs.13962 id = cord-292387-2xv3wgaq author = D′Agostino, Armando title = Brief Psychotic Disorder During the National Lockdown in Italy: An Emerging Clinical Phenomenon of the COVID-19 Pandemic date = 2020-08-06 keywords = BPRS; SARS; patient; psychotic summary = Approximately 2 months after the COVID-19 outbreak in Lombardy and 50 days into national lockdown, we began to hospitalize patients with brief psychotic episodes at a remarkable rate. We report a case series of all consecutive patients admitted to the 2 psychiatric inpatient units of the San Paolo University Hospital who were discharged with a diagnosis of BPD during the COVID-19 pandemic lockdown in Milan, Italy (March 9 to May 18). In order to standardize the evaluation criteria, the following set of instruments was employed: the Brief Psychiatric Rating Scale (BPRS) 20 was performed as a global measure of psychopathology upon admission and at discharge; the presence of stressful life events in the 12 months before the lockdown was assessed using Paykel''s interview for recent life events 21 ; the Structured Clinical Interview for DSM (SCID-II) 22 was performed to evaluate the presence of a personality disorder; and the Temperament and Character Inventory-240 items (TCI-240) 23 was administered to investigate personality dimensions. doi = 10.1093/schbul/sbaa112 id = cord-288639-wy07nao0 author = Earnest, Arul title = Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore date = 2005-05-11 keywords = ARIMA; SARS summary = title: Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore BACKGROUND: The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make real-time predictions on the number of beds occupied in Tan Tock Seng Hospital, during the recent SARS outbreak. The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make realtime predictions on the number of beds occupied in TTSH during the SARS outbreak, starting from 14 Mar 2003, when the CDC was activated, to 31 May 2003 when Singapore was declared SARS free. To the best of our knowledge, this is the first study to suggest the application of a known statistical method such as the ARIMA model, to predict and monitor the utilization of hospital isolation beds during the recent SARS outbreak in Singapore, for which Tan Tock Seng Hospital was the Admissions, predicted and actual number of beds occupied doi = 10.1186/1472-6963-5-36 id = cord-262766-ndn6iwre author = Easom, Nicholas title = 68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit date = 2020-03-06 keywords = SARS; patient summary = Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. In addition, many mild respiratory viral infections were managed as influenza 10 , with significant resource implications, both for healthcare services and patients Here we describe our experience of the first 68 patients we have tested for SARS-CoV-2 at a Regional Infectious Diseases unit (RIDU) in the UK. Specialist Infectious Diseases consultant-delivered assessment of a group of patients who predominantly have mild illness is unlikely to be sustainable, especially as the case-definition broadens to include a wider geographical area and/or COVID-19 patients requiring inpatient care becomes more common in the UK. doi = 10.1101/2020.02.29.20029462 id = cord-322385-sc2vxxnn author = Ebinger, J. title = SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers date = 2020-08-04 keywords = SARS; covid-19 summary = Main Outcomes: Using Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection. Recognizing the range of factors that might influence antibody status in a given individual, we focused our study on not only estimating seroprevalence but also on identifying factors associated with seropositivity and relative antibody levels within the following three categories: (1) pre-existing demographic and clinical characteristics; (2) potential Covid-19 illness related exposures; and, (3) Covid-19 illness related response variables (i.e. different types of self-reported symptoms). In adjusted analyses, we compared differences between serology status (i.e. antibody positive versus negative) in each variable of interest, grouped into one of three categories: (1) preexisting demographic and clinical characteristics (e.g. age, gender, ethnicity, race, and selfreported medical comorbidities); (2) Covid-19 related exposures (e.g. self-reported medical diagnosis of Covid-19 illness, household member with Covid-19 illness, number of people living in the home including children, type of home dwelling, etc); and, (3) Covid-19 related response variables (e.g. self-reported fever, chills, dry cough, anosmia, nausea, myalgias, etc.). doi = 10.1101/2020.07.31.20163055 id = cord-319706-2e9jrv0s author = Ebinger, Joseph E. title = Pre-existing traits associated with Covid-19 illness severity date = 2020-07-23 keywords = SARS; african; covid-19; patient summary = For all patients considered to have Covid-19, based on direct or documented laboratory test result and suggestive signs and/or symptoms, we obtained information from the electronic health record (EHR) and verified data for the following demographic and clinical characteristics: age at the time of diagnosis; sex; race; ethnicity; smoking status defined as current versus prior, never, or unknown; comorbidities, including obesity, as clinically assessed and documented by a provider with ICD-10 coding; and, chronic use of angiotensin converting enzyme (ACE) inhibitor or angiotensin II receptor blocker (ARB) medications. For the primary outcome of illness severity, categorized by escalating levels of care (i.e., hospitalization, intensive care, intubation), the pre-existing characteristics that demonstrated statistical significance in age-and sex-adjusted models included older age, male sex, African American race, obesity, hypertension, diabetes mellitus, and the Elixhauser comorbidity score ( Table 2 ; Fig 3) . doi = 10.1371/journal.pone.0236240 id = cord-289522-7u3d6nfc author = Ebrahimi, Mina title = COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population date = 2020-10-17 keywords = COVID-19; SARS summary = title: COVID-19 Patients: A Systematic Review and Meta-Analysis of Laboratory Findings, Comorbidities, and Clinical Outcomes Comparing Medical Staff versus the General Population This review compared coronavirus disease 2019 (COVID-19) laboratory findings, comorbidities, and clinical outcomes in patients from the general population versus medical staff to aid diagnosis of COVID-19 in a more timely, efficient, and accurate way. Two reviewers separately extracted the data from included studies, considering key characteristics including author, publication year, country, type of study, sample size, laboratory findings, comorbidities, and final clinical outcomes. Further analysis revealed the frequency of clinical manifestations in infected medical staff were similar to patients in the general public (Table 3) . The findings of this COVID-19 meta-analysis review revealed that the normal or abnormal outcome of a patient''s laboratory results may shed light on the stage of the disease and its progression. Laboratory findings, signs and symptoms, clinical outcomes of Patients with COVID-19 Infection: An updated systematic review and meta-analysis doi = 10.24171/j.phrp.2020.11.5.02 id = cord-312849-vgzvpwz9 author = Eckbo, Eric J. title = Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples date = 2020-11-10 keywords = COVID-19; SARS summary = title: Evaluation of the BioFire® COVID-19 Test and Respiratory Panel 2.1 for Rapid Identification of SARS-CoV-2 in Nasopharyngeal Swab Samples The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of SARS-CoV-2 in nasopharyngeal swabs. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RdRP and E genes. This report describes the results of an independent evaluation of the performance characteristics of the BioFire COVID-19 Test and the RP2.1 for detection of SARS-CoV-2. The BioFire COVID-19 Test and Respiratory Panel 2.1 are easy-to-use, highly sensitive, and rapid assays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. This evaluation demonstrates that the assays perform comparably to our laboratory developed real-time PCR assay, with 100% agreement in testing results for clinical specimens and acceptable performance at their stated limits of detection. doi = 10.1016/j.diagmicrobio.2020.115260 id = cord-265682-yac7kzaf author = Eden, John-Sebastian title = An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date = 2020-04-10 keywords = Iran; New; SARS summary = Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is directly linked to the Iranian epidemic, from where genomic data are currently lacking. doi = 10.1093/ve/veaa027 id = cord-331701-izkz1hz4 author = Eden, John-Sebastian title = An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date = 2020-03-17 keywords = Iran; SARS summary = Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. Herein, we show that the genomic analyses of SARS-CoV-2 strains from Australian returned travellers with COVID-19 disease may provide important insights into viral diversity present in regions currently lacking genomic data. However, while we cannot completely discount that the cases in Australia and New Zealand came from other sources including China, our phylogenetic analyses, as well as epidemiological (recent travel to Iran) and clinical data (date of symptom onset), provide evidence that this clade of SARS-CoV-2 is linked to the Iranian epidemic, from where genomic data is currently lacking. doi = 10.1101/2020.03.15.992818 id = cord-288660-z0k2ui3y author = Edler, Alice A. title = Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology date = 2006-02-28 keywords = H5N1; SARS; avian summary = Abstract Avian flu, influenza A subtype H5N1, is an emergent and virulent disease that poses a threat to the health and safety of the world community. Avian flu is responsible for the current outbreak in Asia; H5N1 has now displayed probable human-to-human transmission; it could be a harbinger of a global epidemic. Subtype H5N1, currently known as avian or bird flu, is of particular interest because of its increasing pathogenicity and ability to form a new viral subtype to which there is no native immunity in human hosts. However, if individuals are infected, the current case-fatality rate for avian flu is thought to be greater than 50% in humans [2] and greater than 90% in birds and other mammals. The key to addressing the threat of avian flu in all populations, including anesthesiologists, is prevention of the disease and containment of its spread through traditional, public health preparedness: basic hygiene, Universal Precautions, and special procedures designed to prevent exposure and contain infection in health-care settings. doi = 10.1016/j.jclinane.2005.12.004 id = cord-344017-qldawc8m author = Edouard, S. title = Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France date = 2020-11-11 keywords = IFA; SARS; patient summary = Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. In this study, we are reporting our experience to develop an indirect immunofluorescent assay (IFA) for the detection of anti-SARS-CoV-2 antibodies that we implemented before any other serological test was available in France. ELISA To compare our IFA with commercial ELISA IgG, we randomly selected 70 sera with possible cross-reactivity (including 45 sera with possible nonspecific serological interference and 25 sera from patients diagnosed with common others human coronavirus), 30 sera collected before the pandemic and 100 sera from our cohort of SARS-CoV-2-infected patients among all the sera that we tested by IFA. Some other studies also reported an earlier serological response in severe compared to mild SARS-CoV-2 infection [5, 20, 25] that is consistent with the earlier seroconversion that we found in patients with poor clinical outcome (PClinO). doi = 10.1007/s10096-020-04104-2 id = cord-255229-w2xtxo9a author = Edson, Daniel C title = Identification of SARS-CoV-2 in a Proficiency Testing Program date = 2020-07-20 keywords = SARS; result summary = OBJECTIVES: At the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States, testing was limited to the Centers for Disease Control and Prevention–developed reverse transcription polymerase chain reaction assay. METHODS: The American Proficiency Institute sent 2 test samples to 346 clinical laboratories in order to assess the accuracy of SARS-CoV-2 assays. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. Conclusions: Overall performance in this SARS-CoV-2 RNA detection challenge was excellent, providing confidence in the results of these new molecular tests and assurance for the clinical and public health decisions based on these test results. In this report we present the results of the first US study of SARS-CoV-2 accuracy by API participant laboratories from the 2020 First Test Event. doi = 10.1093/ajcp/aqaa128 id = cord-271090-91lzr4tz author = Edwards, Kathryn M. title = Anticipating SARS-CoV-2 Vaccine Testing, Licensure, and Recommendations for Use date = 2020-06-19 keywords = SARS; phase summary = Because of concerns raised about enhanced disease after wild virus infection in animal studies following vaccination against severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and Middle East respiratory syndromecoronavirus (MERS-CoV) (9, 10), experts have met and proposed immunologic criteria to be evaluated in animals and humans to detect and consequently reduce the risk of enhanced disease (11) . Some of the Phase 1 studies evaluating SARS-CoV-2 vaccines have also included individuals >65 years of age to assess safety and immunogenicity in this population, which is at greater risk for severe COVID-19 disease. With SARS-CoV-2 vaccines, Phase 2 studies are planned to expand the safety profile and to assess immune responses in larger numbers of subjects. The Phase 3 efficacy trials planned for SARS-CoV-2 vaccines in the United States are expected to enroll 20,000 to 30,000 individuals, the numbers projected to be necessary to determine whether the vaccines will prevent significant disease over a period of 6 months follow-up. doi = 10.1016/j.jpeds.2020.06.048 id = cord-278812-5jps95q9 author = Edwards, Sarah J L title = Anthroponotic risk of SARS-CoV-2, precautionary mitigation, and outbreak management date = 2020-07-02 keywords = SARS summary = Following early reports of anthroponotic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and mixed messages over anthroponotic risk, some pets were reportedly abandoned to fend for them selves or killed. Evidence of infection of animals with SARS-CoV-2 has been shown experimentally both in vivo and in vitro for mammals including monkeys, cats, ferrets, rabbits, foxes, and hamsters, while bioinformatic studies also predict infectivity of pigs and wild boar among other mammals. 6 Additional experimental inoculation of animals would not help because small sample sizes and bioinformatic studies alone cannot confirm that a whole species is incapable of being infected by SARS-CoV-2. Sufficient evidence exists of anthroponosis of SARS-CoV-2 on which to base precautionary steps to mitigate the risks it poses. Infection and rapid transmission of SARS-CoV-2 in ferrets Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Potential fecal transmission of SARS-CoV-2: current evidence and implications for public health SARS-CoV-2 infection in farmed minks, the Netherlands doi = 10.1016/s2666-5247(20)30086-0 id = cord-276057-427ji6ze author = Effenberger, Maria title = Faecal calprotectin indicates intestinal inflammation in COVID-19 date = 2020-04-20 keywords = SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-RNA was detected in the faeces in ~50% of patients with COVID-19 3 5 6 ; SARS-CoV-2 viral particles were observed by electron microscopy in stool samples from two patients without diarrhoea 2 ; and one study reported SARS-CoV-2 infection of the oesophagus, stomach, duodenum and rectum. 7 In this pilot study, we explored a relation between GI symptoms, intestinal inflammation (determined by FC) and faecal SARS-CoV-2-RNA in hospitalised patients with COVID-19 who did not require intensive care measures. We report evidence that SARS-CoV-2 infection in patients with COVID-19 indeed instigates an inflammatory response in the gut, as evidenced by diarrhoea, elevated FC (largely expressed by neutrophil granulocytes 7 ) and a systemic IL-6 response. Faecal SARS-CoV-2 RNA was not detected during acute diarrhoea but could be detected in asymptomatic patients with or without previous diarrhoeal symptoms. doi = 10.1136/gutjnl-2020-321388 id = cord-346758-pi1hf6xg author = Egerup, P. title = Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns date = 2020-09-15 keywords = COVID-19; SARS; September summary = Two smaller case reports from China documented SARS-CoV-2 antibodies in newborns with COVID-19 positive mothers indicating possible vertical transmission. This study aimed to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns. We here report the results of a prospective cohort study with unselected serological testing in 1,313 parturient women, 1,189 partners and 1,206 newborns to identify if SARS-CoV-2 infection is associated with obstetric and neonatal complications. The serum from the blood samples from women, partners and newborns were analyzed for SARS-CoV-2 antibodies (IgM and IgG). There was no significant difference between pre-pregnancy characteristics in relation to SARS-CoV-2 antibodies, except blood type and that women with antibodies reported more COVID-19-like symptoms (p=0.025). In this prospective cohort study with serological testing of parturient women, partners and newborns we found no association between COVID-19 and obstetric-or neonatal complications. doi = 10.1101/2020.09.14.20191106 id = cord-315685-ute3dxwu author = Ehaideb, Salleh N. title = Evidence of a wide gap between COVID-19 in humans and animal models: a systematic review date = 2020-10-06 keywords = COVID-19; CoV-2; SARS; model summary = The systematic search identified 101 studies and 326 preprints, of which 400 articles were excluded because they were reviews, non-original articles, unrelated to the COVID-19 infection, or experimental animals that do not support SARS-CoV-2 replication such as pigs, ducks, and chickens ( Fig. 1 and Additional file 2). The aims were to investigate the pathogenesis of COVID-19 (n = 15), testing drugs and vaccines (n = 14), the host Table 1 Search strategy and selection criteria We searched the MEDLINE, as well as BioRxiv and MedRxiv preprint servers for original research describing or using an animal model of SARS-CoV-2 induced COVID published in English from January 1, 2020, to May 20, 2020. We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). We used the search terms (COVID-19) OR (SARS-CoV-2) AND, (animal models), (hamsters), (nonhuman primates), (macaques), (rodent), (mice), (rats), (ferrets), (rabbits), (cats), and (dogs). doi = 10.1186/s13054-020-03304-8 id = cord-320092-0qnvydux author = Ehsani, Sepehr title = COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein date = 2020-10-16 keywords = COVID-19; SARS; hepcidin; iron; protein; spike summary = An implication of this preliminary observation is to suggest a potential route of investigation in the coronavirus research field making use of an already-established literature on the interplay of local and systemic iron regulation, cytokine-mediated inflammatory processes, respiratory infections and the hepcidin protein. c The position of the disulfide bonds in the sequence of the mature human hepcidin is illustrated along with the potential palmitoylation residues (ten cysteines) of the cytoplasmic tail of the SARS-CoV-2 spike protein. If the sequence similarity reported here is actually playing a significant role at the cellular level, could it be that, although the cellular localizations appear to be different based on current knowledge, the SARS-CoV-2 spike protein cytoplasmic tail can partly mimic the structure of hepcidin and interact with ferroportin? In addition, a notyet-fully-established link of relevance here is the observations of a Kawasaki-disease-like systemic vasculitis syndrome in children infected with the novel Fig. 3 Summary of salient facets of coronavirus spike protein and human hepcidin biology. doi = 10.1186/s13062-020-00275-2 id = cord-262415-cj4pjuuc author = Eiros, R. title = Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers date = 2020-07-14 keywords = July; SARS; preprint summary = title: Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers The present study was designed to search for evidence of pericardial and myocardial involvement after past SARS-CoV-2 infection comprehensively studied by clinical assessment, laboratory tests, electrocardiography and cardiac magnetic resonance (CMR) imaging. Overall, the drug therapy aimed at Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. 10 This study examined the prevalence of pericarditis and of myocarditis in a cohort of SARS-CoV-2 positive health-care workers in Salamanca, Spain. However, the strength of this study is the addition of non-hospitalized participants and also the inclusion of participants diagnosed of past SARS-CoV-2 infection through serology, who also had a high prevalence of pericarditis and myocarditis. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. Pericarditis and myocarditis long after SARS-CoV-2 infection: a cross-sectional descriptive study in health-care workers Eiros et al. doi = 10.1101/2020.07.12.20151316 id = cord-349485-iomk99lv author = Eis-Hübinger, Anna M. title = Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples date = 2020-04-22 keywords = SARS summary = title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples To rapidly identify unrecognized cases in hospitals in an efficient, resource-saving and cost effective manner we propose an ad hoc laboratory-based surveillance approach for SARS-CoV-2. It is based upon minipool (MP) testing of nucleic acid preparations of respiratory samples submitted to laboratories for routine diagnostics. The workflow comprises individual nucleic acid (NA) extraction of respiratory samples, pooling of extracted NA samples in batches of 10 and SARS-CoV-2 specific real-time RT-PCR. We report a diagnostic workflow for the laboratory-based surveillance of SARS-CoV-2 in a rapid and cost effective manner. From a public health perspective an easy to establish and cost effective laboratory-based screening strategy may assist in rapid case detection, surveillance and ultimately in a better understanding of this epidemic (7) . doi = 10.1016/j.jcv.2020.104381 id = cord-324800-l8xl4g2a author = Eisenberg, Michael L. title = Coronavirus Disease 2019 (COVID-19) and men’s reproductive health date = 2020-04-22 keywords = SARS summary = As the COVID-19 pandemic rages across the world, the scientific community continues to study the pathophysiology of SARS-Cov-2 virus to guide transmission, susceptibility, and treatment. While cardiac, ocular, and neurologic symptoms of the COVID-19 have been reported, the reproductive implications of coronavirus infection remain unknown. Indeed, the current report was not able to assess any changes in semen quality among the participants thus it remains unknown how and if the fecundability of infected men is impaired. In addition, as more than 80% of those who are infected by the coronavirus are asymptomatic, the reproductive implications for these men would likely be favorable but also remains unknown. But given the current impact of the pandemic on the world, the likelihood the virus will remain for some time, and that over 100 million babies are born every year, the reproductive implications of SARS-Cov-2 should be further studied. doi = 10.1016/j.fertnstert.2020.04.039 id = cord-327214-kcbxyhhh author = Eketunde, Adenike O title = A Review of Postmortem Findings in Patients With COVID-19 date = 2020-07-28 keywords = COVID-19; SARS; patient summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus originated in Wuhan, China, and has spread rapidly across the world. According to Merad and Martin''s study, the hyper inflammation in severe COVID-19 patients shared similarities with cytokine release syndromes, including macrophages activation syndrome. Minimally invasive autopsies of three COVID-19 patients in Chongqing, China revealed damage to the alveolar structure with minor serous and fibrin exudation and hyaline membrane formation [8] . The hypercoagulable state has been linked to a poor prognosis in patients with severe COVID-19, which leads to a microthrombi formation in the lungs, lower limbs, hands, brain, heart, liver, and kidneys, as a result of the activation of the coagulation pathway. There is a strong association with the hyperinflammatory state, which can be explained by most of the signs and symptoms that are exhibited by COVID-19 patients, including most of the pathological findings. Fatal eosinophilic myocarditis in a healthy 17-year-old male with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2c) doi = 10.7759/cureus.9438 id = cord-344884-dcoq9srf author = El Otmani, H. title = Neuro-COVID-19: What are we talking about? date = 2020-06-06 keywords = SARS summary = Q2 In a very short time after the onset of the COVID-19 infection, a ''''flood'''' of reports regarding SARS-Cov-2 related neurological manifestations were published. While more than three and a half million individuals are affected worldwide to date, most arguments of COVID-19related neurological manifestations are supported by case reports or small series [1] [2] [3] . On the other hand, a review of the available data shows that the implication of the SARS-Cov-2 virus as a direct cause of neurological complications is not established yet. In support to this, to date, only 2 cases of meningitis or encephalitis with evidence of viral SARS-Cov-2 detection in CSF are reported [6, 7] . So far, a dozen of COVID-19-related Guillain-Barré syndromes (GBS) have been reported, which seems to be marginal compared to the high prevalence of infected individuals [10] . Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Neurologic Features in Severe SARS-CoV-2 Infection doi = 10.1016/j.neurol.2020.05.004 id = cord-314942-eym2rh8v author = El Tabaa, Manar Mohammed title = New putative insights into neprilysin (NEP)-dependent pharmacotherapeutic role of roflumilast in treating COVID-19 date = 2020-10-01 keywords = IL-6; SARS; covid-19; inflammatory summary = Being a highly selective phosphodiesterase-4 inhibitors (PDE4i), roflumilast acts by enhancing the level of cyclic adenosine monophosphate (cAMP), that probably potentiates its anti-inflammatory action via increasing neprilysin (NEP) activity. Because activating NEP was previously reported to mitigate several airway inflammatory ailments; this review thoroughly discusses the proposed NEP-based therapeutic properties of roflumilast, which may be of great importance in curing COVID-19. Additionally, breaking ET-1 by NEP will prolong the anti-inflammatory effect of 716 roflumilast via maintaining the high cAMP level which is underscored to play an 717 important role in improving the immune system of highly risk COVID-19 groups 718 (Graf et al., 1995; Raker et al., 2016) . Degrading ET-1 can also inhibit pulmonary fibrosis via blocking the ET-1-induced transforming growth factor-β1 (TGF-β1), and at the same time, maintain the high level of cAMP which may contribute for long-term anti-inflammatory effect of roflumilast. doi = 10.1016/j.ejphar.2020.173615 id = cord-299911-v95pf3eg author = El-Ghiaty, Mahmoud A. title = Cytochrome P450-mediated drug interactions in COVID-19 patients: current findings and possible mechanisms date = 2020-06-26 keywords = COVID-19; IL-6; SARS; drug; p450 summary = Based on the conclusions drawn from the currently rapidly evolving knowledge about COVID-19, our hypothesis is built on the potential modulation of CYPs activity by the inflammatory environment provoked by SARS-CoV-2 infection, as well as the pathologic involvement of the liver which harbors the majority of the drug metabolizing enzymes (DMEs). Systemic inflammation and immune response represent a substantial element in many acute and chronic diseases which is strongly implicated in altering drug pharmacokinetics through, mainly, modulating the expression and activity of DMEs. As a main contributor to the metabolic biotransformation of most drugs, CYPs are widely involved in such disease-drug interactions [19] . For decades, IL-6 has been recognized as the major inflammatory element that provokes a significant repressive effect on the expression and activity of different CYPs. Human recombinant interleukin 6 (rhIL-6) has shown concentration-dependent blocking of phenobarbital-mediated induction of CYP2B1/2 mRNA and activity in rat hepatocytes [48] . doi = 10.1016/j.mehy.2020.110033 id = cord-292367-ocbsmmt6 author = El-Masri, Maher M. title = Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date = 2012-02-29 keywords = SARS; infection summary = Such comparison is intended to provide a surrogate measure of the influence that strict enforcement of infection control strategies during the SARS outbreak may have had on the risk of HAIs. Methods A retrospective chart review was conducted on the medical records of 400 intensive care patients who were admitted to the ICU three months before and during the 2003 SARS outbreak. The intent of such comparison is to provide a surrogate measure of the influence that strict enforcement of infection control guidelines might have had on the risk of developing HAIs. A retrospective chart review was conducted on the medical records of 400 patients who were admitted to the intensive care unit of a community-based hospital in Southwestern Ontario. doi = 10.1016/j.iccn.2011.10.003 id = cord-296950-9dldbs6o author = El-Zein, Rayan S title = COVID-19-associated meningoencephalitis treated with intravenous immunoglobulin date = 2020-09-06 keywords = COVID-19; SARS summary = Neurologic manifestations in patients infected with SARS-CoV-2 have been reported such as anosmia, ageusia, ataxia, seizures, haemorrhagic necrotising encephalopathy, and Guillain-Barré syndrome. The SARS-CoV-2 CSF PCR was negative; however, a high index of suspicion remained due to the temporal relationship of his current symptoms and the recent COVID-19 pneumonia. Our report describes a case of encephalitis associated with SARS-CoV-2 which showed clinical improvement with IVIg therapy. Moriguchi et al 5 described what appears to be the first case of COVID-19-associated meningoencephalitis presenting with convulsions and confirmed with a positive SARS-CoV-2 CSF PCR; their patient had abnormal MRI findings of the medial temporal lobe and was treated with favipiravir. Paniz-Mondolfi et al 6 reported a case of COVID-19-associated pneumonia in a 74 years old with Parkinson''s who succumbed to his illness on day 11; however, SARS-CoV-2 was found in the brain capillary endothelium and neuronal cell bodies on postmortem examination. doi = 10.1136/bcr-2020-237364 id = cord-286365-fy0a8mb4 author = ElHawary, Hassan title = Bibliometric Analysis of Early COVID-19 Research: The Top 50 Cited Papers date = 2020-10-13 keywords = COVID-19; SARS summary = CONCLUSION: By highlighting the characteristics of the top 50 cited COVID-19-related articles, the authors hope to disseminate information that could assist researchers to identify the important topics, study characteristics, and gaps in the literature. To that end, the goal of this study was to present a bibliometric analysis to identify and dissect the characteristics of the top 50 cited COVID-19-related articles published early on following the outbreak. 62 The majority of the highly cited research assessed COVID-19''s clinical presentation and disease description while only 7 papers discussed potential treatment. While this limitation is present with any bibliometric analysis, the main goal of this study was to highlight the characteristics of the highly cited research articles early during the COVID-19 pandemic and the dynamic nature of citation count should not diminish the value of the information presented here. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.1177/1178633720962935 id = cord-307489-2liu4anc author = Elavia, Nasha title = An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia date = 2020-05-23 keywords = CoV-2; SARS summary = title: An Atypical Presentation of Acute Pulmonary Embolism With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia Clinical presentation and severity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) varies greatly amongst patients, as supported by recent literature. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) presenting with atypical gastrointestinal symptoms in a patient with SARS-CoV-2 infection. This atypical presentation of PE is unique to our case and highlights the significance of a high index of clinical suspicion for SARS-CoV-2 and its associated thrombogenic effect, even in patients with atypical symptoms. Here, we would like to describe a case of acute bilateral pulmonary embolism (PE) in a patient with SARS-CoV-2 pneumonia who mainly presented with gastrointestinal symptoms. Our patient however presented mainly with gastrointestinal symptoms, which have been reported with SARS-CoV-2; however, with significant hypoxia in the absence of a respiratory viral syndrome although with a low pretest probability for PE, we decided to further evaluate the patient for hypoxia. doi = 10.7759/cureus.8249 id = cord-340535-78bpvtuf author = Elbay, Rümeysa Yeni title = Depression, Anxiety, Stress Levels of Physicians and Associated Factors In Covid-19 Pandemics date = 2020-05-27 keywords = SARS; covid-19 summary = AIM: To investigate anxiety, stress, and depression levels of physicians during the Covid-19 outbreak and explored associated factors in both clinical and general site. Factors found to be associated with higher DAS-21 total scores in frontline workers were as follows: increased weekly working hours, increased number of Covid-19 patients cared for, lower level of support from peers and supervisors, lower logistic support, and lower feelings of competence during Covid-19 related tasks. In an early study investigating immediate psychological response during Covid-19 epidemic among general population in China, 53.8% of participants rated the psychological impact of the outbreak as moderate or severe (1) . In another study investigating long term psychological effects of SARS outbreak on healthcare workers, 23% of staff were found to have moderate or severe depressive symptoms in a 3year follow-up (4) . Based on this perspective, here, we aimed to investigate anxiety, stress and depression levels of physicians during Covid-19 outbreak and explored associated factors in both clinical and general site. doi = 10.1016/j.psychres.2020.113130 id = cord-264326-teahway7 author = Eleftheriou, Phaedra title = In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus date = 2020-05-29 keywords = DPP-4; HCV; SARS; protease summary = According to docking analysis the most promising results were found for HCV protease, DPP-4, α-thrombin and coagulation Factor Xa known inhibitors, with several of them exhibiting estimated free binding energy lower than −8.00 kcal/mol and better prediction results than reference compounds. Since the 3D structure of the active site of the enzyme is crucial for catalytic activity, we proceeded to a comparison of the SARS-CoV-2 main protease, Mpro, with the HIV-1 protease, the HCV protease (NS3 protein) and the human proteases DPP-4, thrombin, Factor Xa, renin and ACE, which constitute known drug targets with approved inhibitors. The structural similarity between the SARS-CoV-2 protease and some of the selected proteases, in combination with the existence of the same amino acids at certain positions of the substrate cleavage site, such as Ser at the P1'' position of the recognition sequence of the HCV protease and thrombin are promising features in the effort to identify effective SARS-CoV-2 protease inhibitors among the approved drugs of the selected proteases. doi = 10.3390/molecules25112529 id = cord-290429-0d34abdo author = Elengoe, Asita title = COVID-19 Outbreak in Malaysia date = 2020-06-17 keywords = COVID-19; SARS summary = The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic outbreak emerged in December 2019 from Wuhan City, Hubei Province, China and spread to the rest of the world. They reported that the virus had 96.3% genetic similarity with a Yunnan bat coronavirus RaTG13 and 70% homology with severe acute respiratory syndrome coronavirus (SARS-CoV) [2] . On the 12 th January 2020, the World Health Organization (WHO) announced the cause of this epidemic outbreak was a novel coronavirus discovered in 2019 (2019-nCoV) or SARS-CoV-2 and named the disease coronavirus disease 2019 (COVID-19) [3] . Coronavirus COVID-19 cases spiked across Asia after a mass gathering in Malaysia. The origin, transmission, and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak -An update on the status Epidemiology, causes, clinical manifestation and diagnosis, prevention, and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review doi = 10.24171/j.phrp.2020.11.3.08 id = cord-296692-t5p09le8 author = Elgin, T.G. title = The changing landscape of SARS-CoV-2: Implications for the maternal-infant dyad date = 2020-09-07 keywords = China; SARS; clinical; covid-19; pregnant summary = In December of 2019 cases of an unknown viral pneumonia were reported from Wuhan, Hubei, China Although much uncertainty remains, regarding the natural history and demographics of COVID19 , the virus appears to primarily cause infection in adults over 51 with case fatality rates increasing dramatically with age [5] . There are, however, emerging case reports of pregnant mothers who test positive for COVID-19 infection and who remain either completely asymptomatic [23] and or manifest mild symptoms in the subsequent 24 hours following delivery. Although clinical evidence is lacking, the case numbers to date of COVID-19 in pregnancy remain very low [32] and case reports of two neonates who tested positive for SARS-CoV-2 shortly after birth lends some credence to the concern. Vertical transmission of coronavirus disease 19 (COVID-19) from infected pregnant mothers to neonates: A review An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes doi = 10.3233/npm-200460 id = cord-274184-hm516x6p author = Elli, Luca title = Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date = 2020-04-27 keywords = PCR; SARS; covid-19; patient summary = From the abovementioned reasons we must deduce that: -in high SARS-CoV-2 incidence areas where PCR assays are not extensively performed, Covid-19 cannot be ruled out by simple clinical examination or epidemiological link; -the greatest amount of efforts and precautions are required to minimize the spread of the disease and to preserve medical staff from infection. In our current situation, which is characterized by high incidence of Covid-19 and relative scarcity of surveillance assays in asymptomatic subjects, for the abovementioned reasons we recommend different modalities of individual protection based on a strict clinical and epidemiological stratification of patients with potential SARS-CoV-2 infection undergoing endoscopic examination. In this setting, regardless of the classification of patients (high/low-risk, , in order to prevent the medical staff from becoming infected, we suggest high-performance personal protection equipment, i.e. a N95 or FFP2/FFP3 respirator, a hairnet, a double pair of gloves, a disposable waterproof surgical gown, a face shield (which we prefer because it allows to protect, and then spare, respirators) or goggles, and work safety clogs (Table 1) . doi = 10.1016/j.dld.2020.04.018 id = cord-310623-zbjgr9jk author = Ellington, Sascha title = Characteristics of Women of Reproductive Age with Laboratory-Confirmed SARS-CoV-2 Infection by Pregnancy Status — United States, January 22–June 7, 2020 date = 2020-06-26 keywords = COVID-19; SARS summary = These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation compared with nonpregnant women, but their risk for death is similar. These findings suggest that among women of reproductive age with COVID-19, pregnant women are more likely to be hospitalized and at increased risk for ICU admission and receipt of mechanical ventilation * https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html. In contrast, however, ICU admission and receipt of mechanical ventilation are distinct proxies for illness severity (8) , and after adjusting for age, presence of underlying conditions, and race/ethnicity, the risks for both (N = 91,412) , by pregnancy status, age group, and race/ethnicity, and relative risk for these outcomes comparing pregnant women to nonpregnant women aged 15-44 years -United States, January 22-June 7, 2020 Among reproductive-age women with SARS-CoV-2 infection, pregnancy was associated with hospitalization and increased risk for intensive care unit admission, and receipt of mechanical ventilation, but not with death. doi = 10.15585/mmwr.mm6925a1 id = cord-285711-2utcn0hw author = Elliott, Robert title = COVID-19 Related Mortality During Management of a Hepatic Abscess date = 2020-09-22 keywords = SARS; covid-19 summary = Declared a pandemic by the World Health Organization on March 11th, 2020, COVID-19 has challenged healthcare systems to limit the spread of community and hospital-acquired of disease. In the setting of an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), healthcare systems have been challenged to limit in-hospital transmission of the virus; a task noted to be incredibly difficult given the suggestion of what appears to be fairly high viral transmissibility (3, 4) . We presented a case of a patient death from SARS-CoV-2 infection prior to the implementation of universal masking. In addition, now having lived this experience with universal masking, we question: (1) if there might be a survival advantage to short-interval masking during the height of seasonal influenza activity and (2) if there may be a benefit to expanded use of N95 respirators in the IR suite during AGP-type interventions performed on individuals presenting with respiratory infections not limited to Covid-19. doi = 10.1016/j.jradnu.2020.09.001 id = cord-035292-pan415s7 author = Elmessaoudi-Idrissi, Mohcine title = Structure-guided discovery approach identifies potential lead compounds targeting M(pro) of SARS-CoV-2 date = 2020-11-11 keywords = SARS summary = Targeting the SARS-CoV-2 M(pro) crystal structure (PDB ID: 6LU7) a combination of in silico screening, molecular docking, and dynamic approaches, a set of 5000 compounds of the ZINC database were screened. As a result, we identified and ranked the top 20 compounds based on the scores of ligand-interaction, their drug-likeness properties, and their predicted antiviral efficacies. Taking the advantage of the main protease (M pro ) structure that became available recently [14] , we carried out a virtual in silico screening of nearly 5000 ZINC compound database to identify new inhibitors targeting the SARS-CoV-2. The docking simulations showed, by a ranking of binding energies score, that compound 2-[2-(2Fig. 1 Structure of SARS-CoV-2 main protease M pro . Based on our computational strategy, the pharmacokinetic properties and drug-likeness of the top 20 ranked scoring molecules that show the potential of M pro inhibitors of the SARS-CoV-2 are shown in supplementary table 1. doi = 10.1007/s13337-020-00627-6 id = cord-350189-2su7oqbz author = Elmén, Joacim title = Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date = 2005-01-14 keywords = LNA; RNA; SARS; siRNA summary = A priori, this suggests that LNA may be used to increase the functional half-life of siRNA in vivo by two different mechanisms, e.g. by enhancing the resistance of the constituent RNA strands against degradation by single-stranded RNases and by stabilizing the siRNA duplex structure that is critical for activity. Next, we examined the effect of making single RNA to LNA exchanges at base-paired positions in the antisense strand of the firefly luciferase siLNA1. Although we cannot exclude that these modifications somehow prevent loading of the antisense strand into RISC, we believe this to be unlikely given the functionality of many significantly more modified siLNAs. Rather, as these positions are all close to the site where RNA target cleavage occurs [between pos. The SARS siRNA (Table 1) has identical closing base-pairs at both ends (A:U) making it likely that enough of both the antisense and sense strand would be incorporated into RISC to observe activity on the respective targets. doi = 10.1093/nar/gki193 id = cord-255495-xnoppq3y author = Elrashdy, Fatma title = On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date = 2020-07-09 keywords = COVID-19; PCR; RNA; SARS summary = It is possible that this "Trojan horse" strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this "silence" time period and then started to re-spread again. The fact that SARS-CoV-2 can be present within the vacuoles or double membrane vesicles (DMVs) within the host cells was proven by the careful post-mortem histopathological analysis of the renal samples of patients with COVID-19 by light microscopy, electron microscopic examination, and immunostaining (Farkash et al., 2020; Su et al., 2020) . Is this "Trojan horse" strategy of the release of the SARS-CoV-2-loaded exosomes or EDMVs represent a reasonable explanation for the appearance of the viral RNA in the recovered COVID-19 patients 7-14 day post discharge? doi = 10.1080/07391102.2020.1790426 id = cord-303659-mzez7v4d author = Elsayed, Sarah M title = The Possibility and Cause of Relapse After Previously Recovering From COVID-19: A Systematic Review date = 2020-09-05 keywords = COVID-19; SARS; relapse summary = There are reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial clearance of the virus. There have been reports of patients who tested positive for SARS-Cov-2 after clinical recovery and initial documented clearance of the virus. The publications included COVID-19 positive patient data and the relapse of disease was confirmed by PCR; the full text was available for these publications. Data were collected in the following categories when available: Study design; Study country; Patient demographics; Clinical signs and symptoms; Laboratory findings; Imaging studies; Dynamics of the oropharyngeal swab test; Treatment of the first presentation; The clinical picture of relapse; Day of a positive result after confirmed negative We tabulated the data using Microsoft Excel (2010, Microsoft Corp, Redmond, WA). The study reports a total of 11 patients (6 females and 5 males), all from China, who tested positive for COVID-19. doi = 10.7759/cureus.10264 id = cord-260180-kojb8efv author = Elsoukkary, Sarah S. title = Autopsy Findings in 32 Patients with COVID-19: A Single-Institution Experience date = 2020-09-17 keywords = COVID-19; Fig; SARS; case; patient summary = METHODS: We report the clinicopathologic findings from 32 autopsy studies conducted on patients who died of COVID-19 including routine gross and microscopic examination with applicable special and immunohistochemical staining techniques. The purpose of this study is to describe clinical and pathologic findings in major organ systems of patients who died from SARS-CoV-2 infection. In this study, we described the unique and multisystem clinical and pathologic findings in 32 autopsies of patients who died from the novel coronavirus, SARS-CoV-2. On histologic examination, we observed findings secondary to the patients'' preexisting conditions in the heart, lungs, liver, and kidneys, as well as changes secondary to SARS-CoV-2 infection such as various stages of DAD and multiple thromboemboli in large and small vessels in multiple organs. While the lung findings are most significant for the majority of those infected, other organ systems are frequently involved including with widespread microscopic thromboses in numerous organs, as well as liver, kidney, and lymph node pathology. doi = 10.1159/000511325 id = cord-351691-3egwvb59 author = Elzupir, Amin O. title = Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2 date = 2020-10-23 keywords = COVID-19; SARS summary = This study investigates the inhibitory effect of SARS-CoV-2 3-chymotrypsin-like protease (3CL(pro)) using caffeine and caffeine-containing pharmaceuticals (3CPs) based on molecular dynamics simulations and free energy calculations by means of molecular mechanics-Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics-generalized-Born surface area (MMGBSA). Of these 3CPs, seven drugs approved by the US-Food and Drug Administration have shown a good binding affinity to the catalytic residues of 3CL(pro) of His(41) and Cys(145): caffeine, theophylline, dyphylline, pentoxifylline, linagliptin, bromotheophylline and istradefylline. This study demonstrates the inhibitory effect of 3CL pro by means of approved caffeine and caffeine-containing pharmaceuticals (3CPs) using the molecular docking approach. An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations doi = 10.1080/07391102.2020.1835732 id = cord-253468-pf0xubii author = Emara, Mohamed H title = Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients date = 2020-09-02 keywords = SARS summary = title: Ketonuria with or without ketoacidosis as the presenting manifestation of SARS-CoV-2 (COVID-19) among uncontrolled Type 2 Diabetic patients We hereby present the data of 3 patients presented to our OPD and were admitted as diabetic ketoacidosis (DKA) and 2-3 days later they developed manifestations suggestive of and proved by swabbing as positive cases. Chest auscultation and chest X ray were unremarkable and hence chest CT scan was requested ( Figure 1 ) and showed picture suggestive of mild-moderate COVID-19, swabbing was done and came positive Case 2: A 51-year-old male, presented by dizziness over last 2-3 days and when examined found to have high RBS and ketonuria, and hence admitted as KDA, and was acidotic (PH 7). A 62-year-old male patient who was not compliant with his medicines over the last 2 months, presented for renewal of medicine without any clinical manifestations, found to have panic RBS measurement, and was positive for urine ketones. doi = 10.1016/j.mehy.2020.110226 id = cord-304544-tqtdjh2m author = Enes, Ak title = Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date = 2020-06-20 keywords = H1N1; NHBE; SARS summary = Comparison of transcriptome of NHBE cells 24 hours after mock-infection and SARS-CoV-2 infection demonstrated that most genes that respond to infection were upregulated (320 genes) rather than being downregulated (115 genes).While upregulated genes were enriched in signalling pathways related to virus response, downregulated genes are related to kidney development. Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. Upregulated MMPs and chemokines demonstrate the response generated by NHBE cells to trigger the immune system, these two subgroups of genes are further discussed below comparatively in SARS-CoV-2 and H1N1 infection. Interestingly, none of the IL-17 ligands were expressed in detectable amounts in NHBE cells, and none of the ligands or receptors were upregulated in response to virus infection, therefore the positive feedback loop is likely to be initiated by activation of NFκB via other signalling pathways. doi = 10.1101/2020.06.20.163006 id = cord-270123-m8utyd1m author = Enmozhi, Sukanth Kumar title = Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach date = 2020-05-05 keywords = Andrographolide; Kcal; SARS; compound summary = This paper evaluates the compound Andrographolide from Andrographis paniculata as a potential inhibitor of the main protease of SARS-COV-2 (Mpro) through in silico studies such as molecular docking, target analysis, toxicity prediction and ADME prediction. And upon certain in vitro and some clinical data chloroquine phosphate and hydroxychloroquine sulphate was advised to be the treatment for COVID-19 and enough randomized trials on these compounds to be provided and allowed the administration of the above drugs to be used for emergency (https://www.fda.gov/emergency-use-authori-zation#covidtherapeutics). Though there are many targets are found for the treatment of COVID-19, the main protease (M pro ) of SARS-CoV-2 was chosen due to interest of treating infected patients, to stop the multiplication of virus within the cells, through which M pro was involved in the release of polypeptides which are functional extensive proteolysis and cleavage of the enzyme itself from the sites of genome, pp1a and ppa1ab . doi = 10.1080/07391102.2020.1760136 id = cord-021805-2j07zw6q author = Epstein, Jonathan H. title = Emerging Diseases in Bats date = 2018-09-28 keywords = Ebola; SARS; bat; virus summary = 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. doi = 10.1016/b978-0-323-55228-8.00040-0 id = cord-302939-z0071rwa author = Erdeve, Ömer title = The Turkish Neonatal Society proposal for the management of COVID-19 in the neonatal intensive care unit date = 2020-06-19 keywords = COVID-19; NICU; SARS; mother summary = • NICUs should prepare emergency plans for COVID-19 to ensure the optimal management of potential victims • The assigned team should coordinate the hospitalization and maintenance of the patient with suspected COVID-19 • In the presence of high-risk factors, it is recommended that the newborn should be admitted and taken into an isolation ward in the NICU as soon as possible • Samples of the patient should be taken by staff that is trained and designated by the NICU • Newborns may be born prematurely and the most common non-specific initial symptoms include respiratory distress, shortness of breath, cyanosis, increased heart rate, lethargy, fever, feeding intolerance and vomiting • The SARS-CoV-2 has not been detected in breast milk, but the choice to breastfeed should be the mother''s and the families • There is no effective anti-coronavirus treatment yet and treatment is generally supportive doi = 10.14744/turkpediatriars.2020.43788 id = cord-271014-xzpvupms author = Erikstrup, Christian title = Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date = 2020-06-25 keywords = IFR; SARS summary = title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. doi = 10.1093/cid/ciaa849 id = cord-320308-pzex799x author = Erol, Adnan title = Role of oxidized LDL-induced “trained macrophages” in the pathogenesis of COVID-19 and benefits of pioglitazone: A hypothesis date = 2020-05-12 keywords = SARS; macrophage summary = CONCLUSIONS: When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. When oxLDL-trained macrophages encounter SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the lung, it causes unregulated cytokine secretion, leading to the alveolar damage. CARD9 is critical adaptor protein and a central integrator in innate immune cell activation that triggers the inflammatory signaling pathway in response to viral infection. Consequently, while SARS-CoV-infection in oxLDL-trained macrophages cannot produce protective type I interferons, they readily potentiates existing low-grade inflammation through ASC-mediated caspase-1 activation [10, 11] . All COVID-19 patients who develop severe respiratory failure display hyper-inflammatory responses with features of either immune dysregulation or macrophage activation syndrome. The information provided here must match the contributors'' statement in the manuscript.Importance of oxidized lipid-trained macrophages in the severity of COVID-19Adnan Erol Comment Role of the funding source Please disclose any funding sources and their role, if any, in the writing of the manuscript or the decision to submit it for publication. doi = 10.1016/j.dsx.2020.05.007 id = cord-253431-fjds5cdr author = Erukainure, Ochuko L. title = Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. (Labiatae) date = 2020-11-03 keywords = 5-O; COVID-19; SARS; figure summary = title: Targeting the initiation and termination codons of SARS-CoV-2 spike protein as possible therapy against COVID-19: the role of novel harpagide 5-O-β-D-glucopyranoside from Clerodendrum volubile P Beauv. Ligand-protein interactions between viral protein (SARS-CoV-2 spike protein), the host receptor target (ACE2) and Harpagide 5-O-b-D-glucopyranoside are presented in Figures 5-7 . Harpagide 5-O-b-D-glucopyranoside displayed a good binding in complex with the host receptor target, initiation and termination sequence of the viral spike protein messenger RNA compared to all studied standard drugs with binding affinities of À7.5, À6.4 and 6.3 kcal mol À1 respectively (Table 5) . In the present study, we investigated the epidemiology of COVID-19 and the potentials of harpagide 5-O-b-D-glucopyranoside, a new iridoid glycoside isolated from C. At molecular level, the viral envelope spike (S) protein of SARS-CoV-2 and angiotensin converting enzyme 2 receptor within the host are central to COVID-19 pathogenesis and response to therapeutic interventions among other biological factors . doi = 10.1080/07391102.2020.1840439 id = cord-280043-bm0qkrod author = Esagian, Stepan M. title = Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic date = 2020-06-04 keywords = COVID-19; SARS; transplant summary = As the coronavirus disease 2019 (COVID-19) outbreak has rapidly evolved into a global pandemic, abdominal organ transplantation programs are currently facing multiple challenges. According to the report of the first case series from China, a significant proportion of patients (23.7%) suffered from comorbidities, which are commonly seen in abdominal transplant candidates, including hypertension (15.0%), diabetes mellitus (7.2%), hepatitis B infection (2.1%), cancer (0.9%), chronic kidney disease (0.7%) and immunodeficiency (0.2%) (7) . Although data for abdominal organ transplant candidates and recipients are still limited, emerging reports have indicated that these patients may present with atypical COVID-19 manifestations. These guidelines address three potential standpoints the epidemic confronts transplantation systems with; first, the risk of donor-derived SARS-CoV-2 infection, which although has not been reported thus far in neither organ or blood product recipients, extensive donor screening protocols have been implemented in many transplant centers in pandemic areas. doi = 10.3389/fmed.2020.00287 id = cord-315064-2mgv9j6n author = Escher, Felicitas title = Detection of viral SARS‐CoV‐2 genomes and histopathological changes in endomyocardial biopsies date = 2020-06-12 keywords = COVID-19; CoV-2; Germany; SARS summary = Accordingly, we prospectively analysed endomyocardial biopsies (EMBs) from a cohort of 104 samples of patients with suspected myocarditis or unexplained heart disease for the presence of SARS-CoV-2 RNA by RT-qPCR and hints for histopathological injury. Up to 8 EMBs each of 104 patients [mean age: 57.90 ± 16.37 years; left ventricular ejection fraction (LVEF): 33.7 ± 14.6%, sex: n = 79 male/25 female] with suspected myocarditis or unexplained heart failure were analysed between 3 February and 26 March 2020 in German clinical centres in accordance with SARS-CoV2 spread in Germany. In this study, we established for the first time the evidence of SARS-CoV-2 genome detection in 5 of 104 EMBs of patients with suspected myocarditis or unexplained heart failure. Our finding of SARS-CoV-2 genome detection in EMBs of patients suffering from myocarditis/inflammatory cardiomyopathy cannot rule out or confirm the infection of cardiac cells but revealed incremental insights into organ-specific infection of SARS-CoV-2 using possibly macrophage migration as a shuttle from the lung to the heart. doi = 10.1002/ehf2.12805 id = cord-293136-lfwqzf8m author = Escosa‐García, Luis title = Ten key points about COVID‐19 in children: the shadows on the wall date = 2020-08-13 keywords = COVID-19; SARS; child summary = It was initially named Pediatric multisystem inflammatory syndrome (PIMS) temporally associated with COVID-19 by the Royal College of Paediatrics and Child Health (RCPCH) 18 To date, some cases of neonatal SARS-CoV-2 infection have been reported 27 28 . Recent data from a German study indicate that viral loads in the very young (age group 0-6 years) do not significantly differ from those of adults 44 To put it briefly, SARS-CoV-2 PCR of nasopharyngeal swab is considered the gold standard diagnostic test for acute COVID-19 disease. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Children and Adolescents: A Systematic Review Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center''s observational study Characteristics and Outcomes of Children With Coronavirus Disease 2019 (COVID-19) Infection Admitted to US and Canadian Pediatric Intensive Care Units doi = 10.1002/ppul.25025 id = cord-305104-jk6ai1od author = Escribese, María M title = Cross‐sectional pilot study exploring the feasibility of a rapid SARS‐CoV‐2 immunization test in health and non‐healthcare workers date = 2020-08-05 keywords = SARS; healthcare summary = All rights reserved Cross-sectional pilot study exploring the feasibility of a rapid SARS-CoV-2 immunization test in healthcare and non-healthcare workers To the Editor: We aimed to generate an immune response map to SARS-CoV-2 in a very specific population of a Medical School were both healthcare workers and non-healthcare workers cohabit, and elucidate the main risk factors that can be associated with COVID-19 diagnosis in each population. Additionally, this pilot study provides the knowledge and the positive controls (healthcare workers with positive RT-PCR) for the development of future methodological strategies aiming to set up new immunological tests for herd immunity follow-up (ELISA, neutralization assays, etc.).This will be helpful if we take into account the shortage of commercial kits for SARS-CoV-2 immunological tests during the pandemic, and the limitations of these tests in terms of specificity and sensitivity (5, 6)(). doi = 10.1111/all.14545 id = cord-349504-oqpjqgv4 author = Escudero, Dolores title = Análisis de SARS-CoV-2 en el aire de una UCI dedicada a pacientes Covid-19 date = 2020-10-10 keywords = SARS; UCI summary = Algunos estudios han documentado que el SARS-CoV-2 puede permanecer en el aire generado por aerosoles hasta 3 horas (7) demostrándose la presencia de genoma viral en el aire y filtros de los hospitales. El estudio se realizó a finales de mayo del 2020 en 5 boxes diferentes de la UCI (Tabla 1), colocando los equipos de extracción en el suelo, cerca de la cabeza del paciente y lo más alejado posible de la salida de aire, recogiéndo las muestras de aire durante un tiempo de 2-4 horas. El análisis mediante RT-PCR cuantitativa no mostró en ningún caso detección del genoma de SARS-CoV-2 en las muestras recogidas por los dos métodos descritos, por lo que en nuestro estudio no hemos podido demostrar la presencia de SARS-CoV-2 en el aire de la UCI ni en la planta de hospitalización. En nuestra UCI todos los boxes estaban equipados con presión negativa de -10 pascales y un intercambio de 15-20 ciclos/h de aire lo cual puede justificar la ausencia de RNA del SARS-CoV-2 en nuestra investigación. doi = 10.1016/j.medin.2020.09.004 id = cord-281699-pxof67pl author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-08-13 keywords = SARS; mutation summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are not under selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene, and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors ( Fig. 1) . doi = 10.1101/2020.08.12.248732 id = cord-331076-ak481qew author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-10-12 keywords = RNA; SARS; mutation summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are under less selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020a) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors (Fig. 1) . Three of the five most common nsp14 mutations, namely 18060C>T, 18736T>C and 18877C>T are associated with increases in both genome-wide mutational load, as well as MoE status, an alternative indicator of mutational rate and virus evolution. doi = 10.7717/peerj.10181 id = cord-283699-c4jjdj5o author = Eslami, Gholamali title = The impact of sofosbuvir/daclatasvir or ribavirin in patients with severe COVID-19 date = 2020-08-19 keywords = SARS; daclatasvir; sofosbuvir summary = With the national standard COVID-19 treatment protocol at the time being lopinavir/ritonavir 200/50 mg two tablets every 12 h plus hydroxychloroquine 400 mg daily, it was decided to conduct a two-arm trial where both arms would receive the standard protocol in addition to either ribavirin or sofosbuvir/ daclatasvir. In this open-label trial, the effects of sofosbuvir/daclatasvir and ribavirin in patients with severe COVID-19 were measured. The time required before observing clinical improvement was significantly less in patients treated with sofosbuvir/daclatasvir, and the side effects of the medication, such as GI bleeding and anaemia, were lower than in the group receiving ribavirin. In this open-label study, treatment of patients with severe COVID-19 with sofosbuvir/daclatasvir was significantly more effective than ribavirin through improved clinical symptoms, lower mortality rates, a shorter duration of both ICU and hospital stays, and fewer side effects. doi = 10.1093/jac/dkaa331 id = cord-288025-skkpkqw6 author = Eslami, Hadi title = The role of environmental factors to transmission of SARS-CoV-2 (COVID-19) date = 2020-05-15 keywords = COVID-19; SARS summary = Human-to-human transmission of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs most often when people are in the incubation stage of the disease or are carriers and have no symptoms. Therefore, in this study, was discussed the role of environmental factors and conditions such as temperature, humidity, wind speed as well as food, water and sewage, air, insects, inanimate surfaces, and hands in COVID-19 transmission. This study aimed to investigate the effect and role of various factors, including environmental factors (climate change, water transfer, air, and food), disinfection of surfaces, and hands in the transmission and prevalence of COVID-19 pandemics. The most well-known methods of surface disinfection to remove SARS-CoV-2 virus are, in short, the use of ethyl alcohol (62-70%), or hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%, dilution ratio 1 to 50) with a contact time of 1 min (Henwood 2020; WHO 2014) . doi = 10.1186/s13568-020-01028-0 id = cord-342024-kaku49xd author = Espejo, Andrea P title = Review of Current Advances in Serologic Testing for COVID-19 date = 2020-06-25 keywords = ELISA; SARS summary = • The use of total antibody or simultaneous IgG/IgM measurements (regardless of method) significantly adds sensitivity to reverse transcription polymerase chain reaction testing protocols early post onset of symptoms and becomes the most accurate diagnostic test at later time points. The SP, RBD, and NP proteins appear to be the main targets of the humoral immune response in coronavirus infections including SARS-CoV-2 and were the antigens used in the majority of the serologic assays examined in this literature review. Overall, while these results are similar to that reported in a review of serologic testing for MERS-CoV and SARS-CoV, they may have been affected by choice of target antigens, the various immunoassay kits, and the level of detail of case history used to categorize the time of sample acquisition post onset of symptoms. doi = 10.1093/ajcp/aqaa112 id = cord-348360-20eq5meh author = Esposito, Dominic title = Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays date = 2020-06-04 keywords = SARS; protein; spike summary = To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Thus, the work presented here is intended to provide a robust method for those wishing to reliably produce SARS CoV-2 spike protein in quantities sufficient for serology assays, structural biology, or simply to better understand some of the production variables affecting the yield. Nevertheless, the approaches outlined here allowed us to improve the production yield of spike protein significantly by modifying cell culture temperature and harvest time, as well as improving the purification process. To produce SARS-CoV-2 antigens for the development of serology assays, we initially followed standard procedures for secreted protein production: transfection using the manufacturer''s protocols, expression at 37°C, harvest at three days post-transfection, tangential flow filtration of the culture supernatant, immobilized metal ion chromatography with linear gradient elution, and size exclusion chromatography. doi = 10.1016/j.pep.2020.105686 id = cord-340279-bq5owwot author = Espíndola, Otávio de Melo title = Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date = 2020-06-04 keywords = SARS summary = key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection doi = 10.1016/j.ijid.2020.05.123 id = cord-347965-zluu0i41 author = Essahib, Wafaa title = SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts date = 2020-09-21 keywords = ACE2; SARS summary = title: SARS-CoV-2 host receptors ACE2 and CD147 (BSG) are present on human oocytes and blastocysts PURPOSE: To visualize SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. RESULTS: SARS-CoV-2 host receptors ACE2 and CD147 are present on the membrane of trophectoderm, epiblast and hypoblast cells in human blastocysts. The aim of our study was to visualize SARS-CoV-2 receptors ACE2 and CD147 on human oocytes and blastocysts. In pre (5 days post fertilization (dpf5) and (dpf6))-and peri (dpf7)-implantation blastocysts, CD147 and ACE2 are present on the membrane of trophectoderm and hypoblast cells, which will both contribute to the embryonic part of the placenta (chorion). The presence of the receptors ACE2 and CD147, especially on the membrane, implicates that SARS-CoV-2 is theoretically able to bind and infect human oocytes and pre-and periimplantation embryos. Samples were washed in 2% BSA/PBS before Fig. 1 Immunofluorescent staining and confocal microscopy for SARS-CoV-2 host receptors ACE2 and CD147 on human oocytes and blastocysts. doi = 10.1007/s10815-020-01952-x id = cord-277399-0w8is9xm author = Esteves, Sandro C. title = SARS‐CoV‐2 pandemic and repercussions for male infertility patients: A proposal for the individualized provision of andrological services date = 2020-05-22 keywords = CoV-2; SARS; patient; sperm summary = The prolonged lockdown of health facilities providing non‐urgent gamete cryopreservation—as currently recommended by many reproductive medicine entities and regulatory authorities due to the SARS‐CoV‐2 pandemic will be detrimental for subgroups of male infertility patients. These groups include infertility patients (eg, azoospermic and cryptozoospermic) undergoing medical or surgical treatment to improve sperm quantity and quality, as well as males of reproductive age affected by inflammatory and systemic auto‐immune diseases who are about to start treatment with gonadotoxic drugs or who are under remission. Sperm banking should be considered in men with HH who respond to therapy, that is, have viable spermatozoa in the ejaculate, in particular, when the continuation of gonadotropin therapy during the SARS-CoV-2 pandemic is neither possible (eg, due to economic or logistic reasons), nor desired. We propose remedies to mitigate the consequences of a prolonged cessation of andrological services due to the SARS-CoV-2 pandemic to vulnerable subgroups of male infertility patients. doi = 10.1111/andr.12809 id = cord-341670-o1v63zg8 author = Estevez-Ordonez, Dagoberto title = Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage date = 2020-05-20 keywords = SARS; patient summary = title: Letter: Perioperative and Critical Care Management of a Patient With Severe Acute Respiratory Syndrome Corona Virus 2 Infection and Aneurysmal Subarachnoid Hemorrhage Postoperative cerebrospinal fluid (CSF) samples were also tested for SARS-CoV-2 viral ribonucleic acid (RNA), which was not detected. CSF sample was obtained on hospital day 6, 5 d after testing positive for SARS-CoV-2 and evaluated by RT-qPCR. At 20 d, no one involved in her care has reported symptoms of infection with COVID-19 or has tested positive for SARS-CoV-2. Testing of CSF in a SARS-CoV-2-infected patient is also reported here, which to our knowledge has not been documented in the peered-reviewed literature. The present approach to the management of this patient with aSAH may provide some insight when caring for patients with urgent/emergent surgical pathologies in the setting of SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges doi = 10.1093/neuros/nyaa197 id = cord-285647-9tegcrc3 author = Estrada, Ernesto title = Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2 date = 2020-08-17 keywords = PPI; SARS; network; process; protein summary = By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19. 25, 26 Therefore, we assume here that perturbations produced by SARS-CoV-2 proteins on the human PPI network are propagated by means of diffusive processes. Here, we propose the use of a time-fractional diffusion model on the PPI network of proteins targeted by SARS-CoV-2. We now consider how a perturbation produced by SARS-CoV-2 on a protein mainly expressed in the lungs can be propagated to proteins mainly located in other tissues (see Table S4 in the supplementary material) by a subdiffusive process. Here, we have studied the particular case in which the time-fractional diffusion equation produces a subdiffusive regime, with the use of α = 3/4 in the network of human proteins targeted by SARS-CoV-2. doi = 10.1063/5.0015626 id = cord-335648-lbmhprjn author = Estrich, Cameron G. title = Estimating COVID-19 prevalence and infection control practices among US dentists date = 2020-10-15 keywords = PPE; SARS; covid-19 summary = Dentists from every US state (n = 2,195) answered questions about COVID-19–associated symptoms, SARS-CoV-2 infection, mental and physical health conditions, and infection control procedures used in their primary dental practices. As early as March 2020, Journal of Dental Research published the infection control guidelines that dentists at Wuhan University used, 7 and, in April and May 2020, the American Dental Association (ADA) and the Centers for Disease Control and Prevention (CDC), respectively, released interim guidance on infection control protocols and changes to the practice and office environments. In this article, we used the first month of study data to estimate the prevalence of COVID-19 among US dentists and to determine the rate of compliance with CDC and ADA infection prevention and control procedures. 14, 15 Respondents who reported providing oral health care in the past month were asked about infection prevention or control procedures in their primary dental practice. doi = 10.1016/j.adaj.2020.09.005 id = cord-278960-3xw4qjoy author = Evangelista, A. T. title = The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 date = 2020-05-20 keywords = SARS summary = The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. In temperate regions of the globe, the incidence of respiratory enveloped viruses, such as influenza and endemic human coronaviruses peak in winter months, usually in January and February, which is considered due to indoor social crowding with droplet and contact transmission and the added effect of low indoor relative humidity (RH). doi = 10.1101/2020.05.15.20103416 id = cord-317622-o10ntfi8 author = Evans, Ronald M. title = Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing date = 2020-09-11 keywords = SARS; VDR; covid-19 summary = In patients, severity of liver disease correlates inversely with VDR expression, levels of vitamin D, and metabolites (Oh et al., 2020) , and hepatocellular injury directly with progressive COVID-19 (Henry et al., 2020; Ji et al., 2020) . Similar effects were observed in non-lung models; e.g., vitamin D deficiency (or VDR knockout) was associated with increased renin and Ang II (and IL-6 and TGFb) levels in diabetic mice (Zhang et al., 2008) . Human intestinal organoids (ACE2 expressing), suggesting a gut enterocyte reservoir for SARS-CoV-2, fuel viral spread and cytokine response in COVID-19 pathogenesis, another potential enteric-phase inflammatory hurdle to oral vitamin D administration (Clevers, 2020) . Heightened basal RAS (e.g., reduced ACE2 expression, higher Ang II levels) activation and inflammatory states (Ajilore and Thames, 2020; Albert and Ridker, 2004; Suthanthiran et al., 2000; Vinciguerra and Greco, 2020) , reported in African Americans, are associated with severe COVID-19 outcomes and relevant risk co-morbidities (e.g., hypertension, diabetes), some linked to vitamin D deficiency (Rostand, 2010; Yancy, 2020) . doi = 10.1016/j.cmet.2020.09.007 id = cord-261307-qmh3wtqo author = Evans, Scott E. title = Inducible Epithelial Resistance against Coronavirus Pneumonia in Mice date = 2020-10-17 keywords = SARS summary = , a single PUL-042 treatment significantly improved survival of otherwise lethal SARS-CoV infection and significantly reduced the lung MERS-CoV burden 3 days after challenge, congruent with our prior work demonstrating a consistent correlation between survival advantage and reduced pathogen burden. Although it is suspected that a second pandemic wave may arise concurrently with seasonal influenza, a patient with a virus-like illness can be preemptively treated with PUL-042 with the expectation that she or he will appreciate a benefit, whether the syndrome results from SARS-CoV-2, influenza A, both viruses, or another pathogen. The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents the latest threat to global health security, and the pressure to identify effective therapeutics during this pandemic is immense. After an early report of a "cytokine storm" in patients with coronavirus disease (COVID-19) , there is increased interest in anti-IL-6 therapy as a treatment option, with ill-defined criteria for use (1). Inducible epithelial resistance against acute Sendai virus infection prevents chronic asthma-like lung disease in mice doi = 10.1165/rcmb.2020-0247le id = cord-325936-rwxg187r author = Eyal, Nir title = AIDS Activism and Coronavirus Vaccine Challenge Trials date = 2020-06-26 keywords = HIV; SARS summary = To minimize risk to participants, live SARS-CoV-2 vaccine challenge trials would need to recruit participants who, in the-likely-event of infection, would remain at relatively low fatality risk. Shortly after HIV sterilizing cure trials transplanted allogenic stem cell in participants, with well over a thousand times the fatal risk of SARS-Cov-2 infection in healthy young participants [17, 18] , AIDS activist David Evans interviewed the participants of these risky trials and concluded, "We should recognize their great capacity to understand the risks they may confront as research participants and, after a careful ethical and scientific review, respect the motivations of those who decide that the benefits of knowing that their contributions may help others outweighs the risks" [19] . That is not the case for COVID-19, which means that adequately communicating about and assessing potential risks and benefits of participating in a challenge study and ensuring appropriate informed consent may be impossible. doi = 10.1007/s10461-020-02953-8 id = cord-285159-gytebbua author = Eydoux, Cecilia title = A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date = 2020-07-07 keywords = RNA; SARS summary = Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). doi = 10.1101/2020.07.07.192005 id = cord-263583-a1zon98c author = Fabbris, Cristoforo title = Is oro/nasopharyngeal swab for SARS-CoV-2 detection a safe procedure? Complications observed among a case series of 4876 consecutive swabs date = 2020-10-13 keywords = SARS summary = In this paper we present the complications encountered in a series of healthworkers who underwent oro/nasopharyngeal swab for detection of SARS-CoV-2. All patients underwent sampling with a sterile collection Citoswab® (Citotest Labware Manufacturing Co., LTD) All reports, possible complications and clinical information were noted from registries of the infectious disease units and medical records. One patient, affected by diabetes mellitus and neutropenia, developed septal abscess (case 2) and another, who later was observed to have septal deviation, had severe anterior and posterior bleeding from an arterial point of the olfactory area, possibly arising from the anterior ethmoidal artery (case 3) requiring surgical cauterization. However arterial rupture can give catastrophic bleed as seen in one patient: we suspect the septal deviation may have misled the swabbing process to the upper part of nares where trauma to the anterior ethmoidal artery may have occurred. In conclusion, oro/nasopharyngeal swabs are safe procedures to detect SARS-CoV-2 infection. doi = 10.1016/j.amjoto.2020.102758 id = cord-298056-svwtfshi author = Fabio, Ciceri title = Early predictors of clinical outcomes of COVID-19 outbreak in Milan, Italy date = 2020-06-12 keywords = COVID-19; China; SARS; patient summary = Multivariable analysis showed older age, coronary artery disease, cancer, low lymphocyte count and high RALE score as factors independently associated with an increased risk of mortality. CONCLUSION: In a large cohort of COVID-19 patients of European origin, main risk factors for mortality were older age, comorbidities, low lymphocyte count and high RALE. 14 In this report we describe the demographical, clinical, radiological and laboratory characteristics, as well as the clinical outcomes and the risk factors for mortality, of the first 500 patients with COVID-19 admitted to San Raffaele Scientific Institute, a tertiary care academic hospital in Milan, Italy. With a clinical observation longer than one months from the last patient admitted, w e were able to identify early predictors of mortality related to patient characteristics, radiological and laboratory findings at hospital admission for COVID-19. doi = 10.1016/j.clim.2020.108509 id = cord-256020-wrui3i2l author = Fadaka, Adewale Oluwaseun title = Understanding the epidemiology, pathophysiology, diagnosis and management of SARS-CoV-2 date = 2020-08-26 keywords = ACE-2; COVID-19; CoV-2; MERS; SARS; figure summary = The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The disease is caused by SARS-CoV-2, a zoonotic pathogen that acquired mutations as it crossed the species barrier from bat to pangolin enabling it to infect humans. 5 The clinical symptoms of COVID-19 include fever, cough, and pneumonia, which makes the disease enormously dangerous with a high case fatality rate. 11 Symptoms of human SARS-CoV-1 infections include headache, fever and respiratory complications such as cough, dyspnea, and pneumonia. 81 The main goal of SARS-CoV-2 diagnosis is to accurately detect the virus and to minimize further transmissions by timely isolation and treatment of infected patients. 112 This implies that variation in ACE-2 expression in COVID-19 patients is likely to affect susceptibility, symptoms and intervention outcomes following SARS-CoV-2 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations doi = 10.1177/0300060520949077 id = cord-281684-m3m4mhye author = Fagre, Anna C. title = A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date = 2020-09-28 keywords = ACE2; CoV-2; SARS summary = title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. However, to date, there has been only a gross histological analysis of the lung pathological changes following infection and the impact of SARS-CoV-2 neutralizing antibody clones on lung immune infiltrates has yet to be fully assessed. Those antibody clones that blocked the interaction of the RBD with ACE2 and bound to native spike protein were then tested for neutralization of SARS-CoV-2 in a cytopathic effect (CPE) assay with Vero E6 cells. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity doi = 10.1101/2020.09.25.313601 id = cord-257584-v38tjof3 author = Fahmi, Muhamad title = Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date = 2020-03-03 keywords = SARS; protein summary = Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45). doi = 10.1016/j.meegid.2020.104272 id = cord-279576-wt4crton author = Fajardo, Álvaro title = Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date = 2020-05-13 keywords = Green; PCR; SARS; SYBR summary = Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . doi = 10.1101/2020.05.13.093609 id = cord-316080-y6ypbdtu author = Fajnzylber, J. M. title = SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality date = 2020-07-17 keywords = COVID-19; SARS summary = We quantified SARS-CoV-2 viral load from participants with a diverse range of COVID-19 severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. Amongst the participants hospitalized with COVID-19, higher prevalence of detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. Amongst hospitalized individuals, the majority still 92 had detectable SARS-CoV-2 RNA at the time of initial sample collection, including 50% with variable, individuals with detectable plasma, nasopharyngeal or sputum viral loads had 124 significantly lower absolute lymphocyte counts, and higher CRP and IL-6 levels compared to 125 those without detectable plasma viremia (Fig 2b-d) . . https://doi.org/10.1101/2020.07.15.20131789 doi: medRxiv preprint DISCUSSION 151 We report a comprehensive analysis of SARS-CoV-2 respiratory tract, plasma, and urine viral 152 loads of 235 participants who were either hospitalized with COVID-19, evaluated as 153 symptomatic outpatients, or had recovered from COVID-19 disease. doi = 10.1101/2020.07.15.20131789 id = cord-316095-jzyb4jn5 author = Falahchai, Mehran title = Dental care management during the COVID‐19 outbreak date = 2020-09-19 keywords = COVID-19; SARS; dental; patient summary = Sixteen English papers were enrolled to answer questions about procedures that are allowed to perform during the COVID‐19 outbreak, patients who are in priority to receive dental care services, the conditions and necessities for patient admission, waiting room and operatory room, and personal protective equipment (PPE) that is necessary for dental clinicians and the office staff. Considering the generation of high amounts of droplets and aerosols during routine dental procedures, the conventional protective measures that are routinely followed by dental clinicians are no longer efficient for prevention of COVID-19 transmission. Urgent dental treatments include management of conditions that require immediate attention such as alleviation of severe pain with/without the risk of infection and balancing the patient load in the hospital emergency departments. According to the data acquired from the screening questionnaires, patients who need emergency/urgent dental treatment can be divided into three groups of apparently healthy, suspected, and confirmed cases. doi = 10.1111/scd.12523 id = cord-270661-e83xe4sp author = Falahi, Shahab title = Transmission routes for SARS-COV-2 infection: Review of Evidence date = 2020-10-06 keywords = SARS summary = Subsequent studies have shown that the virus is also present in saliva; given the evidence of virus transmission from asymptomatic individuals(1) and the presence of the virus in saliva, it has been suggested that even secretory droplets during normal speeching may be a route to transmit SARS-COV-2 (2). In a number of studies, the SARS-CoV-2 genome was identified in blood samples from a number of patients with COVID-19 (15, 16) , and subsequently raised the question: Is SARS-CoV-2 transmitted through transfusion? In a study, all blood samples of asymptomatic people with COVID-19 were negative for SARS-COV-2 PCR and RNAemia was detected in severe and symptomatic cases. Sexual transmission: SARS-COV-2 is present in saliva and feces, and in theory it is possible to transmit through oral-anal intercourse (17) but this sexual habit is not common, so it is unlikely that this route will be a significant mean of transmission. doi = 10.1016/j.nmni.2020.100778 id = cord-340357-gyvvcnuf author = Fallahi, Hamid Reza title = Being a front-line dentist during the Covid-19 pandemic: a literature review date = 2020-04-24 keywords = SARS; coronavirus; infection; transmission summary = This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. The purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the CDC and the ADA guidelines. Due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for 2019-nCoV infection. 2019-nCoV transmission in dental settings occurs through four major routes: (1) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials; doi = 10.1186/s40902-020-00256-5 id = cord-273685-oxvfxmtr author = Fan, Qihong title = Anal swab findings in an infant with COVID‐19 date = 2020-03-17 keywords = SARS summary = In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in pharyngeal swab and anal swab were compared. In this case study the test for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in pharyngeal swab and anal swab were compared. The oropharyngeal specimen showed negative result for SARS-CoV-2 on the 14th day after onset of the illness. However, the anal swab was still positive for SARS-CoV-2 on the 28th day after the onset of the illness. COVID-19, Anal swab, SARS-CoV-2, Fecal-oral transmission confirmed in China with at least 3042 reported deaths. Several reports noted that the stool specimens from the patients with COVID-19 were positive for the novel SARS-CoV-2. However, the anal swabs remained positive for SARS-CoV-2 on the 28th day after the onset of the illness (Table 1) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1002/ped4.12186 id = cord-337297-fkw8780t author = Fan, Siyuan title = Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study date = 2020-07-10 keywords = AIS; COVID-19; SARS; patient summary = Methods: This retrospective single-center case series analyzed critically ill patients with COVID-19 at the intensive care unit of Tongji Hospital, Wuhan, China from February 5 to April 2, 2020. Herein, we conducted a retrospective study to analyze the neurological manifestations of critically ill patients with COVID-19 in intensive care units (ICU) to explore various pathophysiological mechanisms that could contribute to neurological complications in these patients. COVID-19, corona virus disease 2019; AIS, acute ischemic stroke; WBC, white blood cell; ALT, alanine transaminase, cTnI, High-sensitive cardiac troponin I; NT-proBNP, N-terminal prohormone of brain natriuretic peptide; LDL-C, low-density-lipoprotein cholesterol; aPTT, activated partial thromboplastin time; hsCRP, high sensitivity C-reactive protein; LDH, lactate dehydrogenase; IQR, interquartile range. The clinical spectrum of neurological complications in critically ill patients with COVID-19 was broad, including delirium, acute ischemic stroke, intracerebral hemorrhage, hypoxic-ischemic brain injury, flaccid paralysis and rhabdomyolysis. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.3389/fneur.2020.00806 id = cord-318204-t024w7h6 author = Fang, Ferric C title = The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date = 2020-06-08 keywords = COVID-19; CoV-2; SARS summary = As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection doi = 10.1093/cid/ciaa742 id = cord-277188-t33nw4zb author = Fang, Jie title = Efficacy of Early Combination Therapy With Lianhuaqingwen and Arbidol in Moderate and Severe COVID-19 Patients: A Retrospective Cohort Study date = 2020-09-18 keywords = Arbidol; COVID-19; LHQW; SARS summary = RESULTS: The early combined usage of LHQW and Arbidol can significantly accelerate the recovery of patients with moderate COVID-19 by reducing the time to conversion to nucleic acid negativity, the time to chest CT improvement, and the length of hospital stay. One case report of four patients with mild or severe COVID-19 in Shanghai (China) found that combining antiviral drugs (lopinavir/ ritonavir or Arbidol) with TCM (Shufengjiedu capsule) resulted in a significant improvement in clinical symptoms . In conclusion, this retrospective study demonstrated that the early administration of LHQW + Arbidol combination therapy could significantly accelerate recovery in patients with moderate COVID-19 by reducing the time to conversion to nucleic acid Frontiers in Pharmacology | www.frontiersin.org September 2020 | Volume 11 | Article 560209 negativity, the time to chest CT improvement and the length of hospital stay. doi = 10.3389/fphar.2020.560209 id = cord-346092-fo83f99f author = Fang, Li‐Qun title = Geographical spread of SARS in mainland China date = 2009-06-05 keywords = China; SARS summary = Objectives To describe the spatiotemporal diffusion of the severe acute respiratory syndrome (SARS) epidemic in mainland China, and to analyse the spatial pattern of SARS transmission from the Beijing epicentre to its neighbouring areas. SARS cases that got infected in Beijing but were reported in three provinces surrounding Beijing were mapped, and logistic regression using a ''case–control'' design at the county level was performed to analyse the impact of travel‐related risk factors in the diffusion pattern. Results The SARS epidemic in mainland China spanned a large geographical extent but clustered in two areas: first in Guangdong Province, and about 3 months later in Beijing with its surrounding areas in Shanxi Province, Inner Mongolia Autonomic Region, Hebei Province and Tianjin. Using the tracking analysis, we identified geographic features associated with SARS outbreaks in mainland We found that 34 SARS cases became infected in Beijing and travelled to the Inner Mongolia Autonomic Region, Shanxi Province or Hebei Province after onset, and were reported by hospitals outside Beijing. doi = 10.1111/j.1365-3156.2008.02189.x id = cord-274279-f99nd3dx author = Fantini, Jacques title = Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection date = 2020-04-03 keywords = CLQ; SARS summary = Using a combination of structural and molecular modelling approaches, this study showed that chloroquine (CLQ), one of the drugs currently under investigation for SARS-CoV-2 treatment, binds sialic acids and gangliosides with high affinity. A ganglioside-binding site in the Nterminal domain (NTD) of the spike (S) glycoprotein of SARS-CoV-2 was identified, and CLQ was shown to be a potential blocker of the S-ganglioside interaction which occurs in the first step of the viApril 10, 2020; 14:43 ] ral replication cycle (i.e. attachment to the surface of respiratory cells, mediated by the S protein). At this stage, attachment of the NTD to the ganglioside-rich microdomain involved the whole interface (i.e. Table 1 Energy of interaction of each amino acid residue of SARS-CoV-2 spike protein in contact with GM1 molecules. As CLQ and CLQ-OH are potential therapies for SARS-CoV-2 infection, it is important to check whether the amino acid residues identified as critical for ganglioside binding are conserved among clinical isolates. doi = 10.1016/j.ijantimicag.2020.105960 id = cord-347121-5drl3xas author = Farah, I. title = A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform. date = 2020-09-29 keywords = COVID-19; SARS; September; Shivom; data; datum; patient; platform; research summary = The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The platform is a proven research ecosystem used by universities, biotech, and bioinformatics organizations to share and analyze omics data and can be used for a variety of use cases; from precision medicine, drug discovery, translational science to building data repositories, and tackling a disease outbreak. Our approach is designed to provide healthcare professionals with an urgently needed platform to find and analyze genetic data, and securely and anonymously share sensitive patient data to fight the disease outbreak. Among other use-cases, the provided platform can be used to rapidly study SARS-CoV-2, including analyses of the host response to COVID-19 disease, establish a multi-institutional collaborative datahub for rapid response for current and future pandemics, characterizing potential co-infections, and identifying potential therapeutic targets for preclinical and clinical development. doi = 10.1101/2020.09.28.20203257 id = cord-313344-rqvi2ksc author = Farcas, Gabriella A. title = Fatal Severe Acute Respiratory Syndrome Is Associated with Multiorgan Involvement by Coronavirus date = 2005-01-15 keywords = CoV; SARS summary = Severe acute respiratory syndrome (SARS) is characterized by pulmonary compromise; however, patients often have evidence of other organ dysfunction that may reflect extrapulmonary dissemination of SARS coronavirus (SARS-CoV). The purpose of the present study was to investigate the presence of SARS-CoV, the degree of viral dissemination, and the viral loads in multiple organ samples from all patients who died of SARS during the Toronto outbreak (March to September 2003) and underwent a postmortem examination and compare the results with those found in patients who died of other causes during the outbreak. A total of 212 discrete postmortem organ samples, including lung, liver, spleen, kidney, small bowel, large bowel, lymph nodes, heart, and skeletal muscle, were prospectively collected from the 21 patients who died of SARS and underwent autopsies. doi = 10.1086/426870 id = cord-340260-z13aa1wk author = Farewell, V. T. title = SARS incubation and quarantine times: when is an exposed individual known to be disease free? date = 2005-10-19 keywords = SARS; time summary = For the data set of averaged times, Figure 1 presents the proÿle likelihoods, L * P (M ), based on the gamma, log-normal and log-gamma models discussed in Section 2. For the truncated gamma model, the proÿle likelihood never drops below 60 per cent suggesting that any value of M greater than the maximum time observed, 14, is plausible. For public health purposes, it could therefore be argued that, based only on such data and an assumed log-normal model, that a quarantine time of 20 days might be necessary to ensure that SARS cases were not released ''too early''. Finally, to show the e ect of more extreme interval-censoring, we consider extending the set of data in Table II by including additional SARS cases from Hong Kong whose period of possible exposure, which deÿnes the width of the interval within which their incubation time lies, is thought to be less than 10 days rather than 5 days. doi = 10.1002/sim.2206 id = cord-354353-hyz0gmpz author = Farhangrazi, Z. Shadi title = Airborne Particulate Matter and SARS-CoV-2 Partnership: Virus Hitchhiking, Stabilization and Immune Cell Targeting — A Hypothesis date = 2020-09-24 keywords = SARS; covid-19 summary = While long-term exposure to air pollutants such as PM 2.5 and nitrous dioxide contributes to persistent inflammatory responses and cardiopulmonary diseases (7) , which might increase vulnerability to COVID-19, it is also plausible that depending on the environment SARS-CoV-2 "hitchhiking" on airborne PM pollutants might be an additional mechanism for spreading the infection. In summary, although long-term exposure to polluted air might increase vulnerability to COVID-19 through prior adverse cellular effects of settled PM (24), our proposed "hitchhiking" hypothesis offers an additional multi-mechanistic pathogenic process through delivery of low viral titres with diverse PM-virus composites and is applicable to both indoor and outdoor situations, where the pathogenic severity is dependent on PM concentration, composition, shape and size as well as the infectious viral load. Contrary to the suggestions that long-term exposure to PM might increase vulnerability to SAR-CoV-2 infection, inhaled PM might promote some forms of immunity to the virus in some individuals. doi = 10.3389/fimmu.2020.579352 id = cord-322641-mz0b91xr author = Farnsworth, Christopher W title = SARS-CoV-2 Serology: Much Hype, Little Data date = 2020-04-28 keywords = COVID-19; SARS summary = In response to a lack of COVID-19 testing the FDA issued guidance regarding serologic assays, stating that although manufacturers could use the Emergency Use Authorization (EUA) pathway for approval, serologic assays could also be marketed in the US bypassing this approval process (2) . Serology has been suggested to play three roles in the COVID-19 pandemic; 1) diagnosis, 2) identification of convalescent plasma donors, 3) screening populations with the purpose of determining exposure and immunity. If the prevalence of COVID-19 in the population is 20% a test with a sensitivity and specificity of 98% will make the value of a positive result (PPV) 92.5% (Figure 1 ). The importance of specificity of serologic tests for screening low prevalence populations was recently demonstrated in a non-peer reviewed publication (11) . The authors found that 1.5% of those screened were positive for SARS-CoV-2 antibodies and, after analysis, found the estimated prevalence to be 2.4%. doi = 10.1093/clinchem/hvaa107 id = cord-007567-vst954ef author = Farquharson, Carolyn title = Responding to the severe acute respiratory syndrome (SARS) outbreak: Lessons learned in a Toronto emergency department() date = 2003-06-04 keywords = GTA; SARS; patient summary = 3 Epidemiologic evidence indicates that transmission of the illness occurs with close person-toperson contact (to household members, health care workers, or nearby patients who were not protected by contact or respiratory isolation precautions) and through droplet secretions. In an effort to deal with the transmission and onset of illness within health care and community settings, the province of Ontario designated a Provincial Operations Centre (POC), which was responsible for issuing directives to hospitals about patient care and infection control practices. Some had normal chest radiography with no infiltrates demonstrated (yet) but had symptoms of fever, headache, myalgia, and malaise, and 1 of 3 distinct exposures: they had either traveled to Vietnam, China, Hong Kong, Singapore, or Taiwan; they had been exposed to a person with SARS; or they had been a health care worker, patient, or visitor in a hospital in the GTA where there had been recorded cases of SARS transmission. doi = 10.1067/men.2003.109 id = cord-354619-pftjhtpo author = Farronato, Marco title = A Call for Action to Safely Deliver Oral Health Care during and Post COVID-19 Pandemic date = 2020-09-15 keywords = ACE2; COVID-19; DHCW; SARS; patient summary = The oral cavity is purported to be one of the main host sites, both for entry and transmission, implicated in SARS-CoV-2 spread either through contact, droplet, aerosols, or saliva. Evidence suggests that the classic mechanism of transmission, contact and droplet spread, can be contained mostly by isolating symptomatic patients and by the use of facial masks/facial coverings, which de facto provides a physical barrier to the oral cavity and nose, the primary source of infection for droplets and larger aerosol particles. Following the above proposed guidelines, no cases COVID-19 disease transmission after single or multiple dental consultations was registered among the DHCW or patients. Classified as operative and non-operative, depending on their ability to work in the oral cavity or/and provide an essential outside support, the DHCW and the patients visiting the dental practice are undeniably at higher risk of SARS-CoV-2 infection and further transmission [41] . doi = 10.3390/ijerph17186704 id = cord-334099-rtv6xm90 author = Farrow, Robert title = Early Multi-organ Point-of-Care Ultrasound Evaluation of Respiratory Distress During SARS-CoV-2 Outbreak: Case Report date = 2020-04-15 keywords = POCUS; SARS summary = 1, 2 In our early experience during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, with multiple patients presenting with acute dyspnea of suspected parenchymal Highland Hospital / Alameda Health System, Department of Emergency Medicine, Oakland, California pulmonary pathology, we found that the prompt differentiation between an underlying cardiac versus pulmonary source can be instrumental in both triage and early resuscitation. Herein we present a case of SARS-CoV-2 related multifocal pneumonia diagnosed by POCUS in the ED during the initial triage of a return ED visit, which highlights its clinical utility and our proposed imaging pathway for evaluating patients with acute dyspnea during the current SARS-CoV-2 outbreak. While the majority of patients infected with SARS-CoV-2 will experience only mild illness, a subset will progress to multifocal pneumonia, acute respiratory distress syndrome, and cardiomyopathy [10] [11] [12] pathologies that can be identified rapidly with POCUS. doi = 10.5811/cpcem.2020.4.47524 id = cord-273351-vq3budip author = Farré, Núria title = Prolonged QT Interval in SARS-CoV-2 Infection: Prevalence and Prognosis date = 2020-08-21 keywords = ECG; SARS summary = A prolonged QTc was independently associated with a higher mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. QTc prolongation was defined as an increase of at least one millisecond in QTc compared to baseline QTc. According to the protocol at our center at the time of the study, treatment with hydroxychloroquine and azithromycin was recommended to all patients. The variables included in the model were age, baseline QTc > 480 ms, chronic kidney disease, treatment with azithromycin and hydroxychloroquine, ischemic chronic disease, atrial fibrillation or flutter, heart failure, and the presence of any cardiovascular risk factor. Although these differences could be due to a more severe presentation in a group of elderly comorbid patients, SARS-CoV-2 infection could be the cause of this prolonged QTc interval, either as a direct effect of the virus or through systemic inflammation. A prolonged QTc was independently associated with a higher risk of mortality even after adjustment for age, comorbidities, and treatment with hydroxychloroquine and azithromycin. doi = 10.3390/jcm9092712 id = cord-257191-u5xnmsv8 author = Farshi, Esmaeil title = Investigation of immune cells on elimination of pulmonary‐Infected COVID‐19 and important role of innate immunity, phagocytes date = 2020-09-18 keywords = COVID-19; SARS summary = [4] [5] [6] [7] [8] Lethal disease in BALB/c mice infected with a mouse-adapted strain of SARS-CoV, MA15, showed a lack of activation of innate immune response, resulting in a barely detectable antivirus T cell response. 8 On the other hand, aged BALB/c mice that were infected with a human clinical isolate of SARS-CoV (Urbani strain) successfully eliminated the invasive virus within 1 week post-infection; these mice exhibited high and prolonged levels of viral replication, signs consistent with clinical symptoms, and pathologic changes in the lung resembling those seen in elderly SARS patients. In this study, we attempted to identify the types of immune cells that contribute to clearing COVID-19 during the acute phase of the infection in mice models plus human. Cellular immune responses to severe acute respiratory syndrome coronavirus (SARS-CoV) infection in senescent BALB/c mice: CD4+ T cells are important in control of SARS-CoV infection doi = 10.1002/rmv.2158 id = cord-291613-pfgy9ztl author = Farshidpour, Maham title = A brief review of liver injury in patients with Corona Virus Disease-19 during the pandemic date = 2020-07-03 keywords = COVID-19; SARS summary = Corona Virus Disease (COVID)-19 is a respiratory viral infection caused by a newly emergent coronavirus, Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2), which started in Wuhan, China, in December 2019 and has since evolved into a pandemic with a global risk to human health [1] . Although abnormal liver enzymes were regularly described as an extrapulmonary clinical feature, and almost one half of patients experienced grades of hepatic injury [6] [7] [8] [9] , liver damage in patients with SARS infections was primarily manifested in the mild and moderate elevation of alanine and/or aspartate aminotransferases (ALT and AST) with some degree of hypoalbuminemia and hyperbilirubinemia during the early stage of the illness [10, 11] . In this brief review article, we summarized the characteristics and mechanism of liver injury in patients with SARS-CoV-2 infection, with the hope of guiding further study on this important topic. Clinical characteristics of non-ICU hospitalized patients with coronavirus disease 2019 and liver injury: a retrospective study doi = 10.1007/s12664-020-01068-1 id = cord-122092-gdyt02er author = Fatehi, Farzad title = Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date = 2020-10-18 keywords = Fig; RNA; RTC; SARS summary = Comparison of different scenarios is based on tissue damage and viral load, highlighting the impact(s) of antibodies and adaptive cell-mediated immune response on infection dynamics. Surprisingly, our model also suggests that early treatment by either therapy alone can actually increase the duration of infection compared with a later therapy start, likely because suppressing virus production results in a reduced immune response. The model also includes non-structural proteins that are important for the viral life cycle, such as the replicase-transcriptase complex (RTC), and keeps track of the numbers of gRNAs (and subgenomic sgRNAs) at different stages of the replication process. We have included additional reactions into the model that describe remdesivir binding to the RTC complexes on the gRNAs and sgRNAs to capture this (see SI for details), and track the effect of a given, fixed number of remdesivir molecules per cell on the release of viral particles from an infected host cell. doi = nan id = cord-312444-c1dz5o85 author = Faure‐Bardon, V title = How should we treat pregnant women infected with SARS‐CoV‐2? date = 2020-05-14 keywords = SARS; view summary = (Hydroxy) chloroquine has been used in SARS-CoV-2-infected humans with highly controversial results 14,15 but several phase 3 studies are underway to analyse its efficacy both as a cure for patients at each stage of the disease and as a preventive measure. Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with severe coronavirus disease (COVID-19) -Full Text View -ClinicalTrials Study to evaluate the safety and antiviral activity of Remdesivir (GS-5734 TM ) in participants with moderate coronavirus disease (COVID-19) compared to standard of care treatment -Full Text View -ClinicalTrials The efficacy of different anti-viral drugs in COVID 19 infected patients -Full Text View -ClinicalTrials In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine versus placebo in COVID-19 patients at risk for severe disease -Full Text View -ClinicalTrials doi = 10.1111/1471-0528.16270 id = cord-317379-ljdaj80d author = Faure‐Bardon, V. title = Anatomical and timely assessment of protein expression of angiotensin‐converting enzyme 2, SARS‐CoV‐2 specific receptor, in fetal and placental tissues: new insight for perinatal counseling date = 2020-08-15 keywords = ACE2; SARS summary = Beyond theoretical assessment of risk and pathways for vertical transmission, the low incidence of perinatal infections might relate to a lower expression of ACE2 in the placenta and targeted organs. We aimed to evaluate protein expression of ACE2 both in placentas and in all fetal organs from pregnancies not infected with SARS-CoV2 at various gestational ages. Seven placentas were analyzed including 5 from the cases described above, 1 from a 7 weeks''-miscarriage, and 1 from a symptomatic infected pregnant woman with positive SARS-CoV2 RT-PCR delivered by cesarean section at 34 weeks''. These results broaden the insight on likelihood, pathways and morbidities of vertical transmission of SARS-CoV-2, providing a unique anatomical and timely validation of the protein distributions in fetal organs and placentas. The marked placental presence of the specific SARS-CoV2 receptor, ACE2, and its absence from the amnion suggests that ascending vertical transmission could mainly occur following rupture of the amniotic membranes. doi = 10.1002/uog.22178 id = cord-326916-bakwk4tm author = Fauver, Joseph R. title = Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States date = 2020-05-07 keywords = Connecticut; SARS; States; United; covid-19 summary = To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. To delineate the roles of domestic and international virus spread in the emergence of new United States COVID-19 outbreaks, we sequenced SARS-CoV-2 viruses collected from cases identified in Connecticut. We sequenced SARS-CoV-2 genomes from nine of the first COVID-19 cases reported in Connecticut, with sample collection dating from March 6-14, 2020 (Data S1). By combining daily passenger volumes ( Figure 2B ) with COVID-19 prevalence at the travel route origin (Figures 2C and 2D) and accounting for differences in reporting rates, we found that the domestic and international SARS-CoV-2 importation risk started to increase dramatically at the beginning of March 2020 ( Figure 2E ). doi = 10.1016/j.cell.2020.04.021 id = cord-312997-wcqdksfg author = Favresse, Julien title = Clinical performance of the Elecsys electrochemiluminescent immunoassay for the detection of SARS-CoV-2 total antibodies date = 2020-06-02 keywords = SARS summary = In the context of COVID-19, a wide range of serology immunoassays with different SARS-CoV-2 antigen recognition and antibody specificity have been developed to complement RT-PCR assays [1] . This study is the first to report the external validation of a new electrochemiluminescent immunoassay (ECLIA) test, the Elecsys anti-SARS-CoV-2 from Roche Diagnostics ® . This retrospective study was conducted from May 6 to 12, 2020 at the clinical biology Analyses of serum samples obtained 28 days or more after symptom onset provided a sensitivity of 96.7% (95%CI: 82.8-99.9%) and 100% (95%CI: 88.9-100%) with the manufacturer and the optimized cut-off, respectively (Figure 1) . The optimal ROC cut-off showed excellent clinical performance 14 days or more following RT-PCR positivity or following the onset of COVID-19 symptoms. doi = 10.1093/clinchem/hvaa131 id = cord-344356-up53a0k4 author = Feaster, Matt title = High Proportion of Asymptomatic SARS-CoV-2 Infections in 9 Long-Term Care Facilities, Pasadena, California, USA, April 2020 date = 2020-10-17 keywords = SARS summary = Our analysis of coronavirus disease prevalence in 9 long-term care facilities demonstrated a high proportion (40.7%) of asymptomatic infections among residents and staff members. Infection control measures in congregate settings should include mass testing–based strategies in concert with symptom screening for greater effectiveness in preventing the spread of severe acute respiratory syndrome coronavirus 2. Early in the COVID-19 pandemic, the supply of both nasopharyngeal swabs and test kits for SARS-CoV-2 rRT-PCR testing in the United States was extremely limited and made available only for symptomatic persons meeting certain criteria determined by the Centers for Disease Control and Prevention (CDC) (12). Our findings demonstrate a high prevalence of both symptomatic and asymptomatic COVID-19 infection among residents and staff in 9 LTCFs. Because the potential for asymptomatic transmission of SARS-CoV-2 is concerning, for greater effectiveness, infection control efforts in LTCFs should include both mass testing-based strategies and symptom screening. doi = 10.3201/eid2610.202694 id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 keywords = COVID-19; SARS; virus summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). doi = 10.3389/fmicb.2020.01821 id = cord-329240-atisrhas author = Fedorenko, Aliza title = Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date = 2020-06-16 keywords = Phi6; SARS summary = Here we combine microscopy imaging with virus viability assays to study survival of three bacteriophages suggested as good models for human respiratory pathogens: the enveloped Phi6 (a surrogate for SARS-CoV-2), and the non-enveloped PhiX174 and MS2. The observed high virus survival in dry saliva deposited on surfaces, under a wide range of RH levels, can have profound implications for human public health, specifically the COVID-19 pandemic. To study virus survival in microdroplets deposited on a smooth inanimate surface, we sprayed Phi6, MS2, and PhiX174 viruses suspended in three media -human saliva, water, and SM bufferon glass-bottom 12-well plates (Fig. 1, Methods) . The observation that at a given RH, the microscopic hydration conditions of deposited droplets of various media can differ so widely (see along the rows of Fig. 3 ) suggests that RH does not directly affect virus stability and infectivity in drying microdroplets deposited on surfaces, but rather RH indirectly affects survival through its effect on physicochemical conditions at the scale that matters for viruses (~ µm). doi = 10.1101/2020.06.15.152983 id = cord-331871-colmj7uk author = Feehan, A. K. title = Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020 date = 2020-06-24 keywords = SARS summary = Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. This study was designed to estimate SARS-CoV-2 infections in Orleans and Jefferson Parishes (O/JP) and the COVID-19 related IFR by race. . https://doi.org/10.1101/2020.06.23.20138321 doi: medRxiv preprint was used to calculate "presumed recovered." IFR was calculated by dividing cumulative deaths by race, reported by the Louisiana Department of Health, by "presumed recovered" individuals. 2018 population estimates are indicated in Table 1 and multiplied by weighted seroprevalence (percent IgG+) to generate the number of "presumed recovered." Reported deaths are divided by "presumed recovered" to calculate the IFR, which was 1.63% overall. doi = 10.1101/2020.06.23.20138321 id = cord-275604-5u4kikov author = Feehan, Amy K. title = Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 date = 2020-11-17 keywords = SARS; USA summary = Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. We estimated SARS-CoV-2 infections in Orleans and Jefferson Parishes, Louisiana, USA, and determined the COVID-19-related IFR by race. io) considered >50 characteristics, including social determinants of health and US Census population Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. Study participants for whom either or both tests were positive were considered to be infected with SARS-CoV-2. Our study found the overall SARS-CoV-2 exposure rate in this area to be 7.8% and confirmed a recent report of overrepresentation of Black persons with COVID-19 in the New Orleans area (5) . doi = 10.3201/eid2611.203029 id = cord-295455-km0qcmlh author = Fehr, Anthony R. title = Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis date = 2018-07-31 keywords = ADP; HEV; SARS; macrodomain summary = The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Originally described as ADP-ribose-1 00 -phosphatases, both cellular and viral macrodomains enzymatically remove mono-and poly-ADP-ribose from proteins, supporting the notion that protein ADP-ribosylation is a component of the antiviral response. It was unclear how these mutations affected this protein, as neither mutant affected PAR binding and it was unknown whether alphaviruses'' macrodomains had de-ADP-ribosylating activity. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites The conserved macrodomains of the nonstructural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases doi = 10.1016/j.tim.2017.11.011 id = cord-259223-6b07qiw2 author = Feitosa, Eduardo L title = COVID-19: Rational discovery of the therapeutic potential of Melatonin as a SARS-CoV-2 main Protease Inhibitor date = 2020-07-30 keywords = COVID-19; Mpro; PDB; SARS; cell; interaction; melatonin summary = Molecular docking studies described the binding sites and the interaction energies of 74 Mpro-ligand complexes deposited in the Protein Data Bank (PDB). The search for structural similarity used the 10 hit molecules that presented the best interaction energies (Kcal/mol) measured in the docking study among all 74 ligand-Mpro complexes from PDB. The selected hits (top 10 best-scored compounds identified by previous docking study), as well as their respective similar binders, were docked into SARS-CoV-2 main protease (Mpro) with unliganded active site (PDB id: 6Y84). The interaction between melatonin and Mpro (Figure 4) improved the values of binding energy and created a new perspective for a molecule with high therapeutic potential over the COVID-19 pathology to act, so far, only in more severe cases of the disease. To understand the need to clinically evaluate melatonin against Cov-2, we should make a brief introduction to infectious and physiopathological characteristics related mainly to the viral cycle and host immune response in the COVID-19 ( Figure 5) . doi = 10.7150/ijms.48053 id = cord-343515-fad1yyqx author = Felgenhauer, Ulrike title = Inhibition of SARS–CoV-2 by type I and type III interferons date = 2020-10-09 keywords = IFN; SARS; Vero summary = For SARS-CoV-2 (dark gray bars), statistically significant negative correlation coefficients (CC) were obtained for both cell lines, indicating that viral replication is increasingly inhibited by IFN-a. Observations were similar when the input MOI was reduced to 0.001 (Fig. S1 ), except that titers of SARS-CoV-1 in Calu-3 cells were already very low in the absence of any IFN-a, resulting in a nonsignificant effect of additional IFN. Our data thus indicate that (i) if anything, ruxolitinib is an enhancer rather than an inhibitor of SARS-CoV-2 multiplication, and (ii) the boosting effect is most likely due to inhibition of the antiviral JAK/ STAT signaling pathway, because it is not present in the IFN induction-deficient Vero E6 cells. For the statistical testing of the dose-response effect of IFN (type I and III) against SARS-coronaviruses, the typical regression procedures were not applicable because of several values below the detection limit and some ties in the data. doi = 10.1074/jbc.ac120.013788 id = cord-301157-tu3iig9o author = Felsenstein, Susanna title = Presentation, Treatment Response and Short-Term Outcomes in Paediatric Multisystem Inflammatory Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS) date = 2020-10-14 keywords = Multisystem; PIMS; SARS; Syndrome summary = Whilst most children and young people develop mild symptoms, recent reports suggest a novel paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS). Since the advent of the Coronavirus Disease 2019 (COVID-19) pandemic, dominated by respiratory disease and evolution of acute respiratory distress syndrome (ARDS), cardiovascular compromise, excessive systemic inflammation and coagulopathy in adults [1] [2] [3] , several countries affected by the coronavirus disease [4] pandemic have reported an unusually high number of cases of children hospitalized due to a multisystem inflammatory condition, at times requiring intensive care (Table S1) . Temporal distribution of paediatric inflammatory multisystem syndrome temporally associated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (PIMS-TS) cases of this cohort, in relation to COVID-19 like presentations to hospitals in England. The peak of presentations of children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 followed the peak of presentations of patients, adult and paediatric, to English Emergency Departments, with a lag of 4-6 weeks (Figure adapted from https://www.gov.uk/government/news/weekly-covid-19-surveillance-report-published; week 30). doi = 10.3390/jcm9103293 id = cord-354531-7klivhut author = Feng, Liqiang title = An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques date = 2020-08-21 keywords = CMI; Fig; SARS; ad5-s; macaque summary = title: An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques In an attempt to develop a prophylactic vaccine against SARS-CoV-2, we constructed a replication-incompetent recombinant adenovirus, Ad5-S-nb2, that can efficiently express SARS-CoV-2 S protein in infected cells (Fig. 1a) . All non-vaccinated macaques showed no serum neutralizing activities (<1:50) against SARS-CoV-2 either before or 7 days after challenge (Fig. 4f) (Fig. 4g) . This study demonstrated that candidate vaccine Ad5-S-nb2 can elicit S-specific antibody and CMI responses in rodents and in NHPs. A single IM injection with a low-dose of 1 × 10 10 vp Ad5-S-nb2 can confer effective protection against SAR-CoV-2 challenge in aged Chinese rhesus macaques. Consistently, other studies in rhesus macaques also showed that the immune responses elicited by a primary SARS-CoV-2 infection or inactivated whole virus effectively protected against SARS-CoV-2 challenge without observing ADE 18, 19, 29, 30 . doi = 10.1038/s41467-020-18077-5 id = cord-307536-qeo5dfxg author = Feng, Ye title = Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date = 2020-06-30 keywords = SARS summary = title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19. Based on both the epitope counts and HLA score, we 250 eventually selected 13 T-cell epitopes-only vaccine peptides. doi = 10.1101/2020.03.03.962332 id = cord-327681-c2kmog0g author = Feng, Zhilan title = Timely identification of optimal control strategies for emerging infectious diseases() date = 2009-07-07 keywords = SARS summary = RESULTS: Stage-specific infection rate estimates from cases hospitalized before quarantine began exceed those from the entire outbreak, but are qualitatively similar: infectiousness was negligible until symptom onset, and increased 10-fold from prodrome to acute illness. Our model resembles theirs (Fig. 1 ), but we distinguish the prodrome and acute respiratory phase and allow infected people to become infectious before or after becoming ill, at rates-products of contact rates and probabilities of transmission on contact-that may differ among stages. A Mathematica TM notebook that evaluates these expressions for user-supplied parameter values, comparing the impact of non-pharmaceutical interventions on any disease transmitted by close contact, is available from the Table 1 Parameter estimates (b represents infection, r isolation efficiency, f hospitalization; subscripts E, P and R refer to pre-symptomatic, prodrome, and acute respiratory stage) from fitting predicted to observed cumulative admissions to TTSH during the first 30 days of the outbreak (cf. doi = 10.1016/j.jtbi.2009.03.006 id = cord-285574-i0dh1u5i author = Ferini-Strambi, Luigi title = COVID-19 and neurological disorders: are neurodegenerative or neuroimmunological diseases more vulnerable? date = 2020-07-21 keywords = SARS; covid-19 summary = doi = 10.1007/s00415-020-10070-8 id = cord-351736-4x5u4qsy author = Fernandez-Garcia, Cristina title = Severe COVID-19 During Pregnancy and the Subsequent Premature Delivery date = 2020-09-19 keywords = SARS summary = Only a few case of SARS-CoV-2 infection in preterm neonates delivered by mothers with COVID-19 have been reported till date. We report the cases of three premature babies delivered by two mothers with severe COVID-19 pneumonia, whose condition deteriorated to the point that necessitated the use of mechanical ventilation on the mothers as well as accelerated child delivery of the mothers. There have been very few reports of preterm delivery in mothers with COVID-19 and most babies have tested negative to SARS-CoV-2. 3, 4 In the few reported neonates who tested positive to SARS-CoV-2 via PCR, there is no evidence of in utero transmission, since infection in the immediate neonatal period could not be completely excluded. 5, 6 Preterm delivery was required in the three cases described in this report, since the mothers developed severe COVID-19 pneumonia. There was no evidence of in utero transmission, such that all the babies (3) tested negative to SARS-CoV-2 immediately after birth and at 24 hours, 5, and 14 days of life. doi = 10.1016/j.pedneo.2020.09.005 id = cord-294262-yvbufnf4 author = Fernandez-Nieto, D. title = Comment on: “To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out. Characterization of herpetic lesions in hospitalized COVID-19 patients.” date = 2020-06-22 keywords = SARS summary = All 15 patients presented typical clinical lesions and symptoms of herpes 39 simplex/zoster. In spite of performing PCR tests for SARS-CoV-2 from the 42 content of the vesicles in only three patients, the results were all negative. Regarding vesicular rashes or varicella-like COVID-19 exanthems 3 , we previously 44 reported four cases in which we performed both PCR multiplex for herpesvirus and rt-45 PCR for SARS-CoV-2, directly from the content of the vesicles. This reasonably rules out a role of herpes 47 viruses 3 , and a potential infective ability of SARS-CoV-2 through the vesicles. In our current experience, the diagnosis of 55 herpesvirus infection in COVID-19 patients does not usually involve diagnostic doubts, 56 due to the clinical presentation and reported symptoms being typical of the disease, 57 even when lesions are extensive (Figure 1) . doi = 10.1016/j.jaad.2020.06.063 id = cord-335364-qwjuzebd author = Fernandez-Rivas, G. title = Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave date = 2020-06-26 keywords = Barcelona; SARS summary = title: Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave Methods: IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22nd, 2020) by chemiluminescence assays. IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22 nd , 2020) by chemiluminescence assays. Hence, in this study we analyzed the SARS-CoV-2 IgG seroprevalence in Healthcare workers of the Northern Metropolitan Area of Barcelona, Spain. From May 4th to May 22 nd , 2020, all Healthcare workers of the ICS-Northern Metropolitan Area of Barcelona (n=9315) were offered to have serum testing performed for SARS-CoV-2 IgG antibodies. doi = 10.1101/2020.06.24.20135673 id = cord-270888-8j17ul7k author = Fernández-González, Sara Mª title = ¿Infección Por Sars-Cov-2 Como Desencadenante De Un Síndrome Inflamatorio Sistémico? date = 2020-09-09 keywords = SARS summary = Desde entonces este síndrome se ha conocido con diferentes nomenclaturas y, desde Mayo, se conoce como Paediatric inflammatory multisystem syndrome temporally associated with severe J o u r n a l P r e -p r o o f acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (PIMS-TS) [3] [4] [5] . Presentamos el caso de un niño de 4 años con síndrome de respuesta inflamatoria sistémica e IgG positiva para SARS-CoV-2 con IgM y reacción en cadena de la polimerasa (PCR) sobre muestra de frotis nasofaríngeo negativas. Tras 24 horas de inicio de tratamiento presentó una mejoría clínica progresiva con desaparición del exantema, edema e hiperemia conjuntival, así como normalización de constantes (frecuencia cardiaca 71 lpm y tensión arterial 97/52 mmHg, p50) y parámetros analíticos, a excepción de trombocitosis reactiva (plaquetas 579000/L) Estuvo ingresado durante 9 días en planta de hospitalización, hasta completar 7 días de antibioterapia intravenosa en espera de resultados de cultivos y mejoría de parámetros analíticos, manteniéndose estable a nivel hemodinámico y respiratorio sin necesitar soporte vasoactivo ni respiratorio. doi = 10.1016/j.eimc.2020.07.012 id = cord-270112-o2exvfy5 author = Ferrarese, Carlo title = An Italian multicenter retrospective-prospective observational study on neurological manifestations of COVID-19 (NEUROCOVID) date = 2020-05-19 keywords = COVID-19; SARS; neurological summary = We report here the description of a multicenter retrospective-prospective observational study promoted by the Italian Society of Neurology (SIN), involving the Italian Neurological Departments, who will consecutively recruit patients with neurological symptoms and/or signs, occurred at the onset or as a complication of COVID-19. A comprehensive data collection, in the form of electronic case report form (eCRF), will register all possible neurological manifestations involving central nervous systems, peripheral nerves, and muscles, together with clinical, laboratory (including cerebrospinal fluid, if available), imaging, neurological, neurophysiological, and neuropsychological data. More specifically, the aims are to gather data on the following: (1) the appearance of neurologic symptoms and/or signs at COVID-19 onset or during the disease course, (2) the exams performed for the diagnosis of the neurological involvement, (3) the clinical course of both the COVID-19 infection and the neurological events, but also the occurrence of possible long-term neurological complications within a 6-month period of follow-up. doi = 10.1007/s10072-020-04450-1 id = cord-255665-srvz2ay0 author = Ferrari, Marco title = COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions date = 2020-10-14 keywords = COVID-19; SARS summary = title: COVID-19 screening protocols for preoperative assessment of head and neck cancer patients candidate for elective surgery in the midst of the pandemic: a narrative review with comparison between two Italian institutions The study included all patients undergoing surgery under general anesthesia for HNC at two Italian tertiary referral academic hospitals during the peak of the pandemic diffusion of to an internal "grey zone" of COVID-19 surveillance, submitted to further blood tests, chest CT, and nasal/nasopharyngeal swab while maintaining strict isolation. The following data were extracted from institutional databases: patient-related including the 2-week post-discharge period) was considered as the gold standard evaluation (i.e. patients developing symptoms attributed to COVID-19 through nucleic acid-based test on respiratory secretions in this time frame were considered as "false negative" of the screening; doi = 10.1016/j.oraloncology.2020.105043 id = cord-355175-uo9fx6jy author = Ferrazzi, E title = Vaginal delivery in SARS‐CoV‐2‐infected pregnant women in Northern Italy: a retrospective analysis date = 2020-05-28 keywords = SARS; covid-19 summary = Data were collected from the clinical records using a standardised questionnaire on maternal general characteristics, any medical or obstetric co‐morbidity, course of pregnancy, clinical signs and symptoms, treatment of COVID 19 infection, mode of delivery, neonatal data and breastfeeding. Conclusions Although postpartum infection cannot be excluded with 100% certainty, these findings suggest that vaginal delivery is associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. Another clinical series of 11 women with COVID 19 infection who had successful deliveries (10 caesarean and 1 vaginal) has been reported: in all the newborns, the 2019-nCoV nucleic acid test was negative. This paper reports the obstetric outcome of a cohort of COVID-19-affected pregnant women and the rate of SARS-CoV-2 positivity in newborns according to mode of delivery and breastfeeding status. Although postpartum infection cannot be excluded, our study also suggests that vaginal delivery may be associated with a low risk of intrapartum SARS-Cov-2 transmission to the newborn. doi = 10.1111/1471-0528.16278 id = cord-267762-mzon01fd author = Ferreira, A. title = Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection. date = 2020-06-29 keywords = HCQ; SARS summary = Methods: By analyzing the Portuguese anonymized data on private and public based medical prescriptions we have identified all cases chronically receiving HCQ for the management of diseases such as systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. Cross linking the two sets of data has allowed us to compare the proportion of HCQ chronic treatment (at least 2 grams per month) in laboratory confirmed cases of SARS-CoV-2 infection with laboratory confirmed negative cases. Several in vitro studies have shown chloroquine phosphate and hydroxychloroquine sulphate (HCQ) to be effective in both preventing and treating SARS-CoV-2 infection in isolated cells (1) (2) (3) . By analyzing these sets of data, we were able to detect all patients with SARS-CoV-2 confirmed infections and all clinically suspected but non-confirmed patients between Mars 2, 2020 (the date of the first Portuguese case) and the moment of the analysis. The proportion of HCQ chronic treatment was higher in negative patients is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.06.26.20056507 id = cord-295121-4xemmaqt author = Ferreira, Eliane de Oliveira title = Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date = 2020-09-29 keywords = CDI; COVID-19; SARS summary = The outbreak caused by the novel coronavirus SARS-CoV-2 and its associated symptoms, termed COVID-19 disease, originally in Wuhan, China in 2019, has rapidly become a global pandemic (Park, 2020) . Although some of those risk factors for CDI are also related to higher probability rates of mortality in severe SARS-CoV-2 infection, the limited number of CDI cases reported among COVID-19 patients is somewhat surprising. The authors emphasized that when CDI is present as a co-infection with COVID-19 and the diarrhea persists, therapy can be difficult because of the SARS-CoV-2 infection. The dearth of studies regarding secondary infections, such as Clostridioides difficile, in COVID-19 patients makes it difficult to measure the effect of the pandemic on antimicrobial stewardship programs and on long term antimicrobial resistance. In conclusion, it seems highly likely that cases of CDI are being under-reported among COVID-19 patients and the increased use of antibiotics may, in part, be responsible. doi = 10.3389/fmicb.2020.581343 id = cord-330061-q4xi260z author = Ferreira, João Guimarães title = Pneumothorax as a late complication of COVID-19 date = 2020-08-31 keywords = COVID-19; SARS; patient summary = We present a typical laboratory confirmed case of COVID-19 pneumonia, that was hospitalized due to hypoxemia but did not require mechanical ventilation. On the other hand, patients with more severe disease comprise 14% of the cases, with progressive tachypnea and dyspnea after five to eight days from the beginning of the symptoms, low blood oxygen saturation, and/or lung infiltrates in > 50% of the lungs. Regarding laboratory abnormalities in patients with COVID-2019 infections, the most frequent findings for those who need admission to the intensive care unit are leukocytosis, higher neutrophil count, lymphopenia, increased values of CRP, LDH, aminotransferases, total bilirubin, creatinine, cardiac troponin, procalcitonin and D-dimer. Herein, we present a typical and laboratory confirmed case of COVID-19 pneumonia, with clinical course deterioration during the third week of the disease due to a massive hypertensive pneumothorax with no known previous risk factor. Spontaneous pneumothorax and subcutaneous emphysema in COVID-19 patient: case report doi = 10.1590/s1678-9946202062061 id = cord-326983-h6gdck2u author = Ferretti, Andrew P. title = Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date = 2020-10-20 keywords = CD8; HLA; SARS summary = We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). doi = 10.1016/j.immuni.2020.10.006 id = cord-312559-ygh507x2 author = Fiesco-Sepulveda, K. Y. title = Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review date = 2020-05-22 keywords = COVID-19; SARS summary = title: Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, meta-analyses 248 using Latin American cases would also be ideal for determining how COVID-19 could affect this 249 region, which has some differences, such as lower average age or higher exposure to respiratory 250 infections than other regions like Europe (Amariles et al., 2020a). (2020) concluded that the novel virus could come from a bat SARS-like coronavirus isolate, 168 which is in agreement with reports from the GISAID database Clinical features of patients infected 644 with 2019 novel coronavirus in Wuhan The novel coronavirus (SARS-CoV-2) emergency and the role of timely and 674 effective national health surveillance Complete genome sequence of a 2019 novel coronavirus (SARS-COV-2) strain isolated 792 in Nepal. doi = 10.1101/2020.05.16.20104422 id = cord-315152-v3l33up6 author = Figlerowicz, Magdalena title = First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia date = 2020-07-01 keywords = COVID-19; SARS summary = title: First case of convalescent plasma transfusion in a child with COVID-19-associated severe aplastic anemia We present the case of a six-year-old girl with severe COVID-19, in whom SARS-CoV-2 was successfully eliminated after convalescent plasma transfusion. In December 2019, a novel coronavirus disease (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) arose unexpectedly in China. In pediatric patients with a severe or critical course of COVID-19, acute respiratory distress syndrome (ARDS) can occur; toxic shock is also observed. Here, we present a case of using a J o u r n a l P r e -p r o o f convalescent plasma transfusion as a therapeutic method for severe pediatric COVID-19associated aplastic anemia. We present a case of using convalescent plasma in the therapy of a child with severe COVID-19. Effectiveness of convalescent plasma therapy in severe COVID-19 patients doi = 10.1016/j.transci.2020.102866 id = cord-282878-8qgsq2km author = Fignani, Daniela title = SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date = 2020-10-23 keywords = ACE2; SARS; cell; figure; human; pancreatic summary = Finally, using RT-qPCR, RNA-seq and High-Content imaging screening analysis, we demonstrated that pro-inflammatory cytokines, but not palmitate, increases ACE2 expression in the β-cell line EndoC-βH1 and in primary human pancreatic islets. To address this question, we screened the ACE2 expression pattern in human pancreata obtained from adult non-diabetic multiorgan donors and in the insulin-producing human β-cell line EndoC-βH1, using different methodologies, multiple reagents, and publicly available or in-house generated RNA sequencing datasets. Here, we adopted multiple technologies and reagents to thoroughly analyse presence of ACE2, both at mRNA and protein level, in order to evaluate its expression and localization in pancreatic tissue samples obtained from adult non-diabetic multiorgan donors from the INNODIA EUnPOD biobank collection, in enzymatic-and LCM-isolated primary adult human pancreatic islets and in human β-cell line EndoC-βH1. Importantly, a recent report showed that human pancreatic islets can be infected in vitro by SARS-CoV-2 (23), supporting our observations of a specific tropism of the virus due to ACE2 expression. doi = 10.1101/2020.07.23.208041 id = cord-028989-w50thois author = Figueira Gonçalves, Juan Marco title = Clinical challenges in chronic obstructive pulmonary disease in patients who suffered SARS-CoV-2 infection() date = 2020-07-10 keywords = COPD; SARS summary = Reported complications of SARS-CoV-2 infection, such as extensive pneumonia/acute lung damage or adult acute respiratory distress syndrome, the occurrence of myocarditis/cardiac arrhythmias or the development of thromboembolic 2/7 episodes are events that may worsen the baseline condition of the COPD patient surviving the process, having to take into account their existence when planning their outpatient follow-up. Despite the lack of sufficient evidence at the moment, the results reported to date and the pathogenic mechanisms plausibly involved, make it advisable to consider this aspect in those patients with COPD who, after hospital discharge, develop in the medium to long term an increase in dyspnoea not justified by spirometric parameters. In the SARS-CoV-1 epidemic, some of the survivors developed avascular necrosis, pulmonary fibrosis, and dyslipidaemia after viral infection 15, 16 , which may have a relevant impact on those patients who already had some underlying respiratory or cardiovascular condition. doi = 10.1016/j.medcle.2020.04.012 id = cord-298850-tgxfki7n author = Figuero-Pérez, Luis title = Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab date = 2020-10-15 keywords = CoV-2; SARS summary = title: Anakinra as a potential alternative in the treatment of severe acute respiratory infection associated with SARS-CoV-2 refractory to tocilizumab Several studies have proposed that anti-IL-6 receptor antibodies, such as tocilizumab, play an important role in the treatment of severe acute respiratory infection associated with SARS-CoV-2. We present a case report of a 51-year-old man diagnosed with severe respiratory infection associated with SARS-CoV-2 that was refractory to antiviral and anti-IL-6 treatment, with a favourable clinical outcome and analytical improvement after treatment with anti-IL-1 (anakinra). We present the case of a 51-year-old patient with bilateral pneumonia secondary to SARS-CoV-2 infection refractory to treatment with tocilizumab who showed improvement after treatment with anakinra. The "cytokine storm" secondary to SARS-CoV-2 infection determines severe COVID-19 disease. 3 The use of anti-IL-6 antibodies in the treatment of SARS-CoV-2 infection is currently under study, being one of the current pillars of COVID-19 disease treatment. doi = 10.1016/j.reumae.2020.06.008 id = cord-339009-wcoch07b author = File, Thomas M. title = Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date = 2012-08-23 keywords = CoV; SARS; case; patient; respiratory summary = Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world. doi = 10.2165/00151829-200504020-00003 id = cord-324651-8teb5jrn author = Filippini, Antonio title = Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date = 2020-04-30 keywords = SARS; TPC2 summary = title: Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? In the present opinion article we highlight evidence from different laboratories to drive the attention of the scientific community on the role played by endo-lysosomal Two-Pore Channels (TPCs) in viral infection. In particular, cross linking our recent data and existing literature, we focus on evidence indicating that virus intracellular pathway could be targeted by a novel occurring TPCs inhibitor, the flavonoid Naringenin. Intriguingly, our recent evidence has shown that the activity of human TPC channels can be inhibited by a natural flavonoid compound, in fact present in citruses and tomatoes, Naringenin (Pafumi et al., 2017) . In conclusion, these considerations offer a perspective on specific molecular targets, TPCs, and underpin a role for Naringenin as pharmacological blockade of SARS-CoV-2 infectivity providing further support for exploration of TPCs inhibition as novel antiviral therapy. doi = 10.3389/fmicb.2020.00970 id = cord-320902-1hfxju5f author = Filocamo, Giovanni title = Use of anakinra in severe COVID-19: a case report date = 2020-05-11 keywords = COVID-19; SARS summary = As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still''s disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient''s critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). doi = 10.1016/j.ijid.2020.05.026 id = cord-312702-fruzsn26 author = Finch, Courtney L. title = Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date = 2020-05-14 keywords = COVID-19; SARS summary = title: Characteristic and quantifiable COVID-19-like abnormalities in CTand PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) Based on the rather limited X-97 ray findings in the lungs of reported NHP models of SARS-CoV-2 infection with either 98 mild or no clinical signs (11, 25, 27-29), we turned to high-resolution chest CT and 99 Increases in PCLH or PCLH/LV 169 were not seen in the mock-exposed macaques over the entire study (Figure 8a A key advantage of quantifiable CT chest imaging readout over serial euthanasia 212 studies, in addition to potentially reduced experimental animal numbers, is the ability not 213 only to evaluate between-group differences, but also to compare severity and duration of 214 disease at higher resolution in single animals and even in isolated parenchymal areas 215 sequentially. follow-up confirmation of these pilot results in this model of mild-moderate COVID-19 233 is needed to further establish quantifiable lung CT as a reliable disease readout and to 234 forge imaging-pathologic correlates in macaques euthanized at peak radiographic 235 abnormality. doi = 10.1101/2020.05.14.096727 id = cord-313349-ikjivfce author = Finsterer, Josef title = Causes of hypogeusia/hyposmia in SARS‐CoV2 infected patients date = 2020-04-20 keywords = SARS; patient summary = It is well appreciated that SARS‐CoV2 does not exclusively affect the lungs.(1,2) Virus‐RNA can be detected in most of the body compartments, including the cerebrospinal fluid (CSF).(3) Neurological manifestations have been recently investigated in a retrospective study of 214 SARS‐CoV2‐infected patients.(1) This article is protected by copyright. A further argument against hypothesis one is that SARS-CoV2-associated meningitis is rare Accepted Article but smelling/taste abnormalities are frequent. In COVID-19 patients, ACE2-expressing cells of the taste buds and/or olfactory epithelium might be targeted by SARS-Cov2 via a cytopathic effect. 15 Besides the hypothesis of a cytopathic effect on neurosensory cells, the high incidence of smell and/or taste loss in COVID-19 patients might thus reflect the impact of SARS-Cov2 on the synthesis of neurotransmitters (notably serotonin and dopamine) by ACE2-expressing cells. In summary, the most likely cause for transient hypogeusia and hyposmia in SARS-CoV2-infected patients is a direct contact and interaction of the virus with gustatory receptors or olfactory receptor cells. doi = 10.1002/jmv.25903 id = cord-266710-3wdy16tw author = Fintelman-Rodrigues, Natalia title = Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production date = 2020-09-21 keywords = ATV; Fig; LPV; RTV; SARS summary = Molecular dynamics analysis revealed that the root mean square deviation (RMSD) for the SARS-CoV-2 Mpro backbone presented different conformations in complex with ATV or LPV (see Fig. S3 ). As a control, the activity of SARS-CoV-2 Mpro in fractions from infected cells was evaluated by treatment with RTV, which inhibited activity in the molecular range of 31 to 38 kDa without a change in the 70-kDa region (Fig. 2 , RTV lanes). Since the results regarding the pharmacologic activity of ATV and ATV/RTV against SARS-CoV-2 replication in Vero cells were promising, we next investigated whether the proposed drug therapies could inhibit virus replication in a human epithelial pulmonary cell line (A549). We highlight ATV and ATV/RTV because our assay readout to quantify infectious virus particles reveals (i) a good profile of antiviral activity, (ii) higher potencies in respiratory cells, and (iii) the ability to reduce levels of proinflammation mediator in monocytes. doi = 10.1128/aac.00825-20 id = cord-311782-d2t8bzio author = Fiore, Josè Ramòn title = Results from a survey in healthy blood donors in South Eastern Italy indicate that we are far away from herd immunity to SARS‐CoV‐2 date = 2020-08-13 keywords = Italy; SARS summary = We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general population three months after the local start of the epidemic. In our study, we confirm a low rate of antibodies against SARS-CoV-2 on a group of blood donors from a geographical region with a moderate incidence (187 cases/100.000 inhabitants vs the national data of 390 infections/100.000 inhabitants); our results are at variance with those observed in other regions of Italy. doi = 10.1002/jmv.26425 id = cord-313356-ninzeazy author = Fiorillo, Luca title = COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date = 2020-04-30 keywords = COVID-19; SARS; surface; virus summary = title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention doi = 10.3390/ijerph17093132 id = cord-312663-hhd5f823 author = Fiorino, Gionata title = Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date = 2020-03-24 keywords = IBD; SARS summary = The outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. IBD patients are severely worried about the impact of their disease and medications on the risk and the prognosis of COVID-19, and many of them are forced to come to hospital because of active disease, complications and drug administration. Patients scheduled for a follow-up visit are required to stay at home and to complete a questionnaire about IBD symptoms and quality of life, together with their routine laboratory tests, to the nurse and the dedicated doctor, who give recommendations and information about therapy and follow-up procedures. Based on the assumption that the risk of coronavirus infection is not different between the general population and IBD patients, but that IBD flares are difficult to manage in this situation, we advise all patients to continue their therapies, especially if in remission. doi = 10.1093/ecco-jcc/jjaa058 id = cord-330266-uypjqif7 author = Firpo, Mason R. title = Targeting Polyamines Inhibits Coronavirus Infection by Reducing Cellular Attachment and Entry date = 2020-09-23 keywords = DFMO; MHV; SARS; cell; figure summary = To determine if coronaviruses are susceptible to polyamine depletion, we treated Vero-E6 cells with doses of DFMO ranging from 750 μM to 5 mM for 4 days prior to infection with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.1 plaque forming units (pfu) per cell. To determine if DFMO-mediated virus restriction was a result of polyamine depletion, we treated BHK-R cells with DFMO and, at the time of infection, supplemented with the individual polyamines putrescine, spermidine, and spermine at 1 μM, a level that did not affect cellular viability ( Figure 2A ). We observed that DFMO reduced viral titers and that supplementation with any of the individual polyamines rescued virus replication to untreated levels ( Figure 2C ). 19 We observed no changes in plaque size ( Figure 3A ) or morphology ( Figure 3B ) with DFMO supplementation to the media, suggesting that DFMO was not sufficiently antiviral when applied to cells after infection and highlighting that DFMO must be applied prophylactically to reduce coronavirus replication. doi = 10.1021/acsinfecdis.0c00491 id = cord-252767-as841xo0 author = Fischer, Bastian title = SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, March to June 2020 date = 2020-07-16 keywords = CoV-2; SARS summary = We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. We determined seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 3,186 regular blood donors in three German federal states between 9 March and 3 June 2020. To determine an approximation of the actual rate of people who have recovered from COVID-19, representative of the German population, we determined the anti-SARS-CoV-2 IgG seroprevalence of regular blood donors resident in three different German federal states between March and June 2020. The Figure shows the anti-SARS-CoV-2 IgG distribution in blood donors with equivocal (ratio: ≥ 0.8 to < 1.1) and clearly seropositive (ratio: ≥ 1.1) test results. Distribution of anti-SARS-CoV-2 IgG ratios of blood donors with seropositive and equivocal test results, Germany, March-June 2020, (n = 3,186) doi = 10.2807/1560-7917.es.2020.25.28.2001285 id = cord-293517-8derad2p author = Fischer, Johannes C. title = Correction to: The role of passive immunization in the age of SARS-CoV-2: an update date = 2020-10-30 keywords = SARS summary = key: cord-293517-8derad2p authors: Fischer, Johannes C.; Zänker, Kurt; van Griensven, Martijn; Schneider, Marion; Kindgen-Milles, Detlef; Knoefel, Wolfram Trudo; Lichtenberg, Artur; Tamaskovics, Balint; Djiepmo-Njanang, Freddy Joel; Budach, Wilfried; Corradini, Stefanie; Ganswindt, Ute; Häussinger, Dieter; Feldt, Torsten; Schelzig, Hubert; Bojar, Hans; Peiper, Matthias; Bölke, Edwin; Haussmann, Jan; Matuschek, Christiane title: Correction to: The role of passive immunization in the age of SARS-CoV-2: an update journal: Eur J Med Res cord_uid: 8derad2p High activity natural killer cell during target attack. Footprint of previously attached natural killer cell can be identified by patchy membrane residuals on the target cell surface. When will NK-cells join the cellular immune cascade to fight SARS-CoV-2? The role of passive immunization in the age of SARS-CoV-2: an update Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Fischer et al. Eur J Med Res (2020) 25:53 doi = 10.1186/s40001-020-00449-8 id = cord-255888-znfgh78m author = Fisher, Dale title = Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date = 2020-08-18 keywords = SARS summary = SARS-CoV-2 was detected on workers and environmental samples, including a cutting board used to slice imported salmon. We have assessed the survival of SARS-CoV-2 on refrigerated and frozen meat and salmon over 3 weeks to assess the potential of outbreaks being seeded by imported contaminated food. The clusters of infection of COVID-19 among workers in slaughterhouses and meat processing facilities in many countries can be attributed to factors that promote transmission of virus directly between workers, such as crowding, poor ventilation, and shouting in close proximity due to high ambient noise levels. With a significant burden of virus present in infected workers and the environment then contamination of meat with SARS-CoV-2 is possible during butchering and processing. Our laboratory work has shown that SARS-CoV-2 can survive the time and temperatures associated with transportation and storage conditions associated with international food trade. We believe it is possible that contaminated imported food can transfer virus to workers as well as the environment. doi = 10.1101/2020.08.17.255166 id = cord-010050-utbrf4ad author = Fisher, Dale A title = Preventing local transmission of SARS: lessons from Singapore date = 2003-06-02 keywords = SARS; Singapore summary = 4 Instituting this Preventing local transmission of SARS: lessons from Singapore Clinical record At 11:30 on 8 April 2003, a 64-year-old man presented to the National University Hospital emergency department (ED) complaining of light headedness for 3 days, and dry cough and body aches for 2 days. Australia must ensure rapid identification of a potential index case at points of initial contact in hospitals, community clinics and general practices across the country. 1, 2 In countries with the resources to implement full and effective contact and respiratory isolation for all suspect patients, local transmission of the virus has been almost non-existent. Provided there is consistent early identification of imported suspect cases, then Australia''s healthcare system can manage these patients with appropriate isolation to prevent secondary transmission. Each health jurisdiction in Australia must have a plan for managing a local SARS outbreak, which should include prompt hospital and community responses, and an ability to meet potential needs at short notice. doi = 10.5694/j.1326-5377.2003.tb05358.x id = cord-333042-icgsbelo author = Fisher, Kiva A. title = Community and Close Contact Exposures Associated with COVID-19 Among Symptomatic Adults ≥18 Years in 11 Outpatient Health Care Facilities — United States, July 2020 date = 2020-09-11 keywords = CDC; COVID-19; SARS summary = Restricting the analysis to participants without known close contact with a person with confirmed COVID-19, case-patients were more likely to report dining at a restaurant (aOR = 2.8, 95% CI = 1.9-4.3) or going to a bar/coffee shop (aOR = 3.9, 95% CI = 1.5-10.1) than were control-participants. For each reported activity, participants were asked to quantify degree of adherence to recommendations such as wearing a face mask of any kind or social distancing among other persons at that location, with response options ranging from "none" to "almost all." Descriptive and statistical analyses were performed to compare case-patients with control-participants, assessing differences in demographic characteristics, community exposures, and close contact. In addition to dining at a restaurant, case-patients were more likely to report going to a bar/coffee shop, but only when the analysis was restricted to participants without close contact with persons with known COVID-19 before illness onset. doi = 10.15585/mmwr.mm6936a5 id = cord-265278-wf5pbvvt author = Fishman, Jay A. title = Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation date = 2020-09-17 keywords = SARS; covid-19; patient; recipient; transplant summary = In transplant recipiAfter infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viral replication ensues in the respiratory epithelium, followed by viremia and systemic spread to organs by means of the angiotensin-converting-enzyme 2 receptor. 22 Graft rejection and toxic effects from calcineurin inhibitors may be difficult to distinguish from The varied presentation of SARS-CoV-2 infection reflects diversity in host immune responses, notably in immunosuppressed transplant recipients. Although the use of antiinflammatory drugs (e.g., high-dose glucocorticoids or interleukin-6 receptor antagonists) in solid-organ transplant recipients may have the additional benefit of protecting against rejection among patients who are receiving tapering courses of the immunosuppressive agents, especially when calcineurin inhibitors are discontinued because of severe disease, their efficacy in the context of solidorgan transplantation warrants testing in clinical trials. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection doi = 10.1056/nejmcpc2004982 id = cord-295864-kwdvais7 author = Flahault, Antoine title = Has China faced only a herald wave of SARS-CoV-2? date = 2020-03-27 keywords = SARS summary = key: cord-295864-kwdvais7 journal: The Lancet cord_uid: kwdvais7 Serosurveys should be seen as polls before elections; they can be repeated several times, 3 week after week, to monitor the epidemic precisely. There is no reason to wait for the end of the epidemic before doing serosurveys. The results would be tremendously informative to China, first and foremost, and to the entire international community, on the risk of big secondary epidemic waves. The attack rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) calculated by mathe matical models, from estimates of the basic reproduction number, R0, of 2-3, suggests that 50-60% of the population should eventually be infected because the population seems to be entirely naive to the new virus. COVID-19) advice for the public Director-General''s opening remarks at the media briefing on COVID-19 -28 A WHO-UNICEF-Lancet Commission doi = 10.1016/s0140-6736(20)30521-3 id = cord-280915-yk872yaz author = Flaherman, Valerie J title = Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date = 2020-09-18 keywords = SARS; mother summary = In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. doi = 10.1093/cid/ciaa1411 id = cord-264814-v4wnmg03 author = Flanagan, Katie L. title = Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines date = 2020-10-02 keywords = CD8; COVID-19; CoV-2; SARS; cell; dna; table; vaccine summary = Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure. doi = 10.3389/fimmu.2020.579250 id = cord-314822-lmoc0xwi author = Flegel, Willy A. title = CoVID‐19 insights from transfusion medicine date = 2020-07-08 keywords = ABO; SARS summary = 5 The first analyses of patients with CoVID-19 in Wuhan, China did not report a substantial need for blood transfusion. In rapid reporting succession, patients with CoVID-19 infection have been documented to develop cold agglutinin disease, 11 the relatively more common autoimmune haemolytic anaemia 12, 13 or immune thrombocytopenia 14 and their combination as Evans syndrome. 23, 24 The safety profile has to be established, particularly for patients in early stage CoVID-19, where convalescent plasma, if safe, may be most effective. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and Transfusion Medicine: reflections from Italy Blood component use in critical care in patients with COVID-19 infection: a single centre experience Improved clinical symptoms and mortality on severe/critical COVID-19 patients utilizing convalescent plasma transfusion Relationship between ABO blood group distribution and clinical characteristics in patients with COVID-19 More on ''Association between ABO blood groups and risk of SARS-CoV-2 pneumonia'' More on ''Association between ABO blood groups and risk of SARS-CoV-2 pneumonia'' doi = 10.1111/bjh.17005 id = cord-300024-169g2ih5 author = Flemming, S. title = Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date = 2020-05-26 keywords = SARS summary = key: cord-300024-169g2ih5 title: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 cord_uid: 169g2ih5 Abdominal fluid (ascites), bile, liver and gall bladder samples were collected during emergency cholecystectomy of a critically ill patient suffering from COVID-19. Tracheal secretion and throat swab samples were collected immediately prior to surgery as positive controls. All samples were tested for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction (PCR) using validated primers 5 . PCR tests revealed strongly positive results for SARS-CoV-2 RNA in tracheal secretion as well as in throat swab samples, with cycle threshold values of 20 and 25, respectively. The remaining samples all tested negative for SARS-CoV-2 suggesting that the virus does not spread to the abdominal cavity, bile and abdominal organs. A stool sample obtained one day after surgery also tested negative. Recommendations for general surgery activities in a pandemic scenario (SARS-CoV-2) doi = 10.1002/bjs.11713 id = cord-309304-glcxrh7t author = Flemming, Sven title = Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 date = 2020-09-19 keywords = SARS summary = title: Author response to: Comment on: Abdominal fluid samples (negative for SARS‐CoV‐2) from a critically unwell patient with respiratory COVID‐19 Nevertheless, these recommendations should be critically challenged since only the transmission of human papillomavirus from patient to surgeon by surgical smoke (aerosols) has been reported in a very small number of cases. Several recent studies have shown that fecal samples of COVID-19 patients can be positive for SARS-CoV-2, suggesting potential fecal oral transmission and thus a higher risk for gastrointestinal surgeons 3 . The purpose of our case report was to share actual clinical observations and results from a critically ill patient suffering from COVID-19 pneumonia who required emergency surgical treatment. These results have since been supported by a second case report showing negative PCR of peritoneal fluid in a COVID-19 patient who needed emergency surgery due to acute appendicitis. doi = 10.1002/bjs.11898 id = cord-316670-x9x54fxw author = Flinck, Heini title = Comparison of two fully automated tests detecting antibodies against nucleocapsid N and spike S1/S2 proteins in COVID-19 date = 2020-08-29 keywords = Elecsys; SARS summary = Based on our results, the SARS-CoV-2 antibodies can be quite reliable detected 2 weeks after NAAT positivity and 3 weeks after the symptom onset with both tests. In this paper, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. N protein based tests may be more sensitive to detect past COVID-19, but S protein may be a possible target for neutralizing antibodies, and SARS-CoV-2 antibodies against that antigen may better predict the protective immunity (Walls et al. In this study, we compared the performance of the fully automated Elecsys ® Anti-SARS-CoV-2 test detecting antibodies against nucleocapsid N protein and LIAISON ® SARS-CoV-2 S1/S2 IgG test detecting antibodies against spike protein S1-and S2-antigens. Response of anti-SARS-CoV-2 total antibodies to nucleocapsid antigen in COVID-19 patients: a longitudinal study doi = 10.1016/j.diagmicrobio.2020.115197 id = cord-016897-t71f10kv author = Flores, Marco V. title = Preventing Airborne Disease Transmission: Implications for Patients During Mechanical Ventilation date = 2013-05-29 keywords = NIV; SARS; droplet summary = We discuss the risk of transmitting these procedures and the strategies for mechanical ventilation in future airborne epidemics with special consideration given to the issue of protecting health care workers (HCWs). In contrast to the situation regarding severe acute respiratory syndrome (SARS) or tuberculosis prevention in HCWs, little attention has been given to the importance of HCWs personal protective equipment (PPE) (gowns, gloves, masks) for prevention and management of infl uenza. There is also potential for NIV to reduce the need for intubation in patients with infl uenza pneumonia or chronic respiratory disease, facilitate extubation, and widen the provision of ventilator support outside the intensive care unit (ICU). Evaluation of droplet dispersion during non-invasive ventilation, oxygen therapy, nebulizer treatment and chest physiotherapy in clinical practice: implications for management of pandemic infl uenza and other airbone infections Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review doi = 10.1007/978-3-7091-1496-4_34 id = cord-310624-3kojrkz7 author = Flores-Alanis, Alejandro title = The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789 date = 2020-08-27 keywords = CoV-2; MP789; SARS summary = In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved. doi = 10.1186/s13104-020-05242-8 id = cord-319013-oytqcifa author = Focosi, Daniele title = Convalescent Plasma Therapy for COVID-19: State of the Art date = 2020-08-12 keywords = COVID-19; SARS; convalescent; patient; plasma summary = In the first retrospective, randomized controlled trial published to date, 39 patients in New York with severe COVID-19 were transfused with 2 units of ABO-type matched CP with anti-Spike antibody titers of Ն1:320 (measured by a two-step Spike proteindirected ELISA). CP (9 to 13 ml/kg from donors with S-RBD IgG titer of Ն1:640) was associated with a negative SARS-CoV-2 PCR test at 72 h in 87.2% of the CP group versus 37.5% of the BSC group, but clinical improvement at 28 days was statistically different only in patients with severe, but not in life-threatening, disease (104) . Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol Anti-SARS-CoV-2 virus antibody levels in convalescent plasma of six donors who have recovered from COVID-19 doi = 10.1128/cmr.00072-20 id = cord-337602-5evfkk70 author = Focosi, Daniele title = Anti‐A Isohemagglutinin titers and SARS‐CoV2 neutralization: implications for children and convalescent plasma selection date = 2020-06-09 keywords = ABO; SARS summary = . Most importantly, the Italian-Spanish genome-wide association study identified the rs657152 polymorphism in the ABO locus on chromosome 9q34 (and only another polymorphism in chromosome 3p21.31) as the only susceptibility locus for respiratory failure in COVID-19 (6) , suggesting that, in addition to disease acquisition, ABO blood group could also affect disease severity. If confirmed, this hypothesis will have implications for convalescent plasma therapy, since anti-A1 IgG could confer additional benefit over anti-SARS-CoV2 neutralizing antibodies: in fact, while preserving ABO match compatibility, it could be wiser to prefer blood group O donors for CP in COVID-19. All rights reserved Accepted Article considered that hyperimmune serum, arising from pooled diverse ABO groups, contains far lower anti-A isoagglutinin titer than an average O-group convalescent donation. The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis doi = 10.1111/bjh.16932 id = cord-325669-6kjlcakt author = Fogacci, Silvia title = Management of pregnancy-related hypertensive disorders in patients infected with SARS CoV-2: pharmacological and clinical issues date = 2020-09-10 keywords = COVID-19; SARS; pregnant; woman summary = The purpose of the current review is to highlight the safety of drug treatment for COVID -19 in pregnant women treated with anti-hypertensive medications. In accordance with the European Society of Cardiology (ESC) guidelines for the management of CV diseases during pregnancy, 100-150 mg/day acetylsalicylic acid (aspirin) should be recommended to pregnant women with a high or moderate risk to develop pre-eclampsia (class I; level of evidence A) [17] . In accordance with the American Heart Association (AHA) recommendations [25] , methyldopa should only be prescribed in cases of severe hypertension during pregnancy, considering potential maternal and fetal side effects (class I; level of evidence A). In accordance with the latest ESC guidelines for the management of CV disease during the COVID-19 pandemic, drug-drug interactions should be considered before administering azithromycin in patients treated with LMWH [37] , despite possible beneficial effects by azithromycin in patients infected with SARS-CoV-2 [48] . doi = 10.1093/ehjcvp/pvaa105 id = cord-302358-vou46eie author = Fomsgaard, Anna S title = An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage date = 2020-03-30 keywords = SARS summary = With a detection sensitivity of 97.4% (95% CI=86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 minutes at 98°C prior to the RT-qPCR reaction. Analysis of SARS-CoV-2 positive and negative oropharyngeal swaps using the SensiFAST TM kit showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy when samples were heat-processed for 5 min. Analysis of the clinical samples using the RealStar® SARS-CoV-2 RT-PCR kit showed significant inhibition of the RT-qPCR reaction (Figure 1 ) except when the MagNA Pure and QIACube purified samples were used. Moreover, this positive result could not be confirmed by any other NA purification method or SARS-CoV-2 specific RT-qPCR assay and therefore we cannot confirm if this patient sample is truly positive for COVID-19 using the QIACube purification system or false negative using the MagNA Pure system. doi = 10.1101/2020.03.27.20044495 id = cord-265228-afbkp3wm author = Fomsgaard, Anna S. title = An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020 date = 2020-04-09 keywords = SARS summary = The comparison of the SensiFAST Probe No-ROX One-Step Real-time PCR results using the simplified workflow to both NA purification systems is shown in Table 1 , Table 2 Comparison of results obtained with the SensiFAST Probe No-ROX One-Step Real-time PCR a assay on clinical samples, which were prior subjected to various minimal processing methods or nucleic acid extractions b , Denmark, 2020 (n = 87 patient samples c ) SARS-CoV-2 positive and negative oropharyngeal swab-samples heat-processed for 5 min at 98 °C before the RT-qPCR reaction showed a 97.4% sensitivity, 100% specificity and 98.3% accuracy compared with MagNA Pure 96 purified samples when using the SensiFAST assay ( Table 1 ). Due to the alarmingly low accessibility to NA purification reagents and kits, we show an alternative to the MagNA Pure purification step with simple heating for 5 min at 98 °C that results in a sensitivity, specificity, and accuracy of 97.4% (95% CI: 86.2-99.9), 100.0% (95% CI: 84.6-100.0) and 98.3% (95% CI: 91.1-99.9), respectively, using the SensiFAST SARS-CoV-2 RT-qPCR assay (Supplementary Data). doi = 10.2807/1560-7917.es.2020.25.14.2000398 id = cord-275926-rj23z7po author = Fontanella, Marco M. title = Neurosurgical practice during the SARS-CoV-2 pandemic: a worldwide survey date = 2020-05-05 keywords = CoV-2; Italy; SARS summary = 3. Institutional plans for the SARS-CoV-2 outbreak: any special measures adopted for SARS-CoV-2 positive neurosurgical patients were investigated, i.e. their screening rate and method, any changes in surgical indications, planning and activity for oncologic procedures, non-emergency surgeries, and subarachnoid hemorrhages (SAHs). The same correlation was found with regards to the medical perception of disease activity (Q2) in different countries, and only few respondents (3%) claimed their country was not facing the outbreak during the time period studied: among them, neurosurgeons from Germany were probably the most "wrong", since their country had between 10 4 to 10 5 SARS-CoV2 patients during the study period (Fig. 4A) . 5 India and Pakistan have been reported to be the world''s best respondents to the SARS-COV-2 pandemic, 22-24 thus reflecting high rates of neurosurgical activity reorganizations. doi = 10.1016/j.wneu.2020.04.204 id = cord-328683-zvabpty9 author = Fontanet, A. title = SARS-CoV-2 infection in primary schools in northern France: A retrospective cohort study in an area of high transmission date = 2020-06-29 keywords = June; SARS summary = Methods: Between 28-30 April 2020, a retrospective cohort study was conducted among pupils, their parents and relatives, and staff of primary schools exposed to SARS-CoV-2 in February and March 2020 in a city north of Paris, France. Seroepidemiological studies are thus needed to determine the extent of infection in children and to decipher the role they may play in transmission To our knowledge, the number of SARS-CoV-2 secondary transmissions in school setting documented in scientific literature is limited, with very few or no secondary cases in investigations in . The epidemic curve, based on symptoms experienced by participants with SARS-CoV-2 antibodies, had no specific pattern, and transmission does not appear to have been impacted by the closure of schools for holidays on February 14 (end of week 7) ( Figure 2A ). They differ however from the results of the study performed in the high school of the same city in France, in which 38% of pupils, 43% of teaching staff and 59% of nonteaching staff who participated in the investigation had anti-SARS-CoV-2 antibodies 27 . doi = 10.1101/2020.06.25.20140178 id = cord-270355-5mljrk1h author = Fontanet, Arnaud title = Les enseignements du SRAS date = 2007-02-28 keywords = SARS; SRAS summary = Points essentiels Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l''homme; d''où l''importance d''une détection précoce par la surveillance des foyers épidémiques inhabituels. Les virus peuvent ne pas être adaptés à la transmission interhumaine, et donc être plus faciles à maîtriser, lors de leur première émergence chez l''homme ; d''où l''importance d''une détection précoce par la surveillance des foyers épidémiques inhabituels. Un même scénario est plausible dans le contexte de la grippe aviaire, où les virus directement contractés au contact des volailles n''ont heureusement pas encore (ou exceptionnellement) été à l''origine de transmission interhumaine [11] . Modes de transmission, durée d''incubation et période de contagiosité ont été rapidement connus [12] , avant même que l''agent infectieux ne soit identifié, ce qui a permis d''instaurer des mesures de prévention efficaces associant protection contre les germes respiratoires, isolement des cas, quarantaine des contacts, et restriction des déplacements. doi = 10.1016/j.lpm.2006.12.005 id = cord-352228-dzkf7c7l author = Fontanet, Arnaud title = Cluster of COVID-19 in northern France: A retrospective closed cohort study date = 2020-04-23 keywords = April; IAR; SARS summary = Methods: Between 30 March and 4 April 2020, we conducted a retrospective closed cohort study among pupils, their parents and siblings, as well as teachers and non-teaching staff of a high-school located in Oise. Participants completed a questionnaire that covered history of fever and/or respiratory symptoms since 13 January 2020 and had blood tested for the presence of anti-SARS-CoV-2 antibodies. Interpretation: The relatively low IAR observed in an area where SARS-CoV-2 actively circulated weeks before confinement measures indicates that establishing herd immunity will take time, and that lifting these measures in France will be long and complex. Using a combination of serologic assays with high sensitivity and specificity for anti-SARS-CoV-2 antibodies, we conducted a retrospective closed cohort study. This is, to our knowledge, the first study estimating by antibody detection the IAR of SARS-CoV-2 infection in a community affected by COVID-19, and the fist description of a COVID-19 outbreak in a school. doi = 10.1101/2020.04.18.20071134 id = cord-308234-4obggisp author = Ford, Nathan title = Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID‐19: initial assessment date = 2020-04-15 keywords = LPV; SARS summary = RESULTS: From an initial screen of 433 titles, two randomized trials and 24 observational studies provided clinical outcome data on the use of antiretroviral drugs; most studies reported outcomes using LPV/r as treatment. The use of lopinavir/ritonavir (LPV/r) has been supported by data from in vitro studies, animal models and positive clinical outcomes when LPV/r was given to patients infected with severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) diseases also caused by coronaviruses [2] [3] [4] [5] . Lopinavir/ritonavir (LPV/r) is included in rapid guidance issued by researchers from Wuhan University based on clinical use during prior epidemics of severe acute respiratory syndrome (SARS) and MERS coronavirus (CoV) infections [6] . This systematic review identified two randomized trials and 21 observational studies provided clinical outcome data on the use of LPV/r for the treatment of COVID-19, SARS and MERS. doi = 10.1002/jia2.25489 id = cord-315289-4x229n8n author = Foresta, C. title = Gender susceptibility to COVID-19: a review of the putative role of sex hormones and X chromosome date = 2020-09-16 keywords = ACE2; SARS; TMPRSS2 summary = Although it is assumed that older men have more comorbidities than women of similar age, a tentative hypothesis to explain these epidemiologic findings is the role of the angiotensin-converting enzyme 2 (ACE2): SARS-CoV-2 engages ACE2 in alveolar epithelial On the top of the figure, epidemiological data from the Italian Ministry of Health are reported, with respective gender distribution of cases and deaths. The lack of increased ACE2 pool in men due to low estrogens would favor the ACE pathway (red arrows) in the RAS axis, which further promotes tissue injury and disease severity in men, compared with women with the same viral load cells as the entry receptor and employs the serine protease TMPRSS2 for S protein priming [8, 9] . Altogether, available evidence points toward two not-mutually exclusive mechanisms in differential gender susceptibility to COVID-19 by sex hormonal regulation of the two main actors in SARS-CoV-2 infection: ACE2 and TMPRSS2. doi = 10.1007/s40618-020-01383-6 id = cord-311377-ffkwis40 author = Forns, Xavier title = Inmunosupresión en el trasplante hepático en la era Covid-19 date = 2020-06-12 keywords = SARS; los summary = La presencia de linfopenia con neutrofilia, niveles elevados de IL-6, incremento de la proteína C reactiva así como el hallazgo de niveles elevados de citoquinas asociadas a la inmunidad innata como IP-10, MCP-1, MIP-1α y TNFα sugieren que ésta juega un papel muy importante en la respuesta inflamatoria asociada a la infección (que también se observó con el SARS-CoV y MERS-CoV) y por tanto, sea responsable de la evolución hacia la gravedad de Covid La respuesta efectora inmune innata contra los virus se basa mayoritariamente en el interferón (IFN-1) (23). En caso de enfermedad grave Covid 19, la substitución temporal de anticalcineurínicos y micofenolato mofetilo (MMF) por GC permite a estos pacientes evitar efectos indeseables secundarios a la interacción de dichos inmunosupresores con los múltiples medicamentos que reciben para el tratamiento de la infección por SARS-Cov 2. doi = 10.1016/j.gastrohep.2020.06.003 id = cord-325863-3t73v4ng author = Foss, Francine M. title = Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib date = 2020-06-25 keywords = JAK; SARS; patient summary = title: Attenuated Novel SARS Coronavirus 2 Infection in an Allogeneic Hematopoietic Stem Cell Transplant patient on Ruxolitinib We report a mild and attenuated SARS CoV-2 infection in a patient who is 17 months post stem cell transplantation and maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia. Due to the signal transduction role that the JAK-STAT pathway plays in mediating Immune-effector cell activation, there has been interest in pursuing inhibitors of this pathway as potential therapeutic agents in mitigating COVID19-associated lung inflammation 9, 10 . We recently diagnosed COVID19 infection in a patient who was on oral ruxolitinib for management of graft-vs-host disease after allogeneic stem cell transplant and report on his presentation and the evolution of his clinical course. Our patient was 17 months post stem cell transplantation and was maintained on the JAK/STAT inhibitor ruxolitinib, a proposed novel therapy for SARS CoV-2 pneumonia, throughout his clinical course with successful attenuation of symptoms. doi = 10.1016/j.clml.2020.06.014 id = cord-270399-yfko8mpc author = Foster, Allison title = It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date = 2020-10-15 keywords = COVID-19; HIV; SARS summary = title: It''s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury In this report, we discuss a unique case of an HIV-positive patient in New York City who presented with a 2-week history of worsening fatigue, cough, dyspnea, and myalgias and was found to have COVID-19 pneumonia and acute kidney injury. The pathophysiologic mechanisms of acute kidney injury, SARS-CoV-2 renal tropism, and the impact of highly active antiretroviral therapy on COVID-19 pneumonia are discussed. 20 Whether directly through involvement of SARS-CoV-2 interaction with ACE-2 receptor or indirectly from causing hypotension from an undetermined mechanism, this patient''s decline in renal function can be attributed to his acute infection with COVID-19. [24] [25] [26] Our patient''s exceptional clinical course despite having HIV lends to the idea that his HAART regimen as well as his azithromycin use prior to presentation may have decreased the total amount of SARS-CoV-2 viral replication in both the renal parenchyma and pulmonary tissue resulting in a rapid recovery and subsequent hospital discharge. doi = 10.1177/2050313x20965423 id = cord-324255-ize21we2 author = Fouchier, Ron A. M. title = Koch''s postulates fulfilled for SARS virus date = 2003 keywords = SARS summary = Severe acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003). S evere acute respiratory syndrome (SARS) has recently emerged as a new human disease, resulting globally in 435 deaths from 6,234 probable cases (as of 3 May 2003) . We inoculated two macaques with Vero-cellcultured SCV isolated from a fatal SARS case, and monitored their clinical signs, virus excretion and antibody response. The macaques excreted virus from the nose and throat at 2-6 d.p.i., as shown by polymerase chain reaction with reverse transcription (RT-PCR) and by virus isolation (see supplementary information). At gross necropsy, one macaque had severe multifocal pulmonary consolidation, and SCV infection was detected in lung tissue by RT-PCR and virus isolation. However, these were not present in SCV-inoculated macaques (results not shown), were not found consistently in SARS patients, and do not usually cause the lesions associated with SARS. doi = 10.1038/423240a id = cord-307842-7q2jd0mf author = Fox, Alisa title = Robust and specific secretory IgA against SARS-CoV-2 detected in human milk date = 2020-10-26 keywords = SARS summary = The SARS-CoV-2 immune response in human milk has not yet been examined, though protecting infants and young children from COVID-19 is critical for limiting community transmission, and preventing serious illness and death. Milk samples were initially evaluated for IgA binding reactivity by human IgA-specific ELISA to the 88 full trimeric SARS-CoV-2 Spike (Fig. 1) . It was evident that all samples obtained from COVID-19-89 recovered donors (100%), in undiluted form, exhibited binding activity significantly above that of the 90 pre-pandemic control milk samples, which did exhibit some low-level non-specific or cross-reactive 91 activity (Fig. 1a) . It was found 92 that all COVID-19-recovered samples exhibited endpoint titers significantly higher than control samples evident that most of the samples contained SARS-CoV-2-reactive IgA without necessarily containing 146 measurable IgG and/or IgM, which particularly in the case of IgG, would likely be derived in large part 147 from the serum. doi = 10.1016/j.isci.2020.101735 id = cord-301779-y07xjnpe author = Fox, Sharon E title = Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans date = 2020-05-27 keywords = COVID-19; SARS; patient summary = INTERPRETATION: We identify key pathological states, including thrombotic and microangiopathic pathology in the lungs, that contributed to death in patients with severe COVID-19 and decompensation in this demographic. Evidence before this study We reviewed the single study of autopsy in a COVID-19 positive patient by Z Xu and colleagues, published in this journal, and reports of pathology from severe acute respiratory syndrome (SARS) coronavirus and similar viral infections by J Nicholls. Previous evidence [10] [11] [12] [13] [14] reports viral infection causing activation of both maladaptive cytokine pathways and a platelet response, and our findings suggest that these immune functions might be related to severe forms of COVID-19. We do not have evidence of direct infection of megakaryocytes by SARS-CoV-2, but the abundance of these cells in the lungs at autopsy is probably related to the abundance of small, sometimes platelet-rich thrombi, and foci of haemorrhage. doi = 10.1016/s2213-2600(20)30243-5 id = cord-316179-kmdxltie author = Fozouni, P. title = Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date = 2020-09-30 keywords = RNA; RNP; SARS; figure summary = Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. When the SARS-CoV-2 sequence became public in January 2020, we set out to develop a Cas13-based direct-detection assay for viral RNA that would avoid the need for amplification and enable point-of-care testing. We tested the performance of the device for detecting SARS-CoV-2 RNA using the triple-crRNA Cas13a assay and a dilution series with full viral RNA isolated from supernatants of infected Vero CCL-81 cells . (B) RNPs made with crRNA 2 and crRNA 4 individually and in combination (50 nM total RNP concentration for each reaction) were tested against 2.9 x 10 5 copies/µL (480 fM) of SARS-CoV-2 IVT N gene RNA, and compared to fluorescence from no target RNA RNP alone controls ("RNP 2," "RNP 4," and "RNP 2+4"). doi = 10.1101/2020.09.28.20201947 id = cord-343090-dsjq98ks author = Fragkou, Paraskevi C. title = Review of trials currently testing treatment and prevention of COVID-19 date = 2020-05-23 keywords = COVID-19; SARS; Table summary = OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. property to achieve at least 10-fold higher concentrations in epithelial lung fluid than in 202 serum, have led researchers to repurpose them against SARS-CoV-2 (Table 1, Table S1 observations the antifibrotic agent pirfenidone is being evaluated in at least three randomised 215 clinical trials for its efficacy in the prevention of post-COVID-19 pneumonia fibrosis (Table 216 1, Table S1 ). Among the eligible treatment studies, 310 children recruitment (i.e.< 14 years old) was reported in 7 clinical trials in total: 1 testing 311 darunavir with cobicistat (NCT04252274); 2 on human stem cells transfusion 312 (ChiCTR2000029606, ChiCTR2000030944); 1 testing hydroxycholoroquine (EudraCT 313 Phase IV and phase III treatment trials were the most commonly reported interventional study 319 types (n=40, 20% and n=35, 18% respectively) as demonstrated in Table 3 . doi = 10.1016/j.cmi.2020.05.019 id = cord-336782-0zkb39v1 author = Fraile Gutiérrez, V. title = Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine date = 2020-11-02 keywords = COVID-19; Fig; SARS; lung; patient; ultrasound summary = title: Narrative review of ultrasound in the management of the critically ill patient with SARS-CoV-2 infection (COVID-19): clinical applications in intensive care medicine The disease caused by SARS-CoV-2 (COVID-19) is characterized by pneumonia clinical presentation with fever and cough accompanied by multifocal nodular (round or oval) ground-glass opacities in the lungs that can progress to acute respiratory distress syndrome (ARDS) and requires admission to an Intensive Care Medicine Service (ICMS) in a high percentage of patients. Ultrasound can be a very useful tool during the management of the COVID-19 pandemic because it provides real-time non-invasive bedside images of patients admitted to intensive care units (ICU). • It is superior to the simple x-ray for the detection of pneumothorax, pleural effusion, pneumonia, interstitial syndrome, and for the differential diagnosis of acute dyspnea • In the thoracic ultrasound, the clinical signs are the determinant factor regarding the interpretation of the data obtained. doi = 10.1016/j.medine.2020.10.002 id = cord-270458-7imgvale author = Franchini, Massimo title = The impact of the SARS‐CoV‐2 outbreak on the safety and availability of blood transfusions in Italy date = 2020-04-13 keywords = CNS; SARS summary = The CNS has already released since 22 January 2020 a recommendation outlining preventative measures for the transmission of SARS-CoV-2 by transfusion of labile blood components related to travels from the People''s Republic of China. On 2 March 2020, following the recommendations of the European Centre for Disease Prevention and Control (ECDC) [9] and reflecting the decrees of the Italian government, the CNS updated the prevention measures, reducing the period of temporary deferral of donors from the previous 28 to 14 days. Following the declaration of the government of the widespread dissemination of the SARS-CoV-2 infection in Italy, the last update of the CNS on 10 March 2020 extended these measures to the whole national territory of Italy. In Fig. 1 , the trend of positive cases for SARS-CoV-2 infection in Italy, updated on 20 March 2020, is reported with a concise chronology of the main documents released and the trend of blood donations in the same period. doi = 10.1111/vox.12928 id = cord-337753-olc00glo author = Franco, D. title = Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. date = 2020-08-04 keywords = Panama; SARS summary = The protocol EC-CNBI-202-04-46 was approved by the National Committee on Bioethics of Research of Panama to use de-identified epidemiological data to analyze SARS-CoV-2 transmission and spread, as well as to sequence the complete genome of SARS-CoV-2 from Gorgas Memorial Institute of Health Studies (GMI)''s confirmed cases. . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama detected the first SARS-CoV-2 infection one month after Brazil 15 , being the 11 th country with confirmed cases in Latin America (Supplementary Figure 2) . To characterize the distribution of genetic lineages in Panama, we generated 313 SARS-CoV-2 sequences, which represents 7.4 % of the total confirmed cases by April 15 th (Supplementary Figure 4A Figure 4A ). . https://doi.org/10.1101/2020.07.31.20160929 doi: medRxiv preprint Panama has the most confirmed SARS-CoV-2 infections and associated fatalities in Central America, although control strategies were rapidly implemented at the beginning of the outbreak. doi = 10.1101/2020.07.31.20160929 id = cord-311144-tumtzad8 author = Franco-Muñoz, Carlos title = Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date = 2020-09-17 keywords = Colombia; SARS summary = A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016) . The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with J o u r n a l P r e -p r o o f Journal Pre-proof 80-100% of the reported sequences ( Fig. 2A) . doi = 10.1016/j.meegid.2020.104557 id = cord-274341-vrwmxwvm author = Frank, Carlos Henrique Michiles title = Guillain–Barré Syndrome Associated with SARS-CoV-2 Infection in a Pediatric Patient date = 2020-07-12 keywords = GBS; SARS summary = We report the case of a 15-year-old male patient presenting frontal headaches with retro-orbital pain accompanied by fever evolving to weakness and pain of the lower limbs, which ascended to upper limbs. Here, we report a pediatric case involving a progressive acute symmetrical paralysis of the lower and upper limbs, with an upward evolution, which was possibly related to SARS-CoV-2 infection. Given the patient''s clinical history of a rapidly progressive symmetrical weakness with supporting electroneurography findings, a recent SARS-CoV-2 infection confirmed through the PCR test, negative microbiologic results for other etiologies in CSF and normal MRI, a diagnosis of GBS associated with COVID-19 was made. According to the most recently published systematic review on neurological manifestations in patients with COVID-19, studies have shown data ranging from common, non-specific symptoms to more complex and life-threatening conditions, such as cerebrovascular diseases, encephalopathies and GBS [5] . doi = 10.1093/tropej/fmaa044 id = cord-299432-lbv69du4 author = Franklin, Alan B. title = Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen date = 2020-05-12 keywords = SARS summary = Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal waste water treatment plants into the natural aquatic environment where potential wildlife hosts become infected. Here, we propose a plausible mechanism where SARS-CoV-2, the pathogen causing the disease COVID-19, could spillover from infected humans into novel wildlife hosts in North America. While the primary risk associated with the current COVID-19 outbreak appears to be humanto-human transmission of SARS-CoV-2, we believe the existing evidence also supports the plausibility of novel coronaviruses, such as SARS-CoV-2, spilling over to new wildlife hosts through fecal shedding by infected humans and introduction to the natural aquatic environment via the waste water treatment system. doi = 10.1016/j.scitotenv.2020.139358 id = cord-019048-29wzpwvr author = Franks, Teri J. title = Coronavirus date = 2013-08-26 keywords = CoV; DAD; SARS summary = From discovery to mid-September 2013, HCoV-EMC, renamed MERS-CoV, (de Groot 2013 ) caused 132 laboratory-confi rmed cases of severe acute pneumonia including 58 deaths. Certain structural proteins are common to all coronaviruses: the spike glycoprotein S, an envelope glycoprotein that mediates receptor-binding and membrane fusion; the envelope spanning glycoprotein M, which contributes to the thickness of the envelop; the envelope protein E, which has been identifi ed as a virulence factor SARS-CoV ; and the nucleocapsid protein N, with its function in genome encapsidation, RNA synthesis and translation, and as a type I interferon antagonist ( Fig. 13 .2 ). Initial signs and symptoms of SARS are nonspecifi c and common, which generates a wide differential diagnosis of respiratory pathogens including infl uenza virus, parainfl uenza Fig. 13.4 Acute-phase DAD in SARS patient. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection doi = 10.1007/978-3-642-40605-8_13 id = cord-322044-4eejzpmn author = Frediansyah, Andri title = Remdesivir and its antiviral activity against COVID-19: A systematic review date = 2020-08-07 keywords = SARS summary = title: Remdesivir and its antiviral activity against COVID-19: A systematic review BACKGROUND: To summarize the antiviral activities of remdesivir against SARS-CoV-2, the causative agent of COVID-19. Although remdesivir has been used as a compassionate drug for treating COVID-19 patients, it has only moderate efficacy. CONCLUSION: Although remdesivir has shown potent antiviral activities, more efficacy assessments are urgently warranted in clinical trials. The first randomized, double-blind, placebo-controlled, multicenter clinical trial was 175 reported on April 29, 2020 [48] . Prophylactic 341 and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of 342 MERS-CoV infection Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2 Compassionate use 355 of remdesivir for patients with severe Covid-19 The authors whose names are listed immediately below report the following details of affiliation or involvement in an organization or entity with a financial or non-financial interest in the subject matter or materials discussed in this manuscript. doi = 10.1016/j.cegh.2020.07.011 id = cord-285053-ah9z9luw author = Freedman, David O title = In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks date = 2020-09-25 keywords = SARS; flight summary = This review presents a comprehensive table summarizing all peer-reviewed or public health publication of flights with likely, possible or unproven in-flight SARS-CoV-2 transmission from 24 January 2020 to 21 September 2020. Two likely secondary cases (one seated in Row 40 with 5 index cases) had negative Day 0 PCR testing and were PCR+ on Day 14; pre-flight transmission shortly before the relatively short flight cannot be ruled out. A number of these flights have carried COVID-19 cases, 5 but no national databases or unified international registries documenting evacuation flights or their passenger loads are publicly available, and few data have been published to date. On flights N-R with the rigid masking policies (meals served) of Emirates Airlines, no secondary cases were identified on Day 14 screening despite 58 passengers who were PCR+ on a total of 5 flights of 8 hours each with ∼1500-2000 passengers. doi = 10.1093/jtm/taaa178 id = cord-318957-gp5drg71 author = Freedman, Matthew title = Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography date = 2004-06-30 keywords = SARS summary = title: Computer-aided detection of Severe Acute Respiratory Syndrome (SARS) on chest radiography Abstract Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. A computer-aided detection system has been developed that marks locations on chest radiographs of minimal areas of pneumonia. It has been tested on a small series of chest radiographs with minimal SARS pneumonia and provided 88% sensitivity with 1.3 false-positive marks per image. Severe Acute Respiratory Syndrome (SARS) is a newly described infection affecting, in most individuals, the lungs with progressive severe pneumonia. In this process of early detection, the chest radiograph is used as the primary screening method for people presenting with symptoms of potential SARS pneumonia. Severe Acute Respiratory Syndrome: radiographic review of 40 probable cases in Toronto Severe Acute Respiratory Syndrome: radiographic appearances and pattern of progression in 138 patients doi = 10.1016/j.ics.2004.03.323 id = cord-272734-kawim93f author = Freire-Paspuel, Byron title = Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date = 2020-05-22 keywords = CDC; SARS summary = title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies The CDC designed 2019-nCoV CDC EUA kit (IDT, USA) is based on N1 and N2 probes to detect SARS-CoV-2 that have received positive evaluation on recent reports (1) (2) (3) , and and RNase P as an RNA extraction quality control. Other kit avalaible in the market is nCoV-QS (MiCo BioMed; South Corea) that include probes "ORF3a" and "N" probes for SARS-CoV-2 detection but no probe for RNA extraction quality control, with no EUA approval neither from FDA (USA) nor from Korean CDC (4,5,6). Both CoV-QS and 2019-nCoV CDC EUA kits were used at SARS-CoV-2 diagnosis laboratory "LabGal" at "Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos" at Puerto Ayora in Galapagos Islands (Ecuador), where we considered this validation necessary to guarantee the sensibility of SARS-CoV-2 during the surveillance. doi = 10.1016/j.jcv.2020.104454 id = cord-332510-x3znuwc0 author = Freire-Álvarez, Eric title = COVID-19-associated encephalitis successfully treated with combination therapy date = 2020-11-01 keywords = PCR; SARS summary = We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. Conclusion: This case report indicates that COVID-19 may present as an encephalitis syndrome mimicking acute demyelinating encephalomyelitis that could be amenable to therapeutic modulation. Despite most of the patients with altered mental in this cohort had a brain MRI performed, they did not observe any case of acute disseminated encephalomyelitis, an immune mediated disease that often occurs following viral infections [12] . The negative RT-PCR CSF results for SARS-CoV-2 along with the hyperinflammatory systemic response observed and the impressive findings in the MRI after therapy with immunoglobulins and tocilizumab suggest an acute disseminated encephalomyelitis. doi = 10.1016/j.clinpr.2020.100053 id = cord-313316-l147b7jk author = Freudenthal, Bernard title = Misuse of SARS-CoV-2 testing in symptomatic health-care staff in the UK date = 2020-10-22 keywords = SARS summary = An initiative to screen asymptomatic health-care workers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was timely and logical, 1 and contrasted markedly with the UK Government''s testing strategy stated. His opened-out presentation of a brain does not show the paired lateral ventricles and the foramen of Monro, as several authors erroneously down, and the way to do that is to get the amount of testing up". Overzealous redirection of self-isolating staff back to work before they had completed sufficient self-isolation to exclude infectivity was therefore likely to increase spread of the virus to other staff and to patients or care-receivers in a substantial number of cases, especially given the high prevalence and likelihood of SARS-CoV-2 infection among exposed health-care workers during the epidemic. 5 We believe a symptom-agnostic testing approach for SARS-CoV-2 among HCWs is an effective measure of reducing viral transmission. 1 We agree that use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing among health-care workers (HCWs) solely to reduce absenteeism is inappro priate. doi = 10.1016/s0140-6736(20)32147-4 id = cord-308358-2bap7iih author = Friedland, Robert P title = The role for the metagenome in the pathogenesis of COVID-19 date = 2020-10-07 keywords = COVID-19; SARS summary = A common factor associated with aging and other COVID-19 risk factors is the dysbiosis of gut microbiota and resulting low grade inflammation with loss of epithelial barrier function [5] . Germ free animals have defective immune systems and the gut microbiota influences pathogen dissemination, inflammation, organ damage and mortality in murine pneumonia [9] . Changes in diet with aging may well influence short chain fatty acid production, affecting immune homeostasis, barrier function and severity of COVID-19. However, in cases of severe disease of COVID-19, it is the innate response and not the unregulated adaptive immune response via T cells that results in morbidity and death. The influence of the microbiota on immune processes in COVID19 infection may be assessed with metagenomic analysis of nasal, oral and intestinal communities, as well as metabolomics. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals doi = 10.1016/j.ebiom.2020.103019 id = cord-290776-l6ajq6vp author = Frithiof, Robert title = Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients date = 2020-09-29 keywords = SARS summary = title: Presence of SARS-CoV-2 in urine is rare and not associated with acute kidney injury in critically ill COVID-19 patients Patients infected with SARS-CoV-2 requiring intensive care due to coronavirus disease 2019 (COVID-19) frequently develop acute kidney injury (AKI) [1] , but the underlying mechanisms are poorly explored. In this report, SARS-CoV-2 RNA levels were prospectively investigated in urine of patients with upper or lower airway swab test PCR-verified COVID-19, admitted to a Swedish intensive care unit (ICU, n = 81). Nucleic acid was extracted from urine samples using NucliSENS® eMAG® (bioMerieux), and the amount of viral RNA was quantitated by detection of SARS-CoV-2 E and N-genes using real-time RT-PCR according to previously described protocols [5, 6] . In this cohort, SARS-CoV-2 RNA was not more frequently detected in urine of patients that died or developed acute kidney injury. doi = 10.1186/s13054-020-03302-w id = cord-340811-w4x4falm author = Frizzelli, Annalisa title = What happens to people’s lungs when they get coronavirus disease 2019? date = 2020-05-11 keywords = SARS; patient; respiratory summary = Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.23750/abm.v91i2.9574 id = cord-254395-tu4aqczj author = Froggatt, Heather M. title = Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CL(pro) Reporter Assay date = 2020-10-27 keywords = 3CL; CoV-2; Fig; SARS summary = This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible protocols. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level 2 (BSL2) with high-throughput compatible sample processing and analysis. With the aim of generating a protease reporter compatible with SARS-CoV-2 and other present and future coronaviruses to support viral inhibitor screening, we selected CoV 3CL pro as our protease target. (C) Quantification of fluorescence from 293T cells 48 h after transfection with each FlipGFP reporter and either the SARS-CoV-2 3CL pro or an influenza virus protein (A/PR8/1834 NP). To observe whether these FlipGFP constructs background fluoresced without CoV 3CL pro activity, we transfected cells with each reporter or a superfolder GFP (sfGFP) expression plasmid. Development of a FlipGFP CoV 3CL pro reporter-based assay for protease inhibitor screening in human cells. doi = 10.1128/jvi.01265-20 id = cord-299927-ixuvy2g4 author = Frontera, Jennifer title = Global Consortium Study of Neurological Dysfunction in COVID-19 (GCS-NeuroCOVID): Study Design and Rationale date = 2020-05-22 keywords = COVID-19; SARS; Tier; neurological summary = As the COVID-19 pandemic evolves worldwide, reports of a spectrum of mild to severe neurological syndromes among patients infected with SARS-CoV-2 are emerging, including headache, anosmia, ageusia, seizures, coma, encephalitis, Guillain-Barre syndrome, and acute cerebrovascular events including ischemic stroke, intracerebral hemorrhage, and cerebral venous sinus thromboses [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] . [15] reported that 84% (49/58) of patients with severe SARS-CoV-2 infection and acute respiratory distress syndrome had neurological symptoms including encephalopathy, agitation and confusion, and corticospinal tract signs. We established the Global Consortium to Study Neurological dysfunction in COVID-19 patients (GCS-NeuroCOVID) and promptly launched a tiered research program with an early, pragmatic, and nimble design to enable successful implementation during a global pandemic crisis when healthcare systems are stressed. The primary outcome in Tier 1 is the prevalence of new clinical neurological syndromes in SARS-CoV-2 patients including: new onset headache, anosmia/ageusia, clinical seizures/status epilepticus, strokes (ischemic and hemorrhagic), meningitis/encephalitis, hypoxic/ischemic injury, acute encephalopathy, coma, myelopathy, neuropathy, and dysautonomia/sympathetic storming. doi = 10.1007/s12028-020-00995-3 id = cord-271027-4omocd8q author = Fronza, R. title = Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak date = 2020-05-01 keywords = PM2.5; SARS; italian summary = While it is possible to reason that observed variation in the number and severity of cases stem from the initial number of infected individuals, the difference in the testing policies and social aspects of community transmissions, the factors that could explain high discrepancy in areas with a similar level of healthcare still remain unknown. A generalized Poisson model was fitted to estimate the association among the data showing the number of infected cases per million and the atmospheric factors. Binary classifier based on an artificial neural network (ANN) was implemented to test the capacity of the atmospheric variables to predict the epidemic escalation of the number of positive cases per million on the basis of a combination of where l= PM2.5, PM10, NH 3 dM A l and O 3 . The expected number of infected cases in the total of 107 Italian provinces were predicted for the months of March (Spring), June (Summer), September (Autumn) and December (Winter) using the real measured values for PM2.5 and O 3 atmospheric factors from 2018 seasonal datasets. doi = 10.1101/2020.04.26.20080846 id = cord-273074-k8m917i4 author = Fu, Chao-Yang title = Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens date = 2005-12-01 keywords = SARS; SPF summary = title: Preparation and evaluation of anti-SARS coronavirus IgY from yolks of immunized SPF chickens SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot and neutralization test results showed that the IgY obtained was of a high purity and had a strong reactive activity with a neutralization titer of 1:640. In this study, we have successfully immunized specific pathogen-free (SPF) chickens, and then purified a high-titer anti-SARS coronavirus yolk immunoglobulin (IgY) with neutralizing activity against SARS coronavirus. The activity of IgY in sera and yolks diluted at 1:200 in phosphate buffer saline (PBS) from immunized animals was assessed using an indirect ELISA assay as described previously (Huang et al., 2005) (Fig. 1) . The development of high-titer anti-SARS coronavirus IgY described in this study would appear to have potential as a new anti-SARS biological product for passive immunization, as it effectively neutralized the SARS coronavirus. doi = 10.1016/j.jviromet.2005.10.027 id = cord-289101-ko1knslk author = Fu, Weihui title = An open-label, randomized trial of the combination of IFN-κ plus TFF2 with standard care in the treatment of patients with moderate COVID-19 date = 2020-09-20 keywords = COVID-19; IFN; SARS; TFF2 summary = Our previous clinical pilot study indicated that aerosol inhalation of IFN-k plus TFF2 is a safe treatment and is able to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby resulting in an early release from hospitalization without induction of a proinflammatory response [20] . This study demonstrated that the combination inhalation of IFN-k and TFF2 is able to shorten the time of viral RNA negative conversion and CT improvement, and facilitating patients early discharge from the hospital, in the absence of induction of a proinflammatory response and treatment-related adverse events. The primary endpoint was a significantly shorter time (Mean 3¢80 days, 95% CI 2¢07À5¢53) from the start of the study treatment to viral RNA negative conversion for SARS-CoV-2 in all clinical samples, including nasopharyngeal swabs, throat swabs and stool swabs, in experimental group than in control group (7¢40 days, 95% CI 4¢57À10¢23) (p = 0¢031), and difference between means was 3¢60 days (Fig. 2A) . doi = 10.1016/j.eclinm.2020.100547 id = cord-347225-gh51ag2x author = Fu, Weihui title = A clinical pilot study on the safety and efficacy of aerosol inhalation treatment of IFN-κ plus TFF2 in patients with moderate COVID-19 date = 2020-07-29 keywords = COVID-19; IFN; SARS; TFF2 summary = INTERPRETATION: Aerosol inhalation of IFN-κ plus TFF2 is a safe treatment and is likely to significantly facilitate clinical improvement, including cough relief, CT imaging improvement, and viral RNA reversion, thereby achieves an early release from hospitalization. Therefore, to evaluate the efficacy and safety of intranasal inhalation of TFF2 and IFN-k protein for SARS-CoV-2 infection, we conducted an open-label, nonrandomized, clinical trial in adult patients hospitalized with moderate COVID-19 disease in China. In this trial, any AE from the beginning of aerosol inhalation to 5 days after the end of the last aerosol inhalation were taken as an adverse event during treatment (TEAE); The secondary objective of the pilot study was to evaluate the clinical efficacy of IFN-k plus TFF2 as compared to the control group as assessed by days of hospitalization staying, CT imaging improvement and cough relief time and negative reversion of viral RNA after 10 days of treatment. doi = 10.1016/j.eclinm.2020.100478 id = cord-285848-37dmv4ep author = Fu, Xiao-Wei title = Review of possible psychological impacts of COVID-19 on frontline medical staff and reduction strategies date = 2020-08-06 keywords = SARS; medical; staff summary = A large number of studies have reported that infectious epidemic diseases, such as severe acute respiratory syndrome (SARS), induce considerable psychological pressure that continues to impact frontline medical personnel a full year after such incidences [1] . In this paper, we present the findings of a review of studies that have investigated the psychological pressure and causes of stress associated with previous outbreaks of infectious diseases, such as SARS and influenza A (H1N1). The association between nurses'' perceived Stress from SARS and their corresponding 13 Chan et al [15] Hong Kong Questionnaires A total of 8 of the 42 Hong Kong public hospitals Perceived health status during the SARS epidemic 14 Kim et al [18] Seoul and in Kyung-gi province psychological interventions targeting frontline medical staff prior to the outbreak of epidemic infectious diseases in the future to reduce or avoid the pressures and impacts of these epidemics on them. doi = 10.12998/wjcc.v8.i15.3188 id = cord-284376-plwyjhl8 author = Fu, Xinmiao title = Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date = 2020-05-31 keywords = China; EHV; Fig; HCV; Health; PCR; PJP; SARS; Wuhan summary = All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In contrast, corticosteroid use within the month before sampling was not different between The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis. doi = 10.1016/j.jinf.2020.02.019 id = cord-261415-qxl14j2m author = Fu, Yajing title = Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools date = 2020-03-03 keywords = ACE2; SARS summary = In addition, given that uncontrolled pulmonary inflammation is likely a leading cause of fatality in SARS-CoV-2 infection, we also attempt to speculate possible therapeutic interventions that may be applied to attenuate inflammatory responses in order to reduce mortality (Fig. 2) . In SARS-CoV infection, viroporin 3a has also been shown to trigger the activation of NLRP3 (NOD-like receptor protein 3) inflammasome and the secretion of IL-1b in bone marrowderived macrophages, suggesting the induction of cell pyroptosis , which can cause the release of large amounts of proinflammatory factors (Fink and Cookson 2005) . However, previous studies in animal models have shown that in SARS-CoV infection, such anti-S protein-neutralizing antibodies (anti-S-IgG) can also cause severe lung injury by altering inflammatory responses (Liu et al. This animal study suggests that despite viral suppression, the presence of anti-spike protein antibody at the acute stage of SARS-CoV infection can actually cause severe acute lung injury that persists until the late stages. doi = 10.1007/s12250-020-00207-4 id = cord-343569-9th5bcv0 author = Fu, Yu-Zhi title = SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response date = 2020-10-27 keywords = MAVS; SARS summary = [28] [29] [30] To identify SARS-CoV-2 proteins that may inhibit the RLR-mediated induction of downstream antiviral genes, we constructed 17 SARS-CoV-2 protein expression clones and screened for candidates that inhibit the Sendai virus (SeV, an RNA virus)-induced activation of the IFNβ promoter in HEK293 cells by reporter assays (Fig. 1A) . In reporter assays, ectopic expression of the M protein dose-dependently inhibited the SeV-induced activation of We next performed ELISA experiments and found that the secretion of IFN-β and TNF-α following SeV infection or poly (I:C) transfection was also impaired in HEK293-M cells (Fig. 1G ). These results suggest that the M protein impairs the recruitment of TRAF3, TBK1 and IRF3 to the MAVS complex, leading to the inhibition of the innate antiviral response. In this study, we identified the SARS-CoV-2 M protein as a factor underlying the inhibition of host antiviral innate immunity by directly targeting the central adaptor MAVS in the RLR-mediated induction of type I IFNs. Several lines of evidence suggest that M directly targets MAVS to inhibit the innate immune response. doi = 10.1038/s41423-020-00571-x id = cord-297787-t9neub6d author = Fu, Ziyang title = Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date = 2020-07-18 keywords = GRL0617; SARS summary = The co-crystal structure of SARS-CoV-2 PLpro-C111S in complex with GRL0617 suggests that GRL0617 is a non-covalent inhibitor. The antiviral activity of GRL0617 reveal that PLpro is a promising drug target for therapeutically treating COVID-19. The in-vitro 85 IC50 of GRL0617 against SARS-COV-2 PLpro was 2.1 ± 0.2 μM, suggesting a promising lead 86 compound and therefore it was subjected to further structural and mechanistic studies ( Fig. 2A) . Taken together, our NMR and X-ray analysis indicates that GRL0617 162 is a potent PPI (protein-protein interaction) inhibitor for PLpro blocking the binding of ISG15. Our co-crystal structure of PLpro C111S in complex with the potent 175 inhibitor GRL0617 validated that SARS-COV-2 PLpro is a druggable target. Based on the structure, GRL0617 resides in the S3/S4 site of PLpro, naturally it will also 179 inhibit the processing of viral polyproteins of SARS-CoV-2 since these viral polyproteins share the 180 same substrate cleavage sequence with Ub and ISG15. The SARS-coronavirus papain-like 257 protease: structure, function and inhibition by designed antiviral compounds doi = 10.1101/2020.07.17.208959 id = cord-354534-0b7zwzjv author = Fuccillo, E title = Olfactory disorders in coronavirus disease 2019 patients: a systematic literature review date = 2020-09-15 keywords = COVID-19; SARS; olfactory summary = The patients, intervention, comparison and outcomes (''PICO'') criteria for the review were considered as follows: (1) patientspatients with SARS-CoV-2 infection certified on laboratory tests who underwent a clinical evaluation of smell impairment using anamnestic data, a smell questionnaire and/or olfactory tests; (2) interventionclinical evaluation of olfactory disorders; (3) comparisondifferent methods of evaluating olfactory function (subjective and objective); and (4) outcomeprevalence and characteristics of olfactory dysfunction in Covid-19 patients. The reported data show that smell dysfunction was, overall, more prevalent in patients investigated with validated questionnaires and/or tests with odorants (Table 3 ), compared to PubMed (("COVID" OR "COVID-19" OR "SARS-COV-2" OR "coronavirus")) AND ("smell" or "anosmia" or "dysosmia" or "hyposmia" or "parosmia" or "olfaction" or "olfactory") The Journal of Laryngology & Otology individuals evaluated using anamnestic data, simple surveys and/or non-validated questionnaires. doi = 10.1017/s0022215120002005 id = cord-328074-pcvdr052 author = Fuereder, Thorsten title = Circumnavigating the challenges of COVID-19 in oncology date = 2020-05-07 keywords = CPI; SARS summary = authors: Fuereder, Thorsten; Gunsilius, Eberhard; Bartsch, Rupert; Hilbe, Wolfgang At this time, patients with haematological malignancies may well be the most threatened patient population as many are heavily immunosuppressed due to the underlying disease, their treatment, or both, and thus are highly susceptible to severe complications if infected with SARS CoV-2. The European Society of Medical Oncology (ESMO) has meanwhile provided comprehensive guidelines for the management and treatment of lung cancer patients in the SARS CoV-2 era [6] : High priority in stage IV lung cancer remains the initiation of firstor second-line chemotherapy, immunotherapy or TKI therapy. Based on these findings the interleukin-6 inhibitor tocilizumab, which is used for the treatment of severe CPI (and CAR-T cells) induced adverse events, is currently being evaluated in clinical trials in patients with COVID-19. Therefore, no recommendations can be given to delay CPI therapy for cancer patients during the SARS CoV-2 pandemic [7] . doi = 10.1007/s12254-020-00611-2 id = cord-328762-2b1pl8jr author = Fuest, Matthias title = Postmortem conjunctival and nasopharyngeal swabs in SARS‐CoV‐2 infected and uninfected patients date = 2020-08-06 keywords = SARS summary = The specifity of ocular tissue/fluid in detecting SARS-CoV-2 was very low in comparison with standard sample collection from nasopharyngeal swabs (NPS) (Ulhaq & Soraya 2020) . To date, no data are available on the postmortem prevalence of virus RNA in ocular and pharyngeal tissue in SARS-CoV-2 patients. Accordingly, in a prospective cohort study, potential corneal donors (uninfected with negative premortem NPS) in our institution had postmortem conjunctival (COS) and NPS taken starting March 17, 2020. SARS-CoV-2 RNA was not detected in any postmortem NPS or COS in the uninfected group. The absence of virus RNA in our postmortem swabs agrees with the literature on premortem samples, where only 3/315 COS = 0.95% (compared to NPS 604/849 = 71.1%) were positive even in symptomatic eyes, indicating that the human conjunctiva is not a typical site of SARS-CoV-2 replication (Lu et al. All these SARS-CoV-2 patients were diagnosed by premortem positive NPS. doi = 10.1111/aos.14559 id = cord-320912-jfeu4tho author = Fukui, M. title = Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models date = 2020-06-12 keywords = COVID-19; SARS; SIR; distribution summary = This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection dynamics, even with large populations. . https://doi.org/10.1101/2020.06.11.20128058 doi: medRxiv preprint Figure 3 plots the predicted ranking of infection cases given the estimated negative binomial (NB) distribution, in addition to the log-log plots and estimated power law (PL) distributions. The mean is set to the same value as power law case, R 0 = 2.5, Figure 4a shows 10 sample paths of infected population generated through the simulation of the model with α = 1.1. doi = 10.1101/2020.06.11.20128058 id = cord-311333-shvtfxog author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-05-28 keywords = SARS summary = title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. Nasopharyngeal swab, sputum and saliva samples were collected from 9 patients who 69 were admitted to our hospital after a diagnosis of COVID-19. Saliva as a 187 non-invasive specimen for detection of SARS-CoV-2 Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva Detection of noroviruses in fecal specimens by direct RT-PCR 195 without RNA purification doi = 10.1101/2020.05.27.120410 id = cord-340410-s9haq8y1 author = Fukumoto, Tatsuya title = Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date = 2020-06-26 keywords = SARS summary = The virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct PCR and nCoV-DK, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. The nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. The 2019 Novel Coronavirus Detection Kit (nCoV-DK, Shimadzu Corporation, Kyoto, Japan) eliminates the steps of RNA extraction and purification by using the Ampdirect TM technology (Nishimura et al., 2010) , thus significantly reducing the time required for sample preparation and PCR detection from more than 2 hours to about 1 hour. We herein compared efficacy of the nCoV-DK with the direct PCR method requiring RNA extraction and purification. Particularly, it should be noted saliva is a reliable tool to detect the virus by the nCoV-KD even without process of RNA extraction and purification. doi = 10.1016/j.ijid.2020.06.074 id = cord-296551-efqt3tw2 author = Fukushi, Shuetsu title = Pseudotyped Vesicular Stomatitis Virus for Analysis of Virus Entry Mediated by SARS Coronavirus Spike Proteins date = 2007-11-28 keywords = SARS summary = Severe acute respiratory syndrome (SARS) coronavirus (CoV) contains a spike (S) protein that binds to a receptor molecule (angiotensin-converting enzyme 2; ACE2), induces membrane fusion, and serves as a neutralizing epitope. To study the functions of the S protein, we describe here the generation of SARS-CoV S protein-bearing vesicular stomatitis virus (VSV) pseudotype using a VSV∆G∗/GFP system in which the G gene is replaced by the green fluorescent protein (GFP) gene (VSV-SARS-CoV-St19/GFP). Thus, VSV pseudotyped with SARS-CoV S protein is useful for developing a rapid detection system for neutralizing antibody specific for SARS-CoV infection as well as studying the S-mediated cell entry of SARS-CoV. In addition to a significant advantage of the VSV-SARS-St19/GFP for safe and rapid analyses of infection, the VSV⌬G*/SEAP system, in which the G gene is replaced with the secreted alkaline phosphatase (SEAP) gene, may be superior to high-throughput quantitative analysis of S-mediated cell entry. Mix serially diluted VSV-SARS-St19/GFP with DMEM-5%FCS and inoculate the mixture into Vero E6 cells seeded in 96-well culture plates. doi = 10.1007/978-1-59745-181-9_23 id = cord-317591-qa6oxy4j author = Fukushima, Akiko title = Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date = 2009-05-07 keywords = DNA; RNA; SARS summary = To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells. doi = 10.1159/000215946 id = cord-312950-ggywr91e author = Fuller, Julie title = Surveillance for Febrile Respiratory Infections during Cobra Gold 2003 date = 2006-05-17 keywords = FRI; SARS summary = The Naval Health Research Center conducted laboratory-based surveillance for febrile respiratory infections at the 2003 Cobra Gold Exercise in Thailand. To ease these concerns, the Naval Health Research Center (NHRC), with an 8-year history of surveillance and diagnosis of febrile respiratory illness (FRI) within active duty continental United States and deployed forces, was tasked with conducting laboratory-based, active surveillance for respiratory illnesses (including SARS) during the exercise, with the intent of early recognition and response. 7, 8 As concerns over SARS importation were eased with implementation of surveillance, valuable information on circulating respiratory pathogens during such an exercise was collected. Supplies, including viral transport medium, swabs (sterile Dacron), preprinted subject identification labels, FRI log sheets, and informed consent/case forms, were provided to both units. Of the 16 diagnostic specimens received, seven (44%) tested positive for influenza A, 2 (13%) for coronavirus OC43, 2 (13%) for respiratory syncytial virus, and 1 (6%) for rhinovirus. doi = 10.7205/milmed.171.5.357 id = cord-273492-i483r91m author = Fulzele, Sadanand title = COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile date = 2020-05-09 keywords = COVID-19; SARS; target summary = In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Based on the above reports, we did in silico analysis of miRNAs targeting SARS and COVID-19 (recent isolates from different regions) to understand the pathophysiology and identify novel therapeutic targets. In a previous report, host cellular miRNAs-181 binds to the ORF-4 region at the viral genome of porcine reproductive and respiratory syndrome virus (PRRSV) to inhibit its replication [17] . Both KEGG and GO pathway analysis revealed that COVID-19 targeting human cellular miRNAs are involved in the number of age-related complications. doi = 10.14336/ad.2020.0428 id = cord-322650-q8inhgtr author = Fung, Yin-Wan Wendy title = Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date = 2004-08-15 keywords = ERT; SARS summary = title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests doi = 10.1086/422887 id = cord-267856-t3ksa18w author = Funk, Colin D. title = A Novel Strategy to Mitigate the Hyperinflammatory Response to COVID-19 by Targeting Leukotrienes date = 2020-08-06 keywords = COVID-19; SARS; figure summary = We offer a simple treatment paradigm using two generic drugs targeting the hyperinflammatory response that characterizes the turning point from mild to severe/critical COVID-19 by targeting leukotriene biosynthesis with zileuton (Zyflo(®) controlled release formulation) and antagonism of the cysteinyl leukotriene 1 receptor with montelukast (Singulair(®)). By targeting vascular permeability, immune modulating and general inflammation-dampening effects at the CysLT 1 level with montelukast (Dahleń et al., 1981; Maeba et al., 2005; Capra et al., 2007; Tahan et al., 2008; Khodir et al., 2014) and LT biosynthesis with the 5-lipoxygenase inhibitor zileuton, to block both arms of the LT pathway ( Figure 2 ) and remove ligands for another key receptor regulating vascular permeability, CysLT 2 (Moos et al., 2008) , as well as inflammatory cell recruitment and endothelial cell adhesion via BLT 1 receptor (Ford-Hutchinson et al., 1980; Tager et al., 2003; Taube et al., 2006; Sasaki and Yokomizo, 2019) , there is a sound scientific basis for alleviating disease progression from mild to severe-critical stages of COVID-19 (Figures 1 and 2) . doi = 10.3389/fphar.2020.01214 id = cord-269835-mz7i66qp author = Furfaro, Federica title = SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date = 2020-06-11 keywords = COVID-19; Crohn; IBD; SARS; patient summary = The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with inflammatory bowel disease (IBD) who need to undergo endoscopic procedures. In particular, recommendations regarding the use of personal protective equipment to prevent COVID-19 transmission, both for patients and health-care professionals, are proposed and different scenarios in endoscopic IBD management are evaluated to suggest when endoscopy could be rescheduled and replaced by alternative biomarkers. The panel of experts con sidered possible aerosolization during colonoscopy, in particular during the insertion and removal of instruments through the biopsy channel and the presence of the virus in the stool and advised on the use of N95 masks for lower gastrointestinal procedures as a precautionary measure to protect the endoscopist from the risk of possible COVID-19 transmission from the patient if infected by SARS-CoV-2 (ref. doi = 10.1038/s41575-020-0319-3 id = cord-138656-8iyynbup author = Furuyama, Taima N. title = Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant date = 2020-06-20 keywords = East; SARS; d614 summary = title: Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant From November 2002 to May 2004, SARS-CoV-1 (Severe Acute Respiratory Syndrome caused by Coronavirus type 1) affected 26 countries worldwide, accounted 8,096 confirmed cases and 774 deaths (9.6% fatality ratio) (Drosten et al., 2003; Ksiazek et al., 2003; Lee et al., 2003; Peiris et al., 2003; Zhong et al., 2003 ; Centers for Disease Control and Prevention -Department of Health and Human Services, 2004; World Health Organization, 2004; Centers for Disease Control and Prevention, 2017) . MERS-CoV (Middle East Respiratory Syndrome caused by Coronavirus) spread to 27 countries around the globe, totalizing 2,519 confirmed cases and 866 deaths (34.4% fatality ratio) continuously since April 2012 (Zaki et al., 2012; Hijawi et al., 2013; Centers for Disease Control and Prevention, 2019; World Health Organization, 2019 , 2020b . If there is a correlation between the D614G variant prevalence and higher SARS-CoV-2 transmission, then the epidemiological data might reveal a significant correlation between D614G prevalence and the growth rate coefficients of epidemic curves globally. doi = nan id = cord-322837-tqgwgvo0 author = Gable, Lance title = Legal and Ethical Implications of Wastewater SARS-CoV-2 Monitoring for COVID-19 Surveillance date = 2020-06-24 keywords = CoV-2; SARS summary = Even if reliability and efficacy are established, limits on sample and data collection, use, and sharing, must also be considered to prevent undermining privacy and autonomy in order to implement these public health strategies consistent with legal and ethical considerations. The proposed use of wastewater screening to detect SARS-CoV-2 viral RNA has the potential to greatly enhance our technical capabilities to identify, track, pinpoint, and quantify 32 Second, public health authorities could use this information to justify increased testing among people living in homes or working at sites close to where the virus has been found in wastewater, or to implement neighborhood-wide screening programs in these areas. Wastewater screening for SARS-CoV-2 could provide an important tool to detect new outbreaks of COVID-19 and to target resources to intervene to stop the spread of the disease; however, scientific research must establish the efficacy of such testing in identifying communitybased COVID-19 infections before its use can be considered as the basis for public policy. doi = 10.1093/jlb/lsaa039 id = cord-256147-lfwytlj3 author = Gabriella, di Mauro title = SARS-Cov-2 infection: response of human immune system and possible implications for the rapid test and treatment date = 2020-04-16 keywords = SARS; infection summary = Considering the clinical impact of the new outbreak, it is highly important to study the potential responses of the human immune system during the SARS-CoV-2 infection as well as the role of virus-specific T cells and by B-lymphocytes. In order to apply a rapid test able to detect the presence of specific IgM and IgG for SARS-CoV-2, it is important to consider that the IgM values tend to disappear within 2 weeks since the beginning of the infection. The sensitivity and specificity of these tests were evaluated on 397 blood samples from patients who tested positive for the nasopharyngeal swab for SARS-CoV-2 infection and on 128 patients who tested negative and asymptomatic but potentially at risk of developing the infection based on epidemiological criteria [7] . The results of the study showed that out of 397 blood samples from patients with a SARS-CoV-2 infection, 352 tested positive. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis doi = 10.1016/j.intimp.2020.106519 id = cord-280029-g1k3zlax author = Gabutti, Giovanni title = Coronavirus: Update Related to the Current Outbreak of COVID-19 date = 2020-04-08 keywords = COVID-19; China; MERS; SARS summary = The World Health Organization (WHO) has officially named the infection coronavirus disease 2019 (COVID-19), and the virus has been classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS is caused by a virus that emerged in southern China in November 2002 and led to [ 8000 human infections and 774 deaths in 37 countries in the 2002-2003 period [3] ; MERS is related to a virus detected for the first time in Saudi Arabia in 2012, responsible for 2494 laboratoryconfirmed cases of infection and 858 deaths since September 2012 [4] . On January 11 and 12, 2020, the WHO received further details and information from the Chinese National Health Commission regarding the possible association of this epidemic with exposure in a fish market in Wuhan, and the Chinese authorities shared the genetic sequence of a new coronavirus, subsequently identified as SARS-CoV-2 [14] . doi = 10.1007/s40121-020-00295-5 id = cord-273314-p1dlzoh1 author = Gadiparthi, Chiranjeevi title = Gastrointestinal Bleeding in Patients with Severe SARS-CoV-2 date = 2020-06-04 keywords = GIB; SARS summary = Gastrointestinal symptoms are common and frequently reported in Coronavirus Disease-2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, GIB in COVID-19 patients poses unique challenges to patients due to high-risk of concomitant respiratory failure and to endoscopy personnel due to risk of airborne transmission during endoscopic procedures. GI bleeding (GIB) in patients with SARS-CoV-2 poses unique challenges, especially for endoscopists and other procedural staff because of the potential for aerosol spread. In this article, we report 3 hospitalized patients with SARS-CoV-2 infection with GIB and acute blood loss anemia with focus on management strategies. She tested positive for SARS-CoV-2 by RT-PCR assay and developed acute hypoxic respiratory failure requiring supplemental oxygen of 15 L per minute via a nonrebreather mask. On hospital day 5, the patient developed recurrent GIB with a large amount of melena and bright red blood per rectum with hemodynamic instability requiting intensive care unit (ICU) transfer. doi = 10.14309/ajg.0000000000000719 id = cord-353594-z1vxamvp author = Gagiannis, Daniel title = Clinical, Serological, and Histopathological Similarities Between Severe COVID-19 and Acute Exacerbation of Connective Tissue Disease-Associated Interstitial Lung Disease (CTD-ILD) date = 2020-10-02 keywords = ANA; ARDS; COVID-19; SARS; patient summary = Since we observed similarities between COVID-19 and interstitial lung disease in connective tissue disease (CTD-ILD), we investigated features of autoimmunity in SARS-CoV-2-associated respiratory failure. Patients or their relatives had given written informed consent to routine diagnostic procedures (serology, bronchoscopy, radiology) as well as (partial) autopsy in the case of death, respectively, as well as to the scientific use of data and tissue samples in the present study. Our finding that significant ANA titers and/or detection of specific autoantibodies are found in most patients who develop ARDS raises the question if there is a comparable mechanism of lung damage between SARS-CoV-2 infection and exacerbating autoimmune disease. Our observation of CTD-associated autoantibodies together with the CTD-like radiologic and histopathologic lung findings in severe cases of COVID-19 point towards a possible dysregulation of the immune response upon SARS-CoV-2 infection that might fuel organizing pneumonia and trigger interstitial fibrosis, with deleterious effects on the functional outcome in long-term survivors. doi = 10.3389/fimmu.2020.587517 id = cord-300963-1n1f8mf2 author = Gajendran, Mahesh title = Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date = 2020-10-12 keywords = COVID-19; IBD; RNA; SARS; patient summary = Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient''s age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. doi = 10.20524/aog.2020.0547 id = cord-352433-sts48u9i author = Galanti, Marta title = Direct Observation of Repeated Infections With Endemic Coronaviruses date = 2020-07-07 keywords = OC43; SARS; infection summary = BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. However, in Korea, as reported by the Korean Centers for Disease Control and Prevention, viable SARS-CoV-2 was not isolated in cell culture of respiratory samples from potentially reinfected individuals [5] ; thus, these subsequent positive results may have been due to inactive genetic material detected by molecular testing. doi = 10.1093/infdis/jiaa392 id = cord-252600-bvh1o64r author = Galasiti Kankanamalage, Anushka C. title = Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element date = 2018-04-25 keywords = CoV; MERS; SARS summary = We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The structure-guided design of inhibitor (I) encompassed the following steps: (a) we first determined a high resolution X-ray crystal structure of MERS-CoV 3CLpro in complex with GC376 ( Fig. 2/Panel A) . Validation of this idea was obtained by synthesizing extended inhibitor GC813 and determining a high resolution X-ray crystal structure of the MERS-CoV 3CLpro:GC813 complex ( Fig. 2/Panel B) . More importantly, representative aldehyde bisulfite adduct compounds 10a and 10c display potent inhibition toward MERS-CoV in both enzyme and cell-based systems, with low cytotoxicity (CC 50 > 100 mM) ( Table 2 and Fig. 4 ). doi = 10.1016/j.ejmech.2018.03.004 id = cord-313489-i969aqn9 author = Galbadage, Thushara title = Does COVID-19 Spread Through Droplets Alone? date = 2020-04-24 keywords = SARS; covid-19 summary = Social or physical distancing helps reduce the transmission of respiratory droplets containing SARS-CoV-2 and slows the incidence of the disease by reducing the opportunities for potential viral exposures. Precautions to prevent the spread by droplets as recommended by both the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) are to (1) wash hands with soap, (2) avoid touching viral entry points, such as eyes, nose, and mouth, (3) cover the mouth when coughing or sneezing, (4) wear a facemask if sick and (5) practice social distancing by putting 6 feet of distance between individuals. The ability of SARS-CoV-2 to remain viable longer on surfaces taken together with its higher virulence in establishing an infection makes it very likely that this coronavirus uses other modes of transmission in addition to respiratory droplets (Figure 1) . doi = 10.3389/fpubh.2020.00163 id = cord-354261-gdvawnp6 author = Gale, Chris title = National active surveillance to understand and inform neonatal care in COVID-19 date = 2020-06-14 keywords = COVID-19; SARS summary = Vertical transmission of SARS-CoV-2 has yet to be definitively established; neonatal infection with the virus has been detected in the first days after birth to mothers with COVID-19 1 ; however, this could represent early horizontal transmission. For more complete case ascertainment, this BPSU surveillance will link with other related data sources, including ongoing UKOSS surveillance of COVID-19 in pregnancy for maternal cases, Mothers and Babies: Reducing Risk through Audits and Confidential Enquiries across the UK (MBRRACE-UK), for neonatal deaths and stillbirths, and Public Health England (PHE), Health Protection Scotland, Public Health Wales and the Health and Social Care Public Health Agency in Northern Ireland. Active surveillance through established national systems such as the BPSU and UKOSS with very high population-based case ascertainment is among the simplest, quickest and most efficient way to obtain the accurate population level incidence data and to determine true infection rates, clinical characteristics and outcomes, which are needed to inform optimal perinatal and neonatal care. doi = 10.1136/archdischild-2020-319372 id = cord-309317-cgs0sui7 author = Galeotti, Caroline title = Autoimmune and inflammatory diseases following COVID-19 date = 2020-06-04 keywords = Kawasaki; SARS summary = Emerging reports show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection precedes the appearance of various autoimmune and autoinflammatory diseases, including paediatric inflammatory multisystemic syndrome (PIMS) or multisystem inflammatory syndrome in children (MIS-C), thus adding to the growing mystery of this virus and raising questions about the nature of its link with autoimmune and autoinflammatory sequelae. Several emerging reports show that coronavirus disease 2019 (COVID-19), a pandemic respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), could lead to autoimmune and autoinflammatory diseases, such as paedi atric inflammatory multisystemic syndrome (PIMS; which includes Kawasaki-like disease, Kawasaki disease shock syndrome, toxic shock syndrome, myocarditis and macrophage activation syndrome) in children [1] [2] [3] [4] [5] [6] . In the USA, the New York City Health Department on 4 May 2020 reported that 15 children aged 2-15 years had presented with symptoms of MIS-C, including persistent fever and increased levels of inflammatory markers, and many also had rash, abdominal pain, vomiting or diarrhea; ten of the 15 child ren were positive for SARS-CoV-2 infection 6 . doi = 10.1038/s41584-020-0448-7 id = cord-352905-ge3u32hm author = Galimberti, Sara title = Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2 date = 2020-09-02 keywords = CML; COVID-19; SARS; TTV; patient summary = Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Translated in the COVID-19 context, if TKIs would sustain the coronavirus infection or replication, we might expect to observe a significant increase of TTV load during treatment of our patients with nilotinib. In the second phase of our study, we employed the NanoString technology for analyzing the expression of 770 inflammationand immunity-related genes in five CML patients before and after 6 months of treatment with imatinib, with the aim of testing the impact of this TKI on the possible immunological control of viral infection. Considering that it has been proven that at diagnosis, the immunity of these patients is severely impaired (63) , the low infection rate observed during the 2020 pandemic could prove that TKIs play an antiviral role or, at least, could not impair the host response against the new coronavirus. doi = 10.3389/fonc.2020.01428 id = cord-280774-r2xm164s author = Gallizzi, Romina title = Management of pernio‐like cutaneous manifestations in children during the outbreak of covid‐19. date = 2020-09-19 keywords = CoV-2; SARS summary = The increased number of cases of pernio-like lesions compared to the cases per year we usually observe, the mild temperatures of those months in Southern Italy and the concomitant lockdown, led us to hypothesize a possible correlation with SARS-CoV-2 infection. This is useful to highlight, as in our case, the D-dimer of our patients was weakly increased, a condition perfectly correlated with the mild symptoms of SARS-CoV-2 putative infection presented. In a report of 19 adolescent patients with a clinical diagnosis of pernio-like lesions nasopharyngeal swab and IgG serology for SARS-CoV-2 nucleocapsid protein were negative. Why some children who come into contact with the SARS-CoV-2 do not develop striking respiratory symptoms but present pernio-like lesions with negativity on diagnostic tests? This pathogenic mechanism could explain the appearance of pernio-like lesions due to SARS-CoV-2 infection. In conclusion, we think there is a correlation between pernio-like lesions and SARS-CoV-2 infection, but further studies are needed to prove it. doi = 10.1111/dth.14312 id = cord-340857-teq5txm9 author = Galloro, Giuseppe title = SAFETY IN DIGESTIVE ENDOSCOPY PROCEDURES IN THE COVID ERA RECOMMENDATIONS IN PROGRES OF THE ITALIAN SOCIETY OF DIGESTIVE ENDOSCOPY date = 2020-05-13 keywords = China; SARS; patient summary = Based on the most recent scientific literature and strong statements by the most prestigious international health institutions, the Italian Society of Digestive Endoscopy has drawn up some recommendations about the use of personal protective equipment, the correct way of dressing and undressing of endoscopists and nurses, before and after digestive endoscopy procedures. In addition the CDC and some other Authors detected the virus in the feces of CoViD-19 positive patients (in up to 54% of the cases), suggesting a potential fecal-oral transmission (31, 32) . A recent ad-interim guidance, about the preventive measures of infection control (shown in table 3 ) and about the right use of appropriate PPE for healthcare workers performing endoscopy on subjects with CoViD-19, has been published by the WHO (45) . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus infected pneumonia in Wuhan, China. doi = 10.1016/j.dld.2020.05.002 id = cord-307885-butuv3n1 author = Galvani, Alison P. title = Emerging Infections: What Have We Learned from SARS? date = 2004-07-17 keywords = SARS; disease summary = As is typical of an emerging disease, no vaccines or drugs to combat SARS existed, making quarantine, patient isolation, travel restrictions, and contact precautions the only means of limiting transmission. Previously, similar models had guided public health policy, for example, in halting an outbreak of hoof and mouth disease in the United Kingdom in 2001 (5, 6) . The case-fatality rate is a key determinant of the public health impact of an emerging disease and was high for SARS at approximately 15% (11) . The success with which WHO coordinated the global collaboration in containing SARS galvanized the World Health Assembly to grant WHO greater authority to verify outbreaks, conduct investigations of outbreak severity, and evaluate the adequacy of control measures. Transmission dynamics of the etiological agent of severe acute respiratory syndrome (SARS) in Hong Kong: the impact of public health interventions Infectious diseases of humans: dynamics and control doi = 10.3201/eid1007.040166 id = cord-301106-qskwujpa author = Gambato, Martina title = Clinical implications of COVID-19 in patients with chronic liver disease and liver tumor date = 2020-06-05 keywords = COVID-19; SARS summary = On March 31st of this year, the World Health Organization (WHO) declared a pandemic infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing 2019 coronavirus disease (COVID-19). A single case of acute chronic liver failure secondary to SARS-CoV-2 infection in a decompensated alcoholic cirrhotic patient was recently reported. Overall, the reported data are not yet enough for us to know the risk of infection in patients with existing chronic liver disease, or the impact of COVID-19 on their liver status and outcomes. Patients with liver cancer are another special population often coming to the hospital for treatment and monitoring, who may be at higher risk of contracting COVID-19, especially if they are receiving chemotherapy or immunotherapy. In conclusion, liver damage during SARS-CoV-2 infection has been reported quite frequently, especially in patients who developed severe COVID-19 disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan doi = 10.1007/s13304-020-00804-8 id = cord-289905-dvl2pud2 author = Gan, Rosemary title = COVID-19 as a Viral Functional ACE2 Deficiency Disorder with ACE2 Related Multi-organ Disease date = 2020-06-23 keywords = ACE2; COVID-19; RAS; SARS summary = Appreciating the clear differences between SARS and COVID-19 in presentation, poor prognostic indicators related to individuals'' co-morbid status, and biochemical and radiologic profiles, a novel disease model may assist in: 1) the early recognition of atypical (non-respiratory) presentations of disease; 2) early prophylactic treatment intervention for individuals at risk of severe and critical disease which could take place 6 in the community; 3) revised management of pulmonary complications including those related to prone posturing and ventilation protocols; 4) allowing better utilisation of data collated at a global level in the absence of an evidence-based disease model at this time; 5) identification of different markers of disease progression in at-risk individuals. An upregulation of ACE2 expressing cells related to chronic ATII elevation [18] or treatment with ACEinhibitors [19] , may increase the infective potential of SARS-CoV-2 in this group as a consequence of the duality of ACE2 functioning as both a receptor for viral entry to cells and as an enzyme. doi = 10.1016/j.mehy.2020.110024 id = cord-308507-hp6m6qrn author = Gan, Yi-Ru title = Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase date = 2005-10-19 keywords = AVLQSGFR; SARS summary = The results demonstrate that, compared with other compounds reported so far, AVLQSGFR is the most active in inhibiting replication of the SARS coronavirus, and that no detectable toxicity is observed on Vero cells under the condition of experimental concentration. These authors had done studies of docking the octapeptide to SARS-CoV M pro based on the three-dimensional structure of SARS coronavirus main proteinase obtained by Anand et al. The binding results obtained through docking study [10] and structural bioinformatics [7] show that the octapeptide AVLQSGFR is bound to the SARS proteinase through six hydrogen bonds. The present study was initiated in an attempt to conduct an in-depth examination of the antiviral activity of the octapeptide AVLQSGFR against SARS-associated coronavirus by biochemical experimental approaches. We also detected the effect of the octapeptide AVLQSGFR on replication of SARS-associated coronavirus in Vero cells (Fig. 2) . doi = 10.1016/j.peptides.2005.09.006 id = cord-033244-u05rw6sk author = Ganesamoorthi, Arimanickam title = Non-availability of anesthesia scavenging system and decontamination of the outflow gas from the anesthesia machine during this COVID-19 pandemic date = 2020-10-06 keywords = SARS summary = The HMEF/HEPA filter can be connected to the AGS, even if the anesthesia machine ventilator is used for prolonged ventilation of critically ill patients, like an ICU ventilator when a shortage arises in this COVID-19 pandemic (COVID-19: Usage of Dräger anaesthesia devices for long-term ventilation dated 19 may 2020, 2020). Authors'' contributions AG conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable and contributed to the writing and editing of the final version of the manuscript. ViVi conceptualized and formally analyzed the alternative for decontamination of outflow gas from the anesthesia machine when anesthesia scavenging system is unavailable, and contributed to the review of literature, and writing and editing of the final version of the manuscript. doi = 10.1186/s42077-020-00096-5 id = cord-103497-1ls2dvzy author = Ganier, C title = CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date = 2020-05-29 keywords = ACE2; SARS summary = title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). The ACE2 receptor has been shown to mediate uptake of the virus responsible for COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in human cells (Hoffmann, Kleine-Weber, Schroeder, et al. In order to define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). doi = 10.1101/2020.05.29.123513 id = cord-274680-6pui91uu author = Gao, Chun title = Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date = 2020-10-14 keywords = SARS; viral summary = 5 Many studies have found that older patients have a higher risk of having a severe case and they have a higher death rate from COVID-19, which may be related to a weaker host immune response for antiviral defense and an uncontrolled proinflammatory cytokine storm. [10] [11] Therefore, this retrospective study aimed to analyze the clinical characteristics of COVID-19 patients who experienced prolonged viral shedding and to investigate the contributing risk factors. This is a comprehensive report of 112 COVID-19 patients investigating the distinct characteristics and risk factors for prolonged SARS-CoV-2 viral RNA shedding. In our study, we found that COVID-19 patients with prolonged viral shedding were older (p<0.001) and presented with a higher rate of hypertension (p<0.001). This study focused on investigating the risk factors for COVID-19 patients with prolonged viral shedding. In summary, in this study, we investigated the distinct dynamics of the inflammatory response in COVID-19 patients with prolonged viral RNA shedding. doi = 10.1016/j.clim.2020.108611 id = cord-271371-qs7zge3l author = Gao, Jia title = Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-07-28 keywords = SARS summary = As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligandand protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (M(pro)) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of M(pro). We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 M(pro). Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs. Nevertheless, using this fragment-based approach is a feasible strategy for repurposing low-molecular-weight drugs targeting SARS-CoV-2 M pro . doi = 10.1021/acs.jpclett.0c01894 id = cord-297439-xg0pkjrh author = Gao, Jing title = The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China date = 2020-04-22 keywords = SARS summary = Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and lasting positive nucleic acid test result in patients recovered from pneumonia. The CT image is used to assess the disease progress, whereas the continued two times of negative results from SARS-CoV-2 nucleic acid detection had been considered as a criterion for ending antiviral treatment. Our report highlighted the unsynchronized expression in the changes of CT image and nucleic acid detection in COVID-19, and showed the suspected SARS-CoV-2 carrier. On day 16, the 4th result of nucleic acid in throat swab changed to negative, whereas it was positive in sputum ( Fig. 1) , thus continued the antiviral treatment with interferon inhalation and lopinavir/ ritonavir. On day 8 and day 10, SARS-CoV-2 nucleic acid in throat swab were shown the negative at that two time, and the repeated chest CT image showed that the infection range was declined a lot (Fig. 1) . doi = 10.1186/s12931-020-01363-7 id = cord-266090-f40v4039 author = Gao, Wei title = New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system date = 2020-08-03 keywords = SARS; fractional; model summary = title: New investigation of bats-hosts-reservoir-people coronavirus model and application to 2019-nCoV system According to the report presented by the World Health Organization, a new member of viruses, namely, coronavirus, shortly 2019-nCoV, which arised in Wuhan, China, on January 7, 2020, has been introduced to the literature. Whereas the obtained results show the effectiveness of the theoretical method considered for the governing system, the results also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. The obtained results show the effectiveness of the theoretical method considering the governing system and also present much light on the dynamic behavior of the Bats-Hosts-Reservoir-People transmission network coronavirus model. In this subsection, by using VIM we numerically investigate the Bats-Hosts-Reservoir-People coronavirus model. Modeling the dynamics of novel coronavirus (2019-nCov) with fractional derivative Application of variational iteration method to nonlinear differential equations of fractional order doi = 10.1186/s13662-020-02831-6 id = cord-331878-ww9fu8ey author = Gao, Xiaopan title = Crystal structure of SARS-CoV-2 papain-like protease date = 2020-09-02 keywords = Fig; GRL0617; SARS summary = The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. We then determined the structure of SARS-CoV-2 PLpro complex by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The initial hydrolysis rate was plotted as the function of inhibitor concentration and the plot was fitted by the equation Y=Bottom+(Top-Bottom)/(1+(X/IC 50 )) using software GraphPad. To gain structural and biochemical insight into SARS-CoV-2 PLpro domain (nsp3 746-1063aa, Supporting Information Fig. S1 ), we expressed two PLpro variants. For example, several crystal structures of SARS-CoV-2 PLpro C111S mutant complexed by various non-covalent inhibitors have been recently deposited in Protein Data Bank (PDB ID: 7JIT, 7JIR and 7JIV), which support our assertion. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors doi = 10.1016/j.apsb.2020.08.014 id = cord-351644-pl7xpivx author = Gao, Yelei title = Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis date = 2020-04-17 keywords = COVID-19; SARS; topic summary = We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. Data extracted included: 1) Basic information: title, first author, publication year and study design; 2) participants: baseline characteristics and sample size; and 3) results: proportions of individuals using telemedicine for different contents of consultation (e.g. symptoms, therapy and prevention, policy, public service), details of screening of suspected cases, the provision of advice given to people who had symptoms or contact history, and the limitations of telemedicine. https://doi.org/10.1101/2020.04.14.20065664 doi: medRxiv preprint proportion of consultation on public issues (including disease knowledge, epidemic situation and public issues of COVID-19/SARS). doi = 10.1101/2020.04.14.20065664 id = cord-350949-ystkjdwk author = Gao, Yi-jie title = Clinical features and outcomes of pregnant women with COVID-19: a systematic review and meta-analysis date = 2020-08-03 keywords = COVID-19; SARS summary = The meta-analysis showed the following results: the incidence of severe case or death was 12, 95% CI: 0.03-0.20, I 2 = 0%, P = 0.006; the incidence of fever was 51, 95% CI: 0.35-0.67, I 2 = 89%, P < 0.00001; the incidence of cough was 31, 95% CI: 0.23-0.39, I 2 = 38%, P < 0.00001; the incidence of lymphopenia was 49, 95% CI: 0.29-0.70, I 2 = 83%, P < 0.00001; the incidence of positive CT findings was 71, 95% CI: 0.49-0.93, I 2 = 90%, P < 0.00001; the incidence of coexisting disorders was 33, 95% CI: 0.21-0.44, I 2 = 70%, P < 0.00001; the incidence of preterm labor was 23, 95% CI: 0.14-0.32, I 2 = 21%, P < 0.00001; the incidence of caesarean section was 65, 95% CI: 0.42-0.87, I 2 = 90%, P < 0.00001; the incidence of fetal distress was 29, 95% CI: 0.08-0.49, I 2 = 68%, P = 0.007; the incidence of neonatal asphyxia or neonatal death or stillbirth was 9, 95% CI: − 0.03-0.21, I 2 = 0%, P = 0.14; the incidence of neonatal infection was 12, 95% CI: − 0.01-0.26, I 2 = 0%, P = 0.06; and SARS-CoV-2 testing of breast milk was only mentioned in the study by Chen H (2020.2.12), and the incidence was 0, which cannot be calculated by metaanalysis. doi = 10.1186/s12879-020-05274-2 id = cord-253245-433mg0ke author = Gao, Zhiru title = A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date = 2020-08-05 keywords = SARS summary = A recent study reported that four medical workers aged 30-36 years who had re-detectable positive (RP) for SARS-CoV-2 within 5-13 days after being cured and discharged, indicating that some of the recovered patients may still be virus carriers, which caused widespread concern (Lan et al., 2020). Although the results of the three nucleic acid tests were negative for the patient, there were viral residue in the lungs, so even if the patient was discharged, we supposed that virus would transfer positive again after a period of time (Yao et al., 2020) . In addition, initial studies reported that the SARS-CoV-2 RNA could be detected in the feces of 81.8% recovered patients (54/66), even in those with negative throat swabs (Ling et al., 2020) . In other words, even if sometimes the virus nucleic acid tested by RT-PCR is positive in the recovery phase of COVID-19, it will not cause a more serious condition, and antiviral therapy may not be required in most patients. doi = 10.1016/j.meegid.2020.104494 id = cord-324102-75v4ebag author = Garcia Rodriguez, Alejandro title = SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? Case report date = 2020-10-06 keywords = COV-2; SARS summary = title: SARS-COV-2 infection during pregnancy, a risk factor for eclampsia or neurological manifestations of COVID-19? BACKGROUND: There are no published cases of tonic-clonic seizures and posterior bilateral blindness during pregnancy and Severe Acute Respiratory Syndrome (SARS) Coronavirus (COV) 2 (SARS-COV-2) infection. CONCLUSION: The authors conclude that SARS COV-2 infection could promote brain endothelial damage and facilitate neurological complications during pregnancy. That is the reason why we present a case report of a pregnant woman infected with SARS-COV-2 who showed seizures and sudden blindness. Therefore, we consider that SARS-COV-2 infection during pregnancy could increase the risk of suffering posterior reversible leukoencephalopathy or preeclampsia/eclampsia syndrome. To our knowledge, this is the first report of a patient with COVID-19 presenting preeclampsia associated with eclampsia versus posterior reversible leukoencephalopathy without alarm signs or symptoms. We consider further studies are needed to confirm that SARS-COV-2 infection is a risk factor to develop neurological complications of pregnant woman during pregnancy. doi = 10.1186/s12884-020-03275-2 id = cord-103787-qhftb6d7 author = Garcia, Elizabeth P. title = Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date = 2005-10-31 keywords = PCR; RNA; SARS; star summary = Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. doi = 10.1016/s1525-1578(10)60575-2 id = cord-310636-y7n22ykt author = Garcia-Beltran, W. F. title = COVID-19 neutralizing antibodies predict disease severity and survival date = 2020-10-20 keywords = SARS; covid-19; figure; international; rbd summary = A quantitative ELISA that measures IgG, IgM, and IgA antibodies to the receptor binding domain (RBD) of SARS-CoV-2 and a high-throughput neutralization assay using lentiviral vectors pseudotyped with SARS-CoV-2 and WIV1-CoV were developed to assess neutralization potency and cross-neutralizing responses. We determined the sensitivity and specificity of this assay by assessing anti-RBD antibody levels in a cohort of SARS-CoV-2-infected patient serum samples collected between 14 to 42 days after symptom onset ( n = 85) in order to maximize seropositivity for IgG, IgM, and IgA. Anti-RBD IgG, IgM, and IgA levels were measured for each sample by interpolation on to the standard curve and a receiver operating curve (ROC) analysis was used to determined optimal cut-offs that distinguished SARS-CoV-2-infected patients from pre-pandemic controls ( Figure 2C ). However, a principle components analysis (PCA) that included demographic data, pre-existing medical conditions, laboratory data, treatments received, anti-RBD antibody levels and neutralization titers but not clinical outcomes demonstrated clustering of patients by the severity cohorts ( Figure 4A ). doi = 10.1101/2020.10.15.20213512 id = cord-284387-cjziykrz author = Garcia-Castrillo, Luis title = European Society For Emergency Medicine position paper on emergency medical systems’ response to COVID-19 date = 2020-05-04 keywords = SARS; patient summary = Second, protective measures by health services, especially in public and open environments like emergency departments (EDs) where isolation of potentially infected patients is a real challenge or clinical wards is vital [10] . Clinical care of suspected patients with COVID-19 should focus on early recognition, and immediate isolation, as well as appropriate infection prevention measures and control measures with care taken to optimise supportive care. (1) An informative, coordinated campaign for public and healthcare professionals, focused on mechanisms of contagion [4] , personal protection equipment (PPE) use, and a clinical pathway for the suspected patients infected with COVID-19. (5) The development and implementation of cleaning protocols, considering that coronavirus has been isolated on inanimate objects, and healthcare workers were infected by SARS, even without direct contact with sick patients [15] . The patient, relative or general practitioner may alert the emergency number indicating that a potential case of SARS-CoV-2 infection with severe symptoms is seeking care. doi = 10.1097/mej.0000000000000701 id = cord-330807-abi8pra7 author = Garcia-Pachon, Eduardo title = Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization date = 2020-07-04 keywords = SARS summary = title: Asthma prevalence in patients with SARS-CoV-2 virus infection detected by RT-PCR not requiring hospitalization INTRODUCTION: The prevalence of asthma in patients hospitalized with SARS-CoV-2 has been studied and varies widely in the different series. METHODS AND RESULTS: A total of 218 patients (58% of those who tested positive) did not require hospitalization; they had a median age of 45 years (IQR 34–57) and 57% were female. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. The objective of this study was to analyze the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay for SARS-CoV-2 and did not require hospital admission. For this reason we have analyzed the presence of asthma in a consecutive series of patients who tested positive in the RT-PCR assay [12] for SARS-CoV-2 and did not require hospital admission. doi = 10.1016/j.rmed.2020.106084 id = cord-347731-eqxn6auk author = Garcia‐Cremades, Maria title = Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date = 2020-05-12 keywords = HCQ; SARS; viral summary = The data sources included were (i) longitudinal clinical, pharmacokinetic (PK), and virologic data from patients with severe acute respiratory syndrome‐2 (SARS‐CoV‐2) infection who received HCQ with or without azithromycin (n = 116), (ii) in vitro viral replication data and SARS‐CoV‐2 viral load inhibition by HCQ, (iii) a population PK model of HCQ, and (iv) a model relating chloroquine PKs to corrected QT (QTc) prolongation. 12 The drug effect over time on viral replication rate was established by simulating unbound plasma concentrations or unbound lung tissue concentrations using a previously defined partition coefficient (10 2.45 ; HCQ unbound fraction assumed to be ~ 50%) and using the established in vitro sigmoidal efficacy parameters. 3, 9, 10 Viral kinetics were estimated from in vitro replication rate of severe acute respiratory syndrome-coronavirus (SARS-CoV)-1 and unbound drug concentration in plasma and lungs were simulated with HCQ PK model. doi = 10.1002/cpt.1856 id = cord-347308-l19snjyf author = García-Howard, Marcos title = Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 date = 2020-08-06 keywords = COVID-19; SARS; seizure summary = Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. Background: Non-febrile illness seizures may present in previously healthy children as afebrile seizures associated with minor infections, such as mild gastroenteritis or respiratory tract infections, and are linked to a genetic predisposition. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. For the novel human coronavirus SARS-CoV-2, causing COVID-19, fever, cough, and gastrointestinal complaints are the most common symptoms in children, and a hyperimmune response may be present. Additionally, during hospitalization, the patient and her mother were included in a collaborative study of genomic medicine for identifying genetic variants causing hyperimmunity due to SARS-CoV-2 infection. doi = 10.3389/fped.2020.00507 id = cord-337127-pc9hez28 author = García-Salido, Alberto title = Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a date = 2020-09-30 keywords = SARS summary = title: Innate cell response in severe SARS-CoV-2 infection in children: expression analysis of CD64, CD18 and CD11a The immune response to SARS-CoV-2 infection appears to be a critical factor in the development and prognosis of COVID-19 patients 2 . In children, severe forms of the disease like the pediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 appears to be related with some immune dysregulation 3 . We study in this report three children with severe SARS-CoV-2 infection. As can be seen in Figure 1 children with SARS-CoV-2 show levels of CD64 expression that are higher than in previous published reports of bacterial or viral infections or autoinflammatory diseases 5 . In summary, we describe the immunophenotype of three children with severe SARS-CoV-2 infection. Neutrophil CD64 expression as a longitudinal biomarker for severe disease and acute infection in critically ill patients doi = 10.1016/j.medin.2020.09.003 id = cord-355294-gifsqph6 author = García-Suárez, Julio title = Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study date = 2020-10-08 keywords = COVID-19; SARS; malignancy; patient summary = title: Impact of hematologic malignancy and type of cancer therapy on COVID-19 severity and mortality: lessons from a large population-based registry study METHODS: In this population-based registry study, we collected de-identified data on clinical characteristics, treatment and outcomes in adult patients with hematologic malignancies and confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection within the Madrid region of Spain. This case series included consecutive patients with hematologic malignancies aged ≥ 18 years who received a confirmed diagnosis of COVID-19 in the emergency departments, hospital wards (patients infected while hospitalized) or outpatient clinics of these Madrid hospitals up to May 25, 2020. Potential prognostic factors were collected including pre-infection patient characteristics (age, sex, comorbidities, type of hematologic malignancy and therapy), COVID-19 clinical severity, treatments and care setting. Clinical severity of COVID-19 was worse, and mortality rates were higher among older patients and those with a greater number of comorbidities and varied by type of hematologic malignancy and active antineoplastic treatment. doi = 10.1186/s13045-020-00970-7 id = cord-333520-v2sb90rc author = Gardin, Chiara title = Could Mesenchymal Stem Cell-Derived Exosomes Be a Therapeutic Option for Critically Ill COVID-19 Patients? date = 2020-08-26 keywords = ALI; ARDS; COVID-19; MSC; Mesenchymal; SARS; cell summary = Exosomes derived from mesenchymal stem cells (MSCs) are being explored for the management of a number of diseases that currently have limited or no therapeutic options, thanks to their anti-inflammatory, immunomodulatory, and pro-angiogenic properties. Next, we describe some of the most significant clinical evidence of the successful use of MSC-derived exosomes in animal models of lung and heart injuries, which might strengthen our hypothesis in terms of their utility for also treating critically ill COVID-19 patients. Recently, MSC-derived exosomes have been demonstrated to have comparable and even greater effects than cells themselves in improving inflammation and injury in a variety of pre-clinical lung disease models, including ALI/ARDS (Table 1) . From the studies discussed above, it emerged that the rationale for using MSC-derived exosomes, MVs, or EVs in ALI/ARDS is based on several processes, many of which are shared with those identified in the parent MSCs. These include immunomodulation and anti-inflammatory properties on host tissue, reduction of the permeability of alveolar epithelium and endothelium, improvement of alveolar fluid clearance, enhancement of macrophage phagocytosis, and tissue repair through direct mitochondrial transfer with host cells (Figure 2 ). doi = 10.3390/jcm9092762 id = cord-313117-0qur0isb author = Gardinassi, Luiz G. title = Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse date = 2020-06-26 keywords = SARS; covid-19; figure summary = To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. In addition, our approach also detected increased signals of monocytes (Figure 1B) , dendritic cells ( Figure 1C ) and of the mitochondrial respiratory electron transport chain in SARS-CoV-2 infection (Figure 1A) , suggesting a critical role of metabolic pathways for the immune response of COVID-19 patients. doi = 10.3389/fimmu.2020.01636 id = cord-296356-qkvafy69 author = Garman, Elspeth title = SARS Proteomics Reveals Viral Secrets date = 2005-11-30 keywords = SARS; dna summary = The structure of the mutagenic base pair in the confines of a closed polymerase complex exposes some of those strategies. (2005) In a worldwide cooperative research effort involving a multidisciplinary approach, structural and functional characterization of the SARS virus and its host interactions has been swiftly pursued. By sequence alignment and structural comparison with all known H2A domains, as well as examination of functional data, the authors conjecture that proteins from this superfamily form an emerging group of nucleotide phosphatases, all with similar functionality. This has two pivotal consequences for understanding the biology of the virus: A systematic approach is essential, and, even more importantly, a deeper structural and functional knowledge of the many complexes that the SARS CoV proteins form with one another and with proteins of the host organisms will be required-research that is still in its infancy. doi = 10.1016/j.str.2005.10.004 id = cord-331496-5xak7z6b author = Garnett, Emily title = Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date = 2020-08-31 keywords = PCR; SARS summary = We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. In this study, we describe validation of one of the first assays to receive EUA on an automated platform, the Vitros Anti-SARS-CoV-2 Total (CoV2T; Ortho Clinical Diagnostics) antibody assay, for screening of previous exposure to SARS-CoV-2 in our patient population. Seroconversion in our patient population was assessed by correlation of chart review of 55 patients known to be positive for SARS-CoV-2 by RT-PCR and known date of symptom onset with sample reactivity by the CoV2T assay. Specimens from 14 patients with acute infections, previously tested to be negative for SARS-CoV-2 by RT-PCR but positive for another respiratory viral infection by molecular analysis, were nonreactive by the CoV2T assay. doi = 10.1093/ajcp/aqaa157 id = cord-267588-ruuzr6l1 author = Garnett, Lauren title = Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date = 2020-08-08 keywords = RNA; SARS; swab summary = This study aimed to examine the efficacy of six different swabs that are commonly found in hospital settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima), along with more readily available alternative transport mediums (DMEM, PBS, 100% ethanol, 0.9% normal saline and VTM) for their use in molecular detection of SARS-CoV-2. Therefore, our results suggest that the cotton and wood For the portion of the study focusing on alternative transport media, we assessed the ability of DMEM, PBS, 0.9% Normal Saline, and 100% ethanol compared to VTM to be used as medium for the preservation and recovery of viral RNA to be quantified by molecular detection. Despite finding similar levels of viral RNA collected using different swabs and transport media, there is variation when evaluating different respiratory clinical samples while testing for SARS-CoV-2. doi = 10.1016/j.jviromet.2020.113947 id = cord-275088-wbqznzj7 author = Garrido, Pablo F. title = The Lord of the NanoRings: cyclodextrins and the battle against SARS-CoV-2 date = 2020-07-25 keywords = Cyclodextrin; SARS; cholesterol; figure summary = This includes the encapsulation and transport of specific drugs, as adjuvants to stabilize proteins, vaccines or other molecules involved in the infection, as cholesterol trappers to destabilize the virus envelope, as carriers for RNA therapies, as direct antiviral drugs and even to rescue blood coagulation upon heparin treatment. Modified Cyclodextrins in general antiviral formulations Not only native CDs but also CD derivates have been studied as potential drugdelivery platforms to treat several viral diseases. The inclusion conjugates release sACE2 after entering the body via atomization or other drug delivery means, and the released sACE2 would combine with SARS-CoV-2 S-proteins to block the virus''s ability to infect and destroy human cells. Recently, we discuss the mechanism and production of cyclodextrin-soluble angiotensin-converting enzyme 2 (CD-sACE2) inclusion compounds in the treatment of SARS-CoV-2 infections by blocking S-proteins. doi = 10.1016/j.ijpharm.2020.119689 id = cord-274090-eab7i4f6 author = Gaspari, Valeria title = Can Covid‐19 be a sexually transmitted disease? Posterity will judge date = 2020-05-24 keywords = SARS summary = The knowledge of all possible modes of transmission of SARS-CoV-2 infection is the key to improving both the identification of the asymptomatic population and the necessary isolation measures in order to further flatten the curve. The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients (66.67%) has already been demonstrated in recent studies in Wuhan, without being statistically related to gastrointestinal symptoms and/or disease severity. Moreover, the positivity for SARS-CoV-2 on vaginal swab raises the possibility of both sexual and mother-to-child transmission 7 , although further studies are needed on these issues since no definitive proofs have been found. A further step would be adding SARS-CoV-2 serology, pharyngeal, anal and vaginal swabs to our usual STD screening also in the asymptomatic population, in order to identify positive cases and to confirm the SARS-CoV-2 orogenital route of transmission. SARS-CoV-2 possible contamination of genital area: implications for sexual and vertical transmission routes doi = 10.1111/dth.13676 id = cord-344778-2p1mm3vg author = Gasparri, Maria Luisa title = Changes in breast cancer management during the Corona Virus Disease 19 pandemic: an international survey of the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) date = 2020-05-29 keywords = COVID-19; SARS summary = The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. The aim of our survey was to provide a real time international snapshot of modifications of breast cancer management during the COVID-19 pandemic. Two-hundred and fifty-two/377 (67%) responders considered chemotherapy as being riskier for developing severe COVID-19-related complications compared to surgery and radiation therapy. The reported cases of patients diagnosed with SARS-CoV-2 during BC treatment or within 14 days following treatment are 10%, 7% and 4% for chemotherapy, surgery and radiation therapy, respectively. This large international survey among breast cancer centres showed that the COVID-19 pandemic affected management of BC patients, including treatment modifications, longer waiting times and increased use of genomic profile analysis. Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic Recommendations for triage, prioritization and treatment of breast cancer patients during the COVID-19 pandemic doi = 10.1016/j.breast.2020.05.006 id = cord-255552-k1retwa4 author = Gassen, Nils C. title = Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date = 2020-04-15 keywords = CoV-2; SARS summary = Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Targeting of these pathways by exogenous administration of spermidine, AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS-CoV-2 propagation by 85, 88, and >99%, respectively. In the case of highly pathogenic Middle East respiratory syndrome 57 (MERS)-CoV, we recently showed that autophagy is limited by a virus-induced AKT1-dependent 58 activation of the E3-ligase S-phase kinase-associated protein 2 (SKP2), which targets the key autophagy 59 initiating protein Beclin-1 (BECN1) for proteasomal degradation (10). Direct blocking of the negative BECN1 regulator SPK2 by previously 175 described inhibitors SMIP004, SMIP004-7, valinomycin, and niclosamide (10) showed SARS-CoV-2 176 growth inhibition from 50 (SMIP004, SMIP004-7) to over 99% in case of valinomycin and niclosamide 177 (Figure 4a, lower panel, Figure S3d,e) . doi = 10.1101/2020.04.15.997254 id = cord-302920-jkr438p9 author = Gasser, Romain title = Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date = 2020-10-09 keywords = SARS summary = key: cord-302920-jkr438p9 title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 cord_uid: jkr438p9 Characterization of the humoral response to SARS-CoV-2, the etiological agent of Covid-19, is essential to help control the infection. In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. In this study, we selected plasma from a cohort of Covid-19 convalescent patients and selectively depleted immunoglobulin A, M or G before testing the remaining neutralizing capacity of the depleted plasma. This observation may help design efficient antibody-based COVID-19 therapies and may also explain the increased susceptibility to SARS-CoV-2 of autoimmune patients receiving therapies that impair the production of IgM. Decline of humoral 409 responses against SARS-CoV-2 Spike in convalescent individuals Potent neutralizing 413 antibodies from COVID-19 patients define multiple targets of vulnerability doi = 10.1101/2020.10.09.333278 id = cord-271404-tu8u1b1d author = Gaunkar, Ridhima B title = COVID-19 in Smokeless Tobacco Habitués: Increased Susceptibility and Transmission date = 2020-06-25 keywords = SARS; SLT; covid-19 summary = Smokeless tobacco (SLT) consumption is of particular concern in countries in South Asia with high population densities, as it facilitates exposure to SARS-CoV-2 within or between communities by the act of public spitting. SLT-induced higher expression of angiotensin-converting enzyme 2 receptors along with the presence of furin in the oral mucosa and dysfunctional immune responses among SLT habitués increase viral dissemination and an individual''s susceptibility to COVID-19. There has not been much research on the increased risk of contracting COVID-19 for smokeless tobacco (SLT) users, although the use of these products is widely prevalent in South Asia and the Western Pacific region. The known action of the enzyme furin and the nicotine-induced increased expression of the ACE2 receptor result in COVID-19 viral tropism to the oral mucosal tissues in smokeless tobacco habitués [11] [12] [13] [14] [15] [16] [17] [18] [19] . doi = 10.7759/cureus.8824 id = cord-307701-fujejfwb author = Gaurav, Shubham title = Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date = 2020-06-07 keywords = CoV-2; SARS summary = Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the cause of the novel human Corona Virus Disease COVID-19, first reported on November 17 th , 2019 in Wuhan, China [12] . In addition to structural and NSPs, SARS-CoV-2 genome also codes for at least two other viroporin candidates (other than the E protein), namely ORF3a and ORF8 [3] . Moreover, the 29-nucleotide deleted SARS CoV-1 strain had a 23-fold less viral replication as compared to its wild type, suggesting that this mutation effectively attenuated the virus. doi = 10.1101/2020.06.06.137604 id = cord-252286-377y9aqx author = Gauss, Tobias title = Preliminary pragmatic lessons from the SARS-CoV-2 pandemic from France date = 2020-05-13 keywords = ICU; SARS summary = Abstract The first wave of the SARS-CoV-2 pandemic required an unprecedented and historic increase in critical care capacity on a global scale in France. The SARS-CoV-2 pandemic requires an unprecedented and historic increase in critical care capacity on a global scale. The ongoing fight against the pandemic and potential resurgence of the virus made it compelling for the authors to share specific concepts for the management of critical care surge capacity. One particularity of any exceptional situation (mass casualty, pandemic, etc.) is the activation of a structured crisis mode during which authority lies within the crisis committee, relying on a chain of command and clearly defined principles of control. ICU/HDU capacities management required conscious effort to preserve protected space for non-SARS-CoV-2 critical care and respond to the evolving situation. Training was essential to prepare healthcare professionals in the first days of the pandemic for PPE use, airway management, cleaning, cardiac arrest, etc. doi = 10.1016/j.accpm.2020.05.005 id = cord-280979-0vaarrji author = Gauttier, V. title = Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date = 2020-08-14 keywords = CD8; HLA; SARS summary = These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Altogether, these data showed that optimized peptide vaccination against selected SARS-CoV-2 epitopes elicits robust and broad Th1-biased immunogenicity against several structural (S, M, N) and non-structural proteins in HLA-A2 expressing mice and that several peptides induce viral-specific memory CD8 T cells displaying all characteristics of T lymphocyte sentinels in barrier tissues. Using sequence design through reverse vaccinology selection approach based on previous CoVs knowledge on immunodominant epitopes and computational immunology optimization, we developed a combination of 12 CD8 T cell synthetic peptides originating from 11 SARS-CoV-2 structural and non-structural proteins capable to cover HLA polymorphism with high coverage globally and to induce immunogenicity to different proteins independently of HLA alleles expression. doi = 10.1101/2020.08.14.240093 id = cord-343715-y594iewi author = Gavriatopoulou, Maria title = Organ-specific manifestations of COVID-19 infection date = 2020-07-27 keywords = ACE2; COVID-19; China; SARS; Wuhan; clinical; patient summary = Patients infected with this new coronavirus present with a variety of symptoms, which range from asymptomatic disease to mild and moderate symptoms (mild pneumonia), severe symptoms (dyspnoea, hypoxia, or > 50% lung involvement on imaging) and symptoms of critical illness (acute respiratory distress syndrome, respiratory failure, shock or multiorgan system dysfunction). A large retrospective observational study from China showed that among 214 hospitalized patients with confirmed SARS-CoV-2 infection, 36.4% had neurological manifestations [114] . The correlation of disease severity with neurological symptoms was confirmed by another retrospective study from France, reporting a prevalence of 84% of neurological manifestations in 58 hospitalized patients with acute respiratory distress syndrome (ARDS) due to COVID-19 [115] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1007/s10238-020-00648-x id = cord-284526-a5kgo4ct author = Gavriilaki, Eleni title = Endothelial Dysfunction in COVID-19: Lessons Learned from Coronaviruses date = 2020-08-27 keywords = COVID-19; ICU; SARS; endothelial; patient summary = Experience from previous coronaviruses has triggered hypotheses on the role of endothelial dysfunction in the pathophysiology of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which are currently being tested in preclinical and clinical studies. Recent evidence suggests that signs and symptoms of severe coronavirus disease-2019 (COVID-19) infection resemble the clinical phenotype of endothelial dysfunction and share mutual pathophysiological mechanisms [1] . Experience from previous coronaviruses has triggered studies testing hypotheses on the role of the endothelial dysfunction in patients with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Α high rate of VTE (43%, mainly PE) overall was reported in another series of 150 ICU patients in which patients with COVID-19associated acute respiratory distress syndrome (ARDS) had higher rates of thrombotic complications compared with non-COVID-19-ARDS [65] . Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection doi = 10.1007/s11906-020-01078-6 id = cord-283948-rb9rrkxb author = Gavriilidis, Paschalis title = The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series date = 2020-06-25 keywords = COVID-19; SARS summary = title: The Impact of COVID-19 Global Pandemic on Morbidity and Mortality of Liver Transplant Recipients Children and Adults: A Systematic Review of Case Series Currently, the first articles reporting outcomes of liver transplant recipients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are published. The aim of the present study was to summarise the reported evidence of liver transplant recipients infected by SARS-CoV-2 during the global pandemic. A systematic literature search of articles published from inception until April 2020 performed in EMBASE, MED-LINE (PubMed), Cochrane Library, and Google Scholar databases using free text and MeSH terms (corona virus, COVID-19, liver transplantation, liver transplant recipients, global pandemic of COVID-19, severe acute respiratory syndrome, SARS). Of note, D''Antiga reported that children liver transplant recipients although immunosuppressed were not at increased risk to develop severe COVID-19 compared with the general population [7] . doi = 10.14740/jocmr4223 id = cord-302821-b9ikg0xy author = Gawałko, Monika title = COVID-19 associated atrial fibrillation: Incidence, putative mechanisms and potential clinical implications date = 2020-09-01 keywords = COVID-19; SARS; patient summary = Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. Here, we review the available evidence for prevalence and incidence of AF in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and discuss disease management approaches and potential treatment options for COVID-19 infected AF patients. The pathophysiology of COVID-19 related AF is not well understood and proposed putative mechanisms include a reduction in angiotensin-converting enzyme 2 (ACE2) receptor availability, CD147-and sialic acid-spike protein interaction, enhanced inflammatory signalling eventually culmination in inflammatory cytokine storm, direct viral endothelial damage, electrolytes and acid-base balance abnormalities in the acute phase of severe illness and increased adrenergic drive.(28) (Fig. 1) . doi = 10.1016/j.ijcha.2020.100631 id = cord-258722-1o6zhnnj author = Gbinigie, Kome title = Should azithromycin be used to treat COVID-19? A rapid review date = 2020-05-13 keywords = COVID-19; SARS summary = In vivo and in vitro studies were included assessing the safety and effectiveness of azithromycin for treatment of COVID-19, and/or the activity of azithromycin against SARS-CoV-2. In another pre-print, Andreania and colleagues 13 report the results of an in vitro study assessing the activity of azithromycin and hydroxychloroquine against SARS-CoV-2. In vivo research effectiveness Only one trial was identified on the effectiveness of azithromycin for the treatment of COVID-19, conducted by Gautret and colleagues in France and reported in a pre-print 14 (see Table 1 ). The same research team that conducted the in vivo study included in this review conducted a singlearm trial of 80 patients who tested positive for SARS-CoV-2 and showed mild symptoms, 17 to further assess the effectiveness of the combined hydroxychloroquine/azithromycin treatment regime. No in vivo studies were identified assessing the safety or effectiveness of azithromycin as a standalone treatment for COVID-19. doi = 10.3399/bjgpopen20x101094 id = cord-255738-r8zfdsix author = Ge, Feng title = Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date = 2007-03-30 keywords = RNA; SARS; cell; replicon summary = Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric''s group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel''s group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. doi = 10.1016/j.virol.2006.10.016 id = cord-314311-xbpb9nfi author = Ge, Huipeng title = The epidemiology and clinical information about COVID-19 date = 2020-04-14 keywords = COVID-19; China; SARS; Wuhan summary = In November 2002, a novel betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong, China, and resulted in more than 8000 infections and 774 deaths in 37 countries. This review makes a comprehensive introduction about this disease, including the genome structure and receptor of SARS-CoV-2, epidemiology, clinical features, diagnosis, treatment, and prognosis of COVID-19. The clinical manifestations of SARS-CoV-2-infected patients ranged from mild non-specific symptoms to severe pneumonia with organ function damage. The COVID-19 patients around the world were diagnosed based on World Health Organization interim guidance [65] , and China updated the novel coronavirus pneumonia diagnosis and treatment program (trial version) (in Chinese) according to epidemic situation and improved awareness of disease. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1007/s10096-020-03874-z id = cord-295733-f3rt1fyk author = Ge, Tianxiang title = Evaluation of disinfection procedures in a designated hospital for COVID-19 date = 2020-08-22 keywords = RNA; SARS summary = When compared with previous study, more places that could be potentially contaminated by COVID-19 patients were sampled for viral RNA detection, such as the flush button of the toilet bowl, medical refuse transfer trolley, elevators, and the examination rooms for these patients. These areas could not be used for non-COVID-19 patients until all the environmental samples collected were negative for SARS-CoV-2 RNA detection. In this study, surface samples collected from the examination rooms were all negative for SARS-CoV-2 RNA detection, and the samples collected from isolation wards and other places were also negative for viral RNA detection, which indicated that the terminal disinfection was effective. Other researches had revealed the presence of SARS-CoV-2 RNA in aerosol, which indicated the air could be contaminated by the virus, and patients could be infected in the isolation wards [12, 28] . Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients doi = 10.1016/j.ajic.2020.08.028 id = cord-342362-j7vuoer6 author = Gegúndez-Fernández, José A title = Recomendaciones para la atención oftalmológica durante el estado de alarma por la pandemia de enfermedad por coronavirus COVID-19 date = 2020-04-25 keywords = COVID-19; SARS summary = Conclusiones: Durante la pandemia COVID-19, la atención a los potenciales riesgos de salud para la población ocasionados por el coronavirus deberá prevalecer sobre la posible progresión de enfermedades oculares comunes. Recoge recomendaciones de máximos para la atención a pacientes oftalmológicos, tanto COVID positivos como negativos, durante la pandemia por coronavirus SARS-CoV-2. Durante este periodo la atención a los potenciales riesgos de salud para la población general ocasionados por la pandemia COVID-19 debe primar sobre la posible progresión de enfermedades tales como el glaucoma crónico, la retinopatía diabética, la degeneración macular asociada a la edad (DMAE), enfermedades corneales e inflamatorias, entre otras. Las precauciones tomadas para la elaboración de los derivados hemáticos serán las propias establecidas según el informe de la AEMPS 20 de 23/mayo/2013 sobre el uso de Plasma Rico en Plaquetas (PRP) y teniendo en cuenta los criterios de exclusión del Anexo II del Real Decreto 21 1088/2005, el cual especifica que pacientes con infecciones se excluirán durante y como mínimo las dos semanas posteriores al restablecimiento clínico completo de una enfermedad infecciosa y tras la desaparición de síntomas, incluyendo fiebre superior a 38ºC y afección pseudogripal, donde podríamos clasificar la infección por SARS-CoV-2. doi = 10.1016/j.oftal.2020.04.002 id = cord-306881-wrd2rhjz author = Gehrie, Eric title = Transfusion Service Response to the COVID-19 Pandemic date = 2020-06-25 keywords = COVID-19; SARS; blood summary = In this article, we highlight "best practices" that have emerged during the pandemic, focusing on management of blood supply and blood bank operations, rapid incorporation of COVID-19 convalescent plasma into blood bank inventory, and changes to the approach to the patient requiring therapeutic apheresis. Extrapolation from previous experience with SARS-CoV, Middle Eastern respiratory syndrome, and influenza, and with the strong backing of statements by AABB, the Centers for Disease Control and Prevention, and the Food and Drug Administration (FDA), as well as the preliminary experience of other areas that were afflicted by COVID-19 prior to its wide spread in the United States, blood bankers were able to convince most stakeholders that the true risk to the blood supply was not SARS-CoV-2 itself, but rather social distancing practices resulting in an interruption to the critically needed blood supply. doi = 10.1093/ajcp/aqaa111 id = cord-314135-udce22id author = Geisslinger, Franz title = Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? date = 2020-07-06 keywords = ACE2; CoV-2; SARS; cancer; covid-19 summary = The responsible virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causes the coronavirus disease 2019 (COVID-19), which is mainly characterized by fever, cough and shortness of breath. We summarize the available literature on COVID-19 suggesting an increased risk for severe disease progression in cancer patients, and we discuss the possibility that SARS-CoV-2 could contribute to cancer development. The main symptoms of COVID-19, the lung disease following SARS-CoV-2 infection are fever, cough, shortness of breath and respiratory distress syndrome with risk for septic shock. Preliminary evidence suggests that such a cytokine storm in response to infection with SARS-CoV-2 is a major factor, promoting severe COVID-19 progress and subsequently disease fatality [8, 12] . Chemotherapy-and radiation therapy-induced immunosuppression is a major risk factor for cancer patients to acquire a severe and probably fatal SARS-CoV-2 infection. Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: Relation to the acute lung injury and pathogenesis of SARS † doi = 10.3390/ph13070143 id = cord-271723-8qoozmgk author = Gelman, Ram title = Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents date = 2020-06-18 keywords = ACE2; DPP4; GRP78; MERS; SARS summary = title: Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents The ongoing severe acute respiratory syndrome pandemic caused by the novel coronavirus 2 (SARS-CoV-2) is associated with high morbidity and mortality rates, and it has created a pressing global need for effective antiviral therapies against it. Potential therapeutic approaches have been proposed to target various steps in the viral infectious process, including a SARS-CoV-2 S-protein-based vaccine, a TMPRSS2 inhibitor aiming to block the priming of the viral S protein, an anti-ACE2 antibody to block the surface receptor, and a soluble ACE2 analogue which competitively binds with SARS-CoV-2 to slow viral entry into cells and decrease viral spread [27] . receptor, which may also be associated with the antiviral immune response Dipeptidyl peptidase 4 (DPP4), also known as CD26, is a 110 kDa transmembrane glycoprotein expressed on the surface of a wide variety of epithelial cells and some lymphocytes. doi = 10.1080/22221751.2020.1776161 id = cord-326498-8oa5gkrp author = Gemmati, Donato title = COVID-19 and Individual Genetic Susceptibility/Receptivity: Role of ACE1/ACE2 Genes, Immunity, Inflammation and Coagulation. Might the Double X-Chromosome in Females Be Protective against SARS-CoV-2 Compared to the Single X-Chromosome in Males? date = 2020-05-14 keywords = ACE1; ACE2; COVID-19; RAS; SARS; sex summary = Firstly, SARS-CoV-2 has a strong interaction with the human ACE2 receptor, which plays an essential role in cell entry together with transmembrane serine protease 2 (TMPRSS2); it is interesting to note that the ACE2 gene lays on the X-chromosome, thus allowing females to be potentially heterozygous and differently assorted compared to men who are definitely hemizygous. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. Therefore, proper ACE2 functionality is essential for both virus cell entry and local pulmonary homeostasis, and although it has been previously described that polymorphisms in the ACE2 gene do not affect the outcome of SARS [43] , females might have a higher degree of heterodimer assembling than males, which in turn might show different affinity for the SARS-CoV-2 spike receptor. doi = 10.3390/ijms21103474 id = cord-287338-pws42iay author = Gendelman, Omer title = Continuous hydroxychloroquine or colchicine therapy does not prevent infection with SARS-CoV-2: Insights from a large healthcare database analysis date = 2020-05-05 keywords = COVID-19; SARS summary = As such, in this study, we investigated whether a chronic baseline use of anti-inflammatory medications (namely, hydroxychloroquine and colchicine) could provide a potentially beneficial effect in preventing or, at least partially, mitigating the burden of the SARS-CoV-2 infection. In the present study, we have utilized "real-world data" to explore the associations between subjects positive for SARS-COV-2, different underlying co-morbidities and medications, which were not administered for anti-viral treatment purposes. In a population-based study evaluating the clinical characteristics of 1,482 patients hospitalized with COVID-19 in the USA [19] the majority of patients were males (54.4%) with a similar pattern of underlying comorbidities, most commonly hypertension (49.7%), followed by obesity (48.3%), DM (28.3%), and cardiovascular disease (27.8%). Concerning the alleged anti-viral activities of hydroxychloroquine [23] and its potential protective role against infections [24] , the existing scholarly literature reports contrasting findings even though to date no RCT has shown an unequivocal advantage in preventing or improving the major outcomes in COVID-19 patients [25, 26] . doi = 10.1016/j.autrev.2020.102566 id = cord-270218-578lsck9 author = Gentile, Davide title = Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study date = 2020-04-23 keywords = SARS; figure summary = On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pro (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. On a pharmacophore model, built by Pharmit server (http://pharmitcsb.pitt.edu/) [14] starting from the SARS-CoV-2 M pr (PDB ID: 6LU7) and with the complexed ligand N3 (PRD_002214) structure employed as input, the virtual screening on the 164,952 conformers of the 14,064 molecules contained in the MNP library was carried out. To further validate the pharmacophore model descriptors, validate the poses and binding energies, and comprehensively investigate the interactions of the new ligands within the catalytic site of the protease, we conducted a parallel docking study, with Autodock4, and MD simulations on those compounds (1-17) that showed a better affinity (Table 1) . doi = 10.3390/md18040225 id = cord-268330-mo5myrz4 author = Gentile, Pietro title = Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia date = 2020-04-29 keywords = COVID-19; SARS; cell; msc; stem summary = title: Adipose-derived stromal stem cells (ASCs) as a new regenerative immediate therapy combating coronavirus (COVID-19)-induced pneumonia [1] , reported exceptional outcomes in improved pulmonary functional activity, into seven patients who suffered Coronavirus Disease 2019 (COVID19) after an intravenous administration of clinical-grade mesenchymal stem cells (MSCs). [1] , 7 SARS-CoV-2 positive patients, with COVID-19 pneumonia (study group), showed a great improving pulmonary functional activity after an intravenous administration of clinical-grade MSCs [1] . The rationale of the present work is to suggest the possibility to use autologous or allogeneic adipose-derived stromal stem cells (ASCs) (in the last case after decellularization and with good manufacturing practices -GMPlaboratory approval) intravenously or directly through a ventilation mask (aerosol). In the last case, it could be possible to donate human adipose tissue to GMP, EMA, or FDA Laboratory or bank to isolate SVFs and ASCs and re-infuse the cellular product obtained, as certified drugs, in COVID-19 patients. doi = 10.1080/14712598.2020.1761322 id = cord-320815-p9oh54nt author = Gentile, Pietro title = Research progress on Mesenchymal Stem Cells (MSCs), Adipose-Derived Mesenchymal Stem Cells (AD-MSCs), Drugs, and Vaccines in Inhibiting COVID-19 Disease date = 2020-10-01 keywords = COVID-19; SARS; Stem; cell summary = Additionally, recent studies reported improved respiratory activity after intravenous administration of MSCs into patients affected by coronavirus disease 2019 (COVID-19) caused by the Coronavirus 2 (SARS-CoV-2) suggesting their role as anti-viral therapy. In this literature review, the role of regenerative strategies through MSCs, AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. In this current review, the role of regenerative strategies through MSCs, focusing on AD-MSCs, and adipocyte-secreted exosomal microRNAs (A-SE-miRs) as a potential antiviral therapy was reported, comparing the results found with current research progress on drugs and vaccines in COVID-19 disease. Two clinical trials (EUCTR2020-001364-29-ES and EUCTR2020-001266-11-ES) were registered in April 2020, after the pandemic situation produced by COVID-19 but the last one (EUCTR2019-002688-89-ES) based on the possibility "To assess the feasibility, safety, and tolerability of the administration of HCR040, a drug whose active substance is HC016, allogeneic adiposederived adult mesenchymal stem cells expanded and pulsed with H2O2, in patients with acute respiratory distress syndrome. doi = 10.14336/ad.2020.0711 id = cord-332970-atwz3rgf author = Gentile, Pietro title = Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease date = 2020-05-09 keywords = COVID-19; SARS; cell summary = title: Adipose Stem Cells (ASCs) and Stromal Vascular Fraction (SVF) as a Potential Therapy in Combating (COVID-19)-Disease A recent and interesting study reported improved respiratory activity after intravenous administration of mesenchymal stem cells (MSCs) into patients affected by coronavirus disease 2019 (COVID-19). The MSCs could represent an effective, autologous and safe therapy, and therefore, sharing these published results, here is reported the potential use possibilities in COVID-19 of the most common MSCs represented by Adipose Stem Cells (ASCs). Robert Chunhua Zhao''s group [1] reported in a recent study, published in March 2020, an interesting improvement in pulmonary functional activity, into 7 patients affected by Coronavirus Disease 2019 (COVID-19) after a intravenous administration of clinical-grade mesenchymal stem cells (MSCs). In the preliminary study of Robert Chunhua Zhao''s group [1] , 7 patients affected by SARS-CoV-2, with COVID-19 pneumonia displayed a sensible improvement pulmonary function after several intravenous infusion of clinicalgrade MSCs [1] . doi = 10.14336/ad.2020.0422 id = cord-257399-p6of5fno author = Gentry, Chris A title = Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date = 2020-09-21 keywords = CoV-2; March; SARS; infection summary = METHODS: This retrospective cohort study included de-identified information of all veterans in the US Veterans Health Administration clinical administrative database aged 18 years or older with rheumatoid arthritis, systemic lupus erythematosus, or associated rheumatological conditions (based on International Classification of Diseases, 10th edition, diagnostic codes) who were alive on March 1, 2020. We aimed to examine whether patients with rheuma tological conditions receiving chronic hydroxy chloroquine therapy are at less risk of developing SARS-CoV-2 infection compared with a propensity-matched group of patients not receiving hydroxychloroquine. Our study takes advantage of a setting in which a specific group of patients has been receiving chronic hydroxy chloroquine over several months to years as a novel virus emerges among the population, setting up an ideal premise to test the hypothesis that hydroxychloroquine might be effective in preventing SARS-CoV-2 infection. doi = 10.1016/s2665-9913(20)30305-2 id = cord-352741-0pdeehai author = Geramizadeh, Bita title = Histopathologic Findings of Coronavirus in Lung: A Mini-Review date = 2020-10-12 keywords = MERS; SARS summary = In this report, we will review the published reports about the histopathologic findings of lung tissue in the patients infected with SARS-CoV-2 in comparison with 2 other coronaviruses that have caused outbreaks, ie, SARS-CoV-1 and MERS-CoV. The keywords for searching were "lung," " pulmonary," and CoVs, ie, "severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2])," "coronavirus disease (COVID-19)," "pathology," "biopsy," "autopsy," "histopathology," "severe acute respiratory syndrome (SARS)," and "Middle East Respiratory syndrome (MERS)." Histological examination of lung in rare cases reported from SARS-CoV-2 showed "edema, bilateral diffuse alveolar damage with cellular fibromyxoid exudates, desquamation of pneumocytes and hyaline membrane formation," indicating acute respiratory distress syndrome. 19 One histopathologic finding in the new SARS-CoV-2infected lung disease that has not been reported in the previous epidemics of coronaviruses is the presence of pulmonary fibrosis that can be indicative of future pulmonary dysfunction if the patient recovers. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore doi = 10.1177/2632010x20951823 id = cord-330701-k68b0wqe author = Gerc, Vjekoslav title = Cardiovascular Diseases (CVDs) in COVID-19 Pandemic Era date = 2020-06-17 keywords = COVID-19; SARS; disease; patient summary = AIM: The aim of this study is to retreive published papers about COVID-19 infection deposited in PubMed data base and analyzed current results of investigations regarding morbidity and mortality rates as consequences of COVID-19 infection and opinions of experts about treatment of afected patients with COVID-19 who have Cardiovascular diseases (CVDs). COVID-19 infection is caused by a new beta-coronavirus, which the WHO has called (SARS-CoV-2) -Severe Acute Respiratory Syndrome. Initially, the main complications of COVID-19 were thought to be lung-related, then it was quickly observed that COVID-19 is attacking many organs, including the heart muscle, vascular endothelium and the cardiovascular system in general, increasing morbidity and mortality, especially in patients with other cardiovascular risk factors presented (hypertension, diabetes, obesity, cerebrovascular and renal disease). In Wuhan, according to reports of Chinese physicians, in patients infected with COVID-19 and with acute coronary syndrome, the complete clinical picture was very severe and associated with high mortality (9) . doi = 10.5455/msm.2020.32.158-164 id = cord-326888-0p8nctpy author = Gercina, Anne Caroline title = What is the best mouthrinse against Coronaviruses? date = 2020-08-13 keywords = SARS summary = (1) Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post‐surgical infectious complications. The person-to-person transmission of SARS-CoV-2 may occur directly or indirectly through saliva, and a preoperational use of antimicrobial mouthwash is considered to reduce the number of oral microbes. 1 Chlorhexidine mouthwash has been a common antiseptic agent used in dentistry, both preoperative and postoperative use reducing post-surgical infectious complications. All rights reserved Even assuming that 1% of hydrogen peroxide is the best alternative to prevent transmission during oral procedures, its use on postoperative does not seem to be necessary. The purpose of rinsing 1% hydrogen peroxide is to protect the professional from avoiding transmission during the procedure from patients already infected by SARS-CoV-2. Comparison of In Vitro Inactivation of SARS CoV-2 with Hydrogen Peroxide and Povidone-Iodine Oral Antiseptic Rinses doi = 10.1111/ors.12549 id = cord-290851-1e5e033r author = Gerlier, Denis title = Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date = 2011-06-12 keywords = ACE2; SARS; virus summary = Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection doi = 10.1016/j.coviro.2011.05.014 id = cord-318184-atlslk0e author = Germain, N. title = Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France date = 2020-09-11 keywords = SARS; covid-19 summary = We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. First identified in Wuhan (China), in early January 2020, the new severe acute respiratory syndrome virus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID19) , rapidly spread to other countries worldwide causing an unprecedented pandemic 1 . Taking into account the information available, the French Biomedicine Agency updated the guidance on SARS-CoV-2 transmission risk via donated organs and tissues on March 5, 2020 and recommended to exclude donors with symptoms suggestive of COVID-19 (fever, cough, etc.) and donors who had stayed or traveled to high risk regions within the prior 28 days, or . Archived blood specimens collected on the day of donation for donor screening of infectious diseases were retrospectively tested for SARS-CoV-2 antibodies (Fig.2 ). doi = 10.1101/2020.09.11.20192518 id = cord-341838-lkz8ro90 author = Gervasoni, Cristina title = Clinical features and outcomes of HIV patients with coronavirus disease 2019 date = 2020-05-14 keywords = HIV; SARS summary = The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. doi = 10.1093/cid/ciaa579 id = cord-351224-jeedo5mc author = GeurtsvanKessel, Corine H. title = An evaluation of COVID-19 serological assays informs future diagnostics and exposure assessment date = 2020-07-06 keywords = SARS; assay; patient summary = The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. Despite the differences in sensitivity, all laboratory assays had sufficient positive predictive value (PPV) in COVID-19 hospitalized patients when assuming an expected seroprevalence in this population of ≥50% (Table 1) , or when using serology as an adjunct to RT-PCR testing to monitor the clinical course of illness. To determine specificity of the assays, we used a well-defined panel of 147 serum and plasma samples from 147 individuals exposed to human coronaviruses (HCoV-229E, NL63 or OC43), SARS, MERS), or with a range of other respiratory viruses ( Sensitivity was calculated by using a total of 187 sera from 107 individuals in the Netherlands, in whom COVID-19 was confirmed by RT-PCR and antibodies were detected by PRNT50. doi = 10.1038/s41467-020-17317-y id = cord-320535-fo4lzcav author = Geyer, Howard L. title = Movement Disorders in COVID-19: Whither Art Thou? date = 2020-08-12 keywords = COVID-19; SARS summary = The paucity of movement disorders associated with COVID-19 is particularly striking when contrasted with the neurologic syndrome which affected over a million people worldwide in the aftermath of the 1918 "Spanish" influenza, termed by Constanin von Economo encephalitis lethargica. That encephalitis was associated with a wide range of movement disorders, of which post-encephalitic parkinsonism is the best known, although other manifestations in the acute phase included dystonia, tremor, chorea, myoclonus, and oculomasticatory myorhythmia [6, 7] . Although encephalitis has been described as a cardinal neurological manifestation of COVID-19 during the acute phase of illness [8, 9] , we have yet to encounter any of these associated movement disorder presentations. (In the time since this write-up was first prepared, patients with acute movement disorders and COVID-19 have been reported exiguously; we know of four such reports, which describe myoclonus [10, 11] , a hypokinetic-rigid syndrome [12] , and tremor/ataxia [13] . doi = 10.5334/tohm.553 id = cord-292274-upwn9o2m author = Ghaffari, Abdi title = COVID-19 Serological Tests: How Well Do They Actually Perform? date = 2020-07-04 keywords = SARS; covid-19; test summary = While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . Typically, RDT test strips use a drop of blood to detect the presence of patient antibodies (IgG, IgM, or IgA) produced against a specific SARS-CoV-2 antigen ( Figure 2 ). Critics point to gaps in our understanding of immune response to COVID-19 infection, including the ability of serological tests to detect neutralizing antibodies and the capacity of the immune system to provide long-term immunity against SARS-CoV-2. doi = 10.3390/diagnostics10070453 id = cord-325473-hrdanbn1 author = Ghahremanpour, Mohammad M. title = Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 date = 2020-08-28 keywords = SARS; drug summary = 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 5 Thus, M pro is viewed as a promising target for anti SARS-CoV-2 drug design; it has been the focus of several studies since the pandemic has emerged. For instance, a molecular docking study suggested remdesivir as a potential therapeutic that could be used against SARS-CoV-2, 10 which was supported experimentally by an EC50 value of 23 μM in an infected-cell assay. Structural Basis for the Inhibition of SARS-CoV-2 Main Protease by Antineoplastic Drug Carmofur Crystal Structure of SARS-CoV-2 Main Protease Provides a Basis for Design of Improved α-Ketoamide Inhibitors Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition Structure-based Design of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease Targeting the SARS-CoV-2 Main Protease to Repurpose Drugs for doi = 10.1101/2020.08.28.271957 id = cord-332065-afq26621 author = Ghanchi, Hammad title = Racial Disparity Amongst Stroke Patients During the Coronavirus Disease 2019 Pandemic date = 2020-09-10 keywords = SARS; black; stroke summary = The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting with stroke during the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A statistically significant increase in the number of Black and Hispanic patients presenting with strokes was noted in California, Pacific hospitals, Western hospitals, and all hospitals in the United States during various months studied comparing 2020 to 2019. Given the recent pandemic and racial disparity among patients afflicted with SARS-CoV-2 and the possible link of this virus and cerebrovascular accidents (CVA), we sought to analyze whether there was a disparity for stroke patients presenting to hospitals during this time using the Get with the Guidelines (GWTG) National Stroke Database. The primary endpoint of this study is to compare whether there was a significant difference in the proportion of patients in each reported racial category presenting to our institution with stroke during the COVID-19 pandemic caused by SARS-CoV-2. doi = 10.7759/cureus.10369 id = cord-351896-j6h02ab5 author = Ghannam, Malik title = Neurological involvement of coronavirus disease 2019: a systematic review date = 2020-06-19 keywords = COVID-19; SARS; neurological; patient summary = The following search strategy was implemented and these keywords and their synonyms (in the all fields) were combined in each database as follows: ("COVID 19" OR "coronavirus") AND ("brain" OR "CNS" OR "spinal cord" OR "nerve" OR "neurologic" OR "stroke" OR "cerebrovascular" OR "cerebral vein thrombosis" OR "sinus thrombosis" OR "Intracerebral hemorrhage" OR "hemorrhage" OR "myelitis" OR "GBS" OR "Guillain Barre syndrome" OR "neuropathy" OR "radiculopathy" OR "cranial neuropathy" OR "myopathy" OR "myositis" OR "rhabdomyolysis" OR "encephalitis" OR "encephalopathy" OR "meningitis" OR "meningoencephalitis" OR "seizure" OR "convulsion" OR "epilepsy") [ Fig. 1 ]. [11] For each study, the following descriptive, microbiological, and clinical information was extracted: patient demographic data, SARS-CoV-2 testing from nasal swab and CSF, neurological symptoms and signs and their onset in relation to respiratory or gastrointestinal (GI) symptoms or anosmia or dysgeusia, any neurological investigations and CSF or any other relevant laboratory testing (such as CK, LDH, CRP, D-dimer, lupus anticoagulant, fibrinogen, ganglioside antibodies), neurological diagnosis, occurrence of respiratory failure (defined as need for intubation, abnormal PO2 in blood gas, or Glasgow Coma Scale score less than or equal 8), treatments administered for the neurological diagnosis, and final outcome. doi = 10.1007/s00415-020-09990-2 id = cord-285426-iyl12ber author = Ghavami, Shaghayegh Baradaran title = IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date = 2020-09-08 keywords = IBD; SARS summary = Interestingly, in the recent pandemic of coronavirus disease (COVID19) , and the SARS-CoV epidemic in 2003, while the fecal samples of these patients were positive for the virus, they did not present any severe respiratory distress syndrome (4). Remarkably, the angiotensin-converting enzyme-2 (ACE2) is the receptor for SARS-CoV-2 and it is expressed in different organs including the lungs, testis and ileum. showed that when rheumatoid arthritis patients were treated with anti-TNF-α biologicals (infliximab, adalimumab, and certolizumab pegol), the expression of IFN-α-regulated genes was increased in the peripheral blood mononuclear cell (PBMC) compared to the control group. Besides, in IBD patients, particularly those who are under anti-TNF-α treatment, the host innate immune system interferes more efficiently with viral replication cycle and the clinical presentations are more moderate (9, 12) . Are patients with inflammatory bowel disease at increased risk for Covid-19 infection? doi = 10.22074/cellj.2020.7603 id = cord-218639-ewkche9r author = Ghavasieh, Arsham title = Multiscale statistical physics of the Human-SARS-CoV-2 interactome date = 2020-08-21 keywords = PPI; SARS; network summary = Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing strategies. Similarly, they have been used for characterizing the interactions between viral and human proteins in case of SARS-CoV-2 [13] [14] [15] , providing insights into the structure and function of the virus 16 and identifying drug repurposing strategies 17, 18 . Instead, we model the propagation of perturbations from viral nodes through the whole system, using bio-chemical and regulatory dynamics, to obtain the spreading patterns and compare the average impact of viruses on human proteins. Our results shed light on the unexplored aspects of SARS-CoV-2, from the perspective of statistical physics of complex networks, and the presented framework opens the doors for further theoretical developments aiming to characterize structure and dynamics of virus-host interactions, as well as grounds for further experimental investigation and potentially novel clinical treatments. doi = nan id = cord-344012-npob20n0 author = Gheblawi, Mahmoud title = Angiotensin-Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System: Celebrating the 20th Anniversary of the Discovery of ACE2 date = 2020-05-08 keywords = ACE2; Ang; COVID-19; RAS; SARS; angiotensin summary = ACE2 (angiotensin-converting enzyme 2) has a multiplicity of physiological roles that revolve around its trivalent function: a negative regulator of the renin-angiotensin system, facilitator of amino acid transport, and the severe acute respiratory syndrome-coronavirus (SARS-CoV) and SARS-CoV-2 receptor. Our review summarizes the progress over the past 20 years, highlighting the critical role of ACE2 as the novel SARS-CoV-2 receptor and as the negative regulator of the renin-angiotensin system, together with implications for the coronavirus disease 2019 pandemic and associated cardiovascular diseases. 21, 22 Ongoing global efforts are focused on manipulating the ACE2/Ang 1-7 axis to curtail SARS-CoV-2 infection while affording maximal protective effects against lung and cardiovascular damage in patients with In this review, we summarize the diverse roles of ACE2, highlighting its role as the SARS-CoV-2 receptor and negative regulator of the RAS, and the implications for the COVID-19 pandemic. doi = 10.1161/circresaha.120.317015 id = cord-341000-9xs8aukq author = Ghiasvand, Fereshteh title = Symmetrical polyneuropathy in Coronavirus Disease 2019 (COVID-19) date = 2020-05-15 keywords = SARS; writing summary = The knowledge around the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still evolving with the cases increasing globally. A case series presented data of four Severe Acute Respiratory Syndrome (SARS) patients who developed polyneuropathy, myopathy, or both approximately three weeks after the onset of SARS with a probable diagnosis of critical-illness polyneuropathy (CIP) and/or critical-illness myopathy (CIM) [9] . A case of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported with developing weakness and numbness in lower limbs and inability to walk with a likely diagnosis of critical illness polyneuropathy (CIP) [10] . Since no symptoms were present before the development of COVID-19 and toxic neuropathy was excluded after a review of all her medications, critical illness polyneuropathy (CIP) and Guillain-Barré syndrome (GBS) were considered to be the J o u r n a l P r e -p r o o f most likely diagnosis. doi = 10.1016/j.idcr.2020.e00815 id = cord-287172-h8zoplkm author = Ghobrial, Moheb title = The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date = 2020-10-21 keywords = SARS summary = To understand the potential mechanisms underlying SARS-CoV-2 tropism for brain vasculature, we constructed a molecular atlas of the expression patterns of SARS-CoV-2 viral entry-associated genes (receptors and proteases) and SARS-CoV-2 interaction partners in human (and mouse) adult and fetal brain as well as in multiple non-CNS tissues in single-cell RNA-sequencing data across various datasets. Notably, the top regulated pathways included inflammation, angiogenesis, coagulation, cell-extracellular matrix interaction, viral-host interaction, vascular metabolism, blood-brain-barrier permeability, and reactive oxygen species (ROS) in both the adult and the fetal brain endothelium ( Together, these data reveal that CTSB is highly expressed in various endothelial cell clusters of the fetal and adult human brain and that pathways downstream of CTSB might provide a suggestive explanation of some of the neurovascular symptoms observed in COVID-19 doi = 10.1101/2020.10.10.334664 id = cord-310230-9wfb43gt author = Ghorbani, Mahdi title = Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date = 2020-06-27 keywords = ACE2; RBD; SARS summary = Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. 7 Based on the sequence similarity between RBD of nCOV-2019 and SARS-COV and also the tight binding between RBD of nCOV-2019 and ACE2, it is most probable that nCOV-2019 uses this receptor on human cells to gain entry into the body. The focus of this article is to elucidate the differences between the interface of SARS-COV and nCOV-2019 with ACE2 to understand with atomic resolution the interaction mechanism and hotspot residues at the RBD/ACE2 interface using long-timescale molecular dynamics (MD) simulation. The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019 and all its mutant complexes were investigated by the MMPBSA method. Computational Simulations Reveal the Binding Dynamics between Human ACE2 and the Receptor Binding Domain of SARS-CoV-2 Spike Protein doi = 10.1101/2020.06.27.175448 id = cord-344064-l3u4l3se author = Ghosh, Rajesh title = Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves date = 2020-11-03 keywords = Mpro; SARS; figure summary = Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. The leaves of the traditional medicinal plant Torreya nucifera contains eight well-known diterpenoids (18-hydroxyferruginol, hinokiol, ferruginol, 18-oxoferruginol, O-acetyl-18hydroxyferruginol, methyl dehydroabietate, isopimaric acid, kayadiol) and four biflavonoids (amentoflavone, bilobetin, ginkgetin, sciadopitysin) ( Figure 1 ) (Ryu et al., 2010) . Overall, molecular docking studies clearly revealed that selected three biflavonoids (amentoflavone, bilobetin and ginkgetin) interacted with two key residues (His41 and Cys145) of Mpro via alkyl bond(s) interactions ( Figure 2 ). Overall, this study showed that three important biflavonoids of Torreya nucifera leaves (amentoflavone, bilobetin and ginkgetin) can act as SARS CoV-2 Mpro inhibitors. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study doi = 10.1080/07391102.2020.1841680 id = cord-315388-8sv00zqz author = Ghosh, Ritwik title = Famotidine against SARS-CoV2: A hope or hype? date = 2020-06-06 keywords = SARS; famotidine summary = In the absence of a specific anti-viral or vaccine against the novel severe acute respiratory syndrome-corona virus (SARS-CoV2), "repurposing" of old time-tested medications are being tried. Through binding with H 2 R and modulating the effector pathways mediated by protein kinase A (PKA), famotidine potentially regulates innate and adaptive immune responses. Comparison of immunomodulative effects of the histamine-2 receptor antagonists cimetidine, ranitidine, and famotidine on peripheral blood mononuclear cells in gastric cancer patients Histamine Receptor 2 is Required to Suppress Innate Immune Responses to Bacterial Ligands in Patients with Inflammatory Bowel Disease The effect of histamine type 2 receptor antagonists on human immunodeficiency virus (HIV) replication: identification of a new class of antiviral agents A placebocontrolled trial of ranitidine in patients with early human immunodeficiency virus infection Effects of the H2-receptor antagonist famotidine on the pharmacokinetics of atazanavir-ritonavir with or without tenofovir in HIV-infected patients doi = 10.1016/j.mayocp.2020.05.027 id = cord-347104-h168kqjn author = Ghosh, Ritwik title = A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection date = 2020-11-11 keywords = COVID-19; NMOSD; SARS summary = title: A case of area postrema variant of neuromyelitis optica spectrum disorder following SARS-CoV-2 infection J o u r n a l P r e -p r o o f It has recently reported a case of a young man presenting with bilateral severe optic neuritis and myelitis, determined to be simultaneously SARS-CoV-2 and MOG IgG antibody positive, i.e. a variant of NMOSD. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. We herein report a novel case of a previously healthy man who presented with a clinical picture of bouts of vomiting and hiccoughs (area postrema syndrome), which rapidly evolved to acute LETM, all following SARS-CoV-2 infection. doi = 10.1016/j.jneuroim.2020.577439 id = cord-336561-llwjsds8 author = Ghosh, Sanhita title = siRNA could be a potential therapy for COVID-19 date = 2020-04-22 keywords = SARS summary = Thus, the sequence coding for nsp5 can be treated as a potential target for RNAi using siRNA based therapeutics. Further, Alnylam Pharmaceuticals (USA) has designed and synthesized over 350 siRNA targeting highly conserved regions of the available SARS-CoV-2 genome (Hodgson, 2020) . In this context, Conti and co-researchers have demonstrated an in vitro testing of poly (amidoamine) dendrimer nanocarriers for the potential aerosol-based delivery system of siRNA onto lung epithelial cells (Conti et al., 2014) . Thus, for the treatment of COVID-19 siRNA based therapy can be developed against the novel coronavirus SARS-CoV-2, where siRNAs can hit the highly conserved region of SARS-CoV-2 RNA and also can act as an inhibitor to suppress the genetic disorders of the lungs. The cytopathic effect (CPE) was observed in Vero cells when it was infected with SARS and reduced the CPE after siRNA treatment. Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases doi = 10.17179/excli2020-1328 id = cord-304584-jxha3rz8 author = Giacomo, Di title = SARS-COV-2 infection in cancer patients undergoing checkpoint blockade: clinical course and outcome date = 2020-05-03 keywords = SARS summary = The potential interplay between Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) infection and treatment with immune-checkpoint inhibitors (ICI) of cancer patients is presently unknown. Two subsequent swabs tested negative on April 3 and 4 for SARS-CoV-2 infection ( Figure 1) ; thus, the patient was considered cured from COVID-19 and she will resume ICI-therapy shortly. Undoubtedly, no general conclusion can be drawn from the positive outcome of these two patients on the reciprocal interplay between ICI therapy and SARS-CoV-2 infection. Nevertheless, these findings seem to suggest that treatment with ICI is a doable approach during the COVID-19 pandemic, and that SARS-CoV-2 infection does not seem to represent an obstacle to grant cancer patients the best treatment according to their clinical setting. SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerasechain-reaction (rRT-PCR) testing positive (★) or negative (✪). SARS-CoV-2 infection was assessed by real-time-reverse-transcriptase-polymerase-chainreaction (rRT-PCR) testing positive (★) or negative (✪). doi = 10.1016/j.ejca.2020.04.026 id = cord-339436-0k73tlna author = Giagulli, Vito Angelo title = Worse progression of COVID‐19 in men: Is Testosterone a key factor? date = 2020-06-11 keywords = COVID-19; SARS; man; patient summary = Considering that low serum T levels induce detrimental effects on cardiovascular system and predispose to impaired immune response, endothelial dysfunction and systemic inflammation, respectively 28 , herein, we will overview on possible putative mechanisms by which circulating T might affect the prognosis in men with COVID-19 (Table 1) . All rights reserved adipose tissue dysfunction and male hypogonadism, even if subclinical, are associated with higher circulating levels of cytokine (IL-6, IL-1 and TNF-alpha), endothelial dysfunction 163 , and amplified thrombosis risk, possibly prompting to detrimental clinical consequences in case of SARS-CoV-2 infection. It may affect baseline respiratory function, thus increasing the risk of mechanical ventilation requirement once the infection occurred; increase the number of baseline comorbidities, consequently predisposing to poor prognosis or death as certificated by epidemiological studies; fosters hormonal imbalance (decline in circulating serum T and increase in serum estrogen concentration) which are involved in the fine regulation of immune system and coagulative homeostasis in case of infection, and predispose men to poor effective immune response, cytokine dysregulation; endothelial dysfunction and thrombosis. doi = 10.1111/andr.12836 id = cord-329825-e9mepqvn author = Giamarellos-Bourboulis, Evangelos J. title = Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date = 2020-04-21 keywords = HLA; SARS summary = Immune responses of critically ill patients with sepsis can be classified into three patterns: macrophage-activation syndrome (MAS) (Kyriazopoulou et al., 2017) , sepsis-induced immunoparalysis characterized by low expression of the human leukocyte antigen D related (HLA-DR) on CD14 monocytes (Lukaszewicz et al., 2009) , and an intermediate functional state of the immune system lacking obvious dysregulation. Abbreviations are as follows: ALT, alanine aminotransferase; aPTT, activated partial thromboplastin time; AST, aspartate aminotransferase; APACHE, acute physiology and chronic health evaluation; CCI, Charlson''s comorbidity index; INR, international normalized ratio; PSI, pneumonia severity index; SD, standard deviation; SOFA, sequential organ failure assessment Immune classification of patients with SARS-CoV-2 was performed by using the tools suggested for bacterial sepsis, i.e., ferritin more than 4,420 ng/mL for MAS (Kyriazopoulou et al., 2017) , and HLA-DR molecules on CD14 monocytes lower than 5,000, in the absence of elevated ferritin, for the immune dysregulation phenotype (Lukaszewicz et al., 2009) . doi = 10.1016/j.chom.2020.04.009 id = cord-269726-z0frgm7s author = Gidari, Anna title = Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date = 2020-10-10 keywords = COVID-19; PCR; RNA; SARS summary = Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . doi = 10.1007/s10096-020-04057-6 id = cord-311848-8n9ee57a author = Giesen, Nicola title = Evidence-based Management of COVID-19 in Cancer Patients – Guideline by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) date = 2020-09-21 keywords = AII; COVID-19; CoV-2; SARS; cancer; patient summary = It was prepared by the Infectious Diseases Working Party (AGIHO) of the German Society for Haematology and Medical Oncology (DGHO) by critically reviewing the currently available data on SARS-CoV-2 and COVID-19 in cancer patients applying evidence-based medicine criteria. We do not 285 recommend to delay/discontinue radiotherapy, targeted therapy, endocrine therapy or surgery in 286 cancer patients without suspected/confirmed SARS-CoV-2 infection (DII u ) as no impact on mortality 287 of such prior treatments was seen in several large cohort studies of 20, 31, 40, 94 288 In patients with COVID-19, it is strongly recommended to delay/discontinue chemotherapy, if 289 possible, as chemotherapy within two weeks of admission was a major risk factor for severe COVID-290 19 in a large Chinese cohort study (AII u ). Clinical characteristics and risk factors 38 associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multicentre, 39 retrospective, cohort study doi = 10.1016/j.ejca.2020.09.009 id = cord-334278-ajdjfzd2 author = Gilis, M. title = Caractéristiques de la COVID-19 chez les patients âgés de 75 ans et plus, hospitalisés date = 2020-09-30 keywords = COVID; SARS summary = Matériels et méthodes Il s''agit d''une étude prospective observationnelle descriptive monocentrique incluant tous les patients hospitalisés, initialement hors réanimation, avec une COVID-19 confirmée par RT-PCR et/ou par imagerie scanographique entre le 3 mars et le 24 avril 2020. Conclusion Sur la période de mars 2020 alors que l''épidémie de SARS-CoV-2 a touché la France de plein fouet, les virus respiratoires classiques ont rapidement disparu tandis que la COVID-19 touchait plus du tiers des personnes consultant pour un syndrome grippal dans un centre de dépistage hospitalier francilien. Matériels et méthodes Dans notre hôpital, les soignants symptomatiques étaient systématiquement testés par une RT-PCR SARS-CoV2 sur frottis rhinopharyngé. Les soignants COVID avaient été plus souvent en contact avec un cas confirmé d''infection à SARS-CoV-2 (75 % vs 63 %, p < 0,001) mais n''étaient pas plus souvent affectés dans les unités COVID (16 % vs 12 %, p = 0,17). doi = 10.1016/j.medmal.2020.06.131 id = cord-334735-up81jotp author = Gillissen, Adrian title = Das schwere akute Atemwegssyndrom (SARS) date = 2003 keywords = SARS; severe summary = Severe acute respiratory syndrome (SARS) is a viral disease, observed primarily in Southern China in November 2002, with variable flu-like symptoms and pneumonia, in approx. Weitere Fälle wurden aus Vietnam, Singapur und den USA (hier mation about a new syndrome by the end of February 2003, after the first cases outside the Republic of China had been observed. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong Identification of a novel coronavirus in patients with severe acute respiratory syndrome Guideline on management of severe acute respiratory syndrome (SARS) A novel coronavirus associated with severe acute respiratory syndrome SARS: imaging of severe acute respiratory syndrome Coronavirus as possible cause of severe acute respiratory syndrome A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS): infection control Dieses Prinzip ist bei den Neuraminidaseinhibitoren zur Therapie der Influenza bekannt und klinisch umgesetzt [7, 9, 21] . doi = 10.1007/s00063-003-1271-z id = cord-296981-tded20ih author = Gilmore, Kerry title = In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date = 2020-10-05 keywords = SARS; figure summary = We report in vitro efficacy of Artemisia annua extracts as well as artemisinin, artesunate, and artemether against SARS-CoV-2. Subsequent concentration-response studies using a high-throughput antiviral assay, based on immunostaining of SARS-CoV-2 spike glycoprotein, revealed that pretreatment and treatment with extracts, artemisinin, and artesunate inhibited SARS-CoV-2 infection of VeroE6 cells. The selectivity index (SI), calculated based on treatment and cell viability assays, was highest for artemisinin (54), and roughly equal for the extracts (5-10), artesunate (6) and artemether (<7). annua extracts, as well as pure artemisinin, artesunate, and artemether are active against SARS-CoV-2 in vitro. To initially screen whether extracts and pure artemisinin were active against SARS-CoV-2, their antiviral activity was tested by pretreating VeroE6 cells at different time points during 120 minutes with selected concentrations of the extracts or compounds prior to infection with the first European SARS-CoV-2 isolated in München (SARS-CoV-2/human/Germany/BavPat 1/2020). doi = 10.1101/2020.10.05.326637 id = cord-267115-6jqdi417 author = Giobbe, Giovanni Giuseppe title = SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date = 2020-06-24 keywords = CoV-2; Fig; PCW; RNA; SARS; infection summary = Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . doi = 10.1101/2020.06.24.167049 id = cord-291176-evb6yt0r author = Giorgi Rossi, Paolo title = Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date = 2020-08-27 keywords = SARS; covid-19; patient summary = In this report, based on the cohort of all residents in the province of Reggio Emilia who were SARS-CoV-2-positive at nasal and pharyngeal swab and with symptoms (COVID-19 cases) since the inception of the epidemic, we describe patient characteristics and explore their role as putative prognostic factors in predicting the occurrence of hospital admission or death. We considered the following patient characteristics: age, sex, place of birth (Italy or abroad), time span (in days) from symptom onset to diagnosis/ hospitalization, and comorbidities, whose prognostic role was explored both singly (chronic obstructive pulmonary disease, arrhythmia, diabetes, coronary heart disease, heart failure, vascular diseases, obesity) and by computing the Charlson Comorbidity Index, which provides an overall measure of an individual patient''s complexity [12] . While in this study we focused on the risk of hospitalization and death in a cohort of COVID-19 patients diagnosed during the epidemic in Northern Italy, it also provided us with the opportunity to describe the pattern of distribution of the disease in the whole population. doi = 10.1371/journal.pone.0238281 id = cord-269071-jbxbknyt author = Giorgianni, Andrea title = Transient acute-onset tetraparesis in a COVID-19 patient date = 2020-06-02 keywords = SARS summary = Since the main organic, infectious, and immunomediated causes of acute-onset flaccid tetraparesis have been excluded from the anamnestic, neuroradiological, and laboratory data recorded, we can hypothesize that SARS-CoV-2 had a promoter role in the onset of the tetraparetic clinical presentation. A first-reported case of postinfective acute transverse myelitis has been described in the literature [2] , suggesting that spinal cord can be the target of SARS-CoV-2 infection. Therefore, we can deduce that the neuro-shocking and neuro-irritative effect of SARS-CoV-2, in addition to hyperglycemic neuro-stress, can have a promoting and synergistic role in the manifestation of the tetraparetic transient acute clinic. As described in this case, the neuroinvasive and neurotrophic potential of SARS-CoV-2 could have a synergistic and promoter role in determining neuro-irritative and neuro-shocking effects, without necessarily causing neuroimaging evident organic damage. Acute myelitis after SARS-CoV-2 infection: a case report doi = 10.1038/s41393-020-0493-8 id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 keywords = Bat; Human; RNA; SARS; Supplementary; Table; figure; protein summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . doi = 10.1101/2020.03.13.990598 id = cord-311523-erntrh3p author = Gisondi, P title = Dermatologists and SARS‐CoV‐2: The impact of the pandemic on daily practice date = 2020-04-22 keywords = COVID-19; Italy; SARS summary = Since the first case of "pneumonia of unknown aetiology" was diagnosed at the Wuhan Jinyintan Hospital in China on 30 December 2019, what was recognised thereafter as "severe acute respiratory syndrome coronavirus 2" (SARS‐CoV‐2) has spread over the four continents, causing the respiratory manifestations of Coronavirus disease‐19 (COVID‐ 19) and satisfying the epidemiological criteria for a label of "pandemic." The ongoing SARS‐CoV‐2 pandemic is having a huge impact on dermatological practice including the marked reduction of face‐to‐face consultations in favour of teledermatology, the uncertainties concerning the outcome of COVID‐19 infection in patients with common inflammatory disorders such as psoriasis or atopic dermatitis receiving immunosuppressive/immunomodulating systemic therapies; the direct involvement of dermatologists in COVID‐19 care for patients assistance and new research needs to be addressed. doi = 10.1111/jdv.16515 id = cord-287220-mpnuhqwg author = Giuliani, C. title = Breastfeeding during the COVID-19 pandemic: suggestions on behalf of Woman Study Group of AMD date = 2020-05-30 keywords = COVID-19; SARS; mother summary = Woman Study Group of AMD, after reviewing current knowledge about COVID-19 vertical transmission and the compatibility of breastfeeding in COVID-19 mother, the available recommendations from Health Care Organizations and main experts opinions, issued the following suggestions on breastfeeding during the COVID-19 pandemic, addressed both to mothers with and without diabetes It should be considered that following suggestions may change in the future when more evidence is acquired regarding SARS-Cov2 infection. Chen Y et al 5 reported four cases of live born infants, born to pregnant women with the COVID-19 infection in Wuhan: newborns had no clinical signs of disease and were tested negative for the virus at delivery. 14 Moreover, some experts speculate that, similar to the 2002-2003 SARS-Co-V epidemic 15 , specific SARS-CoV-2 antibodies pass via the breast milk from the COVID-19 mother to the infant within a few days after the onset of the disease, possibly moderating the clinical expression of infant''s infection 16 . doi = 10.1016/j.diabres.2020.108239 id = cord-282043-cs1oyohu author = Giustino, Gennaro title = Coronavirus and Cardiovascular Disease, Myocardial Injury, and Arrhythmia: JACC Focus Seminar date = 2020-10-27 keywords = COVID-19; SARS; patient summary = Both direct viral infection and indirect injury resulting from inflammation, endothelial activation, and microvascular thrombosis occur in the context of coronavirus disease 2019. Although originally believed to be a syndrome characterized by acute lung injury, respiratory failure, and death, it is now apparent that severe coronavirus disease 2019 (COVID-19) is further characterized by exuberant cytokinemia, with resultant endothelial inflammation, microvascular thrombosis, and multiorgan failure (2) . Myocardial injury can be detected in w25% of hospitalized patients with COVID-19 and is associated with an increased risk of mortality. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Acute myocardial injury in patients hospitalized with COVID-19 infection: a review Characteristics and clinical significance of myocardial injury in patients with severe coronavirus disease 2019 doi = 10.1016/j.jacc.2020.08.059 id = cord-340984-blkhfhe2 author = Gklinos, Panagiotis title = Neurological manifestations of COVID-19: a review of what we know so far date = 2020-05-26 keywords = COVID-19; SARS; patient summary = Prompt diagnosis and immediate management of the neurological manifestations of the novel coronavirus will not only improve the prognosis of COVID-19 patients but will also prevent the dissemination of the disease due to misdiagnosed cases. COVID-19 is confirmed to be caused by a novel coronavirus (2019 novel coronavirus, 2019-nCoV) and presents with symptoms similar to those of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. However, neurological manifestations of the novel coronavirus are not precepted by all clinicians, thus, leading to inappropriate management of COVID-19 patients presenting with non-specific neurological symptoms initially. This article aims to review the cases, which reported neurological symptoms at presentation or during the course of the disease and discuss the potential mechanisms of Central Nervous System (CNS) involvement in COVID-19. The other study is a retrospective case series in Wuhan, China, which reported the neurological symptoms of COVID-19 patients [13] . doi = 10.1007/s00415-020-09939-5 id = cord-326254-8dlxsf57 author = Glasbey, T. title = Flawed disinfectant recommendations during a pandemic date = 2020-06-15 keywords = SARS summary = We are deeply concerned over the recommendations in the paper by Kampf [1] recently published in this journal as to what disinfectants are appropriate for use with respect to surface disinfection in the setting of the current Coronavirus pandemic. In that recent paper [1] , the author also suggests that the use of disinfectants containing benzalkonium chloride may be problematic as ''data obtained with benzalkonium chloride at reasonable contact times were conflicting. of Kampf are also diametrically opposed to the United States EPA recommendations for suitable disinfectant products given on their List N: ''Products with Emerging Viral Pathogens and Human Coronavirus claims for use against SARS-CoV-2'' [5] . Here, any disinfectant recommended for use against SARS-CoV-2 is required to be included the Australian Register of Therapeutic Goods (ARTG), and the manufacturer or product sponsor is required to hold suitable efficacy data against either the SARS-CoV-2 virus or recognised surrogate [8] . doi = 10.1016/j.infpip.2020.100070 id = cord-279861-gk8cow8k author = Glasser, John W. title = Modeling and public health emergency responses: Lessons from SARS date = 2011-01-28 keywords = SARS; Singapore summary = By overestimating the potential of managing contacts versus cases, moreover, we may even have inadvertently contributed to a lingering misunderstanding of means by which this epidemic was controlled that will affect their future responses to newly-emerging infectious diseases. Given the assumptions outlined above, together with a gamma distribution, these results suggest that for a disease with ℜ 0 = 3, isolation that was 100% effective in blocking transmission could prevent ℜ 0 − 1 infections (and thus lead to epidemic control) if implemented up to 5.2 days after symptom onset, on average (Fig. 1) . Knowledgeable public health practitioners might have cautioned against overestimating the potential impact of managing contacts of SARS patients, and interpreted observations suggesting that infected people were not particularly infectious until acutely ill as an indication for managing cases instead. doi = 10.1016/j.epidem.2011.01.001 id = cord-345356-gn1iwis0 author = Glebov, Oleg O. title = Understanding SARS‐CoV‐2 endocytosis for COVID‐19 drug repurposing date = 2020-06-02 keywords = COVID-19; CoV-2; SARS; cell summary = Given that most viruses use endocytosis to enter the host cell, mechanistic investigation of SARS‐CoV‐2 infection needs to consider the diversity of endocytic pathways available for SARS‐CoV‐2 entry in the human lung epithelium. Taken together, the above evidence suggests that SARS-CoV-2 may employ distinct endocytic pathways for cell entry in the upper and lower respiratory tract (Fig. 1) . This approach would allow tracking of the virus in relation to other endocytic pathways and also to investigate the effect of viral infection on the general membrane trafficking network of the host cell. Taken together, the combination of adequate cell models with the newly developed SARS-CoV-2 toolkit and established tools of membrane trafficking research is well-poised to deliver a key insight into the mechanisms underlying COVID-19 infection. Furthermore, considering that various viruses may use the same endocytic pathways of the host cell [15] , targeting viral entry at the point of endocytosis holds a more general promise for the development of broad-spectrum antiviral drugs [51] . doi = 10.1111/febs.15369 id = cord-272956-0yumc7em author = Gnavi, Roberto title = Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-05-22 keywords = SARS; case summary = Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. doi = 10.1093/cid/ciaa634 id = cord-354733-qxivrhj8 author = Gniazdowski, V. title = Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date = 2020-08-06 keywords = PCR; RNA; SARS summary = Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. doi = 10.1101/2020.08.05.20168963 id = cord-346670-34wfy52f author = Gobeil, Sophie M-C. title = D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date = 2020-10-12 keywords = RBD; SARS; d614 summary = Most structures of the SARS-CoV-2 S ectodomain currently available include two mutations, one to disrupt the furin cleavage site (RRAR to GSAS = S-GSAS), and a double proline mutation (PP) of residues 986-987, designed to prevent conformational change to the post-fusion state (Wrapp et al., 2020) . While the SARS-CoV-2 S ectodomain construct that includes mutations of residues K986 and V987, between the HR1 and CH subdomains (S2 domain), to prolines (PP) (named S-GSAS/PP in this study) (Figure 1 ) is widely used in the field, the origin of this PP construct was based upon the stabilization of the pre-fusion conformation of other coronavirus spikes (Pallesen et al., 2017; Walls et al., 2020; Wrapp et al., 2020) . Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 b sheet ( Figure 7C, S8B) . doi = 10.1101/2020.10.11.335299 id = cord-286290-85l99l13 author = Goddard, N.L. title = Lessons learned from SARS: The experience of the Health Protection Agency, England date = 2005-11-16 keywords = HPA; SARS summary = Lessons learned from mounting a UK response to SARS included: the importance of international collaboration; formation of a UK-wide, multidisciplinary Task Force; flexible case reporting mechanisms; integration of surveillance and laboratory data; generation of prompt and web-accessible guidance and advice; availability of surge capacity; and contingency planning. The global response to SARS provided new opportunities for the UK to collaborate with WHO (Geneva and Western Pacific Region), a number of public health organisations in south east Asia, as well as national public health centres such as the Centers for Disease Control and Prevention in the USA and Health Canada. Surveillance arrangements were revised during the outbreak to encourage initial alerting to HPA Regional Offices and ensure that local public health authorities were aware of the potential cases. 3. Flexible case reporting mechanisms need to be implemented at central, regional and local level during an evolving outbreak to inform appropriate public health measures. doi = 10.1016/j.puhe.2005.10.003 id = cord-264057-z5arb1k5 author = Goel, S. title = Preparations and limitations for prevention of severe acute respiratory syndrome in a tertiary care centre of India date = 2007-05-18 keywords = EMOPD; SARS summary = This short-term observational study of infection control practice was performed in the medical emergency outpatient department (EMOPD) of a tertiary-care hospital in India when threatened by an outbreak of severe acute respiratory syndrome (SARS). Infection control measures such as fumigation and cleaning were noted, as was the EMOPD laboratory function, use of personnel protection and display of information on infectious diseases. The EMOPDs in key hospitals need be able to screen for infectious diseases, especially in view of the threats from SARS and Avian influenza. The need to screen all patients with suspected infectious disease in the medical emergency outpatient department (EMOPD), and for control and prevention of infection, was recognized. In addition, the patient/attendant load, patient flow, and medical staff practice were observed, and information displayed on SARS or other infectious diseases was noted. doi = 10.1016/j.jhin.2007.02.015 id = cord-308857-otsrexqu author = Goel, Saurav title = Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date = 2020-05-28 keywords = COVID-19; CoV-2; SARS; coronavirus; figure; human; mask; surface; virus summary = This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. doi = 10.1016/j.mtchem.2020.100300 id = cord-332592-bfqsyiyf author = Goette, Andreas title = COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation date = 2020-09-26 keywords = ARDS; COVID-19; SARS summary = title: COVID-19-Induced Cytokine Release Syndrome Associated with Pulmonary Vein Thromboses, Atrial Cardiomyopathy, and Arterial Intima Inflammation Coronavirus disease 2019 (COVID-19) is a viral disease induced by severe acute respiratory syndrome–coronavirus-2 (SARS-CoV-2), which may cause an acute respiratory distress syndrome (ARDS). Here, we can present a case of cytokine release syndrome induced by SARS-CoV-2 causing multiorgan failure and death. In summary, the present case shows that severe COVID-19 induces CRS associated with ARDS, acute kidney failure, liver pathologies, vascular intimal inflammation, pulmonary arterial, and venous thromboses and an inflammatory atrial cardiomyopathy. In the present case, we can show that COVID-19 can induce the occurrences of ARDS, which was associated with pulmonary embolism, as well as thrombogenesis, in pulmonary veins and the right atrial appendage. In addition to COVID-19-induced ARDS, CRS might be associated with pulmonary artery, as well as vein thromboses, atrial fibrillation, sinus node dysfunction, right atrial clot formation, and inflammatory invasion of autonomic atrial nerve ganglia. doi = 10.1055/s-0040-1716717 id = cord-278182-75u57fw1 author = Goh, Gerard Kian-Meng title = Shell disorder analysis predicts greater resilience of the SARS-CoV-2 (COVID-19) outside the body and in body fluids date = 2020-03-31 keywords = MERS; SARS summary = A model to classify and predict the levels of respective respiratory and fecal-oral transmission potentials of the various viruses was built before the outbreak of MERS-CoV using AI and empirically-based molecular tools to predict the disorder level of proteins. Using the percentages of intrinsic disorder (PID) of the nucleocapsid (N) and membrane (M) proteins of CoV, the model easily clustered the viruses into three groups with the SARS-CoV (M PID = 8%, N PID = 50%) falling into Category B, in which viruses have intermediate levels of both respiratory and fecal-oral transmission potentials. In 2011-2012, just before the outbreak of the Middle Eastern Respiratory Syndrome (MERS-CoV), we built an empirically-based model that measures the percentage of intrinsic disorder (PID) of the membrane (M) and nucleocapsid (N) proteins in viruses [5, 6] . doi = 10.1016/j.micpath.2020.104177 id = cord-332539-v1bfm57x author = Gohl, Daryl M. title = A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date = 2020-05-11 keywords = ARTIC; PCR; SARS summary = Several variants of the ARTIC protocol exist in which the pooled SARS-CoV-2 amplicons from a sample are taken through a NGS library preparation protocol (using either ligation or tagmentation-based approaches) in which sample-specific barcodes are added, and are then sequenced using either short-read (Illumina) or long-read (Oxford Nanopore, PacBio) technologies. We sequenced these samples using Illumina''s Nextera DNA Flex Enrichment protocol using a respiratory virus oligo panel containing probes for SARS-CoV-2, the ARTIC v3 tiled primers, and a novel tailed amplicon method designed to reduce cost and streamline the preparation of SARS-CoV-2 sequencing libraries. For the Illumina DNA Flex Enrichment protocol, SARS-CoV-2 genome coverage was more complete for samples with lower N1 and N2 Cts (ranging from ~20-30) at comparable read depths and coverage thresholds than with amplicon approaches, similar to the BEI WA isolate data ( Figure 3C , Supplemental Figure S2 -S3). doi = 10.1101/2020.05.11.088724 id = cord-317820-od9l7p1r author = Goker Bagca, Bakiye title = Overview of the COVID-19 and JAK/STAT Pathway Inhibition: Ruxolitinib Perspective date = 2020-06-20 keywords = JAK; SARS; covid-19; stat summary = The virus, which is the cause of the COVID-19 was named as Severe Acute Respiratory Syndromerelated Coronavirus (SARS-CoV-2) by Coronaviridae Study Group of the International Committee on Taxonomy of Viruses (Figure 1a) . As an expected result of SARS-CoV-2 infection, it was reported cytokine storm syndrome triggered by the dysregulated immunity in numerous patients. There are clinical studies including baricitinib, tofacitinib, and ruxolitinib JAK inhibitors against cytokine storm caused by COVID-19. It is reported that tocilizumab which is an approved IL6 receptor antagonist, treatment reduced cytokine release syndrome symptoms in severe patients COVID-19 [66] . It is reported that the usage of ruxolitinib suppresses cytokine levels and JAK/STAT pathway in Epstein-Barr Virus (EBV) -associated hemophagocytic lymphohistiocytosis [71] . In this context, it is clear that ruxolitinib, which is used especially in older age patients, has an important potential in overcoming complications that are caused by over activation of the immune system which is triggered through JAK/STAT signaling pathway. doi = 10.1016/j.cytogfr.2020.06.013 id = cord-296676-2anl2agl author = Goldberg, Michael F. title = Neuroradiologic manifestations of COVID-19: what the emergency radiologist needs to know date = 2020-08-21 keywords = COVID-19; SARS; patient summary = Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global pandemic with a wide spectrum of clinical signs and symptoms. These neurologic manifestations were more common in severely affected patients, tended to occur early in the disease course, and could be the initial, presenting clinical evidence of COVID-19 [4] . Lastly, the authors note that ECMO alone (in the absence of SARS-CoV-2 infection) is a risk factor for intracranial hemorrhage, further limiting the generalizability of this small case series. Regardless, prior studies that evaluated neuroimaging findings of patients infected with other members of the Betacoronavirus genus have also demonstrated significant abnormalities, including intracranial hemorrhage and evidence of acute disseminated encephalomyelitis (ADEM), which could represent sequelae of inflammatory response and/or direct CNS infection [50, 51] . On behalf of the CoCo Neurosciences study group (2020) Retrospective observational study of brain magnetic resonance imaging findings in patients with acute SARS-CoV-2 infection and neurological manifestations doi = 10.1007/s10140-020-01840-y id = cord-351011-v4zmksio author = Golden, Joseph W. title = Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date = 2020-07-09 keywords = CoV-2; Fig; SARS; mouse summary = In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. In comparison with the normal lung architecture in uninfected control animals, infected mice necropsied on day 3, and those succumbing to disease on days 5-11, had varying levels of lung injury including area of lung consolidation characterized by inflammation/expansion of 145 alveolar septa with fibrin, edema and mononuclear leukocytes and infiltration of vessel walls by numerous mononuclear leukocytes (Fig 3A, Fig S4, and Table S1 ). Importantly, in our study some animals at the lower dose survived infection despite significant Infection of K18-hACE2 mice by SARS-CoV-2 produces a disease similar to that observed in acute human cases, with development of an acute lung injury associated with edema, production 285 of inflammatory cytokines and the accumulation of mononuclear cells in the lung. doi = 10.1101/2020.07.09.195230 id = cord-308800-b8gtwdxc author = Goldhaber-Fiebert, Sara N. title = Low-flow Nasal Cannula and Potential Nosocomial Spread of COVID-19 date = 2020-05-18 keywords = SARS summary = 8 Even with single-occupancy rooms, healthcare providers could be exposed to or spread SARS-CoV-2 after touching contaminated surfaces surrounding unsuspected COVID-19 patients presenting for other reasons. Some institutions have begun covering low-flow nasal cannula, at least in certain contexts, 10 11 though discussions with peers across specialities and institutions suggest that practice is far from uniform and is often limited to known COVID-19 patients. 11 By a conservative estimate, if 10% of the occupants of the roughly one-million hospital beds in the US are on low-flow nasal cannula oxygen on any given day, that translates into 100,000 patients in US hospitals whose treatment may also be adding to nosocomial spread of SARS-CoV-2. With many governments currently encouraging everyone to wear cloth masks in public to decrease spread, our healthcare systems should likewise consider the potential risks from the constant blowing of uncovered, loose-fitting, low-flow nasal cannula oxygen. doi = 10.1016/j.bja.2020.05.011 id = cord-275521-dlp055z8 author = Goldman, Emanuel title = Exaggerated risk of transmission of COVID-19 by fomites date = 2020-07-03 keywords = SARS summary = A clinically significant risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission by fomites (inanimate surfaces or objects) has been assumed on the basis of studies that have little resemblance to real-life scenarios. The longest survival (6 days) of severe acute respiratory syndrome coronavirus (SARS-CoV) on surfaces was done by placing a very large initial virus titre sample (10⁷ infectious virus particles) on the surface being tested. 1 Another study that claimed survival of 4 days used a similarly large sample (10⁶ infectious virus particles) on the surface. 3 Yet another study found long survival (5 days) of human coronavirus 229E on surfaces with what I would still consider a substantially large viral load (10³ plaque-forming units) in a cell lysate. For example, in the studies that used a sample of 10⁷, 10⁶, and 10⁴ particles of infectious virus on a small surface area, 1-3 these concentrations are a lot higher than those in droplets in real-life situations, with the amount of virus actually deposited on surfaces likely to be several orders of magnitude smaller. doi = 10.1016/s1473-3099(20)30561-2 id = cord-255365-fog62qdu author = Goldstein, Neal D. title = On the importance of early testing even when imperfect in a pandemic such as COVID-19 date = 2020-08-03 keywords = COVID-19; SARS summary = bias in identified cases of SARS-CoV-2 infections will vary in the face of unknown data surrounding test sensitivity and specificity. The true prevalence of COVID-19 will vary in the tested population (e.g., whether a drive-thru public event, clinical referral, group home, etc.), therefore we allowed for a hypothetical range from 0% to 50%. When the true prevalence of COVID-19 infection is low, as at the start of a pandemic, there will be a greater number of false positives, even under excellent specificity. If we assume 25% prevalence of disease in the tested population, we could realistically anticipate between 0 and 75 false positive results, and between 0 and 100 false negative results per 1000 tests. Serosurveys employing antibody assays can thereby inform public health surveillance regarding the extent of the population who have been infected at any point with SARS-CoV-2, and track herd immunity thresholds. doi = 10.1016/j.gloepi.2020.100031 id = cord-281216-7t647fww author = Goldust, Mohamad title = Performing dermoscopy in the COVID‐19 pandemic date = 2020-05-05 keywords = SARS summary = A novel coronavirus (SARS-CoV-2) that has recently emerged from China in late 2019 has become a global pandemic. Recent data has suggested that SARS -COV2 can remain viable in aerosols for multiple hours. However, cross-infection is a significant concern with contact dermoscopy especially during a viral pandemic. to disinfect hands with 60-70% isopropyl alcohol, provide verbal consents, and wear surgical masks before entering procedure rooms. It is advisable to wear adequate eye protection (goggles or visor) considering that exposed mucous membranes and unprotected eyes can increase the risk of SARS-CoV2 transmission. 4 Mucous membrane dermoscopy should only be performed when the examination has fundamental significance for therapeutic decisions. Aerosol and Surface Stability of SARSCoV-2 as Compared with SARS-CoV-1 Identifying gram-positive cocci on dermatoscopes and smartphone adapters using MALDI-TOF MS: a cross-sectional study 2019-nCoV transmission through the ocular surface must not be ignored doi = 10.1111/dth.13506 id = cord-255325-tl5fm2yu author = Goletic, Teufik title = Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date = 2020-06-19 keywords = SARS summary = Objectives of this research were: To share obtained sequences of the complete genome of SARS-CoV-2 strains from clinical samples of BiH patients diagnosed with COVID-19, and To contribute to the understanding of the interaction of molecular and classical epidemiology findings of COVID 19 in BH and the whole region and give recommendations for the improvement of prevention and future measures. Livno and Banja Luka samples WGS was performed according to the ARTIC amplicon sequencing protocol for MinION for nCoV-2019, which uses two primer pools to generate the sequence, as described elsewhere [7] . The constructed phylogenetic tree in Figure 2 indicates probable multiple independent introduction events as reflected by clustering of each single BiH sequence in a separate cluster, highlighted with red (Livno, EPI_ISL_462753), green (Banja Luka, EPI_ISL_462990), blue (Sarajevo, EPI_ISL_467300) and purple (Tuzla, EPI_ISL_463893). doi = 10.1101/2020.06.19.160606 id = cord-314676-ndke9agh author = Gollapalli, Pavan title = Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 date = 2020-11-04 keywords = ACE2; RBD; S54; S55; SARS summary = title: Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain–human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2 The top hit molecules from this screening were then docked to the SARS-CoV-2 spike glycoprotein RBD-ACE2 interface, after which molecular dynamic simulations of the top scored compound and a reference ligand were performed to compare their binding affinities. To focus on the role of amino acid residues Asn501B and Tyr41A, we performed a docking simulation of the top 5 ligands at the interface of the spike glycoprotein RBD-hACE2 complex (amino acid residues were taken from PDBSum) by setting exhaustiveness to 100 (supplementary material, Table 7 and Figure 4) . The docking calculations at the spike glycoprotein RBD-hACE2 interface showed an even better binding energy and formation of H-bond interactions, and the detailed interaction analysis for the top 5 ligands is reported in Table 2 . doi = 10.1080/07391102.2020.1841681 id = cord-287628-lzqsh3jf author = Gomersall, Charles D. title = Transmission of SARS to healthcare workers. The experience of a Hong Kong ICU date = 2006-02-25 keywords = ICU; SARS summary = CONCLUSIONS: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff exposure times and a sub-standard physical environment. Conclusions: In an ICU in which infection control procedures are rigorously applied, the risk to staff of contracting SARS from patients is low, despite long staff If our protective measures were effective when fully developed and rigorously applied, then the logical con-clusion is that intensive care units should have strategies in place to prevent infection of healthcare workers; all staff should be fully aware of the procedures and be fully trained in the use of protective equipment. In summary, our data indicate that, with infection control measures, the risk to ICU healthcare workers of acquiring SARS is low, despite prolonged exposure to patients with SARS. doi = 10.1007/s00134-006-0081-1 id = cord-300046-orlga9qf author = Gomes da Silva, J. title = Health literacy of inland population in the mitigation phase 3.2. of COVID-19''s pandemic in Portugal - a descriptive cohort study date = 2020-05-14 keywords = COVID-19; Group; Risk; SARS summary = Globally, younger individuals, females, graduates and the Non-Risk Group presented higher relative frequencies of the correct answer along COVID-19''s Questionnaire. However, three exceptions were observed: the Undergraduate Group and the Risk-Group had a high relative frequency stating that COVID-19 has a cure and in mentioning "Social Isolation" as an important preventive measure to adopt when compared to the Graduate Group and the Non-Risk Group, respectively. Males have higher relative frequency in answering the correct number of SNS24 and in stating that children can get sick and transmit the infection by SARS-CoV-2 when compared to females ( Table 2 -Supplementary information). Nonparametric tests reveal a statistically significant association regarding variable "Age", "Gender" and "Risk Factor", with younger individuals, females and individuals from Risk-Group stating more often the correct answer. Nonparametric tests reveal a statistically significant association regarding variable "Gender" and "Risk Factor", with males and individuals from Non-Risk Group answering the correct number. doi = 10.1101/2020.05.11.20098061 id = cord-305742-wf6qxplf author = Gomez, Santiago A. title = Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date = 2020-09-28 keywords = SARS; rbd(s; virus summary = In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. doi = 10.1002/cbic.202000618 id = cord-273626-zy8qjaai author = Gong, Shu‐ran title = The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models date = 2018-07-28 keywords = East; MERS; SARS summary = This illness has been named Middle East respiratory syndrome and the pathogen (MERS-CoV) has been shown to be a type of coronavirus that is highly related to SARS-CoV. Another suitable and well-established model is the common marmoset (Saguinus mystax), which can show more severe clinical signs than rhesus macaques when infected with MERS-CoV. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Middle East Respiratory Syndrome Coronavirus (MERS-CoV) origin and animal reservoir Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques Studies of severe acute respiratory syndrome coronavirus pathology in human cases and animal models Infection, replication, and transmission of middle east respiratory syndrome Coronavirus in Alpacas doi = 10.1002/ame2.12017 id = cord-305266-fuaq4ujb author = Gong, Yue title = Early Research on COVID-19: A Bibliometric Analysis date = 2020-08-05 keywords = COVID-19; SARS; coronavirus summary = In this review, we found that because of the rapid response of researchers worldwide, the number of COVID-19-related publications showed a high growth trend in the first ten days of February; among these, the largest number of studies originated in China, the country most affected by pandemic in its early stages. The Coronavirus Study Group 4 (CSG) of the International Committee on Taxonomy of Viruses designated the causative 5 virus as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease, 6 which subsequently spread globally, was named coronavirus disease of 2019 7 COVID-19, covering topics such as etiology, diagnosis, epidemiology, treatment, 24 prognosis, nursing, prevention and control, were available in the PubMed and China 25 national knowledge infrastructure (CNKI) databases. Escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in Hong Kong doi = 10.1016/j.xinn.2020.100027 id = cord-259699-48jg7ci7 author = González-Calatayud, Dra Mariel title = Observational study of the suspected or confirmed cases of sars COV-2 infection needing emergency surgical intervention during the first months of the pandemic in a third level hospital: Case series date = 2020-10-24 keywords = COVID-19; SARS; patient summary = METHOD: We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial biomarkers (first five days of hospitalization), days of hospital stay, days in the Intensive Care Unit and reason for discharge. We conducted an observational study of patients undergoing surgical intervention in the operating room assigned as COVID, where we considered age, sex, treating department, type of intervention, and initial laboratory tests (first five days of hospitalization): ferritin, D-dimer, total leucocyte count, total lymphocyte count, lymphocytes (%), platelets, lactate dehydrogenase, fibrinogen, and procalcitonin; we also considered days of hospital stay (DOHS), days in the Intensive Care Unit (ICU), and reason for discharge. Indeed, it has been decided to reduce elective surgical treatment, we have also observed that patients undergoing emergency surgery with suspicion or confirmation of SARS-Cov-2 infection have significant mortality depending on the performed surgical procedure, without relevant findings regarding biomarkers. doi = 10.1016/j.amsu.2020.10.038 id = cord-338744-2kizbzns author = González-Castro, A. title = Síndrome post-cuidados intensivos después de la pandemia por SARS-CoV-2 date = 2020-04-27 keywords = SARS summary = El mundo está inmerso en una pandemia por SARS-CoV-2 que Q2 está llevando a los sistemas sanitarios al borde del colapso y a las unidades de cuidados intensivos a trabajar por encima de su capacidad. Dentro de este panorama general, los servicios de cuidados intensivos deben de estar alertados para identificar «la cola de la primera oleada», que englobará un síndrome post-cuidados intensivos (SPCI) de una gran magnitud y con características especiales. En circunstancias normales el SPCI afecta al 30-50% de nuestros pacientes 3 y sus secuelas pueden persistir incluso más allá de los 5 años tras el alta hospitalaria, especialmente en la recuperación del síndrome respiratorio agudo 4 . Si otras condiciones nos mostraron que hasta el 16% de los familiares no habían reducido el nivel de depresión al año del alta 5 ¿estaremos preparados para el SPCI-post Working experiences of nurses during the Middle East respiratory syndrome outbreak Functional disability 5 years after acute respiratory distress syndrome doi = 10.1016/j.medin.2020.04.011 id = cord-277357-lpurk7pe author = González-González, Everardo title = Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date = 2020-08-13 keywords = COVID-19; PCR; SARS summary = title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. doi = 10.1371/journal.pone.0237418 id = cord-314024-n6l2804j author = Gonçalves, Antonio title = Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date = 2020-04-07 keywords = SARS; viral summary = We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We 162 considered a simple case where the drug effectiveness is assumed to be constant after therapy 163 initiation (see methods) and we calculated the minimal efficacy that would be needed to 164 generate more than 2 logs of viral decline at peak viral load in the 13 studied patients (Fig. 1) . For a putative 167 treatment initiated at the time of infection, symptom onset, or 3 days post symptom onset, a 168 median efficacy of at least 60, 90 and 99% in reducing viral replication would be needed, 169 respectively, to generate more than 2 log of decline in the peak viral load (Fig. 1) . doi = 10.1101/2020.04.04.20047886 id = cord-304479-uxp1kg86 author = Goodarzi, Pedram title = Coronavirus disease 2019 (COVID-19): Immunological approaches and emerging pharmacologic treatments date = 2020-08-08 keywords = COVID-19; CoV-2; SARS; clinical; patient; treatment summary = Finally, recently, a case report study from Japan shows that orally inhaled ciclesonide alleviates the local inflammation in the lung of patients with COVID-19 pneumonia and inhibits the propagation of the virus by antiviral activity [60] . In the same way, a recent case-report study showed that the adoptive transfer therapy of human umbilical cord blood derived-mesenchymal stem cells (hUCMSCs) to a Chinese female patient afflicted with acute COVID19 syndromes improved her laboratory tests and CT images [69] . In vitro evidence of activity against SARS-CoV-2 in infected Vero E6 cells reported with high concentrations of the drug [104, 105, 142] FPV significantly improved the latency to relief for pyrexia and cough [99] FPV in patients with COVID-19 led to decrease of viral load and significant improvement in chest imaging compared with the control arm [98] doi = 10.1016/j.intimp.2020.106885 id = cord-288255-p8uzrsbd author = Goossens, Gijs H. title = Obesity and COVID-19: A Perspective from the European Association for the Study of Obesity on Immunological Perturbations, Therapeutic Challenges, and Opportunities in Obesity date = 2020-08-13 keywords = ACE2; COVID-19; SARS; obesity; patient summary = authors: Goossens, Gijs H.; Dicker, Dror; Farpour-Lambert, Nathalie J.; Frühbeck, Gema; Mullerova, Dana; Woodward, Euan; Holm, Jens-Christian Evidence from studies in humans indicates that people with obesity are characterized by systemic low-grade inflammation, higher susceptibility to infections, dampened immune response to infectious agents, as well as higher morbidity and mortality associated with infections, and demonstrate an impaired immune response to vaccinations and antimicrobial treatment [25] [26] [27] [28] . Together, these findings imply that evaluation of cytokine profiles and immune cell subsets in patients with SARS-CoV-2 infection, and a deeper understanding of the underlying processes, will significantly contribute to better treatment strategies and clinical management of COVID-19 [37] . At the same time, the rapidly emerging clinical data require ongoing scrutiny to understand not only the risks and benefits of single drugs to tackle COVID-19, but also the interaction with pharmacological agents commonly used in people with obesity and related NCDs, including type 2 diabetes and cardiovascular diseases, who are especially at risk of or hospitalized with SARS-CoV-2 infection. doi = 10.1159/000510719 id = cord-356090-oj3d9ail author = Gorgun, D. title = Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date = 2020-10-27 keywords = Fig; SARS; membrane summary = Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state. In this study, using a large set of simulations, we describe how the SARS-CoV2 FP binds mammalian cellular membranes and characterize, at atomic details, lipid-protein interactions important for the stability of the bound state. doi = 10.1101/2020.10.27.357350 id = cord-348748-rxyh58eu author = Gorospe, Luis title = COVID-19: Thoracic Diagnostic Interventional Procedures in Troubled Times() date = 2020-09-07 keywords = SARS; covid-19 summary = Some publications have addressed the clinical management of cancer patients in the current SARS-CoV-2 pandemic, but there are no specific guidelines for performing thoracic diagnostic interventional procedures in patients with tumors who are also infected with SARS-CoV-2. Because of this situation, most of the hospital''s clinical activity (like many other centers throughout the country) was focused on the treatment of Covid-19 patients, and large numbers of medical personnel (including pulmonologists, medical oncologists and radiation therapists, thoracic surgeons, pathologists, and radiologists) had been recruited from different departments of the center for the care and management of these patients. 15 Recent articles have reminded us how important it is for radiology departments to be prepared for COVID-19 (from the indication of chest X-rays or CT to the protection of their staff), 16 but there are no specific guidelines for performing diagnostic thoracic interventional procedures in patients with tumor lesions who are also infected with SARS-CoV-2. doi = 10.1016/j.arbr.2020.08.008 id = cord-331680-qlzhtxs0 author = Goryachev, A.N. title = Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date = 2020-11-03 keywords = RNA; SARS; Vero summary = In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. doi = 10.1101/2020.11.02.363598 id = cord-279563-4lu1n0s7 author = Gorzalski, Andrew J. title = High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date = 2020-06-10 keywords = PCR; SARS summary = The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). CONCLUSIONS: The higher analytical sensitivity may explain the assay''s ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. To assess differences in analytical sensitivity between real-time PCR and TMA, we performed a limit-ofdetection (LoD) study by creating a dilution series of purified / quantified SARS-CoV-2 genomic material either in VTM or APTIMA collection matrix. Noting the sensitivity difference demonstrated by the LoD study, we sought to assess the performance of TMA on specimens previously tested by RT-PCR for SARS-CoV-2. The Hologic Panther SARS-CoV-2 transcription mediated amplification test showed higher analytical sensitivity when compared to real time PCR for the detection of SARS-CoV-2. doi = 10.1016/j.jcv.2020.104501 id = cord-277260-7se220oz author = Gosain, Rohit title = COVID-19 and Cancer: a Comprehensive Review date = 2020-05-08 keywords = COVID-19; China; SARS; cancer; patient summary = Since the emergence of the first case in Wuhan, China, in December 2019, tremendous research efforts have been underway to understand the mechanisms of infectivity and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a fatal virus responsible for abysmal survival outcomes. Data from China thus far have shown that cancer patients infected with COVID-19 are at 3.5 times the risk of requiring mechanical ventilation or ICU admission, compared to the general population [9•] . The CALAVI trial will be initiated as a randomized global clinical trial to assess the potential of acalabrutinib in the treatment of the cytokine storm associated with severely ill COVID-19 patients [86] . An exploratory meta-analysis of 32 studies showed evidence of reduced mortality after receiving various doses of convalescent plasma in patients with severe acute respiratory infections of viral etiology [92] . Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China doi = 10.1007/s11912-020-00934-7 id = cord-287991-10jz1dz2 author = Goshen-Lago, Tal title = The Potential Role of Immune Alteration in the Cancer–COVID19 Equation—A Prospective Longitudinal Study date = 2020-08-26 keywords = COVID19; SARS; patient summary = Conclusion: Our results indicate a similar rate of asymptomatic COVID19 infection in cancer patients and healthcare workers in a longitudinal study throughout the pandemic time. During the study interval, there was no documented symptomatic case of COVID19 among the recruited participants, nor in the general patient population of the cancer center or in the healthcare workers cohort. Furthermore, when analyzing the myeloid lineage, we found a substantial increase in myeloid cells in cancer patients compared to healthcare workers (both SARS-CoV-2 IgG-), in line with previous studies [11, 12] . Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. Our results may indicate that due to differential immune cell profile of cancer patients who are treated with immunomodulatory agents, the host response to the SARS-COV2 may lessen symptom severity. doi = 10.3390/cancers12092421 id = cord-257408-ejhhk1iu author = Goss, Matthew B. title = The Pediatric Solid Organ Transplant Experience with COVID‐19: An Initial Multi‐Center, Multi‐Organ Case Series date = 2020-09-18 keywords = SARS; covid-19; patient summary = CONCLUSIONS: Our multi‐institutional experience suggests the prognoses of pediatric transplant recipients infected with COVID‐19 may mirror those of immunocompetent children, with infrequent hospitalization and minimal treatment, if any, required. Many adult centers (2) (3) (4) have suggested that transplant recipients are at particular risk for an arduous clinical course given their immunocompromised state, though highly associated comorbidities exist as confounders and appear to play a significant role in COVID-19 outcomes for the transplant subpopulation (5) . Data were collected via institutions'' respective electronic medical record systems and were reviewed for patient characteristics, history of recent exposure, timing of presentation, symptomatology, laboratory values, immunosuppression management, antiviral treatment strategies, and clinical outcomes. To date, the bulk of the literature examining COVID-19 following transplant is adult focused, with pediatric reports limited to single patient experiences. Comorbidities associated with a severe COVID-19 clinical phenotype among adult transplant recipients, e.g. hypertension, obesity, and diabetes, (14) are less prevalent in the pediatric population. doi = 10.1111/petr.13868 id = cord-262068-9ixq8hwb author = Gottardi, Andrea De title = Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection date = 2020-06-10 keywords = SARS; patient summary = The data that support the findings of this study are available from the corresponding author, upon Clinical characteristics and management of a liver transplanted patient admitted with SARS-CoV-2 infection SUMMARY We present here the case of a 62-year-old man, who was referred to the emergency department with fever and cough for 3 days. Therefore, due to the potential clinical efficacy for COVID-19 patients [11] and based on SARS clinical cases in 2003 [12] , and before the publication of the LOTUS China trial [13] , we started a treatment with lopinavir 200 mg and ritonavir 50 mg 2-0-2, and hydroxychloroquine 200 mg twice daily. Clinical data available so far indicate that up to 53% of the patients with COVID-19 present increased levels of transaminases during the infection and that liver injury is apparently associated with the severity of respiratory symptoms [14, 15] . doi = 10.1016/j.clinre.2020.05.014 id = cord-315617-mhm9wh9q author = Gottschalk, René title = Bioterrorism: is it a real threat? date = 2004-09-02 keywords = SARS; West; agent; biological summary = However, it is the developments over the past years that are causing the greatest concern: new threats to the security of nations are emerging in the form of terrorist organizations that seem to increasingly explore novel ways of spreading terror [1] . Terrorists will know that using highly infectious agents such as the smallpox virus for biological attacks might well mean their spread also to their own followers because they do not have smallpox vaccine or other preventative measures available. tuberculosis, Nipah virus) Third highest priority agents include emerging pathogens that could be engineered for mass dissemination in the future because of: -availability -ease of production and dissemination -potential for high morbidity and mortality rates and major health impact in the aftermath of the 2001 anthrax attacks, with numerous letters allegedly containing B. doi = 10.1007/s00430-004-0228-z id = cord-303539-gimz41yb author = Goudouris, Ekaterini S. title = Laboratory diagnosis of COVID-19() date = 2020-08-31 keywords = COVID-19; SARS; test summary = DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. 25 Some studies report patients with mild (or even asymptomatic) COVID-19 present lower levels of SARS-CoV-2-specific antibodies or may even do not develop detectable levels, while patients with more severe conditions have higher levels of these. 38 The data presented suggest that the diagnosis of COVID-19 should be based on clinical manifestations, contact history, imaging tests, laboratory tests, and not only on serological tests and the search for the genetic material of the virus. The gold standard for the diagnosis of SARS-CoV-2 infection is the identification of viral genetic material by RT-PCR, in different samples, with greater sensitivity in bronchoalveolar lavage and nasopharyngeal swab. doi = 10.1016/j.jped.2020.08.001 id = cord-305755-6jup93v4 author = Gouveia, Duarte title = Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date = 2020-07-22 keywords = SARS; peptide; sample; swab summary = In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analyzed by MS/MS with a short gradient. To foster the development of alternative detection methods for SARS-CoV-2, we performed a proof-of-concept study to assess the potential of MS/MS for proteotyping SARS-CoV-2: (i) in simulated nasal swabs containing different quantities of viral peptides and (ii) in nasopharyngeal swabs from COVID-19 diagnosed patients. doi = 10.1021/acs.jproteome.0c00535 id = cord-351321-6d2mn5ok author = Gouveia, Duarte title = Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date = 2020-06-19 keywords = ADETQALPQR; SARS; peptide; swab summary = Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. To assess the performance of shotgun MS-based proteomics in detecting SARS-CoV-2 peptides in a background matrix consisting of nasopharyngeal swab protein material, we experimentally created tryptic peptidomes from i) a purified virus solution obtained from Vero E6 cells infected with a SARS-CoV-2 reference strain, and ii) nasopharyngeal swabs obtained from two healthy volunteers (Figure 1) . Simili swabs containing specific quantities of SARS-CoV-2 virus and the equivalent of 8.4% of the nasal matrix protein material collected during sampling were analysed by MS/MS with a short gradient. doi = 10.1101/2020.06.19.161000 id = cord-263532-q044i7ym author = Goyal, Bhupesh title = Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy date = 2020-05-13 keywords = CoV; SARS; pro summary = In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M(pro) on its dimerization and, thus, catalytic activity. The individual monomers of SARS-CoV M pro are enzymatically inactive, and two strategies have been employed to develop inhibitors against this enzyme: (i) molecules targeting the substrate binding pocket to block the catalytic activity, and (ii) dimerization inhibitors. 14, 15 In the present review, literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV M pro on its dimerization and, thus, catalytic activity are compiled. The various mutation analyses, N-terminal truncation studies, and MD simulation studies that highlighted key residues of SARS-CoV M pro involved in the stabilization of the catalytically active dimeric structure of the enzyme are listed in Table 2 and are arranged in chronological order. doi = 10.1021/acscombsci.0c00058 id = cord-261615-p81l6zvz author = Grabbe, Stephan title = Systemische Immunsuppression in Zeiten von COVID‐19: Müssen wir umdenken? date = 2020-08-21 keywords = Patienten; SARS; Therapie; die summary = Über eine mögliche therapeutische Wirksamkeit von Chloroquin oder Hydroxychloroquin bei einer COVID-19-Erkrankung wurde bereits in der Laienpresse spekuliert, sodass diese Substanzen vielfach als unkritisch für die Dauerbehandlung von Patienten mit Autoimmunerkrankungen angesehen werden. In der Klinik scheint jedoch die langfristige therapeutische Einnahme von Hydroxychloroquin in Patienten mit systemischem LE nicht vor einer Covid-19-Erkrankung oder einem schweren Verlauf zu schützen [30, 31] . Somit gibt es derzeit keine Hinweise, dass die Therapie mit Chloroquin oder Hydroxychloroquin negative oder schützende Effekte auf eine SARS-CoV-2-Infektion hat oder den Infektionsverlauf ändert. Grundsätzlich gibt es derzeit keine Datenlage für eine generelle Reduktion oder Pausierung einer Immunsuppression bei Patienten mit Autoimmunerkrankungen, da das Risiko einer Untertherapie dieser zumeist schweren Erkrankungen deutlich höher als das eines aggravierten Infektionsverlaufs einer COVID-19-Erkrankung ist. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/ddg.14194_g id = cord-283380-l60yyr6l author = Grabbe, Stephan title = Systemic immunosuppression in times of COVID‐19: Do we need to rethink our standards? date = 2020-08-02 keywords = SARS; covid-19; disease summary = However, it is also currently under discussion whether patients under immunosuppressive therapy also have a higher risk of suffering a severe course of the COVID-19 disease. However, in clinical practice, long-term therapeutic use of hydroxychloroquine in patients with systemic lupus erythematosus does not appear to protect against covid-19 disease or a severe course of the disease [30, 31] . Therefore, the authors recommend that this therapy option should be considered especially in patients with other risk factors for a severe course of SARS-CoV-2 infection. Essentially, there is currently no data available for a general reduction or pause of immunosuppression in patients with autoimmune diseases, since the risk of an insufficient therapy of these mostly severe diseases is clearly higher than that of an aggravated course of COVID-19 disease. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/ddg.14194 id = cord-327247-dbcacphq author = Grace, Sherry L. title = The Occupational and Psychosocial Impact of SARS on Academic Physicians in Three Affected Hospitals date = 2011-04-12 keywords = SARS; care; physician summary = The survey that was developed was based on a literature review and input from key health care professionals and included items on sociodemographic variables (sex, age, specialty, number and ages of children, number of years in practice, and ethnocultural background); health status; attitudes and perceptions toward SARS; SARSrelated coping methods, concerns, and symptoms; and effects on personal relationships and changes to work resulting from the SARS outbreak. On a scale from 1 (a lot) to 5 (not at all), physicians perceived that their work had been seriously affected by the SARS outbreaks (mean‫,97.1ס‬ SD‫.)98.0ס‬ Ways in which their work had been affected included: interruptions to teaching and education (84.5%, N‫,)361ס‬ unwillingness of patients to attend outpatient clinics (79.8%, N‫,)451ס‬ infection control precautions (77.2%, N‫,)941ס‬ inability to see outpatients (71.0%, N‫,)731ס‬ inability to perform regular activities (51.8%, N‫,)001ס‬ interruptions to research (51.8%, N‫,)001ס‬ new involvement in SARS-related work (8.8%, N‫,)71ס‬ and inability to enter work due to symptoms (4.1%, N‫.)8ס‬ doi = 10.1176/appi.psy.46.5.385 id = cord-348455-vcxalkeo author = Graham, N. R. title = Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date = 2020-07-22 keywords = RBD; SARS summary = title: Kinetics and Isotype Assessment of Antibodies Targeting the Spike Protein Receptor Binding Domain of SARS-CoV-2 In COVID-19 Patients as a function of Age and Biological Sex. date: 2020-07-22 The receptor-binding domain of the CoV spike (RBD-S) protein is important in host cell recognition and infection and antibodies targeting this domain are often neutralizing. We first piloted our antigen preps for the RBD-S IgG screening assay using serum 81 samples from a PCR-confirmed severe COVID-19 patient (defined as admission to the Intensive 82 Care Unit, ICU) who was admitted to the hospital 10 days following symptom onset and based 83 on an early report suggesting that SARS-CoV-2 could trigger antibody responses in this 84 timeframe (24). Anti-S titers in patients with a negative RBD-S test were 138 generally low and in RBD-positive samples, followed the same trends as RBD-reactivity, 139 providing further confirmation of robust serological responses to SARS-CoV-2 during acute 140 COVID-19. doi = 10.1101/2020.07.15.20154443 id = cord-277487-jgbjxgh1 author = Graham, Simon P. title = Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date = 2020-06-20 keywords = CoV-2; IFN; SARS; pig summary = doi = 10.1101/2020.06.20.159715 id = cord-353826-owoec2ud author = Graham, Simon P. title = Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date = 2020-07-27 keywords = CoV-2; IFN; SARS summary = Clinical development of the COVID-19 vaccine candidate ChAdOx1 nCoV-19, a replication-deficient simian adenoviral vector expressing the full-length SARS-CoV-2 spike (S) protein was initiated in April 2020 following non-human primate studies using a single immunisation. Analysis of SARS-CoV-2 S proteinspecific murine splenocyte responses by IFN-γ ELISpot assay showed no statistically significant difference between the primeonly and prime-boost vaccination regimens, in either strain of mouse (Fig. 1a) . SARS-CoV-2 S protein-specific antibody responses following ChAdOx1 nCoV-19 prime-only and prime-boost vaccination regimens in mice and pigs SARS-CoV-2 S protein-specific antibody titres in serum were determined by ELISA using recombinant soluble trimeric S (FL-S) and receptor binding domain (RBD) proteins. Small animal models have variable success in predicting vaccine efficacy in larger animals but are an important To analyse SARS-CoV-2 S-specific T cell responses, all mice were sacrificed on day 49 for isolation of splenocytes and pigs were blood sampled longitudinally to isolate PBMC. doi = 10.1038/s41541-020-00221-3 id = cord-272702-7uc4ozjy author = Graham, T. G. W. title = Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date = 2020-09-18 keywords = Fig; RNA; SARS summary = We therefore tested whether we could detect SARS-CoV-2 RNA by adding 1 μ l of each swab sample to 20 μ l TaqPath reactions containing the N1, N2, and RNase P (RP) probes ( Fig 2A) . Taken together, these results show that RT-qPCR with BEARmix can detect SARS-CoV-2 in clinical samples, either using purified RNA or by direct addition of swab samples, albeit with somewhat less sensitivity than commercial TaqPath master mix. To evaluate a complete protocol in which swab samples are collected into PK solution and then added directly to BEARmix RT-PCRs, we prepared contrived swab samples in which live virus was mixed with pathogenfree human nasal fluid prior to dilution into either DNA/RNA Shield, VCM containing 0.4 mg/ml proteinase K, or a solution of 0.4 mg/ml proteinase K in water (Fig 6) . Here we have developed simple, academic laboratory-derived methods for RNA extraction, direct sample addition, and RT-PCR detection that provide low-cost alternatives to the use of commercial kits (Fig 8) . doi = 10.1101/2020.09.16.20193466 id = cord-268406-3v309r41 author = Grajewski, Rafael S. title = A missing link between SARS‐CoV‐2 and the eye?: ACE2 expression on the ocular surface date = 2020-06-12 keywords = SARS summary = We applaud Lange et al.1 for their extensive efforts to analyse entry factors for severe acute respiratory syndrome coronavirus (SARS-CoV-2) into conjunctival epithelial cells covering the ocular surface, which is an important albeit controversially discussed issue1,2 . A missing link between SARS-CoV-2 and the eye?: ACE2 expression on the ocular surface Before incubation with the primary antibody, tissue was subjected to heat-induced epitope retrieval using Target Retrieval Solution pH 9 (catalog #S2367; Dako). The location of ACE2 expression at the ocular surface enables direct contact of SARS-CoV-2 with conjunctival cells, raising the question how often this occurs and if protective mechanisms of tears and conjunctiva might prevent conjunctivitis to happen more frequently. 6 In summary, our results provide an important addition to the results of Lange et al 1 and other works by clearly demonstrating specific ACE2 expression in conjunctival epithelial cells, providing the receptor for direct entry of SARS-CoV-2. doi = 10.1002/jmv.26136 id = cord-301633-t8s4s0wo author = Gralinski, Lisa E. title = Return of the Coronavirus: 2019-nCoV date = 2020-01-24 keywords = MERS; SARS; Wuhan summary = Similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infections, patients exhibited symptoms of viral pneumonia including fever, difficulty breathing, and bilateral lung infiltration in the most severe cases [1] . A range of disease has been observed highlighted by fever, dry cough, shortness of breath, and leukopenia; patients have included mild cases needing supportive care to severe cases requiring extracorporeal membrane oxygenation; however, compared to SARS-CoV (10% mortality) and MERS-CoV (35% mortality), the 2019-nCoV appears to be less virulent at this point with the exception of the elderly and those with underlying health conditions. In the early part of the outbreak, the absence of infection in health care workers argued for inefficient human to human spread and distinguished 2019-nCoV from both SARS-CoV and MERS-CoV. doi = 10.3390/v12020135 id = cord-335938-hscgmis5 author = Gralinski, Lisa E. title = Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury date = 2013-08-06 keywords = Fig; SARS; Serpine1; pfu; Ϫ/Ϫ summary = The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. To model system-wide behaviors following SARS-CoV infection, we performed a dose-response study that included biological sampling at multiple time points, transcriptional and proteomic systems biology data, and mathematical modeling algorithms to identify signaling networks associated with progression from severe to lethal disease outcomes. These data demonstrate the successful use of highly refined modeling algorithms to identify and validate novel genes and pathways that play critical roles in SARS-CoV pathogenesis and the development of ALI following virus infection in the lung. Similar changes in the urokinase, coagulation, and fibrinolysin pathway expression signatures are noted following highly pathogenic SARS-CoV and influenza virus infections (see Fig. S5B and S6 in the supplemental material), arguing for a con-served role for these pathways in virus-induced end-stage lung diseases, like ALI and ARDS. doi = 10.1128/mbio.00271-13 id = cord-344227-rdlinzrn author = Gralinski, Lisa E. title = Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis date = 2018-10-09 keywords = Fig; MA15; SARS; complement summary = As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment. doi = 10.1128/mbio.01753-18 id = cord-340486-wydlqq2z author = Grandbastien, Manon title = SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation date = 2020-06-27 keywords = SARS; asthmatic summary = title: SARS-CoV-2 pneumonia in hospitalized asthmatic patients did not induce severe exacerbation Conclusion Our results demonstrate that asthmatic patients appeared not to be at risk for severe SARS-CoV-2 pneumonia. Moreover, SARS-CoV-2 pneumonia did not induce severe asthma exacerbation. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. However, the 49 relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known. The propensity score allows analyzing 245 an observational nonrandomized study so that it mimics some of the particular 246 characteristics of a randomized controlled trial as it accounts for systematic differences in 247 baseline characteristics between asthmatic and non-asthmatic subjects when estimating the 248 effect of asthma on severe COVID-19 outcomes. This suggests that the risk factors for hospitalization in our patients were 390 related more to the risk factors of SARS-CoV-2 pneumonia than to asthma. doi = 10.1016/j.jaip.2020.06.032 id = cord-349659-6drnriun author = Grant, Benjamin D. title = SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents date = 2020-07-01 keywords = CoV-2; LFA; SARS summary = title: SARS-CoV-2 Coronavirus Nucleocapsid Antigen-Detecting Half-Strip Lateral Flow Assay Toward the Development of Point of Care Tests Using Commercially Available Reagents In this work, we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. 10 Antigen detecting ELISAs were previously developed in 2004 for SARS-CoV-1, with limits of detection of approximately 50 pg/mL and clinical sensitivity as a function of days since onset that was significantly better than the useful time window for the current generation of SARS-CoV-2 serology assays. A dose response curve was generated for the half-strip LFA using two commercially available SARS-CoV-2 nucleocapsid (N) proteins, from Genemedi and Genscript. Analytical Chemistry pubs.acs.org/ac Article and determination of realistic limits of detection for a full strip LFA in multiple sample matrices will help point the way toward the best approach for an antigen detecting LFA for SARS-CoV-2. In this paper, we present a half-strip LFA for the detection of nucleocapsid protein of SARS-CoV-2. doi = 10.1021/acs.analchem.0c01975 id = cord-340656-ltd6ueoi author = Grant, Michael C. title = The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date = 2020-06-23 keywords = COVID-19; SARS; clinical summary = title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries Furthermore, with few included studies (30 in the largest and most recent [12] ), the range of symptoms were limited and the estimates of prevalence are likely to be upwardly biased because only unwell patients (largely those admitted to hospital) were tested in the early phase of the outbreak. We excluded case reports, articles which failed to disaggregate symptoms in adult and paediatric cohorts, studies of patients with prior respiratory infections (e.g. tuberculosis) or co-infections with other viruses (e.g. similar viruses SARS-CoV-1 or HCoV-EMC/2012, etc) and articles which we are unable to translate to English in a timely fashion. Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: A retrospective single center analysis Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms doi = 10.1371/journal.pone.0234765 id = cord-304356-jyp9gjh9 author = Grant, Rogan A. title = Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date = 2020-08-05 keywords = COVID-19; RNA; SARS; cell; figure; pneumonia summary = We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. doi = 10.1101/2020.08.05.238188 id = cord-292544-m7jyydf1 author = Grau-Pujol, Berta title = Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial date = 2020-07-29 keywords = COVID-19; Hospital; SARS; study summary = OBJECTIVES: The aim of this study is to assess the efficacy of the use of pre-exposure prophylaxis (PrEP) with hydroxychloroquine against placebo in healthcare workers with high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in reducing their risk of coronavirus disease 2019 (COVID-19) disease during an epidemic period. As secondary endpoints, we will obtain: i) the SARS-CoV-2 seroconversion in the PrEP group compared to placebo during the 6 months of follow-up in healthcare workers with negative serology at day 0; ii) the occurrence of any adverse event related with hydroxychloroquine treatment; iii) the incidence of SARS-CoV-2 infection and COVID-19 among healthcare workers in the non-PrEP group, among the total of healthcare workers included in the non-PrEP group during the study period; iv) the risk ratio for the different clinical, analytical and microbiological conditions to develop COVID-19; v) a repository of serum samples obtained from healthcare workers confirmed COVID-19 cases for future research on blood markers to predict SARS-CoV-2 infection. doi = 10.1186/s13063-020-04621-7 id = cord-282858-zikoui4h author = Graudenz, Gustavo Silveira title = SARS-CoV-2. Long Distance Airborne Transmission and its Public Health Implications date = 2020-11-02 keywords = SARS; particle summary = Its predecessor, SARS-CoviD-1, the agent that caused Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003, showed strong evidence of opportunistic airborne transmission in different environments, such as collective housing environments (8) , indoor environments such as airplanes (9), and health service institutions (10) . (12) that suggested transmission of SARS-CoV-2 through infected surfaces and contaminated individual protection equipment as well as long distance environment contamination. In health care settings, the Center for Disease Control''s recommendations for prevention of airborne transmission include maintaining a negative pressure environment, fine filtering of exhaust air from infected patients'' rooms, maintaining high air exchange rates (12 air exchanges per hour), shutting recirculation ducts, and establishing pressure cascades (2) in these settings until further evidence of long distance transmission is obtained Unfortunately, these precautionary measures have not yet been applied in most health care facilities in Brazil. Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus doi = 10.6061/clinics/2020/e2343 id = cord-255515-7se14455 author = Graudenzi, Alex title = Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date = 2020-07-06 keywords = SARS summary = To dissect the mechanisms underlying the observed inflation of variants in SARS-CoV-2 genome, we present the largest up-to-date analysis of intra-host genomic diversity, which reveals that the majority of samples present a complex sublineage architecture, due to the interplay between host-related mutational processes and transmission dynamics. Strikingly, our analysis allowed to identify three non-overlapping mutational signatures, i.e., specific distributions of nucleotide substitutions, which are observed in distinct clusters of samples in a mutually exclusive fashion, suggesting the presence of host-related mutational processes. Finally, the analysis of homoplasies, i.e., (low-frequency) variants shared across distinct viral lineages and unlikely due to infection events, demonstrate that a high number of mutations can independently emerge in multiple samples, due to mutational hotspots often related to signatures or, possibly, to positive (functional) selection. doi = 10.1101/2020.07.06.189944 id = cord-293852-r72c6584 author = Greco, S. title = Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date = 2020-10-31 keywords = ACE2; COVID-19; CoV-2; Disease; RNA; SARS; patient summary = Different studies found that the values of cardiac Troponins were increased in COVID-19 patients with more severe disease [4, 5, [68] [69] [70] , indicating an association of SARS-CoV-2 with myocardial damage. Moreover, the single-cell RNA-sequencing (scRNAseq) approach has been used to profile the SARS-CoV-2 host-response in the PBMCs of COVID-19 patients, and to comprehensively characterize the immunological changes [124] [125] [126] [127] [128] [129] [130] . However, SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) induced cytotoxic effects and RNA-seq findings highlighted significant transcriptional changes in gene pathways related to cellular metabolism and immune response [131] [132] [133] . This analysis also revealed several host-derived lncRNAs differentially expressed in COVID-19 patient-derived lung tissue, and in SARS-CoV-2 infected epithelial cells, including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and NEAT1 (nuclear-enriched autosomal transcript 1) [151] (Fig. 5) . doi = 10.1186/s12967-020-02582-8 id = cord-325910-qiay8n43 author = Green, D. A. title = Clinical Performance of SARS-CoV-2 Molecular Testing date = 2020-05-08 keywords = SARS; preprint summary = In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19. For the time-dependent analysis of conversion rates, we considered "initially positive" 216 patients with any "Detected" or "Indeterminate" SARS-CoV-2 result obtained during the 217 first calendar day of testing rather than the first positive test, to reduce bias due to 218 nasopharyngeal sampling inadequacy (Table 1) . Considering ''Detected'' and "Indeterminate" as 239 positive, 1,471 repeat-tested patients had one or more SARS-CoV-2 positive results over 240 time; only 61.9% were positive on the initial test and only 69.3% had a positive result on 241 the first day (Table 1) . doi = 10.1101/2020.05.06.20093575 id = cord-294372-pec1886j author = Greene, Dina N. title = Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date = 2020-10-15 keywords = SARS summary = Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. In the United States, surveillance data suggest that mean age of infected patients is decreasing compared to the early stages of the COVID-19 pandemic. We used SARS-CoV-2 testing data from a national reference laboratory to characterize the age distribution of detected cases between March and July of 2020. Surveillance data in the United States have shown a trend toward decreasing age among persons with laboratory-confirmed SARS-CoV-2 infection. This study found a similar pattern among patients tested by a national reference laboratory, with the median age among patients testing positive being five years lower in June and early July compared to March and April. doi = 10.1371/journal.pone.0240783 id = cord-294921-h44tct43 author = Greninger, Alexander L. title = The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience date = 2020-07-23 keywords = Dr.; SARS summary = Dr. Greninger was working in his research lab, assembling data for an early February grant for funding to understand the function of his favorite coronavirus gene (orf3a) in SARS-CoV-2, while Dr. Jerome continued splitting time between clinical virology and his work at the Fred Hutchinson Cancer Research Center on gene therapies for persistent viruses. From mid-January until the end of February, we received respiratory specimens from about 15 different persons under investigation for COVID-19 for respiratory virus panel testing, but each of them tested negative for SARS-CoV-2, not only at the CDC but also in our lab as we continued the evaluation of our assay. We could not report results from our assay development and validation studies, but our clinicians soon became disappointed by the 5-to 7-day turnaround time for clinical results from the CDC, during which patients waited in isolation for test results. doi = 10.1128/jcm.01416-20 id = cord-285430-o086q2qa author = Gribble, Karleen title = Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date = 2020-07-25 keywords = HIV; SARS summary = BACKGROUND: In an effort to prevent infants being infected with SARS-CoV-2, some governments, professional organisations, and health facilities are instituting policies that isolate newborns from their mothers and otherwise prevent or impede breastfeeding. WEIGHING OF RISKS IS NECESSARY IN POLICY DEVELOPMENT: Such policies are risky as was shown in the early response to the HIV pandemic where efforts to prevent mother to child transmission by replacing breastfeeding with infant formula feeding ultimately resulted in more infant deaths. In the COVID-19 pandemic, the risk of maternal SARS-CoV-2 transmission needs to be weighed against the protection skin-to-skin contact, maternal proximity, and breastfeeding affords infants. However, mothers and infants present a special situation as the risk of mother-to-child transmission of SARS-CoV-2 needs to be weighed against the protection from infectious diseases and the support for bonding and caregiving provided by close maternal proximity and breastfeeding. doi = 10.1186/s13006-020-00306-8 id = cord-349428-i2s41kl7 author = Griffin, Ian title = The Impact of COVID-19 Infection on Labor and Delivery, Newborn Nursery, and Neonatal Intensive Care Unit: Prospective Observational Data from a Single Hospital System date = 2020-06-13 keywords = COVID-19; SARS; mother summary = The study population consisted of maternal-infant dyads whose mothers were identified to be either COVID-19 positive or persons under investigation (PUI) before their admission to labor and delivery (L&D) or at any time before their discharge. Obstetric patients who were COVID-19 positive or PUIs were cared for in a designated suite of single-person airborne infection isolation (AIIRs) negative pressure rooms separate from the main L&D unit through delivery and the postpartum period, while awaiting testing for COVID-19 or if they had tested positive for COVID-19. If a mother tested positive for COVID-19 and newborn infants had been immediately separated at birth from their mother, neonatal isolation precautions were suspended after two negative polymerase chain reaction (PCR)-based nasopharyngeal swab tests, performed at 48 hours and at 5 days of life, respectively. doi = 10.1055/s-0040-1713416 id = cord-294429-isivkz8b author = Grifoni, Alba title = Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals date = 2020-05-20 keywords = CD4; CD8; Fig; SARS; cell; covid-19 summary = To test for the generation of SARS-CoV-2 CD4 + and CD8 + T cell responses following infection, we initially recruited 20 adult patients who had recovered from COVID-19 disease ( Table 1) . Initial definition and assessment of human antigen-specific SARS-CoV-2 T cell responses are best made with direct ex vivo T cell assays using broad-based epitope pools, such as MPs, and assays capable of detecting T cells of unknown cytokine polarization and functional attributes. Data from both the epitope MPs and protein peptide pool experiments can be interpreted in the context of previously reported T cell response immunodominance patterns observed for other coronaviruses, particularly the SARS and MERS viruses, which have been studied in humans, HLA-transgenic mice, wild-type mice and other species. (C) Correlation of SARS-CoV-2−specific CD4 + T cells detected using the epitope prediction approach (CD4_R MP) compared against the sum total of all antigen pools of overlapping peptides (excluding spike), run with samples from the same donors in two different experiment series. doi = 10.1016/j.cell.2020.05.015 id = cord-266168-hxu5u5op author = Grimaud, Emilie title = Delayed acute bronchiolitis in infants hospitalized for COVID‐19 date = 2020-07-10 keywords = SARS summary = To the Editor, Because of the infant''s history, a chest X-ray was performed and returned normal. A term eutrophic male with otherwise unremarkable neonatal history was referred for poorly tolerated high fever at age 2 months. The respiratory and clinical examination findings including hemodynamics were normal. RT-PCR testing of a nasopharyngeal swab was positive for SARS-CoV-2 but negative for RSV and IV. The chest X-ray was normal, and no lung ultrasonography was performed. These two cases of COVID-19 in infants hospitalized for poorly tolerated high fever and neurological symptoms in whom acute bronchiolitis developed following a delay of 2 to 8 days suggest that SARS-CoV-2 infection may cause acute bronchiolitis in the absence of a viral coinfection such as RSV. Pneumonia is the most common respiratory illness among symptomatic children with COVID-19. Infection and rapid transmission of SARS-CoV-2 in Ferrets Wheezing rhinovirus illnesses in early life predict asthma development in high-risk children doi = 10.1002/ppul.24946 id = cord-277440-9nehpbg2 author = Grimm, Christian title = Could an endo-lysosomal ion channel be the Achilles heel of SARS-CoV2? date = 2020-05-06 keywords = SARS; TPC2 summary = Genetic ablation of TPCs or TPC blockers have been previously shown to affect trafficking of both viruses and bacterial toxins through the endo-lysosomal system, reducing infectivity, including, e.g. cholera toxin, diphtheria toxin, Pasteurella multocida toxin, Anthrax toxin, Ebola virus, and MERS-CoV [5] [6] [7] . Indeed, it has been demonstrated before that SARS-CoV, like EBOV, displays late cell entry kinetics and that transport to NPC1+ (Niemann-Pick C1 protein) late endo-lysosomes is a rate-defining step [9] . The two-pore channels (TPC1, TPC2) are required by viruses such as EBOV (Ebola virus), MERS-CoV and SARS-CoV, orchestrating the interplay of virus and endolysosomal milieus such as trafficking from early to late endosomes, fusion of late endosomes with lysosomes, and facilitating releasing of viral RNA into the cytoplasm. doi = 10.1016/j.ceca.2020.102212 id = cord-267436-mivxm8oh author = Groneberg, David A title = Treatment and vaccines for severe acute respiratory syndrome date = 2005-03-10 keywords = SARS; acute; coronavirus; respiratory summary = The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002-2003 outbreak, is a coronavirus that was unknown before the outbreak. 31 The results of a randomised clinical study in Guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose (400-600 mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. Search terms were "severe acute respiratory syndrome", "SARS", "treatment", "coronavirus", "infection", "SARS coronavirus", "vaccination", and "antiviral". Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus doi = 10.1016/s1473-3099(05)01307-1 id = cord-304815-3datxv8j author = Gronvall, Gigi Kwik title = The Scientific Response to a Pandemic date = 2006-02-24 keywords = SARS; laboratory summary = More than 150 scientists and public health practitioners from 25 countries gathered in Lyon, France, to hear speakers from the WHO, the European Commission, scientific journals, Interpol, and public health networks-many of the institutions and individuals who will likely play key roles in the global response to the next pandemic. By discussing the biosafety and biosecurity challenges presented by past epidemics such as SARS, participants recognized the importance of scientific and public health collaboration in combating disease-and the need to plan. Researchers will need to share biological samples between laboratories, sometimes internationally; decision makers and journalists will want the latest information, which may not be peer reviewed; and researchers will risk contracting the disease they research, which could then spread outside of the laboratory. Scientists need access to samples from patients and laboratories in order to conduct research and public health surveillance, as well as to develop diagnostic tests. doi = 10.1371/journal.ppat.0020009 id = cord-325991-dktffiaa author = Gross, Oliver title = COVID-19-associated nephritis: early warning for disease severity and complications? date = 2020-05-06 keywords = SARS summary = title: COVID-19-associated nephritis: early warning for disease severity and complications? COVID-19-associated nephritis: early warning for disease severity and complications? Here we report that analysis of a urine sample on admission to hospital can be used to detect systemic capillary leak syndrome, which can be a predictor of fluid overload, respiratory failure, need for ICU admission, and death. Three of these patients had coincidentally submitted urine samples in the few weeks before their infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On the basis of these findings, we generated an algorithm for early detection of COVID-19-associated nephritis and to assess the risk of respiratory decompensation by capillary leak syndrome (figure). In summary, the respiratory tract is the gateway for SARS-CoV-2 infection, but we postulate that COVID-19associated nephritis, which can be easily screened for through a simple and inexpensive urine sample analysis, might help predict complications. doi = 10.1016/s0140-6736(20)31041-2 id = cord-266648-962r0vm8 author = Grossberg, Laurie B title = Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date = 2020-07-03 keywords = COVID-19; IBD; SARS summary = title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic Although data in patients with IBD contracting COVID-19 are still limited, both providers and patients have particular concerns regarding the risk of infection with SARS-CoV-2 and how to manage their medications during the COVID-19 pandemic. Information regarding risk factors, prevention, routine care (including office visits, testing, endoscopy, and surgery), and medication management of patients with IBD in the setting of COVID-19 was collected from each reference and is summarized in the Results. 10, 11 Other organizations, including the American Gastroenterological Association doi: 10.1093/ibd/izaa174 Published online 3 July 2020 (AGA), the Gastroenterological Society of Australia, and the European Crohn''s and Colitis Organisation (ECCO), agree that there are no data to support an increased risk of infection among patients with IBD. doi = 10.1093/ibd/izaa174 id = cord-280628-ok62havd author = Groß, Sonja title = SARS-CoV-2 receptor ACE2-dependent implications on the cardiovascular system: From basic science to clinical implications date = 2020-04-30 keywords = ACE2; COVID-19; SARS; patient summary = COVID-19 requires the collaboration of nearly 200 countries to curb the spread of SARS-CoV-2 while gaining time to explore and improve treatment options especially for cardiovascular disease (CVD) and immunocompromised patients, who appear to be at high-risk to die from cardiopulmonary failure. Since the coronavirus disease (COVID19) is still an emerging pandemic with more than 2.1 million confirmed cases worldwide [1] , special focus is currently directed towards the understanding of why people are hospitalized, receive intensive care, and frequently die as a consequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. While higher mortality rates among CVD patients are also associated with other respiratory diseases (especially influenza virus-induced flu or previous SARS epidemics), the question was put forward, whether people treated for heart-related illness are more prone to SARS-CoV-2 viral infection, based on first epidemiological evidence, but particularly based on the presumed upregulation of the SARS-CoV-2 entry receptor. doi = 10.1016/j.yjmcc.2020.04.031 id = cord-296767-mgr32ftl author = Große, Karsten title = SARS‐CoV‐2 as an extrahepatic precipitator of acute‐on‐chronic liver failure date = 2020-05-29 keywords = SARS summary = key: cord-296767-mgr32ftl cord_uid: mgr32ftl We read with great interest the report by Qiu and colleages reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. As ACLF following hepatic versus extrahepatic insults may differ in presentation, course, and prognosis, we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. To the Editor We read with great interest the report by Qiu et al 1 reporting the first case of acute-on-chronic liver failure (ACLF) following SARS-CoV-2 infection. 1 As ACLF following hepatic vs extrahepatic insults may differ in presentation, course and prognosis, 2 we herein report the case of a patient with ACLF precipitated by extrahepatic complications of SARS-CoV-2. Acute on chronic liver failure from novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acute-on-chronic liver failure precipitated by hepatic injury is distinct from that precipitated by extrahepatic insults Multiorgan and renal tropism of SARS-CoV-2 doi = 10.1111/liv.14540 id = cord-321308-rwxhdg8r author = Grubaugh, Nathan D. title = Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear date = 2020-07-03 keywords = SARS summary = While clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown. Following the emergence of SARS-CoV-2 in China in late 2019, and the rapid expansion of the COVID-19 pandemic in 2020, questions about viral evolution have come tumbling after. They present compelling data that an amino acid change in the virus'' spike protein, D614G, emerged early during the pandemic, and viruses containing G614 are now dominant in many places around the world. In support of their hypothesis, the authors provided evidence that clinical samples from G614 infections have a higher levels of viral RNA, and produced higher titers in pseudoviruses from in vitro experiments; results that now seem to be corroborated by others [e.g. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry doi = 10.1016/j.cell.2020.06.040 id = cord-354103-4dldgqzf author = Grubic, Andrew D title = COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date = 2020-06-27 keywords = COVID-19; PCR; SARS; patient summary = While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a "stress test" to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. On the same day, the United States Surgeon General echoed the recommendation from the American College of Surgeons and urged hospitals and healthcare systems to consider suspending elective surgical procedures during the outbreak of COVID-19. This pandemic started with identification of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent from a cluster of pneumonias in the Hubei providence of China in December 2019. On March 25, 2000, American College of Surgeons released the guidelines for emergency general surgery in COVID-19 positive patients or those at high clinical suspicion for COVID infection. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases doi = 10.4240/wjgs.v12.i6.259 id = cord-285700-9q6vwoct author = Grzelak, Ludivine title = SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. date = 2020-04-24 keywords = ELISA; Fig; SARS summary = title: SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors. Here, we performed a pilot study to assess the levels of anti-SARS-CoV-2 antibodies in samples taken from 491 preepidemic individuals, 51 patients from Hopital Bichat (Paris), 209 pauci-symptomatic individuals in the French Oise region and 200 contemporary Oise blood donors. To avoid redundancy, we focused LIPS analysis to N, selecting it for its sensitivity regarding an intracellular viral protein not targeted by NAbs and S1 as it is described as a target of most NAbs. To establish the specificity of the assay, we first analyzed the same series of 40 sera we used for S-Flow and found all of the sera to be negative (Fig. S3 ). Sera from pre-epidemic individuals sampled between 2017 and 2019 (first row), hospitalized cases with confirmed COVID-19 (second row), paucisymptomatics individual from the Crépy-en-Vallois epidemic cluster (third row) and healthy blood donors (last row) were surveyed for anti-SARS-Cov-2 antibodies using four serological assays. doi = 10.1101/2020.04.21.20068858 id = cord-260624-rqjeacow author = Gu, Jiang title = Multiple organ infection and the pathogenesis of SARS date = 2005-08-01 keywords = Fig; SARS; cell summary = SARS viral particles and genomic sequence were detected in a large number of circulating lymphocytes, monocytes, and lymphoid tissues, as well as in the epithelial cells of the respiratory tract, the mucosa of the intestine, the epithelium of the renal distal tubules, the neurons of the brain, and macrophages in different organs. In situ hybridization demonstrated SARS viral sequences in the cytoplasm of a large number of intact and degenerating epithelial cells of the lungs as well as in the scanty infiltrating lymphocytes and clustered macrophages ( Fig. 1, C and D) . (C) In situ hybridization of SARS genomic sequence of the lung from a SARS victim who died 62 d after the onset of high fever detected a large number of pulmonary epithelial cells (small arrows) that contained the virus. In the autopsy samples, in situ hybridization and EM demonstrated virus-infected immune cells in the circulating blood, spleen, lymph nodes, and lymphoid tissue of various organs. doi = 10.1084/jem.20050828 id = cord-277307-wabruzfs author = Gu, Wei title = Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date = 2020-05-21 keywords = New; SARS summary = In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region doi = 10.1093/cid/ciaa599 id = cord-294527-fct2y5vn author = Guadarrama-Ortiz, Parménides title = Neurological Aspects of SARS-CoV-2 Infection: Mechanisms and Manifestations date = 2020-09-04 keywords = Barré; COVID-19; CoV-2; Guillain; SARS; patient summary = The human infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern that has caused more than 16.8 million new cases and 662,000 deaths as of July 30, 2020. Although coronavirus disease 2019 (COVID-19), which is associated with this virus, mainly affects the lungs, recent evidence from clinical and pathological studies indicates that this pathogen has a broad infective ability to spread to extrapulmonary tissues, causing multiorgan failure in severely ill patients. In this context, SARS-CoV-2 can also cause viral meningitis and encephalitis, as demonstrated by a recent report of a 64-yearold patient with laboratory-confirmed COVID-19 who presented neurologic manifestations during the infection, including lethargy, clonus, and pyramidal signs in the lower limbs as well as stiff neck and Brudzinski sign (76) . Future studies are required to evaluate the serologic features of anti-glycolipid antibodies in patients with COVID-19 to elucidate possible mechanisms underlying the association between SARS-CoV-2 infection and Guillain-Barré syndrome. doi = 10.3389/fneur.2020.01039 id = cord-339576-0d6sa9pe author = Guallar, María Pilar title = Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date = 2020-06-14 keywords = SARS; covid-19 summary = Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure doi = 10.1016/j.ijid.2020.06.035 id = cord-286713-14i38xtt author = Guarner, Jeannette title = Three Emerging Coronaviruses in Two Decades: The Story of SARS, MERS, and Now COVID-19 date = 2020-02-13 keywords = SARS summary = As a matter of fact, the characteristic electron microscopy appearance was the clue to amplify and sequence nucleic acids from Dr Urbani''s (one of the health care providers who died of severe acute respiratory syndrome [SARS] in 2003) respiratory specimen using a consensus coronavirus primer. The virus was ultimately named SARS-CoV, as febrile patients had severe acute respiratory syndrome and could present with pneumonia and lower respiratory symptoms such as cough and dyspnea. Nine years later, a new coronavirus that causes respiratory disease appeared in the Middle East, thus the name of MERS-CoV. Symptoms of MERS-CoV are nonspecific, but many patients end up with severe acute respiratory distress. SARS-CoV-2 will cause many more deaths than its predecessors, even though the mortality rate is lower than MERS-CoV infections, because there have been so many more cases. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.1093/ajcp/aqaa029 id = cord-337179-qytruuif author = Guazzi, Marco title = The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients date = 2020-05-21 keywords = ACE2; SARS summary = title: The Dilemma of Renin Angiotensin System Blockers in Coronavirus Disease (Covid‐19): Insights on the Lung Fluid Handling and Gas Exchange in Heart Failure Patients The main clinical manifestation of SARS-CoV-2 is severe acute respiratory syndrome which yields to inflammatory reaction and alveolar fluid floading ultimately impairing gas exchange. We gained previous experience on the effects of renin-angiotensin system inhibition on the pulmonary function of HF patients showing a protective effect on the perturbed gas exchange and lung fluid handling, i.e. alveolar capillary stress-failure, an effect especially observed with enalapril treatment, with a positive but statistically not signfiicnat trend for losartan 11, 12 . Based on this, we outline how renin angiotensin blockers may interact with the lung fluid handling and gas diffusion process in patients with HF infected by SARS-CoV-2, and propose areas for further research. doi = 10.1002/ejhf.1910 id = cord-314070-8qz23nn4 author = Gubbi, Sriram title = Catecholamine physiology and its implications in patients with COVID-19 date = 2020-10-28 keywords = COVID-19; PPGL; SARS; catecholamine; patient summary = The risk factors for severe COVID-19 are diverse, yet closely resemble the clinical manifestations of catecholamine excess states (eg, hypertension, cardiovascular disease, immune dysregulation, and hyperglycaemia), suggesting a potentially common basis for disease. 6 Consequently, catecholamine excess states such as PPGL can cause substantial dysregulation of physiological systems, and lead to pronounced changes in pulmonary (vasoplegia), coronary (myocardial infarction), cerebro vascular (stroke), and remaining systemic vascular tone (hypertension), as well as myocardial disease (cardio myopathies), tachyarrhythmias (benign and fatal), hyper coagulability (thromboem bolism), immune dysreg u lation (cytokine storm), and diabetogenic states; these outcomes are the same as the risk factors that lead to adverse outcomes from COVID-19. 19 Increased concentrations of these cytokines and their downstream acute phase reactants (eg, ferritin) have been associated with a higher likelihood of severe disease and mortality in patients with 20 Catecholamines augment the production of IL-6, IL-10, and other cytokines through a self-amplifying feed-forward loop within myeloid cells, an effect mediated through α1-adrenoceptors. doi = 10.1016/s2213-8587(20)30342-9 id = cord-350904-wyg8ikph author = Gubernatorova, E.O. title = IL-6: relevance for immunopathology of SARS-CoV-2 date = 2020-05-20 keywords = ACE2; Angiotensin; IL-6; SARS; cell; covid-19; patient summary = In turn, SARS-CoV-2 infection of recruited immune cells may increase their apoptosis and exacerbate lymphocytosis [32, 33] , and, finally, may lead in some patients to life-threatening conditions, such as respiratory distress syndrome, cytokine storm, and secondary hemophagocytic lymphohistiocytosis. Interestingly, patients requiring intensive care and invasive lung ventilation display negative correlation between IL-6, TNF and IL-1b concentrations and CD4 + and CD8 + T cell counts [75] , confirming previous studies in animal models, which suggested that cytokine storm actually dampens adaptive immunity against SARS-CoV infection [76] . Taking together, Angiotensin II accumulation due to SARS-CoV-2-mediated ACE2 downregulation may cause Angiotensin 1 receptor downstream activation of NADPH oxidase, which, in turn, leads to elevated ROS production and to induction of transcriptional mechanisms that directly promote IL-6 expression, implicated in inflammation-induced injury and immunopathology. doi = 10.1016/j.cytogfr.2020.05.009 id = cord-273382-7w8fli6w author = Guderian, Daniela B. title = In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling date = 2020-09-07 keywords = SARS; aerosol; particle summary = title: In vitro comparison of surgical techniques in times of the SARS-CoV-2 pandemic: electrocautery generates more droplets and aerosol than laser surgery or drilling Five typical surgical intervention techniques (mechanical stress with a passive instrument with and without suction, CO(2) laser treatment, drilling and bipolar electrocoagulation) were examined and compared regarding resulting particle release. The aim of the presented study was therefore to develop an experimental setup for the simultaneous assessment of aerosol and particle formation in various typical ENT interventions. Similarly, no particle or aerosol formation was detected during mechanical impact by use of a passive instrument in direct tissue contact with additional suction (cf. The laser treatment of the tissue did not lead to a detectable particle formation at any of the three points in time of the analysis (see Fig. 3 , third line). doi = 10.1007/s00405-020-06330-y id = cord-330121-eadu2ba3 author = Gudmundsdottir, Ágústa title = Inactivation of SARS‐CoV‐2 and HCoV‐229E in vitro by ColdZyme® a medical device mouth spray against common cold date = 2020-09-25 keywords = SARS summary = It contains glycerol and minor amounts of purified cold-adapted trypsin 5 The entry of coronaviruses into host cells is mediated by the spike (S) glycoprotein that forms homo-trimers protruding from the virus surface 11 . Based on the results presented in this study, CZ-MD was found to inactivate SARS-CoV-2 (98.3%) and HCoV-229E (99.9%) in vitro (Table I) Coronaviruses cause about one-third of the common cold cases 4 Entry of coronaviruses into susceptible cells requires receptor-binding of the S protein and it''s proteolytic processing by host cell proteases that occurs in a concerted action to promote virus-cell fusion 3 . However, the in vitro study presented here clearly demonstrates that the CZ-MD (containing cod trypsin) inactivates SARS-CoV-2 and HCoV-229E. Although the in vitro results presented cannot be directly translated into clinical efficacy, the study indicates that CZ-MD might offer a protective barrier against coronaviruses such as SARS-CoV-2 and a decreased risk of COVID-19 transmission. doi = 10.1002/jmv.26554 id = cord-294120-8fxrqorg author = Guebre-Xabier, Mimi title = NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date = 2020-08-19 keywords = SARS summary = title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge Cynomolgus macaques (Macaca fascicularis) immunized with NVX-CoV2373 and the saponin-based Matrix-M adjuvant induced anti-S antibody that was neutralizing and blocked binding to the human angiotensin-converting enzyme 2 (hACE2) receptor. And, hACE2 receptor 158 inhibition titers of 649, 1,410, and 1,320 in 2.5, 5, and 25 µg NVX-CoV2373 dose groups 159 respectively were 5.2 -11.2-fold higher than in convalescent sera ( Figure 1C) . Finally, 160 SARS-CoV-2 GMT neutralization antibody titers of 17,920 -23,040 CPE 100 in 161 immunized macaques, were 7.9 -10.1-fold higher than in convalescent sera ( Figure 162 1D) . To evaluate the potential efficacy of NVX-CoV2373 vaccine, macaques were 165 challenged with SARS-CoV-2 virus in upper and lower airways. SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 214 elicits immunogenicity in baboons and protection in mice These interests do not alter the authors adherence to policies on 209 sharing data and materials. doi = 10.1101/2020.08.18.256578 id = cord-336909-nnxa5ant author = Guedez-López, Gladys Virginia title = Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2 date = 2020-08-17 keywords = Prometheus; SARS summary = The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. RT-qPCR tests presented a high specificity with a low probability of false positive; however, sensitivity relies on different factors as specimen site, method of collection, viral load and time from the onset of symptoms [3, 7] . Detection rate of IgM, IgG and IgM/IgG antibodies against SARS-CoV-2 with the three ICT strip assays in positive and negative RT-PCR patients along three periods of time since the onset of symptoms is shown in Table 3 . Detection rates of total antibodies (IgM/IgG) obtained with Sienna® and Wondfo® by the two groups of patients along the three stages since the symptoms onset are collected in Table 4 . In this study, we have investigated the diagnostic value of detection of SARS-CoV-2 IgM and IgG antibodies in different stages of the disease, using three ICT strip assays, in comparison with RT-qPCR. doi = 10.1007/s10096-020-04010-7 id = cord-255284-ffh1jl40 author = Guery, B title = Syndrome respiratoire aigu sévère date = 2003-06-30 keywords = Coronavirus; Kong; SARS summary = Cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d''isoler l''agent responsable, un nouveau Coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l''épidémie. Deux éléments notables sont évoqués dans cette publication, tout d''abord le fait que seuls les patients atteints de SARS ont des anticorps témoignant du fait que ce virus circule pour la première fois. À noter que cette faculté existe chez un Coronavirus porcin entraînant des pathologies respiratoires mais, aucun lien de parenté entre ces deux virus n''a été mis en évidence. Dans le cas du SARS, les premières analyses montrent que la contamination nécessite un contact prolongé et répété avec un malade présentant une symptomatologie pulmonaire. ont montré la présente d''ARN du Coronavirus responsable du SARS dans les selles des patients [4] . doi = 10.1016/s0399-077x(03)00200-2 id = cord-337557-ct43uoir author = Guetl, Katharina title = SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia date = 2020-10-27 keywords = SARS summary = title: SARS-CoV-2 positive virus culture 7 weeks after onset of COVID-19 in an immunocompromised patient suffering from X chromosome-linked agammaglobulinemia (4, 5) Here, we report SARS-CoV-2 positive viral culture 7 weeks after onset of COVID-19 in a patient with an underlying immunosuppressive disorder, so-called X chromosome-linked agammaglobulinemia (XLA), demonstrating the potential of prolonged SARS-CoV-2 spreading beyond widely accepted isolation precautions. On April 15, five days after tocilizumab and convalescent plasma administration and five weeks after the initial diagnosis of COVID-19, SARS-CoV-2 RNA was not detectable for the first time. The patient showed progressive clinical recovery, but an alternating course of three negative followed by three positive SARS-CoV-2 RT-PCR results was subsequently observed. In summary, we have to assume that in our patient shedding of infectious SARS-CoV-2 stopped between week 7 and 10 of disease. doi = 10.1016/j.jinf.2020.10.025 id = cord-304899-vruq4r7z author = Guihot, Amélie title = Syndrome respiratoire aigu sévère : une épidémie singulière de pneumonie virale date = 2004-03-31 keywords = SARS; Sras summary = L''agent infectieux étiologique a rapidement été identifié comme étant un nouveau Coronavirus, baptisé Coronavirus associé au Sras (Sras-CoV).La transmission du virus est interhumaine, par les particules respiratoires principalement. n Chine du Sud-Est, au début de l''année 2003, une épidémie de pneumopathie hautement contagieuse et potentiellement mortelle a été signalée par les autorités sanitaires chinoises.Cette entité clinique d''étiologie inconnue a été baptisée Syndrome respiratoire aigu sévère (Sras) par l''Organisation mondiale de la santé (OMS). La ribavirine est un analogue nucléosidique utilisé comme anti-viral dans le traitement de l''hépatite C chronique (Rébétol ® ), en association avec l''interféron α .La ribavirine possédant une activité in vitro contre plusieurs virus respiratoires (virus syncytial respiratoire, virus de la grippe), elle a été utilisée empiriquement par plusieurs équipes chez des patients atteints de Sras. doi = 10.1016/s0755-4982(04)98581-8 id = cord-299499-66qh3r75 author = Guilamo-Ramos, Vincent title = Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date = 2020-09-07 keywords = AYA; SARS; covid-19 summary = In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. doi = 10.1093/cid/ciaa1348 id = cord-285449-frft2h85 author = Guillon, Patrice title = Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies date = 2008-09-25 keywords = CHO; Fut2; SARS summary = Severe acute respiratory syndrome coronavirus (SARS-CoV) is a highly pathogenic emergent virus which replicates in cells that can express ABH histo-blood group antigens. We observed that the S protein/angiotensin-converting enzyme 2-dependent adhesion of these cells to an angiotensin-converting enzyme 2 expressing cell line was specifically inhibited by either a monoclonal or human natural anti-A antibodies, indicating that these antibodies may block the interaction between the virus and its receptor, thereby providing protection. We present data indicating that the S protein/ACE2-mediated adhesion between cells expressing ACE2 and cells coexpressing the S protein and the A histo-blood group antigen can be specifically blocked by anti-A antibodies. To further evaluate the potential effect of the ABO polymorphism on the epidemiology of SARS, we present a model of its transmission dynamics that takes into account the effect of the protection by anti-histo-blood group natural antibodies. doi = 10.1093/glycob/cwn093 id = cord-325014-n7mnhk2v author = Gujski, Mariusz title = Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date = 2020-10-11 keywords = COVID-19; CoV-2; PCR; SARS summary = As the time window for a positive RT-PCR result is short, serological testing, which provides information about whether a person has been exposed to SARS-CoV-2, may be useful for epidemiological purposes to detect the overall burden of previous infection in a given community. The aim of this study was to determine the prevalence of current and past SARS-CoV-2 infections among police employees, a high-risk population due to their professional duties, during the COVID-19 epidemic. Neither sex (p =0.155) nor other variables listed in Figure 2 were significantly associated with the IgG results ( Figure 2 A logistic regression model predicting a positive anti-SARS-CoV-2 IgM+IgA index was developed (Cox and Snell R Square at 0.015 andNagelkerke R Square at 0.033). After including all variables listed in Figures 1 and 2 along with the number of registered cases and deaths due to COVID-19 (per 10,000 inhabitants), only 4 variables showed a correlation with a positive anti-SARS-CoV-2 IgM+IgA index. doi = 10.3390/jcm9103245 id = cord-286870-92eckkhk author = Gul, Seref title = In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials date = 2020-08-05 keywords = 3CL; SARS; figure summary = title: In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials The FDA-approved drug library was used to screen for the identification of molecules with high affinity to the active site of 3CL pro and nsp8 binding site of RdRp ( Figure 1 ). We also determined critical residues responsible for the high binding affinity of drugs to the protease, which may help to develop novel inhibitor molecules through rational drug design and quantitative structure-activity relationship (QSAR) studies. Conservation of these interactions during MD simulations and their contribution to BFE suggests that ergotamine can stably interact with the nsp8 binding site of RdRp. These results indicate that ergotamine and dihydroergotamine are possible candidates for further in vitro testing and clinical evaluation as an anti-SARS-CoV-2 agents. doi = 10.1080/07391102.2020.1802346 id = cord-338775-gh3a0wuf author = Gulersen, Moti title = Histopathological evaluation of placentas after diagnosis of maternal SARS-CoV-2 infection date = 2020-08-15 keywords = CoV-2; SARS summary = Study Design Retrospective cohort study of women diagnosed with SARS-CoV-2 infection who delivered at a single center from April 9th to April 27th, 2020, and had placental specimens reviewed by pathology. Histopathological characteristics were evaluated in each placenta and the incidence of these findings were compared between placentas after diagnosis of maternal SARS-CoV-2 infection and historical controls, as well as between placentas from patients with or without typical symptoms related to infection. Conclusions Based on our data, there are no significant placental histopathological changes that occur after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared to a gestational age-matched historical control group. The results of our study did not demonstrate significant placental histopathological changes 229 occurring after diagnosis of SARS-CoV-2 infection in the third trimester of pregnancy compared 230 to a gestational-age-matched historical control group with a similar incidence of antepartum or Pathology for examination or due to history of melanoma. doi = 10.1016/j.ajogmf.2020.100211 id = cord-280392-ij5gtesw author = Gultom, Mitra title = Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date = 2020-11-10 keywords = AEC; SARS summary = In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. The AEC 131 cultures from 12 different species (rhesus macaque, cat, ferret, dog, rabbit, pig, cattle, goat, llama, 132 camel, and two neotropical bats) were inoculated with 10.000 TCID50 of either IAV or IDV and incubated 133 at 33°C and 37°C. For IDV we observed 137 antigen-positive cells in all AEC model, except for rhesus macaque and one of the neotropical bat 138 species, indicating that the AEC cultures were all well-differentiated and susceptible to virus infection. In the viral sequences in the 96 hpi samples from virus-infected 156 rhesus macaque and cat AEC cultures, we observed no obvious signs of nucleotide transitions that lead 157 to nonsynonymous mutations compared to the respective inoculums ( Fig. 3) , irrespective of 158 temperature and animal species. doi = 10.1101/2020.11.10.374587 id = cord-314687-kyj6etnc author = Gunalan, Vithiagaran title = A putative diacidic motif in the SARS-CoV ORF6 protein influences its subcellular localization and suppression of expression of co-transfected expression constructs date = 2011-10-25 keywords = ORF6; SARS summary = Following this, a mammalian expression plasmid pXJ3''-ORF6 was transfected into Vero E6 cells and Confocal microscopy showed that the ORF6 protein localized to a similar population of intracellular vesicles. These alanine substitution mutants were cloned into the same vector as the wildtype ORF6 gene and titrated against the nsp8 gene, by co-transfection of Vero E6 cells with plasmids encoding for myc-nsp8 and either 2 g pXJ3'' ORF6 Figure 3 The ORF6 protein exerts a transcriptional effect on nsp8 expression. This indicated that the reduction in the suppression of the expression of co-transfected myc-nsp8 by ORF6A53-56 was significant, and therefore that the putative diacidic motif defined by amino acids 53-56 has a role to play in this ability of the ORF6 protein. This indicated that the putative diacidic motif from amino acids 53-56, in addition to being involved in the suppression of the expression of co-transfected myc-nsp8, is also involved in the subcellular localization of the ORF6 protein and therefore these 2 phenomena may be linked. doi = 10.1186/1756-0500-4-446 id = cord-273367-gl266pvt author = Gunawardana, M. title = Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date = 2020-07-28 keywords = July; RNA; SARS; preprint summary = Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. Subject 557 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on 558 symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but 559 tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A) . doi = 10.1101/2020.07.25.20160812 id = cord-329473-dtlwjndn author = Guo, Ao-Xiang title = The clinical characteristics and mortal causes analysis of COVID-19 death patients date = 2020-04-15 keywords = SARS; TMPRSS2 summary = Therefore, we supposed that the expression of ACE2 and TMPRSS2 in human tissues could be used to explain the clinical characteristics of COVID-19 patients, including coexisting disorders, direct causes of death and initial symptoms. Our results also proved that coexisting disorders of hypertension and heart disease and initial symptoms of dyspnea were significantly higher in death patients, which was consistent with the one previous study [7] . While that ACE2 was highly expressed in heart may be related with the attack of SARS-CoV-2 in heart, which may lead to the initial symptoms of palpitate and chest tightness in some patients, and the direct causes of death including circulatory failure, heart disease and cardiac arrest. The expression of the SARS-CoV-2 targets in these important organs such as lung, heart, liver and kidney may help to explain the clinical characteristics of death patients. doi = 10.1101/2020.04.12.20062380 id = cord-261834-x5ltmj30 author = Guo, Cheng-Xian title = Epidemiological and clinical features of pediatric COVID-19 date = 2020-08-06 keywords = COVID-19; SARS; pediatric summary = METHODS: A retrospective study was conducted on children with a definite diagnosis of COVID-19 in mainland China using the web crawler technique to collect anonymous COVID-19 updates published by local health authorities. In this report, we conducted a retrospective review of COVID-19 features in 341 pediatric patients with ages between 0 and 14 years with the overall goal of providing data that could help in the development of guidelines for the prevention and treatment of pediatric COVID-19. This retrospective review was conducted in children aged 0-14 years with a definite diagnosis of COVID-19 from local health authorities between January 15, 2020, and March 15, 2020, in mainland China. Although there is relatively ample information available for adult COVID-19 patients, our knowledge and analysis of the epidemiology and clinical characteristics of pediatric COVID-19 is quite limited. The data was obtained from local China health authorities thus unable to compare the epidemiological and clinical data from US and European studies in children with COVID-19. doi = 10.1186/s12916-020-01719-2 id = cord-270698-9w3ap3gz author = Guo, Hua title = Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date = 2020-05-13 keywords = ACE2; SARS summary = title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. Consistent results were observed by binding affinity assays between SARSand SARSr-CoV spike proteins and receptor molecules from bats and humans. In a host-virus arms race situation, the genes involved tend to display dN/dS ratios Codon-based analysis of molecular evolution 536 Bat ACE2 and SARSr-CoV spike sequences were analyzed for positive selection. Identification of key amino acid 671 residues required for horseshoe bat angiotensin-I converting enzyme 2 to function as a 672 receptor for severe acute respiratory syndrome coronavirus doi = 10.1101/2020.05.13.093658 id = cord-260376-29ih5c9v author = Guo, Jian-Ping title = SARS corona virus peptides recognized by antibodies in the sera of convalescent cases date = 2004-07-01 keywords = Orf; SARS; serum summary = title: SARS corona virus peptides recognized by antibodies in the sera of convalescent cases We synthesized on cellulose membranes 4942 ten-amino-acid peptides which included all of the sequences predicted for the severe acute respiratory syndrome (SARS) corona virus. Peptides incorporating all of the sequences predicted in the open reading frames of the SARS-CoV genome were prepared on derivatized cellulose membranes using a robotic peptide synthesizer (Autospot ASP 222, Intavis Bioanalytical Instruments, Lagenfeld, Germany). These data indicate that the four recovered cases developed antibodies with viral neutralizing potency between the time of acute and convalescent serum sampling. Therefore, those peptides strongly recognized on membranes probed with convalescent sera, but not with acute or control sera, should be the most immunodominant and may include SARS-CoV epitopes that are vulnerable to neutralization by antibody. Shown in Table 2 are the 24 overlapping membrane peptides that were recognized exclusively, or much more strongly, in multiple pairs of convalescent compared with the respective acute sera. doi = 10.1016/j.virol.2004.04.017 id = cord-203191-7ftg6bfx author = Guo, Kai title = Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data date = 2020-05-16 keywords = COVID-19; SARS; cell; drug summary = title: Identification of Repurposal Drugs and Adverse Drug Reactions for Various Courses of Coronavirus Disease 2019 (COVID-19) Based on Single-cell RNA Sequencing Data To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA approved drugs and pre-clinical small-molecule compounds by integrating the gene expression perturbation data by chemicals from the Library of Integrated Network-Based Cellular Signatures (LINCS) project with publically available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We also collected a list of differentially expressed genes (DEGs) in SARS-CoV-2-infected lung BALF using a bulk RNA-Seq analysis to compare against the single-cell-based data. Repurposing analysis in severe COVID-19 patients 60 potent drugs were also selected in severe cases compared to controls (severe vs healthy group) according to their average CS between the replicates, and 25 of them involved in more than one cell subtype ( Figure 2B , Supplementary Tables S8 & S9) . doi = nan id = cord-354943-wxhbwcfr author = Guo, Li title = Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date = 2020-03-21 keywords = COVID-19; PCR; SARS summary = METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. doi = 10.1093/cid/ciaa310 id = cord-320165-1b6sycgv author = Guo, Qirui title = Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date = 2020-09-09 keywords = MHV; Paquinimod; S100A8; SARS; figure summary = S100A8/A9 specific inhibitor, Paquinimod, significantly reduced the number of neutrophils activated by the coronavirus, inhibited viral replication and rescued lung damage a result of SARS-CoV-2 infection. The whole genome wide RNA-seq analysis of the lungs from infected rhesus macaques showed that a number of transcripts were induced or inhibited at day 3 and day 5 after SARS-CoV-2 infection (Supplementary Figure 1A) . Similar to the data from rhesus macaque experiments, compared to other alarmins, S100A8 was robustly induced by SARS-CoV-2 but not by IAV infection in mice ( Figure 2E ). The expression of these B cell related genes was rescued or induced by Paquinimod during MHV infection, which was confirmed by qRT-PCR analysis ( Figure 3M ). Moreover, both Paquinimod and Resatorvid suppressed the activation of coronavirus related neutrophils in lung during SARS-CoV-2 infection ( Figure 4D ). doi = 10.1101/2020.09.09.288704 id = cord-307932-7t41wvw3 author = Guo, Xiaoqin title = Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers date = 2020-02-14 keywords = SARS summary = title: Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers METHODS: A long-term prospective cohort study followed 34 SARS-CoV-infected healthcare workers from a hospital with clustered infected cases during the 2002-2003 SARS outbreak in Guangzhou, China, with a 13-year follow-up. Non-linear exponential decay models were used to estimate the average decay rates of the antibody CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In our cohort, we found that two healthcare workers might have been misdiagnosed with 236 SARS, as the IgG antibodies against both the whole virus and N199 antigen was persistently 237 lower than the cutoff value, for these two patients. Collectively, based on our results, we can infer that the IgG against SARS-CoV can persist at CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.02.12.20021386 id = cord-346987-fbqqf00i author = Guo, Yongwen title = Controls of SARS-CoV-2 transmission in orthodontic practice date = 2020-06-05 keywords = COVID-19; CoV-2; SARS; patient summary = ABSTRACT The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted worldwide concerns because of its high person-to-person infectivity and lethality, and it was labeled as a pandemic as the rapid increase of confirmed cases in most areas around the world became evident. Although the spread of COVID-19 has been effectively controlled in China and many areas have gradually resumed work and classes, orthodontic participants are still under high risks of SARS-CoV-2 infection. What''s more, the close contact between dental staffs and patients as well as the droplets and aerosols generated during treatment containing saliva and blood further increase the risk of SARS-CoV-2 transmission in dental practice 5 . We must constantly bear in mind that the threat of infection is not visible which poses a challenge on the orthodontic practice thus effective control measures should be taken to prevent the transmission of SARS-CoV-2 and protect both practitioners and patients from the COVID-19. doi = 10.1016/j.ajodo.2020.05.006 id = cord-298172-iyxyennq author = Guo, Youjia title = Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date = 2020-10-02 keywords = Fig; S1D7; S3D8; SARS summary = Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Among them, two antibodies were shown to attenuate the interaction of spike proteins with ACE2 and neutralized infection of VeroE6/TMPRSS2 cells by SARS-CoV-2. Mice were immunized with these recombinant spike proteins to generate antibodies against the SARS-CoV-2 virus, followed by cell fusion to generate a hybridoma-producing antibody. The performance of our antibodies in IP experiments prompted us to examine whether they were capable of inhibiting spike-ACE2 binding or even neutralizing SARS-CoV-2 infection. Our antibodies, S1D7 and S3D8, have been shown to attenuate the interaction of spike proteins with ACE2 and neutralize infection of VeroE6/TM2 cells by SARS-CoV-2. doi = 10.1101/2020.10.01.323220 id = cord-271536-pscw933i author = Guo, Zhen-Dong title = Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020 date = 2020-07-17 keywords = ICU; SARS summary = To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. Furthermore, we found that rates of positivity differed by air sampling site, which reflects the distribution of virus-laden aerosols in the wards ( Figure 2 , panel A). SARS-CoV-2 aerosol was detected at all 3 sampling sites; rates of positivity were 35.7% (5/14) near air outlets, 44.4% (8/18) in patients'' rooms, and 12.5% Figure 2 (1/8) in the doctors'' office area. First, SARS-CoV-2 was widely distributed in the air and on object surfaces in both the ICU and GW, implying a potentially high infection risk for medical staff and other close contacts. doi = 10.3201/eid2607.200885 id = cord-302541-0upiu6iq author = Gupta, Abhishek title = Lockdown—the only solution to defeat COVID-19 date = 2020-05-06 keywords = SARS summary = As it is a new strain of coronavirus and little is known about its behaviour except its potential for transmission while being asymptomatic during an incubation period of up to 14 days and its sensitivity to heat, Sophie Bushwick, technology editor at Scientific American, a science magazine, stated on 20 March 2020 that asymptomatic people with COVID-19 have a higher viral load. A lockdown period depends upon the virus'' faster decay rate which is directly related to the melting point of the outer protective lipid bilayers of SARS-CoV2. In the case of SARS-CoV2 being zoonotic, it is presumed that the melting point of its lipid layer should be around 40°C, resulting in its faster decay during the summer. Because coronavirus is transmitted from host to host only, keeping it away from a host for longer than its incubation period through a lockdown can cause its own death and defeat COVID-19. doi = 10.1007/s13410-020-00826-3 id = cord-276908-9jthjf24 author = Gupta, Akanksha title = COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date = 2020-07-06 keywords = COVID-19; RNA; SARS; viral; virus summary = In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. doi = 10.1002/slct.202001709 id = cord-317906-u5z5cpfk author = Gupta, Ishita title = Atypical Neurological Manifestations of COVID-19 date = 2020-06-08 keywords = COVID-19; SARS summary = The novel coronavirus (SARS-CoV-2), belonging to a group of RNA-enveloped viruses and believed to be transmitted by aerosol route, is a worldwide pandemic. However, to our knowledge, there are minimal studies on the neurological manifestations in SARS-CoV-2 positive patients. Our review aims to identify the various neurological manifestations in SARS-CoV-2 positive patients, which could be an added advantage in the early diagnosis and prevention of further complications of the nervous system. Other non-neurological symptoms were diarrhea, anorexia, myalgia, sore throat, dyspnea, chest pain, fatigue, headache, arthralgia, nausea, and vomiting (see Figure 2 and Table 3 ) [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] . The presentation of olfactory symptoms in SARS-CoV-2-affected patients is due to the fact that the illness spreads through the cribriform plate, which is in close proximity to the olfactory region [30] . Neurological manifestations in COVID-19 caused by SARS-CoV-2 doi = 10.7759/cureus.8518 id = cord-330717-uzrxtgrg author = Gupta, Madhu title = The need for COVID-19 research in low- and middle-income countries date = 2020-07-01 keywords = COVID-19; SARS summary = We therefore propose research in three broad areas as urgently needed to inform responses in lowand middle-income countries: transmission patterns of SARS-CoV-2, the clinical characteristics of the disease, and the impact of pandemic prevention and response measures. Targeted research activities should be done to help mitigate the potential burden of COVID-19 in lowand middle-income countries without diverting the limited human resources, funding, or medical supplies from response activities. We propose three broad research questions to inform public health and policy responses to COVID-19 in LMICs: (1) how do the patterns of SARS-CoV-2 transmission differ in resource-poor settings? A more thorough understanding of the relationship between climate, seasonality, and virus transmissibility could provide insights into the potential course of the pandemic in LMICs that tend to be warmer and more humid, supporting preparedness and response efforts in these settings. doi = 10.1186/s41256-020-00159-y id = cord-337032-s4g4g80w author = Gupta, Manoj Kumar title = In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel date = 2020-04-15 keywords = SARS; Vadde; protein summary = Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ''SARS-CoV2 E'' protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. By considering the above information, in the present study, authors employed computational approach for identifying the best possible structure of the ''SARS-CoV2 E'' protein present in the PDB database to understand its structure and function as well as its behaviour towards various phytochemicals. Subsequently, molecular docking of the ''SARS-CoV2 E'' protein with ligands having 250 conformations using the AutoDock tool revealed that the best ten phytochemicals with minimal binding energy are TIP006452 (Belachinal), TIP005365 (Macaflavanone E), TIP003272 (Vibsanol B), TIP003258 (14 R à ,15-Epoxyvibsanin C), TIP005363 (Macaflavanone C), TIP000749 (Luzonoid D), TIP008605 (Grossamide K), TIP009461 ((-)-Blestriarene C), TIP005366 (Macaflavanone F) and TIP005783 (Dolichosterone). doi = 10.1080/07391102.2020.1751300 id = cord-352059-1bjskqyg author = Gupta, Nivedita title = Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories date = 2020-04-28 keywords = China; NIV; Pune; SARS summary = The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, which is the apex laboratory for viral diagnosis and research in India, optimized the conventional and real-time PCR assays targeting different genomic regions of SARS-CoV-2 and initiated testing of suspected cases. Before initiating testing of clinical specimens from suspected cases of SARS-CoV-2, each VRDL shared results from the rRT-PCR runs performed with positive and negative controls with the apex laboratory (NIV, Pune). Expansion of testing capabilities and selection of testing laboratories for SARS-CoV-2: Following the increase in the load of screening samples from suspected cases with symptoms and travel history to China or asymptomatic persons with travel history to Wuhan after January 15, 2020, it was decided that strategically located VRDLs needed to start testing for SARS-CoV-2 in addition to Thereafter, NCDC, Delhi, initiated independent testing; however, results were shared with ICMR on a daily basis. doi = 10.4103/ijmr.ijmr_594_20 id = cord-339786-elrzlbsg author = Gurala, Dhineshreddy title = Acute Liver Failure in a COVID-19 Patient Without any Preexisting Liver Disease date = 2020-08-26 keywords = SARS; liver summary = Studies and data so far on coronavirus infections from China, Singapore, and other countries showed that liver enzymes elevation could be seen in 20-50% of cases. In another study published in the Lancet in February 2020 by Huang et al., an increase in aspartate aminotransferase (AST) was observed in 62% in intensive care unit (ICU) patients compared to 25% in non-ICU patients, indicating that more severe disease correlates with worsening of liver enzymes [10] . Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. Here, we report a case of acute liver failure in an elderly patient with COVID-19 infection who did not have a history of preexisting liver disease. In summary, we describe the first case of acute liver failure caused by the COVID-19 infection. doi = 10.7759/cureus.10045 id = cord-259566-qtlq7a6l author = Guraya, Salman Yousuf title = Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article date = 2020-06-23 keywords = SARS; covid-19; surgical summary = title: Transforming laparoendoscopic surgical protocols during COVID-19 pandemic; big data analytics, resource allocation and operational considerations; a review article Benefits of delaying elective and non-urgent surgery outweighs the risk of performing surgical procedures on patients with asymptomatic or active COVID-19 disease. Limiting the number of operating room personnel, use of disposable instruments, small trocar incisions, negative pressure environment, and setting energy devices at low modes can help reduce disease transmission during laparoendocsopic procedures. This write up provides a brief account of the impact of the COVID-19, big data analytics of response of medical personnel in curtailing and understanding the disease process and the consensus guidelines for carrying out laparoscopic and endoscopic procedures. -Limiting the number of operating room personnel, use of disposable instruments, negative pressure air flow, and setting electrocautery energy devices at low modes can possibly reduce disease transmission during laparoendocsopic procedures. doi = 10.1016/j.ijsu.2020.06.027 id = cord-265128-i0d4lxko author = Gurung, Arun Bahadur title = Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M(pro) enzyme through in silico approach date = 2020-05-22 keywords = CoV; MERS; SARS summary = Among coronaviruses, the main protease (M(pro)) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 M(pro) enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 M(pro), SARS-CoV M(pro) and MERS-CoV M(pro) were studied using molecular docking. Structure-based drug design primarily relies on molecular docking to identify lead molecules against the target proteins from chemical libraries [12, 13] . The natural products such as traditional medicines and plant-derived compounds (phytochemicals) are the rich sources of promising antiviral drugs [14] . The binding energies and inhibition constants of the phytochemicals with the SARS-CoV-2 M pro enzyme were compared with that of a set of twelve FDA approved antiviral drugs-a) Viral doi = 10.1016/j.lfs.2020.117831 id = cord-347366-0gier0lu author = Gurwitz, David title = Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics date = 2020-03-04 keywords = ACE2; SARS summary = A tentative suggestion based on existing therapeutics, which would likely be resistant to new coronavirus mutations, is to use available angiotensin receptor 1 (AT1R) blockers, such as losartan, as therapeutics for reducing the aggressiveness and mortality from SARS‐CoV‐2 virus infections. These tentative suggestions were based on the observation that SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor binding domain for its spike protein (Lu et al., 2020; Wan, Shang, Graham, Baric, & Li, 2020) , similarly to the coronavirus strain implicated in the 2002-2003 SARS epidemic (Dimitrov, 2003; Ge et al., 2013; Li et al., 2003; Prabakaran et al 2004; Turner, Hiscox, & Hooper, 2004) . The tentative suggestion to apply AT1R antagonists such as losartan and telmisartan as SARS-CoV-2 therapeutics for treating patients prior to the development of acute respiratory syndrome remains unproven until tried. doi = 10.1002/ddr.21656 id = cord-329318-eo8auo1f author = Gusarov, Sergey title = COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2 date = 2020-10-26 keywords = COSMO; SARS; descriptor; drug summary = [Image: see text] Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. In this study, we propose a novel set of drug screening descriptors based on COSMO-RS σ-profiles, augmented by dipole moment and induced charge of the phosphorus atom, to evaluate the chemical similarity of the drugs with nucleotides, as RNA replication transcription initiation activators. A novel set of descriptors based on COSMO-RS σ-profiles and chemical thermodynamics is proposed and evaluated using PCA for the initial screening of a series of nucleotides and nucleotide-analog RdRp replication inhibitor drugs to help accelerate the discovery of COVID-19 treatments. The PCA results show that the novel σ-profile-based descriptor set I clearly correlates the leading COVID-19 drugs remdesivir and EIDD-2801 in monophosphate forms and highlights weaker correlations with drugs that have been reported to exhibit anti-SARS-CoV-2 activity. doi = 10.1021/acs.jpclett.0c02836 id = cord-306414-2dv3qced author = Gutierrez, Lucas title = Deciphering the TCR Repertoire to Solve the COVID-19 Mystery date = 2020-06-20 keywords = COVID-19; SARS; TCR; cell summary = Advances in sequencing technologies and single-cell immune profiling can be leveraged to monitor adaptive immune responses in COVID-19 patients and guide future SARS-CoV-2 immunotherapy and biomarker development. Whether the aged and less diverse TCR repertoire impacts the ability to generate a sufficiently robust T cell response against SARS-CoV-2 in older patients remains to be studied. The development of faster and cheaper sequencing technologies, augmented by the advances in computational tools, support the feasibility of using TCR analyses not only to track SARS-CoV-2specific T cell expansion post-COVID-19 infection or in the course of treating patients with COVID-19, but also to establish certain features of the TCR repertoire architecture as predictive biomarkers for patients'' clinical outcome. Thus, a comprehensive characterization of the dynamics and composition of the TCR repertoires to SARS-CoV-2 infection can largely contribute to the evolving understanding of the functional and mechanistic involvement of the adaptive immune cell response and potentially guide the design of effective treatment. doi = 10.1016/j.tips.2020.06.001 id = cord-285739-0enn5bzn author = Gutiérrez Rodríguez, José title = Variables asociadas a mortalidad en una población de pacientes mayores de 80 años y con algún grado de dependencia funcional hospitalizados por COVID-19 en un Servicio de Geriatría date = 2020-07-16 keywords = COVID-19; SARS summary = Ese mismo día, tras un gran esfuerzo organizativo se abren las plantas para pacientes con COVID-19 en nuestro centro hospitalario: un total de 38 camas destinadas a pacientes mayores de 80 años con infección por coronavirus, que precisan hospitalización por presentar insuficiencia respiratoria aguda o descompensación de patología de base y que, en caso de empeoramiento clínico, no serían subsidiarios de beneficio de ingreso en UCI por sufrir algún grado de dependencia funcional y/o deterioro cognitivo 22 . En este ámbito asistencial, los objetivos de este trabajo han sido: a) estudiar las características epidemiológicas, clínica, analíticas y radiológicas de pacientes mayores de 80 años con algún grado de dependencia funcional y/o deterioro cognitivo ingresados con COVID-19 confirmado por diagnóstico de laboratorio, b) determinar la tasa de mortalidad, c) analizar las variables clínicas, terapéuticas, funcionales y mentales que se asocian a mayor riesgo de mortalidad. doi = 10.1016/j.regg.2020.07.002 id = cord-287247-vv0zc0gd author = Gutman, Julie R. title = Malaria and Parasitic Neglected Tropical Diseases: Potential Syndemics with COVID-19? date = 2020-06-01 keywords = Africa; COVID-19; SARS; malaria summary = With many LMICs implementing movement restrictions or ordering their populations to stay at home to limit SARS-CoV-2 transmission, the threat to essential health services is likely to be immediate, causing delays to diagnosis and treatment for other diseases, including malaria and NTDs. During the Ebola epidemic in West Africa, there were substantial reductions in all-cause outpatient visits and patients treated with antimalarial drugs 2 ; modeling the potential for similar disruptions in malaria control due to COVID-19 suggests that there could be up to an estimated 769,000 deaths due to malaria in 2020 (approximately double the number seen in 2018), mostly among children younger than 5 years. 58 Thus, coinfection with parasitic NTDs could result in altered risks and severity of clinical manifestations of SARS-CoV-2 infection, with the potential for decreased development of immunity with increased viral loads. doi = 10.4269/ajtmh.20-0516 id = cord-290378-h4cof32m author = Guy, Tiphaine title = High-flow nasal oxygen: a safe, efficient treatment for COVID-19 patients not in an ICU date = 2020-08-28 keywords = HFNO; SARS summary = SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. Patients infected with SARS-CoV-2 can develop severe pneumonia and respiratory failure, which often require treatment in intensive care units (ICU) in Western European countries (2) . This report describes the use of HFNO to manage SARS-CoV-2 infected patients with respiratory failure on the pulmonology ward rather than in an ICU. The theoretical risk of virus aerosolization resulted in early published reports of critically ill SARS-CoV-2-infected patients in China not recommending the use of HFNO or non-invasive ventilation until the patient had been cleared of COVID-19 (4). While these results should be confirmed in larger studies, we believe that our data strongly suggest that SARS-CoV2 infected patients with non-hypercapnic acute hypoxemic respiratory failure can benefit from HFNO outside an ICU. doi = 10.1183/13993003.01154-2020 id = cord-279406-wwdqh9qs author = Guzman, Norberto A. title = A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy date = 2020-07-30 keywords = ACM; BDNF; ELISA; IACE; SARS; capillary; exosome; figure; human; potential summary = To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses. It would be beneficial to have a sample processing method before separation, to isolate and concentrate the intended viruses or EVs. Immunoaffinity capillary electrophoresis has already been proven to be a useful technology to isolate, separate, and quantify cell-free molecules of biological interest based on the specificity and selectivity not only of antibody reagents, but also of lectin and aptamer reagents, quantifying molecules ranging from microgram/milliliter to femtogram/milliliter [25, 54, 55, 57, 75] . doi = 10.3390/biomedicines8080255 id = cord-327459-tyhy784d author = Gómez-Rial, J. title = A strategy targeting monocyte-macrophage differentiation to avoid pulmonary complications in SARS-Cov2 infection date = 2020-04-23 keywords = SARS summary = Gómez-Rial J, MD 1,2 , Martinón-Torres F, MD, Phd, Assoc Prof 1 The immune dysregulation and cytokine storm observed in severe COVID-19 cases has led to the trial of licensed RA drugs such as Chloroquine, IL-1/IL-6 blockers, TNF or Janus kinase inhibitors in COVID-19 patients [1] In addition we propose that blockade of granulocyte macrophage-colony stimulating factor (GM-CSF) may be an effective strategy to prevent pulmonary complications and fatality in SARS-Cov2 infection. and inflammation-related phenotypic changes in peripheral blood monocytes, and correlation with acute respiratory distress syndrome (ARDS) in severe patients [5] Furthermore, single-cell RNA sequencing of lung bronchoalveolar immune cells infection [6] If these findings are confirmed, they would indicate that in SARS-Cov2, similarly to SARS-Cov1, acute lethal disease is produced by delayed and dysregulated type I interferon response and pulmonary accumulation of inflammatory monocytemacrophages, which are mainly responsible for immunopathology [6, 7] . doi = 10.1016/j.clim.2020.108442 id = cord-298505-r7ihqb96 author = Górski, Andrzej title = Sepsis, Phages, and COVID-19 date = 2020-10-15 keywords = COVID-19; SARS; phage; sepsis summary = In fact, in addition to data obtained in experimental animals, there are already reports of successful phage therapy in patients with sepsis [2] . Phage therapy efficacy has also been studied in a mouse model of neonatal sepsis caused by Escherichia coli, Klebsiella pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Citrobacter freundii and Moraxella catarrhalis. High effectiveness of phage therapy in the treatment of experimental sepsis induced by multidrug resistant P. Further progress in phage therapy of sepsis has recently been achieved by introducing engineered phages used to treat a patient with a disseminated drug resistant mycobacterial infection. In recent years, a number of reports derived from experimental studies in animals and human clinics have suggested the potential value of phage therapy in the treatment of sepsis. The anti-inflammatory and the immunomodulating properties of phages could also be useful in the treatment of severe COVID-19 syndrome including viral sepsis (Table 2) . doi = 10.3390/pathogens9100844 id = cord-326532-2ehuuvnx author = Götzinger, Florian title = COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study date = 2020-06-25 keywords = COVID-19; Europe; ICU; SARS; child summary = This study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across Europe to inform physicians and health-care service planning during the ongoing pandemic. Significant risk factors for requiring ICU admission in multivariable analyses were being younger than 1 month (odds ratio 5·06, 95% CI 1·72–14·87; p=0·0035), male sex (2·12, 1·06–4·21; p=0·033), pre-existing medical conditions (3·27, 1·67–6·42; p=0·0015), and presence of lower respiratory tract infection signs or symptoms at presentation (10·46, 5·16–21·23; p<0·0001). For this cohort study, European members of the Paediatric Tuberculosis Network European Trials Group (ptbnet)-which currently includes 304 clinicians and researchers, most of whom are based at tertiary or quaternary paediatric infectious diseases or paediatric pulmonology units, across 128 paediatric health-care institutions in 31 European countries [15] [16] [17] [18] [19] [20] -were invited to contribute cases of confirmed SARS-CoV-2 infection that had been managed at or managed remotely by their health-care institution (including individuals admitted to other hospitals or identified during community screening) before or during the study period. doi = 10.1016/s2352-4642(20)30177-2 id = cord-348696-86nbwon2 author = Güemes-Villahoz, Noemi title = Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review date = 2020-08-18 keywords = COVID-19; CoV-2; SARS; ocular summary = title: Novel Insights into the Transmission of SARS-CoV-2 Through the Ocular Surface and its Detection in Tears and Conjunctival Secretions: A Review A multicenter study which documented potential risk factors for SARS-CoV-2 transmission in patients requiring intubation [7] reported that unprotected eye contact with secretions from infected patients was the most predictive variable for transmission to healthcare workers. A recent study evaluated the ocular tropism of SARS-CoV-2 in patients with confirmed COVID-19. Of the 56 subjects investigated there was only one patient who gave a history of prior pterygium surgery, with conjunctivitis and a positive PCR result from the conjunctival swab highlighting the importance of an intact ocular surface in resisting virus invasion [25] . Despite ocular complications not being a common clinically detectable manifestation of SARS-CoV-2 infection, recent evidence suggests that ocular exposure may represent a major transmission route for the virus. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection SARS-CoV-2 RNA detection in tears and conjunctival secretions of COVID-19 patients with conjunctivitis doi = 10.1007/s12325-020-01442-7 id = cord-354134-gb2pf5kb author = Güemes-Villahoz, Noemi title = Conjunctivitis in COVID-19 patients: frequency and clinical presentation date = 2020-08-29 keywords = COVID-19; SARS; conjunctivitis summary = Given the current situation of the SARS-CoV-2 pandemic, describing the clinical characteristics of conjunctivitis associated with the novel coronavirus has relevant implications in the future identification of suspected COVID-19 patients and the differential diagnosis from other forms viral conjunctivitis. A study analyzing a sample of 1099 patients hospitalized for COVID-19 disease in China found a prevalence of conjunctivitis symptoms of only 0.8% and other small series have reported a prevalence around 3% [4, 6, 7] . Despite our study showed no difference in the clinical presentation of conjunctivitis in male and female, we found that conjunctivitis was more frequent in males with moderate COVID-19 and women with mild disease. A better understanding of the ocular manifestations of the virus will assist in early identification of SARS-CoV-2infected cases, prioritizing diagnostic testing in patients with clinical findings compatible with conjunctivitis associated with COVID-19. doi = 10.1007/s00417-020-04916-0 id = cord-314926-4bltio08 author = Ha, Le Dang title = Lack of SARS Transmission among Public Hospital Workers, Vietnam date = 2004-02-17 keywords = SARS summary = The severe acute respiratory syndrome (SARS) outbreak in Vietnam was amplified by nosocomial spread within hospital A, but no transmission was reported in hospital B, the second of two designated SARS hospitals. Our study documents lack of SARS-associated coronavirus transmission to hospital B workers, despite variable infection control measures and the use of personal protective equipment. In conclusion, we found no evidence of SARS-CoV transmission among hospital B workers, despite contact with laboratory-confirmed SARS case-patients and variable infection control practices and use of personal protective equipment. This finding may be explained by differences in infection control practices, use of personal protective equipment (including masks for patients as well as healthcare workers), nursing style, environmental features, and clinical factors such as severity of illness and the absence of a highly infectious SARS-CoV spreader. doi = 10.3201/eid1002.030707 id = cord-288231-vg8bwed9 author = Haagmans, Bart L. title = The Application of Genomics to Emerging Zoonotic Viral Diseases date = 2009-10-26 keywords = SARS; host; virus summary = Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. doi = 10.1371/journal.ppat.1000557 id = cord-351649-87g7g5au author = Haagmans, Bart L. title = SARS date = 2009-01-30 keywords = CoV; SARS; vaccine summary = Because the disease in macaques caused by SARS-CoV infection was pathologically similar to that seen in human patients with SARS, and since the virus should induce highly cross-reactive neutralizing antibodies to protect against newly emerging viruses related to SARS-CoV and protect both the gastrointestinal and respiratory tract in the absence of significant side effects. African green monkeys immunized via the respiratory tract with two doses of a recombinant Newcastle disease virus encoding the S protein developed a relatively high titer of SARS-CoV neutralizing antibodies and upon challenge demonstrated a 1000-fold zoonotic coronaviruses. Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region A single immunization with a rhabdovirus-based vector expressing severe acute respiratory syndrome coronavirus (SARS-CoV) S protein results in the production of high levels of SARS-CoV-neutralizing antibodies doi = 10.1016/b978-0-12-369408-9.00036-6 id = cord-260191-0u0pu0br author = Haas, W. title = „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date = 2004-05-29 keywords = HIV; Influenza; SARS; der; die summary = Abstract Some emerging infectious diseases have recently become endemic in Germany.Others remain confined to specific regions in the world.Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms.Several of these emerging infections will be explained.HIV is an example for an imported pathogen which has become endemic in Germany.SARS and avian influenza are zoonoses with the potential to spread from person to person.Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain.Outbreaks of dengue fever in endemic areas are reflected in increased infec-gehäuften Erkrankungen bei Rückkehrern wieder.West-Nil-Virus-Erkrankungen kommen derzeit nur als importierte Erkrankungen in Deutschland vor.Wichtig ist,diese Erkrankungen frühzeitig in die differenzialdiagnostischen Überlegungen des Klinikers einzubeziehen,um die erforderlichen Maßnahmen zur Diagnostik,Therapie und zum Infektionsschutz rechtzeitig einleiten zu können.Dies erfordert ein gutes Zusammenspiel mit dem Labor und dem öffentlichen Gesundheitsdienst. doi = 10.1007/s00108-004-1199-2 id = cord-291747-3du4jluy author = Habashy, Noha H. title = The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking date = 2020-11-11 keywords = SARS summary = title: The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking We evaluated the predicted anti-SARS-CoV-2 effect of major royal jelly protein (MRJP)2 and MRJP2 isoform X1, which recently showed high efficacy against other enveloped RNA-viruses (HCV and HIV). Since the end of 2019 to the present, severe acute respiratory syndrome 47 coronavirus 2 (SARS-CoV-2) has caused widespread infection and is considered 48 a threat to public health security. SARS-CoV-2, severe 865 acute respiratory syndrome-related coronavirus; nsps, non-structural proteins. Structural and 661 molecular modelling studies reveal a new mechanism of action of 662 chloroquine and hydroxychloroquine against SARS-CoV-2 infection The potential antiviral effect of major royal jelly protein2 and its 835 isoform X1 against severe acute respiratory syndrome coronavirus 2 836 (SARS-CoV-2): Insight on their sialidase activity and molecular 837 docking doi = 10.1016/j.jff.2020.104282 id = cord-262250-o7qhncic author = Habel, J. R. title = Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype date = 2020-08-19 keywords = CD8; SARS summary = Using peptide-HLA-I tetramers, we performed direct ex vivo tetramer enrichment to define the frequency and activation profiles of the responding SARS-CoV2-specific CD8 + T-cells in acute and convalescent COVID-19 patients and in prepandemic PBMCs, tonsil and lung tissues from uninfected donors. 17.20176370 doi: medRxiv preprint To further probe the the responsiveness of A2/SARS-CoV-2 CD8 + T-cells from uninfected versus convalescent COVID-19 donors, PBMCs or tonsil cells were stimulated with the S 269 and Orf1ab 3183 peptides and cultured in vitro for 10 days. Our findings show that, while ''early memory'' CD8 + T-cells can be detected in convalescent HLA-A*02:01 COVID-19 patients at frequencies ∼5-fold higher than those from pre-pandemic samples, the SARS-CoV-2-specific response was ∼10-fold lower than that found regularly for CD8 + T-cells directed at IAV or EBV epitopes. Even so, it is the case that SARS-CoV-2-specific CD8 + T-cells were found in all COVID-19 acute and convalescent donors, and in stored pre-pandemic PBMC and tonsil samples (but not lung tissues) from HLA-A*02:01 children, mature adults and the elderly. doi = 10.1101/2020.08.17.20176370 id = cord-349923-cja8i0hw author = Habibzadeh, Parham title = The Novel Coronavirus: A Bird''s Eye View date = 2020-02-05 keywords = China; SARS; coronavirus summary = C oronaviruses typically result in respiratory and enteric infections affecting both animals and humans, and were considered relatively benign to humans before the severe acute respiratory syndrome (SARS-CoV) outbreak in 2002 and 2003 in China. [1] [2] [3] [4] A decade later, Middle East respiratory syndrome coronavirus (MERS-CoV), another pathogenic coronavirus with a clinical picture reminiscent of SARS, was isolated in patients presenting with pneumonia in the Middle Eastern countries. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. doi = 10.15171/ijoem.2020.1921 id = cord-280924-g6062fwk author = Hachim, Mahmood Yaseen title = Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date = 2020-06-10 keywords = IFITM3; SARS; gene summary = title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. To effectively address the ongoing COVID-19 pandemic, there is a recognized need for a framework for rapid identification of novel targets for diagnostic and therapeutic interventions as well as determine clinically approved drugs with high potential for repurposed use against SARS-CoV-2. In this study, we have applied this approach, and our findings have identified IFITM3 as an early upregulated gene and indicate that valproic acid enhances IFITM3 mRNA expression and antiviral action. Our toxicogenomic analysis showed that valproic acid increased the mRNA expression of IFITM3, supporting a new report that the SARS-CoV-2-human protein-protein interaction map showed that valproic acid might be a potential repurposing drug for COVID-19 (34) . doi = 10.3389/fimmu.2020.01372 id = cord-310920-itqwhi6a author = Haddad, Christina title = Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date = 2020-07-02 keywords = RNA; SARS; viral; virus summary = Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. doi = 10.1016/j.ymeth.2020.06.013 id = cord-353475-dtn7h1gj author = Haddad, Hazem title = miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date = 2020-08-20 keywords = RNA; SARS summary = In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. To understand the early steps of COVID-19 infection, we predicted miRNAs sequences targeting the submitted 29903bp of viral ss-RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 complete genomic RNA sequence) from the isolate of Wuhan-Hu-J o u r n a l P r e -p r o o f 1. doi = 10.1016/j.ncrna.2020.08.002 id = cord-340008-2efzyki4 author = Haddadi, Kaveh title = Coronavirus Disease 2019: Latest Data on Neuroinvasive Potential date = 2020-09-17 keywords = CNS; COVID-19; SARS summary = Similar to other respiratory viruses, severe acute respiratory syndrome coronavirus (SARS-COV-2) may enter the brain via the hematogenous or neuronal route; however, only a few reports are available on the neurological complications of COVID-19. Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel coronavirus, originated in China in December 2019 and rapidly progressed into an epidemic infection, such that the World Health Organization (WHO) termed this calamitous virus "coronavirus disease 2019 (COVID-19)". Indeed, while the bulk of research conducted and published thus far has focused on the mechanisms whereby SARS-CoV-2 targets the respiratory system, more recent investigations have reported disconcerting evidence of the entrance of this new coronavirus into the CNS via different ways, resulting in significant damage to this system or even death due to its infection. Some investigators in China reported that more than 30% of their 214 patients with COVID-19 presented with neurological signs and symptoms; they, therefore, concluded that SARS-CoV-2 might attack the CNS through blood or retrograde neuronal routes, causing the destruction of the CNS. doi = 10.30476/ijms.2020.85980.1561 id = cord-328246-boxsf2sz author = Hadi-Alijanvand, Hamid title = Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes date = 2020-07-27 keywords = ABF; ACE2; SARS summary = 48 In the current study, the input structures for PISA to predict the dissociation free energy of the complex are FoldX-generated mutant 3D structures of ACE2 in association with the RBD of the S1 protein. Free energy of ACE2 binding to RBD of SARS-CoV-2 spike protein 1 is also estimated in the current work by using MM-GBSA approach for mutations in ACE2 that are reported for Iranian ethnic groups by NAMD 2.13. In the current study, we predict the effect of 240 widespread missense mutations in the ACE2 gene reported for different human populations and especially eight ones specific for Iranian ethnic populations on the binding affinity between ACE2 and S1 RBD of SARS-CoV-2 with different computational approaches from bioinformatic methods to a thermodynamic integration procedure. We report the predicted affinities of 240 mutated versions of ACE2 to S1 of SARS-CoV-2 using the mentioned fast structure-based computational methods in Figure 1 . doi = 10.1021/acs.jproteome.0c00348 id = cord-321580-3ru92tra author = Hadler, James L title = Will SARS-CoV-2 prevention efforts affect the coming influenza season in the United States and northern hemisphere? date = 2020-09-07 keywords = SARS summary = The initial country-level responses to SARS-CoV-2 have provided substantial evidence of their collective impact on the COVID-19 pandemic and, incidentally, on seasonal influenza epidemics. As a country, it has perhaps the largest influenza sentinel surveillance system in the world, including active testing for influenza, and it was the first country to implement highly successful NPIs against SARS-CoV-2, giving it the best opportunity to see a possible change in influenza before the expected seasonal decline. To know what might happen with influenza this coming fall and winter, we need to know what has happened prospectively in southern hemisphere countries, especially those that like the US have used fewer NPI''s and used them with less rigor and, correspondingly, been less successful in controlling SARS-CoV-2 transmission. Nonpharmaceutical interventions used to control COVID-19 reduced seasonal influenza transmission in China doi = 10.1093/infdis/jiaa571 id = cord-356030-bbj4r81i author = Haehner, Antje title = Predictive Value of Sudden Olfactory Loss in the Diagnosis of COVID-19 date = 2020-06-11 keywords = SARS; covid-19 summary = The aim of this study was to investigate the frequency of olfactory loss in an outpatient population who presented to a coronavirus testing center during a 2-week period and to evaluate the diagnostic value of the symptom "sudden smell loss" for screening procedures. METHODS: In this cross-sectional controlled cohort study, 500 patients who presented with symptoms of a common cold to a corona testing center and fulfilled corona testing criteria completed a standardized diagnostic questionnaire which included the patients'' main symptoms, time course, and an additional self-assessment of the patients'' current smell, taste function, and nasal breathing compared to the level before the onset of symptoms. CONCLUSION: Considering the high frequency of smell loss in non-hospitalized COVID-19 patients, acute olfactory impairment should be recognized as an early symptom of the disease and should be tested for on a regular basis. doi = 10.1159/000509143 id = cord-258708-da6x5rxa author = Hafiane, Anouar title = SARS-CoV-2 and the cardiovascular system date = 2020-07-16 keywords = ACE2; COVID-19; SARS; patient summary = The coronavirus disease COVID-19 is a public health emergency caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In COVID-19, particular attention has been given to the role of angiotensin-(Ang) converting enzyme 2 (ACE2), and the binding site for SARS-CoV-2 cellular entry (3). One of the clinical features of patients infected with SARS-CoV-2 included abnormal features such as acute cardiac injury (12%) (22) . Significance of the SARS-CoV-2 infection in the CV system is reflected through incidences of acute myocardial injury, arrhythmias, ACS, sepsis, septic shock, viral myocarditis, and heart failure. Coronavirus Disease 2019 (COVID-19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin-Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection 19) and Cardiovascular Disease: A Viewpoint on the Potential Influence of Angiotensin‐Converting Enzyme Inhibitors/Angiotensin Receptor Blockers on Onset and Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Infection doi = 10.1016/j.cca.2020.07.019 id = cord-272211-nkv6irr7 author = Hagan, Liesl M. title = Mass Testing for SARS-CoV-2 in 16 Prisons and Jails — Six Jurisdictions, United States, April–May 2020 date = 2020-08-21 keywords = SARS; testing summary = To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. To better understand SARS-CoV-2 prevalence in these settings, CDC requested data from 15 jurisdictions describing results of mass testing events among incarcerated and detained persons and cases identified through earlier symptom-based testing. In May 2020, CDC requested data from 15 jurisdictions (the Federal Bureau of Prisons [BOP], 10 state prison systems, and four city or county jails), describing SARS-CoV-2 mass testing events † and cases identified before mass testing. High SARS-CoV-2 prevalence detected during mass testing events in a convenience sample of correctional and detention facilities suggests that symptom-based testing underestimates the number of COVID-19 cases in these settings. doi = 10.15585/mmwr.mm6933a3 id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 keywords = Coronavirus; Protein; RNA; Replication; SARS; Virus summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). doi = 10.3390/v4113245 id = cord-266031-tlrsco40 author = Haghani, Milad title = Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCoV literature date = 2020-09-21 keywords = Covid-19; MERS; SARS; literature; study summary = To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. The decision on which general database to use (e.g. Web of Science (WoS) or Scopus) was mainly made on the basis of the number of indexed Covid-19 studies in particular, as the sector of the coronavirus literature that is currently emerging (compared to the literatures on SARS and MERS that have already stabilised). In this cluster, one can observe terms such as those associated with general public health including "wold health organisation", "public health", "public The map of keyword co-occurrences associated with the Covid-19 literature health service", "global health", as well as those associated with disease outbreaks including "emergency", "health risk" "epidemics", "pandemic", "outbreak", "viral diseases", "virus infection", "communicable disease", "transmission", "travel". doi = 10.1007/s11192-020-03706-z id = cord-300078-svu06v9c author = Haghani, Milad title = Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date = 2020-06-01 keywords = Covid-19; MERS; SARS; study summary = To compare the scientometric aspects of the studies on SARS, MERS and Covid-19, three separate datasets of publications on these three topics were retrieved from Scopus through three separate search strategies. Figures A1 and A2 in the Appendix illustrate the map associated with the SARS literature overlaid respectively with the average year of publication and average number of citations associated with the studies where these keywords have occurred. Maps of term occurrences based on the analysis of the title and abstract of studies on SARS, MERS and Covid-19 have also been presented in Figures 7, 8 and 9 respectively. An inspection of the maps overlaid with the average year of publications for SARS and MERS in Figures A1 and A3 in the Appendix suggests that, on average, this cohort of studies are generally the last to emerge in the published domain compared to the two other major clusters, but they receive relatively high citations on average (according to Figures A2, A4 and A6). doi = 10.1101/2020.05.31.126813 id = cord-343029-85ga6r7d author = Haghpanah, Abdolreza title = Potential mechanisms of SARS‐CoV‐2 action on male gonadal function and fertility: Current status and future prospects date = 2020-10-27 keywords = ACE2; ASA; SARS; dna summary = The aim of this review was to provide new insights into different possible mechanisms of involvement of male gonads with SARS‐CoV‐2 including investigating the ACE2 axis in testis, hormonal alterations in patients with COVID‐19, possible formation of anti‐sperm antibodies (ASA) and subsequently immunological infertility as a complication of SARS‐CoV‐2 infection. Considering the fact that the testis is highly enriched in ACE2 receptors and its vulnerability to SARS-CoV-2 invasion, detectable changes in semen analysis, alteration in sex hormones balance and, most importantly, anti-sperm antibodies (ASA) formation and sperm DNA fragmentation are considered to play a major role in male infertility. Search phrases used for different databases strategy included the following: "severe acute respiratory syndrome coronavirus 2", "2019 nCoV", "SARS-CoV-2", "coronavirus", "COVID-19", "reproductive system", "fertility", "infertility", "germ cells", "gamete", "spermatogonia", "spermatogenesis" "spermatozoa", "spermatozoan", "testis", "Sertoli cells", "Leydig cells", "Androgen", "steroidogenesis", "spermiogenesis", "spermiation", "development", "fertilization", "gonadal function", "sex hormones", "angiotensin-converting enzyme 2 receptor", "ACE2", "anti-sperm antibodies", "ASA", "sperm DNA fragmentation index", "DFI", and "semen analysis". doi = 10.1111/and.13883 id = cord-291561-sxvgue36 author = Haixu, Liang title = Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date = 2019-11-25 keywords = ASF; ASFV; China; Fig; GETV; SARS; virus summary = A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. doi = 10.1016/j.jinf.2019.11.014 id = cord-353391-o0s2h0y0 author = Haj Bloukh, Samir title = A Look Behind the Scenes at COVID-19: National Strategies of Infection Control and Their Impact on Mortality date = 2020-08-04 keywords = March; SARS; UAE; covid-19; figure summary = To investigate the importance of serum vitamin D levels, median age, temperature, and humidity we compare infection control measures and their impact on COVID-19-related fatalities in Portugal, Sweden, and Switzerland ( Figure 1 ). A study compared community-wide mask compliance in relation to the number of confirmed SARS-CoV-2 cases/fatalities in Hong Kong, Singapore, and other countries [29] . This mask-wearing strategy combined with social distancing, personal hygiene, cancellation of social gatherings, use of the home office, and school closures resulted in the effective control of the SARS-CoV-2 transmission compared to other neighboring countries [29] . We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. We investigated the SARS-CoV-2 pandemic in the United Arab Emirates (UAE) as an example of a highly populated, globally interconnected country with an equatorial hot climate and excellent control of the COVID-19 outbreak. doi = 10.3390/ijerph17155616 id = cord-291719-1ku6cmwj author = Hajjo, Rima title = A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date = 2020-10-06 keywords = BCG; CGS; COVID-19; SARS; gene summary = METHODS: We developed and employed a systems biology workflow capable of identifying small-molecule antiviral drugs and vaccines that can boast immunity and affect a wide variety of viral disease pathways to protect from the fatal consequences of emerging viruses. RESULTS: Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. Herein, we describe a unique drug and vaccine repurposing workflow, and list high confidence proteins and pharmacological classes of compounds, that work as BCG mimics at the system level by inducing beneficial long lasting trained immune response. Earlier studies suggested that the documented beneficial off-target effects of BCG in protecting from non-TB infections, including perhaps COVID-19, involve a potentiation of innate immune responses through epigenetic mechanisms (56) (57) (58) . doi = 10.1007/s11095-020-02930-9 id = cord-262635-fdwd99ah author = Hajra Martínez, Ismael El title = Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus date = 2020-08-07 keywords = SARS summary = key: cord-262635-fdwd99ah title: Presence of SARS-Coronavirus-2 in the ileal mucosa: another evidence for infection of GI tract by this virus cord_uid: fdwd99ah abdominal CT scan, a thickening of the terminal ileum was observed suggesting the presence of acute ileitis. The patient received empirical treatment with ciprofloxacin and metronidazole without any improvement. Microbiological stool examinations were negative, also for SARS-CoV-2 rRT-PCR test. April 29 th , the study was completed with an ileo-colonoscopy with ileal biopsy. The mucosa of ileum and colon was macroscopically normal, and the biopsy showed no damage. However, RT-PCR test on ileal tissue was positive for SARS-CoV-2 RNA. We repeated the SARS-CoV-2 rRT-PCR test on nasopharyngeal swab and it again came back negative. The patient improved over the next few days without any specific treatment. Evidence for Gastrointestinal Infection of SARS-CoV-2 Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis doi = 10.1053/j.gastro.2020.05.101 id = cord-341234-2zgfcrwc author = Hallak, Jorge title = Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil date = 2020-09-02 keywords = ACE2; CoV-2; SARS; patient summary = title: Concise practice recommendations for the provision of andrological services and assisted reproductive technology for male infertility patients during the SARS-CoV-2 in Brazil Recently, a group of 27 experts from 15 countries and five continents has argued that postponing andrological services and male infertility care during the COVID-19 pandemic could permanently compromise the prospects of biological parenthood for ''time-sensitive'' patients, thus resulting in a devastating psychological impact on men undergoing fertility-related treatment (1) . A recent probabilistic pilot study conducted in seven districts of the city of São Paulo to estimate the prevalence of herd immunity showed that about 5.2% individuals had SARS-CoV-2 IgG antibodies, corresponding to an overall infection rate We reiterate that andrological services and male infertility care cannot be considered low priority during the current SARS-CoV-2 pandemic, particularly for the most vulnerable patients, like those with cancer, patients using immunosuppressive therapy, and the azoospermic/cryptozoospermic men under medical or post-surgical treatment to improve spermatogenesis. doi = 10.1590/s1677-5538.ibju.2020.06.03 id = cord-273064-c58nf9vb author = Hallowell, Benjamin D. title = Severe Acute Respiratory Syndrome Coronavirus 2 Prevalence, Seroprevalence, and Exposure among Evacuees from Wuhan, China, 2020 date = 2020-09-17 keywords = SARS; United; Wuhan summary = At arrival in the United States and again at the quarantine facility, evacuees were asked to complete a US Traveler''s Health Declaration form disclosing any symptoms; they were also screened for illness and fever, asked about symptoms in the past 72 hours, and asked about any high-risk exposures (including working in or visiting healthcare settings; caring for or visiting persons with fever, respiratory illness, or a confirmed COVID-19 diagnosis; or visiting any live animal markets) in Wuhan in the past 14 days. The survey captured information on demographics, clinical signs/ symptoms, travel outside of Hubei Province, face mask use, limitation of time spent in public, and past high-risk exposures (including contact with confirmed COVID-19 case-patients; persons with fever, acute respiratory illness, or both; healthcare and laboratory facilities; and animals and live animal markets). doi = 10.3201/eid2609.201590 id = cord-257751-n7w1psr4 author = Halperin, Daniel T. title = Coping With COVID-19: Learning From Past Pandemics to Avoid Pitfalls and Panic date = 2020-06-30 keywords = SARS; States; United; child; covid-19 summary = As we wrestle with how best to mitigate COVID-19, it is imperative to concur on the likely main drivers of transmission (notably, infection clusters resulting from prolonged indoor respiratory exposure) in order to clearly explain risk and to determine the most effective, realistic behavioral and other means to reduce illness and mortality. What is clear, based on evidence from several countries (and despite media attention to statistically anomalous cases of healthy and younger victims), is that severe outcomes and deaths from COVID-19 are overwhelmingly associated with preexisting (and especially multiple) serious illnesses such as diabetes and heart disease, [14] [15] [16] more so in men and particularly when exacerbated by obesity and smoking. Moreover, the fact that between 96% (in the United States 16 ) and more than 99% (in Italy 14 ) of COVID-19-related deaths, at any age, have occurred in persons with preexisting conditions could suggest that even very old but otherwise healthy people may not be at greatly elevated risk of dying from the disease. doi = 10.9745/ghsp-d-20-00189 id = cord-278260-3o91v72a author = Halstead, Scott B title = COVID 19 Vaccines: Should we fear ADE? date = 2020-08-12 keywords = ADE; DENV; SARS summary = Within months large numbers of vaccinated children developed a severe breakthrough disease, called "atypical measles." [6] A similar outcome, "vaccine associated enhanced respiratory disease (VAERD)," was observed in infants, 4 -12 months of age, who were given formalininactivated respiratory syncytial virus (RSV) and a few months later infected by RSV. The biological behavior of some coronaviruses in non-human species together with evidence that human coronavirus antibodies enhanced infection of SARS or MERS CoVs in Fc receptor-bearing cells, in vitro, have led to speculations that ADE contributes to disease severity in humans. [11] It has been reported that high levels of SARS CoV-1 IgG antibodies circulated in severe SARS cases and that anti-S IgG neutralizing antibody (NAb) responses developed significantly faster after the onset of clinical symptoms in fatal compared with recovered cases leading some to attribute enhanced tissue damage to ADE. With others, we conclude that the differences in clinical, epidemiological and pathological features of SARS and DENV diseases suggest that iADE does not contribute to the severity of natural human coronavirus infections. doi = 10.1093/infdis/jiaa518 id = cord-260247-akujsk0s author = Hamed, Ehab title = Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar date = 2020-11-02 keywords = SARS summary = title: Rates of recurrent positive SARS-CoV-2 swab results among patients attending primary care in Qatar The group suggested recurrent positive rt-PCR results of more than 21 days following the resolution of symptoms as criteria for reinfection. Utilising the criteria set by the COCOREC study group, this record-based study reports on the cases with recurrent positive RT-PCR nasopharyngeal swab for SARS-CoV-2 results in primary health care corporation (PHCC) settings in Qatar. The study population included patients attending with documented SARS-CoV-2 rt-PCR results during the study period. What are the rates of recurrent rt-PCR SARS-CoV-2 positive results of more than 21 days, and what are the population characteristics? No previous studies reported to the rates of recurrent positive rt-PCR for SARS-CoV-2 infections. Given the extensive reporting of the SARS-CoV-2 infections, the number of case reports of recurrent positive and reinfection to date is extremely low, which agrees with our findings. doi = 10.1016/j.jinf.2020.10.029 id = cord-268206-ino9srb6 author = Hamed, Manal A. title = An overview on COVID-19: reality and expectation date = 2020-06-01 keywords = COV-2; COVID-19; RNA; SARS summary = Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. In the current SARS-COV-2 pandemic, Wu and McGoogan (2020) showed that patients with chronic diseases, including diabetes, were at higher risk for severe COVID-19 infection and mortality. The former (S) is the wild type which is milder while the latter (L) is the novel one which resulted in high binding affinity between SARS-COV-2 virus with angiotensin-converting enzyme 2 receptor in human cells. The use of convalescent plasma was recommended before as an important treatment during outbreaks of Ebola virus, Middle East respiratory syndrome coronavirus, SARS-COV-1, H5N1 avian influenza, and H1N1 influenza (Zhou et al. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. doi = 10.1186/s42269-020-00341-9 id = cord-263616-igprqlqr author = Hamid, Hytham K. S. title = Considerations for transanal surgery during COVID‐19 pandemic date = 2020-07-15 keywords = SARS summary = key: cord-263616-igprqlqr authors: Hamid, Hytham K. title: Considerations for transanal surgery during COVID‐19 pandemic date: 2020-07-15 journal: J Surg Oncol DOI: 10.1002/jso.26085 sha: doc_id: 263616 cord_uid: igprqlqr nan To the Editor, Elective colorectal cancer surgery at the oncologic hub of Lombardy inside a pandemic COVID-19 area Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis Prolonged presence of SARS-CoV-2 viral RNA in faecal samples Evidence for gastrointestinal infection of SARS-CoV-2 Detection of SARS-CoV-2 in different types of clinical specimens Isolation of 2019-nCoV from a stool specimen of a laboratory-confirmed case of the coronavirus disease 2019 (COVID-19) Detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child Coronavirus disease (COVID-19) in a paucisymptomatic patient: epidemiological and clinical challenge in settings with limited community transmission doi = 10.1002/jso.26085 id = cord-277659-afysef1e author = Hamilton, F. title = Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date = 2020-07-04 keywords = PCR; SARS summary = Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCW''s). In this paper, we report the kinetics and performance of this assay in three populations: confirmed (PCR +ve) and suspected COVID-19 patients, confirmed (PCR +ve) healthcare workers, and pre-pandemic controls with respiratory infection. The sensitivity of the Abbott SARS-CoV-2 IgG assay was estimated with 95% Confidence Intervals at different time points post symptom onset (DISCOVER patients) or first PCR positive result (healthcare workers). doi = 10.1101/2020.07.03.20145722 id = cord-341776-y7kpp10x author = Hamm, C. title = Zusammenhang zwischen Angiotensinblockade und Influenza-A-Inzidenz date = 2020-06-05 keywords = SARS summary = key: cord-341776-y7kpp10x cord_uid: y7kpp10x So wird unter anderem diskutiert, ob Medikamente, die auf das Renin-Angiotensin-Aldosteron-System (RAAS) wirken, für eine Infektion mit Coronaviren sensibilisieren. Bekannt ist, dass ACE2-Rezeptoren bei Influenza-A-induzierten Lungenschäden, insbesondere beim schweren akuten respiratorischen Syndrom (SARS), eine wichtige Rolle spielen. Ziel der im Folgenden vorgestellten epidemiologischen Studie war es daher, den Zusammenhang zwischen der Häufigkeit einer Influenzainfektion und der Therapie mit ACE-Hemmern bzw. Obwohl nicht sicher ist, ob diese Beobachtung auch auf SARS-CoV-2 übertragbar ist, ist sie in der derzeitigen Pandemieunsicherheit ein Beitrag, der bei eingeschränkten Therapieoptionen hohe Aufmerksamkeit hervorrufen muss. Wenn das Risiko zu erkranken geringer ist, verläuft dann die Erkrankung auch anders? Insgesamt stützt diese Beobachtung derzeit sicherlich die Empfehlung aller kardiologischen und Hypertoniefachgesellschaften [5] , die Therapie mit ACE-Hemmern oder ARB auch in Zeiten der COVID-19-Pandemie uneingeschränkt fortzuführen. Renin-angiotensin-aldosterone system blockers and the risk of Covid-19 Renin-angiotensin-aldosteronesysteminhibitors and risk of Covid-19 doi = 10.1007/s00108-020-00827-8 id = cord-348773-ulnc9gdv author = Hammoud, H. title = Post mortem pathological findings in COVID-19 cases: A Systematic Review date = 2020-10-14 keywords = COVID-19; October; SARS; international summary = Methods: A systematic search of electronic databases (PubMed, ScienceDirect, Google scholar, Medrxiv & Biorxiv) was carried out from December 2019 to August, 15th 2020, for journal articles of different study designs reporting postmortem pathological findings in COVID-19 cases. Articles were included if they met the following eligibility criteria: (1) addressed pathological reports of COVID-19 autopsies or postmortem cases, (2) involved human subjects (at least one case), (3) all study designs were involved (case report, case series, cross-sectional, case-control, randomized and non-randomized studies), (4) no language restrictions were applied. (13, 19, 20, 22-32, 34, 38-41, 44-65, 67) Regarding the included organs, this review described the histopathology of different organs as follows; Lung and pulmonary system was the most common described organ in 42 articles, ( is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Regarding the postmortem pulmonary pathology, our review showed that different histopathological findings had been identified among COVID-19 cases. doi = 10.1101/2020.10.11.20210849 id = cord-339381-vvh06d2c author = Han, Deheng title = SARS‐CoV‐2 was found in the bile juice from a patient with severe COVID‐19 date = 2020-06-12 keywords = SARS summary = In the case report, the novel coronavirus was found in the bile specimen from a patient with severe COVID‐19 by real‐time fluorescent RT‐PCR. SARS-CoV-2 was found in the bile juice from a patient with severe COVID-19 Coronavirus disease 2019 (Covid-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to 163 countries/areas since December 2019. Previous studies have reported that the SARS-CoV-2 could be detected in sputum, faeces, tears, urine and other specimens of infected patients [3, 4] . In the case report, the novel coronavirus was found in the bile specimen from a patient with severe Covid-19. In view of the patient''s medical history, the attending doctor considered bile duct obstruction as one of the reasons for liver function failure. To our knowledge, this is the first case in which bile juice SARS-CoV-2 was detected. doi = 10.1002/jmv.26169 id = cord-275993-isff6lp2 author = Han, Dong P title = Development of a safe neutralization assay for SARS-CoV and characterization of S-glycoprotein date = 2004-08-15 keywords = SARS; protein summary = Similar to other coronaviruses, spike (S)-glycoprotein of the virus interacts with a cellular receptor and mediates membrane fusion to allow viral entry into susceptible target cells. S-protein of coronaviruses, which is thought to function as a trimer (Delmas and Laude, 1990) , is responsible for both binding to cellular receptors and inducing membrane fusion for virus entry into target cells (Collins et al., 1982; Godet et al., 1994; Kubo et al., 1994) . Despite difficulties in detecting S-protein directly by immunoassays, proteins expressed from both pcDNA-S and pHCMV-S constructs were able to pseudotype MuLV particles to produce SARS pseudoviruses that could readily infect Vero E6 cells (Fig. 3A) . To assess whether SARS pseudoviruses we generated could be used to quantify virus-neutralizing antibodies, we examined their susceptibility to convalescent sera from SARS-CoV-infected patients. Pseudotyping of murine leukemia virus with the envelope glycoproteins of HIV generates a retroviral vector with specificity of infection for CD4-expressing cells doi = 10.1016/j.virol.2004.05.017 id = cord-294136-e69ao8j0 author = Han, Dongsheng title = COVID-19: Insight into the asymptomatic SARS-COV-2 infection and transmission date = 2020-08-27 keywords = COV-2; COVID-19; China; SARS summary = successfully isolated SARS-CoV-2 from throat swabs of two asymptomatic patients in a cell culture of Caco-2 cells, suggesting the potential for presymptomatic transmission [16] ; (5) Increasing studies show clear epidemiological evidence of human-to-human asymptomatic spread of COVID-19 (described in the following section); (6) Asymptomatic infection tends to be, but is not only, identified among young people (<20 years old) [14, 15, [17] [18] [19] ; And (7) the majority (>90%) of asymptomatic patients appears to have a milder clinical course during hospitalization [15] , but the severity of the symptoms of the secondary patients infected by SARS-COV-2 from asymptomatic patients varies based on their physical constitution [2, 20] . As the transmission of SARS-COV-2 may occur in the early course of infection and a high viral load in respiratory samples could be detected [13] , RT-PCR testing for this virus is more suitable for screening at earlier stages of infection in key populations, such as patients with obvious symptoms and close contacts of asymptomatic patients [35] . doi = 10.7150/ijbs.48991 id = cord-265350-k9yus2sv author = Han, Guan-Zhu title = Pangolins Harbor SARS-CoV-2-Related Coronaviruses date = 2020-04-06 keywords = SARS summary = Several recent studies identified SARS-CoV-2-related viruses in Malayan pangolins (Manis javanica), providing new insights into the host distribution and evolution of SARS-CoV-2-related viruses [3] [4] [5] [6] [7] . SARS-CoV and SARS-CoV-2 have been taxonomically classified into a single viral species, Severe acute respiratory syndrome-related coronavirus [8] . Whereas SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), two highly contagious CoVs that emerged in humans during the past two decades, might ultimately have bat origins, both of them were introduced into human populations through intermediate hosts [9] . Phylogenetic analysis based on the synonymous sites of RBD, whose evolution is less likely to be influenced by natural selection, shows that RaTG13 is more closely related to SARS-CoV-2 than are the GD pangolin CoVs (Figure 1B) , indicating that the high amino acid similarity between the GD pangolin CoVs and SARS-CoV-2 in the RBD might be due to convergent evolution [3] . doi = 10.1016/j.tim.2020.04.001 id = cord-351625-1we9wi1g author = Han, Huan title = Descriptive, Retrospective Study of the Clinical Characteristics of Asymptomatic COVID-19 Patients date = 2020-10-07 keywords = SARS; covid-19; patient summary = Since asymptomatic patients may be a greater risk of virus transmission than symptomatic patients, public health interventions and a broader range of testing may be necessary for the control of COVID-19. IMPORTANCE Asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a potential problem for pandemic control through public health strategies. Since asymptomatic patients have no clinical symptoms which can easily prevent timely diagnosis and treatment, they may cause a greater risk of virus transmission than symptomatic patients, which poses a major challenge to infection control. Thus far, many studies have analyzed the clinical characteristics of SARS-CoV-2-infected patients presenting levels of illness ranging from mild to severely critical (10, 11) . In this study, we enrolled 25 asymptomatic and 27 symptomatic COVID-19 patients and performed systematic analysis of different clinical characteristics. In this study, we systematically compared different complete blood counts, serum biochemistries, and immunologic responses from SARS-CoV-2-infected asymptomatic and symptomatic individuals. doi = 10.1128/msphere.00922-20 id = cord-303941-3lg1bzsi author = Han, Hui-Ju title = Bats as reservoirs of severe emerging infectious diseases date = 2015-07-02 keywords = Ebola; MERS; SARS; bat summary = Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Currently, bats have been considered to be natural reservoirs of SARS-CoV, MERS-CoV, NiV, HeV, Ebola virus, and Marburg viruses. The viruses discussed above tend to be restricted to certain geographic regions with a particular bat reservoir, such as HeV and NiV associated with flying foxes in Australia and Southeast Asia and Ebola virus associated with Egyptian fruit bats in Africa. Bats have been proposed as the natural reservoirs of viruses causing severe diseases in humans, such as NiV and HeV in Southeast Asia and Australia, Ebola and Marburg viruses in Africa, SARS-CoV in Asia and MERS-CoV in Middle East. doi = 10.1016/j.virusres.2015.05.006 id = cord-344038-20n74z3o author = Han, Mi Seon title = Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date = 2020-04-16 keywords = SARS summary = In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate''s clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother''s respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . doi = 10.1093/cid/ciaa447 id = cord-301115-sedfbjlw author = Han, Mingfeng title = Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date = 2020-08-28 keywords = RNA; SARS; covid-19 summary = title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity The results of our analysis demonstrated that the initial SARS-CoV-2 RNA loads varied in patients, but were comparable in different patient groups stratified by age, gender, comorbidities and disease severity. We compared the measured SARS-CoV-2 RNA levels in sputum specimens from COVID-19 patients at admission among groups divided according to age, sex, underlying diseases and disease severity (Fig. 2a) . a, b The measured SARS-CoV-2 RNAs levels in sputum (a) and throat swab (b) specimens from COVID-19 patients at admission were compared according to the age, sex, comorbidity, and the disease severity. In this study, we analyzed the clinical features including SARS-CoV-2 RNA load and immunological characteristics of peripheral blood in a patient cohort with COVID-19 from Anhui Province, China. doi = 10.1007/s00430-020-00693-z id = cord-255895-6at9gelt author = Han, Namshik title = Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date = 2020-08-25 keywords = Proguanil; SARS; Sulfasalazine; drug; figure summary = We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Importantly, treatment of Calu-3 and Vero E6 cell lines with Proguanil and Sulfasalazine led to a significant downregulation of the mRNA of key cytokines (Figures 4G-J and S8), which are dictated by the p38/MAPK signalling pathway and shown to become elevated during SARS-CoV-2 infection and replication (CXCL3, IFNB1 and TNF-A). Here we have used a series of computational approaches, including bespoke methods for data integration, network analysis, computer simulation and machine learning, to identify novel SARS-CoV-2 induced pathways that could be targeted therapeutically by repurposing existing and approved drugs ( Figure S9 ). doi = 10.1101/2020.08.24.265496 id = cord-330849-yt44k88m author = Han, Rachel H. title = Planning for Mental Health Needs During COVID-19 date = 2020-10-08 keywords = COVID-19; SARS; health; mental; pandemic summary = The purpose of this article, written from the perspective of military medical planners, is to present available data on the prevalence of specific mental health concerns and conditions from previous recent pandemics and COVID-19, as well as to provide data-informed recommendations for meeting the psychological needs of affected individuals. A combination of the following keywords in the title and/or abstract was used in searches of literature on the Southeast Asian Respiratory Syndrome (SARS), H1N1 influenza (H1N1), Middle Eastern Respiratory Syndrome (MERS), Ebola, and COVID-19 pandemics: mental health OR mental illness OR psychiatry OR psychology OR therapist OR PTSD OR posttraumatic OR post-traumatic stress disorder OR behavioral health OR anxiety [disorder] OR GAD OR depression/depressed OR complex grief AND data analysis OR statistic* OR prevalence OR percentage OR increase OR decrease. doi = 10.1007/s11920-020-01189-6 id = cord-313099-rpdlk1b6 author = Han, Xiaoyu title = Severe Acute Respiratory Syndrome Coronavirus 2 among Asymptomatic Workers Screened for Work Resumption, China date = 2020-09-17 keywords = SARS summary = After the outbreak in Wuhan, China, we assessed 29,299 workers screened for severe acute respiratory syndrome coronavirus 2 by reverse transcription PCR. We noted 18 (0.061%) cases of asymptomatic infection; 13 turned negative within 8.0 days, and 41 close contacts tested negative. A s the population of Wuhan, China, returns to work, asymptomatic cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being discovered among workers receiving health checkups for work resumption. We report on cases of asymptomatic SARS-CoV-2 infection among persons during work resumption screening in Wuhan. Among 29,299 persons screened by RT-PCR, we confirmed 18 (0.061%) cases of SARS-CoV-2 infection. Half the cases in our study showed negative IgM and IgG at the time of positive RT-PCR, suggesting recent infections (<14 days). In addition, 13 cases had negative RT-PCR assays <8 (range 3-14) days, suggesting a favorable prognosis for persons with asymptomatic infections. In addition, all 41 close contacts of the asymptomatic case-patients tested negative by RT-PCR. doi = 10.3201/eid2609.201848 id = cord-323072-4rsgeag7 author = Han, Xueqing title = The expression of SARS–CoV M gene in P. Pastoris and the diagnostic utility of the expression product date = 2004-12-01 keywords = SARS; protein summary = Since the outbreak of SARS in 2003, several laboratory diagnostic methods have been established, including real-time RT-PCR assay, whole-virus-based immunofluorescence assay (IFA), recombinant protein-based enzyme-linked immunosorbent assay (ELISA) and immunochromatographic tests, antigencapturing enzyme-linked immunosorbent assay, and Western blot (WB) assay. To test whether the recombinant M protein is effective as an ELISA antigen for detecting SARS-CoV patient serum, the sera from four healthy people and four SARS patients were used. Detection results of eight human sera by ELISA using purified recombinant M protein as antigen.# 1-4: sera from four healthy people, respectively, # 5-8: sera from four SARS patients, respectively. The results were in complete accordance with those of other assays, thus indicating that the recombinant M protein may be useful as an ELISA antigen for detecting specific antibodies to SARS-CoV in human sera. Recombinant protein-based enzyme-linked imunosorbent assay and immunochromatographic tests for detection of immunoglobulin G antibodies to severe acute respiratory syndrome (SARS) coronavirus in SARS patients doi = 10.1016/j.jviromet.2004.08.015 id = cord-295142-5sqkdpi8 author = Han, Y. title = The active lung microbiota landscape of COVID-19 patients date = 2020-08-23 keywords = BALF; SARS; covid-19 summary = The bronchoalveolar lavage fluid (BALF), containing microenvironment information on bronchioles and lung alveoli from the lower respiratory tract, is one of key sample types for characterizing the host inflammatory response and microbiota of COVID-19 patients as lung is one of main organs for the infection of SARS-CoV-2 (7, 8) . In this study, we systematically profiled the transcriptionally active microbiota landscape in BALF from COVID-19 patients and healthy individuals, identified microorganism composition in healthy individuals and COVID-19 patients, found disease-specific active microbes in the COVID-19 patient group, revealed the interaction between several bacteria or viruses and SARS-CoV-2. The diversity analysis revealed that the infection of SARS-CoV-2 probably caused a different lung microbiota composition in the COVID-19 patient group compared with the healthy group. Our study provides insight into the active microbiota in the lungs of COVID-19 patients and will contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. doi = 10.1101/2020.08.20.20144014 id = cord-354536-c9v9kbw8 author = Han, Yan-Jie title = Advances and challenges in the prevention and treatment of COVID-19 date = 2020-07-09 keywords = Coronavirus; MERS; RNA; SARS; virus summary = This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. doi = 10.7150/ijms.47836 id = cord-277870-o79wph9r author = Han, Yanqiang title = Potential inhibitors for the novel coronavirus (SARS-CoV-2) date = 2020-09-18 keywords = 3CL; Mpro; SARS summary = In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. In this study, we chose 3CL Mpro as the therapeutic target to ab initio investigate its inhibition mechanism and binding ability of these most promising drug molecules by ligand-protein docking program (Rosetta) and molecular dynamics (MD) simulations. Through molecular docking and kinetic analysis, we found that for repurposed drugs, the Chloroquine molecule has the strongest interaction with the 3CL Mpro, indicating that Chloroquine is the best potential inhibitor for SARS-CoV-2, followed by Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir. For docking and binding analysis, seven clinically approved inhibitors (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) were selected from previous reported virtual screening works or were found to be highly effective in the control of SARS-CoV-2 infection in vitro [6, 12] . doi = 10.1093/bib/bbaa209 id = cord-319590-f9qcabcx author = Han, Yanxiao title = Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2 date = 2020-04-14 keywords = RBD; SARS summary = Molecular dynamics simulations revealed that the α-helical peptides maintain their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2. 17 In this work, we design and simulate several peptide inhibitors against SARS-CoV-2, which included components from the virus-binding domains of ACE2; based on the recently released crystal structure (PDB code: 6M17 9 ). We have also designed other inhibitors that are closer to the ACE2 protein, whose parts are connected by peptide bonds, and which contain all 15 residues that initially bind to RBD in the 6M17 crystal structure. To examine how these potential inhibitors bind to RBD of SARS-CoV-2, we prepared these systems in the initial position known from the crystal structure (PDB: 6M17) and simulated them in physiological solution (Methods), as shown in Figure 2a −d. In Figure 2a , 200 ns long simulations showed that the helical structure of inhibitor 1 deforms from the left sideloose end unfolding, although it still binds to the RBD of SARS-CoV-2. doi = 10.1021/acsnano.0c02857 id = cord-271211-frkk6w0a author = Han, Yu title = The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID‐19): A Chinese perspective date = 2020-03-12 keywords = MERS; SARS summary = The Chinese government has taken emergency measures to control the outbreak and has undertaken initial steps in the diagnosis and treatment of 2019 novel coronavirus infection disease (COVID‐19). A study in South Korea showed that many environmental surfaces of patients with MERS were contaminated by MERS-CoV, and virus RNA was detected from environmental surfaces within 5 days after the last positive PCR of patients'' respiratory samples. 12 Guangzhou CDC also found SARS-CoV-2 in the house of a confirmed patient, 13 which serves as evidence of contact transmission. 20 The Lancet also reminded doctors not to ignore SARS-CoV-2 transmission via ocular surfaces as infected droplets and bodily fluids may easily contaminate the human conjunctival epithelium. 27 A study showed that during the outbreak of SARS-CoV, of all exposed health care workers, 7.5% were asymptomatic SARSpositive cases. SARS-CoV-2 viral load in upper respiratory specimens of infected patients doi = 10.1002/jmv.25749 id = cord-284366-snajbvr9 author = Han, Zhiyong title = Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date = 2020-07-01 keywords = PCR; SARS summary = [3] [4] [5] The diagnosis of COVID-19 considers clinical symptoms, GGO lesions in chest CT or Xray images, and positive RT-PCR test results for the presence of SARS-CoV-2 RNA in patient samples. For example, the guidelines of the National Health Commission of China state that patients must meet the following 4 benchmarks before they can be discharged: (i) be afebrile for at least 3 consecutive days, (ii) have significantly improved respiratory function, (iii) produce two negative SARS-CoV-2 RT-PCR test results at least 24 hours apart, and (iv) have significant improvement in lung GGO lesions determined by chest CT or X-ray imaging. In Table 1 , we summarize the information about patients who tested positive for SARS-CoV-2 RNA in post-discharge, follow-up examinations in China as described in the 12 published reports. Our analysis indicates that many of the discharged patients tested positive for SARS-CoV-2 RNA when feces or anal swabs were employed, even though they tested negative at the same time when nasopharyngeal or oropharyngeal or sputum samples were examined. doi = 10.1002/jmv.26250 id = cord-304016-4o2bpedp author = Hanage, William P. title = COVID-19: US federal accountability for entry, spread, and inequities—lessons for the future date = 2020-11-02 keywords = Health; OSHA; SARS; United; covid-19 summary = In this article we assess the impact of missteps by the Federal Government in three specific areas: the introduction of the virus to the US and the establishment of community transmission; the lack of national COVID-19 workplace standards and enforcement, and lack of personal protective equipment (PPE) for workplaces as represented by complaints to the Occupational Safety and Health Administration (OSHA) which we find are correlated with deaths 16 days later (ρ = 0.83); and the total excess deaths in 2020 to date already total more than 230,000, while COVID-19 mortality rates exhibit severe—and rising—inequities in race/ethnicity, including among working age adults. Finally, despite the initial federal failure to report COVID-19 data by race/ethnicity [6] , a combination of specific studies, state reporting, investigative journalism, and data trackers has revealed that a persistent feature of the pandemic has been the existence of racial/ethnic inequities in cases, hospitalizations, and mortality, especially with regard to increased risk among US Black, Latinx, and American Indian/Alaska Native populations compared to the US white non-Hispanic population [3-5, 7, 8, 69, 70] . doi = 10.1007/s10654-020-00689-2 id = cord-333264-jdvb8px4 author = Hanke, Leo title = An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction date = 2020-09-04 keywords = ACE2; Fig; RBD; SARS; cell; ty1 summary = Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. The S ectodomain was purified from filtered supernatant on Streptactin XT resin (IBA Lifesciences), followed by size-exclusion chromatography on a Superdex 200 in 5 mM Tris pH 8, 200 mM NaCl. The RBD domain (RVQ-VNF) of SARS-CoV-2 was cloned upstream of an enterokinase cleavage site and a human IgG1 Fc. This plasmid was used to transiently transfect FreeStyle 293F cells using the FreeStyle MAX reagent. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1038/s41467-020-18174-5 id = cord-171703-n22tr8f2 author = Hanmo, Li title = Robust estimation of SARS-CoV-2 epidemic at US counties date = 2020-10-22 keywords = COVID-19; SARS; September summary = In this work, we propose a robust approach of integrating test data and death toll to estimate COVID-19 transmission characteristics by a Susceptible, Infectious, Resolving (but not infectious), Deceased and reCovered (SIRDC) model initially studied in 7 . We have developed a novel approach to integrate test data and death toll to estimate probability of contracting COVID-19, as well as the time-dependent transmission rate and the number of active infectious individuals at the county level in the US. Furthermore, when we reduce the infectious period by 10% (or equivalently 4.5 days in total), while the transmission rate (β t in SIRDC model) is held the same, the PoC SARS-CoV-2 is reduced by 5 times for 26 counties in Washington and 146 counties in Texas, shown in Extended Data Figure 4 . doi = nan id = cord-338541-0yiuh017 author = Hannan, Md. Abdul title = Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response date = 2020-07-10 keywords = Autophagy; SARS; cell; immune summary = title: Intermittent fasting, a possible priming tool for host defense against SARS-CoV-2 infection: Crosstalk among calorie restriction, autophagy and immune response As a healthy practice, calorie restriction in the form of intermittent fasting (IF) in several clinical settings has been reported to promote several health benefits, including priming of the immune response. A comprehensive review has therefore been planned to highlight the beneficial role of fasting in immunity and autophagy, that underlie the possible defense against SARS-CoV-2 infection. In this review, we revisit the current knowledge of fasting as a possible important mediator that is involved in the diverse pathophysiological phenomena, including host immune response, autophagy, and the pathogenesis of SARS-CoV-2 infection. During adaptive immunity, autophagy plays an important role in major histocompatibility complex (MHC)-antigen presentation, lymphocyte development, thymic selection, inflammatory signaling, and cytokine regulation [10] . doi = 10.1016/j.imlet.2020.07.001 id = cord-269564-r5mmsnbx author = Hans, Diana title = Rapidly Fatal Infections date = 2008-05-31 keywords = MRSA; SARS; Staphylococcus; TSS; patient summary = Reports have suggested a mortality rate of 30% to 70% despite aggressive treatment [35] TSS is most commonly caused by Staphylococcus aureus and group A streptococcus. Unfortunately, complicated group A streptococcus infections are shown to have a high mortality rate despite aggressive antibiotic therapy, and penicillin has been shown to have limited effects if not initiated early in the disease. Fifty-three percent of the patients were positive for MRSA, and the risk factors associated with colonization included recent antibiotic use (within 3 months), hospitalization within the past year, skin or soft tissue infection on admission, and HIV infection [68] . PVL-positive S aureus pneumonia typically occurred in younger patients (median age, 14.8 years) who were previously healthy, and 75% were found to have had a viral infection in the preceding days. Two deadly viral infections that have emerged in recent years include severe acute respiratory syndrome (SARS) and influenza A (H5N1), also known as avian influenza or bird flu. doi = 10.1016/j.emc.2008.01.003 id = cord-343185-lbmbp9ca author = Hansen, C. B. title = SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals date = 2020-07-29 keywords = ELISA; July; RBD; SARS summary = Here we have developed novel flexible ELISA-based assays for specific detection of SARS-CoV-2 antibodies against the receptor-binding domain (RBD): An antigen sandwich-ELISA relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Detection of IgM, IgA and IgG antibodies against SARS-CoV-2 protein N was evaluated by analyzing 136 positive samples and 174 negative controls and ROC curve analyses were assessed to estimate the assay performance . To provide a better insight into antibody seroconversion during SARS-CoV-2 infection and reactivity against different locations on protein S and protein N, we conducted IgM, IgA and IgG detection in 90 positive samples against 14 protein fragments and short peptides located on the protein S and protein N structures, full-length RBD, protein S and protein N (Figure 2A ). We have developed an ELISA-based platform for detection SARS-CoV-2 antibodies comprising an indirect RBD S-ELISA for pan Ig detection and direct ELISAs for in-depth analyses of the IgM, IgA and IgG isotype responses towards RBD and protein N. doi = 10.1101/2020.07.27.20162321 id = cord-320158-6dh9e5rg author = Hansen, Richard title = Adaptations to the current ECCO/ESPGHAN guidelines on the management of paediatric acute severe colitis in the context of the COVID-19 pandemic: a RAND appropriateness panel date = 2020-09-01 keywords = ASC; COVID-19; RAND; SARS summary = CONCLUSION: Our COVID-19-specific adaptations to paediatric ASC guidelines using a RAND panel generally support existing recommendations, particularly the use of corticosteroids and escalation to infliximab, irrespective of SARS-CoV-2 status. [10] [11] [12] Panellists rated the appropriateness of specific interventions at various time points during a patient''s admission with ASC (admission, first-line therapy, rescue therapy, continued medical therapy on discharge and surgery) in the context of their SARS-CoV-2 swab status and the presence or absence of symptoms or signs of COVID-19 infection. After the second round of voting, agreement was present for all scenarios (DI<1) except two, both relating to SARS-CoV-2positive patients with symptoms or signs of infection; the use of ciclosporin with corticosteroids as rescue therapy and the use of prophylactic anticoagulation after discharge A detailed list of all scenarios, complete with median score, appropriateness rating and DI is shown in online supplementary table 2. doi = 10.1136/gutjnl-2020-322449 id = cord-296054-s8pibdeg author = Hanson, K. E. title = Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 date = 2020-10-21 keywords = NPS; SARS summary = title: Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2 We prospectively compared health care worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of coronavirus disease 2019 (COVID-19) in 354 patients. More cases were detected by the use of NPS (n = 80) and saliva (n = 81) than by the use of ANS (n = 70), but no single specimen type detected all severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Larger studies that compare the performance of patient self-collected ANS and straight saliva to health care worker-collected NPS for SARS-CoV-2 detection are needed. Therefore, we performed a prospective comparative study to evaluate the performance of patient self-collected ANS and saliva versus that of health care providercollected NPS for SARS-CoV-2 diagnostic testing. This study represents one of the largest prospective comparisons of specimen types to date and demonstrates excellent agreement between provider-collected NPS and patient self-collected saliva and ANS. doi = 10.1128/jcm.01824-20 id = cord-296588-q2716lda author = Hanson, Kimberly E title = Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date = 2020-06-16 keywords = COVID-19; SARS; patient; test summary = OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. doi = 10.1093/cid/ciaa760 id = cord-337973-djqzgc1k author = Hao, Siyuan title = Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date = 2020-08-28 keywords = ALI; HAE; SARS summary = title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Our observation that SARS-CoV-2 was unable to infect epithelial cells from the 299 basolateral side supports that the viral entry receptor ACE2 is polarly expressed at the apical 300 side 30, 31 . We 332 determined that 1 pfu of SARS-CoV-2 in Vero-E6 cells has a particle (viral genome copy) 333 number of 820, suggesting that a load of 2.46 x 10 5 particles is required to productively infect 1 334 cm 2 of the airway epithelium, which is much higher than the small DNA virus parvovirus human 335 bocavirus 1 (HBoV1) we studied 55 . doi = 10.1101/2020.08.27.271130 id = cord-307811-6e3j0pn7 author = Hao, Wei title = Binding of the SARS-CoV-2 Spike Protein to Glycans date = 2020-07-02 keywords = MERS; SARS; protein summary = Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. Previous studies of many other viruses suggested that SARS-CoV-2 S protein may use other molecules on host cell surface as attachment factors to facilitate binding to the high-affinity receptor ACE2. 36 A recent study suggested that HS may bind to the receptor binding domain (RBD, the C-terminal region of the S1 subunit, Fig. 2 ) of the SARS-CoV-2 spike protein and change its conformation. 38 In this study, we systematically examined and compared the binding of the SARS-CoV-2 S protein subunits, full-length molecule and its trimer to different HS using microarray experiments (Fig. 2) . In addition to binding protein-based receptors, many viruses can interact with cell surface glycans, including GAGs and sialic acid-containing oligosaccharides. doi = 10.1101/2020.05.17.100537 id = cord-297941-7yut9vt4 author = Haq, M. title = Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan date = 2020-09-30 keywords = CoV-2; SARS summary = In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV2 antibodies and the risk factors of COVID 19 in healthcare-workers but little is known from developing countries. Methods: This cross-sectional study was conducted on prevalence of SARS CoV2 antibody and risk factors for seropositivity in HCWs in tertiary care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan. To our knowledge this is the first study of assessing SARS-CoV-2 antibodies of HCWs form both public and private tertiary care hospitals in Peshawar, Pakistan. To our knowledge this is the first study on prevalence of SARS CoV-2 antibodies in HCW of tertiary care hospitals in Pakistan. The risk of becoming positive for SARS-CoV-2 antibodies did not increase with history of direct contact with COVID patients within or outside the hospital. doi = 10.1101/2020.09.29.20203125 id = cord-293564-6xtg8uqt author = Hara, Tasuku title = Infection risk in a gastroenterological ward during a nosocomial COVID‐19 infection event date = 2020-04-22 keywords = SARS summary = A case of presumably nosocomial COVID‐19 was detected in the gastroenterological ward; however, appropriate precautions against contact and droplet prevented a subsequent infection cluster. To assess the risk of COVID-19 infection, the exposure-risk category and underlying conditions and their relationship with a positive PCR result were examined. Exposure-risk categories, which is based on whether patients and healthcare professionals use personal protective equipment, were assessed using Interim U.S. Guidance for Risk The basic reproduction number (R0: the number of people a single patient is expected to infect) for COVID-19 is estimated at 2.2 (1.4-3.9). 6,7 Therefore, the CCI was used in this study to assess the risk conferred by underlying diseases for COVID-19. No patient in the low-exposure risk category or with high-risk underlying conditions was infected with SARS-CoV-2 at this hospital. The authors thank all members of the Department of Gastroenterology and Hepatology, Fukuchiyama City Hospital. doi = 10.1002/jmv.25853 id = cord-264772-v3a2qmj5 author = Harada, Kouji H. title = Letter to the Editor on “An Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)”, Back to Basics date = 2020-06-18 keywords = SARS summary = authors: Harada, Kouji H.; Harada Sassa, Mariko; Yamamoto, Naomichi Imperative Need for Research on the Role of Environmental Factors in Transmission of Novel Coronavirus (COVID-19)" highlights an imperative need for research on SARS-CoV-2 in environmental sciences. Here we highlight research showing the importance of basic sanitations to control the spread of infectious diseases applicable to the prevention of COVID-19. 4 The aerosol transmission route for SARS-CoV-2 in aerosols 5 means effective ventilation, including both natural and mechanical ventilation, is an important, easy and basic way to reduce risk of transmission. 8 A case study of the nosocomial spread of SARS in a Vietnam hospital with 33 SARS patients during the 2003 SARS outbreak demonstrated the effectiveness of face masks, gloves, hand sanitizer, and cross-ventilation in the hospital in reducing cross-infection rates. Although comparisons of the cost-effectiveness of basic versus advanced technologies are not yet available, COVID-19 cases in low-and middle-income countries are rapidly rising. doi = 10.1021/acs.est.0c02850 id = cord-259968-cr3zf4oa author = Harb, Roa title = Evaluation of Three Commercial Automated Assays for the Detection of anti-SARS-CoV-2 Antibodies date = 2020-08-06 keywords = SARS summary = key: cord-259968-cr3zf4oa cord_uid: cr3zf4oa The Diasorin assay detects IgG antibodies to the S1 and S2 subunits of the spike protein and the signal is expressed in arbitrary units (AU/mL). The Roche assay detects total antibodies to the nucleocapsid protein and the signal is reported as a cutoff index (COI). Cutoffs for positive samples by the Abbott, Diasorin, and Roche assays are ≥ 1.4, ≥ 15 AU/mL, and ≥ 1.0 COI, respectively. Clinical performance of the roche sars-cov-2 serologic assay Clinical performance of the elecsys electrochemiluminescent immunoassay for the detection of sars-cov-2 total antibodies Performance characteristics of four high-throughput immunoassays for detection of igg antibodies against sars-cov-2 Middle, values for Diasorin SARS-CoV-2 IgG for expected negative (n=344) and expected positive (n=65) specimens. Right, values for Roche SARS-CoV-2 total antibodies for expected negative (n=141) and expected positive (n=65) specimens. B) Distribution of anti-SARS-CoV-2 antibody results in expected positive specimens at 0-11 (n=12) doi = 10.1093/clinchem/hvaa193 id = cord-329944-ywusapij author = Harbourt, D. title = Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing date = 2020-07-03 keywords = July; SARS summary = title: Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing Skin, currency, and clothing samples were exposed to SARS-CoV-2 under laboratory conditions and incubated at three different temperatures (4C, 22C, and 37C). Herein, we model the stability of SARS-CoV-2 77 across animal skin, paper currency, and clothing. . https://doi.org/10.1101/2020.07.01.20144253 doi: medRxiv preprint 9 190 SARS-CoV-2 remained viable at 37°C on skin samples for up to 8 h (Fig 1 and Fig 2) . Significant differences 200 were observed in virus stability between the skin samples and all other tested surfaces (Fig S2) . The results in this study demonstrate the continued inverse relationship between virus stability 259 and temperature which is seen both in the laboratory and in the field when evaluating different was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.07.01.20144253 id = cord-280231-jo3grxd5 author = Hardenberg, Jan‐Hendrik title = Covid‐19, ACE2 and the kidney date = 2020-08-02 keywords = ACE2; AKI; SARS; covid-19 summary = Corona-virus disease 2019 (Covid-19) is a global pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 15 A cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter collectrin (also known as B 0 AT1), with or without the receptor SARS-CoV2 binding domain (RBD), of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 F I G U R E 1 Evolution of the "anginotensin converting enzyme" (ACE) family. 25 That Covid-19 patients develop acute kidney injury (AKI) would not be a surprise. Progressive respiratory failure, not renal failure, is the primary T A B L E 1 A brief overview of Covid-19 patients, acute kidney injury (AKI) and renal-replacement therapies (RRT) Stepwise multivariate binary logistic regression analyses showed that severity of pneumonia was the risk factor most commonly associated with lower odds of proteinuric or haematuric remission and recovery from AKI. doi = 10.1111/apha.13539 id = cord-344204-qq2vqzc2 author = Hariharan, Apurva title = The Role and Therapeutic Potential of NF-kappa-B Pathway in Severe COVID-19 Patients date = 2020-11-07 keywords = COVID-19; SARS; TNF summary = Severe presentations of COVID-19 such as severe pneumonia and acute respiratory distress syndrome (ARDS) have been associated with the post-viral activation and release of cytokine/chemokines which leads to a "cytokine storm" causing inflammatory response and destruction, mainly affecting the lungs. Immunomodulation at the level of NF-κB activation and inhibitors of NF-κB (IκB) degradation along with TNF-α inhibition will potentially result in a reduction in the cytokine storm and alleviate the severity of COVID-19. During previous coronavirus outbreaks, such as SARS-CoV and the Middle East Respiratory syndrome coronavirus (MERS-CoV) , it was reported that viral proteins such as nsp1, nsp3a, nsp7a, spike, and nucleocapsid protein all caused excessive NF-κB activation, possibly contributing to severe disease and high case-fatality rate (DeDiego et al. Herein, we review current literature on the effect of SARS-nCoV-2 infection on NF-κB activation and discuss the potential therapeutic role of inhibitors of this pathway in the treatment of COVID-19. doi = 10.1007/s10787-020-00773-9 id = cord-255498-npk4zv4i author = Harikrishnan, Pandurangan title = Saliva as a Potential Diagnostic Specimen for COVID-19 Testing date = 2020-06-11 keywords = SARS summary = Various clinical specimens like blood, pharyngeal swabs, saliva, anal swabs and urine showed the presence of the virus in infected patients. WHO recommends specimens from upper respiratory tract like nasopharyngeal (NP), oropharyngeal (OP) swab or wash in ambulatory patients, and lower respiratory specimens like sputum, endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease for the quantitative assessment of SARS-CoV-2 RNA level through real-time reverse transcription polymerase chain reaction (rRT-PCR). 17 Azzi et al collected saliva from 25 COVID-19 patients (confirmed by NP swabs) through the drooling technique and all were tested positive for the presence of SARS-CoV-2, while there was an inverse association between lactate dehydrogenase (LDH) and Cycle threshold (Ct) values (considered as semiquantitative indicators of viral load). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. doi = 10.1097/scs.0000000000006724 id = cord-336012-8klkojpo author = Harilal, Divinlal title = SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date = 2020-06-18 keywords = RNA; SARS; USA summary = Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. doi = 10.1101/2020.06.06.138339 id = cord-309986-p7pqla6l author = Harkin, Timothy J title = Delayed diagnosis of COVID-19 in a 34-year-old man with atypical presentation date = 2020-05-18 keywords = COVID-19; SARS summary = [1] [2] [3] Infection with SARS-CoV-2 is confirmed by real-time RT-PCR, typically done on naso pharyngeal (NP) swabs or, less commonly, samples from the lower respiratory tract, including broncho alveolar lavage (BAL). 5 Here, we present a man who developed rapidly progressive pulmonary disease and, following two negative NP tests, was diagnosed with COVID-19 on the basis of broncho scopic biopsy and BAL after 9 days of illness. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course. normal in the first 48 h (appendix p 1), serum and BAL galactomannan were negative, and the pathological finding of acute lung injury in the lesion was already present on day 2, which argue against this explanation. doi = 10.1016/s2213-2600(20)30232-0 id = cord-353329-ju3vwlow author = Haroon, Khawaja Hassan title = COVID-19 Related Cerebrovascular Thromboembolic Complications in Three Young Patients date = 2020-09-28 keywords = COVID-19; SARS summary = We describe clinical, radiological and laboratory findings of three young patients who presented with ischemic stroke and cerebral venous sinus thrombosis to our hospital within the first few weeks of COVID-19 outbreak. His CT of the brain, CT angiogram and CT perfusion ( Fig. 1a -e) showed acute established infarct in the right frontal lobe and basal ganglia, large matched defect in the right MCA territory and occlusion of right CCA and right terminal ICA with no evidence of dissection as well as lung findings suggestive of COVID-19 pneumonia. He was transferred to medical ICU for close monitoring and his follow-up non-contrast CT of the head (Fig. 1f ) revealed large right MCA territory infarct. Our first and second patient showed significant arterial lesions, while the third patient showed a high burden of cerebral venous sinus thrombosis with raised D-dimers and inflammatory markers, leading to stroke. doi = 10.1159/000511179 id = cord-289520-i6pv90s9 author = Harris, Carlyn title = An evidence-based framework for priority clinical research questions for COVID-19 date = 2020-03-31 keywords = COVID-19; MERS; SARS; clinical summary = RESULTS: From the research objectives for SARS-CoV and MERS-CoV, ten themes in the literature were identified: Clinical characterisation, prognosis, diagnosis, clinical management, viral pathogenesis, epidemiological characterisation, infection prevention and control/transmission, susceptibility, psychosocial, and aetiology. Outbreaks, especially of novel agents, create a pressing need to collect data on clinical characterization, treatment, and validation of new diagnostics to inform rapid public health response. We compared our findings to the 2018 systematic review on SARS and MERS to determine which questions have already been addressed, what information is lacking, and provide recommendations for data sharing and clinical study designs to be conducted during the current outbreak. These observational studies are practical in the fast-paced outbreak setting, as they are easier than randomised controlled The First Few X (FFX) WHO Protocol https://www.who.int/publications-detail/the-first-few-x-(ffx)-cases-and-contact-investigation-protocol-for-2019-novel-coronavirus-(2019-ncov)-infection) What are the risk factors for death or severe illness? doi = 10.7189/jogh.10-011001 id = cord-299093-zp07aqpm author = Harrison, Andrew G. title = Mechanisms of SARS-CoV-2 transmission and pathogenesis date = 2020-10-14 keywords = ACE2; COVID-19; CoV-2; Coronavirus; SARS; severe summary = Thus, evasion of IFN signaling by SARS-CoV-2 and impaired IFN production in J o u r n a l P r e -p r o o f human peripheral blood immune cells might contribute to the productive viral replication, transmission, and severe pathogenesis during COVID-19, although further testing is warranted to fully dissect these putative evasion pathways [95] . For instance, Krt18-hACE2 and betaactin-hACE2-transgenic mice rapidly succumb to SARS-CoV-2 infection with lung infiltration of inflammatory immune cells inducing severe pulmonary disease, accompanied by evident thrombosis and anosmia, which partially recapitulate human COVID-19 [114] [115] . Furthermore, upon viral challenge, lymphocytes have expanded in rhesus macaque models around 5 dpi with complementary B-cell responses against SARS-CoV-2 Spike appearing 10-15 dpi in blood samples [125] ; expansion of these adaptive immune compartments was analogous to those observed in COVID-19 patients [37, 125, [132] [133] [134] . doi = 10.1016/j.it.2020.10.004 id = cord-314796-bek92zs9 author = Hartung, Hans-Peter title = COVID-19 and management of neuroimmunological disorders date = 2020-05-22 keywords = COVID-19; SARS summary = The pathogen was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the diseasecoronavirus disease 2019 (COVID-19) -has caused the first recorded non-influenza pandemic. On the basis of their presumed mode of action and evidence from their use in patients, β-interferons, glatiramer acetate and teriflunomide are safe in COVID-19 because they do not cause relevant immunosuppression or increase the risk of viral infections. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. Nevertheless, an immediate and ongoing neurological challenge posed by the COVID-19 pandemic is the management of patients who are undergoing immunotherapy for existing neuroimmunological disease. The complement-blocking mAb eculizumab, which is approved for treatment of NMOSD, has not been associated with an increased risk of viral infections. However, COVID-19 affects the management of patients with neurological diseases in many ways. doi = 10.1038/s41582-020-0368-9 id = cord-259200-65b267ic author = Harypursat, Vijay title = Six weeks into the 2019 coronavirus disease outbreak: it is time to consider strategies to impede the emergence of new zoonotic infections date = 2020-05-05 keywords = MERS; SARS summary = Subsequent to the severe acute respiratory syndrome (SARS) outbreak in China 2003, and the Middle East respiratory syndrome (MERS) outbreak in the Middle East in 2012, global concerns regarding the pathogenicity and epidemic/pandemic potential of novel human coronaviruses began to emerge, with some experts predicting that novel coronaviruses could likely again cross the species barrier and present humans with future pandemic-potential infections. 2019-nCoV is the seventh coronavirus species that is now known to infect humans, is also zoonotic in origin, and is the causative organism for the current viral pneumonia epidemic in China. The complete ban on market trading and sale of wild game meat in China on January 26th, 2020 will help prevent zoonotic transmission of 2019-nCoV in the current epidemic and, to a certain degree, help prevent emergence of new zoonotic infections. doi = 10.1097/cm9.0000000000000760 id = cord-265598-4h3wx81q author = Hasan, Abdulkarim title = Histopathology Laboratory Paperwork as a Potential Risk of COVID-19 Transmission among the Lab Personnel date = 2020-08-06 keywords = SARS; covid-19 summary = Methods We tracked paper-based forms from time of test ordering till the release of the pathology report by calculating the time taken for the papers to reach the lab and the exposure of each staff group to the received papers from both high and moderate COVID-19 risk areas. Conclusion More than 80% of the manual paper request forms will take less than 24 hours to be handled by laboratory personnel; carrying a high potential risk for viral transmission. In this study we focused on defining the major hospital departments that request histopathology (by frequency and percent), measuring the time from handling the paper by clinician staff till handling by laboratory personnel, and comparing the possibility of COVID-19 transmission by paperwork to laboratory personnel, according to their exposure time to these papers. More studies are required to detect stability of the SARS-COV-2 on different surfaces and the potential risk of COVID-19 transmission through papers. doi = 10.1016/j.infpip.2020.100081 id = cord-315754-dq2empne author = Hasan, Anwarul title = A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin date = 2020-04-22 keywords = ACE-2; SARS summary = Angiotensin-converting enzyme-2 (ACE-2) is one of the most important receptors on the cell membrane of the host cells (HCs) which its interaction with spike protein (SP) with a furin-cleavage site results in the SARS-CoV-2 invasion. Genomic analysis of the new CoV has shown that its SP differs from that of other viruses (Du et al., 2017; Li, 2016) , indicating that the protein has a site activated by a HC enzyme called furin (Millet & Whittaker, 2015) (Figure 1 ). The furin activation site (FAS) makes the new CoV much different in cell entry than SARS, and probably affects the stability of the virus and, consequently, the transmission process (Li et al., 2015; Millet & Whittaker, 2014; Yamada & Liu, 2009) . A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 doi = 10.1080/07391102.2020.1754293 id = cord-297786-jz1d1m2e author = Hasan, Md. Mahbub title = Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date = 2020-08-26 keywords = Bangladesh; CoV-2; SARS summary = Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Then, we studied the variants present in different isolates of Bangladesh to investigate the pattern of mutations, identify UMs, and discuss the pseudo-effect of these mutations on the structure and function of encoded proteins, with their role in pathogenicity. To understand the SARS-CoV-2 viral transmission in Bangladesh, we performed phylogenetic analysis on the selected 207 viral genomes reported from different districts of Bangladesh along with selected 467 globally submitted sequences as reported from 42 countries and 6 continents ( Figure 1 ). doi = 10.1101/2020.08.25.267658 id = cord-278123-mq56em3z author = Hasan, Mohammad Rubayet title = Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date = 2020-07-24 keywords = RNA; SARS summary = Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. doi = 10.1371/journal.pone.0236564 id = cord-333547-88dkh6xd author = Hasan, Shadi W. title = Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date = 2020-10-19 keywords = CoV-2; RNA; SARS summary = Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. A limited number of studies have shown that the shedding period of SARS-CoV-2 in stool samples varies considerably, and can still be detected up to 27.9 ± 10.7 days after infection in some cases [9, 11] . Consequently, the main objectives of this study were: (i) to detect the presence of SARS-CoV-2 virus in municipal (untreated) wastewater and treated effluents of wastewater treatment plants (WWTPs) in the UAE; (ii) to quantify the viral concentration in viral gene copies per liter; and (iii) to explore whether these measurements mirror infections in the population in order to comment on the utility of this method to track the epidemiology of the disease. doi = 10.1016/j.scitotenv.2020.142929 id = cord-255264-2kj961en author = Hasan, Syed Shahzad title = Social distancing and the use of PPE by community pharmacy personnel: Does evidence support these measures? date = 2020-05-01 keywords = PPE; SARS summary = While the United States adopted a universal mask approach and Turkey recommended the use of masks and protective goggles for their pharmacy personnel, almost all of the countries recommended against routine use of face mask and other PPE (gloves or aprons/gowns), except when dealing with suspected COVID-19 patients or performing activities requiring close contact (unable to maintain recommended social distance) with the patients. Though the observation from such case study cannot be regarded as conclusive, the assumption, for now, should be that airborne transmission of SARS-CoV-2 is possible unless being discredited in the future, and therefore we opine that the wearing of appropriate PPE is of utmost importance for healthcare workers, including community pharmacy personnel dealing with individuals may or may not be infected on a day-to-day basis, regardless if they manage to observe social distancing in their workplace or if they perform close contact activities. doi = 10.1016/j.sapharm.2020.04.033 id = cord-279223-qvih5qas author = Hascoët, Jean-Michel title = Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date = 2020-09-29 keywords = PCR; SARS summary = Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Thus, although the mother was considered cleared at 6 weeks after the onset of infection, which was confirmed by negative nasopharyngeal and stool SARS-CoV-2 RT-PCR tests after delivery, we tested stool and pharynx swab samples from asymptomatic baby-girl D. Two additional babies and their mothers were tested at birth because the mothers had symptomatic infection, documented with positive SARS-CoV-2 RT-PCR results, at 28 and 31 days before delivery, respectively. Despite the first newborn was asymptomatic and the screening performed as part of routine systematic testing, SARS-CoV-2 RNA detection through early nasopharyngeal sampling and the persistent detection of virus in stool strongly suggest possible vertical maternofetal infection. doi = 10.3389/fped.2020.568979 id = cord-270743-yyl50z94 author = Haseli, Sara title = Reply to “MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss” date = 2020-06-10 keywords = SARS summary = title: Reply to "MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss" We read with great interest the letter by Eliezer and Hautefort discussing our recent report in Academic Radiology of magnetic resonance imaging (MRI) findings in a patient with coronavirus disease-2019 (Covid-19) and enumerating the possible mechanisms of SARS-CoV-2-induced anosmia 1 . In the apparent absence of anatomical changes on MRI and to assess a putative loss of neuronal function in anosmia of Covid-19, we performed 18 FDG PET/CT scan in a patient with isolated anosmia under neutral olfactory condition, which revealed hypoactivity of the left orbitofrontal cortex, thus suggesting a probable neuroinvasive mechanism for anosmia of Covid-19 8 . MRI evaluation of the olfactory clefts in patients with SARS-CoV-2 infection revealed an unexpected mechanism for olfactory function loss. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients. doi = 10.1016/j.acra.2020.05.025 id = cord-276139-l13hbucu author = Hashem, A. M. title = Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients date = 2020-09-23 keywords = SARS summary = Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Here, we studied the kinetics of SARS-CoV-2 specific antibodies to S1 and N viral proteins in blood samples collected between 4 to 70 days post-symptoms onset from a cohort of 87 COVID-19 patients with different disease presentations (i.e. mild, moderate or severe) or outcomes (i.e. survival vs death). Comparing the kinetics of antibody response in COVID-19 patients who had fatal outcomes to those who survived the infection also showed that early induction of anti-N IgG and IgM during the first 15 days post-disease onset is indicative of fatal outcomes (Figure 4c) . In this study we studied the characteristics and kinetics of SARS-CoV-2 specific antibody response (nAbs, IgG and IgM) in a series of serum samples collected from a total of 87 confirmed COVID-19 hospitalized patients over a period of 70 days post-symptoms onset. doi = 10.1101/2020.09.21.20198309 id = cord-341101-5yvjbr5q author = Hashem, Anwar M. title = Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date = 2020-05-06 keywords = Chloroquine; HCQ; SARS; virus summary = While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro doi = 10.1016/j.tmaid.2020.101735 id = cord-260644-5moccf8c author = Hashemi, Seyed Ahmad title = Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date = 2020-11-07 keywords = SARS summary = title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Some researchers evaluated and compared the whole genome sequence of SARS-CoV-2 isolated in various parts of the world and identified some mutations. The high-frequency mutations of the SARS-CoV-2 genome were seen in nsp6, RNA polymerase, helicase, membrane glycoprotein, RNA primase, nucleocapsid phosphoprotein, and spike protein genes (Yin, 2020) . In the first step, we used the sequence of S protein of SARS-CoV-2, published in Gene bank with accession number MT252819.1, for appropriate restriction endonuclease selection and primer design. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity doi = 10.1016/j.meegid.2020.104625 id = cord-278945-q5lzf5o4 author = Hashemi, Seyed Ahmad title = Report of death in children with SARS‐CoV‐2 and Human metapneumovirus (hMPV) co‐infection: is hMPV the trigger? date = 2020-08-07 keywords = SARS summary = To investigate the presence of other respiratory viruses, we performed a panel of virus detection through PCR and RT‐PCR tests to detect influenza virus, parainfluenza virus, Human metapneumovirus, Human bocavirus, adenovirus, and respiratory syncytial virus on nasopharyngeal swabs of all 74 SARS‐CoV‐2 positive dead patients. Although surveys confirmed that children could be infected with SARS-CoV-2 (1-3), there is evidence showing people more than 50 years old are more susceptible to the COVID-19. Case presentation Blood tests, including blood cell differential count, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) were performed for all patients admitted to the hospital with suspicion of infection with SARS-CoV-2. Besides, all patients underwent a chest CT scan that is the most sensitive test for COVID-19 identification (5, 6) , and SARS-COV-2 detection was performed using real-time PCR. We found the influenza virus, Human bocavirus, respiratory syncytial virus, parainfluenza virus, and hMPV in some SARS-CoV-2 positive samples. doi = 10.1002/jmv.26401 id = cord-277509-khvuiwl1 author = Hashemi, Seyyed Alireza title = Ultra-sensitive viral glycoprotein detection NanoSystem toward accurate tracing SARS-CoV-2 in biological/non-biological media date = 2021-01-01 keywords = Fig; SARS summary = The working electrode of developed sensor is activated upon coating a layer of coupled graphene oxide (GO) with sensitive chemical compounds along with gold nanostars (Au NS) that can detect the trace of viruses in any aquatic biological media (e.g., blood, saliva and oropharyngeal/ nasopharyngeal swab) through interaction with active functional groups of their glycoproteins. Herein, we have addressed this demand via developing a rapid and highly sensitive diagnostic kit that do not require any extraction or biological marker and can detect trace of different kinds of pathogenic animal/human viruses such as SARS-CoV-2, infectious bronchitis virus (IBV), avian influenza and Newcastle Disease Virus (LaSota and V4 strains) via active functional groups of their viral glycoproteins upon demonstration of differentiable fingerprints of each virus at diverse voltage positions. doi = 10.1016/j.bios.2020.112731 id = cord-255972-u7v0es5w author = Hashikawa, Andrew title = Child Care in the Time of COVID-19: A Period of Challenge and Opportunity. date = 2020-07-17 keywords = Care; ECE; SARS; child summary = Existing CFOC standards do not address the new concerns expressed by ECE workers during the pandemic, which include: determining the risks for ECE workers, establishing whether physical distancing in young children is feasible and effective, providing more details about cleaning and disinfecting, defining new group size requirements, defining the proper use of SARS-CoV-2 screening tests, handling readmission of children with symptoms or positive COVID-19 tests, and establishing guidelines for temperature checks (type of thermometer, fever threshold for exclusion, when to take temperatures after the initial screening). Even though there remain gaps in COVID-19 specific information that need further research, there is an important role for pediatric health experts to provide some structured guidance based on both expert group consensus and best available evidence to assist ECE directors in operating their programs and in providing consistent messaging to parents. doi = 10.1016/j.jpeds.2020.07.042 id = cord-305581-0bqxwh1o author = Hassan, Sk. Sarif title = Molecular phylogeny and missense mutations of envelope proteins across coronaviruses date = 2020-09-12 keywords = SARS summary = The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations. In the Table 1 , total number of available CoV genomes of respective hosts as well as distinct number of envelope proteins are presented. It is noted that the envelope (E) protein of the CoVs of Pangolin and Chimpanzee are found to be 100% conserved as presented in Table 1 and consequently no mutation was found over there. Among 79 available complete CoV genomes of Bat, twenty-five sequences possess various mutations in the three domains of the E protein as presented in the Fig.2 . Based on mutation characteristics and amino acid conservations over the E proteins across various host CoVs, this report predicts potential close kins of human SARS-CoV2 as the Pangolin-CoV and Bat-CoV which was also reported in a recent study [21] . doi = 10.1016/j.ygeno.2020.09.014 id = cord-306085-gnrnsxej author = Hassan, Sk. Sarif title = SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences date = 2020-07-05 keywords = SARS summary = The envelope protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane domain and (C)-terminus in 15 (0.414%) genomes among 3617 available SARS-CoV2 genomes. Here, we present the non-synonymous mutations of the envelope protein over the available 3617 SARS-CoV2 genomes (Table 1) . It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contain the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes.  In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617 on which the present study of mutation over the envelope protein is made. More precisely, it is to be mentioned that 10(0.386\%) out of 2588 genomes from the USA, 3(0.806\%) from Asia, 1 (0.348\%) from Europe and 1 (0.274\%) from Oceania contain the missense mutations over the envelope proteins of SARS-CoV2 genomes. doi = 10.1016/j.ygeno.2020.07.001 id = cord-312999-3erodkv9 author = Hassan, Sk. Sarif title = Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date = 2020-09-06 keywords = ORF10; Pangolin; SARS summary = SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Based on the mutations, conserved and non-conserved residues in ORF10 proteins are identified and marked in different colors in (Figure There are altogether 22 distinct missense mutations which were examined across 22 unique ORF10 variants of SARS-CoV-2. doi = 10.1101/2020.09.06.284976 id = cord-338055-2d6n4cve author = Hassan, Sk. Sarif title = A unique view of SARS-CoV-2 through the lens of ORF8 protein date = 2020-08-26 keywords = Bat; ORF8; Pangolin; SARS summary = In this present study, we identified the distinct mutations present across unique variants of the SARS-CoV-2 ORF8 and classified them according to their predicted effect on the host, i.e disease or neutral and the consequences on protein structural stability. The ORF8 sequences of SARS-CoV-2, Bat-CoV RaTG13 and Pangolin-CoV have almost the same positive and negative charged amino acids, therefore we can say that probably they have similar kind of electrostatic and hydrophobic interactions, 135 which also contribute to the functionality of the proteins. • QKV07730.1: The T11A mutation occurred as the second mutation in this sequence, which was predicted to be of disease-increasing type and the polarity was changed from hydrophilic to hydrophobic, hence the structure and 305 function of the protein are expected to differ. doi = 10.1101/2020.08.25.267328 id = cord-297127-nhgm09db author = Hasseli, Rebecca title = National registry for patients with inflammatory rheumatic diseases (IRD) infected with SARS-CoV-2 in Germany (ReCoVery): a valuable mean to gain rapid and reliable knowledge of the clinical course of SARS-CoV-2 infections in patients with IRD date = 2020-09-02 keywords = COVID-19; IRD; SARS; patient summary = OBJECTIVES: Patients with inflammatory rheumatic diseases (IRD) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be at risk to develop a severe course of COVID-19. 2 In this situation, patients with inflammatory rheumatic diseases (IRD) may face a particular risk as their disease, especially when clinically active, and their immunomodulatory treatment may impact the course of COVID-19 infection. However, firm knowledge of the course of SARS-CoV-2 infection in patients with IRD is missing, and therefore, evidence-based recommendations for the management of COVID-19 in patients with rheumatic disorders and antirheumatic treatments are lacking. As necessary data cannot be extracted from clinical charts or health insurance records, the DGRh and the Justus-Liebig University Giessen decided to establish a web-based registry, which allows a rapid and timely collection of IRD cases with confirmed SARS-CoV-2 infections in Germany to analyse the clinical course of SARS-CoV-2 infections in patients with IRD and to develop guidance for the management of patients with IRD during the COVID-19 pandemic. doi = 10.1136/rmdopen-2020-001332 id = cord-322562-3gvsn9vf author = Hatada, Ryo title = Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7) date = 2020-06-15 keywords = FMO; Fragment; IFIE; SARS summary = Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). As illustrated in a recent book of in silico drug design, 8 the fragment molecular orbital (FMO) method 9−12 provides an efficient tool for performing ab initio quantum-chemical calculations for biomolecular systems and accurately analyzing their intermolecular interactions in terms of the interfragment interaction energies (IFIEs). Table 1 compiles the results of IFIE and decomposed contributions (PIEDA) interacting with Fragment 1 of the ligand, where the listing threshold is set as 2.0 kcal/mol The distance between the main chain >CO of Thr190 and the N−H part of Fragment 1 is as close as 1.99 Å as illustrated in Figure 6 , suggesting that they are forming a typical hydrogen bond. doi = 10.1021/acs.jcim.0c00283 id = cord-329840-f3dsu36p author = Hati, Sanchita title = Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date = 2020-05-11 keywords = ACE2; SARS; protein summary = In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. In the backdrop of significant mortality rate for SARS-CoV-2 (hereinafter referred to as CoV-2) infection, it is important to know if the thiol-disulfide balance plays any role on the binding of the spike glycoprotein on to the host cell receptor protein ACE2. Using these reported structures, molecular dynamics simulations and electrostatic field calculations were performed to explore the impact of thioldisulfide balance on CoV/CoV-2 and ACE2 binding affinities. The structural and dynamical changes due to the change in the redox states of cysteines in the interacting proteins were analyzed and their effects on binding free energies were studied. doi = 10.1101/2020.05.07.083147 id = cord-330478-g9n2mfni author = Hattenbach, Lars-Olof title = Krisenstrategien der Kliniken während der Pandemie date = 2020-07-01 keywords = COVID-19; SARS; der summary = authors: Hattenbach, Lars-Olof; Reinhard, Thomas; Walter, Peter; Roider, Johannes; Feltgen, Nicolas; Hesse, Lutz; Schrecker, Jens; Eter, Nicole Hintergrund Die SARS-CoV-2(Severe Acute Respiratory Syndrome Coronavirus 2)-Pandemie hat während der ersten Monate des Jahres 2020 weltweit zu tiefgreifenden Veränderungen der medizinischen Versorgung mit massiven Einschränkungen bei chirurgischen Eingriffen und nichtdringlichen ambulanten wie stationären Behandlungen geführt [1] [2] [3] [4] . Jüngere Publikationen zeigen jedoch, dass das Risiko einer Ansteckung durch Tränenflüssigkeit selbst bei COVID-19-Patienten eher gering ist und auch die Häufigkeit des Auftretens einer Konjunktivitis nur bei etwa 1 % liegt [12] [13] [14] . Despite the challenge of a significant shift of medical resources during the SARS-CoV-2 pandemic, medically urgently necessary ophthalmological treatments are continuously provided by maximum care clinics; however, based on currently available data, it cannot be ruled out whether treatment of emergency patients was delayed during the pandemic. doi = 10.1007/s00347-020-01162-x id = cord-328381-bfvdhai8 author = Hattermann, K. title = Susceptibility of different eukaryotic cell lines to SARS-coronavirus date = 2005-01-13 keywords = SARS summary = In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown). doi = 10.1007/s00705-004-0461-1 id = cord-295946-p9enjxiq author = Hattori, Shin-ichiro title = GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection date = 2020-08-20 keywords = Fig; GRL-0920; SARS; WK-521 summary = We assessed various newly generated compounds that target the main protease (M(pro)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. When VeroE6 cells were exposed to SARS-CoV-2 WK-521 at a multiplicity of infection (MOI) of 0.05 and cultured in the presence of various concentrations of the two indole chloropyridinyl esters GRL-0820 and GRL-0920, the compounds were found to be highly potent against SARS-CoV-2 WK-521 with 50% effective concentration (EC 50 ) values of 15 Ϯ 18 and 2.8 Ϯ 0.3 M, respectively, using RNA-qPCR (Table 1) . When VeroE6 TMPRSS2 cells were exposed to SARS-CoV-2 WK-521 and cultured in the presence of various concentrations of lopinavir and nelfinavir, many virus-infected cells were seen at 1 and 10 M and stained in green, indicating that these two compounds had no detectable antiviral activity in the assay. doi = 10.1128/mbio.01833-20 id = cord-254900-fg5wd0nh author = Havenga, M.J.E. title = Serum‐free transient protein production system based on adenoviral vector and PER.C6 technology: High yield and preserved bioactivity date = 2007-12-13 keywords = DE1; PER.C6; PER.E2A; SARS; cell; e2a summary = Because of these features it can be envisioned that the use of adenoviral vectors results in higher protein yields derived from mammalian cells cultured in suspension as compared to current DNA transfection protocols for which processes at scale like cell uptake and nuclear localization, present major technical hurdles. Based on the data obtained thus far it was concluded that an DE1/DE2A adenoviral vector can be efficiently produced at 348C on PER.E2A cells and can subsequently serve as a tranducing agent for PER.C6 cells without inducing viral backbone replication or high level viral capsid protein expression in human A549 indicator cells. As shown in Figure 2C the yield of SARS anti-body produced did not significantly differ demonstrating that cleared vector stock directly harvested from he PER.E2A cell line can be used for production of recombinant protein without compromising yield. doi = 10.1002/bit.21757 id = cord-316215-4mj7n0ax author = Haveri, Anu title = Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020 date = 2020-03-19 keywords = Finland; January; SARS summary = Suspicion of COVID-19 led to her direct transfer to the Lapland Central Hospital in Rovaniemi, where she was isolated and sampled on 28 and 29 January for laboratory confirmation of SARS-CoV-2 infection ( Figure 1 ). SARS-CoV-2 infection was confirmed from nasopharyngeal samples on 29 January by the Helsinki University Hospital Laboratory (HUSLAB), and further confirmed at the Finnish Institute for Health and Welfare (THL) ( Table) . Presence of serum IgM and IgG antibodies against SARS-CoV-2 was analysed by immunofluorescence assays (IFA) based on Vero E6 cells infected with passage 4 of the patient''s isolate SARS-CoV-2/ Finland/1/2020 virus and transferred onto microscope slides and fixed with acetone ( Figure 2 ). Western blot of mock-and SARS-CoV-2 infected Vero E6 cells using patient serum collected 20 days after onset of symptoms, Finland, January-February 2020 No neutralising SARS-CoV-2 antibodies were detected in the close contacts nor in the control population samples collected during 2019 in Finland. doi = 10.2807/1560-7917.es.2020.25.11.2000266 id = cord-288284-fghu8ouc author = Hawryluck, Laura title = Clinical review: SARS – lessons in disaster management date = 2005-01-13 keywords = SARS; Toronto; care summary = Infectious diseases, whether they be natural (e.g. SARS [severe acute respiratory syndrome] and influenza) or the result of bioterrorism, have the potential to create a large influx of critically ill into our already strained hospital systems. Core to any disaster management plan are leaders with clear responsibilities to coordinate efforts and develop policies to contain the disease; to coordinate resource allocation and manpower; to advise and share information regarding infection control and treatment; to share data and research endeavours; to maintain staff morale; and to provide information to various levels of government, health care institutions, front-line workers and the public [1, 13] . The model we propose (Fig. 1 ) is one of a Central Critical Care Crisis Team, composed of leaders of different subteams of multidisciplinary professionals responsible for domains of crucial importance: clinical management, infection control, education, communication, team morale, manpower and system thinking, data collection, research and, finally, lobbying to ensure resources are available to meet critical care needs. doi = 10.1186/cc3041 id = cord-277313-5f5lrn3c author = Hayakawa, Satoshi title = Covid‐19 pandemic and pregnancy date = 2020-08-10 keywords = COVID-19; China; SARS; infection summary = 20 However, fortunately, clinical data suggest no deleterious outcomes of pregnant women who are infected with COVID-19 during pregnancy compared with those infected with SARS-CoV or MERS. In another report from Wuhan, of 13 pregnant women who developed COVID-19 during pregnancy, one woman delivered a dead fetus at 34 weeks of gestation, but the cause of fetal death was speculated to be severe maternal pneumonia and multiple organ failure rather than viral infection of the fetus. 22 Another report showed that 3 of 33 pregnant women who developed COVID-19 during pregnancy in Wuhan showed evidence of intrauterine infection by cord blood PCR test. While early studies showed no evidence of vertical transmission of SARS-CoV-2 from mother-to-child in late pregnancy, 21 recent reports have shown possible in utero transmission. Coronavirus disease 2019 (COVID-19) in pregnant women: A report based on 116 cases doi = 10.1111/jog.14384 id = cord-252428-w6tsf478 author = Hayashi, Takuma title = Highly conserved binding region of ACE2 as a receptor for SARS-CoV-2 between humans and mammals date = 2020-09-29 keywords = ACE2; SARS summary = The multiple sequence alignments of the ACE2 proteins shows high homology and complete conservation of the five amino acid residues: 353-KGDFR-357 with humans, dogs, cats, tigers, minks, and other animals, except for snakes. (B) The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks. The multiple sequence alignments of the sampled ACE2 proteins revealed high homology and high conservation of the five amino acid residues: 353-KGDFR-357 with specific reference to humans, dogs, cats, tigers, minks, and other animals, except for snakes ( Figure 1 (A) and Supplementary Materials). The multiple sequence alignments of the ACE2 proteins by ClustalW revealed the complete conservation of the five amino acid residues: 353-KGDFR-357 between humans, dogs, cats, tigers, and minks (Figure 1(B) ). doi = 10.1080/01652176.2020.1823522 id = cord-342915-r9kv67we author = Hayden, Frederick G. title = Advances in antivirals for non‐influenza respiratory virus infections date = 2013-11-01 keywords = RSV; SARS; infection; respiratory; virus summary = Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. doi = 10.1111/irv.12173 id = cord-334624-chnibsa1 author = Hayn, Manuel title = Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date = 2020-10-30 keywords = Fig; IFN; Nsp15; SARS summary = Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation. SARS-CoV-1 ORF6 is about 4-fold less potent in antagonizing type I IFN signaling (Fig. 243 4b) but induces higher levels of autophagy (Fig. 4c) . Examination of the functional conservation showed that SARS-CoV-2 Nsp15 was less 319 efficient in blocking innate immune activation, both type I IFN induction and signaling, than SARS-320 Hepatitis C virus viruses to block anti-viral autophagic turnover 50 and thus may represent a common studies will see more mechanistic data to explain the molecular details of the impact of SARS-CoV-2 343 proteins on innate immune activation. doi = 10.1101/2020.10.15.340612 id = cord-288153-2qsh2dlk author = Hays, Priya title = Clinical sequelae of the novel coronavirus: does COVID-19 infection predispose patients to cancer? date = 2020-05-27 keywords = MAPK; SARS; cancer summary = Major signaling pathways implicated in aberrant cellular growth are activated, the ensuing cytokine storm weakens the immune system response to tumors, and patients may develop cancer as a result of superimposed mutagenic and/or carcinogenic events. There may be a distinct association between novel coronavirus infection and the onset of cancer through the activation of the MAPK and JAK-STAT signaling pathways and the NF-κB transcription factor. The turning on of oncogenic signaling pathways and the acute inflammatory response that results upon coronavirus infection can be hypothesized as being cancer inducing, or leading to the risk of developing cancer, especially if the patient has a superimposed mutagenic or carcinogenic event occurring concomitantly, even if the virus does not cause a chronic infection like viruses such as HCV, HCV and EBV. Oncologic sequelae of the novel coronavirus • Viral infection induces a robust immune response, a ''cytokine storm'' leading to tissue damage and inflammation, which may predispose to cancer. doi = 10.2217/fon-2020-0300 id = cord-313246-2gtiqrnj author = Hazra, Aniruddha title = Coinfections with SARS-CoV-2 and other respiratory pathogens date = 2020-07-03 keywords = SARS summary = 3 The same specimen can be tested via RT-PCR for a respiratory panel (RP) of other common pathogens, including adenovirus, coronavirus 229E/HKU1/NL63/OC43, human metapneumovirus, influenza A/B, parainfluenza 1-4, respiratory syncytial virus, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis, and rhinovirus/enterovirus (BioFire FilmArray respiratory panel 2). This report examines patients with influenza-like illness symptoms who were simultaneously tested for SARS-CoV-2 and the above panel from March 12, 2020, through April 15, 2020. During the observed period, 2,535 specimens were simultaneously tested for SARS-CoV-2 and RP pathogens on 2,458 symptomatic patients. Notably, the median age of coinfected patients was nearly 20 years younger than those only infected with SARS-CoV-2. During the study period, the Illinois Department of Public Health noted a decline in influenza tests positivity from 14.9% to 1.6% between the weeks ending March 14, 2020, and April 11, 2020, respectively. Rates of coinfection between SARS-CoV-2 and other respiratory pathogens doi = 10.1017/ice.2020.322 id = cord-330692-rqwkkfp0 author = He, Daihai title = Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date = 2020-06-26 keywords = SARS summary = title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom We found that the on-going COVID-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. The fast spread and high fatality of the coronavirus disease 2019 (COVID-19) remind us of the first pandemic in last century, the 1918-19 influenza pandemic. A comparison between the YLLs for COVID-19 and 1918-19 influenza should be conducted, because YLL is the other important indicator of the severity of a pandemic. If we assume a 0.5% IFR for COVID-19 in 2020 and a 2% infection fatality rate in 1918, we may calculate and compare the infections based on reported deaths which should be more reliable than reported cases. doi = 10.1016/j.ijid.2020.06.075 id = cord-264148-qpcvxwti author = He, Feng title = Coronavirus disease 2019: What we know? date = 2020-03-28 keywords = COVID-19; SARS summary = doi = 10.1002/jmv.25766 id = cord-299899-is815pol author = He, Jingjing title = Proportion of asymptomatic coronavirus disease 2019 (COVID‐19): a systematic review and meta‐analysis date = 2020-07-21 keywords = China; SARS; covid-19 summary = The pooled proportion of asymptomatic infection among 1152 COVID‐19 children from 11 studies is 27.7% (95% CI: 16.4–42.7%), which is much higher than patients from all aged groups. However, patients infected with SARS-CoV-2 could also be asymptomatic, confirmed by positive Nucleic acid testing results during the illness. While a variety of studies on asymptomatic infection have been reported, the proportion of asymptomatic patients in confirmed COVID-19 cases is not well characterized. Original articles reporting asymptomatic infection in confirmed COVID-19 patients were included for meta-analysis. Noticeably, one study from Wuhan showed that 98/1021(9.6%) nucleic acid testing negative patients had lgG positive results, suggesting possible recovery from asymptomatic SARS-CoV-2 infection 54 . Characteristics of asymptomatic patients with SARS-CoV-2 infection in Jinan, China. Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha, China. Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection doi = 10.1002/jmv.26326 id = cord-277186-sj8ngpk8 author = He, Qigai title = Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA date = 2005-04-19 keywords = ELISA; N195; SARS summary = Specific binding of the MAb S-A5D5 to both purified N195 and SARS CoV nucleocapsid antigen was effectively inhibited by human SARS positive serum and guinea pig anti-N195 serum. The monoclonal antibodies were characterized by SARS CoV-infected Vero cells and nucleocapsid-spike fusion protein-based IFA, Western blot, and N195 proteinbased ELISA. The isotype of the promising monoclonal antibody, designated as S-A5D5, was determined and was further applied to develop a specific and sensitive antigen capture ELISA for the detection of SARS CoV. The specific reactivity of the MAb S-A5D5 with purified N195 protein (Fig. 3A ) was identical to that of the human SARS positive serum (Fig. 3B) , while no reaction was observed when non-antibody secreting hybridoma was tested (Fig. 3C) . Therefore, this antigen capture ELISA, based on MAb to N protein, might provide a more sensitive method for early detection of SARS CoV infection. doi = 10.1016/j.jviromet.2005.03.004 id = cord-255586-wshvvgxg author = He, Shengyang title = Clinical characteristics of “re-positive” discharged COVID-19 pneumonia patients in Wuhan, China date = 2020-10-15 keywords = SARS; covid-19; positive summary = The demographic features, clinical symptoms, laboratory results, comorbidities, co-infections, treatments, illness severities and chest CT scan results of 267 patients were collected from 1st January to 15th February 2020. | (2020) 10:17365 | https://doi.org/10.1038/s41598-020-74284-6 www.nature.com/scientificreports/ disease progression, no differences were found, suggesting this group of COVID-19 patients could be difficult to detect by using standard clinical data. All raw clinical and laboratory results were collected from electronic medical records system of the Central Hospital of Wuhan, followed by a follow up visit up to 14 days (also known as the discharge quarantine) to test for a re-positive nucleic acid assay. Definition of "re-positive": when a confirmed COVID-19 patient is detected SARS-CoV-2 RNA positive during the 14 days post-discharge quarantine (random test timing). Since understanding of the mechanisms of SARS-CoV-2 infection is still lacking, a careful discharge protocol should be applied (e.g. negative results of the nucleic acid tests of respiratory pathogens for 3 consecutive times), and post-discharge quarantine should be strictly observed, especially for severe and critical COVID-19 patients. doi = 10.1038/s41598-020-74284-6 id = cord-254855-gmy9zyad author = He, Sijia title = PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date = 2020-07-06 keywords = PSGL-1; SARS summary = Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. Together, these results demonstrate that PSGL-1 expression in the virus-producer cells severely diminishes the infectivity of virions bearing SARS coronavirus S proteins. We and other previously reported that PSGL-1-mediated inhibition of virion infectivity is through steric hindrance of particle attachment to target cells, which does not depend on the presence of viral envelope glycoproteins (1, 5) . We performed a virion attachment assay and observed that the lentiviral particles pseudotyped with SARS-CoV or SARS-CoV-2 S protein produced from PSGL-1-expressing cells were impaired in their ability to attach to target cells (Fig. 2D) . These results demonstrate that the presence of PSGL-1 on virus particles can structurally hinder virion interaction with the target cells even in the presence of remaining S proteins, consistent with previous studies of PSGL-1 and HIV-1 infection (1, 5) . doi = 10.1101/2020.05.01.073387 id = cord-334443-3pyu8ucs author = He, Yu title = Public health might be endangered by possible prolonged discharge of SARS-CoV-2 in stool date = 2020-03-05 keywords = SARS summary = According to a recent report, since December 8 2019, a novel identified coronavirus, SARS-CoV-2(previously named as 2019-nCOV) is causing outbreak of pneumonia in Wuhan, China and become the major concern throughout the world [1] . Those early reports may not represent actual rate of gastrointestinal symptoms caused by SARS-CoV-2, because in early stages of the outbreak, the limited resources for detection were only provided to those patients with severe symptoms like respiratory distress syndrome. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Detection and monitoring of SARS coronavirus in the plasma and peripheral blood lymphocytes of patients with severe acute respiratory syndrome doi = 10.1016/j.jinf.2020.02.031 id = cord-301693-3hsu2u1k author = He, Yuwen title = Value of Viral Nucleic Acid in Sputum and Feces and Specific IgM/IgG in Serum for the Diagnosis of Coronavirus Disease 2019 date = 2020-08-06 keywords = CoV-2; Guangzhou; SARS summary = To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We undertook a study on the viral nucleic acids of SARS-CoV-2 in swabs (nasal, pharyngeal), sputum and feces, as well as antibodies in the serum of COVID-19 patients admitted to the First Affiliated Hospital of Guangzhou Medical University, China. doi = 10.3389/fcimb.2020.00445 id = cord-323514-jaom3p6s author = He, Yuxian title = A single amino acid substitution (R441A) in the receptor-binding domain of SARS coronavirus spike protein disrupts the antigenic structure and binding activity date = 2006-05-26 keywords = R441A; RBD; SARS summary = Abstract The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has two major functions: interacting with the receptor to mediate virus entry and inducing protective immunity. Coincidently, the receptor-binding domain (RBD, residues 318–510) of SAR-CoV S protein is a major antigenic site to induce neutralizing antibodies. We also demonstrated that the RBD-Fc bearing R441A mutation could not bind to soluble and cell-associated angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV and failed to block S protein-mediated pseudovirus entry, indicating that this point mutation also disrupted the receptor-binding motif (RBM) in the RBD. In this study, we used the RBD-Fc as a model to study how a single residue mutation in the RBD can abolish the major function of full-length S protein, since this molecule can efficiently bind to the receptor ACE2 and contains multiple conformation-dependent epitopes (Conf I-VI) capable of inducing highly potent neutralizing antibodies [29] . doi = 10.1016/j.bbrc.2006.03.139 id = cord-323908-8dgngwmw author = He, Zhesheng title = Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies date = 2020-05-31 keywords = SARS summary = title: Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity. These compounds could serve as potential anti-SARS-CoV-2 lead molecules for further drug studies to combat COVID-19. The interactions between the gold atom with the binding pockets of proteins were studied by density functional theory (DFT) calculations. doi = 10.1101/2020.05.28.120642 id = cord-320829-uepneyug author = He, Zhongping title = Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date = 2005-08-10 keywords = CD8; SARS summary = title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS doi = 10.1016/j.ijid.2004.07.014 id = cord-340883-zf8jbhdl author = He, Zhongping title = Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date = 2007-03-27 keywords = PCR; SARS summary = title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR. doi = 10.1186/1743-422x-4-32 id = cord-032751-pmclolvh author = Head, Katharine J. title = A National Survey Assessing SARS-CoV-2 Vaccination Intentions: Implications for Future Public Health Communication Efforts date = 2020-09-23 keywords = COVID-19; CoV-2; SARS; vaccine summary = Research Question 2: What are the SARS-CoV-2 vaccine behavioral intentions of adults in the U.S. when a health care provider recommends the vaccine? Importantly, because vaccine intent and/or need may be different for people who were previously infected with SARS-CoV-2 and perceived threat variables (discussed below) are usually only measured for future threats, only participants who answered "no" to the question "do you believe that you''ve had COVID-19" are included in the current study (n = 3,159). Step 3 of the hierarchical regression model, with all variables included, less education was associated with lower intent to receive a SARS-CoV-2 vaccine. The health belief variables that were significant in the full regression model were all positively associated with intent to receive a SARS-CoV-2 vaccine. doi = 10.1177/1075547020960463 id = cord-353731-7xn7m662 author = Heaton, Brook E. title = SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date = 2020-08-18 keywords = SARS; SRPK1 summary = sgRNA sequencing data indicated that the host gene with the highest probability of being 125 required for SARS-CoV-2 infection was the serine/arginine-rich protein kinase, SRPK1 126 ( Figure 1B) . We next wanted to define the degree to which inhibition of SRPK1 mediated N 141 phosphorylation would affect viral replication, especially since other non-SRPK1 kinases 142 have been predicted to be responsible for SARS-CoV-2 protein phosphorylation 12,13 . SRPIN340 treatment of cells infected with the 183 alphacoronavirus 229E (which is only distantly related to betacoronavirus SARS-CoV-2) 184 inhibited the virus by more than 1,000-fold at non-toxic concentrations of the drug ( Figure 185 2G-H). Human papillomavirus type 1 E1^E4 protein is a potent 533 inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits 534 phosphorylation of host SR proteins and of the viral transcription and replication 535 regulator E2 doi = 10.1101/2020.08.14.251207 id = cord-313174-ig0h2s6l author = Hecht, Jonathon L. title = SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers date = 2020-08-02 keywords = ACE2; SARS summary = title: SARS-CoV-2 can infect the placenta and is not associated with specific placental histopathology: a series of 19 placentas from COVID-19-positive mothers Herein, we describe 19 placentas from mothers with COVID-19 studied for gross and histopathologic findings, viral expression by in situ hybridization (ISH) and immunohistochemistry (IHC), and ACE2 and TMPRSS2 expression by IHC. Ten placentas of COVID-19 negative mothers (delivered either before the pandemic or with negative tests) with clinical histories focusing on infections by an RNA virus (one case each of Zika exposure, HIV infection, and Hepatitis C infection), two cases of intrauterine fetal demise, and with histopathologies associated with congenital infections and coagulopathies (one case each of high stage and grade acute chorioamnionitis, high grade maternal vascular malperfusion (MVM), high grade fetal vascular malperfusion (FVM), high grade villitis of unknown etiology (VUE), chronic histiocytic intervillositis, and multiple intervillous thrombi) were identified from the pathology database using this diagnostic terminology and used as this set of controls. doi = 10.1038/s41379-020-0639-4 id = cord-343357-5nhyumxl author = Heegaard, Peter M. H. title = Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date = 2020-09-25 keywords = ACE2; SARS; covid-19 summary = We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. doi = 10.3389/fmicb.2020.573756 id = cord-331428-6pvr2vew author = Heffernan, Kevin S. title = Exercise as medicine for COVID-19: on PPAR with emerging pharmacotherapy date = 2020-08-17 keywords = COVID-19; SARS summary = Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating peroxisome proliferator-activated receptor alpha (PPARα), possibly contributing to lipotoxicity, inflammation and untoward respiratory effects. While we all eagerly await the development of a vaccine, scientists and clinicians have begun exploring "off-label" use of various drugs with that hope that strategic repurposing may help manage and treat COVID-19.(1) Fenofibrate (a peroxisome proliferator-activated receptor alpha agonist) is one such medication that holds promise given its favorable effects on inflammation and endothelial function. This paper will explore the hypothesis that exercise may be a useful adjuvant in a setting of COVID-19 management/rehabilitation due to its effects on PPAR and vascular endothelial function. (3) Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating PPAR, possibly contributing to lipotoxicity and untoward respiratory effects. Peroxisome Proliferator-Activated Receptor α Agonists Increase Nitric Oxide Synthase Expression in Vascular Endothelial Cells doi = 10.1016/j.mehy.2020.110197 id = cord-325112-7ie23c7f author = Heimer, Carol A. title = The uses of disorder in negotiated information orders: information leveraging and changing norms in global public health governance date = 2018-10-04 keywords = Fidler; Health; IHR; SARS; disease; information; order summary = Using SARS and the International Health Regulations (IHR) as a starting point, this article examines negotiated information orders in global public health governance and the irregularities in the supply of data that underlie them. Negotiated information orders within and among the organizations in a field (here, e.g., the World Health Organization, member states, government agencies, and international non‐governmental organizations) spell out relationships among different categories of knowledge and non‐knowledge – what is known, acknowledged to be known, and available for use in decision making versus what might be known but cannot be acknowledged or officially used. Thus although the long silence of the Chinese government was not technically a violation of the IHR, it nevertheless appeared dishonest and inappropriate to the international community, undermining rather than supporting emerging cooperative norms and in fact harming global public health by allowing the new disease to spread beyond China''s borders. doi = 10.1111/1468-4446.12495 id = cord-337712-ylqgraos author = Heinz, Franz X. title = Profile of SARS-CoV-2 date = 2020-10-30 keywords = ACE2; CoV-2; Fig; SARS; virus summary = Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . doi = 10.1007/s00508-020-01763-1 id = cord-292250-jjhpwgfa author = Heinz, Nicole title = A case of an Infant with SARS‐CoV‐2 hepatitis early after liver transplantation date = 2020-06-25 keywords = POD; SARS summary = We present a case of a pediatric liver transplant recipient diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection four days after receiving a living donor liver allograft from her mother. The team decision to proceed with the transplant contemplated the rate of progression of chronic liver failure, the risk of patient mortality before the epidemic abated, the perceived lower risk at the onset of the epidemic compared to the weeks/months ahead and the fact that neither the donor nor recipient demonstrated signs or symptoms of SARS-CoV-2 infection. Follow-up evaluation in the outpatient clinic on POD 30 was notable for resolution of all symptoms including diarrhea, but liver enzymes were again elevated in the setting of a subtherapeutic tacrolimus trough (Table 1, Figure 2) . On POD 36 the patient remained clinically well, liver enzymes had improved and tacrolimus trough was at target. A case of an Infant with SARS-CoV-2 hepatitis early after liver transplantation doi = 10.1111/petr.13778 id = cord-282108-hhnnloxp author = Heister, Paula M. title = Pharmacological hypothesis: TPC2 antagonist tetrandrine as a potential therapeutic agent for COVID‐19 date = 2020-09-15 keywords = SARS; TPC2; channel; tetrandrine summary = The putative mechanism of action of tetrandrine that underlies its potential use as a coronavirus disease 2019 (COVID-19) treatment is its ability to block the two-pore channel 2 (TPC2) in host cells and thus inhibit virus replication at low micromolar concentrations. While this paper was in preparation, a large-scale study exploring SARS-CoV-2 human protein-protein interactions to identify potential therapeutic candidates identified verapamil as a contender, but initial in vitro screening did not show a promising effect at the concentrations used. If indicated by the above, clinical trials to investigate tetrandrine''s potential, using an established oral dose, as an acute therapeutic or prophylactic agent against SARS-CoV-2 infection, provided safety can be confirmed for the particular length of use. 7. If indicated by the above, clinical trials to investigate the potential role of established calcium channel blockers as therapeutic agents in SARS-CoV-2 infection. doi = 10.1002/prp2.653 id = cord-325282-20l9xcmg author = Helal, Mohamed A. title = Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia date = 2020-09-16 keywords = CD147; SARS; protein summary = title: Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The entry of the virus into host cells is facilitated by binding of its transmembrane spike (S) protein with angiotensin-converting enzyme 2 (ACE-2) receptor (Hoffmann et al., 2020) . To understand the mechanism of interaction of the SARS-CoV-2 spike protein with the CD147 receptor, we have performed a four-stage in-silico study. The recently reported crystal structure of SARS-Cov-2 spike protein complex with ACE2 (PDB ID: 6LZG) reveals that the virus utilizes the external subdomain of the spike Receptor Binding Domain (RBD) to recognize the human ACE2 receptor . doi = 10.1080/07391102.2020.1822208 id = cord-297432-2edncbgn author = Helleberg, Marie title = Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date = 2020-07-23 keywords = COVID-19; PCR; SARS summary = A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. doi = 10.1093/infdis/jiaa446 id = cord-255415-sr81j7my author = Heller, Lindsay K. title = Mustela Vison ACE2 Functions as a Receptor for Sars-Coronavirus date = 2006 keywords = ACE2; SARS summary = However, SARS-CoV-like viruses isolated from palm civets appeared to be under strong selective pressure and are genetically most similar to viruses infecting humans early in the outbreak. Human, palm civet, rat, mouse, chicken, and mink ACE2 were compared to identify differences that are important in species specificity and to discern regions within ACE2 that may impact its function as a SARS-CoV receptor. Expression of ACE2 RNA in SARS-CoV susceptible human (Huh7, HEK293T), African green monkey (VeroE6), and Mv1Lu cell lines 7 was analyzed by RT-PCR (chapter 4.8 this volume). 7 The complete open reading frame of human ACE2 (hACE2) or mvACE2 was amplified from RNA isolated from the Huh7 or Mv1Lu cell line, respectively. Our data demonstrate that mvACE2 RNA is expressed by SARS-CoV susceptible Mv1Lu cells, that it is closely related to palm civet ACE2, and that mvACE2 is a functional receptor for SARS-CoV. doi = 10.1007/978-0-387-33012-9_90 id = cord-286298-pn9nwl64 author = Helmy, Yosra A. title = The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date = 2020-04-24 keywords = COVID-19; China; CoV-2; MERS; RNA; SARS; virus summary = Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. doi = 10.3390/jcm9041225 id = cord-252456-971d0sir author = Hemida, Maged Gomaa title = The SARS-CoV-2 outbreak from a one health perspective date = 2020-03-16 keywords = CoV; MERS; SARS; virus summary = The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . doi = 10.1016/j.onehlt.2020.100127 id = cord-327454-o1mrpgvj author = Hemmati-Dinarvand, Farshad title = Mysterious Virus: A Review on Behavior and Treatment Approaches of the Novel Coronavirus, 2019-nCoV date = 2020-05-06 keywords = ACE2; China; SARS; coronavirus summary = Instead, the extremely pathogenic CoVs, containing Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), mostly contaminate lower airways and lead to pneumonia (5) . Based on the genomic structure and phylogenetic analysis, the family Coronaviridae is currently classified into two subfamilies, Sarbecovirus containing SARS-CoV are two major zoonotic pathogenic coronaviruses (Table 1) . Accordingly, the International Committee on Taxonomy of Viruses named it severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently reported that between the SARS-CoV genome sequence and the novel coronavirus exist 82% similarity, thus, named 2019-nCoV by WHO (18) . This theory may be indicating that 2019-nCoV uses the same SARS-CoV mechanism i.e. through angiotensin-converting enzyme2 (ACE2) receptor and the TMPRSS2 protease to infect the human cells. Sequence analysis has shown that some of the 2019-nCoV clusters and bat-associated SARS76 CoV viruses (SARSr-CoV) can use the ACE2 receptor to enter the host cell. doi = 10.1016/j.arcmed.2020.04.022 id = cord-299560-np6nfvf2 author = Hendaus, Mohamed A. title = Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date = 2020-05-20 keywords = RDV; RNA; SARS summary = Replication of SARS-CoV-2 depends on the viral RNAdependent RNA polymerase (RdRp) (Elfiky & Azzam, 2020) which is the most probable target of the investigational nucleotide analogue remdesivir (RDV) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . RDV exhibits broad-spectrum antiviral activity against RNA viruses, and former studies with RdRps from Ebola virus (EBOV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have shown that delayed chain-termination is RDV''s conceivable mechanism of action ( Figure 2 ) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . On April 29, 2020, Gilead revealed results from the openlabel, Phase 3 SIMPLE trial evaluating 5-day and 10-day dosing durations of the investigational antiviral remdesivir in hospitalized patients with severe manifestations of COVID-19 disease. doi = 10.1080/07391102.2020.1767691 id = cord-282560-tofppr3b author = Henderson, Jack A. title = Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors date = 2020-09-21 keywords = Cys; Cys270; MERS; SARS summary = Here, we report the pK(a) calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. 14, 15 Our previous work employing the hybrid-solvent based continuous constant pH molecular dynamics (CpHMD) simulations 16 demonstrated that the elucidation of proton-coupled conformational dynamics offers a deeper understanding of the structure-dynamics-function relationships 17 and inhibition mechanisms 18-20 of aspartyl proteases. We performed pH replica-exchange CpHMD simulations to estimate the pKa values of Asp/Glu/His/Cys/Lys side chains and assess possible proton-coupled dynamics in SARS-CoV, SARS-CoV-2, and MERS-CoV PLpros. To provide support for the protonation states determined by GB-CpHMD titrations and test the proton-coupled dynamics of the BL2 loop, we performed conventional all-atom fixed-charge MD simulations of SARS-CoV-2 PLpro with the catalytic side chains fixed in the charged states and Cys270 fixed in the protonated or deprotonated state. doi = 10.1063/5.0020458 id = cord-022266-nezgzovk author = Henderson, Joan C. title = Tourism and Health Crises date = 2009-11-16 keywords = Asia; DVT; SARS; crisis; health; tourism; travel summary = Such situations and approaches to their resolution represent the subject of this chapter in which health risks when traveling and on arrival at destinations are considered, with a section devoted to infectious diseases affecting humans and animals and birds. Health is a major public and private concern in general and a key element in destination choice and visitor satisfaction, with individuals and the tourism industry likely to shun environments where there might be a risk to tourist well-being. Some studies have concluded that the health of as many as 50% of participants is impaired by the experience of international tourism (Dawood, 1989) and the rise in foreign travel has been accompanied by an increased incidence of disease, especially that of a tropical nature (Connor, 2005) . Some initiatives to minimize unnecessary dangers and avoid serious injuries in the fi eld of adventure tourism are operator accreditation schemes, strict health and safety rules, codes of conduct, staff training and the education and prior assessment of participants (Bentley and Page, 2001) . doi = 10.1016/b978-0-7506-7834-6.50008-9 id = cord-023140-ytal7wog author = Henderson, Joan C. title = Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore date = 2004-12-09 keywords = SARS; Singapore; crisis; hotel summary = title: Responding to crisis: severe acute respiratory syndrome (SARS) and hotels in Singapore The sudden outbreak of severe acute respiratory syndrome (SARS) in Singapore in 2003 was a grave crisis for the tourism industry as a whole and highlights the importance of effectively managing and planning for such occurrences. It focuses on how the epidemic impacted on Singapore''s hotel sector and management reactions to it, affording insights into the problems caused by outbreaks of infectious disease at destinations and possible responses. The epidemic of SARS in 2003 was an exceptional crisis for Singapore''s hotels and an exacting test for its managers, in which advances to near normality were dictated by outside developments and agencies as much as their own efforts. Managing a health-related crisis: severe acute respiratory syndrome (SARS) in Singapore Chaos, crises and disasters: a strategic approach to crisis management in the tourism industry doi = 10.1002/jtr.505 id = cord-293367-0fe62h2f author = Henderson, Lauren A. title = American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS‐C) Associated with SARS‐CoV‐2 and Hyperinflammation in COVID‐19. Version 1 date = 2020-07-23 keywords = COVID-19; MIS; SARS; Task summary = Since its initial description in December 2019 in Wuhan China, coronavirus disease 2019 , caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly evolved into a worldwide pandemic affecting millions of lives.(1) Unlike adults, the vast majority of children with COVID-19 have mild symptoms. Reports in the literature and unpublished observations by members of the panel both note that some patients with MIS-C can decompensate rapidly; however, the risk factors that predispose patients to such severe and progressive illness have not been identified.(10, 13) Accordingly, children with abnormal vital signs, concerning physical examination findings, significantly elevated inflammatory markers, or signs of cardiac involvement will need to be admitted to the hospital for supportive care while Tier 2 testing is completed. doi = 10.1002/art.41454 id = cord-325593-ww2vq3n4 author = Hendren, Nicholas S. title = Unique Patterns of Cardiovascular Involvement in COVID-19 date = 2020-05-14 keywords = COVID-19; SARS summary = However, to our knowledge, a framework describing the variable presentations of cardiac involvement in COVID-19 within the broader spectrum of symptomatic SARS-CoV-2 infection has not been previously proposed. First, the prevalence of mixed cardiopulmonary disease as assessed by elevated cardiac troponin levels, is variable, but occurs in 10-25% of patients hospitalized with COVID-19 3, 4 . ACovCS with cardiac predominate disease may be more apparent at hospital presentation relative to mixed cardiopulmonary disease because the predominate cardiac manifestations (e.g. chest pain due to a myocardial infarction) often results in symptoms which lead patients to seek emergent care. Just as there is variability in cardiac presentations of COVID-19, SARS-CoV-2 infection overall has a wide spectrum of disease penetrance with many patients displaying few to no symptoms, while an unfortunate minority develop severe life limiting disease. Other factors which may influence the variable presentation of COVID-19 include mutations in the circulating SARS-CoV-2 virus though it remains uncertain whether such observations explain the regional differences in the outcomes of COVID-19. doi = 10.1016/j.cardfail.2020.05.006 id = cord-344853-s2p2csrx author = Hendren, Nicholas S. title = Description and Proposed Management of the Acute COVID-19 Cardiovascular Syndrome date = 2020-04-16 keywords = ACE2; COVID-19; SARS; myocardial; patient summary = A substantial minority of patients hospitalized develop an acute COVID-19 cardiovascular syndrome, which can manifest with a variety of clinical presentations but often presents as an acute cardiac injury with cardiomyopathy, ventricular arrhythmias, and hemodynamic instability in the absence of obstructive coronary artery disease. S ince the index cases were first reported in Wuhan, China, in December 2019, coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic infecting >1 million individuals by early April 2020. In this document, we focus on a prominent myocarditis-like syndrome involving acute myocardial injury often associated with reduced left ventricular ejection fraction in the absence of obstructive coronary artery disease. Additional studies, including collection of endomyocardial tissue by biopsy and autopsy studies, are required to delineate the pattern and proportion of ACovCS related to acute myocarditis versus general myocardial injury caused by systemic cytokine dysregulation. doi = 10.1161/circulationaha.120.047349 id = cord-257533-i85dyg8n author = Henn, Wolfram title = Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity date = 2020-06-23 keywords = SARS; vaccine summary = title: Allocation criteria for an initial shortage of a future SARS-CoV-2 vaccine and necessary measures for global immunity Although healthcare systems around the world currently are fully absorbed with the day-today challenge of slowing down the spread of the SARS-CoV-2 virus, ongoing research makes it very likely that a protective vaccine will be developed within a rather short period of time [1, 2] . Given the unprecedented public attention to the issue, these criteria must be medically adequate, socially fair, transparent, verifiable, and easily understandable for non-experts, in order to bridge thehopefully short but anyway relevant-initial shortage of vaccine supply without creating social discomfort or even unrest. As current data clearly show that COVID-19 mortality is strongly associated with age [7] , it should be the leading and also easily verifiable medical parameter for the distribution of the expected vaccine during an initial scarcity. doi = 10.1016/j.vaccine.2020.06.058 id = cord-295545-ruxz77i8 author = Hennighausen, Lothar title = Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date = 2020-05-11 keywords = SARS; stat summary = The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2. A study in pneumocytes demonstrated that ACE2 expression is induced by interferons (Ziegler, 2020) , possibly through the transcription factors Signal Transducer and Activator of Transcription (STAT) 1 and 2, as the authors suggest. Ace2 mRNA levels vary widely between cell types, with high expression detected in lactating mammary and intestinal tissues ( Figure 1A -B) and Type II Pneumocytes (Ziegler, 2020) . To explore the possibility that Ace2 gene expression in SARS-CoV-2 target cells is regulated not only by interferons but also by a range of cytokines through the family of STAT transcription factors, we mined available scRNA-seq data (Ziegler, 2020) (Table 1) . doi = 10.1101/2020.05.11.089045 id = cord-352863-6cttilm8 author = Hennighausen, Lothar title = Activation of the SARS-CoV-2 receptor Ace2 through JAK/STAT-dependent enhancers during pregnancy date = 2020-09-06 keywords = ACE2; SARS summary = Expression of the ACE2 gene in type II pneumocytes is activated by interferons (Ziegler et al., 2020) , opening the possibility that the cytokine storm in COVID-19 patients, and peptide hormones in general, might lead to increased levels of ACE2 in a range of putative SARS-CoV-2 target tissues. Next, we mined RNA-seq data from our lab and demonstrated increased Ace2 expression throughout pregnancy and lactation ( Figure 1B ) with a pattern similar to that of other prolactin-regulation genes (Lee et al., 2018; Yamaji et al., 2013) . Our study directly demonstrates that the Ace2 gene is expressed in mammary tissue and activated during pregnancy and lactation through intronic enhancers built on the transcription factor STAT5. While SARS-CoV-2 has been detected in breast milk in at least seven studies and our research has demonstrated that its receptor ACE2 is present in mammary tissue and highly induced during lactation, the impact of these findings on COVID-19 requires further investigations. doi = 10.1016/j.celrep.2020.108199 id = cord-350101-t34myl7l author = Henrique Braz‐Silva, Paulo title = SARS‐CoV‐2: What can saliva tell us? date = 2020-05-11 keywords = SARS summary = The World Health Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. Organisation (WHO) declared on 11 March 2020 that the epidemic of the new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic now called COVID-19. In addition to the diagnosis itself, the study of saliva in cases of COVID-19 will help understanding its pathogenesis, since it has been recently reported that epithelial cells of the oral cavity showed abundant expression of the angiotensin-converting enzyme II (ACE2), a receptor playing a key role in the entry of SARS-CoV-2 into the cells (Xu et al., 2020) . Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: A diagnostic validity study doi = 10.1111/odi.13365 id = cord-343273-zaaraiy7 author = Hensley, Lisa E. title = Interferon-β 1a and SARS Coronavirus Replication date = 2004-02-17 keywords = SARS summary = Here, we report that recombinant human interferon (IFN)-β 1a potently inhibits SARS coronavirus replication in vitro. The IFN-β 1a preparation employed in this study was selected because it is currently used as part of the most effective treatment regimen for relapsing forms of multiple sclerosis (8) , and more importantly, because it was shown to have antiviral activity (as measured in a vesicular stomatitis virus cytopathic assay system) 14 times greater than the currently available treatment using IFN-β 1b (9) . In the current study, Vero E6 cells were treated with concentrations (5,000 to 500,000 IU/mL) of IFN-β 1a either 24 h before or 1 h after inoculation with the SARS-CoV (multiplicity of infection 0.1 PFU/cell), and monitored for cytopathic effect and production of infectious SARS-CoV at 24, 48, and 72 h postinfection. Production of infectious SARS-CoV was potently inhibited (>99.5% or 2.00 log 10 PFU/mL) at 24 h postinfection by pretreatment of Vero E6 cells with IFN-β 1a at all concentrations tested (Figure 1 ). doi = 10.3201/eid1002.030482 id = cord-346763-xdfl659q author = Herman, A. title = Drug reaction with eosinophilia and systemic symptoms syndrome in a patient with COVID‐19 date = 2020-08-13 keywords = SARS; dress summary = We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. We report a case of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome in a patient with COVID-19. According to the scoring system for classifying DRESS cases (RegiSCAR) reported by Kardaun et al., 1 a drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome was diagnosed as follows: fever ≥38.5°C (0), enlarged lymph nodes (0), eosinophilia (1), atypical lymphocytes (1), skin rash extent >50% body surface area (1), skin rash suggesting DRESS (1), biopsy suggesting DRESS (0), organ involvement (liver, kidney, lung) (2), resolution ≥15 days (0), viral titers (HBV/HCV) negative (1) . Drug reaction with eosinophilia and systemic symptoms syndrome (DRESS) syndrome associated with azithromycin presenting like septic shock: a case report Drug reaction with eosinophilia and systemic symptoms (DRESS) associated with azithromycin in acute Epstein-Barr virus infection doi = 10.1111/jdv.16838 id = cord-285469-b61y9ezi author = Hernández-Fernández, Francisco title = Cerebrovascular disease in patients with COVID-19: neuroimaging, histological and clinical description date = 2020-07-09 keywords = COVID-19; CVD; Fig; SARS; patient summary = The aim of our study is to describe the clinical characteristics, laboratory findings, neuroimaging and available pathological anatomy data, as well as the presentation, therapeutic management and clinical outcomes of patients with acute CVD in a healthcare setting with a high incidence of transmission of this virus. We registered all hospitalized patients with COVID-19 reported during this period, and included all patients diagnosed with acute CVD, both ischaemic and haemorrhagic, treated consecutively by neurology, neurosurgery and the intensive care unit. Bivariates studies were designed to contrast the main variables among CVD patients, between ischaemic/haemorrhagic subtypes within the COVID-19 group, and to assess clinical prognosis. The other three haemorrhagic cases were detected on varying days of clinical evolution because having been intubated, sedated and treated for SARS-CoV-2 infection, the neurological manifestations were masked prior to tracheal extubation, when difficulty arousing these patients was observed. doi = 10.1093/brain/awaa239 id = cord-300774-5mrkmctl author = Hernández-Mora, Miguel Górgolas title = Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date = 2020-10-25 keywords = SARS; TCZ; Tocilizumab; patient summary = INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . doi = 10.1016/j.ijid.2020.10.045 id = cord-347968-jhnr8k3j author = Herrera, David title = Is the oral cavity relevant in SARS-CoV-2 pandemic? date = 2020-06-23 keywords = COVID-19; SARS; oral summary = CONCLUSIONS: Antiseptic mouth rinses, such as those containing cetylpyridinium chloride or povidone-iodine, may be able to decrease the severity of COVID-19 by reducing oral viral load in infected subjects and decreasing the risk of transmission by limiting viral load in droplets, generated in normal life, or in aerosols, produced during dental procedures. The information presented in this narrative review supports the use of antiseptic mouth rinses, both as a single preprocedural use and as daily use during a limited period of time, to impact the transmission and/or pathogenicity of SARS-CoV-2, since they have shown to reduce the oral viral load and, therefore, they may reduce the severity of the disease in an infected subject and may reduce the risk of transmission, by reducing the viral load in aerosols, expelled during dental procedures, or in droplets generated when breathing, talking, sneezing, coughing, etc. doi = 10.1007/s00784-020-03413-2 id = cord-294644-xuafsnxm author = Herrmann, Burkhard L. title = Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten date = 2020-08-13 keywords = SARS summary = title: Die Prävalenz von SARS-CoV-2-IgG-AK liegt bei 1,2%: Screening bei asymptomatischen ambulanten Patienten Patients with newly diagnosed COVID-19 (coronavirus disease 2019) develop antibodies against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The prevalence of 1.2% of SARS-CoV-2-IgG-antibodies and consequently the rate of infection in asymptomatic outpatients in Northrhine-Westfalia (Germany) is low. Inwiefern sich im Rahmen einer ambulanten Vorstellung (Einzugsgebiet Nordrhein-Westfalen [NRW], Deutschland) SARS-CoV-2-IgG-AK im Screening nachweisen lassen, wurde in einer monozentrischen prospektiven Erhebung an 415 Patienten ohne zurückliegenden wissentlichen Kontakt mit SARS-CoV-2 oder COVID-19 untersucht. Alle Patienten willigten in die Untersuchung ein und gaben an, zum Zeitpunkt der Abnahme unter keinen Symptomen einer akuten Infektion wie Husten, Fieber oder Dyspnoe zu leiden. Alle Patienten wurden durch den Autor eigenständig anamnestiziert und verneinten einen Kontakt mit Menschen, die positiv auf SARS-CoV-2 getestet wurden oder an COVID-19 erkrankt sind. Mit einer Prävalenz von 1,2% wurden SARS-CoV-2-AK in der Studienpopulation (ambulante, asymptomatische Patienten) nachgewiesen. doi = 10.1007/s15006-020-0750-y id = cord-344316-mwnnmwnw author = Herst, C.V. title = An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors’ CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design date = 2020-04-28 keywords = EBOV; SARS summary = title: An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors'' CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. Wilson We set out to see if we could drive CTL expansion directed against NP43-53 to occur after vaccinating C57BL/6 mice with Ebola Zaire NP43-53 (VYQVNNLEEIC), 50 and to subsequently conduct an in-vivo EBOV challenge study to see if this peptide was protective. We show here that the H2-D b restricted epitopes VSV (RGYVYQGL) and OVA (SIINFEKL), when administered to C57BL/6 mice, each produce a CD8+ We used this adjuvanted microsphere peptide vaccine platform to immunize C57BL/6 mice with NP43-53, the CTL+ class I peptide antigen from the Ebola Ziare NP protein identified as protective by Wilson et al. doi = 10.1016/j.vaccine.2020.04.034 id = cord-337093-7pxfzuq0 author = Hess, David C. title = COVID-19-Related Stroke date = 2020-05-07 keywords = ACE2; SARS summary = The SARS-CoV-2 virus binds to angiotensin-converting enzyme 2 (ACE2) present on brain endothelial and smooth muscle cells. Depletion of ACE2 by SARS-CoV-2 may tip the balance in favor of the "harmful" ACE1/angiotensin II axis and promote tissue injury including stroke. There is a rationale to continue to treat with tissue plasminogen activator for COVID-19-related stroke and low molecular weight heparinoids may reduce thrombosis and mortality in sepsis-induced coagulopathy. The SARS-CoV-2 virus binds to the angiotensin-converting enzyme 2 (ACE2) via its spike (S) protein [9] . The depletion of ACE2 by the SARS-CoV-2 virus coupled with the age-related decline in ACE2 and increase of ACE-1-Ang II tips the balance in favor of ACE-1/ angiotensin II with proinflammatory and organ damaging effects. Binding to and depletion of ACE2 may tip the RAS balance in favor of the ACE-1-angiotensin II-AT1 axis and contribute to endothelial dysfunction, organ damage, and stroke. doi = 10.1007/s12975-020-00818-9 id = cord-315462-u2dj79yw author = Hewitt, Judith A. title = ACTIVating Resources for the COVID-19 Pandemic: In vivo Models for Vaccines and Therapeutics date = 2020-10-01 keywords = ACE2; COVID-19; SARS; disease; model summary = The selection of appropriate animal models of infection, disease manifestation, and efficacy measurements is important for vaccines and therapeutics to be compared under ACTIV''s umbrella using Master Protocols with standardized endpoints and assay readouts. Models of SARS-CoV-2 infection include mice (ACE2 transgenic strains, mouse adapted virus, and AAV transduced ACE2 mice), hamsters, rats, ferrets and non-human primates (NHPs). Following infection by the intranasal route, golden Syrian Hamsters demonstrate clinical features, viral kinetics, histopathological changes, and immune responses that closely mimic the mild to moderate disease described in human COVID-19 patients (Chan et al., 2020b; Imai et al., 2020; Sia et al., 2020) . In an initial study of SARS-CoV-2 infection of hACE2-hamsters, clinical signs were observed including elevated body temperatures, slow or reduced mobility, weight loss and mortality (1 out of 4 animals). Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease. doi = 10.1016/j.chom.2020.09.016 id = cord-336117-hit4kza8 author = Heymann, D.L. title = Emerging Infections, the International Health Regulations, and Macro-Economy date = 2014-02-27 keywords = IHR; SARS; human summary = Under the IHR, countries are able to work transparently with WHO and its scientific experts and collaborating laboratories to conduct joint risk assessments of public health events such as outbreaks of infectious diseases; to make evidence-based recommendations to help prevent or control their international spread; and, by providing valid and transparent information to national focal points, to help prevent unnecessary panic and misunderstanding about risk. Precautionary measures to prevent international spread of the infection were immediately recommended by the WHO -it was first recommended that persons who were ill with similar symptoms and contact with geographic areas where outbreaks were occurring defer their travel until they were well. The IHR 1969 were revised in 2005, incorporating many of the lessons learned during the SARS outbreak, and now ensure broader disease coverage, and in addition require countries to develop core capacities in public health laboratory and epidemiology in order to detect and respond to diseases where and when it occurs, and before it spreads internationally (Box 1). doi = 10.1016/b978-0-12-375678-7.00624-6 id = cord-009153-zxx4m1kz author = Heymann, David L title = Dangerous pathogens in the laboratory: from smallpox to today''s SARS setbacks and tomorrow''s polio-free world date = 2004-05-15 keywords = SARS; laboratory; poliovirus summary = THE LANCET • Vol 363 • May 15, 2004 • www.thelancet.com COMMENTARY Less than a year after an unprecedented international public-health effort interrupted human-to-human transmission of the coronavirus that causes severe acute respiratory syndrome (SARS-CoV), some human beings are again infected. 2 Auspiciously, the new SARS cases are occurring as WHO''s Biosafety Advisory Group prepares to examine the long-term containment of poliovirus stocks, the risks of which will rapidly increase after interruption of transmission and the ending of immunisation with oral poliovirus vaccine. 3 The recent outbreak of nine cases of SARS in China, with one death, underlines again the challenges of maintaining appropriate biosafety conditions in laboratories working with dangerous pathogens. During the SARS outbreak last year, many specimens were obtained from human cases of SARS COMMENTARY Dangerous pathogens in the laboratory: from smallpox to today''s SARS setbacks and tomorrow''s polio-free world and sent to many different national and international laboratories for various studies. doi = 10.1016/s0140-6736(04)16234-x id = cord-308736-kpz0o1ag author = Heßling, Martin title = Ultraviolet irradiation doses for coronavirus inactivation – review and analysis of coronavirus photoinactivation studies date = 2020-05-14 keywords = SARS; UVC summary = Methods: Coronavirus inactivation experiments with ultraviolet light performed in the past were evaluated to determine the UV radiation dose required for a 90% virus reduction. To answer the important question regarding SARS-CoV-2 and other coronaviruses as to which irradiation doses are needed for inactivation, the existing coronavirus photoinactivation results of the last 60 years have been reviewed and analyzed in this study. In most studies, the authors did not intend to investigate the log-reduction doses of coronaviruses, but rather virus inactivation in various applications. Most authors did not measure the UVC absorption properties of their biological materials because it was of no importance for their research task; thus, it is almost impossible to extract the role of the absorption in the calculation of the necessary irradiation doses for a 90% virus reduction. To date, UVC radiation has been effective against all coronaviruses in all published investigations, although the absorption properties of the sample media reduced inactivation success. doi = 10.3205/dgkh000343 id = cord-296657-mymndjvd author = Higuchi, Yusuke title = High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date = 2020-09-16 keywords = ACE2; RBD; SARS summary = The extracellular domain of modified ACE2 fused to the Fc region of the human immunoglobulin IgG1 had stable structure and neutralized SARS-CoV-2 pseudotyped lentivirus and authentic virus with more than 100-fold lower concentration than wild-type. Engineering ACE2 decoy receptors with directed evolution is a promising approach to develop a SARS-CoV-2 neutralizing drug that has affinity comparable to monoclonal antibodies yet displaying resistance to escape mutations of virus. Three cycles of screening resulted in an identification of mutant ACE2 clones with more than 100-fold higher binding affinity to the RBD and lower half-maximal inhibitory concentration (IC50) for SARS-CoV-2 pseudotyped lentivirus as well as authentic virus. We engineered ACE2 to bind the RBD of the SARS-CoV-2 spike protein with the combination of surface display of mutagenized library and fluorescence-activated cell sorting (FACS) to perform the evolution in 293T human cells. doi = 10.1101/2020.09.16.299891 id = cord-294582-flkjekyo author = Hijikata, Atsushi title = Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs date = 2020-05-25 keywords = ACE2; SARS; drug summary = In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Among these methods, SBDR is the most promising to find Abbreviations ACE2, angiotensin I-converting enzyme 2; MERS, Middle East respiratory syndrome; RBD, receptor-binding domain; SARS-CoV, severe acute respiratory syndrome coronavirus; SBDR, structure-based drug repositioning; WHO, World Health Organization. Also, the structural models of the complexes between SARS-CoV-2 proteins and potential drugs were proposed by comparing the ligand molecules of the proteins and approved, experimental, or natural drugs. A total of 11 ligand molecules were matched to 21 approved/experimental and 5 natural drugs, and the complex models of the SARS-CoV-2 proteins with several promising drugs, those with high similarity score or placed in higher ranking, were constructed as follows. doi = 10.1002/1873-3468.13806 id = cord-283579-aejbfk3l author = Hilda, Awoyelu Elukunbi title = Phyloevolutionary analysis of SARS-CoV-2 in Nigeria date = 2020-06-14 keywords = Nigeria; SARS summary = Conclusion The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. Knowledge on the outbreak and spread of SARS-CoV-2 in Nigeria would help in providing preventive measures and reduce transmission among populations at risk. Comparative analysis of strains within clades was performed on Geneious Prime (https://www.geneious.com/) based on statistical analysis to determine positions in the genomic sequences from Nigeria that significantly differ between other strain. Figures 2a -g showed consensus similarities and variants between 3 strains from Wuhan, China and Nigeria, including human SARS-CoV-2 human genome. Comparative analysis of the strain from Nigeria, 2 strains from Wuhan sharing the same clade and the reference human SARS-CoV-2 genome was done. The study evidently showed the entire outbreak of COVID-19 infection in Nigeria stemmed from a single introduction sharing consensus similarity with the reference SARS-CoV-2 human genome from Wuhan. doi = 10.1016/j.nmni.2020.100717 id = cord-266016-555e3ndo author = Hildenwall, Helena title = Paediatric COVID‐19 admissions in a region with open schools during the two first months of the pandemic date = 2020-06-21 keywords = SARS summary = While it appears that most children get mild symptoms if they become infected with the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) (1), there have been concerns that they may present with high viral loads and contribute to asymptomatic transmission (2) . We carried out a two-month review of paediatric admissions aged 0-17 years who tested positive for SARS-CoV-2 in the Stockholm region, where approximately 514,000 (24%) of all Swedish children live. A total of 63 admitted children aged 0-17 years tested positive for SARS-CoV-2 during the study period. Infants represented more than half of all symptomatic admissions (16/30, 53%) whereas the proportion of all SARS-CoV-2 positive admitted children Paediatric admissions accounted for a minor part of the total admissions due to COVID-19 as a primary diagnosis during the first two months of the pandemic in Stockholm (30/4347, 0.7%). doi = 10.1111/apa.15432 id = cord-346658-ij5sr88p author = Hilgenfeld, Rolf title = Sometimes Intermediates Do the Job! date = 2006-04-07 keywords = SARS summary = The mode of binding of this inhibitor to the target enzyme was found to be related (although not identical) to what had been seen earlier in a complex between the rhinovirus (HRV-2) 3C proteinase and compound AG7088 (Figure 1A) , a vinylogous ethyl ester developed by Agouron Inc. The structural insight along with information on the flexibility of the enzyme [9] enabled researchers world-wide to use structure-based design [5] and virtual screening methods [10] to prepare new inhibitors of the SARS-CoV M pro . Several lopinavir derivatives showed somewhat improved binding affinities, but it came as a big surprise that some of the intermediate benzotriazole esters resulting from the activation of the acid components by HBTU were nanomolar inhibitors of the M pro ! The discovery of compounds binding noncovalently to the M pro may, in the end, constitute a more important milestone on the way to clinically useful inhibitors of the coronavirus main proteinase than identification of the acylating agents. doi = 10.1016/j.chembiol.2006.03.002 id = cord-328960-46zui1sl author = Hillen, Hauke S. title = Structure of replicating SARS-CoV-2 polymerase date = 2020-04-27 keywords = RNA; SARS summary = Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). doi = 10.1101/2020.04.27.063180 id = cord-331517-o5ejfq86 author = Hirayama, Takehisa title = Guillain-Barré syndrome after COVID-19 in Japan date = 2020-10-29 keywords = Barré; SARS summary = We report the first case of Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection in Japan. In previous reports, most patients with SARS-CoV-2-infection-related GBS had lower limb predominant symptoms, and antiganglioside antibody tests were negative. Our findings support the notion that non-immune abnormalities such as hyperinflammation following cytokine storms and microvascular disorders due to vascular endothelial damage may lead to neurological symptoms in patients with SARS-CoV-2 infection. 4 In the present report, we discuss a case of axonal-type GBS associated with SARS-CoV-2 infection, where the patient was tested for various antiganglioside antibodies. Furthermore, we review the cases of SARS-CoV-2-infection-related GBS reported to date, in order to provide insight into the clinical characteristics and pathological mechanisms underlying the disease. In conclusion, our report supports the notion that patients with GBS associated with SARS-CoV-2 infection tend to test negative for antiganglioside antibodies. ► Patients with Guillain-Barré syndrome (GBS) associated with SARS-CoV-2 infection may test negative for many known antiganglioside antibodies. doi = 10.1136/bcr-2020-239218 id = cord-258250-zueo1xfa author = Hirotsu, Yosuke title = Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date = 2020-08-12 keywords = PCR; SARS summary = title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . doi = 10.1016/j.ijid.2020.08.029 id = cord-269519-8hr8wyrr author = Hirotsu, Yosuke title = Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date = 2020-07-07 keywords = SARS; virus summary = Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. doi = 10.1016/j.jcv.2020.104543 id = cord-278987-3s5p9yw6 author = Hirotsu, Yosuke title = Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship date = 2020-04-17 keywords = SARS summary = title: Environmental cleaning is effective for the eradication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in contaminated hospital rooms: A patient from the Diamond Princess cruise ship The patient stayed in room A for 3 days, during which he had the SARS-CoV-2 infection. SARS-CoV-2 is detectable in several types of clinical samples including bronchial lavage fluid, nasopharyngeal swab, pharyngeal swab, sputum, saliva, and feces. 4, 5 Transmission of SARS-CoV-2 via surfaces in hospitals is of great concern to medical staff and patients. 6 A recent study showed that environmental contamination can occur via contact with patients with SARS-CoV-2 and upper respiratory tract symptoms. Double-quencher probes improved the detection sensitivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by one-step RT-PCR Surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient All authors report no conflicts of interest relevant to this article. doi = 10.1017/ice.2020.144 id = cord-356364-ipi81ce3 author = Ho, Bo-Lin title = Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date = 2015-12-14 keywords = Fig; MERS; SARS summary = In the present study, MERS-CoV main protease (M(pro)) is expressed; the dimerization of the protein and its relationship to catalysis are investigated. The colorimetry-based peptide substrate, TSAVLQ-para-nitroanilide (TQ6-pNA) (purity 95-99% by HPLC; GL Biochem Ltd, Shanghai, China), was used to measure the proteolytic activity of MERS-CoV M pro and its mutants throughout the course of the study as described previously [25, 28] . In addition, although the K d values of wild-type SARS-CoV M pro without or with substrates show no significant difference (Table 2) , it was possible to detect substrate-induced dimerization at a protein concentration of 1 μM by AEC [33] . Biochemical and AUC studies indicated that MERS-CoV M pro shows almost the same proteolytic activity as SARS-CoV M pro ; although it is a monomer in aqueous buffer and displays substrate-induced dimerization (Fig 6) . doi = 10.1371/journal.pone.0144865 id = cord-299835-92karhpl author = Ho, Khek Y. title = Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date = 2004-02-17 keywords = SARS; patient; respiratory summary = title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. doi = 10.1086/381558 id = cord-345296-4z7yfj5s author = Ho, Mei-Shang title = Neutralizing Antibody Response and SARS Severity date = 2005-11-17 keywords = SARS; antibody; patient summary = Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. Using the Taiwan nationwide laboratory-confirmed severe acute respiratory syndrome (SARS) database, we analyzed neutralizing antibody in relation to clinical outcomes. To adjust the time effects and other covariates of interest, the relationship between antibody titer, based on logarithmic transformation of base 2 (serum dilution) and other potential factors, i.e., age, sex, infection source, and duration of illness, was quantified by linear mixed models (18) , which took into account the correlation between repeated measurements of each study participants. In the model, patients with a more severe clinical course had earlier and higher antibody responses; we then examined the death rate of the early responders (Table 6 ). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways doi = 10.3201/eid1111.040659 id = cord-281793-tj4m01s4 author = Ho, Mitchell title = Perspectives on the development of neutralizing antibodies against SARS-CoV-2 date = 2020-05-20 keywords = ACE2; RBD; SARS summary = Crossreactive antibodies (e.g., 47D11, S309, and VHH-72) that bind highly conserved epitopes on the RBDs of SARS-CoV and SARS-CoV-2 could have broad neutralization activities against viral infection. The receptor binding domain (RBD) of the SARS-CoV-2 S protein contains several novel residues that might be introduced through recombination with the pangolin coronavirus, indicating a possible critical step in the evolution of the ability of SARS-CoV-2 to infect humans [10] . isolated a human monoclonal antibody (named "rRBD-15") that inhibits the interaction of the RBD of SARS-CoV-2 and the ACE2 and neutralizes the pseudovirus infection [5] . The structure complex of 47D11 and the RBD (or the S1/S protein) would reveal a novel conserved site on the RBD for broad-neutralizing antibodies against SARSr-CoVs. In addition to 47D11, another human antibody (S309) isolated from memory B cells of a SARS survivor infected in 2003 neutralizes SARS-CoV-2 [18] . doi = 10.1093/abt/tbaa009 id = cord-323871-2hx4fuk2 author = Ho, Sheau Ling title = Structural bioinformatics analysis of free cysteines in protein environments date = 2009-03-14 keywords = SARS; cysteine; residue summary = For non-membrane proteins: the hydrophobic residues such as leucine, valine, isoleucine and alanine were more frequently seen in the spatial neighborhood around free cysteines; the same was observed for the aromatic phenylalanine residue. Thus, we applied a structure-base sequence alignment of these nine coronavirus main proteinases to identify any spatial correspondences involving cysteine among them. It can be observed that this multiple sequences alignment figure shows a strong conservation of hydrophobic residues (valine, leucine, isoleucine, alanine phenylalanine and proline) and small residues (serine and glycine) in proximity to cysteine residues. A superimposition (stereo image) of the structures of SARS 3CLpro demonstrates that cysteine residues not only favor positioning in a hydrophobic environment but also develop hunched posture in the surroundings of aromatic residues, see Fig. 3 . doi = 10.1016/j.jtice.2008.07.015 id = cord-298083-4h3tg6hg author = Ho, Tin-Yun title = Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein date = 2004-01-23 keywords = SARS summary = In order to analyze the antigenicity and receptor-binding ability of SARS-CoV S protein, we expressed the S protein in Escherichia coli using a pET expression vector. By biotinylated ELISA and Western blot using biotin-labeled S protein as the probe, we identified 130-kDa and 140-kDa proteins in Vero cells that might be the cellular receptors responsible for SARS-CoV infection. Taken together, these results suggested that recombinant S protein exhibited the antigenicity and receptor-binding ability, and it could be a good candidate for further developing SARS vaccine and anti-SARS therapy. These data suggested that comparison of primary amino acid sequences does not provide insight into the receptor-binding specificity or antigenic properties of SARS-CoV S protein. To analyze the antigenicity of recombinant S protein, we performed Western blot and ELISA using sera from SARS patients or from spike-immunized rabbits. doi = 10.1016/j.bbrc.2003.11.180 id = cord-339514-0aa58pi6 author = Ho, Yu title = Assembly of human severe acute respiratory syndrome coronavirus-like particles date = 2004-06-11 keywords = SARS summary = Viral particles of human severe acute respiratory syndrome coronavirus (SARS CoV) consist of three virion structural proteins, including spike protein, membrane protein, and envelope protein. In this report, virus-like particles were assembled in insect cells by the co-infection with recombinant baculoviruses, which separately express one of these three virion proteins. Sucrose gradient purification followed by Western blot analysis and immunogold labeling showed that the spike protein could be incorporated into the virus like particle also. Recombinant baculoviruses encoding E, M, and S protein genes were used to infect Sf21 insect cell, and the expression of each protein was checked by Western blot at 4 dpi (data not shown). The packaging signal of coronavirus RNA was previously identified by using defective interfering viral particles [26] , since the SARS-CoV is a highly infectious virus, it would be much more feasible to identify this signal by using VLPs. Moreover, S protein-containing VLPs should be able to specifically target to the host cell of the SARS CoV and serve as a safe and efficient tool to deliver Western analysis confirmed the presence of S and E proteins mainly in fractions 16-18. doi = 10.1016/j.bbrc.2004.04.111 id = cord-342456-5gp3cry0 author = Hoagland, Daisy A. title = Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date = 2020-07-13 keywords = ACE2; RNA; SARS; figure summary = Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. doi = 10.1101/2020.07.12.199687 id = cord-281948-xv7vuypd author = Hoang, Ansel title = COVID-19 in 7780 pediatric patients: A systematic review date = 2020-06-26 keywords = COVID-19; MIS; SARS; child summary = We included published or in press peer-reviewed cross-sectional, case series, and case reports providing clinical signs, imaging findings, and/or laboratory results of pediatric patients who were positive for COVID-19. Data collected included the type of article (e.g., case series), country of origin, number of pediatric patients, demographic information, and all clinical symptoms (e. Compared to that review and other COVID-19 pediatric systematic reviews, [18À21] this manuscript has several key advantages: (1) we summarize 131 studies that includes 7780 children from 26 different countries, (2) this report synthesizes underlying pediatric medical conditions and delineates bacterial and viral coinfections, (3) we quantitatively describe clinical symptoms and imaging findings, (4) herein, we conglomerate the mean and standard deviation of frequently used laboratory analytes in COVID-19 positive children, (5) our report presents antiviral therapies by specific agents, and (6) our systematic review offers a preliminary comparison of patients with/without MIS-C. doi = 10.1016/j.eclinm.2020.100433 id = cord-334162-j8m2zqbr author = Hoechter, D. J. title = Besonderheiten der kardiopulmonalen Reanimation zu Zeiten von SARS-CoV-2 date = 2020-07-15 keywords = Patienten; SARS; und summary = Als Beispiel seien hier die Empfehlungen der Deutscher Gesellschaft für Anaesthesiologie und Intensivmedizin (DGAI) und des Berufsverbands Deutscher Anästhesisten (BDA) zu den Besonderheiten des Atemwegsmanagements bei Patienten mit vermuteter oder gesicherter COVID-19-Erkrankung und bei Patienten ohne Infektion während der Coronapandemie genannt [13] . Besteht bei dem Patienten ein begründeter oder bestätigter Verdacht auf COVID-19 sollen Laienhelfer, die über keine Schutzausrüstung verfügen, auf die Thoraxkompressionen verzichten und ggf. Dabei wird angenommen, dass es bei der Defibrillation wahrscheinlich zu keiner oder allenfalls zu einer kurzzeitigen und geringen Aerosolbildung kommt und die mittlerweile flächendeckende Nutzung von Klebepads den Anwender Distanz zum Patienten halten lässt. Bei innerklinischen Reanimationen von Patienten mit vermuteter oder bestätigter Infektion mit SARS-CoV-2 sollen folgende Besonderheiten hervorgehoben werden: Die Verwendung von Frühwarnsystemen (wie beispielsweise dem "early warning score") wird verstärkt empfohlen, um kritisch kranke Patienten frühzeitig zu erkennen und die Notwendigkeit zur Durchführung einer Reanimation möglichst zu vermeiden [5, 10] . doi = 10.1007/s00101-020-00814-6 id = cord-350817-tmszrtju author = Hoepel, Willianne title = Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date = 2020-07-13 keywords = SARS; anti; covid-19; figure; spike summary = Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. Taken together, these data demonstrate that anti-Spike IgG immune complexes generated from serum of severely ill COVID-19 patients induce a strong pro-inflammatory response by (otherwise immunosuppressive) human M2 macrophages, which is characterized by high production of classical cytokine storm mediators such as IL-1β, IL-6, IL-8, and TNF. As shown in Figure 4A , the used human macrophage model highly expressed all FcγRs. To determine whether FcγRs are involved in activation by anti-Spike immune complexes, we blocked the different FcγRs with specific antibodies during stimulation, and analyzed cytokine production. In conclusion, our data show that anti-Spike IgG from serum of severely ill COVID-19 patients strongly amplifies pro-inflammatory responses by human macrophages, and can contribute to subsequent endothelial barrier disruption and thrombosis. doi = 10.1101/2020.07.13.190140 id = cord-300964-knc0ruou author = Hoffman, Tove title = Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 date = 2020-04-14 keywords = COVID-19; SARS summary = We evaluated a commercially available test developed for rapid (within 15 minutes) detection of SARS-CoV-2-specific IgM and IgG by 29 PCR-confirmed COVID-19 cases and 124 negative controls. In the present study, we evaluated a commercially available assay, the COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China), developed for detection of SARS-CoV-2-specific antibodies. None of the 24 healthy volunteers, without any known history of SARS-CoV-2 infection/COVID-19, tested positive for IgM or IgG. In this study we evaluated a commercial rapid test for detection of SARS-CoV-2-specific IgM and IgG. If this was the case for one or more of the included patients, the actual sensitivities should be higher, i.e. when evaluated only on samples known to contain detectable levels of SARS-CoV-2-specific IgM and/or IgG. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis doi = 10.1080/20008686.2020.1754538 id = cord-274852-84m62t4x author = Hogan, Catherine A. title = Retrospective Screening for SARS-CoV-2 RNA in California, USA, Late 2019 date = 2020-10-17 keywords = SARS summary = To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. The study period corresponded to the onset of the 2019-2020 respiratory virus season, during which the number of cases of influenza A, influenza B, and respiratory syncytial virus increased and the frequency To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. Our pooled screening strategy for investigating local community transmission of SARS-CoV-2 in the San Francisco Bay area of California during late 2019 during the onset of the respiratory virus season identified no COVID-19 cases. doi = 10.3201/eid2610.202296 id = cord-335077-ievtvhge author = Hogan, Catherine A. title = Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens date = 2020-07-23 keywords = Accula; SARS summary = The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. The aim of this study was to evaluate the test performance characteristics of the Accula SARS-CoV-2 test in a clinical setting against a high-complexity reference standard. The manufacturer''s instructions comprise the following steps: collection of NP swab, lysis of viral particles in SARS-CoV-2 buffer, transfer of nucleic acid solution to a test cassette that contains internal process positive and negative controls, reverse transcription of viral RNA to cDNA, nucleic acid amplification, and detection by lateral flow. We included 100 samples (50 positive, 50 negative) previously tested by the SHC-LDT and subsequently tested with the Accula SARS-CoV-2 POCT. In individuals with moderate to high pretest probability of SARS-CoV-2, reflex testing of negative samples on a separate EUA assay should be performed. doi = 10.1128/jcm.01072-20 id = cord-270122-xijsj0d8 author = Hogan, Robert Edward title = COVID-19 in Patients With Seizures and Epilepsy: Interpretation of Relevant Knowledge of Presenting Signs and Symptoms date = 2020-08-24 keywords = COVID-19; SARS summary = Realizing the need for current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and clinical presentation of COVID-19, especially in relationship to patients with seizures and epilepsy. Overall, findings indicate seizures and epilepsy are rare, especially in mild COVID-19 cases, but may occur in more severe cases later in the disease course. Realizing both the need for and limitation of current information, this summary provides a focused summary of pertinent clinical diagnostic information about neurological involvement of SARS-CoV-2 virus and COVID-19, especially in relationship to patients with seizures and epilepsy. 27 As compared to population-based studies of the initial clinical presentation of COVID-19, studies in patients with seizures and epilepsy are lacking. While a neuroinvasive mechanism of SARS-CoV-2 virus CNS infection remains a postulated cause of clinical neurological disease, 16 investigation of new-onset neurological impairments associated with COVID-19 found lack of evidence for direct acute insult of SARS-CoV-19 virus to the CNS. doi = 10.1177/1535759720948549 id = cord-327431-dnppshnv author = Hognon, Cécilia title = Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date = 2020-05-27 keywords = SARS; SUD summary = In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. 28, 37 In this letter, we report an extended all-atom molecular dynamics (MD) study of the interactions produced between a dimeric SUD domain and a short RNA G4 sequence. To further examine the conformational space spanned by the G4/SUD complex, and in particular the role of the RNA in favoring the dimerization and the structure of the interface, we resorted to enhanced sampling MD simulations to obtain the 2D free energy profile along two relevant collective variables: first, the distance between G4 and SUD, and second, the separation between the two SUD subdomains. doi = 10.1101/2020.04.07.029447 id = cord-347818-93ixqyfp author = Hojyo, Shintaro title = How COVID-19 induces cytokine storm with high mortality date = 2020-10-01 keywords = ACE2; COVID-19; IL-6; SARS summary = Thus, IL-6 serves as a possible mechanism of treatment for severe COVID-19 patients, raising the possibility that one therapeutic option for the disease may be targeting excessive inflammation caused by IL-6 receptor (IL-6R) signaling with monoclonal antibody therapy or treatment with chemical modulators to block the signaling cascade while maintaining a sufficient antiviral primary immune response. IL-6-STAT3 signaling as a potential cause of the ARDS via cytokine storms in COVID-19 patients IL-6 amplifier, machinery for excessive inflammation SARS-CoV-2 infection induces the endocytosis of ACE2 together with SARS-CoV in target cells including epithelial cells and endothelial cells, resulting in an increase of serum angiotensin II (Ang II) levels due to the reduction of ACE2 surface expression (Fig. 1) [17, 48] . doi = 10.1186/s41232-020-00146-3 id = cord-310291-z79x349o author = Holland, LaRinda A. title = An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) date = 2020-07-01 keywords = Arizona; SARS summary = title: An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) Here, we report on early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sentinel surveillance in Tempe, Arizona. Genomic characterization identified an isolate encoding a 27-amino-acid in-frame deletion in accessory protein ORF7a, the ortholog of SARS-CoV immune antagonist ORF7a/X4. In anticipation of COVID-19 spreading in Arizona, we initiated a surveillance effort for the local emergence of SARS-CoV-2 starting 24 January 2020. To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we performed next-generation sequencing (NGS; Illumina NextSeq, 2ϫ76) directly on specimen RNA, thereby avoiding cell culture passage and potentially associated mutations. We found that the SARS-CoV-2 AZ-ASU2923 genome has an 81-nucleotide (nt) deletion in the ORF7a gene, resulting in a 27-amino-acid in-frame deletion (Fig. 2B) . Severe acute respiratory syndrome coronavirus gene 7 products contribute to virus-induced apoptosis doi = 10.1128/jvi.00711-20 id = cord-273918-knlc3bxh author = Holmes, Emily A title = Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science date = 2020-04-15 keywords = COVID-19; SARS; health; mental; research; social summary = 1,2 Furthermore, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, might infect the brain or trigger immune responses that have additional adverse effects on brain function and mental health in patients with Research funders and researchers must deploy resources to understand the psychological, social, and neuroscientific effects of the COVID-19 pandemic. We use the term mental health sciences to reflect the many different disciplines, including, but not limited to, psychology, psychiatry, clinical medicine, behavioural and social sciences, and neuroscience, that will need to work together in a multidisciplinary fashion together with people with lived experience of mental health issues or COVID-19 to address these research priorities. doi = 10.1016/s2215-0366(20)30168-1 id = cord-312340-hpuoren5 author = Holstein, Sarah A. title = Oncology Treatment in the Era of COVID‐19: We Cannot Afford to Hit the Pause Button date = 2020-06-02 keywords = COVID-19; SARS summary = Given the expected duration of the pandemic, it is imperative that treatment of the patient''s cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Given the expected duration of the pandemic, it is imperative that treatment of the patient''s cancer remain the priority and that advances in drug development continue through appropriately designed clinical trials. Despite the barriers that lead to this low rate of participation, clinical trials remain the cornerstone for improving oncology patient outcomes through the development of new therapies. To this end, there are many groups, including ASCO and the American Society of Hematology, that have created registries in order to collect data on outcomes of oncology patients infected with SARS-CoV-2. It is imperative that comprehensive immune profiling studies be performed to evaluate the immune responses in these patient populations and that oncology patients be included in COVID-19 clinical trials. doi = 10.1002/cpt.1920 id = cord-344901-mgnaprgt author = Holz, Frank G. title = SARS-CoV-2: Herausforderung für alle date = 2020-03-30 keywords = SARS summary = key: cord-344901-mgnaprgt authors: Holz, Frank G. title: SARS-CoV-2: Herausforderung für alle date: 2020-03-30 journal: Ophthalmologe DOI: 10.1007/s00347-020-01097-3 sha: doc_id: 344901 cord_uid: mgnaprgt nan Der Augenarzt, Dr. Li Wenliang, war in China einer der ersten, der auf eine "SARS-ähnliche" Epidemie hinwies. Er selbst hat sich an einem asymptomatischen Glaukom-Patienten infiziert und ist an Komplikationen der Erkrankung verstorben [3] . Insbesondere Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection The China Medical Treatment Expert Group for Covid-19, Guan W et al (2020) Clinical characteristics of Coronavirus disease 2019 in China Chinese doctor, silenced after warning of outbreak, dies from Coronavirus doi = 10.1007/s00347-020-01097-3 id = cord-290068-s1gdbsfx author = Hon, KLE title = Clinical presentations and outcome of severe acute respiratory syndrome in children date = 2003-05-17 keywords = Kong; SARS summary = title: Clinical presentations and outcome of severe acute respiratory syndrome in children In addition, we treated patients who had moderate symptoms of high fluctuating fever and notable malaise with intravenous ribavirin (20 mg/kg daily, given in three doses) and hydrocortisone (2 mg/kg every 6 h) immediately after admission. Lymphopenia (0·3-3·0ϫ10 9 /L) was reported in all patients, but the teenagers were generally more severely affected than the younger children. 2, 3 Ribavirin is a broad-spectrum antiviral agent and has been used for treatment of severe respiratory syncytial virus infection in We noted two distinct patterns of clinical presentation among the children we studied. On this basis, we did an open-label study in which oral gabapentin 300 mg thrice daily was given for every other chemotherapy treatment in nine patients with breast cancer. The patient reported severe nausea after the first two chemotherapy treatments. doi = 10.1016/s0140-6736(03)13364-8 id = cord-289282-4oz6r7op author = Hon, Kam Lun title = Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date = 2020-06-01 keywords = COVID-19; SARS; respiratory summary = title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS doi = 10.1002/ppul.24810 id = cord-326864-i1r3bv4p author = Hon, Kam Lun title = Coronavirus disease 2019 (COVID-19): latest developments in potential treatments date = 2020-06-29 keywords = COVID-19; MERS; SARS; treatment summary = 4 COVID-19 is a respiratory tract infection that causes mild symptoms in the majority of cases, but can also lead to ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 : latest developments in potential treatments drugsincontext.com mortality and morbidity. SARS-CoV is closely related to civet and bat CoVs, but it is phylogenetically divergent from other coronaviruses associated with human infections, including ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com OC43, NL63, 229E, and HKU1. In a clinical trial involving 199 patients with laboratory-confirmed SARS-CoV-2 infection, lopinavir-ritonavir treatment was not associated with any clinical improvements compared with standard care. 25 Long and colleagues reported that corticosteroid therapy using methylprednisolone, dexamethasone, and hydrocortisone was beneficial in treating ISSN: 1740-4398 REVIEW -Coronavirus disease 2019 (COVID-19): latest developments in potential treatments drugsincontext.com SARS-CoV patients, 78 and significantly prolonged survival time in clinical cases. doi = 10.7573/dic.2020-4-15 id = cord-287228-0qm939ve author = Hong, Ke title = Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date = 2020-10-27 keywords = PCR; RNA; SARS summary = In one study including 70 patients with COVID-19, 21% clinically recovered patients with two consecutive negative results of nucleic acid detection experienced a later positive testing for SARS-CoV-2, and the longest duration of viral RNA positivity in this study was 45 days following infection [4] . A total of 2860 COVID-19 patients were hospitalized and followed in this hospital since the epidemic, and those with persistent or intermittent viral RNA positivity in respiratory samples (including the nasopharyngeal, oropharyngeal and sputum samples) for at least 4 weeks were included in our study, regardless of the age and their clinical status. However, in most of these studies, PCR testing was used as a marker to indicate the existence of virus, and patients with positive viral RNA was considered infectious though they have been infected for months without further clinical symptoms. doi = 10.1080/22221751.2020.1827983 id = cord-333863-mtljy3s6 author = Hong, Nan title = Evaluation of ocular symptoms and tropism of SARS‐CoV‐2 in patients confirmed with COVID‐19 date = 2020-04-26 keywords = COVID-19; OSDI; SARS summary = Patients with COVID-19 may show prodromal symptom of conjunctivitis in cases where eye goggles were not worn while in close proximity with COVID-19 positive patients, leading to suggestions that ocular exposure might be a potential route of SARS-CoV-2 infection (Lu et al. Previously hospitalized patients (admission date from 19 January to 29 February 2020) in the isolation ward of the First Affiliated Hospital of Zhejiang University, diagnosed as COVID-19 positive based on their clinical symptoms and positive SARS-CoV-2 test results of their sputum swab specimens, were the target subject population. After the onset of COVID-19, the mean scores of the SEEQ and OSDI questionnaires were significantly raised, suggesting a degraded ocular surface condition (Table 2) . In our study, fifteen subjects (27%) reported new onset ocular irritation symptoms or aggravated pre-existing ocular surface irritation symptoms after infection of SARS-CoV-2. doi = 10.1111/aos.14445 id = cord-269522-38dhwggn author = Hong, Xia title = Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() date = 2009-08-27 keywords = PTSD; SARS; subject summary = title: Posttraumatic stress disorder in convalescent severe acute respiratory syndrome patients: a 4-year follow-up study() OBJECTIVE: To measure the incidence and impact of posttraumatic stress disorder (PTSD) in a cohort of 70 subjects with severe acute respiratory syndrome (SARS). To study the impact of PTSD, we used the Impact of Event Scale (IES), Zung Self-Rating Anxiety Scale (SAS), Zung Self-Rating Depression Scale (SDS), Symptom Checklist 90 (SCL-90), Short Form-36 (SF-36 Health Survey) and Social Disability Screening Schedule (SDSS). In one study of 63 survivors of SARS at 3 months postdischarge from hospital in Singapore, the rate of possible PTSD, inferred from an Impact of Event Scale (IES) Score of N26, was 41.7% [15] . In a study of 195 survivors of SARS at 1 month postdischarge from hospital in Hong Kong, 10% to 18% of them reported symptoms related to PTSD [16] . doi = 10.1016/j.genhosppsych.2009.06.008 id = cord-330597-nftwj0d5 author = Hopfer, Helmut title = Hunting coronavirus by transmission electron microscopy – a guide to SARS‐CoV‐2‐associated ultrastructural pathology in COVID‐19 tissues date = 2020-09-27 keywords = COVID-19; CoV-2; SARS; patient summary = Using micrographs from infected cell cultures and autopsy tissues, we show how coronavirus replication affects ultrastructure and put the morphological findings in the context of viral replication, which induces extensive remodelling of the intracellular membrane systems. To better understand the ultrastructural morphology of SARS-CoV-2 infection and COVID-19, we will first briefly discuss the pathogenesis of COVID-19 and coronavirus replication in general and then examine the TEM findings in more detail. All rights reserved Coronaviruses including SARS-CoV-2 and the morphological changes associated with replication can be visualised by TEM in infected cell lines (figure 3A-G) [81] [82] [83] [84] [85] 87, 88] or organoids [96, 97] . Based on the cell culture findings outlined above, we expect to find the same SARS-CoV-2 morphology and distribution in vesicles of autopsy and biopsy tissues of COVID-19 patients. doi = 10.1111/his.14264 id = cord-264919-0jlg2gkc author = Hopp, Marie-Thérèse title = Unravelling the debate on heme effects in COVID-19 infections date = 2020-06-12 keywords = ACE2; COVID-19; SARS; TMPRSS2 summary = doi = 10.1101/2020.06.09.142125 id = cord-274591-p34kk4up author = Horby, Peter W, title = Prospects for Emerging Infections in East and Southeast Asia 10 Years after Severe Acute Respiratory Syndrome date = 2013-06-17 keywords = Asia; East; SARS; Southeast summary = The region is certainly a hot spot of socioeconomic and environmental change, and although some changes (e.g., urbanization and agricultural intensification) may reduce the probability of emerging infectious diseases, the effect of any individual emergence event may be increased by the greater concentration and connectivity of livestock, persons, and products. The SARS epidemic provided a dramatic demonstration of the weaknesses in national and global capacities to detect and respond to emerging infectious diseases, and it was in many ways a watershed event that had a transformative effect on many of the clinical, public health, and other professionals involved. Surveillance and response capacities have improved in the last decade, and East and Southeast Asia are far better prepared to detect and respond to emerging infectious diseases. doi = 10.3201/eid1906.121783 id = cord-320627-7vi6skvh author = Horejsh, Douglas title = A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry date = 2005-01-19 keywords = SARS; beacon; molecular summary = We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. In this report, we describe the construction of molecular beacon-conjugated beads that we have called ''BeadCons'', whose specific hybridization with complementary target sequences can be resolved by flow cytometry (see Figure 1 ). In the multiplex detection experiment, the test sample contained 0.5 ml of the positive oligo DNA (100 mM stock) diluted in 9.5 ml of a complex mixture of oligonucleotides (equimolar levels of 10 mM each, equalling a 100 mM total concentration; sequences listed in Supplementary Table 1 ). doi = 10.1093/nar/gni015 id = cord-328409-px92ff89 author = Hornuss, Daniel title = COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date = 2020-05-13 keywords = COVID-19; PCR; SARS summary = After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Als Diagnostik der Wahl zur schnellen Identifikation von COVID-19-Fällen hat sich dabei die PCR-Analyse auf SARS-CoV-2 aus tiefen nasopharyngealen oder oropharyngealen Abstrichen etabliert [3] . doi = 10.1055/a-1170-6061 id = cord-333465-cha7ndv5 author = Horspool, A. M. title = Interplay of antibody and cytokine production reveals CXCL-13 as a potential novel biomarker of lethal SARS-CoV-2 infection date = 2020-08-31 keywords = August; RBD; SARS summary = Patient mortality, sex, blood type, and age were all associated with differences in antibody production to SARS-CoV-2 antigens which may help explain variation in immunity between these populations. We evaluated anti-193 SARS-CoV-2 antibody production to 3 antigens (RBD, N, and S1) in 82 in-patients 194 Table 1 ) by developing a novel rapid-ELISA technique. Our survey of SARS-CoV-2 positive patients demonstrated that antibody (IgG) 198 production to RBD, N, and S1 proteins developed over the first 10 to 20 days post-199 symptom onset (Figure 1a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. To accurately assess 223 differences in antibody production independently of disease outcome, we quantified anti-224 SARS-CoV-2 IgG production in patients who survived infection grouped by biological sex, 225 . . https://doi.org/10.1101/2020.08.24.20180877 doi: medRxiv preprint significantly increased in patients that did not survive SARS-CoV-2 infection compared to 272 those that did (Figure 4d ). doi = 10.1101/2020.08.24.20180877 id = cord-292209-d1ty9etr author = Horta, Bernardo L title = Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date = 2020-10-29 keywords = Brazil; SARS; study; test summary = Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. The present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in 133 sentinel cities throughout Brazil, as part of the EPICOVID-19 study (www.epicovid19brasil.org). In summary, the analyses of the three waves of national serological surveys in Brazil showed important inequalities in the prevalence of antibodies against SARS-CoV-2 according to family wealth, education and ethnic groups. Yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against SARS-CoV-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. doi = 10.26633/rpsp.2020.135 id = cord-331617-1ytcd0ax author = Horvath, Karl title = Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date = 2020-05-15 keywords = Personen; SARS; test summary = Da weitgehend alle zur Diagnose eingesetzten Tests nicht vollständig fehlerfrei funktionieren, ist auch bei der Testung auf Vorliegen von SARS-CoV-2 spezifischen AK damit zu rechnen, dass es einen Anteil von Personen gibt, der vom Test falsch klassifiziert wird. Wie groß dieser jeweilig falsch klassifizierte Anteil an allen getesteten Personen ist, d.h. wie sicher ein positives oder negatives Testresultat ist, ist abhängig von der Sensitivität und Spezifität des jeweiligen Tests sowie von der gegebenen Vortestwahrscheinlichkeit. Mit anderen Worten beschreibt die Vortestwahrscheinlichkeit das Risiko, dass bei einer bisher ungetesteten Person eine SARS-CoV-2 Infektion vorliegt bzw. Zu bedenken ist auch, dass sich die Prävalenz einer SARS-CoV-2 Infektion und damit die Vortestwahrscheinlichkeit mit Fortschreiten der Pandemie ändern wird. Auch bei nahezu idealen Testeigenschaften sind bei geringer Vortestwahrscheinlichkeit (wie sie bei der Testung von Personen ohne Symptome und Risikofaktoren für eine SARS-CoV-2 Infektion besteht) positive Testresultate häufig falsch. doi = 10.1016/j.zefq.2020.05.005 id = cord-297775-ug4ovsws author = Hosie, Margaret J title = Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date = 2020-09-23 keywords = SARS summary = High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. Recent reports from Dutch mink farms of both mink-to-cat and mink-tohuman transmission of the virus provide support for this scenario (5, 9) We used a range of laboratory techniques to show that two domestic cats from households with suspected cases of COVID-19, and which displayed either mild or severe respiratory disease, were infected with SARS-CoV-2. As we do not have the owner''s virus sequence, we cannot determine whether the observed mutations in cat 2''s viral genome arose in a human prior to transmission. Table 1 details the SNPs observed in the cat 2 viral genome, and their frequency in the existing UK human population and among existing feline SARS-CoV-2 sequences. doi = 10.1101/2020.09.23.309948 id = cord-274286-07arhrv9 author = Hosier, H. title = First case of placental infection with SARS-CoV-2 date = 2020-05-05 keywords = SARS; international summary = Conclusion: This case demonstrates, for the first time, SARS-CoV-2 invasion of the placenta, highlighting the potential for severe morbidity among pregnant women with Covid-19. Levels of anti-SARS-CoV-2 IgG and IgM antibodies in the case study patient were among the highest observed in 56 Covid-19 + patients admitted to Yale New Haven Hospital. This report describes a case of second-trimester Covid-19 associated with preeclampsia and SARS-CoV-2 infection of the placenta. Further studies of placenta from women with Covid-19 may help address whether this is a histological feature associated with placental SARS-CoV-2 infection. RNA was extracted from homogenized placenta, umbilical cord, fetal lungs, heart kidney tissues (27-160 mg; stored in formalin) and maternal oral, nasal, and rectal swabs, saliva, urine, plasma, and serum post-operatively and tested for the presence of SARS-CoV-2 and human RNase P using the US CDC qRT-PCR assay as described 7 . doi = 10.1101/2020.04.30.20083907 id = cord-032811-sdbj26ca author = Hosoki, Koa title = Reply date = 2020-09-29 keywords = SARS summary = They suggest that suppression of angiotensin-converting enzyme-2 (ACE-2) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could impair the hydrolysis of des-Arg 9 -bradykinin and stimulate the bradykinin receptor type 1 (BKB1) pathway to induce leakage of fluid into the lungs. 4 However, other studies suggest that SARS-CoV-2 may upregulate the expression of ACE-2 in patients with coronavirus disease 2019 (COVID-19) or influenza pneumonia in alveolar epithelial cells, endothelial cells, and lymphocytes in perivascular tissue than in uninfected control autopsy lung. 7 We favor a third hypothesis, where excessive and prolonged secretion of type I and type III IFNs in the airways contributes to loss of lung epithelial barrier function during COVID-19 and other RNA virus infections (Fig 1, A) . Because IFN-l contributes to loss of lung epithelial barrier function, 8 we hypothesize that entry of SARS-CoV-2 via ACE-2 can stimulate secretion of IFN-l and induce leakage of fluid into the lungs (Fig 1, A) . doi = 10.1016/j.jaci.2020.09.008 id = cord-310299-isdsestc author = Hosseini, Akram A. title = Delirium as a presenting feature in COVID-19: neuroinvasive infection or autoimmune encephalopathy? date = 2020-06-09 keywords = CSF; SARS summary = 1 We report two cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) infection with acute onset of altered mental status and delirium with normal respiration and metabolic balance in the first 48 hours. Despite normal brain CT at 48 hours, MRI on day 6 showed three hyperintense foci on diffusion-weighted images, but no overt restriction, consistent with T2-shine-through suggesting cellular infiltration/inflammation or small infarcts ( Figure 1 ). 1,2 However, there is currently no report of limbic encephalitis associated with COVID-19 that presented with delirium in the absence of respiratory, metabolic or systemic features, while patients may be hidden sources of spreading the virus in busy clinical settings. The detection of SARS-CoV2 in the CSF in a patient with meningo-encephalitis supports neurotropic and neuroinvasive potential of the virus 2 presumably through the blood vesselrich meninges once the blood brain barrier is damaged. Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) doi = 10.1016/j.bbi.2020.06.012 id = cord-292751-tk1oggi9 author = Hosseini, Elahe Seyed title = The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date = 2020-09-24 keywords = COVID-19; RNA; SARS; coronavirus summary = Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.1016/j.virol.2020.08.011 id = cord-331277-fjsuo3yy author = Hoste, Alexis C.R. title = Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: A screening tool and a point-of-care test date = 2020-08-11 keywords = ELISA; SARS summary = Two serological tools based on a Double Recognition assay (Enzyme-Linked Immunosorbent Assay, DR-ELISA and Lateral Flow Assay, DR-LFA) to detect total antibodies to SARS-CoV-2, have been developed based on the recombinant nucleocapsid protein. Therefore, the aim of the present work was the development of serological tools to determine the presence of antibodies against SARS-CoV-2 in the population, as an indicator of an ongoing or previous infection. In the current study, a Double Recognition Enzyme-Linked Immunosorbent Assay (DR-ELISA) was developed to determine the presence of immunoglobulins of different classes (IgG, IgM and IgA) to SARS-CoV-2 in human serum, to support the diagnosis of COVID-19. In the present study, we developed two serological assays using the recombinant N protein Table 1, a group of 14 serum samples from early days post infection, positive to COVID-19 by respiratory-PCR yet still negative in the commercial serological assay (with seroconversion a few days later) were also tested in our assays. doi = 10.1016/j.diagmicrobio.2020.115167 id = cord-255413-8o884nyp author = Hotez, Peter J. title = The Potential Role of Th17 Immune Responses in Coronavirus Immunopathology and Vaccine-induced Immune Enhancement date = 2020-04-17 keywords = SARS; Th17 summary = From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. From studies conducted in laboratory animals, there are additional concerns about immune enhancement and the role of potential host immunopathology resulting from experimental human COVID-19 vaccines. Beyond direct virus-induced pathology, immune enhancement associated with eosinophilic infiltration and immunopathology is a potential safety concern linked to first-generation vaccines to prevent severe acute respiratory syndrome (SARS) (12) . While vaccinia and other vectored vaccines induce substantial immune enhancement in both the lungs and liver of experimental animals (20) (21) (22) (23) (24) , which in some cases have been linked to viral expression of the N protein (15) , none of these studies specifically examined Th17 responses. A double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge Severe acute respiratory syndrome-associated coronavirus vaccines formulated with delta inulin adjuvants provide enhanced protection while ameliorating lung eosinophilic immunopathology doi = 10.1016/j.micinf.2020.04.005 id = cord-256303-bpa571ys author = Hotez, Peter J. title = Will COVID-19 become the next neglected tropical disease? date = 2020-04-10 keywords = SARS summary = The daily World Health Organization (WHO) Coronavirus Situation Reports highlight the rapid spread of COVID-19 across Europe, the United States, and many of the advanced nations in East Asia [1] . If SARS CoV2 becomes a major respiratory virus pathogen in resource-poor countries of the tropics and subtropics, we might envision unprecedented levels of global morbidity and mortality. Accordingly, PLOS Neglected Tropical Diseases will consider articles from the community of scientists and public health experts in Asia, Africa, and Latin America now shifting their efforts to combat the COVID-19 pandemic. However, as John Lennon once said, "life is what happens to you while you''re busy making other plans," and on that basis we now invite our community of NTD scientists to submit COVID-19 papers on what may become a global health terror on a scale that rivals or even exceeds some of the world''s major neglected tropical diseases. doi = 10.1371/journal.pntd.0008271 id = cord-260412-yjr83ef6 author = Hotez, Peter J. title = Developing a low-cost and accessible COVID-19 vaccine for global health date = 2020-07-29 keywords = RBD; SARS summary = Our group is developing a two-pronged approach to advance recombinant protein-based vaccines to prevent COVID-19 caused by SARS-CoV-2 and other coronavirus infections. One vaccine is based on a yeast-derived (Pichia pastoris) recombinant protein comprised of the receptor-binding domain (RBD) of the SARS-CoV formulated on alum and referred to as the CoV RBD219-N1 Vaccine. In addition to their low cost and suitability for use in public immunization programs in lowand middle-income countries, we pursued RBD recombinant protein-based vaccines as a technology to maximize safety relative to other platforms, such as virus vectors that have previously been found to induce immune enhancement. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1), a SARS Vaccine Candidate Potential for developing a SARS-CoV receptor-binding domain (RBD) recombinant protein as a heterologous human vaccine against coronavirus infectious disease (COVID)-19 Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain (RBD219-N1) Formulated with Alum Induces Protective Immunity and Reduces Immune Enhancement doi = 10.1371/journal.pntd.0008548 id = cord-307858-274a699i author = Hotez, Peter J. title = COVID-19 vaccines: neutralizing antibodies and the alum advantage date = 2020-06-04 keywords = SARS summary = A chemically inactivated virus vaccine (PiCoVacc) and a recombinant proteinbased vaccine (CoV-RBD219N1) were recently shown to elicit high levels of protective immunity in rhesus macaques or in mice against homologous virus challenge with SARS-CoV-2 or SARS-CoV, respectively 2,3 . Similarly, mice vaccinated with CoV-RBD219N1, based on the recombinant RBD protein of SARS-CoV, which is now investigated as a COVID-19 vaccine candidate, exhibited virus-neutralizing antibody titres between 640 and 1,280 upon SARS-CoV homologous viral challenge 3 . Therefore, an emerging story in COVID-19 vaccine development is the potential importance of inducing high levels of neutralizing antibodies to the S protein or its RBD. A key finding so far is that aluminium adjuvant formulations, such as those used for PiCoVacc and CoV-RBD219N1, appear to promote high titres of neutralizing antibody. A potential concern about the use of aluminium adjuvants is based on the claim that T H 2-type immune responses might promote vaccine-enhanced respiratory disease (VAERD) 9 . doi = 10.1038/s41577-020-0358-6 id = cord-031001-x4iiqq5e author = Hou, Fan Fan title = Personnel protection strategy for healthcare workers in Wuhan during the COVID-19 epidemic date = 2020-07-20 keywords = SARS; Wuhan summary = DESIGN: During the COVID-19 pandemic, 943 healthcare staff sent from Guangzhou to Wuhan to care for patients with suspected/confirmed COVID-19 received infection precaution training before their mission and were equipped with Level 2/3 personal protective equipment (PPE), in accordance with guidelines from the National Health Commission of China. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53 out of 1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126 out of 2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively. The seropositivity for SARS-CoV-2 antibodies (IgG, IgM, or both IgG/IgM positive) was 3.4% (53/1571) in local healthcare workers from Wuhan with Level 2/3 PPE working in isolation areas and 5.4% (126/2336) in healthcare staff with Level 1 PPE working in non-isolation medical areas, respectively (Table 3) . doi = 10.1093/pcmedi/pbaa024 id = cord-339012-4juhmjaj author = Hou, Wei title = Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date = 2020-07-28 keywords = MRV; PEDV; SARS; Vero; cell; gene summary = Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and "synaptic clefts" between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The detected sets of differential expressed genes (DEGs) for PEDV and MRV were analyzed by gene set enrichment analysis (GSEA) using functional bioinformatic programs to retrieve biological processes (pathways and Gene Ontology terms [GO-term]) and associations with chemical compounds, including drugs. doi = 10.1101/2020.07.28.224576 id = cord-350855-gofzhff7 author = Hou, Yixuan J. title = SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract date = 2020-05-27 keywords = ACE2; CoV-2; SARS; figure summary = High-sensitivity RNA in situ mapping revealed the highest ACE2 expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) vs distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. We measured the relative infectivity of the SARS-CoV-2 GFP virus in primary 283 cells based on the average peak titers and observed that infectivity exhibited the same 284 pattern as the ACE2 expression levels from the upper to lower respiratory tract ( Figure 285 6Bi-6Biv). Gene 1230 expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human 1231 airway epithelial cells and lung tissue doi = 10.1016/j.cell.2020.05.042 id = cord-252232-vgq6gjpx author = Hou, Yuxuan title = Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry date = 2010-06-22 keywords = ACE2; CoV; SARS summary = Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry. doi = 10.1007/s00705-010-0729-6 id = cord-329200-o5hxpl8f author = Houlihan, Catherine F title = The complexities of SARS-CoV-2 serology date = 2020-09-23 keywords = SARS summary = Our understanding of individual and population-level immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains incomplete and developing reliable serological assays to detect previous infection has been an intense focus of the global scientific effort. For public health planning we need scalable assays validated against large banks of samples from individuals who had proven seasonal (non-severe acute respiratory syndrome) coronaviruses and those who had well characterised symptomatic and asymptomatic confirmed SARS-CoV-2 infection. In The Lancet Infectious Diseases, the National SARS-CoV-2 Serology Assay Evaluation Group 1 provide the first large comparative investigation of the performance of four widely available commercial assays and a single in-house assay. Antibody responses to SARS-CoV-2 are predominantly directed at the spike glycoprotein, which the virus requires for entry, and the nucleocapsid protein, which binds the viral RNA genome. 2,3 The DiaSorin, Siemens, and in-house assays measured these potentially protective antibodies, with the inhouse ELISA using trimerised spike protein, which shows a high correlation with neutralisation. doi = 10.1016/s1473-3099(20)30699-x id = cord-278176-o9glkhyv author = Houng, Huo-Shu H title = Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date = 2004-09-01 keywords = PCR; SARS summary = The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. It was demonstrated that the RT-PCR assay with 91% amplification efficiency could be used for consistent detect ion of the SARS-CoV viral RNA extracted from samples containing as little as 0.005 pfu per reaction with an anticipated C T value of 40 cycles (data not shown). It was demonstrated in this study that the cloned pHCV1 plasmid could be used to replace viral cDNA as a stable and rational SARS-CoV copy number standard for the SARS-CoV RT-PCR assay. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays doi = 10.1016/j.jviromet.2004.04.008 id = cord-267960-r5m7o9dp author = Hourdel, Véronique title = Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date = 2020-09-25 keywords = Illumina; SARS; United summary = In this study, we aimed at implementing an ampliconbased sequencing approach to obtain SARS-CoV-2 consensus genomes directly from clinical specimens, adaptable into the field conditions, with the two easily manageable nextgeneration sequencers, the nanopore MinION and the Illumina iSeq100 TM system. Sputum specimens and respective isolates RNA extracts were tested with the SARS-CoV-2 real-time RdRP gene duplex reverse transcription (RT)-PCR developed by the French National Reference Center for Respiratory Viruses and the real-time E gene RT-PCR from the Charité protocol (see WHO Coronavirus disease COVID-19 technical guidance: Laboratory testing for 2019-nCoV in humans, available from https://www.who. Globally, using our amplicon-based approach, combined with the MinION platform, we were able to obtain the near fulllength genome of the studied viral specimens in around 8 h, from samples to sequences data. Viral consensus genomic sequences were rapidly and easily obtained for the two SARS-CoV-2 clinical specimens and their respective isolates, by using the two different sequencing platforms, MinION and iSeq100 TM system. doi = 10.3389/fmicb.2020.571328 id = cord-291642-xfkdxnfb author = Howley, Fergal title = Late presentation of ‘Lemierre’s syndrome’: how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic date = 2020-10-10 keywords = Lemierre; SARS; syndrome summary = title: Late presentation of ''Lemierre''s syndrome'': how a delay in seeking healthcare and reduced access to routine services resulted in widely disseminated Fusobacterium necrophorum infection during the global COVID-19 pandemic We describe an atypical case of Lemierre''s syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe an atypical case of Lemierre''s syndrome involving the brain, liver and lungs following a dental infection in a young male who delayed seeking dental or medical attention due to a lack of routine services and concerns about the SARS-CoV-2 outbreak. We describe a severe case of Lemierre''s syndrome, requiring ICU admission and intubation, where presentation and initiation of treatment were delayed by the SARS-CoV-2 pandemic. doi = 10.1136/bcr-2020-239269 id = cord-353873-88ud20oq author = Hoyler, Marguerite M. title = The importance of challenges in COVID-19 screening and testing in the obstetric patient population date = 2020-05-28 keywords = SARS summary = We reviewed with interest the recent article and accompanying infographic published by Herman and colleagues regarding anesthesia management of the obstetric patient in the era of COVID-19. [1] We commend the authors for a compelling visual summary of strategies to help care for patients as well as protect obstetric anesthesia providers from possible SARS-CoV-2 transmission. These observations support a low threshold for testing parturients for COVID-19, even if they present with symptoms that occur in normal pregnancy; this is particularly important in communities with high rates of SARS-CoV-2 infection. As part of obstetric anesthesia care considerations, and particularly in communities and institutions with high burdens of SARS-CoV-2 infection, it may be prudent to routinely manage parturients as high risk for COVID-19 infection and to encourage conservative measures that J o u r n a l P r e -p r o o f doi = 10.1016/j.jclinane.2020.109938 id = cord-291916-5yqc3zcx author = Hozhabri, Hossein title = The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date = 2020-08-05 keywords = ACE2; COVID-19; China; CoV-2; Coronavirus; MERS; PCR; RNA; SARS summary = doi = 10.3390/ijerph17165648 id = cord-291459-m56dy8us author = Hraiech, Sami title = Lack of viral clearance by the combination of hydroxychloroquine and azithromycin or lopinavir and ritonavir in SARS-CoV-2-related acute respiratory distress syndrome date = 2020-05-24 keywords = SARS summary = In order to evaluate these results in intensive care unit (ICU) patients, we retrospectively assessed in moderate-to-severe ARDS the efficacy of hydroxychloroquine-azithromycin combination regarding viral disappearance at both day 6 of the treatment and day 6 of evolution of ARDS as compared with patients treated with lopinavir-ritonavir and a control group without any anti-viral treatment. Negative nasopharyngeal PCR for SARS-CoV-2 at day 6 following the initiation of treatment were observed in 5 (38%) patients from the lopinavir-ritonavir group as compared with 3 (18%) patients from the hydroxychloroquine-azithromycin group and 2 (20%) from the control group (p = 0.39). At day 6 following ARDS onset, PCR was negative in only 9 patients, 5 from the lopinavir-ritonavir group, 2 from the hydroxychloroquine-azithromycin group and 2 from the control group. doi = 10.1186/s13613-020-00678-4 id = cord-299781-9d5g5xaw author = Hrusak, Ondrej title = Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment date = 2020-04-07 keywords = COVID-19; SARS; child summary = title: Flash Survey on SARS-CoV-2 Infections in Pediatric Patients on anti-Cancer Treatment While we should not underestimate the risk of developing a more severe course of COVID-19 than observed here, the intensity of preventive measures should not cause delays or obstructions in oncological treatment. The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causing the Coronavirus Disease (COVID-19) pandemic in 2020 was identified in December, 2019. 11 To evaluate this, we used a flash survey to determine whether there was current evidence that pediatric patients with cancer in SARS-CoV-2 affected areas had been tested for this virus or had developed severe COVID-19 disease. More research is needed to better understand the epidemiology of SARS-CoV-2 infection and COVID-19 in pediatric patients with cancer or other immunocompromised children. doi = 10.1016/j.ejca.2020.03.021 id = cord-269707-titu9lm4 author = Hsieh, Ching-Lin title = Structure-based design of prefusion-stabilized SARS-CoV-2 spikes date = 2020-07-23 keywords = Fig; S-2P; SARS summary = Here, we characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting ~10-fold higher expression than its parental construct and the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2. In addition to salt bridges, filling loosely packed hydrophobic cores that allow the protein to refold can help stabilize the prefusion state, as shown by previous cavity-filling substitutions in RSV F and HIV-1 Env (12, 20, 22) . Adding one disulfide (S884C/A893C) to a single proline variant (F817P) also reduced the expression level, although the quaternary structure of the spikes was well maintained (table S2, Combo40). HexaPro expressed 9.8-fold higher than S-2P, had ~5°C increase in Tm, and retained the trimeric prefusion conformation (Fig. 3D) . doi = 10.1126/science.abd0826 id = cord-322451-cwpz4akv author = Hsin, Dena Hsin-Chen title = Heroes of SARS: professional roles and ethics of health care workers date = 2004-07-27 keywords = HCW; SARS; Taiwan summary = To examine the professional moral duty of health care workers (HCWs) in the outbreak of severe acute respiratory syndrome (SARS) in 2003. In a number of countries in order to encourage HCW, the government and the public started to give the title of ''hero'' to nurses and doctors who are working in the frontline of SARS outbreak. While the ethical ideal of self-less sacrifice of life for curing disease is promoted in the public image and media, discussions with HCW in several countries suggests that being a hero is not what modern medical practice is for some HCWs. Most HCWs in Taiwan are working in the commercial hospital, where the hirer pushes them to focus their effort of work on business competition rather than the basic role of helpers to human''s health. Nurses'' professional care obligation and their attitudes towards SARS infection control measures in Taiwan during and after the 2003 epidemic doi = 10.1016/j.jinf.2004.06.005 id = cord-255476-p0gyyl3c author = Hsu, Albert L. title = Placental SARS‐CoV‐2 in a Pregnant Woman with Mild COVID‐19 Disease date = 2020-08-04 keywords = SARS; covid-19; woman summary = Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality.(1) COVID‐19 manifestations appear similar between pregnant and non‐pregnant women.(2) OBJECTIVES/STUDY DESIGN: We present a case of placental SARS‐CoV‐2 virus in a woman with mild COVID‐19 disease, then review the literature. Evidence of placental COVID‐19 raises concern for placental vasculopathy (potentially leading to fetal growth restriction and other pregnancy complications) and possible vertical transmission – especially for pregnant women who may be exposed to COVID‐19 in early pregnancy. In this case study, we present a case of placental SARS-CoV-2 virus in a woman with an uncomplicated pregnancy and mild COVID-19 disease. To date, there is still no other published work about SARS-CoV-2 virus by immunohistochemistry in the placentas of women with mild COVID-19 disease. Despite her having mild COVID-19 disease in pregnancy, we demonstrate placental vasculopathy and presence of SARS-CoV-2 virus across the placenta. Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of the placenta in pregnancies with COVID-19 positive mothers and neonates at birth doi = 10.1002/jmv.26386 id = cord-290257-2u228xe9 author = Hsu, Chih-Cheng title = Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan date = 2006-05-05 keywords = SARS; Taiwan; health summary = title: Confidence in controlling a SARS outbreak: Experiences of public health nurses in managing home quarantine measures in Taiwan This paper assesses factors related to public health nurses'' confidence in managing community SARS control programs. The third section contained questions (using 10-point Likert scale: 1 5 the worst to 10 5 the best) about the effectiveness of the nurse''s institution in managing the SARS epidemic, including the nurse''s assessment of (1) the institutional functioning on community home quarantine, (2) the quality of training received for controlling infectious disease outbreaks, and (3) the adequacy of support (for both manpower and financing) received from superior health agencies force commander said the epidemic situation was stable and advised people to return to their routine. In summary, public health nurses'' confidence in the control of a SARS outbreak and people''s compliance with quarantine measures are 2 major factors that can affect the success of a SARS-control program. doi = 10.1016/j.ajic.2005.11.008 id = cord-340651-g3518bq2 author = Hsu, Chung-Hua title = An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study date = 2007-05-29 keywords = NHM; SARS; patient summary = title: An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study The cases were too few to be conclusive, the initial observations seem to indicate NHM appears to be safe in non-criticallly ill patients and clinical trials are feasible in the setting of pandemic outbreaks. In view of the possible beneficial effect of NHM on SARS or SARS-like infectious diseases, we conducted this randomized, double-blind clinical trial with placebo-control to examine its effectiveness. To our knowledge, this is the first double-blind and placebo-controlled clinical pilot study on supplementary treatment of SARS or SAR-like diseases. doi = 10.1093/ecam/nem035 id = cord-298079-hgdyxk98 author = Hsu, Jeffrey J. title = Heart Transplantation in the Early Phase of the COVID‐19 Pandemic: A Single‐Center Case Series date = 2020-07-12 keywords = COVID-19; SARS summary = Here, we describe our center''s experience with orthotopic heart transplantation (OHT) in one of the country''s pandemic epicenters, where we performed eight OHTs in the first two months after community spread began in late February 2020. 3 Further, the effects of SARS-CoV-2 in highly immunosuppressed patients in the early post-transplant period are currently unclear. Current recommendations from the International Society of Heart and Lung Transplantation (ISHLT) is for all potential donors to undergo PCR-based testing for SARS-CoV-2. In our eight cases performed during the period of pandemic onset (Table) , none have become infected with SARS-CoV-2 to date, despite the growing number of cases in Los Angeles (Figure 1) . Similarly, the impact of SARS-CoV-2 infection in a patient with a newly transplanted cardiac graft is unclear, as to our knowledge, there are have yet to be any cases reported at the time of this communication. More evidence is needed to determine the risks of SARS-CoV-2 infection in newly transplanted patients. doi = 10.1111/ctr.14042 id = cord-254072-evgw0as5 author = Hsu, Li-Yang title = Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts date = 2003-06-17 keywords = SARS; patient summary = title: Severe Acute Respiratory Syndrome (SARS) in Singapore: Clinical Features of Index Patient and Initial Contacts We describe the clinical, laboratory, and radiologic features of the index patient and the patient''s initial contacts affected with probable SARS. According to the World Health Organization, a suspected case of SARS is defined as documented fever (temperature >38°C), lower respiratory tract symptoms, and contact with a person believed to have had SARS or history of travel to an area of documented transmission. We describe the clinical features of the index patient in Singapore and the patient''s initial group of contacts affected with probable SARS. Nine days after admission, the patient began to improve clinically, the laboratory abnormalities returned towards normal, and the chest x-ray abnormalities stabilized and resolved. When the index patient was seen in early March, the clinical features and highly infectious nature of SARS were not known. doi = 10.3201/eid0906.030264 id = cord-297463-mmmwi8de author = Hsu, You-Ren title = Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors date = 2013-03-15 keywords = SARS summary = title: Detection of Severe Acute Respiratory Syndrome (SARS) Coronavirus Nucleocapsid Protein Using AlGaN/GaN High Electron Mobility Transistors AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect the SARS coronavirus (SARS-CoV) nucleocapsid protein interaction without fluorescent labeling. We demonstrated AlGaN/GaN was highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleic acid-protein interaction. Here, we demonstrated using the AlGaN/GaN HEMT-based sensors to detect the SARS-CoV CTD s protein. Here, we demonstrated that the AlGaN/GaN HEMTs also have the capability of detecting nucleic acid-protein interaction with high sensitivity. The detection limit of AlGaN/GaN HEMTs sensor for SARS-CoV N protein of dsDNA immobilized device was 0.003 nM, and two orders lower than AMPs immobilized nanowire FET 17 . In summary, AlGaN/GaN HEMTs can detect the nucleic acid binding protein at a low detection limit. doi = 10.1149/05006.0239ecst id = cord-330944-54xmnum8 author = Hsu, You-Ren title = Investigation of C-terminal domain of SARS nucleocapsid protein–Duplex DNA interaction using transistors and binding-site models date = 2014-03-31 keywords = SARS summary = AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. With a quantitative analysis of the signals from the sensors through binding-site models, we are able to reveal how many binding sites are on the receptor (dsDNA) for certain ligands (SARS-N protein) and what the dissociation constants are for ligand-receptor complexes. The chemical reaction for the surface-immobilized receptor (dsDNA) and the free ligand (SARS-N protein-CTD) in bulk solution can be expressed as the following equations: Therefore, we conclude that for a one-binding-site model, the most significant change of the surface coverage ratio is within the range of the ligand concentration between one order higher and one order lower than the value of the dissociation constant. doi = 10.1016/j.snb.2013.11.087 id = cord-279754-95zawygq author = Hsu, Yu-Chen title = Risk and Outbreak Communication: Lessons from Taiwan''s Experiences in the Post-SARS Era date = 2017-04-01 keywords = CDC; SARS; Taiwan summary = After the SARS outbreak, Taiwan''s Centers for Disease Control (Taiwan CDC) followed the WHO outbreak communication guidelines on trust, early announcements, transparency, informing the public, and planning, in order to reform its risk communication systems. After the SARS outbreak, Taiwan''s Centers for Disease Control (CDC) followed the WHO outbreak communication guidelines-on trust, announcing early, transparency, informing the public, and planning-to reform its risk communication systems. In order to analyze the efficiency of risk communication on influenza vaccination, Taiwan CDC has monitored the toll-free hotline to identify topics that are of most concern to the public (eg, who are the target population, where to get the shot, adverse event reporting). The government of Taiwan has demonstrated considerable improvement in its risk communication practices during public health emergencies since the SARS outbreak in 2003. doi = 10.1089/hs.2016.0111 id = cord-307460-v6xgkg1p author = Hsu, Yu-Lung title = Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan date = 2020-06-13 keywords = SARS summary = key: cord-307460-v6xgkg1p authors: Hsu, Yu-Lung; Lin, Hsiao-Chuan; Wei, Hsiu-Mei; Lai, Huan-Cheng; Hwang, Kao-Pin title: Temperature and the difference in impact of SARS CoV-2 infection (COVID-19) between tropical and non-tropical regions in Taiwan cord_uid: v6xgkg1p Therefore, we believe that, all things being equal, the transmission of SARS CoV-2 differs 32 between tropical and non-tropical regions. This is because countries greatly 34 differ with respect to population density, disease burden, health care quality, infection control Stability of SARS coronavirus in human specimens and 42 environment and its sensitivity to heating and UV irradiation Epidemiology and clinical 45 presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 46 3 years using a novel multiplex real-time PCR method The pediatric burden of human coronaviruses 49 evaluated for twenty years Coronaviruses in the Pediatric Population Hsu 57 and Hsiao-Chuan Lin interpreted data Distribution of COVID-19 patients around the world 64 Distribution of local cases of COVID-19 in Taiwan doi = 10.1016/j.tmaid.2020.101790 id = cord-321691-46la29tm author = Hsueh, Po-Ren title = SARS Antibody Test for Serosurveillance date = 2004-09-17 keywords = ELISA; SARS; Taiwan summary = A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. A peptide-based enzyme-linked immunosorbent assay (ELISA) can be used for retrospective serosurveillance of severe acute respiratory syndrome (SARS) by helping identify undetected chains of disease transmission. Such surveillance may be key to tracking the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) because mild and asymptomatic cases of SARS-CoV infection that do not meet the World Health Organization''s case definition (1) have been identified by immunoassays (2) (3) (4) , and SARS-CoV-like viruses have been isolated from wild mammals (5) . The diagnostic sensitivity of the peptide ELISA was 100% on a panel of 69 convalescent-phase serum samples from SARS patients provided as a reference panel by the Center for Disease Control, Department of Health, Taiwan. The peptide ELISA was evaluated for specificity on serum samples drawn from patients associated with typical and atypical respiratory pathogens other than SARS-CoV (National Taiwan University Hospital). doi = 10.3201/eid1009.040101 id = cord-294854-rvrgcugn author = Hu, Biying title = The cytokine storm and COVID‐19 date = 2020-06-27 keywords = COVID-19; MERS; SARS summary = An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread throughout the world 1 . It has been reported that a cytokine storm is Accepted Article associated with the deterioration of many infectious diseases, including severe acute respiratory syndrome (SARS) 3 and Middle East respiratory syndrome (MERS) 4 . It is considered to be the main cause of disease severity and death in Accepted Article COVID-19 patients 5 , and is related to high levels of circulating cytokines, severe lymphopenia, thrombosis, and massive mononuclear cell infiltration in multiple organs 21 . Anakinra, an IL-1 receptor antagonist that blocks the activity of pro-inflammatory cytokines IL-1α and IL-1β, has been reported to improve respiratory function and increase the survival rate of COVID-19 patients 73 . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of Accepted Article coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, double-blinded, phase IIb clinical trial (CloroCovid-19 Study) doi = 10.1002/jmv.26232 id = cord-353914-zzla4frm author = Hu, Bo title = Cardiac involvement of COVID-19: Looking forward to novel discoveries and clinically valuable evidence() date = 2020-09-01 keywords = SARS summary = Since the Coronavirus Disease-2019 (COVID-19) outbreak, several clinical studies [1] [2] [3] have discovered the evidence of myocardial injury as significant elevation of cardiac troponin among the infected patients, especially those required intensive care. From our experiences, myocardial injury is almost in COVID-19 patients of severe and critical types and/or with underlying cardiovascular diseases [1] [2] [3] . Currently, the number of infected people has reached 3.6 million, while cases with myocarditis were extremely rare in the published clinical studies and case reports. In line with our study [1] , although SARS-CoV-2 infection can be detected in myocardial tissue, cardiac involvement of COVID-19 is possibly more integrated with systemic disorders. Clinical investigation of SARS-CoV-2 myocarditis should focus on young patients without any underlying cardiovascular diseases. We look forward to novel discoveries and clinically valuable evidence regarding to cardiac involvement of COVID-19. Suspected myocardial injury in patients with COVID-19: evidence from front-line clinical observation in Wuhan, China doi = 10.1016/j.ijcard.2020.05.049 id = cord-304480-azosg1tt author = Hu, Donghua title = Studies on the interactions of Ti-containing polyoxometalates (POMs) with SARS-CoV 3CL(pro) by molecular modeling date = 2006-09-05 keywords = 3CL; SARS summary = The ligand-receptor interaction of POMs/3CL pro generally causes energy decreasing and conformation changing; accordingly these changes should influence the enzyme catalytic activity of the SARS-CoV 3CL pro . What is more, during the course of POMs/SARS-CoV 3CL pro complex formation, the atom charge loading properties and the electrostatic characteristic are very vital elements that keep the enzyme-inhibitor interaction. The investigation results show that: (1) POMs interact with the 3CL pro receptor in enzyme active site region, with several polarized residues including the enzyme catalyst residues of His41/Cys145; (2) The total binding energies of the five POM/SARS-CoV 3CL pro complexes lead to the following order of complex stability: 1,2-PTi 2 /3CL pro > 1,4-PTi 2 /3CL pro > 1,5-PTi 2 /3CL pro > 1,6-PTi 2 /3CL pro > 1,11-PTi 2 /3CL pro . (3) Electrostatic energy and hydrogen bond interaction contribute much to the enzyme-inhibitor complex formation between POMs and SARS-CoV 3CL pro . doi = 10.1016/j.jinorgbio.2006.08.013 id = cord-292880-zegtr19k author = Hu, Fuying title = Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 date = 2020-08-13 keywords = COVID-19; SARS summary = title: Corticosteroid, oseltamivir and delayed admission are independent risk factors for prolonged viral shedding in patients with Coronavirus Disease 2019 Here, we reviewed medical records of patients with laboratory-confirmed COVID-19 in Tianmen, a city in Hubei province adjacent to Wuhan, to describe the clinical features, epidemiological characteristics and risk factors associated with prolonged viral shedding of COVID-19. Time from illness onset to hospital admission (P < 0.001), radiographic extent (P = 0.002), lymphocyte count (P = 0.038), albumin (P = 0.046), hs-CRP (P = 0.010), and prescription of antibiotics (P < 0.001), arbidol (P = 0.020), oseltamivir (P <0.001), corticosteroid (P < 0.001) and immunoglobulin (P < 0.001) were also associated with prolonged viral shedding. In the present study, we described the epidemiological and clinical characteristics of patients in Tianmen city, Hubei province, and concluded that delayed admission, and prescription of corticosteroid and oseltamivir were significantly associated with prolonged viral shedding. doi = 10.1111/crj.13243 id = cord-277739-eb4z3u66 author = Hu, Ke title = Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial date = 2020-05-16 keywords = SARS; covid-19; patient summary = title: Efficacy and Safety of Lianhuaqingwen Capsules, a repurposed Chinese Herb, in Patients with Coronavirus disease 2019: A multicenter, prospective, randomized controlled trial In the latest publication, Lianhuaqingwen (LH) capsule (Shijiazhuang Yiling Pharmaceutical Co. Ltd., Shijiazhuang, China) was a manufactured product of the traditional Chinese medicine formula marketed in China that could significantly inhibit SARS-CoV-2 replication, alter the viral morphology and confer anti-inflammatory activity in vitro . On the basis of usual treatment, we sought to explore the safety and efficacy of LH capsules in patients with Covid-19 by conducting a multicenter randomized controlled trial in mainland China. Eligibility criteria consisted of the following: 1) Laboratory-confirmed cases with according to the Protocol for Diagnosis and Treatment of Novel Coronarvirus Pneumonia (4 th edition) which was issued by the National Health Commission (General Office Of The National Health And Health Commission, 2020) (Panel 1); 2) Being symptomatic (either having fever, coughing, or fatigue) plus radiologic abnormalities consistent with pneumonia; 3) Patients aged 18 years or greater of either sex. doi = 10.1016/j.phymed.2020.153242 id = cord-269825-k685efoh author = Hu, Parker title = Early comprehensive testing for COVID-19 is essential to protect trauma centers date = 2020-07-01 keywords = COVID-19; SARS; trauma summary = We recorded the daily number of trauma patients diagnosed with SARS-CoV-2 infection, the presence of clinical symptoms or radiological signs of COVID-19, and the results of verbal symptom screen (for new admissions). Positive verbal screen results, presence of ground glass opacities on admission chest CT, and presence of clinical symptoms were not significantly different in patients with or without SARS-CoV-2 infection (p > 0.05). [14] [15] [16] While the position is becoming well defined for those patients with known, established disease, there is little available data to guide trauma centers that may be required to treat significant numbers of asymptomatic infected new patients during this ongoing crisis. The screening and testing procedure in the trauma bay subsequently identified four additional SARS-CoV-2-infected patients. All new trauma patients should be regarded as SARS-CoV-2 positive until testing can be completed to minimize exposures to staff and limit nosocomial spread of disease. doi = 10.1097/ta.0000000000002870 id = cord-340163-ex03l0pc author = Hu, Tingting title = A comparison of COVID-19, SARS and MERS date = 2020-08-19 keywords = COVID-19; MERS; SARS summary = In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The latest diagnostic criteria of COVID-19, SARS and MERS including clinical presentations, labora tory diagnosis and radiological feature Latest treatment and prevention methods of Published in a peer-reviewed article Availability of the full text publication Availability of the paper in English According to a study among 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China, the male-to-female ratio was 1.06:1, and the median age was 56 years (interquartile range, 42-68; range, 22-92 years) (Wu & McGoogan, 2020; Wang et al., 2020) . CXR findings In the early phase, CXR of COVID-19 patients is not highly recommended for clinical diagnosis because of its low sensitivity in detecting SARS-CoV-2 pneumonia. doi = 10.7717/peerj.9725 id = cord-277014-iz8jo44e author = Hu, Weihua title = Disorders of sodium balance and its clinical implications in COVID-19 patients: a multicenter retrospective study date = 2020-10-16 keywords = SARS; covid-19; patient summary = This study indicates that severity of the disease, the length of stay in the hospital of surviving patients, and mortality were higher among COVID-19 patients with sodium balance disorders. CONCLUSION: Sodium balance disorder, particularly hyponatremia, is a common condition among hospitalized patients with COVID-19 in Hubei, China, and it is associated with a higher risk of severe illness and increased in-hospital mortality. reported hyponatremia to be much common (50%) amongst hospitalized COVID-19 patients in the United States [13] , and recently study further suggested that serum sodium concentration was inversely correlated with IL-6, and hyponatremia was associated with a more severe outcome of COVID-19 disease [14] . The associative disorders of serum sodium balance, their clinical characteristics, severity, and outcomes in SARS-CoV-2 infected patients have not been established. It was revealed that disease severity, the length of hospital stay for surviving patients, and mortality were high among COVID-19 patients with sodium balance disorders. doi = 10.1007/s11739-020-02515-9 id = cord-334518-mjr6u7ak author = Hu, X. title = Development and clinical application of a rapid and sensitive loop-mediated isothermalamplification test for SARS-CoV-2 infection date = 2020-05-23 keywords = COVID-19; LAMP; SARS summary = To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on the serial upper respiratory samples from an asymptomatic carrier, and the insistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. . https://doi.org/10.1101/2020.05.20.20108530 doi: medRxiv preprint As described in the Materials and Methods, we developed a rapid and simple RT-LAMP assay to detect SARS-CoV-2 RNA, and positive reactions resulted in a color change from purple to blue due to decreased magnesium concentration in the presence of extensive Bst DNA polymerase activity, while negative reactions retained the purple color. doi = 10.1101/2020.05.20.20108530 id = cord-294069-7zr77r71 author = Hu, Xiaowen title = The distribution of SARS-CoV-2 contamination on the environmental surfaces during incubation period of COVID-19 patients date = 2020-09-30 keywords = CoV-2; SARS summary = In this study, we sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the environmental surfaces during the incubation period of coronavirus disease 2019 (COVID-19) patients. In addition, we synchronously sampled the high-touch environmental surfaces in the quarantine room, aiming to detect the SARS-CoV-2 distribution on the environmental surfaces during the incubation period of COVID-19 patients. Then, medical staffs stayed in hotel immediately sampled their nasopharyngeal swabs and environmental surfaces, and transferred them to the hospital for further diagnosis Additionally, the frequency of washing behaviors of patients at the quarantine room, including face washing, hands washing, tooth brushing, bathing and excrement, were shown in Table 2 . Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient doi = 10.1016/j.ecoenv.2020.111438 id = cord-312652-zhccmfgw author = Hu, Xiumei title = Impact of Heat-Inactivation on the detection of SARS-CoV-2 IgM and IgG Antibody by ELISA date = 2020-06-20 keywords = CoV-2; IgM; SARS summary = According to Chinese Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (Trial Version 7), SARS-CoV-2 specific IgM becomes detectable around 3-5 days after onset and IgG reaches a titration of at least 4-fold increase during convalescence compared with the acute [9] . In order to establish a safe and accurate method for detecting SARS-CoV-2 specific antibodies, we retrospectively assessed the impact of sera heat-inactivation at 56℃ for 30 minutes on the levels of SARS-CoV-2 IgM or IgG antibodies. Therefore, our analysis provide evidence that sera inactivated by heating at 56℃ for 30 minutes could reduce the risk of virus contamination, and would not impair the detection efficacy of SARS-CoV-2 IgM or IgG testing using this ELISA assay. In summary, sera inactivated by heating at 56℃ for 30 minutes could minimize the risk of virus contamination and did not impair the positive detection rate using SARS-CoV-2 antibody detection kit (ELISA-immunoassay) and eventually represents a valuable contribution to a safer COVID-19 serological diagnosis. doi = 10.1016/j.cca.2020.06.032 id = cord-346555-3hrbea6d author = Hu, Xiumei title = Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS‐CoV‐2 date = 2020-06-28 keywords = SARS summary = Since many coronaviruses are sensitive to heat, heating inactivation of samples at 56°C prior to testing is considered a possible method to reduce the risk of transmission, but the effect of heating on the measurement of SARS‐CoV‐2 antibodies is still unclear. CONCLUSION: Our results indicate that heat inactivation of serum at 56°C for 30 minutes interferes with the immunoanalysis of antibodies to SARS‐CoV‐2. The current outbreak of coronavirus disease 2019 (COVID19) caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is posing a serious threat to public health. The signal intensity of the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before and after heat inactivation The changes in the IgM and IgG levels of 9 serum samples from non-COVID-19 group detected by AFIA before (blue dot) and after heat inactivation (red dot) Heat inactivation of serum interferes with the immunoanalysis of antibodies to SARS-CoV-2 doi = 10.1002/jcla.23411 id = cord-276957-pk33dl8q author = Hu, Xuejiao title = Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection date = 2020-08-26 keywords = LAMP; SARS; covid-19 summary = To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. The detection results obtained using the RT-LAMP assay showed good concordance with those obtained using the RT-qPCR In Cohort I, 35 of 37 nasopharyngeal swabs from 24 COVID-19 patients were confirmed to be SARS-CoV-2 positive according to the criteria of RT-qPCR (28 samples) and NGS confirmation (7 samples) (see Table S3 in the supplemental material). Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on serial upper respiratory samples from an asymptomatic carrier, and the inconsistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. doi = 10.1128/msphere.00808-20 id = cord-309898-sju15hev author = Hu, Yiwen title = Comparative analysis of nanomechanical features of coronavirus spike proteins and correlation with lethality and infection rate date = 2020-11-02 keywords = MERS; RBD; SARS summary = The key result of our work is that both, the overall flexibility of upward RBD and the mobility ratio of RBDs in different conformations, represent two significant factors that show a positive scaling with virus lethality and an inverse correlation with the infection rate. Figure 2 depicts data that shows that the lowest-frequency normal modes of MERS-CoV, SARS-CoV and SARS-CoV-2 spike proteins are all associated with a swing motion of upward receptor-binding domain (RBD) to different extents. Figure 4 provides a correlation diagram for MERS-CoV, SARS-CoV and SARS-CoV-2 spike protein, where the overall flexibility of upward RBD is evaluated by the average fluctuation of open-state RBD and the mobility ratio is quantified as the ratio of maximum fluctuations over upward and downward RBDs. The data shows that both factors have positive correlation with case fatality rate and inverse relationship with the virus infectivity. doi = 10.1016/j.matt.2020.10.032 id = cord-267533-nmgtan4e author = Hu, Zhigang title = Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date = 2020-10-29 keywords = COVID-19; RNA; SARS summary = By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin. doi = 10.1007/s10096-020-04085-2 id = cord-342938-rzhsnkn4 author = Huang, Bo-Ruei title = Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan date = 2020-06-30 keywords = SARS summary = title: Co-infection of Influenza B Virus and SARS-CoV-2: A Case Report from Taiwan 1, 2 Here, we report a unique case of influenza B virus co-infection with SARS-CoV-2 in Taiwan. The co-infection of influenza virus and SARS-CoV-2 is unusual, and to date, most reported cases are from China. Beside co-infection of influenza virus, increased co-infection of other virus or bacteria had also been reported among In our case, the newly developed dry cough and fever during hospitalization was the warning sign and the subsequent chest image confirmed clinical deterioration, which prompted the initiation of hydroxychloroquine. Single dose baloxavir marboxil was also superior to oseltamivir in reducing the viral load one day after the initiation of the trial regimen in patients with uncomplicated influenza. The clinical characteristics of pneumonia patients co-infected with 2019 novel coronavirus and influenza virus in Wuhan Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia doi = 10.1016/j.jmii.2020.06.011 id = cord-313028-0nhgxoim author = Huang, Chaolin title = Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China date = 2020-01-24 keywords = ICU; MERS; SARS; patient summary = INTERPRETATION: The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Following the pneumonia cases of unknown cause reported in Wuhan and considering the shared history of exposure to Huanan seafood market across the patients, an epidemiological alert was released by the local health authority on Dec 31, 2019, and the market was shut down on Jan 1, 2020. 16 Secondary infection was diagnosed if the patients had clinical symptoms or signs of nosocomial pneumonia or bacteraemia, and was combined with a positive culture of a new pathogen from a lower respiratory tract specimen (including the sputum, transtracheal aspirates, or bronchoalveolar lavage fluid, or from blood samples taken ≥48 h after admission). In view of the high amount of cytokines induced by SARS-CoV, 22, 24 MERS-CoV, 25, 26 and 2019-nCoV infections, corticosteroids were used frequently for treatment of patients with severe illness, for possible benefit by reducing inflammatory-induced lung injury. doi = 10.1016/s0140-6736(20)30183-5 id = cord-322908-e3gok0ot author = Huang, Fangfang title = A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19) date = 2020-05-20 keywords = COVID-19; CoV-2; Coronavirus; SARS; chinese summary = In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19. In this review, we summarized potential Chinese herbal medicines ( Table 2 ) that may treat COVID-19 by targeting proteins such as Spike protein, ACE2, 3CLpro, PLpro and RdRp. We also predicted the binding affinities between these compounds and COVID-19 related targets by molecular docking, with a focus on six compounds: quercetin, andrographolide, glycyrrhizic acid, baicalin, patchouli alcohol, and luteolin. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1016/j.phrs.2020.104929 id = cord-278951-vxrwrzlj author = Huang, Hsien-Hao title = Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak date = 2006-12-31 keywords = SARS summary = title: Declining Emergency Department Visits and Costs During the Severe Acute Respiratory Syndrome (SARS) Outbreak Background The immediate and long-term impact of severe acute respiratory syndrome (SARS) outbreak on emergency department (ED) visits and hospital expenditures for these visits has not been thoroughly investigated. 14 This study found that a substantial mean reduction in the number of ED visits occurred during the SARS epidemic, with a peak of 51.6% and a mean of 32.1% (95% CI of the mean difference, 27.6-36.6%) during the 4-month (April-July) epidemic period in a designated SARS hospital in Taiwan ( Figure 1 ). The higher total cost for each patient during the SARS epidemic was primarily attributed to increases in the number of laboratory investigations, radiographic examinations, ancillary procedures and medications required ( Figure 5 ). doi = 10.1016/s0929-6646(09)60106-6 id = cord-260697-oepk0b1d author = Huang, J. title = COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches date = 2020-08-01 keywords = Lopinavir; Ritonavir; SARS; covid-19 summary = We applied the Synthetic Minority Oversampling Technique (SMOTE) to overcome the rare recurring events in certain age groups and performed Virtual Twins (VT) analysis facilitated by random forest regression for medical treatment-recurrence classification. Here, we report the clinical, radiological, laboratory, and drug treatment findings of 93 recurring patients from 414 patients in Shenzhen, along with our machine learning approaches for identifying the best drug combinations that reduce recurring rates in all population, different age groups and obese patients. The interaction among age, hospitalization delay and drug treatment on SARS-CoV-2 recurring rate is shown in Figure 3 . Interestingly, we found out that the combination of anti-influenza virus drug, oseltamivir, with Interferon/Lopinavir/Ritonavir/Arbidol, has very good outcome (recurring rate of 0.172), supporting the hypothesis of co-infection of influenzas and SARS-CoV-2. . https://doi.org/10.1101/2020.07.29.20164699 doi: medRxiv preprint Supplement Table Table S1 : Clinical characteristics, laboratory findings, treatments, and outcomes of Covid-19 patients with and without recurrence of SARS-CoV-2 PCR positivity during hospitalization. doi = 10.1101/2020.07.29.20164699 id = cord-301556-f3m9gwvo author = Huang, Jessie title = SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response date = 2020-09-18 keywords = ACE2; SARS; cell; figure summary = Serially passaging these epithelial spheres generated >10 30 iAT2s per starting sorted tdTomato+ cell over 225 days in culture (Hurley et al., 2020) , generating cells that maintained expression of AT2 marker genes including surfactants as shown by single cell RNA sequencing (scRNA-Seq) ( Figure 1C -D, Figure S1 ) and providing a stable source of human primary-like AT2 cells for viral infection disease modeling. Compared to other published datasets of SARS-CoV-2 infection models in Calu-3, J o u r n a l P r e -p r o o f A549-ACE2, and primary (non-alveolar) normal human bronchial epithelium (NHBE) (Blanco-Melo et al., 2020) , iAT2s were able to uniquely capture the downregulation of AT2-specific programs, such as decreased surfactant gene expression and loss of lamellar body gene ontology (GO) terms (comparative gene set enrichment based on lung-related GO biological processes; Figure S3 ). doi = 10.1016/j.stem.2020.09.013 id = cord-293765-xpc4yizb author = Huang, Jia-Ling title = Th2 predominance and CD8+ memory T cell depletion in patients with severe acute respiratory syndrome() date = 2005-02-24 keywords = CD8; SARS summary = To define the dynamics of the immune spectrum in SARS, serum levels of cytokines, chemokines, immunoglobulins, complement and specific antibodies against SARS-associated coronavirus (SARS-CoV) were assayed by enzyme-linked immunosorbent assay (ELISA), and phenotypes of peripheral lymphocytes were analyzed by flow cytometry in 95 SARS-infected patients. IL-10 levels in the serum of SARS patients were continuously elevated for the 5 months observed in this study (2.47-4 .57 times that of normal control levels; Fig. 1C , P < 0.001, correlation coefficient = 0.514, one-way ANOVA; minimum detectable dose < 3.9 pg/ml). In this study, we found that infection with SARS-CoV triggered vigorous immune disturbances characterized by the following: (1) typical anti-viral nonspecific and specific humoral responses; (2) perturbation of cytokine and chemokine levels; and (3) severe impairment of cellular immunity, including lymphopenia in acute phase and loss of CD8+ memory T cells in convalescent phase. doi = 10.1016/j.micinf.2004.11.017 id = cord-330200-l6bnxi40 author = Huang, Jianping title = Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date = 2020-04-27 keywords = RNA; SARS; viral summary = title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. doi = 10.1101/2020.04.22.20071258 id = cord-302608-fw4pmaoc author = Huang, Jiao-Mei title = Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-19 keywords = CoV-2; SARS summary = However, RBD and key amino acid residues supposed to be crucial for human-to-human and cross-species transmission are homologues between SARS-CoV-2 and pangolin CoVs. These results from our analysis suggest that SARS-CoV-2 is a recombinant virus of bat and pangolin CoVs. Moreover, this study also reports mutations in coding regions of 125 SARS-CoV-2 genomes signifying its aptitude for evolution. The host specificity of virus particle is determined by amino acid sequence of RBD and is usually dissimilar among different CoVs. Therefore, RBD is a core determinant for tissue tropism and host range of CoVs. This article presents SARS-CoV-2 phylogenetic trees, comparison and analysis of genome, spike protein, and RBD amino acid sequences of different CoVs, deducing source and etiology of COVID-19 and evolutionary relationship among SARS-CoV-2 in human. The S-protein amino acid sequence identity between SARS-CoV-2 and related beta-CoVs showed that bat/Yunnan/RaTG13 shares highest similarity of 97.43%. doi = 10.1101/2020.03.16.993816 id = cord-341970-pho6dksc author = Huang, Jun title = Immunization with SARS-CoV S DNA vaccine generates memory CD4(+) and CD8(+) T cell immune responses date = 2006-06-05 keywords = CD8; SARS summary = In the present study, mice were immunized i.m. with SARS-CoV S DNA vaccine, and three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses when the cells were stimulated in vitro with a pool of peptides overlapping entire SARS spike protein. Moreover, mice boosted with SARS S DNA vaccine exhibited a 3-30-fold increase in the frequency of IFN-␥-producing cells in spleens (P < 0.01) and lymph nodes (P < 0.05), respectively (Fig. 1) , compared with the prime immunization. To further ascertain whether the frequency of SARS-CoV S specific CD4 + and CD8 + T cell responses was increased after boost vaccination, mice were boosted i.m. with SARS-CoV S DNA vaccine, seven days after injection, IFN-␥-and IL-2-producing CD4 + and CD8 + T cells were determined in lymph nodes, spleen and lungs. doi = 10.1016/j.vaccine.2006.03.058 id = cord-262145-i29e3fge author = Huang, Kuan-Ying A. title = Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date = 2020-10-19 keywords = RBD; SARS summary = A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. The MAbs with 161 strong anti-RBD binding have a relatively long heavy chain CDR3 length (50% 162 binding concentration <0.5 µg/ml versus >0.5 µg/ml, p=0.03, two-tailed Mann-163 Whitney test; Supplemental Figure 3 The 32 anti-spike glycoprotein MAbs were systematically examined by plaque 173 reduction neutralisation (PRNT) assay for neutralisation of wild type SARS-CoV-2 174 virus (see methods; summarised in Table 1 ). Potent neutralising antibodies to the RBD of SARS-CoV-2 spike glycoprotein were 188 identified and we thus analyse the blockade of the ACE2-RBD interaction by anti-189 RBD antibodies in two assays ( Figure 3 , Table 1 The structure of VHH72-Fc bound to RBD is known (17) and its footprint on the 198 RBD does not overlap that of ACE2, so inhibition is thought to occur by steric 199 hindrance. doi = 10.1101/2020.08.28.267526 id = cord-267246-hq7g62p5 author = Huang, Su-Hua title = Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism date = 2015-07-31 keywords = ORF6; SARS; npipb3 summary = title: Phage display technique identifies the interaction of severe acute respiratory syndrome coronavirus open reading frame 6 protein with nuclear pore complex interacting protein NPIPB3 in modulating Type I interferon antagonism METHODS: This study identified SARS-CoV ORF6-interacting proteins using the phage displayed human lung cDNA libraries, and examined the association of ORF6–host factor interaction with Type I IFN antagonism. RESULTS: The highest affinity clone to ORF6 displayed the C-terminal domain of NPIPB3 (nuclear pore complex interacting protein family, member B3; also named as phosphatidylinositol-3-kinase-related kinase SMG-1 isoform 1 homolog). The nucleotide sequences of the C terminus (amino acid residues 936e1050) of NPIPB3 (Accession Number Q92617) fused with the coat protein of ORF6-interacting phage clone 40 was amplified using PCR, and then cloned into bacterial expression vector pET32a for coimmunoprecipitation in vitro and mammalian expression vector pDsRed1-C (BD Biosciences Clontech) for colocalization assay. doi = 10.1016/j.jmii.2015.07.002 id = cord-277619-83bve5z0 author = Huang, Victoria W. title = Head and neck survivorship care in the times of the SARS‐CoV‐2 pandemic date = 2020-05-02 keywords = HNC; SARS summary = In this present commentary, we discuss the unique mental health challenges and burdens of patients with head and neck cancer in the times of the SARS‐CoV‐2 pandemic and approaches to mitigate these stressors through telemedicine to reduce future burdens to the patient and the health care system. With the uncertainties of the SARS-CoV-2 pandemic and a head and neck cancer (HNC) diagnosis, the potential mental health consequences of such delays to treatment warrant further discussion. 24 With HNC patients already a vulnerable population, delaying treatment in the times of the SARS-CoV-2 pandemic can place additional strain on the mental health and QOL of patients, resulting in future burdens on the health care system. With examples of utilizing technology from China, providers need to address the mental health burden of a HNC diagnosis for patients who are being asked to delay treatment to ensure comprehensive cancer care. doi = 10.1002/hed.26235 id = cord-309074-pys4aa60 author = Huang, Victoria W. title = Telehealth in the times of SARS-CoV-2 infection for the Otolaryngologist date = 2020-05-30 keywords = CoV-2; SARS; telemedicine summary = OBJECTIVE: In response to the American Academy of Otolaryngology – Head and Neck Surgery''s recommendations to limit patient care activities in the times of SARS-CoV-2, many elective surgeries have been canceled without patient clinics transitioning to virtual visits. In response to these evolving needs, the American Academy of Otolaryngology -Head and Neck Surgery (AAO-HNS) telemedicine committee has put forth new recommendations to prioritize novel applications of telehealth to help limit coronavirus disease pandemic spread while maintaining quality care 8 . As testing in the U.S. becomes more available in this era of SARS-CoV-2, telemedicine continues to take the main role of "forward triage", evaluating patients with respiratory symptoms before they arrive in hospitals 23 With the AAO-HNS recommending all otolaryngologists to limit patient care activities to time-sensitive, urgent, and emergent medical conditions, elective surgeries have been canceled with many outpatient clinics rescheduling appointments and transitioning to virtual visits 7, 8 . doi = 10.1016/j.wjorl.2020.04.008 id = cord-337854-5ogip9tz author = Huang, Wanqiu title = The determination of release from isolation of COVID-19 patients requires ultra-high sensitivity nucleic acid test technology date = 2020-07-02 keywords = SARS summary = In our study, we developed an improved strategy, termed as nestRPA (nest recombinase polymerase amplification), which could greatly improve the sensitivity of nucleic acid detection for SARS-CoV-2 than RPA or qPCR. Using nestRPA technology, we found that positive plasmid containing SARS-CoV-2 with the concentration of 1 copy/ul could also be stably detected by Fragment 5 and nucleic acid detection results were negative using qPCR. Our results suggested that the ultra-sensitive nucleic acid detection technique has important implications for early identification of those asymptomatic carriers infected with SARS-CoV-2. In addition, many experts of COVID-19 prevention and treatment clearly pointed out that the inaccurate sample collection were also one of the important reasons for the false negative result of SARS-CoV-2 nucleic acid [6] [7] [8] . If all the links in the detection of SARS-CoV-2 nucleic acid could be strictly administrated, false negative could be completely eliminated, and the discontinuation of isolation will no longer be a dilemma for us. doi = 10.1016/j.jinf.2020.06.075 id = cord-344636-go5cw92q author = Huang, Wei E. title = RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date = 2020-04-25 keywords = LAMP; RNA; SARS summary = In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample. doi = 10.1111/1751-7915.13586 id = cord-325657-s2vdazq0 author = Huang, Yan-Jang S. title = SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge date = 2020-07-17 keywords = Aedes; SARS summary = Three widely distributed species of mosquito; Aedes aegypti, Ae. albopictus and Culex quinquefasciatus, representing the two most significant genera of arbovirus vectors that infect people, were tested. In this study, the susceptibility of three mosquito species, Ae. aegypti, Ae. albopictus and Cx. quinquefasciatus, were determined through the intrathoracic inoculation with SARS-CoV-2. No virus was detected in the 277 inoculated mosquitoes collected and titrated at time points beyond 24 h, suggesting a rapid loss of infectivity and the lack of replication after injection. Based upon the lack of detectable infectious virus in any of the 277 samples collected at all time points beyond 24 h post-inoculation, we conclude that SARS-CoV-2 is unable to replicate in mosquitoes and that even if a mosquito fed on a person with virus in the blood, that the mosquito would not be a vector if feeding on a naïve host. doi = 10.1038/s41598-020-68882-7 id = cord-330067-ujhgb3b0 author = Huang, Yi title = CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes date = 2007-10-02 keywords = SARS; sequence summary = To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. In CoVDB, with the aim of facilitating gene retrieval, we tried to unify the naming of these non-structural proteins from different groups of coronaviruses. When we compared their putative amino acid sequences to the corresponding ones in other group 1 coronavirus genomes using BLAST, as well as searching for conserved domains using motifscan, results showed that the putative proteins encoded by these ORFs belonged to a protein family in Pfam originally assigned as ''Corona_NS3b'' (accession number PF03053). database, CoVDB, of annotated coronavirus genes and genomes, which offers efficient batch sequence retrieval and analysis. doi = 10.1093/nar/gkm754 id = cord-351532-2yd4wg9v author = Huang, Yin-Qiu title = No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study date = 2020-07-14 keywords = IFN; LPV; RBV; SARS summary = title: No Statistically Apparent Difference in Antiviral Effectiveness Observed Among Ribavirin Plus Interferon-Alpha, Lopinavir/Ritonavir Plus Interferon-Alpha, and Ribavirin Plus Lopinavir/Ritonavir Plus Interferon-Alpha in Patients With Mild to Moderate Coronavirus Disease 2019: Results of a Randomized, Open-Labeled Prospective Study The proportion of patients with SARS-CoV-2 nucleic acid negativity in the LPV/r+IFN-α-treated group (61.1%) was higher than the RBV+ IFN-α-treated group (51.5%) and the RBV+LPV/r+IFN-α-treated group (46.9%) at day 14; however, the difference between these groups was calculated to be statistically insignificant. The office of National Health Commission of the People''s Republic of China, and the National Administration Bureau of Traditional Chinese Medicine have jointly issued different versions of the "Guidelines for diagnosis and treatment of novel coronavirus pneumonia", in which LPV/r, IFNa, and RBV are recommended for on-trial use in patients with COVID-19. doi = 10.3389/fphar.2020.01071 id = cord-268370-kfjujs4z author = Huang, Yu-Tung title = Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study date = 2009-05-31 keywords = SARS; Taiwan summary = title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study The purpose of this study was to explore the effect of the SARS outbreak on hospitalization for chronic ambulatory-care-sensitive conditions (ACSCs) in Taiwan. Methods We applied a population-based interrupted time series study design and used the time series auto-regressive integrated moving-average model to compare the actual and predicted admission rates of seven selected chronic ACSCs. The analyses were based on National Health Insurance hospital inpatient claims data from 1997 to 2003. We applied a population-based interrupted time series design to compare the actual with predicted hospitalization for ACSCs after the SARS outbreak, to identify conditions with increased hospitalization that might have been caused by untimely or inappropriate primary care during the SARS outbreak. We found that the actual hospitalization rates for six selected ACSCs, particularly respiratory conditions, were significantly lower than their predicted rates for at least 1 month during the SARS period. doi = 10.1016/s0929-6646(09)60082-6 id = cord-329011-spiuqngp author = Huang, Yuan title = Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 date = 2020-08-03 keywords = ACE2; CoV-2; RBD; SARS summary = The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. A large number of glycosylated S proteins cover the surface of SARS-CoV-2 and bind to the host cell receptor angiotensinconverting enzyme 2 (ACE2), mediating viral cell entry [8] . The SARS-CoV-2 S protein is highly conserved among all human coronaviruses (HCoVs) and is involved in receptor recognition, viral attachment, and entry into host cells. Structure of the S1 subunit The binding of virus particles to cell receptors on the surface of the host cell is the initiation of virus infection; therefore, receptor recognition is an important determinant of viral entry and a drug design target. Therefore, the development of antibodies targeting this functional motif may cross-bind and neutralize these two viruses and related CoVs. Antiviral peptides prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infection. doi = 10.1038/s41401-020-0485-4 id = cord-351662-rmkcb6o3 author = Huang, Zhifeng title = Characteristics and roles of SARS‐CoV‐2 specific antibodies in patients with different severities of COVID‐19 date = 2020-07-24 keywords = COVID-19; SARS summary = We aimed to quantify the levels of SARS‐CoV‐2‐specific IgM, IgA, and IgG antibodies, identify changes in them based on COVID‐19 severity, and establish the significance of combined antibody detection. The rise times for specific IgM and IgG levels are different, and combined detection could be more advantageous in the diagnosis of COVID-19 [5] . In this study, SARS-CoV-2-specific IgM, IgA, and IgG levels were measured in patients with varying severities of COVID-19, the relationship between specific antibody levels and disease severity was classified, and the significance of combined antibody detection was clarified, providing a reference for the clinical diagnosis of COVID-19. We also found that while IgA and IgG levels were significantly higher in the severe & critical patients than in moderate patients, there was no difference in IgM between the two groups. Levels of IgA and IgG were higher in severe & critical COVID-19 patients than in moderate COVID-19 patients, while IgM levels were no different between the two groups. doi = 10.1111/cei.13500 id = cord-277490-xrgnt6l5 author = Huang, Zhongwei title = Optimal temperature zone for the dispersal of COVID-19 date = 2020-05-16 keywords = SARS summary = Abstract It is essential to know the environmental parameters within which the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can survive to understand its global dispersal pattern. Our findings suggest that there is an optimal climatic zone in which the concentration of SARS-CoV-2 markedly increases in the ambient environment (including the surfaces of objects). The aerodynamic characteristics and propagation of SARS-CoV-2 in aerosols have been reported (Liu et al., 2020) . Therefore, it is essential to understand the survival of SARS-CoV-2 in the ambient environment to prevent COVID-19. Transmission of a 2009 Pandemic Influenza Virus Shows a Sensitivity to Temperature and Humidity Similar to That of an H3N2 Seasonal Strain Evidence that higher temperatures are associated with lower incidence of COVID-19 in pandemic state, cumulative cases reported up to Association between ambient temperature and COVID-19 infection in 122 cities from China doi = 10.1016/j.scitotenv.2020.139487 id = cord-320511-qnxj7d9l author = Hueston, Linda title = The antibody response to SARS-CoV-2 infection date = 2020-08-27 keywords = IFA; NAT; SARS summary = METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for IgG, IgA and IgM was developed, and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Diagnosis is primarily by detecting SARS-CoV-2-specific RNA by nucleic acid testing (NAT), but this has limitations, including the possibility of false-negative results due to low virus load in patients with minimal disease, inadequate respiratory tract sampling or mutations in the target sequence, and false-positive results due to contamination or nonspecific amplification. The objective of this study was to develop and evaluate an immunofluorescent antibody (IFA) test for SARS-CoV-2-specific IgG, IgM and IgA, and apply it to document the serological response in individuals with confirmed COVID-19. Since the start of the epidemic in Australia, the Public Health Laboratory Network recommended collecting acute and convalescent sera for serological assays on individuals being tested for SARS-CoV-2 infection, in addition to respiratory tract samples for NAT, though this has not been universally adopted [5] . doi = 10.1093/ofid/ofaa387 id = cord-342144-awtiqxx5 author = Hufert, F. title = Coronaviren: von der banalen Erkältung zum schweren Lungenversagen: Chronologie einer Pandemie date = 2020-04-01 keywords = MERS; SARS; der; die; und; von summary = Ein klinischer Nutzen konnte beim Einsatz der eigentlich für die Behandlung von Humane-Immundefizienz(HIV)-Infektionen verwendeten Proteaseinhibitoren Lopinavir und Ritonavir (Kaletra ® ) zur Therapie des SARS-CoV nachgewiesen werden [6] . Im Dezember 2019 trat in China erstmalig ein neues Coronavirus auf, das zunächst als 2019-nCoV bezeichnet wurde und nach aktueller Nomenklatur des International Committee on Taxonomy of Viruses (ICTV) nun als SARS-CoV-2 bezeichnet wird [7] . So ist der kombinierte Einsatz der Proteaseinhibitoren Lopinavir und Ritonavir bei SARS-CoV-Patienten von klinischem Nutzen [6] . Eine weitere Studie mit MERS-CoV-Infizierten wird in Saudi-Arabien durchgeführt, bei der mit Lopinavir/Ritonavir plus Interferon-β behandelt wird [30] ; Daten zu den Ergebnissen liegen noch nicht vor. konnte gezeigt werden, dass die zelluläre Protease TMPRSS2 für die Infektiosität von SARS-CoV-2 essenziell ist und eine Hemmung dieser Protease mithilfe von Camostat-Mesilat die Vermehrung des Virus u. doi = 10.1007/s00112-020-00910-2 id = cord-007713-611sp7uo author = Hughes, J. M. title = Emerging infectious diseases: the public’s view of the problem and what should be expected from the public health community date = 2005 keywords = SARS; disease; health summary = In 2003 alone, a newly recognized coronavirus spread across five continents sickening more than 8,000 people and causing 774 deaths from a new disease designated severe acute respiratory syndrome (SARS) [4] , the exotic animal trade resulted in the first cases of human monkeypox in the Western hemisphere [5] , and highly pathogenic strains of avian influenza virus killed humans and devastated the poultry industry in parts of Asia [6] -further heightening fears of pandemic influenza. Improving preparedness and response: lessons learned from recent outbreaks -Strengthening existing and developing new national and international partnerships -Training and educating a multidisciplinary workforce -Ensuring "full use" of investments -Encouraging transparency and political will -Fostering a global commitment to address inequities -Developing and implementing preparedness plans and research agendas -Proactively communicating with health professionals, the media, and the public While the first line of defense in controlling an outbreak remains strong national surveillance systems that can readily detect outbreaks, the SARS experience highlighted the importance of global disease detection efforts [13] . doi = 10.1007/3-211-29981-5_17 id = cord-270837-xvauo76d author = Hui, David S. title = The 1-Year Impact of Severe Acute Respiratory Syndrome on Pulmonary Function, Exercise Capacity, and Quality of Life in a Cohort of Survivors date = 2005-10-31 keywords = Dlco; ICU; SARS summary = Our assessment included: lung volume (total lung capacity [TLC], vital capacity, residual volume, functional residual capacity), spirometry (FVC, FEV1), diffusing capacity of the lung for carbon monoxide (Dlco), inspiratory and expiratory respiratory muscle strength, 6-min walk distance (6MWD), chest radiographs (CXRs), and HRQoL by Medical Outcomes Study 36-Item Short-Form General Health Survey questionnaire. The lung function tests at 12 months showed significantly lower percentage of predicted FVC, VC, TLC, RV, and Dlco in survivors who required ICU support than those who were treated on medical wards, although no significant difference was noted for 6MWD and respiratory muscle strength between the two groups ( Table 5) . The 1-year lung function indexes (percentage of predicted FVC, VC, TLC, RV, and Dlco) in survivors who required ICU support were remarkably lower than those of patients who were treated on medical wards, although no significant differences were noted for 6MWD, respiratory muscle strength, and health status between the two groups. doi = 10.1378/chest.128.4.2247 id = cord-270857-8424oq4x author = Hui, David S. title = Exhaled Air Dispersion During Oxygen Delivery Via a Simple Oxygen Mask date = 2007-08-31 keywords = HPS; SARS; oxygen summary = We studied the dispersion of exhaled air through a simple oxygen mask applied to a human patient simulator (HPS) during the delivery of different oxygen flow in a room free of air currents. 7 As part of our influenza pandemic preparedness, we studied the safety of oxygen therapy by examining exhaled air dispersion from a simple oxygen mask attached to a human patient simulator (HPS) during the delivery of oxygen at different levels of flow. 33 Using a laser visualization technique and a mathematical model that was different from the one used in the current study for data analysis, we have previously shown a maximal dispersion distance of approximately 0.4 m during the application of oxygen at 4 L/min via a simple mask to the HPS, which was programmed at a respiratory rate of 12 breaths/min and a tidal volume of 0.5 L. doi = 10.1378/chest.07-0636 id = cord-290758-kz0qfy3r author = Hui, David S. title = The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China date = 2020-02-29 keywords = SARS; Wuhan summary = title: The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -The latest 2019 novel coronavirus outbreak in Wuhan, China The 2019-nCoV infection in Wuhan appears clinically milder than SARS or MERS overall in terms of severity, case fatality rate and transmissibility, which increases the risk of cases remaining undetected. The rapid identification and containment of a novel coronavirus virus in a short period of time is a reassuring and a commendable achievement by China''s public health authorities and reflects the increasing global capacity to detect, identify, define and contain new outbreaks. The latest analysis show that the Wuhan CoV cluster with the SARS CoV.10 (Novel coronavirus -China (01) Whilst several important aspects of MERS-CoV epidemiology, virology, mode of transmission, pathogenesis, diagnosis, clinical features, have been defined, there remain many unanswered questions, including source, transmission and epidemic potential. doi = 10.1016/j.ijid.2020.01.009 id = cord-333368-kjrk8nn9 author = Huizinga, Gabrielle P title = The Collision of Meta-Inflammation and SARS-CoV-2 Pandemic Infection date = 2020-09-03 keywords = COVID-19; SARS; obesity summary = While obesity and diabetes may complicate the delivery of supportive care in critical illness regardless of the underlying disease, lessons learned from the interaction of obesity with other systemic inflammatory syndromes suggest that obesity modifies biologic factors related to SARS-CoV-2 infection and the COVID-19 syndrome. In seasonal and pandemic influenza, however, obese individuals may be more susceptible to severe viral respiratory disease even if they mount a serologic response to vaccination 25 A c c e p t e d M a n u s c r i p t 11 Along with possible impairments in pathogen clearance, obese hosts are more likely to experience the breakdown of respiratory epithelium during a pulmonary infection, which leads to increased fluid in the airway space. doi = 10.1210/endocr/bqaa154 id = cord-271815-yr1dq258 author = Hulkower, Rachel L. title = Inactivation of surrogate coronaviruses on hard surfaces by health care germicides date = 2011-06-30 keywords = MHV; SARS; TGEV summary = Methods The efficacy of health care germicides against 2 surrogate coronaviruses, mouse hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), was tested using the quantitative carrier method on stainless steel surfaces. This study was undertaken using the carrier method to evaluate 6 chemical germicides commonly used in health care settings for their efficacy in reducing infectivity of coronaviruses on environmental surfaces. The efficacy of 6 hospital surface germicides was tested against 2 coronaviruses, MHV and TGEV, used as surrogates for SARS-CoV. 3, 15, 17, 24 The results of this study show that, of the commonly used hospital germicides tested, only the ethanol-based germicides were able to achieve this level of reduction of infectious virus after 1 minute of contact time. Studies of hospital germicide efficacy against adenovirus 8 using the same carrier-based method with 1-minute contact times found greater log 10 reduction factors by OPA (4.37) than were observed in this study for TGEV (2.27) and MHV (1.71). doi = 10.1016/j.ajic.2010.08.011 id = cord-329454-69z28yli author = Humar, Atul title = Severe acute respiratory syndrome and the liver date = 2004-01-30 keywords = SARS; coronavirus summary = Liver enzyme abnormalities are common in SARS patients, although hepatic impair-ment has not been reported to be a prominent feature of this illness. However, this is the first report to associate hepatic SCoV infection and liver pathologic features. Defining the basis for susceptibility to severe inflammatory outcomes after coronavirus infection has obvious implications for the study and treatment of clinical SARS. Although the exact mechanisms for resistance and susceptibility to MHV3 coronavirus infection have not be determined, studies have shown that in resistant mice, infection leads to a T helper type 1 (TH1)-dominant response that, through the production of interferon, neutralizing antibodies, and cytotoxic T cells, results in viral clearance. A novel coronaviruses associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases doi = 10.1002/hep.20069 id = cord-322007-xy66t0ls author = Humbert, S title = COVID-19 as a cause of immune thrombocytopenia date = 2020-05-20 keywords = SARS summary = ITP has been described during the course of several viral infections: HIV, EBV, CMV, HCV but only once during severe acute respiratory distress coronavirus 2 (SARS-CoV-2) [2] . As immune thrombocytopenia was the most relevant diagnosis and due to severe bleeding, we started prednisone (1 mg/kg/day) and one course of intravenous immunoglobulins 1 g/kg. We describe here the second case of SARS-CoV-2-induced ITP. COVID-19 is caused by SARS-CoV-2, responsible for severe pneumonia in less than 20% of cases. COVID-19 thrombocytopenia could be secondary to direct platelet-virus interaction via pathogen recognition receptors (PRR). In our case, thrombocytopenia is lower than what is usually observed during COVID-19 and may be secondary to an immune-related mechanism. The suddenness and severity of thrombocytopenia could be explained by the patient''s advanced age as coronavirus induced higher antibodies production in older people [10] . Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 doi = 10.1016/j.medmal.2020.05.003 id = cord-312561-9o2fhi6e author = Hung, I.F.N. title = Viral Loads in Clinical Specimens and SARS Manifestations date = 2004-09-17 keywords = NPA; SARS summary = A retrospective viral load study was performed on clinical specimens from 154 patients with laboratory-confirmed severe acute respiratory syndrome (SARS); the specimens were prospectively collected during patients'' illness. Viral load in nasopharyngeal aspirates (n = 142) from day 10 to day 15 after onset of symptoms was associated with oxygen desaturation, mechanical ventilation, diarrhea, hepatic dysfunction, and death. We compared the viral load in these specimens with the presence or absence of diarrhea, oxygen desaturation, mechanical ventilation, lymphopenia, hepatic dysfunction, abnormal urinalysis findings, and death rate by chi-square or Fisher exact test for categorical variables and by Mann-Whitney U test for continuous variables. A high viral load in serum was also associated with oxygen desaturation, mechanical ventilation, hepatic dysfunction, and death (all p < 0.01) but not with diarrhea or abnormal urinalysis findings. The importance of SARS-CoV as a respiratory pathogen is supported by the strong association of viral load in NPA with oxygen desaturation, mechanical ventilation, and death. doi = 10.3201/eid1009.040058 id = cord-314734-ai0hz4uq author = Hung, Ivan Fan-Ngai title = SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: a case series date = 2020-06-12 keywords = Hong; Kong; SARS summary = Thus, the Diamond Princess cruise ship, which was quarantined because of an onboard outbreak of COVID-19 in February, 2020, provides an opportunity to define the shedding pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient antibody responses before and after the onset of symptoms. Participants were prospectively screened by quantitative RT-PCR (RT-qPCR) of nasopharyngeal and throat swabs, and serum IgG and IgM against internal nucleoprotein and the surface spike receptor-binding protein (RBD) of SARS-CoV-2 at baseline (upon entering quarantine) and on days 4, 8, and 12 of quarantine. Evidence before this study We searched PubMed on March 14, 2020, with no date restrictions, for articles in English, using the terms "Covid-19", "coronavirus", "antibody", "viral load", "cruise ship", "quarantine", "shedding", and "seroconversion". By Feb 20, 2020, 76 passengers from Hong Kong were hospitalised in Japan after testing positive for SARS-CoV-2 by throat swab RT-PCR, of whom two individuals died from complications of the infection (appendix). doi = 10.1016/s1473-3099(20)30364-9 id = cord-331835-nuhrd92z author = Hung, Kevin K. C. title = The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong date = 2018-11-27 keywords = Hong; Kong; SARS summary = title: The role of the hotel industry in the response to emerging epidemics: a case study of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong METHODS: This case study focuses on the epidemic outbreaks of SARS in 2003 and H1N1 swine flu in 2009 in Hong Kong, and the subsequent guidelines published by the health authority in relation to the hotel industry in Hong Kong which provide the backbone for discussion. This case study will use the example of the Metropole Hotel in Hong Kong in the international spread of Severe Acute Respiratory Syndrome (SARS) in 2003, and the effect of the government mandated quarantine of the Metropark Hotel during the swine flu 2009 in Hong Kong. After the SARS outbreak in Hong Kong the health authority established the Guidelines for Hotels in Preventing Severe Acute Respiratory Syndrome (SARS) [24] doi = 10.1186/s12992-018-0438-6 id = cord-256572-sqz8yc7b author = Huo, Jiandong title = Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date = 2020-05-06 keywords = ACE2; RBD; SARS; cr3022 summary = The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 Å of the Fab/RBD complex. Potent nanomolar affinity neutralising human monoclonal antibodies against the SARS-CoV RBD have been identified that attach at the ACE2 receptor binding site (including M396, CR3014 and 80R (Ter Meulen et al., 2006; Sui et al., 2004; Zhu et al., 2007) ). We determined the crystal structure of the SARS-CoV-2 RBD-CR3022 Fab complex (see Methods and Table S3 ) to investigate the relationship between the binding epitopes of ACE2 and CR3022. Full interpretation of the detailed interactions between CR3022 and the RBD was enabled by the second crystal form which diffracted to high resolution, 2.4 Å, and the structure of which was refined to give an R-work/R-free of 0.213/0.239 and good stereochemistry (Methods, Table S3, Figure S5 ). doi = 10.1101/2020.05.05.079202 id = cord-293946-4bquxdqa author = Huong, Nguyen Quynh title = Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date = 2020-08-10 keywords = Nam; Nguyen; SARS; Viet; bat summary = In this study we investigated the presence and diversity of coronavirus sequences in the field rat trade distribution chain, wildlife farms specializing in raising rodents for human consumption, and bat guano "farms" and roosts near human dwellings to better understand the natural hosts of coronaviruses and the risk for these interfaces to facilitate spillover into humans. Out of 70 sites, coronavirus positives were detected at 58 including 100% (24/24) of live rat trade sites, 60.7% (17/28) of rodent wildlife farm sites, 94.1% (16/17) of bat guano farm sites, and at the one natural pteropid bat roost. Significant findings of this study are the high proportion of coronavirus positive wildlife (bats and rodents) and the increasing proportion of positives found along the rat trade supply chain from sub-interfaces close to the capture site (rat traders) to restaurants. doi = 10.1371/journal.pone.0237129 id = cord-256092-bph9ys72 author = Hussain, Aneela N. title = Role of testosterone in COVID-19 patients - a double-edged sword? date = 2020-09-17 keywords = COVID-19; SARS summary = Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Current data suggest a direct correlation between the lower level of serum testosterone, inflammatory cytokines, disease severity, and poor clinical outcomes among male patients with COVID-19. Lower levels of testosterone result in the upregulation of ACE2 and TMPRSS2 receptors, facilitating SARS-CoV-1 entry into the alveolar cells, and deregulating a lung-protective pathway (4) . Thereby we hypothesize that low testosterone levels in males have a direct correlation with the severity of disease and a worse outcome in COVID-19. Patients with low testosterone have reportedly developed severe manifestations requiring assisted ventilation because of the upregulation of ACE-2 receptors in lower respiratory cells, increased risk of lung damage, and respiratory muscle catabolism. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China doi = 10.1016/j.mehy.2020.110287 id = cord-346930-gl573ip9 author = Hussain, Azhar title = Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date = 2020-05-24 keywords = COVID-19; RNA; SARS summary = Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. Since the emergence of the virus in China in December of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the globe resulting in the current global pandemic. Arbidol (also known as Umifenovir) is a promising repurposed antiviral agent with a unique mechanism of action targeting the S protein/ACE2 interaction and inhibiting membrane fusion of the viral envelope to the host cell [7] . doi = 10.7759/cureus.8260 id = cord-315288-fcx4q6mp author = Hussain, Mohammed Hassan title = Tracheal swab from front of neck airway for SARS-CoV-2; a bronchial foreign body date = 2020-08-27 keywords = CoV-2; SARS summary = We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. We report the case of a bronchial foreign body, following a tracheostomy site swab for SARS-CoV-2, aiming to raise awareness and vigilance. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. This case highlights the need for clear guidance on how samples for SARS-CoV-2 are taken from patients with front of neck airways (laryngectomy/tracheοstomy) and the potential pitfalls involved. Patients with front of neck airways, either in the form of a laryngectomy or tracheostomy stoma site, present a challenge in terms of testing for SARS-CoV-2. There is a need for clear guidance on how to test patients with front of neck airways for SARS-CoV-2. doi = 10.1136/bcr-2020-237787 id = cord-344658-4z2697q6 author = Hutasoit, Novana title = Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology date = 2020-08-29 keywords = COVID-19; SARS summary = title: Sars-CoV-2 (COVID-19) Inactivation Capability of Copper-Coated Touch Surface Fabricated by Cold-Spray Technology The primary intention was to alleviate the tendency of SARS-CoV-2 (COVID-19) virus to linger longer on touch surfaces that attract high-to-medium volume human contact, such as the push plates used in publicly accessed buildings and hospitals. This work showcases the capability of cold-spray as a potential copper-coating solution for different in-use parts and components that can act as sources for the spread of the virus. In this work the authors have deposited copper coatings onto the stainless steel push-plates in a matter of 7 mins only, which is a marvellous demonstration of the application of the cold spray coating process for ongoing and future challenges arising from the pandemic. Table 1 and Fig. 2 presents the viricidal activity results of SARS-CoV-2 virus when exposed to three different metallic surfaces and compared with COVID-19 only and positive control solutions. doi = 10.1016/j.mfglet.2020.08.007 id = cord-293715-lipme817 author = Hutchison, Lisa title = Neuropsychiatric Symptoms in an Adolescent Boy with Multisystem Inflammatory Syndrome in Children (MIS-C) date = 2020-06-30 keywords = MIS; SARS summary = BACKGROUND: Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID-19) is an emergent syndrome affecting children globally in the wake of the SARS-CoV-2 pandemic. METHOD: This case describes a 14-year-old boy who developed prominent neuropsychiatric symptoms including delirium followed by impairments in executive functioning in the context of MIS-C with positive SARS-CoV-2 antibodies. The recent SARS-CoV-2 pandemic has been associated with emergence of a new syndrome referred to as Multisystem Inflammatory Syndrome in Children (MIS-C) related to coronavirus disease-2019 (COVID19) . Given the paucity of knowledge concerning this syndrome''s effect on the nervous system, the intent of this case report is to describe the neuropsychiatric symptoms in one 14-year-old boy presenting with multisystem inflammatory syndrome and positive SARS-CoV-2 antibodies. Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicenter cohort doi = 10.1016/j.psym.2020.06.015 id = cord-341474-06113cn0 author = Huynh, Tien title = In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease date = 2020-05-14 keywords = Mpro; SARS; figure summary = Besides the identification of several high-potency drugs and/or molecules, we unveiled the consensus binding mechanism that a ligand prefers to bind the "anchor" site of the Mpro pocket, which might facilitate the future design and optimization of an inhibitor for the SARS-CoV-2''s Mpro. To verify the docking results, as an example, we further performed the MD simulation to investigate the stability of entecavir''s pose with the best affinity score inside the Mpro pocket (Figure 5a ). As shown in Figure 3c , our docking result verifies that the Boc group indeed occupies the "anchor" site, further validating the binding mechanisms discovered in this work for stabilizing the ligand inside the Mpro''s pocket. We found that the docking affinity scores of several molecules (such as nelfinavir and entecavir) are very close to those of the ligands found experimentally (N3 and O6K), and their binding stabilities with the Mpro were verified in MD simulations. doi = 10.1021/acs.jpclett.0c00994 id = cord-275257-upj8mvzn author = Hwang, E. Shelley title = Surgical Oncologists and the COVID-19 Pandemic: Guiding Cancer Patients Effectively through Turbulence and Change date = 2020-06-14 keywords = COVID-19; SARS; cancer; care; pandemic; patient summary = Perspectives are provided on: (1) maintaining a safe environment for surgical oncology care; (2) redirecting the multidisciplinary model to guide surgical decisions; (3) harnessing telemedicine to accommodate requisite physical distancing; (4) understanding interactions between SARS CoV-2 and cancer therapy; (5) considering the ethical impact of professional guidelines for surgery prioritization; and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. The panel provides perspectives on: (1) creating a safe environment for surgical oncology care, (2) redirecting the multidisciplinary model to guide surgical decisions, (3) harnessing telemedicine to accommodate requisite physical distancing, (4) understanding interactions between SARS CoV-2 and cancer therapy, (5) considering the ethical impact of professional guidelines for surgery prioritization, and (6) advocating for our patients who require oncologic surgery in the midst of the COVID-19 pandemic. doi = 10.1245/s10434-020-08673-6 id = cord-294122-ou3wj4rz author = Hwang, Stephen W title = Population mortality during the outbreak of Severe Acute Respiratory Syndrome in Toronto date = 2007-05-29 keywords = Greater; SARS; Toronto summary = BACKGROUND: Extraordinary infection control measures limited access to medical care in the Greater Toronto Area during the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak. The objective of this study was to determine if the period of these infection control measures was associated with changes in overall population mortality due to causes other than SARS. METHODS: Observational study of death registry data, using Poisson regression and interrupted time-series analysis to examine all-cause mortality rates (excluding deaths due to SARS) before, during, and after the SARS outbreak. An interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak. The interrupted time series analysis found no significant change in mortality rates in the Greater Toronto Area associated with the period of the SARS outbreak in 2003, as indicated by the fact that the observed rates remained almost entirely within the 95% CI for the predicted rates. doi = 10.1186/1471-2458-7-93 id = cord-349117-xfir3m5p author = Hyseni, Inesa title = Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays date = 2020-09-10 keywords = CoV-2; MNT; PNT; SARS; pseudotype summary = After fully characterising lentiviral pseudotypes bearing the SARS-CoV-2 spike protein, we employed them in pseudotype-based neutralisation assays in order to profile the neutralising activity of human serum samples from an Italian sero-epidemiological study. SARS CoV-2 strain 2019-nCov/Italy wild-type virus (LV), which was handled in a level 3 bio-containment facility (BSL 3), was used as positive control in order to evaluate the spike glycoprotein expression, while a ∆-envelope pseudotype, prepared with the same procedure, was used as a negative control. To verify the expression of the spike protein in the SARS-CoV-2 pseudotypes, the spike was detected by Western blot; sera from convalescent SARS-CoV-2 patients, which have been shown to have a high neutralising titre in microneutralisation with a live virus, were used as the primary antibody, and goat anti-Human IgG as the secondary antibody. doi = 10.3390/v12091011 id = cord-320612-vam0bli3 author = Höring, Steffen title = Management of a Hospital-Wide COVID-19 Outbreak Affecting Patients and Healthcare Workers date = 2020-10-26 keywords = April; SARS; patient summary = Here, we report a large nosocomial outbreak of SARS-CoV-2 that occurred at a satellite hospital of the University Hospital Aachen, Germany, with 26 patients and 21 healthcare workers infected. Considering the numerous COVID-19 cases among patients and HCW, a hospital-wide screening was initiated on April 8 for all remaining SARS-CoV-2-negative patients and entire hospital staff. On the other hand, we analyzed the first cases among hospital staff, starting with the potential index nurse tested positive for SARS-CoV-2 on the 6th of April. By the time the outbreak emerged, the hospital policy already comprised preemptive infection control measures in order to prevent intrahospital spread of SARS-CoV-2. The second route of transmission addressed by our measures was infected HCW, who potentially spread SARS-CoV-2 to patients as well as to their co-workers. In the post-outbreak period, we have continued to screen all patients on their day of admission and all geriatric inpatients once weekly for SARS-CoV-2 in order to detect new cases timely. doi = 10.1007/s42399-020-00597-2 id = cord-291809-b7sosrc7 author = Iacovoni, Attilio title = A case series of Novel-Coronavirus infection in heart transplantation from two centers in the pandemic area in the North of Italy date = 2020-06-26 keywords = SARS; covid-19 summary = BACKGROUND Little is known about the coronavirus SARS-CoV-2 disease (COVID-19) in solid organ transplanted patients. (5) It has been speculated that 10 SARS-CoV-2 damages the host through two overlapping mechanisms, the first is the direct damage 11 of the virus itself, the second is an abnormal host response that may lead to a cytokine storm Aim of this study is to report a series of heart transplanted patients with SARS-CoV-2 infection 3 from two Heart Transplant Centers in the North of Italy describing clinical characteristics, 4 prognosis and the impact of COVID-19 on heart transplant programs. The high case fatality rate observed in heart transplanted patients may be due 3 to the characteristics of the cohort evaluated in the analysis. These characteristics may therefore explain the 12 higher incidence SARS-CoV-2 infection, the more severe clinical presentation and the higher 13 mortality rate in transplanted patients. Case report of COVID-19 in a kidney transplant recipient: Does 21 immunosuppression alter the clinical presentation? doi = 10.1016/j.healun.2020.06.016 id = cord-328289-3h3kmjlz author = Iadecola, Costantino title = Effects of COVID-19 on the nervous system date = 2020-08-19 keywords = COVID-19; CoV-2; SARS; patient summary = Another Parkinson''s disease patient with obesity, hypertension and diabetes, exhibited at autopsy, in addition to hypoxic-ischemic neuronal damage, microhemorrhages, white matter lesions and enlarged perivascular spaces, but no evidence of SARS-CoV-2 in the brain (Kantonen et al., 2020) . The encephalopathy is most likely a consequence of systemic factors, such as cytokine sickness, hypoxia and metabolic dysfunction due to peripheral organ failure, while the strokes seem to be related more to hypercoagulability and endothelial injury than to SARS-CoV-2 vasculitis affecting brain vessels. In some cases, the possibility of a SARS-CoV-2 encephalitis could not be ruled out based on the potential for the virus to infect neurons (Song et al., 2020) , but definitive clinical and pathological evidence of neurotropism is lacking. doi = 10.1016/j.cell.2020.08.028 id = cord-261414-vqvctafm author = Ian Gallicano, G. title = Molecular targeting of vulnerable RNA sequences in SARS CoV-2: identifying clinical feasibility date = 2020-11-12 keywords = Fig; SARS; cell summary = Here we show that siRNAs and miRNAs inhibit SARS CoV-2 spike protein production in a dose-dependent manner in both HEK293 cells and a primary human airway tracheal cell line. Two cell types, HEK293 cells and primary human tracheal cells (hpTCs) were employed to test the hypothesis that siRNAs or miRNAs could suppress SARS CoV-2 spike expression. As a result, electroporation was used to introduce spike cDNA into hpTCs. Twenty four hours after electroporation of spike plasmid, 200 nM of each small RNA (the concentration seen to virtually completely suppress spike in HEK293 cells) was transfected resulting in marked reduction in spike protein expression in both siRNA1 + 2 and miRNA1 + 2 samples (Fig. 3A) . The data in Fig. 3B , C reveal that siRNA1/NT (non-transfection reagent) suppressed spike protein production in a dose-dependent manner in HEK293 cells (Fig. 3B ). doi = 10.1038/s41434-020-00210-0 id = cord-263945-yli5suxb author = Iancu, Gabriela Mariana title = Viral exanthema as manifestation of SARS-CoV-2 infection: A case report date = 2020-08-28 keywords = COVID-19; CoV-2; SARS summary = RATIONALE: The clinical manifestations of the SARS-CoV-2 infection are mainly respiratory but the virus can cause a variety of symptoms. PATIENT CONCERNS: We present the case of SARS-CoV-2 infection in a previously healthy woman who presented with respiratory symptoms and developed anosmia, diarrhea, and an erythematous maculo-papular rash on day 15 from symptom onset. [6] Pathogenetically, the appearance of cutaneous lesions during the SARS-CoV-2 infection can be explained by an immune response initiated by the viral nucleotides which activate Langerhans cells with the secondary involvement of keratinocytes (maculopapular, urticarial and chicken pox-like rashes), by microthrombi formation and cutaneous vasculopathy (chilblain lesions, livedo reticularis, erythema multiforme-like rash, gangrene), or by reaction to the medication administered (urticaria, erythroderma, erythema multiforme, etc.). [7, 8] We report a case of disseminated exanthema that appeared after 15 days of treatment for SARS-CoV-2 infection in a patient without other medical and dermatological problems in the past. doi = 10.1097/md.0000000000021810 id = cord-331094-22366b81 author = Ianevski, Aleksandr title = Potential Antiviral Options against SARS-CoV-2 Infection date = 2020-06-13 keywords = COVID-19; CoV-2; SARS; Vero; figure summary = We also screened 136 safe-in-man broad-spectrum antivirals against the SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. After the initial screening, we identified apilimod, emetine, amodiaquine, obatoclax, homoharringtonine, salinomycin, arbidol, posaconazole and nelfinavir as compounds that rescued virus-infected cells from death (AUC from 285 to 585; Table S1 ). We next profiled transcriptional responses to nelfinavir, amodiaquine or both drugs in virus-or mock-infected Vero-E6 cells at 24 h. Anti-SARS-CoV-2 activity of safe-in man broad-spectrum antivirals in Vero-E6 cells. Here, we found that combinations of nelfinavir with salinomycin, amodiaquine, obatoclax, emetine or homoharringtonine were synergistic against SARS-CoV-2 in Vero-E6 cells. Thus, the amodiaquine and nelfinavir combination could result in better efficacy and decreased toxicity for the treatment of SARS-CoV-2 and perhaps other viral infections. Transcriptomic analysis of mock-and SARS-CoV-2-infected Vero-E6 cells treated with nelfinavir, amodiaquine or both drugs. doi = 10.3390/v12060642 id = cord-348855-lnltoj1n author = Iannaccone, Giulia title = Weathering the Cytokine Storm in COVID-19: Therapeutic Implications date = 2020-06-29 keywords = COVID-19; SARS; TNF; patient summary = The exaggerated cytokine release in response to viral infection, a condition known as cytokine release syndrome (CRS) or cytokine storm, is emerging as the mechanism leading to ARDS and MOF in COVID-19, thus endorsing the hypothesis that properly timed anti-inflammatory therapeutic strategies could improve patients'' clinical outcomes and prognosis. CS are the cornerstone of treatments for cytokine storms and macrophage activation syndrome in autoimmune/autoinflammatory diseases [18] ; in the COVID-19 scenario they may be useful in the more severe forms of CRS to curb the systemic inflammatory response and prevent the occurrence of ARDS, if appropriately timed [10, 19] , 20]. Tocilizumab is now already included in many practice guidelines for COVID-19 management, especially for the treatment of critically ill patients with severe refractory hypoxemia in a later stage after the high-viral-load initial phase all over the world, while we wait for more definite data from multiple ongoing clinical trials [42] . doi = 10.1159/000509483 id = cord-254120-1q8tqeg7 author = Iannone, Primiano title = The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness. date = 2020-04-11 keywords = N95; SARS; grade summary = The WHO, ECDC and CDC have issued conflicting guidelines on the use of respiratory filters (N95) by HCWs. Methods We searched PubMed, Embase and The Cochrane Library from the inception to March 21, 2020 to identify randomized controlled trials (RCTs) comparing N95 respirators versus surgical masks for prevention of COVID-19 or any other respiratory infection among HCWs. The grading of recommendations, assessment, development, and evaluation (GRADE) was used to evaluate the quality of evidence. However, wearing N95 respirators can prevent 73 more (95% CI 46-91) clinical respiratory infections per 1000 HCWs compared to surgical masks (2 RCTs; 2594 patients; low quality of evidence). We therefore conducted a systematic review aimed at assessing the efficacy of N95 respirators versus surgical masks for the prevention of respiratory tract infections transmission among HCWs. The evidence from the review can then be used for the development of an appropriate GRADE framework for public health policy guidelines. doi = 10.1101/2020.04.06.20054841 id = cord-273426-55vu6b3u author = Iba, Toshiaki title = Coagulopathy of Coronavirus Disease 2019 date = 2020-05-26 keywords = ARDS; COVID-19; SARS; patient summary = Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. Conclusions: Severe acute respiratory syndrome coronavirus 2/ coronavirus disease 2019 frequently induces hypercoagulability with both microangiopathy and local thrombus formation, and a systemic coagulation defect that leads to large vessel thrombosis and major thromboembolic complications, including pulmonary embolism in critically ill hospitalized patients. (Crit Care Med 2020; XX:00-00) Key Words: coagulopathy; coronavirus; coronavirus disease 2019; disseminated intravascular coagulation; hypercoagulability; thromboembolism I ncreasing communications worldwide have reported that hospitalized, critically ill coronavirus disease 2019 (COVID-19) patients are frequently developing laboratory abnormalities compatible with hypercoagulability and clinically a high prevalence of thromboembolic events (1). doi = 10.1097/ccm.0000000000004458 id = cord-312684-3i2r2ahr author = Iba, Toshiaki title = Coagulopathy in COVID‐19 date = 2020-06-18 keywords = COVID-19; SARS; patient summary = For example, the coronavirus that caused severe acute respiratory syndrome (SARS) in 2002 (SARS-CoV-1) were reported to be associated with thrombocytopenia (55%), thrombocytosis (49%), and prolonged activated partial thromboplastin time (aPTT) (63%), but the incidence of bleeding was not high [5, 6] . In this respect, Chinese experts noted that in severe cases, patients can develop acute respiratory distress syndrome (ARDS), with coagulation predominant-type coagulopathy [9] . The excess production of proinflammatory cytokines, increased levels of damage-associated molecular patterns (DAMPs), the stimulation of cell-death mechanisms and vascular endothelial damage are the major causes of coagulation disorder in any severe infection (Fig. 1) . The major targets of the SARS-CoV-2 are the lung epithelial cell, lymphocyte, and the vascular endothelial cell, and these findings can explain that the clinical presentation of severe COVID-19 is characterized by ARDS, shock, and coagulopathy [12, 47] . doi = 10.1111/jth.14975 id = cord-268827-qwcbvtna author = Ibanez, Agustin title = COVID-19 in older people with cognitive impairment in Latin America date = 2020-08-18 keywords = COVID-19; SARS summary = 9 If SARS-CoV-2 can impair proteostasis through ORF8 binding and cause dysregulated endoplasmic reticulum protein traffick ing, then α-synuclein could aggregate uncontrollably. The COVID-19 pandemic in Latin America and Caribbean countries (LACs) has failed to capture the attention exiguous. 7 Many hospitals in LACs have inadequate protective equipment and there is scarce support for health-care workers who become sick. implemented control measures, is third highest among LACs. The public health conditions in these countries are complex and pose unique challenges; one underlying explanation for the surge in cases might be a large informal economy, in which workers need to leave their house every day to clean other households or to stand, for instance, at crowded traffic corners to sell their goods or shine shoes. For instance, with 20% of over 11 000 health workers in Mexico ill with COVID-19-one of the highest rates in the world-hospital staffing is and attract the resources necessary to control it. doi = 10.1016/s1474-4422(20)30270-2 id = cord-312160-2820aftb author = Ibrahim, Mahmoud A.A. title = In silico Drug Discovery of Major Metabolites from Spices as SARS-CoV-2 Main Protease Inhibitors date = 2020-10-08 keywords = CoV-2; SARS summary = Stabilities and binding affinities of the two identified natural spices were calculated over 40 ns molecular dynamics simulations and compared to an antiviral protease inhibitor (lopinavir). The binding energies of the investigated spices compounds with SARS-CoV-2 M pro were estimated using molecular mechanical-generalized Born surface area (MM-GBSA) approach with modified GB model (igb=2) implemented in AMBER16 software [27] . The physicochemical parameters of the most promising natural spices as SARS-CoV-2 M pro inhibitors were predicted using the online Molinspiration cheminformatics software %ABS was estimated as follows [28] : The online web-based tools of SwissTargetPredicition (http://www.swisstargetprediction.ch) were applied to predict the biological targets for the most promising natural spices as SARS-CoV-2 M pro inhibitors. Since the main protease of SARS-CoV-2 (M pro ) plays a critical role in the viral replication process, structure-based computational modeling of ligand-receptor interactions and molecular dynamics has been used to screen metabolites from common spices as potential M pro inhibitors. doi = 10.1016/j.compbiomed.2020.104046 id = cord-331109-a8e7r80d author = Ibrahim, Yassmin S. title = Case Report: Paralytic Ileus: A Potential Extrapulmonary Manifestation of Severe COVID-19 date = 2020-08-31 keywords = COVID-19; SARS; patient summary = We report two cases of SARS-CoV-2 infection complicated by paralytic ileus. Several authors have postulated that the angiotensin-converting enzyme 2 receptors, the host receptors for COVID-19, that are present on enterocytes in both the small and large bowel might mediate viral entry and resultant inflammation. We describe two cases of severe COVID-19 pneumonia who developed paralytic ileus during their disease course, which may represent one of the luminal manifestations of severe SARS-CoV-2 infection. 7 A review of 29 studies noted that 12% of patients with SARS-CoV-2 infection had gastrointestinal symptoms, including diarrhea, nausea, and vomiting. In conclusion, we report paralytic small and large bowel ileus as a complication of COVID-19. The added value of the present case report is the detailed histopathological evidence supporting a role for COVID-19-induced micro-thrombosis, thereby compromising microcirculatory function and resultant colonic bowel dilatation and perforation in the first patient. doi = 10.4269/ajtmh.20-0894 id = cord-268453-87b298uk author = Ibáñez, Sebastián title = Hydroxychloroquine and chloroquine in COVID-19: should they be used as standard therapy? date = 2020-06-03 keywords = COVID-19; HCQ; SARS summary = In the absence of a vaccine and specifically designed antivirals, the medical community has proposed the use of various previously available medications in order to reduce the number of patients requiring prolonged hospitalizations, oxygen therapy, and mechanical ventilation and to decrease mortality from coronavirus disease 2019 (COVID-19). HCQ was, in vitro, at least as effective as chloroquine in inhibiting SARS-CoV-2 infection, although it should be noted that studies on its mechanisms of action are not as extensive as with CQ [30] . The evidence for the use of hydroxychloroquine or chloroquine in COVID-19 is not good so far, not only because of the negative results of most of the studies but also because of their design, when publishing results of a very low number of patients, when reporting favorable results but without having a control group that allows comparison, when choosing results for which it will be very difficult to find significant differences, such as mortality, or for which their clinical relevance is uncertain. doi = 10.1007/s10067-020-05202-4 id = cord-304457-8g36h1bz author = Idelsis, E.-M. title = Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date = 2020-08-01 keywords = IFN; PCR; SARS; patient summary = Conclusions: In a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly negativized the virus on day 4 of treatment when comparing with IFN-alpha2b. The RT-PCR after treatment with IFNs on day 14 for hospital discharges was negative to SARS-CoV-2 in 100% and 91% of patients of HeberFERON and control cohorts, respectively. These results confirm the validity of early intervention with the treatment of IFNs in patients with COVID-19, whereas demonstrated in the trial, the combination of type I and type II IFNs impacts strongly in the reduction of the risk for a severe disease likely through the efficient implementation of a timely controlled inflammatory antiviral response against the SARS-CoV-2 infection. Evaluation of the Effect and Safety of HeberFERON vs Heberon Alpha in Patients Infected with Corona Virus SARS-CoV-2 (Study ESPERANZA/HOPE): TRIALS doi = 10.1101/2020.07.29.20164251 id = cord-268283-eja8fkwv author = Iftikhar, Hafsa title = Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach date = 2020-06-09 keywords = 3cl; FDA; SARS; drug summary = In this regard, several recent studies have been conducted using computational methods to screen libraries of approved drugs or drug-like molecules to identify potential inhibitors of different viral proteins, particularly, RdRp and 3CL-protease [13] [14] [15] [16] [17] . Here, we applied a computer aided drug discovery approach by targeting three important enzymes (RdRp, 3CL-protease and helicase) of SARS-CoV-2 and identified three FDA-approved drugs and three other drug-like molecules as potential therapeutics. In this study, we used a virtual screening based strategy to identify already approved drugs or drug-like molecules that can bind to any of the three key viral enzymes, 3CL-protease, RdRp and helicase, and potentially inhibit the function of these enzymes. In our studies we performed computational screening by targeting three important enzymes of SARS-CoV-2 including RdRp, 3CL-protease and helicase, to identify not only the already approved drugs for repurposing but also the drug candidates or lead structures that can be chemically modified to develop potential drugs. doi = 10.1016/j.compbiomed.2020.103848 id = cord-298679-w0yp4u19 author = Iftimie, Simona title = Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date = 2020-09-03 keywords = COVID-19; SARS; patient summary = Logistic regression analyses showed that fever, pneumonia, acute respiratory distress syndrome, diabetes mellitus and cancer were the variables that showed independent and statistically significant associations with mortality. This is one of the first studies to describe the factors associated with mortality in patients infected with SARS-CoV-2 in Spain, and one of the few in the Mediterranean area. The objective of the present study has been to characterize our patients'' epidemiology and to identify the risk factors associated with mortality for this disease in our geographical area. Logistic regression analyses showed that the presence of fever, pneumonia, acute respiratory distress syndrome, type 2 diabetes mellitus and cancer were the only variables that showed an independent and statistically significant association with mortality when they were adjusted for differences in age, gender, smoking status and alcohol intake (Tables 2 and 3) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.1371/journal.pone.0234452 id = cord-306177-5wefp31y author = Iheagwam, Franklyn Nonso title = Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants date = 2020-09-12 keywords = COVID-19; CoV-2; SARS; TMPRSS2 summary = e Unites States Food and Drug Administration-(USFDA-) approved drugs [26] , drugbank [27, 28] , traditional Ayurvedic, Chinese and natural medicine [20, [28] [29] [30] [31] , dark chemical matter, and fooDB [25] are some of the ZINC database subsets that have been rigourously screened for molecules to combat SARS-CoV-2 with main protease, RNA-dependent RNA polymerase, and angiotensin-converting enzyme-2 as the major therapeutic targets. Hence, this study analysed a plethora of natural products (NPs) from African medicinal plants with known bioactivities in human as therapeutic candidates targeting and inhibiting SARS-CoV-2 RNA synthesis, replication, structural protein function, and host-specific receptors/enzymes. In the course of drug discovery, structure-based virtual screening is a computational approach utilised to identify promising novel small chemical ligands from curated chemical compound databases with potential activity against drug targets [48] . doi = 10.1155/2020/1878410 id = cord-326581-31trqhi1 author = Ihling, Christian title = Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients date = 2020-06-22 keywords = SARS summary = title: Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. 2 On the basis of the prospective goals of this coalition, the aim of this "proof-of-principle" study is to highlight the potential of MS in identifying SARS-CoV-2 proteins, even from highly diluted samples, such as gargle solutions of COVID-19 patients. All samples had been classified as SARS-CoV-2-positive by three reverse-transcription and quantitative polymerase chain reaction (RT-qPCR) analyses identifying E-, S-, and N-gene RNAs. For protein precipitation, 1 mL of acetone (−20°C) was added to 750 μL of gargle solution and stored overnight at −20°C. We present a protein MS-based method to specifically detect SARS-CoV-2 virus proteins from highly diluted gargle solutions of COVID-19 patients. Using this approach, we were able to identify peptides originating from SARS-CoV-2 nucleoprotein in gargle solution samples. doi = 10.1021/acs.jproteome.0c00280 id = cord-284498-54j6ys8s author = Ihsanullah, Ihsanullah title = Coronavirus 2 (SARS-CoV-2) in water environments: Current status, challenges and research opportunities date = 2020-10-16 keywords = CoV-2; SARS; covid-19; wastewater; water summary = Some of the significant challenges and research opportunities are the development of standard techniques for the detection and quantification of SARS-CoV-2 in the water phase, assessment of favorable environments for its survival and decay in water; and development of effective strategies for elimination of the novel virus from water. Development of effective standard techniques for the detection and quantification of SARS-CoV-2 in water, assessment of the existing water purification technologies and development of novel advanced water treatment systems are major challenges and open research opportunities. Furthermore, careful surveillance of water and wastewater to be used as an early warning tool for such outbreaks in future, understanding the survival and decay mechanism of the novel virus in water and wastewater, analysis of potential pathways of SARS-CoV-2 into water bodies are other potential research opportunities for environmental researchers [40] [41] [42] [43] [44] . doi = 10.1016/j.jwpe.2020.101735 id = cord-035163-tqh5wv12 author = Ijaz, M. Khalid title = Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date = 2020-09-08 keywords = Health; SARS; virus summary = In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . doi = 10.7717/peerj.9914 id = cord-312996-qzu8pkyt author = Iles, R. K. title = A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date = 2020-08-22 keywords = MALDI; PCR; SARS; protein summary = Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. doi = 10.1101/2020.08.22.20176669 id = cord-352580-l6vkzja0 author = Iltaf, Samar title = Frequency of Neurological Presentations of Coronavirus Disease in Patients Presenting to a Tertiary Care Hospital During the 2019 Coronavirus Disease Pandemic date = 2020-08-18 keywords = COVID-19; SARS summary = Background Coronavirus disease 2019 (COVID-19), caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), usually presents clinically with cough, fever, shortness of breath, and loss of taste and/or smell. COVID-19 can also present with neurologic signs and symptoms, including headache, hyposmia/anosmia, encephalopathy, meningoencephalitis, Guillain-Barré syndrome, stroke, and seizure. This subjective survey addressed 10 neurological manifestations of COVID-19: headache, altered sensation, nausea and vomiting, sudden hemiparesis (stroke), numbness and paresthesia, vertigo, ataxia, seizure, encephalitis/meningitis, Guillain-Barré Syndrome (GBS), and myelitis. Our study confirmed that headache (6%), altered level of consciousness and encephalopathy (2%), hemiparesis (stroke; 0.6%), GBS (0.3%) and seizure (0.3%) were the most frequently reported neurological presentations [5, 6, 7, 8] . A case study reported that a patient positive for SARS-CoV-2 presented with isolated sudden onset anosmia but no other symptoms of COVID-19 [11] . doi = 10.7759/cureus.9846 id = cord-312619-7jpf81yz author = Ilyas, Sadia title = Disinfection technology and strategies for COVID-19 hospital and bio-medical waste management date = 2020-08-12 keywords = BMW; COVID-19; SARS; covid; waste summary = The exposure to COVID-waste may potentially increase the virus spread by increasing the reproductive number (R 0 ) from its determined range between 2.2 to 3.58 Thus, effective management of COVID-waste including the appropriate disinfect and disposal techniques are necessary to control the pandemic spread, which has not been focused yet albeit posing a similar threat as SARS-CoV-2 itself can have to the public health. The present article reviews the disinfection technologies to control/prevent the novel coronavirus spread and the proper management of COVID-waste including the effective strategies and reprocessing possibilities of the used items. Not only the COVID-waste generated by the hospitals, health centers, and self-quarantines, but the waste generated during the disinfection of public area or, where an infected person visited have been directed to treat as medical waste and collection of those waste in double-packed designated bags are mandatory before sending to burning at the high-temperature incinerator facility. doi = 10.1016/j.scitotenv.2020.141652 id = cord-290948-cuu78cvl author = Imbert, Isabelle title = The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date = 2008-02-05 keywords = GST; RNA; SARS summary = Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. doi = 10.1016/j.virusres.2007.11.017 id = cord-011813-lm105z6n author = Imperiale, Michael J. title = Recurring Themes date = 2020-07-08 keywords = SARS summary = to ask whether mSphere would be interested in publishing a summary of a conference being held at that time in Singapore to commemorate the 20th anniversary of the first Nipah virus outbreak. Having attended a similar conference on Ebola and other emerging infectious diseases a couple of years earlier, I knew that the topics of discussion and the information presented at such a meeting are of interest and importance to the microbial sciences community. I therefore told Benhur that we were absolutely interested: the report from the Nipah@20 conference is published with this editorial (1). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was beginning its journey from Wuhan, China to the rest of the world, and as of the time I am writing this, well over 10 million cases and half a million deaths have been reported. As the authors of the Nipah@20 conference summary note, the similarities in terms of what the world needs to respond to such emerging diseases are many. doi = 10.1128/msphere.00633-20 id = cord-298036-2zurc60t author = Imre, Gergely title = Cell death signalling in virus infection date = 2020-09-12 keywords = IRF-3; RNA; SARS; cell; death; virus summary = Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . doi = 10.1016/j.cellsig.2020.109772 id = cord-293056-kz3w0nfh author = Indes, Jeffrey E. title = Early Experience with Arterial Thromboembolic Complications in Patents with COVID-19 date = 2020-08-28 keywords = CoV-2; SARS summary = A retrospective case-control study design was used to identify, characterize and evaluate potential risk factors for arterial thromboembolic disease in SARS-CoV-2 positive patients. Although not statistically significant, in patients with arterial thromboembolism, patients who were SARS-CoV-2 positive compared to those testing negative or not tested tended to be male (66.7 % v. Treatment of arterial thromboembolic disease in the COVID-19 positive patients included open thromboembolectomy in 6 patients (40%), anticoagulation alone in 4 (26.7%) and 5 (33.3%) did not require or their overall illness severity precluded additional treatment. The SARS-CoV-2 positive group included patients with a range of COVID-19 16 symptomatology (mild to severe) as well as those tested as part of routine preoperative 17 preparation. Patients with arterial thrombosis who were SARS-CoV-10 2 positive had significantly higher D-dimer levels, BMI, were younger, and less often on 11 antiplatelet medications as compared to patients who were SARS-CoV-2 negative or not tested. doi = 10.1016/j.jvs.2020.07.089 id = cord-290895-tb0xald0 author = Indu, Purushothaman title = Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach date = 2020-10-26 keywords = COVID-19; FDA; SARS summary = title: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. RESULTS: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥ -8 kcal/mol. In this study, FDA J o u r n a l P r e -p r o o f approved small molecule antiviral drugs were screened against protein targets of SARS-CoV-2 using a computational based approach. In our study, other screened antiviral drugs such as Indinavir, Tipranavir, and Pibrentasvir showed dock energy value more than -8 kcal/mol and these drugs might also serve as an inhibitors of Mpro target of SARS-CoV-2. doi = 10.1016/j.jiph.2020.10.015 id = cord-254821-px4fe7mn author = Infantino, Maria title = Diagnostic accuracy of an automated chemiluminescent immunoassay for anti‐SARS‐CoV‐2 IgM and IgG antibodies: an Italian experience date = 2020-05-10 keywords = SARS; antibody summary = Sixty‐one COVID‐19 patients and 64 patients from a control group were tested by iFlash1800 CLIA analyzer for anti‐SARS CoV‐2 antibodies IgM and IgG. The more relaxed rules of the FDA''s "Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency" issued on 16 March 2020, 9 has allowed the market easier access to these tests as well as easier and faster diagnostics, but the lack of control in the production process is also dangerous making these tests potentially less reliable. 11 The aim of the this study was to assess the diagnostic performance of a novel fully automated CLIA for the quantitative detection of anti-SARS-CoV-2 IgM and IgG antibodies. 16 As with most existing studies on the diagnostic performance of the SARS-CoV-2 antibodies, our preliminary data showed that most COVID-19 patients have both IgM and IgG, and only few of them have isolated IgG or IgM antibodies. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Assessment of immune response to SARS-CoV-2 with fully-automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays doi = 10.1002/jmv.25932 id = cord-271751-46oo9xv5 author = Ingraham, Nicholas E. title = Shining a light on the evidence for hydroxychloroquine in SARS-CoV-2 date = 2020-04-28 keywords = SARS; hydroxychloroquine summary = Chloroquine and hydroxychloroquine seem effective in killing SARS-CoV in vitro [1, 3] . Recent reports show it also may be effective at killing SARS-CoV-2-infected cells in vitro [4] . To date, no pre-clinical studies have evaluated the efficacy of hydroxychloroquine in the current SARS-CoV-2 pandemic. A recent article published in Chinese found no benefit with chloroquine in a 1:1 randomized trial with 30 patients [6] . Until data from randomized controlled trials are available, we suggest caution utilizing hydroxychloroquine off label for patients with COVID-19. There are currently no evidence supporting hydroxychloroquine as prophylaxis, but unfortunately these data are being extrapolated to the indication potentially resulting in drug shortages for patients with rheumatic diseases who require this medication. Preliminary study of hydroxychloroquine sulfate in treating common coronavirus disease (COVID-19) patients in 2019 Hydroxychloroquine and azithromycin as a treatment of COVID-19: preliminary results of an open-label nonrandomized clinical trial doi = 10.1186/s13054-020-02894-7 id = cord-283197-jjye8t6j author = Ingraham, Nicholas E. title = Fact Versus Science Fiction: Fighting Coronavirus Disease 2019 Requires the Wisdom to Know the Difference date = 2020-04-29 keywords = SARS; hydroxychloroquine; trial summary = This commentary uses a recent study of hydroxychloroquine to demonstrate the dire need for randomized clinical trials, but more importantly, to explore the potential consequences of misinformation, how fear fuels its impact, and offer guidance to maintain scientific integrity without relinquishing hope. As of March 25, there remains no randomized control trial in humans with evidence that chloroquine or hydroxychloroquine is beneficial in SARS-CoV or SARS-CoV-2. Premature acceptance of efficacy is not new (swine flu vaccination [10] or recombinant human activated protein C [11] ), but it is these prior experiences that influence current standards to require high quality and often multiple randomized control trials to change practice. However, despite warnings from healthcare leaders and public health agencies, there continues to be a premature adoption of hydroxychloroquine as treatment based on limited preclinical data and misinformed interpretation of a nonrandomized study. doi = 10.1097/cce.0000000000000108 id = cord-309370-g8d3w7it author = Insausti-García, Alfredo title = Papillophlebitis in a COVID-19 patient: Inflammation and hypercoagulable state date = 2020-07-30 keywords = COVID-19; SARS; patient summary = We believe that the inflammatory reaction and the coagulation alteration present in our patient due to Sars-Cov2 coronavirus may have acted as risk factors for the development of papillophlebitis. It has been suggested to result from idiopathic inflammation of retinal vascular and, possibly of the capillaries of the optic disc; however it is mandatory to work out a hypercoagulable state (hereditary or acquired thrombophilia factors), vasculitic syndromes, blood hyperviscosity, and other recognized systemic vascular inflammatory disorders. On left eye fundus examination, and color and red free retinographies, severe inflammation of the optic nerve head was observed accompanied by retinal venous vasodilatation and tortuosity, cotton-wool spots and moderate superficial hemorrhages in all four quadrants. 8 In addition to the respiratory tract infection and to these acute ocular manifestations, the current pandemic caused by the SARS-CoV-2 is associated with coagulation activation and a disproportionate systemic inflammatory response. doi = 10.1177/1120672120947591 id = cord-307860-iqk1yiw4 author = Ionescu, Mihaela Ileana title = An Overview of the Crystallized Structures of the SARS-CoV-2 date = 2020-10-24 keywords = 3cl; ACE2; CoV-2; PDB; RNA; SARS summary = Structures retrieved from PDB (August 12, 2020) were analyzed for relevant information on COVID-19 infection, synthesis of new inhibitors, SARS-CoV-2 interaction with host receptors, and the neutralizing antibodies interactions with spike glycoprotein. The first X-ray structure found (PDB ID 6LU7) belongs to the nonstructural protein 5 (3C-like protease) of the SARS-CoV-2 in complex with the Michael acceptor-based inhibitor N3 (PRD_002214). There is a cryo-EM crystal structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp12/nsp8/nsp7) with the antiviral drug remdesivir (PDB ID 7BV2) [37] . Previous studies on the crystal structures of SARS-CoV S glycoprotein mutants neutralized by 80R-specific antibodies have been considered a hope for the immunotherapeutic Fig. 8 The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites doi = 10.1007/s10930-020-09933-w id = cord-342453-1vj9p7vm author = Ip, A. title = Hydroxychloroquine in the treatment of outpatients with mildly symptomatic COVID-19: A multi-center observational study date = 2020-08-25 keywords = August; SARS summary = Methods: We examined the association between outpatient hydroxychloroquine exposure and the subsequent progression of disease among mildly symptomatic non-hospitalized patients with documented SARS-CoV-2 infection. [15] [16] [17] [18] In this multi-center observational cohort study we report progression from mildly symptomatic SARS-CoV-2 infection diagnosed as an outpatient progressing to subsequent need for in-patient hospitalization according to outpatient exposure to hydroxychloroquine. This retrospective, observational, multicenter cohort study within the Hackensack Meridian Health network (HMH) utilized EHR-derived data of patients with documented SARS-CoV-2 infection who received care initially within an outpatient setting. Our primary objective was to evaluate the association between hydroxychloroquine exposure and subsequent need for hospitalization in a population of patients with documented SARS-CoV-2 infection diagnosed in the outpatient setting. In this multicenter retrospective observational cohort study of mildly symptomatic outpatients with polymerase chain reaction documented SARS-CoV-2 infection, we noted an association (OR 0.53; 95% CI, 0.29, 0.95) between outpatient exposure to hydroxychloroquine and a reduction in subsequent need for hospitalization. doi = 10.1101/2020.08.20.20178772 id = cord-307213-i8yijbiu author = Ip, Jonathan Daniel title = Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date = 2020-11-02 keywords = Illumina; SARS summary = title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. A total of 28 serial respiratory specimens from 12 patients were successfully sequenced 49 using nanopore and Illumina sequencing. Temporal profiles of 310 viral load in posterior oropharyngeal saliva samples and serum antibody responses during 311 infection by SARS-CoV-2: an observational cohort study A neutralizing human antibody 370 binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Viral load dynamics and disease 397 severity in patients infected with SARS-CoV-2 in Zhejiang province, China doi = 10.1016/j.cmi.2020.10.030 id = cord-349821-5ykwwq75 author = Ippolito, G. title = Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date = 2006-09-09 keywords = SARS; States; United; case; infection summary = The term ''highly infectious diseases'' describes infections caused by pathogens that are transmissible from person to person, cause severe or life-threatening illness; present a serious hazard in healthcare settings and in the community; and require specific control measures, which may include management of cases in a highly secure isolation unit. In Canada, where SARS ''paralysed the Greater Toronto Area healthcare system for weeks'' [27] , and the Toronto public health department investigated 2132 potential cases of SARS, identified over 23,000 contacts as requiring quarantine and logged more than 316,000 calls on its SARS hotline [28] , a national review commission identified systemic deficiencies in response capacity, including ''inadequacies in institutional outbreak management protocols, infection control and infectious disease surveillance'', and found that these deficiencies resulted at least in part from failure to implement lessons learned from earlier public health emergencies [22] . doi = 10.1007/s00018-006-6309-y id = cord-307070-tqxvu3pu author = Iqbal, Phool title = Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date = 2020-09-20 keywords = COVID-19; PCR; SARS summary = However, improvement was observed in the clinical condition of the patients who were managed as per COVID-19 protocol based upon the clinical signs and symptoms after correlating with diagnostic chest imaging studies. The infectious disease team advised testing with COVID-19 serology (immunoglobulin (Ig) M and IgG antibodies through lateral flow assay), the results of which were positive, indicating recent infection. The infectious disease team was consulted and based upon his clinical presentation and previous investigations, the patient was maintained on the local management protocol for COVID-19 infection. Moreover, biomarkers such as CRP, ferritin, lymphocyte counts, lactate dehydrogenase, and N-terminal pro b-type natriuretic peptide, along with radiological findings in CXR or features such as unilateral or bilateral pneumonia, ground-glass opacities, or consolidations in a chest CT scan, can suggest COVID-19 infection even in such patients where RT-PCR alone is negative [4] . doi = 10.7759/cureus.10555 id = cord-274602-q9i2k304 author = Iqbal, Yousaf title = Psychiatric presentation of patients with acute SARS-CoV-2 infection: a retrospective review of 50 consecutive patients seen by a consultation-liaison psychiatry team date = 2020-09-10 keywords = COVID-19; SARS; psychiatric summary = BACKGROUND: Reports of psychiatric morbidity associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection tend to be limited by geography and patients'' clinical status. AIMS: To describe the psychiatric morbidity associated with SARS-CoV-2 infection (confirmed by real-time polymerase chain reaction) in referrals to a consultation-liaison psychiatry service in Qatar. 12 Finally, all current studies in hospital settings have restricted themselves to symptomatic patients with COVID-19, although psychiatric consultation-liaison services will also be referred patients who have tested positive for SARS-CoV-2 but are physically asymptomatic. The current study aimed to complement existing data by characterising the psychiatric morbidity associated with acute SARS-CoV-2 infection in patients referred to a consultation-liaison psychiatry service in Qatar. As such it offers a broad clinical picture of the psychiatric problems associated with acute SARS-CoV-2 infection, occurring in a general hospital setting, and including patients who are symptomatic and asymptomatic for COVID-19 infection. doi = 10.1192/bjo.2020.85 id = cord-277110-e27lm7rr author = Iria, Neri title = Major cluster of pediatric “ true ” primary chilblains during the COVID‐19 pandemic: a consequence of lifestyle changes due to lockdown date = 2020-06-13 keywords = COVID-19; SARS; chilblain summary = We reported demographical, laboratory and clinical features, history of close contact with COVID‐19 patients, presence of similar skin lesions in other family members, precipitating and risk factors for chilblain onset. All rights reserved In April 2020, we observed a growing number of chilblain-like manifestations similar to coldinduced lesions during the pandemic, with the opportunity to study 8 cases, 2 children and 6 adolescents, and report here our results. The aim of this study is to verify whether the chilblain-like lesions were a cutaneous clue for SARS-CoV-2 infection or due to other causes. All rights reserved -PCR-assay on blood samples for Parvovirus B19 DNA and Enterovirus RNA -PCR-assay on skin biopsy for Parvovirus B19, Mycoplasma pneumoniae and SARS-CoV-2 was performed in a single patient (12.5%). Various cutaneous findings were observed in adults infected with COVID-19 and, simultaneously, a marked increase of chilblain-like lesions occurred worldwide among children during the COVID-19 pandemic 10, 11 In our cases we exclude SARS-CoV-2 infection. doi = 10.1111/jdv.16751 id = cord-272653-01wck9f3 author = Isaacs, David title = Apocalypse perhaps date = 2020-08-24 keywords = SARS; pandemic summary = The exact starting date of the novel coronavirus pandemic COVID-19 will never be known, but China informed the World Health Organization (WHO) about the disease on New Year''s Eve, 31 December 2019. Transmission of severe acute respiratory syndrome (SARS)-CoV-2, the virus that causes COVID-19, was accelerated by traditional travel of 3 billion people for 40 days before the Chinese New Year on 25 January 2020. 2,3 When the Australian Chief Medical Officer activated the pandemic emergency response plan, weeks before the World Health Organization declared a pandemic, the Government was legally obliged to act. 12 The authors conclude that staff were being infected through community transmission and that PPE was effective in protecting front-line health-care workers. At a time when world leaders want to blame each other for aspects of the COVID-19 pandemic, the war metaphor is particularly menacing. Managing mental health challenges faced by healthcare workers during covid=19 pandemic doi = 10.1111/jpc.15011 id = cord-341648-z4lflkmo author = Isaacs, David title = To what extent do children transmit SARS‐CoV‐2 virus? date = 2020-06-16 keywords = SARS summary = A current child care outbreak in Sydney was initiated and spread by infected adults. 6 An unreviewed study of 15 New South Wales schools found nine staff and nine students who had tested positive for SARS-CoV-2. 7 It is possible that asymptomatic and mildly infected children are important transmitters of SARS-CoV-2, but the evidence to date suggests children rarely spread the virus. 8 Studies suggest school closures in China, Hong Kong and Singapore had little or no effect on control of the 2003 outbreak with the related SARS virus, which like infection with SARS-CoV-2 was much milder in children than adults. 9 In conclusion, the available evidence to date suggests children are unlikely to be major transmitters of SARSEpidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China School closure and management practices during coronavirus outbreaks including COVID-19: A systematic review doi = 10.1111/jpc.14937 id = cord-291024-9g4om4sf author = Isakbaeva, Elmira T. title = SARS-associated Coronavirus Transmission, United States date = 2004-02-17 keywords = SARS; case; patient summary = To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. To that end, we obtained serial biologic specimens and clinical and exposure data for 5 to 10 weeks after onset of illness from seven laboratory-confirmed U.S. SARS patients and their household contacts. We detected SARS-CoV in fecal and respiratory specimens and found that SARS case-patients may have high concentrations of virus in stools during the 2nd week of illness and continue to shed the virus in feces until at least 26 days after onset of symptoms. All upper respiratory specimens in the first 2 weeks after onset were negative for SARS-CoV by RT-PCR; this finding differs from a report in Hong Kong, where viral RNA was detected in nasopharyngeal aspirates of 68% of case-patients at day 14 (21) . doi = 10.3201/eid1002.030734 id = cord-279765-sb1ifyfx author = Isakova-Sivak, Irina title = A promising inactivated whole-virion SARS-CoV-2 vaccine date = 2020-10-15 keywords = SARS summary = In this regard, the study by Shengli Xia and colleagues 7 is timely because it provides valuable evidence for the safety and immunogenicity of a β-propiolactone inactivated aluminium hydroxideadjuvanted whole-virion SARS-CoV-2 vaccine candidate developed by China National Biotec Group and the Beijing Institute of Biological Products (BBIBP-CorV), which was tested in randomised, double-blind, placebocontrolled phase 1/2 clinical trials in healthy individuals aged 18 years and older. Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Effect of an inactivated vaccine against SARS-CoV-2 on safety and immunogenicity outcomes: interim analysis of 2 randomized clinical trials Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBIBP-CorV: a randomised, double-blind, placebo-controlled, phase 1/2 trial doi = 10.1016/s1473-3099(20)30832-x id = cord-338517-1mxcssjj author = Ishay, Yuval title = Antibody response to SARS‐Co‐V‐2, diagnostic and therapeutic implications date = 2020-08-26 keywords = COVID-19; RBD; SARS; antibody; patient summary = The phage display method, allowing rapid and wide display of proteins directly correlated to their associated genes, can detect NAbs against SARS-CoV from both naïve and immune antibody libraries, capable of blocking the binding of S1 domain, thereby showing virus neutralization and prophylaxis capability either in vitro or in the animal models (31, 33, 36) . Another method, possibly allowing the production and utilization of existing NAbs, may include the use of Epstein-Barr virus (EBV) transformation of human B cells to improve the isolation of NAbs from the memory B cells harvested from the SARS-CoV infected patients (11) . Experimental and clinical data on the use of convalescent plasma products and humanized monoclonal antibodies for H5N1 influenza infection have also shown positive outcomes, and this treatment was proposed as a mean for overcoming anti-viral drug resistance (62, 79, 80) . In a study involving 20 patients with severe pandemic influenza A (H1N1) 2009 virus infection, administration of convalescent plasma reduced respiratory tract viral load, serum cytokine response, and mortality (81) . doi = 10.1002/hep4.1600 id = cord-311948-3v311fnd author = Ishiguro, Takashi title = Clinical Course and Findings of 14 Patients with COVID-19 Compared with 5 Patients with Conventional Human Coronavirus Pneumonia date = 2020-08-27 keywords = SARS summary = Because her symptoms, laboratory data, and radiological findings were mild with patchy GGOs detectable only by CT ( Figure 11 ), we did not administer antibiotics or antivirals, and she remained in stable condition during hospitalization. Only one of the SARS-CoV-2 pneumonia patients was in severe condition on admission (Table 3) , but 5 patients worsened during hospitalization, and one patient (Case 5) required HFNC therapy. Abnormal X-ray shadows were not detectable in 4 (36.3%) of the 11 SARS-CoV-2 pneumonia patients throughout their course, but abnormal shadows were found in the other patients on admission or during hospitalization. 10 Abnormal shadows were not detected on initial chest X-ray in 5 of our 11 patients with SARS-CoV-2 pneumonia. (11) We administered ritonavir/lopinavir to 5 of the 11 SARS-CoV-2 pneumonia patients, and chest X-ray findings gradually began to improve 3 days after the initiation of these agents in 3 patients. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1016/j.rmcr.2020.101207 id = cord-335377-zrbn637z author = Ishimaru, Daniella title = RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date = 2012-12-26 keywords = RNA; S3L2; SARS; Stem; figure; loop summary = Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. We further show that kissing dimer formation plays a role in frameshift-stimulation and modulates the relative abundance of full-length and subgenomic viral RNAs. Plasmids containing wild-type pseudoknot as well as the ÁS3 pk mutant were described in Plant et al (1) . Our previous NMR analysis of exchangeable imino protons of the SARS-CoV pseudoknot ( Figure 1A , wild-type pk) provided unequivocal evidence for the existence of Stem 3 (1). Surprisingly, in the context of the SARS-CoV Stem 3 sequence, 5 0 -cuug-3 0 tetraloop-capped mutants readily formed extended duplex structures as revealed by native gel and NMR analysis. doi = 10.1093/nar/gks1361 id = cord-276481-os1nf3cs author = Ishizaki, Tatsuro title = Estimation of the impact of providing outpatients with information about SARS infection control on their intention of outpatient visit date = 2004-09-30 keywords = SARS; outpatient summary = Abstract To examine the effect of provision of information about the infection control in the specific infection disease treatment unit in a city hospital on the outpatient''s intention of outpatient service use, respondents who underwent outpatient medical care at the hospital (N = 821) were asked whether or not they intended to continue the outpatient visit at the hospital if a severe acute respiratory syndrome (SARS) patient was admitted to the unit. This study examined the effect of providing outpatients with information about SARS infection control in the infectious disease treatment unit in a community hospital on their intention to continue outpatient visits, and estimated the cumulative total number of outpatients as well as the cumulative total expenditures for outpatient care at the hospital during a 180-day period after the admission of a SARS patient to the hospital. doi = 10.1016/j.healthpol.2004.04.008 id = cord-252714-idlyl4ga author = Islam, M. Saiful title = Current knowledge of COVID-19 and infection prevention and control strategies in healthcare settings: A global analysis date = 2020-05-15 keywords = COVID-19; China; IPC; SARS summary = 1,2 Outbreaks of newly emerging or remerging infectious diseases present a unique challenge and a threat to healthcare providers (HCPs) and other frontline responders due to limited understanding of the emerging threat and reliance on infection prevention and control (IPC) measures that may not consider all transmission dynamics of the emerging pathogens. We searched publications in English on ''PubMed'' and Google Scholar for the period between January 1 and April 27, 2020, using the following search terms: "2019-nCoV" or "COVID-19" or "2019 novel coronavirus" or "SARS-CoV-2." To identify COVID-19 IPC guidelines, we visited the websites of the international public health agencies such as CDC, ECDC, WHO, as well as the Australian Government Department of Health, the Bureau of Disease Prevention and Control of the National Health Commission of the People''s Republic of China, and Public Health England. doi = 10.1017/ice.2020.237 id = cord-339524-r0a6a1jw author = Islam, M. T. title = A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades date = 2020-10-13 keywords = October; SARS summary = title: A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2. 137 A set of 15 primers ( Table 1) was designed based on the ARMS for differentiating six major 138 clades of SARS-CoV-2: S, L, V, G, GH, and GR. Hence, the single-variant specific PCRs were able to identify the 228 SARS-CoV-2 positive sample containing GR-clade of the virus. This study proposes a simple and exclusive ARMS-based SNP-discriminating method using 257 conventional PCR to establish multiplex-assays in detecting SARS-CoV-2 mutation clades. doi = 10.1101/2020.10.08.20209692 id = cord-339352-c9uh8vjx author = Islam, Muhammad Torequl title = Environmental Integrants Affecting the Spreadability of SARS-CoV-12 date = 2020-07-28 keywords = SARS summary = The SARS-CoVs can survive in water and remain infectious for long periods (days to weeks), therefore, these may affect people and other animals if aerosols are generated (Casanova et al. It has been demonstrated that SARS-CoVs have low stability in the environment, very sensitive to oxidants (e.g., chlorine) and are inactivated significantly faster in water. However, SARS-CoV-2 has been found in the fecal samples and anal swabs of some patients, therefore, there is a possibility of fecal-oral (including waterborne) transmission of this virus (Rosa et al. Additionally, it is also necessary to study all the environmental components that affecting the survival, replication, spreadability or transmission and pathogenicity of SARS-CoV-2 in human and other animals. Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Selenium and RNA virus interactions: Potential implications for SARS-CoV-2 infection (COVID-19) TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes doi = 10.1007/s12560-020-09435-z id = cord-308370-9av7qw10 author = Islam, Rajib title = A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 date = 2020-05-12 keywords = PCA; QSAR; SARS summary = To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. The aim of this study is to explore and identify the binding affinities and interactions of these antiviral phytochemicals against the main protease of SARS-CoV-2 using computational and statistical tools. In this study, a-ketoamide-11r is considered as a control ligand because it is recently reported as a good inhibitor against main protease , which shows binding affinity of -7.8 kcal/mol. Among the studied 40 phytochemicals, hypericin, cyanidin 3-glucoside, baicalin, glabridin, and a-ketoamide-11r show the highest binding affinity and strong interactions with both or at least one of the catalytic residues (Cys145 and His41) of the main protease. doi = 10.1080/07391102.2020.1761883 id = cord-320490-3jmo35jc author = Ismail, Saba title = Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date = 2020-04-12 keywords = HLA; MEPVC; SARS; TLR3; energy; mol summary = In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . doi = 10.1101/2020.04.05.026005 id = cord-332374-cbiw6yvb author = Israeli, Ofir title = Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date = 2020-06-10 keywords = SARS summary = Very recently, two studies [6] [7] used a direct no-buffer RT-qPCR approach which identified > 90% of the tested clinical samples. In this study, we tested the diagnostic efficiency following thermal inactivation (65°C for 30min and 95°C for 10min) without addition of lysis buffers ("no buffer") or following lysis by three buffers (Virotype, QuickExtract and 2% Triton-X-100) and compared it to diagnosis after standard RNA extraction. Samples included buffers spiked with SARS-CoV-2, at concentrations 0.1-100,000 PFU/ml and 30 clinical samples, previously diagnosed as positive (20) and negative (10). The limit of detection was 1 PFU/ml: In this concentration samples in the no buffer mode and Virotype at 95°C were not detected, while the RNA extraction mode averaged the lowest critical threshold ( Ct=29.8) followed by QuickExtract and Triton. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step doi = 10.1101/2020.06.10.144196 id = cord-283749-j4600733 author = Itoyama, Satoru title = ACE1 polymorphism and progression of SARS date = 2004-10-22 keywords = SARS; case summary = Angiotensin converting enzyme (ACE1) insertion/deletion (I/D) polymorphism was previously reported to show association with the adult respiratory distress syndrome, which is also thought to play a key role in damaging the lung tissues in SARS cases. Despite the small sample size, the frequency of the D allele was significantly higher in the hypoxemic group than in the non-hypoxemic group (p =0.013), whereas there was no significant difference between the SARS cases and controls, irrespective of a contact history. Genotypic distribution and allele frequency of the ACE I/D polymorphism in SARS cases and controls with or without contact history to SARS patients were compared (Table 4 ). The ACE insertion/deletion polymorphism has also been reported to be a risk factor of the diseases mentioned above [17] and this might be associated with systemic angiopathy and influence progression of SARS in the lung. Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore doi = 10.1016/j.bbrc.2004.08.208 id = cord-345493-3bb1zuqp author = Itoyama, Satoru title = Identification of an alternative 5′‐untranslated exon and new polymorphisms of angiotensin‐converting enzyme 2 gene: Lack of association with SARS in the Vietnamese population date = 2005-06-03 keywords = ACE2; SARS; exon summary = We analyzed genetic variations of angiotensin‐converting enzyme 2 (ACE2), considering that it might influence patients'' susceptibility to severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) or development of SARS as a functional receptor. © 2005 Wiley‐Liss, Inc. We analyzed genetic variations of angiotensinconverting enzyme 2 (ACE2), considering that it might influence patients'' susceptibility to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) or development of SARS as a functional receptor. A case control study involving 44 SARS cases, 16 anti-SARS-CoV antibodypositive contacts, 87 antibody-negative contacts, and 50 non-contacts in Vietnam, failed to obtain any evidence that the ACE2 gene polymorphisms are involved in the disease process in the population. Using the PCR-based cloning procedure, we identified for the first time an alternative exon upstream of the original exon 1 of ACE2 that is expressed in various organs, including the lung and trachea, primary-cultured bronchial epithelial cells, and the small intestine. doi = 10.1002/ajmg.a.30779 id = cord-345092-1ztfcpsb author = Iwasaki, Masae title = Inflammation Triggered by SARS-CoV-2 and ACE2 Augment Drives Multiple Organ Failure of Severe COVID-19: Molecular Mechanisms and Implications date = 2020-10-08 keywords = ACE2; AT1R; Ang2; COVID-19; IL-6; SARS; cell; patient summary = Severe patients of COVID-19 often develop acute respiratory distress syndrome and multiple organ dysfunction/failure with high mortality that may be closely related to the hyper-proinflammatory status called the "cytokine storm." Massive cytokines including interleukin-6, nuclear factor kappa B (NFκB), and tumor necrosis factor alpha (TNFα) released from SARS-CoV-2-infected macrophages and monocytes lead inflammation-derived injurious cascades causing multi-organ injury/failure. ARB/ACE-I, angiotensin receptor blocker/ACE2 inhibitor; AT1aR, angiotensin receptor subtype 1a; C3, complement component 3; E-cadherin, epithelial cadherin; gp130, glycoprotein 130; IL, interleukin; JAK, Janus kinase; MAPK, mitogenactivated protein kinase; MCP-1, monocyte chemoattractant protein 1; mIL-6R, membrane interleukin 6 receptor; MMP9, matrix metallopeptidase 9; MyD88, myeloid differentiation primary response 88; NFκB, nuclear factor kappa-light-chain-enhancer of activated B cells; NFκB, nuclear factor kappa B; PI3K/Akt, phosphoinositide-3-kinase/protein Kinase B; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; sIL-6R, soluble interleukin 6 receptor; SOCS3, the suppressor of cytokine signaling-3; STAT3, signal transducers and activators of transcription; sTNFα, soluble tumor necrosis factor alpha; Tfh, follicular helper T cell; Th0, naive T cell; Th17, T helper 17 cell; TMPRSS2, transmembrane protease serine 2; TNFα, tumor necrosis factor alpha; TPO, thrombopoietin; VEGF, vascular endothelial growth factor. doi = 10.1007/s10753-020-01337-3 id = cord-275439-cdlcv1c9 author = Iwasaki, S. title = Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date = 2020-05-19 keywords = SARS summary = We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in nine COVID-19 patients. SARS-CoV-2 was detected in saliva in 8 of 9 (89%) patients and in all 11 samples taken within 2 weeks after disease onset. The diagnosis of COVID-19 is made by PCR testing of samples collected by nasopharyngeal or oropharyngeal swabs, with the nasopharyngeal route being the standard with a sensitivity for the virus in the range of 52-71% [1] [2] [3] [4] [5] . demonstrated the saliva to be more sensitive for SARS-CoV-2 detection patients than nasopharyngeal swabs 14 . We prospectively compared SARS-CoV-2 detection between nasopharyngeal samples and saliva samples in 9 patients with COVID-19. Our results were consistent to these data; the virus was detected in all the saliva samples taken within 2 weeks after symptom onset. Data are shown as mean ± SD (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.05.13.20100206 id = cord-025980-85jbwmfv author = Iwasaki, Sumio title = Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva date = 2020-06-04 keywords = SARS summary = We prospectively compared the efficacy of PCR detection of SARS-CoV-2 between paired nasopharyngeal and saliva samples in 76 patients including ten coronavirus disease 2019 (COVID-19) patients. Figure 1C shows To our knowledge, a few studies compared viral load between nasopharyngeal and saliva samples. The viral loads were 5-times higher in saliva than in nasopharyngeal samples in one study (5) , whereas they were lower in saliva in two studies (6, 8) . Our results showed that the viral load was equivalent at earlier time points but lower in saliva than in nasopharyngeal samples at convalescent phase. Saliva is more sensitive for SARS-CoV-2 detectionin COVID-19 patients than nasopharyngeal swabs. Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1016/j.jinf.2020.05.071 id = cord-010384-wyp7hrde author = Iwen, Peter C title = Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-04-10 keywords = SARS; specimen summary = The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. doi = 10.1093/labmed/lmaa018 id = cord-272450-8a3ir06y author = Iwen, Peter C title = Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-19 keywords = SARS; specimen summary = The purpose of this report is to provide a clear and concise understanding of laboratory biosafety practices necessary to prepare laboratorians to safely process clinical specimens from a patient that might contain this new pathogen. Although it is recognized that these laboratory sections do follow BSL-2 blood-borne pathogen standards, additional practices might be considered following a risk assessment to prevent exposures to aerosols and droplets when processing specimens that might contain SARS-CoV-2. With this classification, the interim guidance from the CDC suggests that the following practices may be performed in the standard BSL-2 laboratory when handling a specimen that might contain SARS-CoV-2: pathologic examination and processing of formalin-fixed or otherwise inactivated tissues, molecular analysis of extracted nucleic acid preparations, electron microscopic studies with glutaraldehyde-fixed grids, routine examination of bacterial and mycotic cultures, routine staining and microscopic analysis of fixed smears, final packaging of specimens for transport, and inactivation of specimens such as the placing of specimens in a nucleic acid extraction buffer. doi = 10.1093/ajcp/aqaa047 id = cord-312884-anlp8lab author = Iyer, Gayatri R. title = Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants date = 2020-09-04 keywords = ACE2; IFITM3; SARS; TMPRSS2; covid-19 summary = Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. The aim of the present study was to identify variants in these five selected candidate genes from the clinical exome data available with us for more than 100 individuals and make an attempt to classify them as relevant to the present COVID-19 aetiopathology, especially for the Indian population. The selected candidate gene variants were assessed in our internal cohort of 103 individuals, who had earlier provided consent, to perform a pilot study on the susceptibility and disease severity of Indians for COVID-19. Since host genetic polymorphisms have been demonstrated to be associated with vulnerability to human infection, in this study five candidate genes-ACE2, TMPRSS2, CD209, IFITM3, and MUC5B-were selected based on their relevance to the current pandemic. doi = 10.3389/fgene.2020.00861 id = cord-342538-5bwsm290 author = Izquierdo Lara, R. W. title = Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date = 2020-09-22 keywords = CoV-2; Netherlands; SARS; sample summary = Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina). doi = 10.1101/2020.09.21.20198838 id = cord-345139-gyvlikye author = Izquierdo-Domínguez, Adriana title = Pérdida del sentido del olfato durante la pandemia COVID-19 date = 2020-06-12 keywords = COVID-19; SARS summary = Mientras que la función olfatoria normal se define como normosmia, los trastornos cuantitativos se clasifican en pérdida parcial (hiposmia) o total (anosmia) del olfato 4 . Se habla de estudio cuantitativo al referirse a la cantidad de olor necesitado para ser detectado (umbral olfativo) y tiene por objeto el estudio de las variaciones olfativas en función de la concentración de la sustancia olorosa y de la cantidad de los olores detectados, dando un resultado de anosmia (pérdida total), hiposmia (pérdida parcial) o normosmia (olfato normal). Durante la pandemia COVID-19, se aconseja a aquellos pacientes con pérdida repentina y grave del sentido del olfato, iniciar medidas de distanciamiento social, aislamiento domiciliario preventivo y realizar pruebas de diagnóstico para el SARS-CoV-2 cuando sea posible. doi = 10.1016/j.medcli.2020.06.006 id = cord-347813-9vfwl7c0 author = Jackson, M. L. title = Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2 date = 2020-07-02 keywords = County; SARS; covid-19 summary = Interventions considered were (a) encouraging telecommuting; (b) reducing contacts to seniors and nursing home residents; (c) modest reductions to contacts outside of the home; (d) encouraging self-isolation of persons with COVID-19 symptoms; (e) rapid testing and household quarantining. This report presents findings from an agent-based model of SARS-CoV-2 transmission that can help guide decisions about mitigating the impact of COVID-19 during this re-opening. 6 The per-contact probability of transmitting SARS-CoV-2 in homes and in non-home settings was estimated by fitting simulated daily COVID-19 hospitalizations to hospitalizations in King County from 28 February -27 May 2020, in the presence of social distancing interventions as actually implemented in King County. Rather than estimating the impact of generic reductions in Reff, this report uses an agent-based model to estimate the impact of specific policies on SARS-CoV-2 transmission and COVID-19 hospitalizations. 15 used also agent-based models to explore the impact of combinations of social distancing measures on SARS-CoV-2 transmission. doi = 10.1101/2020.06.30.20143735 id = cord-312486-rumqopg0 author = Jacob, Chaim Oscar title = On the genetics and immunopathogenesis of COVID-19 date = 2020-09-10 keywords = ACE2; CoV-2; Kawasaki; SARS; cell; covid-19; patient; severe summary = The question is whether ACE2 expression levels are pertinent to SARS-CoV-2 infection only in the tissues relevant to viral entry and the lungs as its major target, [44, 45] or, given that COVID-19 in its severe form is a systemic disease with multi-organ disfunction [46, 47] , ACE2 expression levels may be important in multiple organs and tissues other than those of the respiratory system. However, the activation of multiple complement pathways, dysregulated neutrophil responses, endothelial injury, and hypercoagulability appear to be interlinked with SARS-CoV-2 infection and instead serve to drive the severity of the disease [91] . Regarding SLE, the prototypic systemic autoimmune disease, a group of investigators suggested that inherent epigenetic dysregulation causing hypomethylation and overexpression of ACE2, the functional receptor for SARS-CoV-2, might facilitate viral J o u r n a l P r e -p r o o f entry, viremia, and increased likelihood of cytokine storm in such patients [153] . doi = 10.1016/j.clim.2020.108591 id = cord-337105-jlmh79qv author = Jacob, Fadi title = Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date = 2020-09-21 keywords = CoV-2; SARS; cell; figure; infection summary = We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. QPCR analysis also showed higher levels of ACE2 and TMPRSS2 expression in CPOs at 50 DIV and 100 DIV than in hippocampal organoids ( Figure S2D ) Together, these results show that our CPOs exhibit a similar transcriptome as adult human choroid plexus tissue and express markers for choroid plexus epithelial cells and SARS-CoV-2 receptors, representing a suitable experimental model to study SARS-CoV-2 infection. Our finding that dysregulated gene expression varies widely among hepatocyte, intestinal, and choroid plexus organoids infected with SARS-CoV-2 suggests unique responses in different cell types and highlights the need for diverse human cellular model systems when studying the disease. doi = 10.1016/j.stem.2020.09.016 id = cord-317693-l08q2lhp author = Jacob, Michelle Cristine Medeiros title = Animal-based food systems are unsafe: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) fosters the debate on meat consumption date = 2020-07-07 keywords = SARS; bushmeat; food summary = CONCLUSION: To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases (5) . Uses of bushmeat vary from COMMENTARY SNAPSHOT SARS-CoV-2 fosters a debate on permanently banning wildlife consumption in an effort to prevent further public health threats related to foodborne zoonotic diseases. To ban the access to bushmeat without a rational analysis of all human meat production and consumption in the global animal-based food system will not help us to prevent future outbreaks. FNS, food and nutrition security; SARS, severe acute respiratory syndrome subsistence-based rural consumption and subsistencecommercial hunting to a luxury commodity in urban areas (18) . doi = 10.1017/s1368980020002657 id = cord-325460-4fhegc0z author = Jacobs, Werner title = Fatal lymphocytic cardiac damage in coronavirus disease 2019 (COVID‐19): autopsy reveals a ferroptosis signature date = 2020-09-22 keywords = E06; SARS; covid-19; figure summary = Immunohistochemical staining with E06, a monoclonal antibody binding to oxidized phosphatidylcholine (reflecting lipid peroxidation during ferroptosis), was positive in morphologically degenerating and necrotic cardiomyocytes adjacent to the infiltrate of lymphocytes, near arteries, in the epicardium and myocardium. We examined the patient''s myocardial tissue for markers of ferroptosis, an iron-catalysed form of regulated cell death that occurs through excessive peroxidation of polyunsaturated fatty acids and is also proposed to detrimentally contribute to some forms of ischaemia-reperfusion injury, stroke, and degenerative diseases. Renal tissue from the COVID-19 patient with myocarditis and multiple organ dysfunction syndrome showed morphological signs of acute tubular necrosis, intratubular oxalate crystals, as well as E06 positivity in proximal tubuli (A). By comparison, in the case of sudden death due to myocarditis of other aetiology, immunohistochemical staining with E06 (B) and anti-4-HNE antibody (D) in the renal tissue showed no presence of these ferroptosis markers (non-specific staining in the corticomedullary junction is also present on control stains). doi = 10.1002/ehf2.12958 id = cord-285362-7dc2gox0 author = Jacot, Damien title = Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses date = 2020-09-07 keywords = SARS summary = title: Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses We analyzed SARS-CoV-2 viral loads from 22''323 RT-PCR results according to samples types, gender, age, and health units. Quantitative reverse transcription polymerase chain reaction (RT-PCR) represents a 24 key diagnostic tool for patients with suspected SARS-CoV-2 infection. The report of RT-PCR SARS-CoV-2 viral loads raised also several 38 questions regarding the use of this information for the laboratory as an internal quality assessment 39 tool, as well as (i) to predict contagiousness of patients and hence to guide epidemiological 40 decisions, especially for hospitalized patients and (ii) to predict the patient prognosis and assess for the E-gene PCR was those described by Corman and colleague (4) . Clinical progression and 218 viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study SARS-CoV-2 Viral Load in Upper 224 Respiratory Specimens of Infected Patients doi = 10.1016/j.micinf.2020.08.004 id = cord-035274-hu8zshq8 author = Jadali, Zohreh title = Neurologic manifestations of COVID-19: what can we learn from other coronaviruses date = 2020-11-11 keywords = SARS summary = Like other coronaviruses, SARS-CoV-2 is neurotropic and may spread to the nervous system via similar mechanisms. Neurotropic and neuroinvasive properties of SARS-CoV-2 are supported by several observations including the presence of virus particles in the cerebrospinal fluid of patients with significant nervous system symptoms [3] . Currently, it is difficult to distinguish whether neurological complications of COVID-19 are a consequence of direct or indirect effects of viral infection. Another mechanism relies on blood circulation and angiotensin-converting enzyme 2 (ACE2) receptors that are expressed on glial cells, neurons, and capillary endothelium and are involved in virus entry [4] . Molecular mimicry that could be associated with the development of autoimmunity is another mechanism by which SARS-CoV-2 may trigger an immune response against nervous system-specific proteins [5] . Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ACE2: Angiotensin-converting enzyme 2 COVID-19 and SARS-Cov-2 infection: pathophysiology and clinical effects on the nervous system The author(s) read and approved the final manuscript. doi = 10.1186/s41983-020-00240-w id = cord-350821-0qfoc553 author = Jahromi, Reza title = Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date = 2020-06-01 keywords = COVID-19; SARS summary = title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 In this study, we present the effect of surfactants on coronavirus (SARS-CoV-2) virucidal efficiency in sanitizing fluids. Sodium dodecylbenzenesulfonate (SDBS), sodium laureth sulfate (SLS), and two commercial dish soap and liquid hand soap were studied with the goal of evaporation rate reduction in sanitizing liquids to maximize surface contact time. Twelve fluids with different recipes composed of ethanol, isopropanol, SDBS, SLS, glycerin, and water of standardized hardness (WSH) were tested for their evaporation time and virucidal efficiency. Twelve sanitizing fluids with different recipes, as shown in Table 1 , were prepared to examine the effect of individual components and mixtures on evaporation rate and SARS-CoV-2 virucidal efficiency of the solutions. Furthermore, the addition of 3% dish soap to the ethanol solution (S1) increased the evaporation time by about 63% from 24 to 39 s (of fluid S9), as shown in Figure 2 . doi = 10.1101/2020.05.29.124107 id = cord-146679-g7qioapl author = Jaimes, Javier A. title = Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses date = 2020-02-14 keywords = SARS summary = title: Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses To obtain an initial assessment of shared and/or specific features of the 2019-nCoV spike (S) envelope glycoprotein, a protein sequence alignment was performed to compare the sequence of the Wuhan-Hu-1 strain of the novel coronavirus with that of the closely related human SARS-CoV S strain Tor2 sequence ( Supplementary Fig. 1 ). The relatively high degree of sequence identity for the RBD is consistent with the view that 2019-nCoV, like SARS-CoV, may use ACE2 as its host cell receptor, The composition of residues found at the two known coronavirus S cleavage sites was performed using alignment data ( Fig. 2B and C). doi = nan id = cord-291991-on70zzn0 author = Jaimes, Javier A. title = Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site date = 2020-05-28 keywords = SARS summary = Here we provide context and clarify the role of the novel SARS-CoV-2 S1/S2 cleavage site in virus 90 emergence and infection, and perform a direct assessment of the proteases cleaving this site by use of 91 biochemical assays. To directly address the proteases cleaving the SARS-CoV-2 S1/S2 site, we used a biochemical peptide 95 cleavage assay (Jaimes et al., 2019), which was previously used to screen emerging influenza viruses 96 (Straus and Whittaker, 2017) . The comparative data with SARS-CoV S1/S2 site reveals that the acquisition of the 4 109 amino acid insert distinctively broadens the activating protease repertoire of the SARS-CoV-2 S1/S2 110 cleavage site to all major classes of proteolytic enzymes known to potentially activate coronavirus S 111 proteins. Activation of the SARS coronavirus spike 195 protein via sequential proteolytic cleavage at two distinct sites A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at 258 the S1/S2 cleavage site of the spike protein doi = 10.1016/j.isci.2020.101212 id = cord-339570-vf79fefg author = Jain, Vidhi title = Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists date = 2020-06-22 keywords = SARS summary = title: Implications of SARS CoV-2 positivity in amniotic membranes for ophthalmologists While the former highlighted the importance of human secretions like tears as a potential source of transmission of the virus, the latter explored the possibility of SARS-CoV-2 in amniotic membrane grafts. The amniotic membrane, while having great potential for healing ophthalmologic wounds, was recently shown to be RT-PCR positive for viral RNA in two critically ill pregnant females with COVID-19 [3] . While there is no confirmed data on the survival of SARS CoV-2 in cryopreserved amniotic membranes, it is clear that temperature strongly influences viral persistence (>2 weeks survival at 4°C vs only 2 days at 20°C) [5] . In light of these findings, we strongly suggest ophthalmologists to observe extreme caution while handling body fluids and placental membranes during the current COVID-19 pandemic. Amniotic membrane harvesting during COVID-19 pandemic Detection of SARS-COV-2 in placental and fetal membrane samples doi = 10.1038/s41433-020-1051-5 id = cord-303069-ss6g3jkg author = Jakhar, Renu title = An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date = 2020-05-26 keywords = MHC; SARS summary = A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. The aim of this study is to analyze envelope protein strains using in silico approaches looking for the conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine [22, 23, 24] . Envelope protein from the SARS-CoV-2 was analyzed using the IEDB MHC-1 binding prediction tool to predict the T cell epitope suggested interacting with different types of MHC Class I alleles. Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus doi = 10.1101/2020.05.26.115790 id = cord-269101-7altkx5u author = Jakhmola Mani, Ruchi title = Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study date = 2020-10-28 keywords = ACE2; COVID-19; Nigella; SARS summary = title: Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study An amazing herb, Nigella sativa, having antiviral, antihypertensive, antidiarrhoeal, analgesics, and anti-bacterial properties, needs to be explored for its efficacy against SARS-CoV-2, the causative agent of COVID-19. sativa bioactive constituents were similar to the pathways followed in SARS-COV-2 pathology, like renin-angiotensin system, kidney functions, regulation of blood circulation, blood vessel diameter, etc. To study the effectiveness of N.sativa against SARS-CoV-2, protein interactions studies were carried out for receptors predicted via swiss target prediction for this plant''s bioactive constituents, to understand their beneficial effect on SARS-CoV-2 in humans. sativa bioactive constituents by protein interaction and docking studies as well as proven their binding efficiency with ACE2 receptor and now this can be studied further in wet lab and be formulated as the medicine to combat the deadly disease COVID-19. doi = 10.1080/07391102.2020.1839560 id = cord-278721-g5zqebju author = Jakhmola, Shweta title = Comorbidity Assessment Is Essential During COVID-19 Treatment date = 2020-08-04 keywords = COVID-19; Netherlands; SARS summary = Our study revealed that deaths associated with cardiovascular diseases and diabetes are highly significant (p < 0.0001) compared to hospitalized in countries like Italy, France, and Spain unlike the Netherlands. Deaths from kidney diseases (Italyp < 0.0001; Swedenp < 0.0001; Netherlandsp = 0.0001; Francep = 0.0033) and neurological ailments (Francep = 0.0001; Netherlandsp < 0.0001) are significantly higher than the total hospitalized patients affected by the particular comorbidity. The information about numbers of hospitalized or deceased COVID-19 patients with associated comorbidities from individual countries was already provided in their respective reports. The death proportions due to Heart Diseases including, cardiovascular diseases and hypertension, were significantly higher (p < 0.0001) compared to the total hospitalized patients in Italy, Sweden, and Spain. Notably we found that heart diseases, including hypertension along with cardiovascular diseases, are the most frequent association with SARS-CoV2 infection in most countries (Italy, France, Spain, and Sweden) except the Netherlands. doi = 10.3389/fphys.2020.00984 id = cord-295041-5vpawtef author = Jakhmola, Shweta title = SARS-CoV-2, an Underestimated Pathogen of the Nervous System date = 2020-09-28 keywords = ACE-2; CNS; COVID-19; SARS; virus summary = Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. doi = 10.1007/s42399-020-00522-7 id = cord-276797-86hc3lbi author = Jamieson, Denise J. title = Emerging infectious disease outbreaks: Old lessons and new challenges for obstetrician-gynecologists date = 2006-06-30 keywords = Nile; SARS; States; United; West summary = Objective The purpose of this study was to summarize 3 recent high-profile infectious disease threats that have affected the United States: severe acute respiratory syndrome, West Nile virus, and anthrax. Results The 3 emerging infectious diseases pose very different threats: Severe acute respiratory syndrome is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. This systematic review summarizes 3 recent, highprofile infectious disease threats that have affected the United States: (1) SARS, (2) West Nile virus, and (3) anthrax. The 3 emerging infectious disease threats that are described in this systematic review pose very different and novel health threats: SARS is a newly identified pathogen that caused an international pandemic; the West Nile virus investigation involved an old pathogen that was identified in a new location; and the anthrax attacks involved the intentional introduction of a pathogen. doi = 10.1016/j.ajog.2005.06.062 id = cord-339726-eg0hajzl author = Jamrozik, Euzebiusz title = Coronavirus Human Infection Challenge Studies: Assessing Potential Benefits and Risks date = 2020-08-25 keywords = HCS; SARS; vaccine summary = Novel research designs, particularly where such studies might be controversial as in the case of SARS-CoV-2 HCS, require especially careful ethical evaluation including rigorous risk-benefit assessments as well as timely, thorough, public engagement ( WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020; Bambery et al. To be ethically acceptable, SARS-CoV-2 HCS would need to have multiple risk minimization strategies in place, including (i) selection of low risk participants (e.g., healthy young adults 1 ), (ii) careful strain selection and development, (iii) careful titration of viral dose, (iv) early diagnosis and availability of all necessary medical care, (v) long-term follow-up of participants, (vi) compensation for any lasting harms, and (vii) stringent infection control including measures to protect and screen research staff for infection (WHO Working Group for Guidance on Human Challenge Studies in COVID-19 2020). Tensions between public health and vaccine research priorities: A comparative modelling assessment of the risks and benefits of SARS-CoV-2 vaccine field trials versus human challenge studies doi = 10.1007/s11673-020-10030-x id = cord-284978-vh1x6pg9 author = Jang, Hongje title = Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date = 2013-02-18 keywords = HCV; SARS; figure summary = Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . doi = 10.1002/ange.201209222 id = cord-307556-k2lavvca author = Jang, Hongje title = Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide date = 2013-02-18 keywords = HCV; SARS summary = Herein, we developed a multiplexed helicase assay based on graphene oxide (GO) for high-throughput screening of inhibitors of HCV NS3 helicase and severe acute respiratory syndrome coronavirus (SARS CoV) helicase. [10] Herein, we show that the GOHA can be used for measuring the activities of HCV NS3 helicase and SARS CoV helicase in a single mixed solution using two distinct DNA substrates tethered to different fluorophores, and furthermore, for multiplexed high-throughput screening to discover highly selective small-molecule inhibitors of these helicases ( Figure 1 ). A 96-well plate mGOHA was used to screen a 10 000 compound library to discover inhibitors of SARS CoV helicase and HCV NS3 helicase (Figure 3) . [17] Two compounds, antiHCV-Hel-2 and -3, showed a dose-dependent decrease in the Luc/MTT values with the respective half-maximal effective concentrations (EC 50 ) of 188.1 AE 32.6 and 56.8 AE 7.4 mm, indicating that they dose-dependently blocked HCV RNA replication in the cultured Huh-7 cells (Figure 5 b,c) . doi = 10.1002/anie.201209222 id = cord-286014-cc99e24x author = Jang, T.-N title = Severe acute respiratory syndrome in Taiwan: analysis of epidemiological characteristics in 29 cases date = 2003-11-05 keywords = Kong; SARS; Taiwan summary = To describe the clinical characteristics and outcomes of patients with severe acute respiratory syndrome (SARS). The first probable SARS patient in Taiwan returned from China via Hong Kong early in the global outbreak in February 2003. 7 We analyse the clinical, laboratory, and radiological features of patients with probable SARS who were seen at the Shin Kong Wu Ho-Su Memorial Hospital (SKMH) in Taipei, Taiwan. 16 In our study, SARS-associated coronavirus RNA was detected in oropharyngeal swabs by RT-PCR in 16 (55.1%) of 29 patients at initial presentation. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome in Singapore: clinical features of index patient and initial contacts Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China doi = 10.1016/j.jinf.2003.09.004 id = cord-300138-1s87msv2 author = Jang, Youngeun title = Olfactory and taste disorder: The first and only sign in a patient with SARS-CoV-2 pneumonia date = 2020-04-20 keywords = SARS summary = 3 Recently, Giacomelli et al 4 reported that 20 of 59 (33.9%) of SARS-CoV-2-positive hospitalized patients had an olfactory or taste disorder. 4 SARS-CoV-2 can be transmitted in the asymptomatic or paucisymptomatic stages; therefore, olfactory and taste disorders can be significant signs for its early detection to control transmission. He had been self-quarantined for 14 days since March 12 due to close contact with a confirmed SARS-CoV-2-positive patient, who was his cohabitant. Although he had no clinical symptoms or signs of COVID-19 such as fever, myalgia, cough, and sore throat, on March 26 (the final day of his quarantine) he was confirmed positive based on a polymerase chain reaction (PCR) test (Rdrp gene, cycle threshold value of 30.28 on sputum and 33.47 on nasopharyngeal and oropharyngeal swab). This case of a SARS-CoV-2-positive patient with radiologically proven pneumonia on chest CT, who presented with only olfactory and taste disorders and no other clinical manifestations, suggests that previous cases with asymptomatic infections could have been misclassified. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study doi = 10.1017/ice.2020.151 id = cord-017354-cndb031c author = Janies, D. title = Large-Scale Phylogenetic Analysis of Emerging Infectious Diseases date = 2008 keywords = H5N1; SARS; influenza; phylogenetic; sequence; tree summary = doi = 10.1007/978-3-540-74331-6_2 id = cord-305931-0pgu2gvh author = Janus, Scott E title = COVID19: a case report of thrombus in transit date = 2020-06-17 keywords = CoV-2; SARS summary = In view of the fact that the utility of tissue plasminogen activator in this population is not well studied, we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. 4 Although the utility of tissue plasminogen activator (TPA) for thrombus in transit in other clinical settings has previously been reported, 5 the literature regarding cardiovascular events in SARS-CoV-2 remains scarce; we therefore describe the case of a 64-year-old male who presented with Learning points SARS-CoV-2 pneumonia, who was found to have extensive clot in transit on echocardiography and underwent successful lytic therapy. In view of the fact that the utility of TPA in this population is not well studied, 10 we present this case of rapid improvement in oxygenation after successful lytic therapy for thrombus in transit in this patient with SARS-CoV-2. doi = 10.1093/ehjcr/ytaa189 id = cord-349477-3qhpu7v0 author = Jarynowski, A. title = An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland date = 2020-10-15 keywords = Jarynowski; Kempa; Poland; SARS; covid-19; poviat summary = Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. Demographic (like age, mobility, migration etc.), social ("income","PiS_support") and COVID-related factors (population size,forest_density,population_density,arrival_SARS) are the ground for our proposal of proper sanitary staff allocation. The aim of this paper is an exploratory and preliminary quantitative evaluation of the geographical spread on the level of county/poviat (NUTS-4) of SARS-CoV-2 virus (and COVID-19 disease caused by it) in Poland during the Spring wave of infections. The main statistical approach is calculating multiple regressions with Akaike selection criteria on the SARS-CoV-2 arrival time to each poviat and the number of COVID-19 cases based on socio-economic variables. doi = 10.1101/2020.10.14.20090985 id = cord-338979-ew046wcr author = Jasti, Madhu title = A review of pathophysiology and neuropsychiatric manifestations of COVID-19 date = 2020-06-03 keywords = COVID-19; China; SARS summary = This novel coronavirus reportedly had symptoms resembling that of Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV) seen in the year 2003 [3] . A recently published study that looked at 214 cases of severe coronavirus illness treated in Wuhan during the early phase of the global pandemic reported that about 36% of patients displayed neurological symptoms [11] . There have been a fair number of reports suggesting SARS-CoV-2 infecting the neurons, raising questions about the direct effects of the virus on the brain that play a role in patients'' deaths. By contrast, there have been a few case reports which mention no penetrance of virus into the central nervous system as evidenced by the absence of SARS-CoV-2 in CSF and that the CNS effects are secondary to elevated inflammatory markers as CSF analyses during the acute stage showed pleocytosis with increased IL-8 and TNF-α concentrations [17] . doi = 10.1007/s00415-020-09950-w id = cord-351694-nb7230s1 author = Jatt, Lauren P. title = Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings date = 2020-06-16 keywords = SARS summary = title: Widespread severe acute respiratory coronavirus virus 2 (SARS-CoV-2) laboratory surveillance program to minimize asymptomatic transmission in high-risk inpatient and congregate living settings We describe a widespread laboratory surveillance program for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) at an integrated medical campus that includes a tertiary-care center, a skilled nursing facility, a rehabilitation treatment center, and temporary shelter units. As part of its coronavirus disease 2019 (COVID-19) response, VAGLAHS implemented a widespread laboratory surveillance program for SARS-CoV-2 in both hospital and residential facilities. Finally, on March 31, the laboratory at VALBHS initiated SARS-CoV-2 testing using the cobas system and began accepting specimens from other VA facilities, substantially increasing testing capacity and further decreasing turnaround time to a median of 1 day (IQR, 1-1). On April 3 and April 6, 57 residents who originally tested negative but lived in the same SNF unit as the SARS-CoV-2 positive individuals were retested, and 2 additional asymptomatic cases were identified. doi = 10.1017/ice.2020.301 id = cord-283352-0l1ggmhx author = Javelot, H title = Panic and pandemic: narrative review of the literature on the links and risks of panic disorder as a consequence of the SARS-CoV-2 pandemic date = 2020-08-10 keywords = COVID-19; SARS; disorder; panic summary = Abstract Although the ''panic'' word has been abundantly linked to the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic in the press, in the scientific literature very few studies have considered whether the current epidemic could predispose to the onset or the aggravation of panic attacks or panic disorder. The current SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic is likely to induce, beyond its potentially dramatic impact on health, serious psychological consequences, particularly in terms of the often reported "panic" state it triggered, and the medical disorder potentially linked to this state, i.e., panic disorder [1] [2] [3] [4] [5] . In this review, we propose to address : (i) the way in which the international literature has used to date the terminology of "panic" in relation to the SARS-CoV-2 pandemic, (ii) the very concept of panic attack, panic disorder and the specificity of the respiratory component frequently associated with it, (iii) and finally, a synthesis of the links and risk factors between COVID-19 and "respiratory" panic disorder. doi = 10.1016/j.encep.2020.08.001 id = cord-301943-qdtfjdxr author = Javelot, H title = Panique et pandémie: revue de la littérature sur les liens entre le trouble panique et l''épidémie à SARS-CoV-2 date = 2020-05-21 keywords = COVID-19; SARS; panique; trouble summary = Résumé L''état de panique associé à la pandémie liée au SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) incite à s''interroger sur les troubles anxieux que cette situation pourrait générer ou aggraver. D''éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d''hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l''infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. D''éventuelles situations co-morbides entre un tel trouble et la COVID-19 (coronavirus disease 2019) doivent inciter à certaines précautions en matière de prescriptions médicamenteuses, notamment en lien avec les traitements, ou situations, sources d''hypokaliémie : (i) le salbutamol, source potentielle de surconsommation, notamment chez les patients anxieux, (ii) l''infection par le SARS-CoV-2 et plus encore en cas de diarrhées et/ou vomissements. doi = 10.1016/j.encep.2020.05.010 id = cord-328209-uc37poce author = Javid, Babak title = Impact of population mask wearing on Covid-19 post lockdown date = 2020-04-16 keywords = SARS summary = Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high, the reduction on deaths was dramatic as the effective R approached 1, as might be expected after aggressive social-distancing measures such as wide-spread lockdowns. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. COVID-19 has a higher hospitalization and mortality rate than influenza 5 , and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high (Fig. 1a) , the reduction on deaths was dramatic as the effective R approached 1 (Fig. 1b) , as might be expected after aggressive socialdistancing measures such as wide-spread lockdowns 5 . doi = 10.1101/2020.04.13.20063529 id = cord-354900-bzv4yhqi author = Jawhara, Samir title = How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections date = 2020-10-12 keywords = COVID-19; SARS; glucan summary = During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. This short review focuses on the role of baker''s yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available. Of note, the SARS-CoV-2 particles first invade the respiratory mucosa and infect other cell types, causing a series of immune responses and the overproduction of cytokines ''cytokine storm'' , which may be related to the critical condition of COVID-19 patients [21] . doi = 10.1186/s13099-020-00385-2 id = cord-300399-21xozruq author = Jayamohan, Harikrishnan title = SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date = 2020-10-18 keywords = CRISPR; CoV-2; PCR; RNA; SARS; covid-19; sample summary = This review paper examines current molecular diagnostic tools (Fig. 1) , such as amplification-based (including CRISPR-Cas based), antibody and antigen tests, and sequencing, utilized for the detection of SARS-CoV-2. In addition, we also discuss sample preparation aspects that are relevant to wider utilization and point-of-care (POC) deployment of COVID-19 diagnostic tests (PCR, isothermal amplification, and sequencing-including library preparation). RT-PCR broadly involves four steps-lysis of SARS-CoV-2 in the sample, purification of the viral RNA, reverse transcription to complementary DNA (cDNA), and amplification of specific regions of the cDNA, and finally, optical detection of the amplified cDNA. The assay can detect the virus from respiratory swab samples with sensitivity comparable to that of the US Centers for Disease Control and Prevention (CDC) SARS-CoV-2 real-time RT-PCR assay in 30-40 min. Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples doi = 10.1007/s00216-020-02958-1 id = cord-263457-puf8gjir author = Jayarangaiah, Apoorva title = COVID-19-Associated Coagulopathy: An Exacerbated Immunothrombosis Response date = 2020-07-31 keywords = COVID-19; SARS; figure; platelet summary = Activated leukocytes potentiate a procoagulant state via release of intravascular tissue factor, platelet activation, NETosis, and inhibition of anticoagulant mechanisms. 4, 5 The predominant underlying mechanism in COVID-19-related mortality is hypothesized to be widespread tissue damage and endothelial injury from an overactivated immune system via exaggerated T-cell responses and increased cytokine secretion, leading to a cytokine storm. 70 In conclusion, a viral-mediated coagulant state culminates in the presence of endothelial injury and dysfunction and cytokine-driven inflammatory conditions, leading to activation of TF-mediated thrombosis. The current COVID-19 pandemic has resurrected the concept of immunothrombosis as it is a relevant model to demonstrate the potentiating effects of the immune system and the coagulation system and the detrimental effects associated with their unrestrained activation, as evidenced by microthrombi and overt venous and arterial thrombi (Figure 4 ). A procoagulant state in COVID-19 is the result of a direct viral-related endothelial injury, leukocyte-and cytokinemediated platelet activation, TF release, and NETosis augmented by an unchecked activation of the complement system. doi = 10.1177/1076029620943293 id = cord-253252-s8fm5rfa author = Jayaweera, Mahesh title = Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy date = 2020-06-13 keywords = SARS; aerosol; covid-19; droplet; figure; transmission summary = This review paper intends to outline the literature concerning the transmission of viral-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. There have been myriads of hypotheses corroborating that certain threshold levels of humidity, temperature, sunlight, and ventilation will speed up the virus-laden droplet and aerosol transmission, aggravating the spread of the SARS-CoV disease (Morawska, 2006) . Nevertheless, the effectiveness of the use of masks for the control of SARS-CoV-2-laden aerosol transmission from an infected person to a susceptible host is uncertain and not fully conceivable. Researchers have speculated that both droplets and aerosols generated from non-violent and violent expirations of SARS-CoV-2-infected people may be responsible for the nonnosocomial and nosocomial transmission of COVID-19 disease. doi = 10.1016/j.envres.2020.109819 id = cord-315453-mbv8vb2r author = Jean, Shio-Shin title = Old and re-purposed drugs for the treatment of COVID-19 date = 2020-06-01 keywords = SARS; covid-19; treatment summary = EXPERT OPINION: Although strong evidence of well-designed randomized controlled studies regarding COVID-19 therapy is presently lacking, remdesivir, teicoplanin, hydroxychloroquine (not in combination with azithromycin), and ivermectin might be effective antiviral drugs and are deemed promising candidates for controlling SARS-CoV-2. In future, clinical trials regarding a combination of potentially effective drugs against SARS-CoV-2 need to be conducted to establish the optimal regimen for the treatment of patients with moderate-to-severe COVID-19. Recently, US Food and Drug Administration (FDA) approved the phase 3, double-blind ODYSSEY study (ClinicalTrials.gov Identifier: NCT04326426, initiated on 12 April 2020) to investigate the efficacy and safety of tradipitant at a dosage of 85 mg orally twice daily for the treatment of inflammatory lung injury following critical COVID-19 infection [35] . Apart from remdesivir that was shown to have acceptable clinical efficacy against moderate-to-severe COVID-19 and acceptable side effects, the potential antiviral drugs that are likely useful in the treatment of patients with mild-to-moderate COVID-19 included hydroxychloroquine, teicoplanin, and ivermectin. doi = 10.1080/14787210.2020.1771181 id = cord-321867-7n88rl6p author = Jee, J. title = Oncologic Immunomodulatory Agents in Patients with Cancer and COVID-19 date = 2020-08-12 keywords = SARS; covid-19 summary = A recent retrospective study found a possible trend toward worse outcomes associated with corticosteroid use in cancer patients, although no analysis was performed to correct for possible selection bias in which sicker patients received those medications [11] . For all analyses we considered the number of patients who developed a primary composite endpoint of respiratory failure (use of nonrebreather, high-flow nasal oxygen, or mechanical ventilation) or death within 28 days of SARS-CoV-2 diagnosis. When patients were stratified by level of respiratory support, corticosteroid use was associated with worse outcomes in the pre-2L oxygen cohort (HR 2.3, 95% CI 1.1-4.9), a trend not observed in the post-2L oxygen (HR 0.9, 95% CI 0.4-1.9) and post-critical cohorts (HR 0.8, 95% CI 0.5-1.4), though these additional analyses were limited by All rights reserved. . https://doi.org/10.1101/2020.08.11.20145458 doi: medRxiv preprint from neutropenia 60 to 180 days prior to SARS-CoV-2 diagnosis did not have worse outcomes. doi = 10.1101/2020.08.11.20145458 id = cord-342340-q6j7vy8u author = Jefferies, Sarah title = COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study date = 2020-10-14 keywords = COVID-19; New; SARS; Zealand summary = METHODS: We did a descriptive epidemiological study of all laboratory-confirmed and probable cases of COVID-19 and all patients tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New Zealand from Feb 2 to May 13, 2020, after which time community transmission ceased. Demographic features and disease outcomes, transmission patterns (source of infection, outbreaks, household transmission), time-to-event intervals, and testing coverage were described over five phases of the response, capturing different levels of non-pharmaceutical interventions. This descriptive epidemiological study examined a cohort of all confirmed and probable COVID-19 cases and all people tested for SARS-CoV-2 infection in New Zealand up to May 13, 2020 , which marked the easing of the most restrictive non-pharmaceutical interventions, after which community transmission ceased. doi = 10.1016/s2468-2667(20)30225-5 id = cord-307242-e20gtx0z author = Jegouic, Sophie M. title = Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date = 2020-05-22 keywords = SARS; figure summary = Similar western blot analysis of total protein extracts following induction of logarithmic phase E.coli cultures with IPTG confirmed the expression of His-tagged S antigen of the predicted molecular weight in all cases ( Figure 3 , upper panel). Nevertheless, we found that S protein fragments prepared for gel electrophoresis using non-reducing loading buffer could be used successfully for epitope mapping of 2 S reactive monoclonal antibodies, 3G9, an unpublished mouse mAb generated to SARS S, and CR3022, a human mAb also isolated originally to SARS [19] but shown to cross-react with SARS-CoV-2. To provide an additional level of validation and to add epitope specificity to the data, 2 of the sera scoring positive by S1 ELISA were used as probes on western blots using full length S expressed in insect cells (cf. Optimization of the Production Process and Characterization of the Yeast-Expressed SARS-CoV Recombinant Receptor-Binding Domain ( RBD219-N1 ), a SARS Vaccine Candidate doi = 10.1101/2020.05.21.109298 id = cord-353200-5csewb1k author = Jehi, Lara title = Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date = 2020-08-11 keywords = COVID-19; SARS; model; patient summary = OBJECTIVE: To characterize a large cohort of patients hospitalized with COVID-19, their outcomes, develop and validate a statistical model that allows individualized prediction of future hospitalization risk for a patient newly diagnosed with COVID-19. DESIGN: Retrospective cohort study of patients with COVID-19 applying a least absolute shrinkage and selection operator (LASSO) logistic regression algorithm to retain the most predictive features for hospitalization risk, followed by validation in a temporally distinct patient cohort. MEASUREMENTS: Demographic, clinical, social influencers of health, exposure risk, medical co-morbidities, vaccination history, presenting symptoms, medications, and laboratory values were collected on all patients, and considered in our model development. Hospitalization risk prediction and outcomes in COVID-19 PLOS ONE | https://doi.org/10.1371/journal.pone.0237419 August 11, 2020 2 / 15 ethical restrictions by the Cleveland clinic regulatory bodies including the institutional review Board and legal counsel. We also develop and validate a statistical model that can assist with individualized prediction of hospitalization risk for a patient with COVID-19. doi = 10.1371/journal.pone.0237419 id = cord-321549-r7bmtloy author = Jendrny, Paula title = Scent dog identification of samples from COVID-19 patients – a pilot study date = 2020-07-23 keywords = SARS; dog; sample summary = METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. As dogs can be trained quickly, the aim of the present study was to test the concept of using dogs reliably and in real-time to discriminate between samples of SARS-CoV-2 infected patients and non-infected controls. The individuals were only tested for SARS-CoV-2 virus and therefore one cannot exclude that a former infection, especially with another human coronavirus like HCoV-OC43 resulted in false positive indications of the dogs and that cross detection occurred. Detection dogs were able to discriminate respiratory secretions of infected SARS-CoV-2 individuals from those of healthy controls with high rates of sensitivity and specificity. doi = 10.1186/s12879-020-05281-3 id = cord-270257-5f95gve3 author = Jeon, Sangeun title = Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date = 2020-03-28 keywords = SARS summary = Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. In near future, these already FDA-approved drugs could be further developed following clinical trials in order to provide additional therapeutic options for patients with COVID-19. We screened approximately 3,000 FDA-and IND-approved drug library against SARS-CoV to identify antiviral drug candidates (manuscript in preparation). Among the 48 drugs that were evaluated in our study, 24 drugs showed potential antiviral activities against SARS-CoV-2 with IC 50 values in Second, ciclesonide is another interesting drug candidate for further development although its antiviral potency was much lower (IC 50 = 4.33 µM) than niclosamide. Prior to our evaluation of 48 drugs against SARS-CoV-2 infection, we also tested antiviral activity of several other drugs based on the cytopathic effect of the virus in the presence of each drug ( Figure 2 ). doi = 10.1101/2020.03.20.999730 id = cord-346008-6v2gdz4a author = Jeong, Areum title = Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea date = 2020-06-02 keywords = COVID-19; SARS summary = title: Changes in the Clinical Practice of Ophthalmology during the Coronavirus Disease 2019 (COVID-19) Outbreak: an Experience from Daegu, Korea Due to close contact during examination, frequent exposure to tears and ocular discharge, and the inevitable sharing of equipment, ophthalmologists and patients are at a higher risk of SARS-CoV-2 infection. To prevent the transmission of COVID-19 in clinics, we follow steps based on three levels of control measures: administrative control, environmental control, and the use of personal protective equipment (PPE). If any of the aforementioned conditions are met, the patient is masked, isolated, and instructed to visit the COVID-19 screening center for reverse transcription polymerase chain reaction. Patients who have fever but negative test results postpone the appointment or attend the clinic. To reduce the exposure time, all patients should wear a mask in the waiting room. Characteristics of ocular findings of patients with coronavirus disease 2019 (COVID-19 doi = 10.3947/ic.2020.52.2.226 id = cord-276493-hoaxv5e0 author = Jeong, Gi Uk title = Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date = 2020-07-14 keywords = COVID-19; RBD; RNA; SARS summary = With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. doi = 10.3389/fmicb.2020.01723 id = cord-342776-hkjhqgie author = Jewett, Anahid title = The Potential Effect of Novel Coronavirus SARS-CoV-2 on NK Cells; A Perspective on Potential Therapeutic Interventions date = 2020-07-10 keywords = COVID-19; SARS summary = While studies on SARS-CoV-2 effects on immune cell function continue to progress, we know very little about the significance of depletion of key immune effectors by the virus in the mortality and morbidity of the disease. It also underscores the necessity for the future comprehensive studies of NK cells in SARS-CoV-2 infected individuals and animal models to better understand the role and significance of reported NK cell depletion and functional inactivation in disease morbidity and mortality, in hope to design effective therapeutic interventions for the disease. In particular, in the peripheral blood of patients that were infected with SARS, it was noted that there were significantly lower numbers of natural killer (NK) cells compared to healthy subjects (14) . As mentioned above the infectious agent of COVID-19 disease depletes NK cells in the peripheral blood, and potentially even in the lung tissues of patients, thereby, disabling and depleting the core immune effectors necessary to remove the virus and regulate uncontrolled immune activation. doi = 10.3389/fimmu.2020.01692 id = cord-026811-6bdzut3d author = Jha, Ashish K. title = Emerging Treatment and Prevention Strategies against COVID-19: A Brief Update date = 2020-05-16 keywords = COVID-19; HCQ; SARS summary = We have highlighted here the potential therapeutic role of remdesivir, chloroquine/ hydroxychloroquine (HCQ), lopinavir/ritonavir, and convalescent plasma in patients with SARS-CoV-2 infection. However, interpretation of the result of this study is limited by the lack of a randomized control group, small sample size, exclusion of serious cases (creatinine clearance <30 mL/min and >five-time elevation of serum aminotransferase), variable duration of remdesivir administration, noncollection of viral load data, adverse effects, and short-term follow-up. Early results obtained from more than 100 patients enrolled in studies conducted in the China showed the superiority of chloroquine compared with the controls in terms of reduction of exacerbation of pneumonia, duration of symptoms, and delay of viral clearance, all in the absence of severe side effects. A systematic review and exploratory meta-analysis from 32 studies of SARS coronavirus infection and severe influenza showed a statistically significant reduction in the pooled odds of mortality following treatment with convalescent plasma compared with placebo (odds ratio = 0.25; 95% confidence interval [CI]:0.14-0.45; I[2] = 0%). doi = 10.1055/s-0040-1712547 id = cord-341415-g781zhu6 author = Jhaveri, Kenar D. title = Thrombotic microangiopathy in a patient with COVID-19 date = 2020-06-07 keywords = SARS; patient summary = We describe a patient with coronavirus disease 2019 (COVID-19) and clinically significant kidney biopsy proven thrombotic microangiopathy(TMA). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was confirmed in the patient by reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay or serologic testing at our center. On day 20, the patient underwent a kidney biopsy that revealed severe acute thrombotic microangiopathy with cortical necrosis (Figure 1 ). While beta 2 glycoprotein-1 IgM levels were elevated, other laboratory and clinical features of anti-phospholipid antibody were absent( Table 2) . We report the first case of TMA associated with SARS-CoV-2 with presence of diffuse cortical necrosis and widespread microthrombi in the kidney biopsy. Physicians treating patients with COVID-19 should keep microangiopathic disease in the differential diagnosis when systemic findings of hemolysis are present along with thrombocytopenia and AKI. Coagulopathy and Antiphospholipid Antibodies in Patients with Covid-19 Acute Kidney injury in patients hospitalized with COVID doi = 10.1016/j.kint.2020.05.025 id = cord-305591-ir3wz6nr author = Ji, Danyang title = Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date = 2020-06-01 keywords = PQS; RNA; SARS summary = We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). We confirm Gquadruplex structure forming in the top-ranked PQSs by multiple spectroscopic assays in vitro and characterize the crosstalk between G-quadruplexes and viral helicase by microscale thermophoresis (MST) and molecular docking. Our analysis of Gquadruplex-forming sequences in SARS-CoV-2 provides insights into the design of anti-viral treatment by targeting the viral helicase and G-quadruplex structures. Interestingly, PQSs at positions 13385 and 24268 with the highest G-scores indicating high probability to adopt G-quadruplex structures only share high sequence similarity to the bat CoVs (see Supplementary Information S1 available online at https://academic.oup.com/bib and Table 2 ). In comparison, our G-quadruplex search across the genome of SARS-CoV-2 also identified a number of GG PQSs. PQS at position 13385 was confirmed to adopt G-quadruplex structures, which also contains a [GAAAG] sequence in the middle ( Table 1 ). doi = 10.1093/bib/bbaa114 id = cord-260772-n5q2yi7j author = Ji, Dong title = Reply to: ‘No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease’ date = 2020-05-06 keywords = SARS summary = title: Reply to: ''No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease'' Secondly, this is in keeping to our hypothesis that dysregulated hepatic innate immunity in patients with MAFLD contribute to the pathogenesis of COVID-19. 2 The liver is enriched with innate immune cells (such as macrophages, natural killer, natural killer T, and γδ T cells) 3 and due to its rich blood supply from the small bowel, circulation of the virus via the hepatic reticular system is expected. Hepatic innate immunity populations are potent cytokine producers and there are reports that obesity and NAFLD were associated with increased production of pro-inflammatory cytokines like TNF-α by adipose cells and Kupffer cells. No evidence for an increased liver uptake of SARS-CoV-2 in metabolic associated fatty liver disease of the link between the dysregulated hepatic innate immunity and COVID-19. doi = 10.1016/j.jhep.2020.04.039 id = cord-332458-2kwfcgz9 author = Ji, Henry title = Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus date = 2020-03-25 keywords = SARS summary = title: Novel decoy cellular vaccine strategy utilizing transgenic antigen-expressing cells as immune presenter and adjuvant in vaccine prototype against SARS-CoV-2 virus A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. A novel approach modifying cells to express viral markers to elicit protective immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these presented viral proteins can be recognized by the host immune system, thus, an efficient protective immune response might be elicited. doi = 10.1016/j.medidd.2020.100026 id = cord-349210-8t4a5qqo author = Ji, Ping title = Immunomodulatory Therapeutic Proteins in COVID‐19: Current Clinical Development and Clinical Pharmacology Considerations date = 2020-08-10 keywords = COVID-19; SARS; clinical; patient summary = Immunomodulatory biological therapies are being evaluated in clinical trials for the management of the systemic inflammatory response and pulmonary complications in patients with advanced stages of COVID‐19. A randomized, open-label, controlled trial for the efficacy and safety of adalimumab in patients with elevated TNF-α levels in the critical stages of severe COVID-19 is ongoing in Shanghai, China, with the main outcome of time to clinical improvement. A Phase 2 trial of the efficacy and safety of infliximab was initiated to evaluate whether early institution of TNF-α inhibitor therapy in patients with severe COVID-19 infections could prevent further clinical deterioration and reduce the need for advanced cardiorespiratory support and early mortality at a 5 mg/kg IV single dose. extrinsic factors ( Route of administration: As described before, the immunomodulatory therapeutic proteins currently in clinical trials for the treatment of COVID-19 mostly are directed towards patients with moderate and severe stages of the disease. doi = 10.1002/jcph.1729 id = cord-335538-thd5oaef author = Ji, Xiaoyang title = TWIRLS, a knowledge‐mining technology, suggests a possible mechanism for the pathological changes in the human host after coronavirus infection via ACE2 date = 2020-07-13 keywords = ACE2; SARS; twirl summary = First, TWIRLS can process and summarize the massive biomedical literature on coronaviruses, and then collect, classify, and analyze reported coronavirus studies to reveal host-related entities based on the distribution of specific genes in the text of the articles. We obtained text data (referred to as the local samples) from all related peer reviewed articles published by human researchers that contained the keyword "coronavirus" including the title, abstracts, and author and affiliation information (total 3,182,687 words). TWIRLS first calculates the specific co-distribution between CSHGs in local samples, then determines the distance between each pair of CSSEs and performs dichotomy clustering according to the linkage relationship between CSSEs and CSHGs. This step classified the 623 entities into 32 categories represented as C0-C31 (see category number in Table S1 , Sheet 1 second column). Interestingly, CSHGs in the 2 connections of ACE2 and DPP4 associated with category C5 were also enriched in category C3, inferring that the information summarized in category C3 probably describes the underlying mechanisms of the pathological changes after coronavirus infection. doi = 10.1002/ddr.21717 id = cord-275482-ncrhb75f author = Jia, Hong Peng title = Infection of Human Airway Epithelia by Sars Coronavirus is Associated with ACE2 Expression and Localization date = 2006 keywords = ACE2; SARS summary = In contrast with results in polarized epithelia, poorly differentiated primary human tracheobronchial epithelia or A549 cells grown on tissue culture plastic expressed little ACE2 mRNA or protein. (D) β-galactosidase levels determined in primary human airway epithelia cultured under ALI or resubmerged conditions that were infected from the apical with SARS-S protein pseudotyped FIV. These results indicated that SARS-CoV infects undifferentiated human airway epithelial cells poorly or not at all, while well-differentiated conduction airway epithelia are susceptible. Our studies revealed the novel observation that SARS-CoV infection of human airway epithelia is dependent upon the state of epithelial differentiation and ACE2 mRNA and protein expression. In conclusion, studies in models of human airway epithelial differentiation and polarity reveal that SARS-CoV infects well-differentiated cells from the apical surface and preferentially exits from the apical side. doi = 10.1007/978-0-387-33012-9_85 id = cord-024020-6opgzgcj author = Jia, Hongpeng title = Sustained research fund and dedicated research center for preparing next pandemic date = 2020-04-11 keywords = SARS; research summary = doi = 10.1093/pcmedi/pbaa012 id = cord-290066-umthoftd author = Jia, Xingwang title = False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 date = 2020-10-08 keywords = SARS summary = title: False Negative RT-PCR and False Positive Antibody Tests ——Concern and Solutions in the Diagnosis of COVID-19 We read with interest that antibody testing using a rapid immunochromatographic assay is reliable in the diagnosis of severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ) infection 1 . positive antibody results could be eliminated after five times dilution with normal human serum, when the RF level was lower than 10 IU/mL. The false positive antibody results could also be eliminated after 5 times dilution with normal human serum. Although the RT-PCR test has become the standard method for the diagnosis of SARS-CoV-2 infection, false-negative rates have been reported. Therefore, the combination of serum IgM/IgG antibody detection, the nucleic acid test, CT scan and clinical features improves the accuracy of COVID-19 diagnosis. Reliability and usefulness of a rapid IgM-IgG antibody test for the diagnosis of SARS-CoV-2 infection: A preliminary report doi = 10.1016/j.jinf.2020.10.007 id = cord-353777-t8q99tlq author = Jia, Yong title = Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date = 2020-04-11 keywords = CoV-2; SARS summary = The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020. The discrepant phylogenies for the spike protein and its 23 receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARSDespite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that 25 leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27 th January 2020 from 26 doi = 10.1101/2020.04.09.034942 id = cord-288010-i9zrojoo author = Jia, Yuanyuan title = Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China date = 2020-05-15 keywords = SARS summary = title: Characterization of eight novel full-length genomes of SARS-CoV-2 among imported COVID-19 cases from abroad in Yunnan, China 6 However, limited studies on full-length genome characterization of SARS-CoV-2 from COVID-19 cases imported from abroad. Here, we characterized the genotype and mutation characteristics of SARS-CoV-2 isolated from eight imported cases from abroad in Yunnan, China. To further characterize the characteristics of virus variation, the sequence analyses based on SARS-CoV-2 full-length nucleotide and amino acid sequences was performed using the strain Wuhan-Hu-1 (Genbank no. Moreover, three novel mutations, including D1962V in nsp3 from the strain YN_Im03, L1375F in nsp3 and A829T in S protein from the isolate YN_Im04 were first identified in this study according to the comparison with 11,231 genomic sequences available at GISAID on 4/26/2020. In summary, we characterized the full-length genomes of SARS-CoV-2 strains from eight COVID-19 cases imported from abroad in Yunnan, China. doi = 10.1016/j.jinf.2020.05.016 id = cord-303135-rx21ajiw author = Jian, Li title = Perspective: COVID-19, implications of nasal diseases and consequences for their management date = 2020-05-01 keywords = ACE2; SARS summary = This leads us to the question whether treatment in patients with allergic rhinitis, normally INCS, or in severe patients with CRSwNP, nowadays including biologics to suppress type 2 immune reactions, should be continued in case of a SARS-CoV-2 infection. SARS-CoV-2 may also infect patients with severe asthma and CRSwNP, who might be under treatment with a type 2 biologic drug such as dupilumab, omalizumab, or mepolizumab. However, we begin to recognize that diseases of the upper airways or their management by corticosteroids and biologics do not seem to increase the risk of infection nor the risk for severe COVID-19. In research perspective, because the airway passage of nose and nasopharynx is the main entry for respiratory viruses including the SARS-CoV 2, the expression and its regulation of the ACE2 receptor and the TMPRSS2 protease are key topics for research and targets for interventions. SARS-CoV-2 entry genes are most highly expressed in nasal goblet and ciliated cells within human airways doi = 10.1016/j.jaci.2020.04.030 id = cord-298216-iq7fenxm author = Jiang, Chao title = Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season date = 2020-05-13 keywords = SARS; influenza summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to sweep the world, causing infection of millions and death of hundreds of thousands. The respiratory disease that it caused, COVID-19 (stands for coronavirus disease in 2019), has similar clinical symptoms with other two CoV diseases, severe acute respiratory syndrome and Middle East respiratory syndrome (SARS and MERS), of which causative viruses are SARS-CoV and MERS-CoV, respectively. This is a discussion and comparison of the virus structures, transmission characteristics, clinical symptoms, diagnosis, pathological changes, treatment and prevention of the two kinds of viruses, CoVs and IAVs. It hopes to provide information for practitioners in the medical field during the epidemic season. In December 2019, a novel coronavirus, SARS-CoV-2, caused a pneumonia epidemic 44 in Wuhan, Hubei province of China. Lung pathology of severe 567 acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Molecular pathology analyses of two fatal 572 human infections of avian influenza A(H7N9) virus doi = 10.1016/j.micinf.2020.05.005 id = cord-340351-ee8wjp5u author = Jiang, Fa-Chun title = Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms date = 2020-09-17 keywords = SARS summary = We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. Approximately 3 hours after the 2 patients were identified as positive for SARS-CoV-2 RNA, we sampled the environmental surfaces of the 2 rooms in the centralized quarantine hotel in which they had stayed. One surface sample from the faucet in patient B''s room was positive for SARS-CoV-2 RNA; the C t was 28.75 for the ORF1ab gene. We also detected SARS-CoV-2 RNA in the surface swab samples of the pillow cover, duvet cover, and sheet. SARS-CoV-2 RNA has been detected on environmental surfaces in isolation rooms where the symptomatic or paucisymptomatic patients stayed for several days (3) (4) (5) . doi = 10.3201/eid2609.201435 id = cord-304839-lesa5u2n author = Jiang, Fang title = Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19) date = 2020-03-04 keywords = SARS; Wuhan summary = In late December 2019, a cluster of cases with 2019 Novel Coronavirus pneumonia (SARS-CoV-2) in Wuhan, China, aroused worldwide concern. On January 7, 2020, researchers rapidly isolated a novel coronavirus (SARS-CoV-2, also referred to as 2019-nCoV) from confirmed infected pneumonia patients. 3 We reviewed the published clinical features, symptoms, complications, and treatments of patients with COVID-19 to help health workers around the world combat the current outbreak. Keywords used were "COVID-19," "2019 novel coronavirus," "SARS-CoV-2," "2019-nCoV," "Wuhan coronavirus," and "Wuhan seafood market pneumonia virus." After careful screening, six published articles with confirmed cases were identified and included in this review. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan doi = 10.1007/s11606-020-05762-w id = cord-286217-3uklf2u2 author = Jiang, He-wei title = SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses date = 2020-07-14 keywords = Fig; SARS; Supplementary; protein summary = Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We detected the SARS-CoV-2-specific IgG and IgM proteins bound to the array using fluorescent-labeled anti-human antibodies, thereby generating a global assessment of each patient''s humoral antibody response. All of the samples and the controls were probed on the proteome microarray, and after data filtering and normalization, we constructed the IgG and IgM profile for each serum and performed clustering analysis to generate heatmaps (Figs. To statistically analyze the IgG responses against SARS-CoV-2 proteins, we calculated the p-values followed by multiple testing correction (or q-values), and applied significant analysis of microarray (SAM) to identify significant positive proteins (Supplementary Fig. 7 and Data 2). doi = 10.1038/s41467-020-17488-8 id = cord-285758-c18arb6s author = Jiang, Shibo title = SARS Vaccine Development date = 2005-07-17 keywords = RBD; SARS summary = The spike (S) protein of SARS-CoV is the major inducer of neutralizing antibodies, and the receptor-binding domain (RBD) in the S1 subunit of S protein contains multiple conformational neutralizing epitopes. (30) reported that mucosal immunization of African green monkeys with an attenuated parainfluenza virus expressing S protein resulted in production of neutralizing antibodies and protected animals from infection by challenge with SARS-CoV. These findings suggest that RBD contains the major neutralizing epitopes in the S protein and is an ideal SARS vaccine candidate because RBD contains the receptor-binding site, which is critical for virus attachment to the target cell for infection (15, (17) (18) (19) . Epitope mapping and biological function analysis of antibodies produced by immunization of mice with an inactivated Chinese isolate of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.3201/eid1107.050219 id = cord-290671-6p23qxb8 author = Jiang, Shibo title = An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies date = 2020-01-31 keywords = SARS summary = We have recently designed and engineered a pan-CoV fusion inhibitor, EK1 peptide, which could inhibit infection of five human coronaviruses, including SARS-CoV and MERS-CoV, and three bat-SL-CoVs [7] . Intranasal application of EK1 peptide before or after viral challenge, EK1 peptide can protect human DPP4-transgenic mice from MERS-CoV infection, suggesting its potential prophylactic and therapeutic effect against 2019-nCoV infection. The recently developed SARS-CoV and MERS-CoV neutralizing monoclonal antibodies (mAbs) and nanobodies with protective efficacy are specific to the S1 subunit of S protein, particularly the RBD [5, [8] [9] [10] . One of the rapid approaches is to evaluate the currently available SARS-CoV neutralizing antibodies with cross-neutralizing and protection activity against 2019-nCoV infection. The spike protein of SARS-CoV-a target for vaccine and therapeutic development A novel neutralizing monoclonal antibody targeting the N-terminal domain of the MERS-CoV spike protein doi = 10.1080/22221751.2020.1723441 id = cord-349070-bqv03u2e author = Jiang, Shih Sheng title = Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date = 2004-01-15 keywords = PCR; SARS summary = title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. doi = 10.1086/380841 id = cord-267458-uofy7jyx author = Jiang, Xiao-Lin title = Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China date = 2020-04-22 keywords = CoV-2; SARS summary = title: Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China We report a three-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Herein, we report a 3-family cluster study of eight patients associated with asymptomatic and pauciasymptomatic (one mild symptom only) SARS-CoV-2 transmission in Shandong Province, China. The first positive SARS-CoV-2 patients in this cluster were identified on January 21, 2020 triggering an epidemiological investigation by the local center for disease control and prevention. Our findings show that the transmission of SARS-CoV-2 by individuals with asymptomatic or paucisymptomatic infections is possible. Patient 5 (asymptomatic) was identified to be infected with SARS-CoV-2 after frequent contact with Patients 3 and 4 during work and home visits. In this study, we detected SARS-CoV-2 in two environmental swabs from the household of Patient 3. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period doi = 10.1093/infdis/jiaa206 id = cord-292972-p7ifetgw author = Jiang, Xuan title = Does SARS‐CoV‐2 has a longer incubation period than SARS and MERS? date = 2020-02-24 keywords = SARS summary = However, based on our analysis of a larger dataset available so far, we find there is no observable difference between the incubation time for SARS-CoV-2, severe acute respiratory syndrome coronavirus (SARS-CoV), and middle east respiratory syndrome coronavirus (MERS-CoV), highlighting the need for larger and well-annotated datasets. The symptom onset date of the first identified patient infected by SARS-CoV-2 was December 1st, 2019, which is about 14 days before the subsequent reported cases. 3 The first estimate of mean incubation time was based on the exposure information of 10 confirmed early SARS-CoV-2 infected cases in Wuhan, China and was predicted to be 5. The reported estimate of the SARS-CoV-2 incubation time was based on limited case data. For the MERS datasets, for example, we found only five reports published with accessible raw data, but one report had several patients with incubation times ranged from 0 to 21 days. doi = 10.1002/jmv.25708 id = cord-258255-hzmcrenk author = Jiang, Xuejun title = Asymptomatic SARS‐CoV‐2 infected case with viral detection positive in stool but negative in nasopharyngeal samples lasts for 42 days date = 2020-04-24 keywords = SARS summary = Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs([1]), but the presence of SARS‐CoV‐2 RNA in feces of COVID‐19 patients indicates the possibility of transmission via fecal‐oral route([2‐4]). Currently, the identification of this disease is mainly conducted by using nasopharyngeal swabs [1] , but the presence of SARS-CoV-2 RNA in feces of COVID-19 patients indicates the possibility of transmission via fecal-oral route [2] [3] [4] . Herein, we report the distinctive clinical characteristics of an asymptomatic case in which SARS-CoV-2 viral nucleotide detection was positive in anal swabs but negative in nasopharyngeal swabs for such a long period (42 days). This case will further provide the new information that, besides confirmed COVID-19 patients, the asymptomatic SARS-CoV-2 infected case can be persistently tested positive in the stool samples but negative in nasopharyngeal swabs for a long time. Detectable SARS-CoV-2 viral RNA in feces of three children during recovery period of COVID-19 pneumonia doi = 10.1002/jmv.25941 id = cord-328373-cubp1cc1 author = Jiang, Yanfang title = Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date = 2020-11-04 keywords = PCR; SARS summary = In the current study the use of a novel digital PCR assay to detect SARS-CoV-2 in both clinical patient-derived samples and environmentally derived samples was investigated, with the ultimate aim of reducing the rate of false negative results. Thirty-two patient samples including nasopharyngeal swabs, throat swabs, oropharyngeal swabs, phlegm, plasma/blood, and eye conjunctiva were collected at multiple timepoints during the disease course, and tested for the presence of SARS-CoV-2 via RT-PCR. SARS-CoV-2 nucleic acid sequences were detected in all clinical patient samples (respiratory tract samples including nasopharyngeal and oropharyngeal swabs). To prevent false-negative SARS-CoV-2 nucleic acid-based test results, and develop a new sensitive detection assay, we evaluated the performance of real-time RT-PCR and digital PCR for detecting SARS-CoV-2 nucleic acid in clinical patient-derived samples and environmentally derived samples. Strikingly, digital PCR detected SARS-CoV-2 nucleic acids in several samples that had previously tested negative via real-time RT-PCR, including 3 patient-derived samples and 5 environmentally derived samples. doi = 10.1016/j.cca.2020.10.032 id = cord-290218-dvyeg5fk author = Jiang, Yi title = RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date = 2020-09-04 keywords = RNA; SARS summary = Interestingly, the structure of complexed nsp12 is almost identical to nsp12 in apo RdRp, with an RMSD of 0.5 Å [17] , coinciding with the high processivity of the viral RNA polymerase, which does not need to consume extra energy for conformation changes in the active site during the replication cycle (Fig. 3B ). These "sliding poles" are stabilized by interactions formed between the positively charged residues at the extended N-terminal of nsp8 and bases in RNA backbones ( Fig. 3E ) and reported to account for the known processivity of the RdRp, which is required for replicating the long coronavirus genomes [39] . Although the sequence identity of nsp12 across the RNA viruses is low, the polymerase active site is structurally highly conserved, suggesting that RdRp inhibitors may serve as a potential J o u r n a l P r e -p r o o f broad-spectrum antiviral drug against RNA viruses. doi = 10.1016/j.bbrc.2020.08.116 id = cord-323737-6ajqy0ch author = Jiang, Yuanyuan title = Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus date = 2020-10-04 keywords = Hesperidin; RNA; SAM; SARS summary = title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify potential inhibitors targeting 2 0 -O-MTase of SARS-CoV-2. To identify inhibitors targeting nsp16, we first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs. Supplementary Table 1 lists the detailed genome and protein information that were employed in this study. As seen from MM-PBSA results and docking studies, drugs including Hesperidin, Osi-027, Rimegepant, Sonedenoson, and Gs-9667 had higher binding affinities than SAM with the 2 0 -O-MTase of SARS-CoV-2. doi = 10.1080/07391102.2020.1828172 id = cord-190207-en96o8zo author = Jim''enez-Avalos, Gabriel M. title = High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease date = 2020-08-30 keywords = SARS; SBS summary = title: High-Throughput Virtual Screening of 4487 flavonoids: New insights on the structural inhibition of SARS-CoV-2 Main Protease Here, a PAIN-filtered flavonoid database was screened against four sites of the protease: a free (normal) conformation of the Substrate Binding Site (NSBS), an induced-fit state of the SBS (ISBS), a Dimerization Site (DS) and a Cryptic Site (CS). In the case of SBS, the top 30 ligands with the lowest binding energies from NSBS and ISBS were contrasted and the ones present in both lists were selected as the final candidates. Each putative binding site had its respective solvent-accessible surface area (SASA) found in PyMol v.2.4 (44) , using as input the hydrogen-curated structure of M PRO obtained before. A previous study on SARS-CoV-1 3CL PRO reported two glycosylated flavonoids as inhibitors, whose sugar moieties interacted with the active sites''s S1 and S2 subsites through hydrogen bonds (31) . doi = nan id = cord-334884-ig6n9cet author = Jiménez-Alberto, Alicia title = Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors date = 2020-06-25 keywords = Mpro; SARS summary = The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. Taking this into consideration, we performed in silico evaluation of a set of approved drugs as potential inhibitors of Mpro from SARS-CoV-2; our findings show that several molecules warrant further analysis as treatment options against COVID-19. The SARS-CoV-2 Mpro structure and two of its main conformers, extracted from the molecular dynamics simulation trajectory file, were processed with AutoDockTools (Morris et al., 2009 ). Next, solvent-explicit molecular dynamics simulations were performed on Mpro; the resulting trajectory showed that the protein has a highly flexible active site as the amino acids surrounding the binding site had high RMSF (Root-Mean-Square Fluctuation) values. doi = 10.1016/j.compbiolchem.2020.107325 id = cord-316096-3fnwosst author = Jin, Huali title = Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice date = 2005-03-25 keywords = SARS; dna summary = After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. All DNA vaccine constructs, encoding the E protein, the M glycoprotein, and the N protein of SARS-CoV, were obtained as follows: these genes were amplified from the cDNA by PCR amplifications using each set of specific primers, respectively. In the present study, it was consistent with their work that the N protein construct could induce the highest SARS-specific IgG, T cell proliferation, and in vivo CTL response (lysis rate of 50.6%) compared with M protein gene (lysis rate of 17%) and E protein gene (lysis rate of 5.6%) (Fig. 4) . In summary, the administrations with all three SARS-CoV DNA vaccines in our study were able to induce high levels of the antigen-specific IgG antibody, the T cell proliferation, IFN-c, DTH, and in vivo CTL responses. doi = 10.1016/j.bbrc.2005.01.048 id = cord-334790-lav794w0 author = Jin, Huijuan title = Consensus for prevention and management of coronavirus disease 2019 (COVID-19) for neurologists date = 2020-04-01 keywords = COVID-19; SARS; patient summary = 1 Clinical symptoms of 2019-nCoV have mostly resembled that of severe acute respiratory syndrome coronavirus (SARS-CoV) of 2003. The nervous system manifestations were significantly more common in patients with severe infection, manifested as ischaemic stroke and cerebral haemorrhage diagnosed by clinical symptoms and head CT, impaired consciousness and skeletal muscle injury. Symptoms related to the development of acute cerebrovascular diseases Among patients with SARS-CoV-2 infection, middle-aged and elderly people accounted for the majority of strokes, especially in critically ill patients. According to the ''Technical guidelines for prevention and control of new coronavirus infection in medical institutions (First Edition)'' 16 developed by General Office of the National Health Commission of the People''s Republic of China and clinical characteristics of these patients, we propose the following precautions for neurologists, especially for those who are working in high-risk areas. doi = 10.1136/svn-2020-000382 id = cord-325234-skshcrh1 author = Jin, Tingxu title = SARS-CoV-2 presented in the air of an intensive care unit (ICU) date = 2020-08-15 keywords = CoV-2; SARS; patient summary = Therefore, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, it is necessary to 1) determine whether SARS-CoV-2 particles are present in the indoor air and 2) determine whether recovered patients are still shedding virus, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. To date, some studies have reported the presence of SARS-CoV-2 particles in the air in isolation rooms from hospitals treating COVID-19 patients (Yuanfang J,2020; Guo, Wang, Zhang, Li, & Chen,2020; Joshua L. Therefore, our study aims to 1) determine whether SARS-CoV-2 particles are present in the indoor air, with an objective to test the hypothesis of airborne transmission of SARS-CoV-2, and 2) determine whether recovered patients are still shedding SARS-CoV-2 particles, thus providing much-needed environmental evidence for the management of COVID-19 patients during the recovery period. Our findings revealed the presence of SARS-CoV-2 in the indoor air of the ICU and indicate that the virus may be shed via aerosol for days, even after a patient has tested negative. doi = 10.1016/j.scs.2020.102446 id = cord-286854-0s7oq0uv author = Jin, Xi title = Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site date = 2020-07-03 keywords = COVID-19; Furin; SARS; Wuhan; ZJ01 summary = title: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes. Sequence alignment analysis indicated 38 mutation sites for ZJ01 compared with other SARS-CoV-2 family members ( Figure 2(A) ). Further comparative alignment analysis of GZ02 (SARS viral strain), Wuhan-Hu-1 (the earliest sequenced SARS-CoV-2), RaTG13, HKU9-1 (the potential ancestor of SARS and SARS-CoV-2), HKU-1 and OC43 showed that the variation of FCS sequence had certain regularity in coronavirus evolution ( Figure 4(B) ). We speculated that, despite the gene similarity between ZJ01 and Wuhan-Hu-1, the mutation near the FCS changed the protein structure conformation and surface electrostatic potential of ZJ01, which further influenced its binding capacity with Furin. doi = 10.1080/22221751.2020.1781551 id = cord-341804-rnj3wtg4 author = Jin, Zhe title = Drug treatment of coronavirus disease 2019 (COVID-19) in China. date = 2020-06-27 keywords = COVID-19; RNA; SARS summary = This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. However, more evidence is needed either for 4 supporting or opposing the systemic therapeutic administration of glucocorticoids in 5 patients with SARS-CoV-2 infection (Qin et al., 2020 a variety of immune cells 20 and improves the immunity, while IFN-β takes effect by inhibiting the adsorption of certain 1 viruses, enhancing phagocytosis of natural killer cells and mononuclear macrophages Tocilizumab is a recombinant humanized anti-IL-6 receptor (IL-6R) monoclonal antibody, 21 13 which can specifically bind to soluble and membrane-bound IL-6 receptors and inhibit 1 signal transduction mediated by IL-6, thereby reducing inflammation and blocking cytokine 2 storm caused by COVID-19 (Scheinecker et al., 2009) . doi = 10.1016/j.ejphar.2020.173326 id = cord-334976-53cd16w5 author = Jo, Seri title = Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro date = 2020-08-04 keywords = CoV-2; SARS; flavonoid summary = An in silico docking study showed that the binding modes of herbacetin and pectolinarin are similar to those obtained from the catalytic domain of SARS-CoV 3CLpro. Baicalin showed an effective inhibitory activity against SARS-CoV-2 3CLpro and its docking mode is different from those of herbacetin and pectolinarin. The proteolytic assay using SARS-CoV-2 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The compound showed the severely reduced fluorescent intensity and thus represented their SARS-CoV-2 3CLpro inhibitory activity. Among them, baicalin, herbacetin and pectolinarin revealed the prominent inhibitory activity against SARS-CoV-2 3CLpro. The binding modes of herbacetin and pectolinarin were similar to those obtained from the docking study of the catalytic domain of SARS-CoV 3CLpro 21 . In the previous results of SARS-CoV 3CLpro 21 , only the three effect flavonoids (herbacetin, pectolinarin, and rhoifolin) were mentioned. doi = 10.1080/14756366.2020.1801672 id = cord-348899-vynk8q8c author = Jo, Seri title = Inhibition of SARS-CoV 3CL protease by flavonoids date = 2019-11-14 keywords = CoV; SARS; Triton; flavonoid summary = A synthetic peptide labelled with an Edans-Dabcyl FRET (Fluorescence resonance energy transfer) pair 12 was used to search SARS-CoV 3CLpro inhibitory compounds against a flavonoid library. The proteolytic assay using the SARS-CoV 3CLpro in the presence of Triton X-100 has been performed to differentiate the artificial inhibitory activity of chemicals through non-specific binding with proteases by forming aggregate or complexation. The three compounds showed the severely reduced fluorescent intensity and thus represented their SARS-CoV 3CLpro inhibitory activity. The interactions between SARS-CoV 3CLpro and three inhibitory flavonoids were analysed to predict their binding affinities. We have created a library of flavonoids to systematically investigate SARS-CoV 3CLpro inhibitory compound by a FRET method. Herbacetin, rhoifolin and pectolinarin were the best inhibitory compounds against SARS-CoV 3CLpro in the flavonoid library. In order to predict the flavonoid scaffolds needed to interact with the catalytic site of SARS-CoV 3CLpro, an induced-fit docking study was performed and analysed. doi = 10.1080/14756366.2019.1690480 id = cord-310631-ru5f69qg author = Joachim, Denner title = SARS-CoV-2 and enhancing antibodies date = 2020-05-07 keywords = SARS summary = In contrast, other CoV infections including the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS) and the recent COVID-19 are characterised by a higher pathogenicity in certain human populations and may be lethal. In persons infected by SARS-CoV enhancing antibodies and neutralising antibodies may partly counteract each other''s function. In the case, cross-reactive enhancing antibodies exist, the infection with the new SARS-CoV-2 may be enhanced by these pre-existing antibodies against common CoV. Common CoV circulate every year in the human population [1] and it sounds logical that the amount of anti-CoV antibodies including potentially enhancing antibodies is higher in older persons. The assumption of ADE with pre-existing enhancing antibodies against common CoV may also explain why in some regions the infection rate with SARS-CoV-2 and its pathogenicity is higher compared with other regions. The possible existence of enhancing antibodies is also of importance for the development of a vaccine against SARS-CoV-2. doi = 10.1016/j.jcv.2020.104424 id = cord-262184-uxyb4vih author = Jockusch, Steffen title = A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses that Cause SARS and COVID-19 date = 2020-06-18 keywords = Fig; SARS summary = We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. Using the criteria above, our study examines 11 nucleotide analogues with sugar or base modifications (structures shown in Fig. 1 ) for their ability to inhibit the SARS-CoV-2 or SARS-CoV RdRps: Ganciclovir 5''-triphosphate, Carbovir 5''-triphosphate, Cidofovir diphosphate, Stavudine 5''-triphosphate, Entecavir 5''-triphosphate, 2''-O-methyluridine-5''-triphosphate (2''-OMe-UTP), 3''-O-methyluridine-5''triphosphate (3''-OMe-UTP), 2''-fluoro-2''-deoxyuridine-5''-triphosphate (2''-F-dUTP), desthiobiotin-16aminoallyl-uridine-5''-triphosphate (Desthiobiotin-16-UTP), biotin-16-aminoallyl-2''-deoxyuridine-5''triphosphate (Biotin-16-dUTP) and 2''-amino-2''-deoxyuridine-5''-triphosphate (2''-NH 2 -dUTP). We then performed polymerase extension assays with the library of nucleoside triphosphate analogues (Fig. 1) either alone or in combination with natural nucleotides: 2''-OMe-UTP, 3''-OMe-UTP, 2''-F-dUTP, 2''-NH 2 -dUTP, Biotin-UTP, desthiobiotin-16-UTP, Sta-TP, Cid-DP + UTP + ATP, Car-TP + UTP + ATP + CTP, Gan-TP + UTP + ATP + CTP, or Ent-TP + UTP + ATP + CTP, following the addition of a pre-annealed RNA template and primer to a pre-assembled mixture of the SARS-CoV and/or SARS-CoV-2 RdRp (nsp12) and the two cofactor proteins (nsp7 and nsp8). doi = 10.1016/j.antiviral.2020.104857 id = cord-350211-vuxs5wtt author = Johanna, Barón‐Sánchez title = Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date = 2020-07-28 keywords = PCR; SARS; los summary = Sin embargo, algunos autores sugieren que el virus puede infectar el sistema nervioso central (SNC), 17 donde el nivel de expresión de ECA2 es muy bajo, [18] [19] [20] [21] así, aunque la etiopatogenia de la anosmia por el virus SARS-CoV-2 no está todavía clara, esta podría estar medida por una infección directa la mucosa olfatoria, provocando destrucción de las neuronas sensoriales olfativas, por lo que la recuperación sería mas lenta y habría mayor probabilidad de que la perdida olfatoria permaneciera por mas tiempo, pudiendo incluso quedar un déficit permanente residual, 15 o por una afectación directa del lóbulo frontal como se ha reportado recientemente. doi = 10.1016/j.nrl.2020.07.006 id = cord-265529-0n9xxa9h author = John Hann, Angus title = Controversies regarding shielding and susceptibility to COVID‐19 disease in liver transplant recipients in the United Kingdom date = 2020-06-17 keywords = SARS summary = The objective of this case series is to report on SARS-CoV-2 infection in liver transplant recipients and discuss the role of immunosuppression, comorbidities and shielding. In the UK, transplant recipients were classified as individuals vulnerable to SARS-CoV-2 infection due to immunosuppression. A report from a high incidence area of northern Italy did not see fatalities in SARS-CoV-2-infected liver transplant patients, unless they were elderly and comorbid. 6 Therefore, these authors suggest that immunosuppression alone is not a risk factor for development of severe SARS-CoV-2 disease. We highlight three contrasting cases of SARS-CoV-2 infection in liver transplant recipients from the early stages of the pandemic in the UK (Table 1) . We suggest that liver transplant recipients are at high risk for severe SARS-CoV-2 infection and should continue to undergo strict isolation until the pandemic has passed, or robust evidence proves a lack of risk. doi = 10.1111/tid.13352 id = cord-305534-936peb1n author = Johnson, Kemmian D. title = Pulmonary and Extra-Pulmonary Clinical Manifestations of COVID-19 date = 2020-08-13 keywords = COVID-19; MERS; SARS; patient summary = The severe acute respiratory syndrome coronavirus−2 (SARS-CoV-2) has been recently identified as the culprit of the highly infectious, outbreak named coronavirus disease 2019 (COVID-19) in China. While it is known that COVID-19 manifests similarly to the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2012 Middle East Respiratory Syndrome (MERS), primarily affecting the pulmonary system, the impact of the disease extends far beyond the respiratory system and affects other organs of the body. In the severe disease state, the patient''s clinical course is complicated by the development of pneumonia with ARDS, acute hypoxic respiratory failure, and/or death (7) . Several retrospective studies have consistently reported pulmonary manifestations in patients with COVID-19, which include cough, shortness of breath, sputum production, respiratory failure, and ARDS (Table 1) (5, 7, (9) (10) (11) (12) (13) (14) (15) (16) (17) . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.3389/fmed.2020.00526 id = cord-309728-7vfotgrr author = Johnson, Kristen M. title = Managing COVID‐19 in Renal Transplant Recipients: A Review of Recent Literature and Case Supporting Corticosteroid‐sparing Immunosuppression date = 2020-05-26 keywords = COVID-19; SARS; patient summary = PHARMACOTHERAPY Volume **, Number **, 2020 We present the case and outcomes of a renal transplant recipient with SAR-CoV-2 treated in our hospital whose immunosuppressive therapy was managed with only a modest reduction in calcineurin inhibitor target trough concentration and antiproliferative dose reduction. We have described the case of a renal transplant recipient who was successfully treated for COVID-19 with supportive care along with steroid-sparing immunosuppression regimen changes that included dose-reduced antiproliferative therapy and a modest decrease in tacrolimus target trough level. [22] [23] [24] Finally, currently published cases of SARS-CoV-2 in renal transplant recipients have demonstrated variable results in progression of respiratory disease and survival when substituting higher doses of corticosteroids for complete cessation of maintenance calcineurin inhibitor and antiproliferative therapy. 8, 11 Conclusion It is difficult to compare and draw conclusions regarding optimal immunosuppressant management in renal transplant recipients treated for SARS-CoV-2 from the limited data presented in currently published cases along with significant confounding variables. doi = 10.1002/phar.2410 id = cord-292578-co5essuw author = Johnson, Marina title = Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2 date = 2020-08-02 keywords = RBD; SARS summary = OBJECTIVES: The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS: A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). CONCLUSION: Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality. In summary, the MSD multiplexed coronavirus panel assay evaluated in this study is highly reproducible, specific and sensitive for the detection of anti-SARS-CoV-2 antibody over 14 days since the onset of COVID-19 symptoms. doi = 10.1016/j.jcv.2020.104572 id = cord-301622-mn59vszt author = Jomah, Shahamah title = Clinical efficacy of antivirals against novel coronavirus (COVID-19): A review date = 2020-08-03 keywords = LPV; RTN; SARS; covid-19 summary = However, several agents are included in Infectious Diseases Society of America (IDSA) Management Guidelines for treatment of COVID-19 patients; including antimalaria (chloroquine, hydroxychloroquine), antivirals (lopinavir/ritonavir), antibacterial (azithromycin, and immunomodulators (Tocilizumab) based on their beneficial role reported by practicing physicians or small scale clinical trials. Additional keywords such as treatment", "antiviral", "protease inhibitors", "lopinavir ritonavir", "ribavirin", Remdesivir", "arbidol",Östalmovir", "Favipiravir", human studies, randomized controlled trials (RCT), prospective or retrospective cohort designs, case-control designs, case series and case report, with COVID-19 produced more than 300 trails. A randomized control trial including 199 severe COVID-19 patients revealed that lopinavir group had significantly shorter time for clinical improvement compared to standard therapy. Prospective, randomized, controlled, open-label multicenter trial [27] • 236 moderate/severe confirmed COVID-19 cases randomized; 116 to receive Favipiravir for 10 days and 120 to receive Umifenovir (Arbidol) for 10 days and all patients received conventional therapy. doi = 10.1016/j.jiph.2020.07.013 id = cord-336837-rerp1g1w author = Jones, Nick K title = Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 date = 2020-06-19 keywords = Methodology; SARS; hcw summary = These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent ''hubs'' of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely. Testing for SARS-CoV-2 RNA was performed with real-time RT-PCR using throat and nose swab samples of HCWs from Cambridge University Hospitals NHS Foundation Trust (CUHNFT) and their symptomatic household contacts. In the HCW symptomatic and HCW symptomatic household contact screening arms combined (reflecting all individuals with self-reported symptoms at the time of testing), 13/771 (1.7%) tests were positive, which was significantly lower than 30/221 (13%) in the original study period (Fisher''s exact test p<0.0001). In particular, during the last 2 weeks of the study period (11th to 24th May 2020), we identified only four positive SARS-CoV-2 samples from 2016 tests performed, two from the HCW asymptomatic and two from the HCW symptomatic/symptomatic household contact arms. doi = 10.7554/elife.59391 id = cord-293938-40zyv1h8 author = Jonsdottir, Hulda R. title = Coronaviruses and the human airway: a universal system for virus-host interaction studies date = 2016-02-06 keywords = East; MERS; SARS; human summary = The emergence of both Severe Acute Respiratory Syndrome and Middle East Respiratory syndrome CoVs as well as the yearly circulation of four common CoVs highlights the importance of elucidating the different mechanisms employed by these viruses to evade the host immune response, determine their tropism and identify antiviral compounds. Tracheobronchial HAE cultures recapitulate the primary entry point of human respiratory viruses while the alveolar model allows for elucidation of mechanisms involved in viral infection and pathogenesis in the alveoli. Given the documented history of coronaviruses overcoming the species barrier and causing severe disease in humans, it is important to investigate the zoonotic potential of close evolutionary relatives of common HCoVs in a culture model that recapitulates the aspects of the human airway, e.g. morphology and receptor distribution. The establishment of transgenic animal models for human disease is attainable when either the virus receptor has been identified, which is not the case for all HCoVs, or when viruses can be adapted to a different host. doi = 10.1186/s12985-016-0479-5 id = cord-324165-afdmsbw2 author = Joo, Heesoo title = The effects of past SARS experience and proximity on declines in numbers of travelers to the Republic of Korea during the 2015 MERS outbreak: A retrospective study date = 2019-08-31 keywords = MERS; SARS summary = The results from regression models and sensitivity analyses demonstrated that areas with ≥100 SARS cases and closer proximity to the ROK had significantly larger percentage decreases in traveler volumes during the outbreak. This evaluation estimates the changes in numbers of non-citizen short-term visitor arrivals from selected areas to the ROK during the 2015 MERS outbreak and examines the correlation between travel volume declines and previous experience of the most similar sizable outbreak, the 2003 severe acute respiratory syndrome (SARS) outbreak. Although WHO did not recommend any travel restrictions to the ROK during the 2015 MERS outbreak [17] , WHO noted that raising awareness about Table 4 Monthly marginal percentage change between actual (2015) and baseline projected (average of 2013 and 2014) non-citizen arrivals to the Republic of Korea (ROK) associated with areas that experienced ≥100 probable severe acute respiratory syndrome (SARS) cases and distance to the Republic of Korea. doi = 10.1016/j.tmaid.2019.05.009 id = cord-346787-uo8k6qic author = Jorgensen, Sarah CJ title = Remdesivir: Review of pharmacology, pre‐clinical data and emerging clinical experience for COVID‐19 date = 2020-05-23 keywords = COVID-19; MERS; SARS; remdesivir summary = 3 The remdesivir dosing regimen being evaluated in clinical trials (200 mg IV on day 1, then 100 mg IV on days 2 through 5 or 10) was substantiated by in vitro data and bridging the PK with the rhesus monkey experience to humans. Prophylactic and therapeutic remdesivir treatment significantly reduced MERS-CoV-induced clinical signs, viral titers in respiratory specimens and the severity of lung lesions compared to control animals. 14 In the SARS-CoV-2 study, remdesivir was again initiated shortly before viral titers are expected to peak at 12 hours post-inoculation and a dosing regimen equivalent to the regimen being tested in human COVID-19 clinical trials was used (10 mg/kg load ~ 200 mg in humans, then 5 mg/kg daily ~ 100mg daily in humans x 6 days). In a summary of safety data reported by the FDA from the a remdesivir clinical trial comparing 5 and 10day treatment courses in patients with COVID-19, Grade 3 and 4 ALT and/or AST elevations occurred in 7% patients. doi = 10.1002/phar.2429 id = cord-329904-e05ywn5e author = Jose, Merin title = Fatal Superimposed Bacterial Sepsis in a Healthy Coronavirus (COVID-19) Patient date = 2020-05-29 keywords = SARS; infection summary = We present a case of a healthy COVID positive individual, with no underlying comorbidities, who rapidly deteriorated overnight on readmission to the hospital after initial discharge and succumbed to this disease due to a superimposed bacterial infection with COVID pneumonia. This case report highlights the importance of educating COVID-19 positive patients about the precautions, as well as signs and symptoms of a superimposed bacterial infection, when their plan of care is in a home setting. It also emphasizes the potential role of checking procalcitonin levels as a part of routine laboratory investigation at initial presentation in all suspected as well as confirmed COVID-19 cases to rule out an on-going bacterial infection that can prove fatal in the course of the disease. Our emphasis from this case report is to highlight the risk of superimposed bacterial infection in COVID-19 patients. doi = 10.7759/cureus.8350 id = cord-344647-jr85915d author = Joseph, Adrien title = Acute kidney injury in patients with SARS-CoV-2 infection date = 2020-09-03 keywords = AKI; COVID-19; SARS summary = Acute Kidney Injury (AKI) is a frequent complication of severe SARS-CoV-2 infection but data are scarce in ICUs. AKI has been previously reported with an average incidence of 11% (8-17%) overall, with highest ranges in the critically ill (23%; 14-35%) [2] [3] [4] . Different applications of the Kidney Disease Improving Global Outcomes (KDIGO) criteria for AKI, in particular different methods to estimate missing baseline creatinine and handling urinary output, can cause important variations of estimated incidence [5, 6] and may contribute to the discrepancies among these studies. High levels of IL-6 have been associated with the development of severe disease [24, 25] and acute respiratory distress syndrome [8] during COVID-19 infection, but the role of inflammation markers in COVID-19-induced-AKI remains speculative [7] . Our study suggests a tremendously high incidence of AKI in our cohort of critically ill COVID-19 patients, along with an independent association between AKI and outcome. doi = 10.1186/s13613-020-00734-z id = cord-271944-oxtus5vb author = Joseph, Rudman title = Seizure And COVID-19: Association and Review of Potential Mechanism date = 2020-10-13 keywords = COVID-19; SARS; patient summary = Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, this highly transmissible virus has since spread rapidly around the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a novel coronavirus that causes Coronavirus Disease of 2019 (COVID19) , a disease that can present with a variety of symptoms [1] . The most common symptoms at the onset of COVID-19 illness are fever, cough, and fatigue; in severe cases, patients may develop severe pneumonia, acute respiratory distress syndrome, and organ failure [4] . This article presents a review of the current literature on seizures linked with SARS-COV 2 infection and describes possible underlying mechanisms. describes the demographic data, time to onset of neurological symptoms, diagnostic criteria, intervention, and outcomes from 11 studies of seizures associated with SARS-COV-2 infection. doi = 10.1016/j.npbr.2020.10.001 id = cord-324251-wgtatr8v author = Joshi, Madhvi title = Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology date = 2020-07-13 keywords = SARS summary = title: Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID. Positive selection of ORF3a and 477 ORF8 genes drives the evolution of SARS-CoV-2 during the 2020 COVID-19 pandemic Full-genome sequences of the first two SARS-CoV-2 485 viruses from India doi = 10.1101/2020.07.10.197095 id = cord-353612-9ux181xg author = Josset, Laurence title = Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus date = 2013-04-30 keywords = EMC; HCoV; SARS summary = Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. In addition, several kinase inhibitors (including SB203580, LY294002, and U0126) and a glucocorticoid (dexamethasone) were also predicted to be negative regulators of genes changed similarly after SARS-CoV and HCoV-EMC infection at late times postinfection (see Table S2 in the supplemental material). Importantly, this kinase inhibitor was predicted to regulate genes that were DE similarly by SARS-CoV and HCoV-EMC at late times postinfection (see Table S2 in the supplemental material) and could therefore inhibit both viruses'' replication. doi = 10.1128/mbio.00165-13 id = cord-356195-5pcaxpp9 author = Jothimani, Dinesh title = COVID-19 and Liver. date = 2020-06-15 keywords = ACE2; COVID-19; SARS; patient summary = Similar to SARS Co-V, Angiotensin Converting Enzyme2 (ACE2) appears to be the susceptible receptor for COVID-19 and is expressed in more than 80% of alveolar cells in the lungs. Interestingly, the level of ACE2 expression in cholangiocytes was similar to type 2 alveolar cells of the lungs, indicating that the liver could be a potential target for SARS-CoV-2. Summary of recently published studies are in described in Table 2 With the knowledge of current evidence, it is clear that elevated liver enzymes are observed predominantly severe and critical cases of COVID-19 compared to mild infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection doi = 10.1016/j.jhep.2020.06.006 id = cord-265617-e91s6xo8 author = Jouali, Farah title = SARS-CoV-2 Genome Sequence from Morocco, Obtained Using Ion AmpliSeq Technology date = 2020-07-30 keywords = SARS summary = This study describes a genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sampled from a male patient with SARS-CoV-2 who was likely infected in Casablanca, Morocco. As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here, we present the sequence of a SARS-CoV-2 genome that was obtained from a mildly symptomatic Moroccan patient. The five patients were found to be PCR positive for SARS-CoV-2 after a real-time reverse transcriptase PCR (RT-PCR) assay using a Da An gene kit (Sun Yat-sen University, China). The SARS-CoV-2 viral genome sequencing was performed manually using the Ion AmpliSeq technology and the Ion Torrent personal genome machine (PGM). The libraries were prepared using the Ion AmpliSeq library kit version 2.0 (Life Technologies) and Ion AmpliSeq SARS-CoV-2 research assay panel according to the manufacturer''s instructions. The genome sequence was compared to the complete genome of the SARS-CoV-2 Wuhan-Hu-1 isolate using the Betacoronavirus BLAST tool and showed 99.8% similarity. doi = 10.1128/mra.00690-20 id = cord-325038-q7gxw1go author = Joyce, Andrew A title = Changes in Interventional Pain Physician Decision-Making, Practice Patterns, and Mental Health During the Early Phase of the SARS-CoV-2 Global Pandemic date = 2020-08-31 keywords = SARS; volume summary = The survey consisted of a series of questions assessing prepandemic physician demographics and practice patterns, as well as new beliefs and behaviors following government-based medical policy changes resulting from the SARS-CoV-2 global pandemic (Supplementary Data). Multiple linear and logistic regression models were fit to continuous and dichotomous dependent variables, respectively, with independent variables consisting of the following: age, sex, training background (primary residency), number of years since completion of training, geographic region (Northeast, Midwest, South, Northwest, and international), regional density (rural, suburban, or urban) of practice location, practice setting (private practice, academic/university, hospital system employee, or other), prepandemic clinic/ procedure volumes, and personal relationship with someone who had tested positive for SARS-CoV-2 infection (defined as a positive test for the respondent, someone they live with, a personal patient, staff member they work with, or colleague in the group). doi = 10.1093/pm/pnaa294 id = cord-351930-puhm3w42 author = Juan, J. title = Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies date = 2020-05-06 keywords = COVID-19; SARS; case summary = . https://doi.org/10.1101/2020.05.02.20088484 doi: medRxiv preprint are fever, cough, dyspnea/shortness of breath and fatigue; third, on admission, most cases have patchy shadowing or ground-glass opacity on CT of the chest, and that normal or low leukocyte, lymphocytopenia and raised CRP are the most common laboratory findings observed in COVID-19-infected pregnant patients; fourth, the rate of severe COVID-19 pneumonia is relatively low but there are two reported maternal deaths, as of April 23, 2020; fifth, COVID-19 does not appear to increase the risk of adverse pregnancy outcomes such as preeclampsia; sixth, only a few pregnancies have resulted in a spontaneous miscarriage or abortion; seventh, of those who have delivered, the gestational age at delivery ranged from 28 to 41 weeks and the majority of cases have had Cesarean delivery; and eighth, in the case-series there have been no reported cases of neonates tested positive for SARS-CoV-2, however, in the case-reports there has been one case each with positive SARS-CoV-2 in amniotic fluid and neonatal throat swab. doi = 10.1101/2020.05.02.20088484 id = cord-291687-kwu0otpi author = Judson, Gregory L. title = Cardiovascular Implications and Therapeutic Considerations in COVID-19 Infection date = 2020-06-13 keywords = COVID-19; China; SARS; disease; patient summary = A review of 44,672 confirmed COVID-19 cases from Wuhan, China, demonstrated increased mortality in patients with cardiovascular disease (10.5%), diabetes (7.3%), and hypertension (6%), which was significantly higher than the overall case-fatality rate of 2.3% [22] . These initial cases series have shown a similar relationship between underlying cardiac comorbidities with a higher prevalence of hypertension, diabetes, coronary artery disease, and obesity in patients requiring mechanical ventilation [24] . Early studies reported a prevalence of acute cardiac injury of 12% in the entire cohort as defined by either high sensitivity troponin (Hs Tn) or the MB fraction of creatinine kinase (CK-MB) [ 99 th percentile or new echocardiographic or electrocardiographic abnormalities with greater elevations in cardiac biomarkers among patients requiring ICU care [1, 20] . Case cohort studies included data in patients for whom the outcome and illness course helped further elucidate the role of cardiac injury in COVID-19 disease. doi = 10.1007/s40119-020-00184-5 id = cord-328587-vctvcyim author = Jun, Sun title = The hypothesis that SARS-CoV-2 affects male reproductive ability by regulating autophagy date = 2020-07-10 keywords = ACE2; SARS summary = According to the existing clinical data, some patients not only suffer from respiratory diseases, but also have complications such as acute renal injury and even renal necrosis [2] [3] [4] , in addition, SARS-CoV-2 was also found in recent semen analysis of male patients [5] . Previous clinical data have shown that in addition to respiratory diseases, some male patients with COVID-19 are accompanied by kidney damage and even renal failure [2] [4], which suggest that SARS-CoV-2 may affect male fertility. Furthermore, clinical data also show that the receptor protein ACE2 that mediates the entry of SARS-CoV-2 into host cells is not only expressed in alveolar cells, but also highly expressed in male renal tubular cells [4] [21] [30] .All these suggest that SARS-CoV-2 not only causes damage to the respiratory system of patients, but also has a certain impact on the reproductive system of male patients. doi = 10.1016/j.mehy.2020.110083 id = cord-014878-n6a9cq47 author = Jun-yi, Ma title = The characteristics and dynamic changes of X-ray chest film in 50 patients with severe acute respiratory syndrome date = 2003 keywords = SARS summary = The characteristics and dynamic changes of chest film in 50 SARS patients in Hebei Province were analysed by the authors and reported as follows. X-ray chest films of all the patients taken every 2--3 days in the hospitalized period were collected and those with significant changes were analysed. Because there lacks definite epidemiological contacting history in part of the patients, the disease shows no specificity in clinical manifestation and blood cell examination, and the therapeutic effect could give no help to diagnosis, it is of vital importance in clinical practice to decide whether there is lesion occurring in the lung through X-ray chest film examination for early diagnosis of SARS. The figure of chest film of SARS patients is characterized as follows: ( 1 ) Lesions often oc-curred at the lower field and outer zone of the lung; (2) Lesions are mostly multiply presented; Characteristics of X-ray chest film figure in patients with SARS doi = 10.1007/bf02838621 id = cord-285162-srkd3wh0 author = Jung, F. title = How we should respond to the Coronavirus SARS-CoV-2 outbreak: A German perspective date = 2020-06-05 keywords = Germany; March; SARS summary = Figure 1 shows that until March 20 (day 80), the daily cases of new confirmed infections increased with doubling times between 1-5 days, showing a strong exponential rise of positive tests for SARS-CoV-2 infections in Germany. Common elements of these Asian states were the immediate action of governments to implement certain social distancing strategies and the wearing of face masks in public to reduce the number of new cases, which has proven to be effective to prevent transmission from infected individuals [15] . This led to a longer phase of exponential growth of SARS-CoV-2 infections and deaths in Germany, France and Italy and caused cumulative case numbers to grow significantly higher in comparison to the East-Asian countries (Fig. 2) . Until the end of March (day 91), Japan, however, has managed to stabilize these at under 5,000 confirmed cases, while Germany had almost 71,000 and France almost 52,000 confirmed SARS-Cov-2 infections. doi = 10.3233/ch-209004 id = cord-296319-fwn97wds author = Juno, J. A. title = Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19 date = 2020-05-21 keywords = RBD; SARS; figure summary = In 139 summary, antibody responses against both S and the RBD are consistently elicited in 140 SARS-CoV-2 infected individuals, the endpoints titres of which correlate significantly 141 with neutralising activity (r=0.55 and r=0.61 respectively) and ACE2 binding 142 inhibition (r=0.72 and r=0.72 respectively) in the plasma ( Figure S2) . 143 144 B cell responses to S antigens following SARS-CoV-2 infection 145 We next examined the frequency and specificity of class-switched B cells in 146 convalescent subjects using SARS-CoV-2 spike or RBD proteins as flow cytometric 147 probes. Clear antigen-specific populations of CD19 + IgD -B cells (gating in Figure S3 ) 148 binding spike, spike and RBD or RBD alone could be resolved in our cohort of 149 recovered from SARS-CoV-2 subjects, with minimal background staining in 150 uninfected controls (Figure 2A ; Figure S4 ). doi = 10.1101/2020.05.17.20104869 id = cord-258084-nkr3lrov author = Juthani, Prerak title = Coronavirus Disease 2019 (COVID-19) Manifestation as Acute Myocardial Infarction in a Young, Healthy Male date = 2020-07-11 keywords = COVID-19; SARS summary = In this case report, we describe a 29-year-old nonobese hospital food service associate who presented with diffuse abdominal and chest pain; he was found to be positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with significantly elevated levels of troponin T and multiple acute phase reactants; his EKG demonstrated ST-elevations consistent with anterolateral infarction. In this case report, we discuss a young patient who tested positive for SARS-CoV-2 and subsequently developed significant cardiovascular complications. We believe that this case is unique because this was a young, athletic patient with minimal risk factors for coronary disease who tested positive for COVID-19 and developed an acute MI with STEMI and required stent placement. It is a reminder to us that cardiovascular complications must be considered in the COVID-19 population, even in those patients with minimal risk factors for heart disease. doi = 10.1155/2020/8864985 id = cord-338923-hc7gagnq author = Jääskeläinen, AJ title = Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation date = 2020-06-15 keywords = CoV-2; SARS summary = We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). In this study, we assessed the specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 antibodies, including two rapid lateral flow tests, in comparison with a neutralisation test. doi = 10.1016/j.jcv.2020.104512 id = cord-279132-florvm7z author = K., Branimir title = From apparent to true – from frequency to distributions (II) date = 2020-08-17 keywords = COVID-19; SARS; bayesian summary = According to Roda et al (2) , one of the main reasons for the variability in predicting the COVID-19 epidemic is the lack of data on the actual dynamics of the infection spread, which results in so-called nonidentifiability in model calibration. The authors determined the model parameters using the Bayesian approach and Markov chain Monte Carlo, and concluded that the COVID-19 epidemics in Wuhan and Seattle had likely been spreading for several weeks before they became apparent and were far more extensive than initially reported. Feroze (7) used Bayesian structural time series models to investigate the pattern of SARS-CoV-2 spread in India, Brazil, USA, Russia, and the UK between March 1 and June 29, 2020 to assess the impact of mitigation measures and predict the dynamics of the epidemic over the next 30 days. Dehning et al (9) used the SIR epidemiological model framework in combination with Bayesian inference to analyze the effective growth rate of the number of new cases over time. doi = 10.3325/cmj.2020.61.381 id = cord-341524-zvic4xc9 author = KARAKURT, Hamza Umut title = Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks date = 2020-06-21 keywords = MMP9; SARS summary = We analysed transcriptome of SARS-CoV-2 infected human lung epithelial cells, compared it with mock-infected cells, used network-based reporter metabolite approach and integrated the transcriptome data with protein-protein interaction network to elucidate the early cellular response. The response in signalling pathways, gene expression, protein levels and metabolic profiles are regulated as a result of interactions in multilayer biological networks, hence a holistic view of the cellular response can be elucidated by an integrated approach. Here, we provide an analysis of transcriptional response after 24 h of infection, further, we integrated transcriptome profile with metabolic and protein-protein interaction networks to reveal multilayer mechanistic details of the SARS-CoV-2 infection in NHBE cells. Significant upregulation in expression of matrix metalloproteinase 9 (MMP9) in NHBE cells indicates that drugs which target MMP9 have potential uses in SARS-CoV-2 infection. This complex network structure between signalling pathways indicated that RAGE receptor targeting drugs have the potential to be used in SARS-CoV-2 patients to suppress symptoms. doi = 10.3906/biy-2005-115 id = cord-291552-qv6koo6g author = KWAN, AMBROSE CHI‐PONG title = Severe acute respiratory syndrome‐related diarrhea date = 2005-02-23 keywords = SARS summary = Background: Severe acute respiratory syndrome (SARS) is an emerging infectious disease and diarrhea has been reported in up to 76% of cases. The purpose of the present paper was to carry out a retrospective study of the clinical and demographic data of SARS patients with diarrhea in Princess Margaret Hospital. Patient data, need of ventilatory care, survival, number of bowel movements per day, total potassium supplement, lowest serum potassium and lowest serum albumin level were retrieved from the records and entered into a database for further analysis. described the clinical course of 75 patients in United Christian Hospital in Hong Kong and reported that 73% had watery diarrhea 7.5 ± 2.3 days after the onset of symptoms. We noted that female patients and residents of Amoy Gardens Estate were associated with diarrhea, and loglinear analysis showed that there was no significant interaction between these two factors. Outbreak of severe acute respiratory syndrome (SARS) at Amoy Gardens doi = 10.1111/j.1440-1746.2005.03775.x id = cord-288017-f9b3t0ts author = Kabeerdoss, Jayakanthan title = Understanding immunopathological fallout of human coronavirus infections including COVID‐19: Will they cross the path of rheumatologists? date = 2020-08-10 keywords = COVID-19; HCQ; IFN; SARS summary = High risks for fatal disease in COVID‐19 include older age, metabolic syndrome, male gender, and individuals who develop delayed type I IFN response. 54 In a macaque model of SARS-CoV infection too, aged macaques had more severe lung pathology, lower expression of type I IFN and higher expression of pro-inflammatory cytokines as compared to younger macaques. 80 to patients with COVID-19 that it is a mild immunomodulatory F I G U R E 2 Hydroxychloroquine (HCQ) inhibits SARS-CoV-2 entry and inhibits virus-induced type I interferon (IFN) signaling and proinflammatory cytokines production. While male gender, older age and people with metabolic syndrome seem to be at a higher risk of contracting more severe SARS-CoV-2 infection, younger females of African and Asian ancestry have higher risk for developing SLE; male gender among lupus patients, however, is an independent risk factor for severe disease. Evasion by stealth: inefficient immune activation underlies poor T cell response and severe disease in SARS-CoV-infected mice doi = 10.1111/1756-185x.13909 id = cord-294800-akr4f5p8 author = Kabir, Md. Tanvir title = nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date = 2020-07-10 keywords = COVID-19; China; MERS; RNA; SARS; vitamin summary = They also summarized that as viral load is quite high during the time of hospital admissions, use of potent antiviral agents at an early stage might prove Abbreviations: ACE2, angiotensin converting enzyme 2; AP, antigen presentation; APCs, antigen presentation cells; APN, aminopeptidase N, ARBs, angiotensin II receptor blockers; ARDS, acute respiratory distress syndrome; CDC, Centers for Disease Control; nCOVID-19, novel coronavirus disease 2019; CoVs, coronaviruses; DPP4, dipeptidyl peptidase 4; dsRNA, double-strand RNA; EC 50 , half maximal effective concentration; ED, emergency department; ELISA, enzymelinked immunosorbent assay; EUA, emergency use authorization; FDA, Food and Drug Administration; GGO, ground-glass opacity; HCV, hepatitis C virus; HIV, human immunodeficiency virus;, MHC, major histocompatibility complex; or HLA, human leukocyte antigen; ICU, intensive care unit; IL-6, interleukin 6; LPV/r, lopinavir/ritonavir; mAbs, monoclonal antibodies; MERS, Middle East respiratory syndrome; N7-MTase, N7-methyltransferase; NSAIDs, nonsteroidal anti-inflammatory drugs; PRRs, pattern recognition receptors; PUI, patient under investigation; RdRp, RNA-dependent RNA polymerase; RSV, respiratory syncytial virus; S protein, spike protein; SAM, S-adenosyl-methionine; SARS, severe acute respiratory syndrome; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; WHO, World Health Organization. doi = 10.3389/fcell.2020.00616 id = cord-353072-n92atcrx author = Kadkhoda, Kamran title = COVID-19: an Immunopathological View date = 2020-04-22 keywords = COVID-19; SARS summary = Unravelling these mechanisms can assist basic scientists, laboratory medicine practitioners, clinicians, public health practitioners, funding agencies, and health care policymakers in responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This is consistent with high-level surface expression of angiotensin-converting enzyme 2 (ACE2), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, on pneumocytes (2) . In the context of COVID-19, since ACE2 is highly expressed in the gastrointestinal (GI) tract (9), shedding the virus in the stool is prolonged (10); however, diarrhea is uncommon likely because virus-specific effector memory T cells typically home to the mucosal surfaces they had previously encountered with an infection with a common CoV, i.e., upper and lower respiratory tract. It has recently been shown that SARS-CoV and the Middle East respiratory syndrome (MERS)-CoV take advantage of non-or subneutralizing antibodies and enter cells via surface CD32a receptors (Trojan horse mechanism) (11, 12) . doi = 10.1128/msphere.00344-20 id = cord-311905-4yu29b49 author = Kakoulidis, Ioannis title = SARS-CoV-2 infection and glucose homeostasis in pregnancy. What about antenatal corticosteroids? date = 2020-05-06 keywords = SARS summary = METHODS: We performed a literature search on PubMed, regarding the use of corticosteroids in patients with SARS-CoV-2 infection, in pregnancies complicated by SARS-CoV-2, as well as their impact on glycemia in pregnant women with or without diabetes. While the healthcare community worldwide struggles to manage the novel SARS-CoV-2 (Severe Acute Respiratory Coronavirus 2; Covid-19) pandemic, it is of great importance to ensure that optimal care continues to be given to special groups of patients such as pregnant women. Therefore, extreme caution should be given, regarding the use of antenatal corticosteroids, in case of pregnant women with SARS-CoV-2 requiring preterm delivery [1, 3, 4, 16] . Since there are few small studies in the 6 literature regarding the management of pregnant women with SARS-CoV-2 (and possibly lacking reliable conclusions), the decision about the use of antenatal corticosteroids should be carefully made in consultation with infectious disease specialists, obstetricians and neonatologists [4, 16] . Timedependent changes in insulin requirement for maternal glycemic control during antenatal corticosteroid therapy in women with gestational diabetes: a retrospective study doi = 10.1016/j.dsx.2020.04.045 id = cord-350505-uh8r2vyz author = Kalantar-Zadeh, Kourosh title = Considering the Effects of Microbiome and Diet on SARS-CoV-2 Infection: Nanotechnology Roles date = 2020-05-01 keywords = CoV-2; Prevotella; SARS summary = [Image: see text] The impact of dietary patterns and the commensal microbiome on susceptibility to and severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has been largely ignored to date. 2 Therefore, the elucidation of host cytokine molecular pathways and microbiota components 17 as well as bacterial reactions in association with cytokine responses may provide novel microbiome-based therapeutic approaches to SARS-CoV-2 infection. Considering the presented discussion, nutritional and dietary strategies directed at restoring the well-known beneficial microbiota, which can possibly suppress viral infection in the elderly and those with underlying health problems, may be an effective strategy to mitigate the harmful effects of this virus. One approach, as a whole and to be undertaken prior to any viral infection, could include strengthening the intestinal barrier against pathogens, increasing intestinal motility, and reducing an underlying pro-inflammatory state by adopting a Many different direct or indirect microbiome pathways could contribute to SARS-CoV-2-gut interactions. doi = 10.1021/acsnano.0c03402 id = cord-257611-z0sng9sx author = Kalantari, Hamidreza title = Determination of COVID-19 prevalence with regards to age range of patients referring to the hospitals located in western Tehran, Iran date = 2020-10-07 keywords = COVID-19; SARS summary = We decided to examine suspected samples of pneumonia outbreak caused by the new coronavirus SARS-CoV-2 and provide information about the mortality rate due to this infection in different age groups in Iran. In this descriptive-cross-sectional study, a total of 784 samples of naso/oropharyngeal swabs of suspected patients with COVID-19 symptoms who had referred to Imam Khomeini, Shahid Fayaz-Bakhsh and Modarres hospitals in Tehran from February 24, 2020 to March 24, 2020 were examined by RT-PCR method. Therefore, in this study, we aimed at targeting these three genes using real-time RT-PCR method to examine suspected samples of COVID-19 and to determine the mortality rate due to this infection in different age groups in Iran. This was in accordance with the results of the present study, in which the highest number of deaths and positive cases were reported in people in the age group of >70 years. doi = 10.1016/j.genrep.2020.100910 id = cord-306438-db2rqz4d author = Kalathiya, Umesh title = Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site date = 2020-05-14 keywords = ACE2; RBD; SARS; figure; spike summary = An important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. These findings identify a novel small molecule binding-site formed by the spike protein oligomer, that might assist in future drug discovery programs aimed at targeting the coronavirus (CoV) family of viruses. Our current study focuses on understanding the variability of the trimer spike glycoprotein in SARS-CoV-2 with respect to the genomes from other coronavirus strains, and identifying the changes in the molecular properties due to conformational flexibility in the spike protein. Our data suggest a mechanism whereby Chitosan (and possibly its derivatives), as well as macrolide type molecules, might bind to a pocket formed by the spike protein trimer and provide a novel domain to focus on for future drug discovery projects. doi = 10.3390/jcm9051473 id = cord-301876-d2j9wpqk author = Kalita, Parismita title = Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2 date = 2020-05-04 keywords = SARS; vaccine summary = Few groups have designed subunit vaccines against SARS-CoV-2; however, their workflow involved either use of single protein for vaccine design [24, 25] or used only CTL epitopes without considering the importance of B-cell or HTL epitopes [26] . B-cell epitopes for the screened SARS-CoV-2 proteins were predicted using the ABCPred server (http://crdd.osdd.net/raghava/abcpred/). A total of 6 HTLs, 18 CTLs, and 9 B-cell epitopes derived from the three proteins were used to design the subunit vaccine (566 amino acid residues) against SARS-CoV-2 (Supplementary Figure 1) . Based on extensive bioinformatics analysis, we used three proteins to design a multi-epitope subunit vaccine against novel coronavirus SARS-CoV-2. Computational studies suggest that our multi-epitope based subunit vaccine has a probability of showing good protective efficacy and safety against SARS-CoV-2 infection in humans. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach doi = 10.1016/j.micpath.2020.104236 id = cord-341987-lsvifqyo author = Kalyanasundaram, Sridhar title = Novel Corona Virus Pandemic and Neonatal Care: It’s Too Early to Speculate on Impact! date = 2020-08-03 keywords = SARS; covid-19; infection summary = We discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 (COVID-19) in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. In this article, we discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. Another recent case study published in Nature Communication reported transplacental transmission of COVID-19 from a positive pregnant mother during the last trimester to her offspring which occurred due to maternal viremia, placental infection, and neonatal viremia following placental infection [34] . doi = 10.1007/s42399-020-00440-8 id = cord-292025-dr611nse author = Kam, Kai-qian title = Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children date = 2020-06-13 keywords = CoV-2; SARS summary = From 23 March 2020 to 3 April 2020, all inpatient pediatric confirmed COVID-19 cases diagnosed via positive SARS-CoV-2 polymerase chain reaction (PCR) from nasopharyngeal swabs using the real-time reverse transcription (rRT)-PCR assay for the E gene were included in this study. In the 9 infected children with detectable SARS-CoV-2 in buccal specimens, the mean difference of Ct values between buccal and nasopharyngeal specimens for all infected patients was 10.7 (range, 6.1-16.1), and this was statistically significant (P < .001). Our findings confirm that SARS-CoV-2 can be detected in buccal specimens of infected children and that the viral load is the highest in the first week of illness or diagnosis. In our study, the average viral loads of buccal SARS-CoV-2 were consistently lower than the respective nasopharyngeal specimens, with substantial differences between the average Ct values. Two COVID-19-infected children had negative buccal specimens despite detectable nasopharyngeal viral load. doi = 10.1093/jpids/piaa068 id = cord-324307-2zbm4iwn author = Kam, Kai-qian title = A Well Infant With Coronavirus Disease 2019 With High Viral Load date = 2020-02-28 keywords = COVID-19; SARS summary = A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. doi = 10.1093/cid/ciaa201 id = cord-334695-cjxlw1tu author = Kam, Yiu-Wing title = Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date = 2009-11-17 keywords = 16hbe; SARS; cell; figure summary = title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro We observed that SARS-CoV spike glycoprotein can be efficiently cleaved by several airway proteases and that this processing enhances entry of SARS-CoVpp. Furthermore, we have identified the putative cleavage sites of airway proteases and, by site-directed mutagenesis, have determined the role of specific amino acid residue for proteolytic processing of the envelope glycoprotein, and for SARS-CoVpp entry into human airway epithelial cells (16HBE) in vitro. In an effort to directly demonstrate that airway protease mediated virus entry enhancement is due to the presence of cleavage site on the SARS spike glycoprotein, 16HBE cells were pre-incubated with wild-type (SARS-CoVpp) or mutant (R667App) pseudotypes on ice, which allowed virus attachment but not entry. doi = 10.1371/journal.pone.0007870 id = cord-275846-7onenxg7 author = Kamikubo, Yasuhiko title = Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2 date = 2020-03-27 keywords = SARS summary = Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Here, we developed the world''s first influenza-based epidemiological method as a useful proxy to detect the spread of SARS-CoV-2 and the establishment of partial herd immunity in countries. These results prompted us to hypothesize that (i) S type SARS-CoV-2 exit Wuhan or other epicenter in China earlier than L type virus without recognition by infectious disease surveillance systems of China and other countries; (ii) the infection by S type induced herd immunity that provides at least partial protection against spread of SARS-CoV-2. doi = 10.1101/2020.03.25.20043679 id = cord-347351-emdj66vj author = Kampf, Günter title = Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date = 2020-09-18 keywords = CoV-2; RNA; SARS; covid-19; patient; transmission summary = Originating from a single travel-associated primary case from China, the first documented chain of multiple human-to-human transmissions of SARS-CoV-2 outside of Asia allowed a detailed study of transmission events and identified several factors (e.g. cumulative face-toface contact, direct contact with secretions or body fluids of a patient, personal protective equipment) to classify contacts as low or high risk [32] . In the close surrounding of COVID-19 patients in hospitals SARS-CoV-2 RNA is detected more frequently compared to surfaces outside the patient rooms but samples were so far consistently negative for infectious virus. General disinfection of frequently touched surfaces in the public such as shopping carts or door handles is, however, unlikely to add any protective value because even in COVID-19 wards inanimate surfaces were mainly contaminated in the permanent and immediate surrounding of symptomatic patients (detection of viral RNA, not of infectious virus) and only rarely one room away [138] suggesting that the risk to find SARS-CoV-2 on frequently touched surfaces in the public is low. doi = 10.1016/j.jhin.2020.09.022 id = cord-338468-c0jv3i1t author = Kanduc, Darja title = From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry date = 2020-07-16 keywords = CoV-2; SARS; hexapeptide; human; protein summary = Results: Immunoreactive epitopes present in SARS-CoV-2 were mostly composed of peptide sequences present in human proteins that—when altered, mutated, deficient or, however, improperly functioning—may associate with a wide range of disorders, from respiratory distress to multiple organ failure. In the wake of such results, in order to validate (or, as well, invalidate) the cross-reactivity hypothesis, investigation was expanded here by analyzing the peptide sharing between the human host and immunoreactive epitopes that are also present in SARS-CoV-2. Table 2 documents that numerous immunoreactive SARS-CoV-2 epitopes are composed mostly or, in many instances, uniquely of peptide sequences shared with human proteins. This study shows that hexapeptides from immunoreactive epitopes present in SARS-CoV-2 are widespread among a high number of human proteins. Table S2 : Hexapeptide sharing between 233 epitopes present in SARS-CoV-2 and human proteins. Table S3 : List and short description of 460 human proteins that share hexapeptides with the 233 SARS-CoV-2 epitopes. doi = 10.3390/antib9030033 id = cord-308400-8wihm63b author = Kanellopoulou, A. title = Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort date = 2020-11-13 keywords = November; SARS summary = Background: To assess the level of knowledge and trust in the policy decisions taken regarding the coronavirus disease (COVID-19) pandemic among Epirus Health Study (EHS) participants. Variables assessing knowledge and beliefs towards the pandemic were summarized overall and by gender, age group (25-39, 40-49, 50-59, 60+ years) and period of report (before the lifting of lockdown measures in Greece: March 30th to May 3rd, and two post-lockdown time periods: May 4th to June 31st, July 1st to August 31st). Therefore, the primary objective of this 123 study was to investigate the levels of knowledge and beliefs on the COVID-19 pandemic and the magnitude 124 of trust upon Greek authorities and how these measures differed according to age, gender and time period 125 among the participants of an ongoing Greek cohort study, the Epirus Health Study (EHS). doi = 10.1101/2020.11.10.20229146 id = cord-262029-zzn74cjr author = Kang, Chang Kyung title = In vitro activity of lopinavir/ritonavir and hydroxychloroquine against severe acute respiratory syndrome coronavirus 2 at concentrations achievable by usual doses date = 2020-05-29 keywords = COVID-19; SARS summary = We examined the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2, at concentrations which can be used to treat coronavirus-19 patients with little concern of toxicity. Its in vitro antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19, has been recently suggested [4] . Therefore, the screening of poten-tial antivirals to fight COVID-19 is urgently needed and led us to assess the in vitro activity of lopinavir/ritonavir and hydroxychloroquine on SARS-CoV-2 at clinically administrable doses. We examined the in vitro activity of the oral antivirals lopinavir/ritonavir and hydroxychloroquine against SARS-CoV-2 at their patient administrable doses. In conclusion, this in vitro experimental study showed that lopinavir/ritonavir, at its clinically relevant concentration, showed significant anti-SARS-CoV-2 activity when it was administered following viral infection. 1. Lopinavir/ritonavir showed significant anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity both in terms of the prevention of cytotoxicity and reducing the viral load at plasma concentrations achievable by usual doses. doi = 10.3904/kjim.2020.157 id = cord-263594-jd9ako6c author = Kang, Sisi title = A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date = 2020-09-11 keywords = Fig; SARS summary = Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Severe acute 57 respiratory distress syndrome-associated coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein 58 is a highly immunopathogenic and multifunctional viral protein (14) (15) (16) (17) (18) (19) , which elicited high titers 59 of binding antibodies in humoral immune responses (20) (21) (22) . Herein, 66 we report a human mAb derived from COVID-19 convalescent, with specific targeting to SARS-67 CoV-2 N protein and functionally compromising complement hyper-activation ex vivo. Isolation of N protein-directed mAbs 69 To profile antibody response to SARS-CoV-2 N protein in early recovered patients, we collected 70 six convalescent blood samples at seven to 25 days after the onset of the disease symptoms. doi = 10.1101/2020.09.10.292318 id = cord-276487-8vkrh70j author = Kang, Sisi title = Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites date = 2020-04-20 keywords = Fig; NTD; SARS summary = title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2. In this study, we report the crystal structure of SARS-CoV-2 nucleocapsid N-terminal domain (termed as SARS-CoV-2 N-NTD) as a model for understanding the molecular interactions that govern SARS-CoV-2 N-NTD binding to ribonucleotides. Since full-length SARS-CoV-2 N protein aggregated status were found in our expression and purification studies (Supporting Information Fig. S2 ), as well as previously reported data on other coronavirus nucleocapsid protein, we next investigated the structural studies on N-terminal region of SARS-CoV-2 N protein (termed as SARS-CoV-2 N-NTD). doi = 10.1016/j.apsb.2020.04.009 id = cord-273035-sewfb3q8 author = Kang, Xixiong title = Proteomic Fingerprints for Potential Application to Early Diagnosis of Severe Acute Respiratory Syndrome date = 2005-01-01 keywords = PBS; SARS; acute summary = Background: Definitive early-stage diagnosis of severe acute respiratory syndrome (SARS) is important despite the number of laboratory tests that have been developed to complement clinical features and epidemiologic data in case definition. Results: The discriminatory classifier with a panel of four biomarkers determined in the training set could precisely detect 36 of 37 (sensitivity, 97.3%) acute SARS and 987 of 993 (specificity, 99.4%) non-SARS samples. We established a decision tree algorithm consisting of four unique biomarkers for acute SARS in the training set and subsequently validated the accuracy of this classifier by use of a completely blinded test set. To identify the serum biomarkers that could distinguish SARS from non-SARS samples, we used a training set of specimens (37 SARS acute and 74 controls; Tables 1 and 2) and constructed the decision tree classification algorithm using 10 989 peaks [99 peaks ϫ (37 ϩ 74) spectra] of statistical significance identified in the low energy readings (see Materials and Methods). doi = 10.1373/clinchem.2004.032458 id = cord-267831-uu883ofc author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-06-15 keywords = SARS; virus summary = We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry doi = 10.1101/2020.04.21.053058 id = cord-291323-kbjyd5g3 author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-08-25 keywords = Apilimod; SARS; VSV; Vacuolin-1; ZEBOV summary = We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We describe here potent inhibitory effects on content release and infection by chimeric vesicular stomatitis virus (VSV) containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small-molecule inhibitors of the main endosomal phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, PIKfyve. We have constructed chimeric forms of vesicular stomatitis virus (VSV) bearing the fusion proteins of Zaire ebolavirus (ZEBOV) or SARS coronavirus 2 (SARS-CoV-2) and shown that two small-molecule inhibitors of an endosomal lipid kinase (PIKfyve) inhibit viral infection by preventing release of the viral contents from endosomes. doi = 10.1073/pnas.2007837117 id = cord-252234-3txk22yj author = Kaniyala Melanthota, Sindhoora title = Elucidating the microscopic and computational techniques to study the structure and pathology of SARS‐CoVs date = 2020-08-07 keywords = SARS summary = Coronavirus replication is initiated with the binding of virion particles to the receptors of the cells, further directing the translation of the viral genome in the cytoplasm and synthesis of membrane-bound proteins. Previous studies have shown the use of a scanning electron microscope (SEM) for obtaining surface information and TEM for revealing inner components of the SARS-CoV particle. Table 1 compares various microscopy techniques for understanding the structure of SARS-CoV and its effect in host cells. The E6 cell lines were subjected to thin-layer electron microscopy and the images revealed typical coronavirus particles within the rough endoplasmic reticulum, specifically in cisternae, as well as in vesicles and several large clusters of extracellular particles were found attached to the surface of the plasma membrane. Apart from studying how the virus enters the cell, immunofluorescence was also used to investigate antibody response to the SARS-CoV and use it as an efficient detection method. doi = 10.1002/jemt.23551 id = cord-254505-mjj8xrer author = Kannan, Saathvik R. title = Infectivity of SARS-CoV-2: there Is Something More than D614G? date = 2020-09-15 keywords = SARS summary = To gain insight into the distribution of mutations in SARS-CoV-2 nonstructural proteins (nsps) and structural proteins, we analyzed protein sequences (n = 7232) from the United States (n = 6302), Europe (n = 420), China (n = 104), and India (n = 406), and determined the mutations with respect to Wuhan-Hu-1 isolate (NCBI Reference Sequence: NC_045512.2). The results of the temporal analysis of the mutation frequency of P323L (nsp12), C241U (5''UTR) and D614G (S-protein) show that P323L was consistently present in the viruses that had D614G mutation and C241U started coevolving with D614G sometime late January 2020 (Fig. 1b) . A mutation of D614 to G614 should result in the loss of these interactions, which could alter the dynamics of S-protein conformational changes during SARS-CoV-2 infection. Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex cell doi The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity cell doi doi = 10.1007/s11481-020-09954-3 id = cord-275348-jna496x7 author = Kapadia, Sagar U. title = SARS vaccine based on a replication-defective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector date = 2008-06-20 keywords = SARS; VSV; VSVΔG summary = A SARS vaccine based on a live-attenuated vesicular stomatitis virus (VSV) recombinant expressing the SARS-CoV S protein provides long-term protection of immunized mice from SARS-CoV infection (Kapadia, S.U., Rose, J. We found that the vaccine given intramuscularly induced a neutralizing antibody response to SARS-CoV that was approximately ten-fold greater than that required for the protection from SARS-CoV infection, and significantly greater than that generated by the replication-competent vector expressing SARS-CoV S protein given by the same route. In order to evaluate this vector as a SARS vaccine candidate, we also developed a SARS-CoV neutralization assay using a pseudotyped VSV recombinant expressing a green fluorescent protein. SARS-CoV neutralizing antibody titers of these sera were determined by incubating VSVΔG-EGFP/SΔtail-HA virus with serial dilutions of these sera, and the virusserum mixtures were transferred to a monolayer of Vero E6 cells. doi = 10.1016/j.virol.2008.03.002 id = cord-304340-9mrtic2k author = Karacan, Ilker title = The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey date = 2020-05-15 keywords = COVID-19; Istanbul; SARS summary = Although SARS-CoV-2 has a lower mutation rate than expected [18] , real-time tracking of the virus isolates in populations may help epidemiological understanding of the disease and early detection of important mutational or recombination events. Herein, we analyzed full-length SARS-CoV-2 genomes from three patients in Istanbul together with their clinical findings. Sample Collection: Nasopharyngeal swabs were collected from unrelated patients and tested for SARS-CoV-2 presence as a standard care protocol for routine diagnosis in Umraniye Training and Research Hospital (UEAH), Istanbul. The physical examination in the emergency department revealed a body temperature of 36.8°C, blood pressure of 120/70 mm Hg, the pulse of 100 beats per minute, respiratory rate of 20 breaths per minute, and oxygen saturation of 97% while the patient was breathing ambient air. Herein, we report three virus genomes isolated in Istanbul for the first time together with patients'' clinical findings. doi = 10.14744/nci.2020.90532 id = cord-311105-8edwb59c author = Karamese, M. title = The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey date = 2020-06-26 keywords = SARS summary = title: The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world. In this study, we retrospectively analyzed RT-PCR results of 10,000 cases from April 2 to May 30, 2020 in Kars, Iğdır, and Ardahan cities that are located on the Eastern of Turkey. All the cases were suspected of SARS-CoV-2 infection because of the symptoms or close contact with a COVID-19 patient. . https://doi.org/10.1101/2020.06.25.20138131 doi: medRxiv preprint that are located on the Eastern of Turkey; however, 7853 cases were evaluated who had typical respiratory infection symptoms such as fever, cough and shortness of breath, or close contact with a COVID-19 patient. To our knowledge, this is one of the first epidemiologic study about the RT-PCR positivity of SARS-CoV-2 suspected cases in our country. doi = 10.1101/2020.06.25.20138131 id = cord-268339-jxm69ndw author = Karamitros, Timokratis title = SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date = 2020-03-28 keywords = SARS summary = We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify smalland large-scale intra-host variations in the viral genome. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays. Here, we explore intra-host genomic variants and low-frequency polymorphic quasispecies in Next Generation Sequencing (NGS) data derived from patients infected by SARS-CoV-2. The S1 subunit consists of a signal peptide and the NT and receptor binding (RB) domains, with the latter sharing only 40% amino acid identity with other SARS-related CoVs. Our analysis revealed that similarly to other genomic regions, the S1 subunit hosts many low-frequency SNVs, characterized by higher density compared to the rest of the S gene sequence (Figure 1-E) . doi = 10.1101/2020.03.27.009480 id = cord-353963-d3gk3519 author = Karampela, Irene title = Could Respiratory Fluoroquinolones, Levofloxacin and Moxifloxacin, Prove to be Beneficial as an Adjunct Treatment in COVID-19? date = 2020-06-06 keywords = SARS summary = A recent in silico study has shown that the fluoroquinolones, ciprofloxacin and moxifloxacin, may inhibit SARS-CoV-2 replication by exhibiting stronger capacity for binding to its main protease than chloroquine and nelfinavir, a protease inhibitor antiretroviral drug. Based on their potential antiviral activity and immunomodulatory properties, the favorable pharmacokinetics and safety profile, we propose the use of respiratory fluoroquinolones as adjuncts in the treatment of SARS-CoV-2 associated pneumonia. However, preliminary clinical trials reported conflicting results regarding the use of the anti-malarial and anti-inflammatory chloroquine and the macrolide azithromycin, while the antiviral remdesivir has not been shown to significantly decrease COVID-19 mortality (1, 2) . Considering the potential antiviral activity of respiratory fluoroquinolones against SARS-CoV-2, along with their immunomodulatory properties, their favorable pharmacokinetics and the excellent safety profile, we propose their use as adjuncts in treating patients presenting COVID-19. Therefore, randomized clinical trials of respiratory fluoroquinolones are necessary to explore their potential Arch Med Res E20_832 3 therapeutic effect as an adjunct in the treatment of SARS-CoV-2 associated pneumonia. doi = 10.1016/j.arcmed.2020.06.004 id = cord-253380-oymg1bba author = Karataş, Ayşe title = Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma date = 2020-07-03 keywords = SARS summary = title: Prolonged Viral Shedding in a Lymphoma Patient with COVID-19 Infection Receiving Convalescent Plasma Herein we report a patient with a history of autologous stem cell transplantation (ASCT) for lymphoma whose RT-PCR test remained positive for SARS-CoV-2 for 74 days. The prolonged RT-PCR positivity, despite convalescent plasma infusion, may suggest that the given antibodies may be ineffective in terms of viral clearance. In patients with hematological malignancies or immunosuppression, such as ASCT, may lead to prolonged viral shedding, and strict isolation is warranted for long-term SARS-CoV-2 infection control. A case whose viral shedding lasted 60 days is reported from China Our patient had also undergone bone ASCT thus, underlying immunosuppression might lead to prolonged shedding. In patients with hematological malignancies or immunosuppression such as ASCT may lead to J o u r n a l P r e -p r o o f prolonged viral shedding and strict medical precautions and isolation rules should be followed for SARS-CoV-2. doi = 10.1016/j.transci.2020.102871 id = cord-261959-pvufajw4 author = Karathanou, Konstantina title = A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2 date = 2020-09-10 keywords = ACE2; SARS; figure summary = Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. The surface of the Severe Acute Respiratory Syndrome (SARS)-CoV-2 virion is decorated with large membrane-anchored spike proteins S (Figure 1 ) that bind to Angiotensin Converting Enzyme 2 (ACE2) receptor of the host cell (Briefing, 2020; Hoffmann et al., 2020; Li et al., 2003; Xiao et al., 2003; Zhou et al., 2020) . To derive clues about intra-molecular interactions with potential role in shaping structural dynamics of protein S, we computed two-dimensional graphs of all Hbonds of protein S in structures proposed for the closed, open, and pre-fusion conformation, and for ACE2 bound to an RBD fragment. doi = 10.1016/j.jsb.2020.107617 id = cord-303363-uu9hb1c9 author = Karimi, Mehran title = Implications of SARSr-CoV 2 infection in thalassemias: Do patients fall into the “high clinical risk” category? date = 2020-05-11 keywords = COVID-19; SARS; patient; thalassemia summary = We''re all flying blind regarding coronavirus, but it''s fair to think if thalassemic patients are particularly vulnerable to SARS-COV-2 infection or are at potential higher risk of complications from COVID-19 than normal population, specially when they become older. Therefore, it is recommended that patients with diabetes maintain a good glycemic control, because it might help reduce the risk of infection itself and may also modulate the severity of the clinical expression of the disease (39) . Hemoglobin disorders including thalassemias are generally not associated with respiratory diseases but anemia and iron-overload involving the heart, lungs (pulmonary hypertension), liver disease, diabetes and even the immune system, can encounter these patients to have higher risk of complications from SARS-COV-2 infection than normal population, specially when they become older. The few reported cases of SARS-CoV-2 infection in people with thalassemias might reflect the efforts to minimise social contacts or other unclarified reasons, such as lower beta globin protein as a possible target of COVID-19 in these patients (51) . doi = 10.23750/abm.v91i2.9592 id = cord-316186-254z62e4 author = Kario, Kazuomi title = COVID‐19 and hypertension—evidence and practical management: Guidance from the HOPE Asia Network date = 2020-07-09 keywords = Asia; COVID-19; SARS summary = 1 Early clinical experience suggested that older age and the presence of a number of comorbidities, including hypertension, cardiovascular disease, diabetes mellitus and chronic respiratory disease increased the risk of death in patients with 3 In addition, the renin-angiotensin aldosterone (RAS) system (specifically the angiotensin-converting enzyme 2 [ACE2] protein) has been identified as playing an important role in facilitating entry of coronaviruses, including SARS-CoV-2, into target cells, especially in the lungs. Despite the theoretical possibility that use of RAS inhibitors increases the risk of infection with SARS-CoV-2 and the severity of COVID-19 illness, analyses including patients from the current pandemic indicate that this does not seem to be the case ( Table 2 ). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China doi = 10.1111/jch.13917 id = cord-009573-ghv9uezx author = Karlberg, J title = Do sensational media reports about severe acute respiratory syndrome affect the mindset of healthcare workers? date = 2007-01-02 keywords = SARS summary = The doctor at Huddinge Hospital called the Karolinska Hospital, and told the mother that an isolation room would be available for them at the hospital. That afternoon, the mother and son arrived at the Astrid Lindgren''s Children''s Hospital of the Karolinska Hospital, and a doctor and nurse met them. Because the doctors and other hospital staff now regarded her son as a suspected SARS case, the mother was concerned about returning home to her daughter and mother. A few days later the mother called the hospital and was told that the laboratory results were negative for SARS. We are concerned because, at the time of writing, there has not been any report of this suspected SARS case to the Swedish Institute for Infectious Disease Control or to WHO. We believe that heightened anxiety about SARS, brought about by the popular media''s exaggerated reporting of the outbreak in Hong Kong, affected the way Swedish healthcare professionals reacted. doi = 10.1111/j.1651-2227.2003.tb00508.x id = cord-338683-nzgnpi6f author = Karligkiotis, Apostolos title = Changing paradigms in sinus and skull base surgery as the COVID‐19 pandemic evolves: Preliminary experience from a single Italian tertiary care center date = 2020-06-08 keywords = SARS; covid-19; pandemic; patient summary = The aim of the present paper is to report our preliminary experience with the management of urgent and nondeferrable endoscopic surgeries for sinus and skull base diseases, during the COVID-19 period, describing the evolving recommendations which have been implemented day by day, as new evidences emerged, until reaching the actual protocol of precautions. At the beginning, no specific protection was recommended during surgery and all health care workers in the operating room (OR) continued to wear standard surgical masks and gowns, leaving viral-filtering-PPE available to be used only in case of confirmed COVID-19 patients. 10 In order to investigate the health of the patients belonging to the PANDEMIC-group after their last postoperative medication, a telephone interview was carried out retrospectively, examining the following factors: fever, cough, dyspnoea, anosmia, dysgeusia, gastrointestinal signs/symptoms, myalgias, fatigue, headache, pharyngodynia, rhinorrhea, active pneumonia, need for hospitalization for any reason, potential swab or serological tests performed, and if they had been in contact with COVID-19 positive individuals. doi = 10.1002/hed.26320 id = cord-316498-f43apjul author = Karlsson, Jan Olof G title = May Mangafodipir or Other SOD Mimetics Contribute to Better Care in COVID-19 Patients? date = 2020-10-10 keywords = INO; SARS summary = The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate—MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. The Manganese diPyridoxyL EthylDiamine (MnPLED)-type mangafodipir (manganese dipyridoxyl diphosphate-MnDPDP), a magnetic resonance imaging (MRI) contrast agent that possesses MnSOD mimetic activity, has shown promising results in various forms of inflammation, in preclinical as well as clinical settings. Intravenously administration of mangafodipir will, in contrast to INO [1] : "Everyone will be exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and most people will become infected; the disease is known as COVID-19. When it comes to mangafodipir, its combined MnSOD mimetic and redox metal binding activity may be of particular importance when attacking the inflammatory storm in SARS-CoV-2 patients. doi = 10.3390/antiox9100971 id = cord-293710-f1tzt6jb author = Karolyi, M. title = Late onset pulmonary embolism in young male otherwise healthy COVID-19 patients date = 2020-09-23 keywords = SARS summary = SARS-CoV-2 infection is associated with increased risk of thrombosis in severely ill patients but little is known about the risk in outpatients with mild to moderate disease. Studies showed reduced mortality in hospitalized COVID-19 patients treated vs not treated with anticoagulants in patients with a sepsis-induced-coagulopathy (SIC) score ≥ 4 or D-Dimer > 6 times upper limit of normal [4] . We describe a case series of four outpatients with proven SARS-CoV-2 infection who developed pulmonary embolism (PE) with a delay of 2-4 weeks after symptom onset with complete resolution of initial symptoms. The characteristics of outpatients who are suitable for anticoagulation have to be determined.In conclusion, new onset of dyspnea and tachycardia after initial resolution of COVID-19 symptoms ("disease trajectory characterised by two peaks") should raise suspicion of PE and a CT scan should be considered. doi = 10.1007/s10096-020-04044-x id = cord-268817-wx96wwpg author = Karp, Donna Grace title = Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date = 2020-08-20 keywords = ADAP; PCR; SARS; covid-19 summary = Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. 6 In this study, we report the development and validation of a highly sensitive and specific SARS-CoV-2 total antibody assay on a Hamilton MicroLab STAR liquid-handling platform (Fig. 1) , based on the ADAP STAR assay-ready workstation. The successful implementation of the automated high-throughput ADAP SARS-CoV-2 total antibody assay solution as described herein can help meet the surge in demand for COVID-19 infection testing. To evaluate the assay''s sensitivity, 57 serum specimens from COVID-19 patients were subjected to the ADAP SARS-CoV-2 total antibody analysis. doi = 10.1177/2472630320950663 id = cord-260034-a1y0enrg author = Karsulovic, Claudio title = mTORC inhibitor Sirolimus deprograms monocytes in “cytokine storm” in SARS-CoV2 secondary hemophagocytic lymphohistiocytosis- like syndrome date = 2020-07-13 keywords = SARS summary = title: mTORC inhibitor Sirolimus deprograms monocytes in "cytokine storm" in SARS-CoV2 secondary hemophagocytic lymphohistiocytosislike syndrome Human M1 monocytes in vitro were able to express higher levels of IL-6 and IL-1β after LPS stimulation (8) (Fig. 1) . When monocytes are treated in vitro with sirolimus, and mTORC blocker, they are unable to express M1 proteins even in presence of LPS. With this data and previous reports of its use in influenza pneumonia (13) , it seems reasonable to think that the SARS-CoV2 induced sHLH-Like syndrome could be successfully slowed or terminated by sirolimus, due to its action blocking the migration of monocytes to lung tissue. We propose at least compassionate use of sirolimus in SARS-CoV2 patients who are classified as high risk of ominous progression or are currently using tocilizumab, corticosteroids and/or J o u r n a l P r e -p r o o f protease inhibitors and Hscore shows high probability of sHLH. doi = 10.1016/j.clim.2020.108539 id = cord-025129-ry85kv9q author = Kashyap, Uddip title = Enhanced Design of PPE Based on Electrostatic Principle to Eliminate Viruses (SARS-CoV-2) date = 2020-05-23 keywords = SARS; charge summary = In this work, we propose a sanitization procedure of the personal protective equipment (PPE), such as gloves and masks, before and after the use, by employing high voltage charge generator (30 kV) from a very low DC source of 5 V to eliminate the virus from the surface of PPE. The high electric field alters the induced dipole of the protein of the virus, causing permanent damage in terms of electroporation. The negative terminal of the high voltage output can be grounded, and the positive terminal is connected to a metallic layer with a coating of CNT or ablate nano-grooves with Lithography. However, in the current work, the step-up negative high voltage charge is grounded, and the positive charges are allowed to accumulate over the metallic surface. The high electric field alters the induced dipole of the protein of the virus (Sharp and Honig 1990) , causing permanent damage in terms of electroporation (Liu et al. doi = 10.1007/s41403-020-00101-1 id = cord-261876-7rsc803x author = Kaslow, David C. title = Certainty of success: three critical parameters in coronavirus vaccine development date = 2020-05-25 keywords = MERS; SARS; incubation; period; vaccine summary = In considering the "certainty of success" in development of human coronavirus vaccines, particularly SARS-CoV-2, a third, related critical parameter is proposed—infectious inoculum intensity, at an individual-level, and force of infection, at a population-level. Reducing the infectious inoculum intensity (and force of infection, at a population-level) is predicted to lengthen the incubation period, which in turn is predicted to reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. The one factor that emerges for consideration in SARS-CoV-2 vaccine development and implementation is reducing the infectious inoculum intensity (and force of infection, at a populationlevel) to lengthen the incubation period, reduce the severity of illness, and increase the opportunity for an anamnestic response upon exposure to the circulating virus. doi = 10.1038/s41541-020-0193-6 id = cord-289852-4uxb70rh author = Kassem, Dina H. title = Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis date = 2020-09-30 keywords = COVID-19; SARS; cell; patient summary = Thus, harnessing the immunomodulatory properties of mesenchymal stem cells (MSCs) to ameliorate that cytokine-storm can indeed provide a golden key for the treatment of COVID-19 patients, especially severe cases. In fact, MSCs transplantation can improve the overall outcome of COVID-19 patients via multiple mechanisms; first through their immunomodulatory effects which will help to regulate the infected patient inflammatory response, second via promoting tissue-repair and regeneration, and third through their antifibrotic effects. Similar studies are also warranted to compare the therapeutic benefit of a certain MSCs type, and its derived EVs. Antimicrobial activity of mesenchymal stem cells: current status and new perspectives of antimicrobial peptide-based therapies Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ILL COVID-19 patients: the case for compassionate use Human umbilical cord-derived mesenchymal stem cell therapy in patients with COVID-19: a phase 1 clinical trial doi = 10.3389/fcell.2020.587866 id = cord-267307-kyh0xsrp author = Kasting, Monica L. title = Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date = 2020-11-04 keywords = COVID-19; SARS; effectiveness summary = Public health efforts should focus on increasing perceived severity and threat of SARS-CoV-2-related disease, while promoting NPI as effective in reducing threat. A six-item measure was used to assess participants'' perceptions of the effectiveness of NPIs to prevent SARS-CoV-2 infection and spread. Three of the six items measured the perceived effectiveness of preventing yourself from spreading COVID-19 to others and included: 1) wearing a mask anytime you leave the house to go out in public, 2) practicing social distancing by leaving at least six feet between you and other people (this does not include people you live with), and 3) covering your mouth when you cough. Any variable that was significant at p<0.01 in bivariate comparisons was included in an adjusted logistic regression model with the binary lower/ higher perceived effectiveness of COVID-19 prevention measures as the outcome. doi = 10.1371/journal.pone.0241662 id = cord-352969-rpt7xja6 author = Kataria, Ashish title = COVID-19 in Kidney Transplantation: Epidemiology, Management Considerations, and the Impact on Kidney Transplant Practice date = 2020-07-15 keywords = COVID-19; SARS; patient; study; transplant summary = 1, 4 Solid organ transplant (SOT) patients including kidney transplant recipients (KTRs) are at a uniquely increased risk of serious complications from COVID-19 because of immunosuppressive (IS) medication use, elderly age (>65 y), and preexisting comorbidities like diabetes, hypertension, and cardiovascular diseases. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. Kidney transplant recipients may be at a uniquely increased risk of serious complications from COVID-19 as compared to the general population because of a chronically immunosuppressed state and a high prevalence of comorbidities like diabetes, heart disease, and lung disease. 71, 72 At this time, there is no evidence to suggest that kidney transplant patients are at an increased risk of thrombotic events compared with the general population for disease of similar severity. doi = 10.1097/txd.0000000000001031 id = cord-322955-7dw32xby author = Kathwate, Gunderao H title = In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins date = 2020-06-12 keywords = SARS; cell; epitope; protein; vaccine summary = title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Those properties are calculated by different methods at IEDB server (http://tools.iedb.org/bcell/ )like Kolaskar-Tongaonkar antigenicity scale provide physiology of the amino acid residues(45), Emini Surface accessible score for accessible surface of the epitope(46), Secondary structure of epitopes also has role in antigenicity. High scored and common peptides predicted by various tools were selected for deriving sequence of potential vaccine candidate. We designed a multi-epitopes vaccine construct from S-protein of SARS-CoV2. From various epitopes predicted by the online server based on common sequence and high score three TCR and two BCR epitopes were selected as part of COVID19 vaccine. This vaccine codes epitopes form S protein of SARS-CoV2 virus for T and B cell receptors. doi = 10.1101/2020.06.03.131755 id = cord-319707-j8y9gt2o author = Kato, Verstrepen title = Neurological manifestations of COVID-19, SARS and MERS date = 2020-06-19 keywords = COVID-19; MERS; SARS; Syndrome summary = The novel coronavirus, SARS-CoV-2, is likewise a causative pathogen for severe viral pneumonia with the risk of progression to respiratory failure and systemic manifestations. Articles related to the topic were identified by following terms: "Severe Acute Respiratory Syndrome", "Middle East Respiratory Syndrome", Coronavirus disease 2019", "Neurology", "MERS", "SARS", "COVID-19", "Stroke", "Epilepsy", "Guillain-Barré Syndrome", "Encephalitis", "Myelitis", "Meningitis", "Neurological Sequels", "Polyneuropathy" and "Carotid Dissection". Several recent articles report associated cases of encephalitis, acute flaccid paralysis and other neurological symptoms, such as Guillain-Barré syndrome or ADEM, as possible complications of a HCoV infection [6] . Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Neurological complications of middle east respiratory syndrome coronavirus: a report of two cases and review of the literature doi = 10.1007/s13760-020-01412-4 id = cord-314489-e5r5s5ee author = Katsidzira, Leolin title = The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date = 2020-05-11 keywords = Africa; SARS summary = The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . doi = 10.1093/cid/ciaa552 id = cord-310064-p8u424ch author = Katz, Andrew P. title = False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date = 2020-06-12 keywords = PCR; SARS summary = [4] [5] [6] The virus responsible for COVID-19, SARS-CoV-2, poses a particular risk to providers involved in the care of otolaryngology patients due to examinations and surgeries involving the nasopharynx, oropharynx, and upper aerodigestive tract, which harbor high concentrations of viral particles. 6 In line with other institutions across the globe, these protocols call for preoperative testing of asymptomatic patients using reverse transcriptase polymerase chain reaction (RT-PCR) given reports of asymptomatic carriers of SARS-CoV-2 capable of transmission. Tahamtan and Ardebili discuss possible factors causing false negative results of SARS-CoV-2 RT-PCR, namely mismatches between the testing primers and viral genome or low viral loads in samples due to timing of disease or location of collection. In the most recent patient with positive preoperative testing without symptoms (patient #3), pathologists recommended immediate re-testing based on the borderline titers in her test results rather than delaying surgery for weeks for a potential COVID-19 infection. doi = 10.1002/hed.26317 id = cord-274097-11hvriqy author = Katz, Louis M. title = Is SARS‐CoV‐2 transfusion transmitted? date = 2020-06-16 keywords = RNA; SARS summary = The few studies of SARS-CoV-2 RNA in donors or of donors developing COVID-19 after giving blood are a mix of small series wherein prospectively test-positive units were quarantined and not transfused or involved units quarantined after donation to permit the donor time to get ill before units are distributed. In a lookback to recipients of 17 transfused components from seven South Korean donors who developed COVID-19 6 to 15 days after donation, there was no associated clinical morbidity in the recipients; however, archived samples tested by PCR after the donors reported their illnesses were negative. 21 Precise estimates of the prevalence of asymptomatic/presymptomatic infection and especially of whether RNA-emia or, more germane to this topic, viremia occur in the absence of illness (especially in healthy donors or the larger well population who might be qualified to donate) are among the key missing data needed to inform our debate about any risk of TTI and subsequent TTD. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations doi = 10.1111/trf.15831 id = cord-327622-ezgufe24 author = Kaur, Ramandeep title = Practical strategies to reduce nosocomial transmission to healthcare professionals providing respiratory care to patients with COVID-19 date = 2020-09-23 keywords = COVID-19; NIV; SARS; patient summary = • When removing the endotracheal tube, simultaneously turn off the ventilator • Avoid disconnecting ETT from the ventilator circuit before extubation to reduce spray of contaminated aerosols 9 Transport • Place a filter between the artificial airway and the transport ventilator circuit • Use HME that has filter function (HME-F) • Consider clamping the ETT before disconnection from ventilator circuit 10 Bronchoscopy assist* 2 in vivo [44, 45] • For spontaneously breathing patients, place a surgical mask on patient''s face (Fig. 7a, b) • Use NIV mask with examination port for patients on NIV (Fig. 7d) • Use swivel adapter to insert bronchoscope for intubated patient (Fig. 7c) Abbreviations: HFNC high-flow nasal cannula, IPPB intermittent positive pressure breathing, HME heat moisture exchanger, ETT endotracheal tube, NIV non-invasive ventilation *Based on CDC guidelines, these procedures should ideally be performed in airborne infection isolation rooms entrainment or nonrebreather mask [53] . doi = 10.1186/s13054-020-03231-8 id = cord-300899-yi2mx91a author = Kaur, Satinder title = Understanding COVID-19 transmission, health impacts and mitigation: timely social distancing is the key date = 2020-07-18 keywords = COVID-19; China; SARS summary = COVID-19 is a highly infectious disease caused by SARS-CoV-2, first identified in China and spread globally, resulting into pandemic. Various measures are undertaken to prevent infection such as maintaining hygiene, using facemasks, isolation/quarantine, social/physical distancing, in extreme cases lockdown (restricted movement except essential services) in hot spot areas or throughout the country. Python programming is conducted for change point analysis (CPA) using Bayesian probability approach for understanding the impact of restrictions and mitigation methods in terms of either increase or stagnation in number of COVID-19 cases for eight countries. COVID-19 is caused by novel strain of virus SARS-CoV-2 emerged from China and now declared as pandemic due to its presence across the continents in more than 213 countries. Rise in number of cases in different weeks is presented in Table 1 where it can be observed that India, France and Japan had experienced increase in fifth week, that in USA and Spain in the fourth week, Italy in the third week except for Iran and China in second week. doi = 10.1007/s10668-020-00884-x id = cord-328396-p2gvpe8i author = Kaur, Savneet title = The Enigma of Endothelium in COVID-19 date = 2020-08-04 keywords = ARDS; COVID-19; SARS summary = In the current perspective, we envisage a key role of mEC in the pathogenesis of coronavirus disease 2019 caused by the novel coronavirus, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV2). These studies along with the fact that the pulmonary epithelium is more resistant to injury than the endothelium signify that SARS-CoV-2-induced ARDS and associated coagulopathy may be caused by a direct endothelial infection by the virus in the lungs (Matthay et al., 2019) . A summary of such recent reviews and short reports is provided in Table 1 (Alvarado-Moreno and Majluf-Cruz, 2020; Amraei and Rahimi, 2020; Cure and Cure, 2020; Froldi and Dorigo, 2020; Guler et al., 2020; Gupta et al., 2020; Gustafson et al., 2020; Mangalmurti et al., 2020; Marchetti, 2020; Mondal et al., 2020; Panfoli, 2020; Pons et al., 2020; Sardu et al., 2020b; Teuwen et al., 2020) . doi = 10.3389/fphys.2020.00989 id = cord-258701-jyzxu9nk author = Kaushal, Darwin title = Endoscopy in Otorhinolaryngology During Corona Outbreak: A Proposal for Safe Practice date = 2020-08-13 keywords = COVID-19; SARS; endoscopy summary = In this article, we propose essential steps that can be implemented at the departmental and institutional levels to do endoscopic diagnostic procedures effectively during COVID-19 outbreak and to break the transmission chain. Coronavirus disease 2019 (COVID-19) is a type of viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Person-toperson transmission is thought to occur among close contacts mainly via respiratory droplets produced when an infected person coughs or sneezes, which is very common in endoscopic procedures in Otorhinolaryngology. • Deep cleaning and fumigation of the room should be performed when a reverse transcriptase-polymerase chain reaction COVID-19 positive patient undergoes a procedure. • When possible, procedures on COVID-19 suspect/positive patients should be performed as the last procedure, and the endoscopy room should be thoroughly ventilated for at least 1 h before the next procedure by using blowers or natural ventilation. doi = 10.1007/s12070-020-02048-9 id = cord-288733-c51lfwd6 author = Kavanagh, Oisín title = Inhaled Hydroxychloroquine to Improve Efficacy and Reduce Harm in the Treatment of COVID-19 date = 2020-07-15 keywords = SARS summary = An analysis of clinical trials registered on ClinicalTrials.gov revealed that this may continue as many studies combine HCQ with agents that prolong the QT interval. Here we describe an inhaled formulation of HCQ which has passed safety studies in clinical trials for the treatment of asthma and discuss how this approach may reduce side-effects and improve efficacy. Chloroquine and hydroxychloroquine (HCQ) were two of the earliest drugs to 33 receive attention as possible repurposable treatment options for COVID-19 3 . Concerns associated with severe side effects 41 are such that the FDA and EMA now formally recommend against taking HCQ for COVIDEffects of chloroquine on 178 viral infections: An old drug against today''s diseases? FDA Drug Safety Communication: FDA cautions 199 against use of hydroxychloroquine or chloroquine for COVID-19 outside of the 200 hospital setting or a clinical trial due to risk of heart rhythm problems Optimizing hydroxychloroquine 210 dosing for patients with COVID-19: An integrative modeling approach for effective 211 drug repurposing doi = 10.1016/j.mehy.2020.110110 id = cord-331039-qgom2e3n author = Kavitha, Kuppuswamy title = 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates date = 2020-09-22 keywords = CoV-2; Lopinavir; SARS; pro summary = A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 M(pro) and the top 2 lead compounds based on binding affinity were found to be 1,2,4 triazolo[1,5-a] pyrimidin-7-one compounds. The objectives of this study were i) to identify evolutionarily important active site amino acids by structure-based sequence alignment of SARS-CoV-2 and SARS-CoV M pro enzymes ii) to identify potential non-covalent M pro inhibitors by screening protease-inhibitor-like compounds available in the ZINC database by molecular docking studies iii) prediction of absorption, distribution metabolism, excretion and toxicity properties of the top-scoring inhibitors using in silico methods iv) to validate the stable binding of the lead compounds with SARS-CoV-2 M pro by molecular dynamics (MD) simulations and v) to calculate thermodynamic binding energies for each lead compound -SARS-CoV-2 M pro complex using Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) calculations. doi = 10.1016/j.bpc.2020.106478 id = cord-018101-zd4v222b author = Kawashima, Kent title = Disease Outbreaks: Critical Biological Factors and Control Strategies date = 2016-05-31 keywords = SARS; disease; individual; infection; pathogen summary = doi = 10.1007/978-3-319-39812-9_10 id = cord-262412-bs7quwov author = Kaya, Gürkan title = Clinical and Histopathological Features and Potential Pathological Mechanisms of Skin Lesions in COVID-19: Review of the Literature date = 2020-06-30 keywords = COVID-19; SARS; lesion; patient summary = Clinical manifestations are as follows (see Table 1 ): generalized or localized rash (erythematous, papulovesicular, maculopapular, petechial, morbilliform, symmetrical drug-related intertriginous and flexural exanthema (SDRIFE)-like, digitate papulosquamous pityriasis rosea-like), generalized urticaria, varicelliform rash, herpes lesions (zoster), purpuric lesions (retiform purpura), livedoid lesions (livedo reticularis, livedo racemosa), acro-ischemic lesions (dry gangrene, blisters, cyanosis), erythema multiforme-like, chilblain-like lesions (COVID toes) and other lesions such as urticarial vasculitis, acute generalized exanthematous pustulosis (AGEP)-like rash, eosinophilic panniculitis, COVID mask, periorbital dyschromia, oral ulcers and COVID red half-moon nail sign. In a recent report, the postmortem histology of COVID-19 patients revealed lymphocytic endotheliitis in lung, heart, kidney, liver and small intestine, a pathological picture reminiscent of what is seen in skin lesions, suggesting that SARS-CoV-2 infection facilitates the induction of endothelial inflammation in several organs as a direct consequence of viral involvement and of host inflammatory response [61] . doi = 10.3390/dermatopathology7010002 id = cord-302147-6r67g5zk author = Kayaaslan, Bircan title = Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact date = 2020-10-16 keywords = SARS summary = title: Semen Does Not Cause Additional Risk for SARS-CoV-2 Transmission during Sexual Contact The author emphasizes that even if semen has a very low possibility for transmission of the virus, the disease can be transmitted by the respiratory route due to the very close contact between partners. We think that even if severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is detected in a patient''s semen sample, it is quite difficult to say that the transmission between partners has solely been through semen. However, sexual contact carries a high risk in terms of SARS-CoV-2 transmission between partners through the respiratory secretions, not semen. Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 No evidence of severe acute respiratory syndrome-coronavirus 2 in semen of males recovering from coronavirus disease 2019 Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection doi = 10.1159/000511618 id = cord-293692-t5rfvyvj author = Kazi, Sajida title = The delights and perils of publishing, knowledge-sharing and critique during a pandemic: Observations from COVID-19 coagulopathies date = 2020-05-16 keywords = COVID-19; SARS summary = Despite the limited data, the high-stakes milieu and risk of litigation have led several institutions to adopt a more aggressive approach of using intermediate or full-dose anticoagulation for most of their critically ill COVID-19 patients admitted to the Intensive Care Unit [22] . The dissemination of knowledge during times of international crisis is guided by the principles first set out in the World Health Organization''s 2016 statement on data-sharing during public health emergencies, which incorporated lessons from the Ebola and Zika outbreaks, and was undersigned by many notable foundations and journals [23] . These principles have been adopted for use in the current pandemic through a call to share "research data and findings relevant to the novel coronavirus (COVID19) outbreak" in the same fashion [24] . Sharing research data and findings relevant to the novel coronavirus (COVID-19) outbreak doi = 10.1016/j.thromres.2020.05.023 id = cord-318029-xd7nuahh author = Ke, Chunjin title = 2019 novel coronavirus disease (COVID-19) in hemodialysis patients: a report of two cases date = 2020-04-30 keywords = SARS; covid-19 summary = authors: Ke, Chunjin; Wang, Yufeng; Zeng, Xing; Yang, Chunguang; Hu, Zhiquan OBJECTIVE: To analyze the diagnosis and treatment of patients with chronic renal failure complicated with novel coronavirus pneumonia, and to evaluate the effect of blood purification technology on the treatment and prognosis of such patients METHODS: Two COVID-19 cases undergoing hemodialysis with chronic renal failure were retrospectively analysed in our hospital. On January 8, 2020, the Chinese Center for Disease Control and Prevention officially announced the pneumonia was caused by a new type of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2] . Hyperviremia and cytokine storm are important causes for COVID-19''s evolution to severe pneumonia, even to multiple organ dysfunction in a few cases [6] . Blood purification technology seems to be helpful for preventing COVID-19 patients with chronic renal failure from severe pneumonia or even multiple organ dysfunction. Interferon and cytokine responses to SARS-coronavirus infection doi = 10.1016/j.clinbiochem.2020.04.008 id = cord-294073-65h2mkdy author = Ke, Jia title = Strategies and recommendations for the management of gastrointestinal surgery during the COVID-19 pandemic: experience shared by Chinese surgeons date = 2020-07-03 keywords = COVID-19; SARS; patient summary = We also recommend that each hospital should establish a group of diagnostic experts with responsibilities for risk stratification, especially for patients under investigation who need urgent surgery. • It is known that fever is one of the most common symptoms of COVID-19 and that patients with certain GI diseases (e.g. acute appendicitis, gastric perforation, intestinal obstruction) who required urgent care with emergency GI surgery often present with high fever as well. COVID-19-positive patients with GI bleeding with hemodynamic stability should undergo conservative treatments first, including angioembolization, before endoscopic treatment due to the high risk of endoscopy being an aerosol-generating procedure. For confirmed/high-risk COVID-19 patients and PUIs, diagnostic and therapeutic GI endoscopies should be performed in a negative-pressure room with Level Three precautions. For all surgical personnel involved in GI surgery for confirmed/ high-risk COVID-19 patients or for PUIs for COVID-19, we recommend the following protective measures (Figure 1 ). doi = 10.1093/gastro/goaa030 id = cord-287304-h6wj7m8u author = Keil, Roger title = Governing the Sick City: Urban Governance in the Age of Emerging Infectious Disease date = 2007-12-07 keywords = SARS; Toronto; city; governance; health; new; public; urban summary = While there has been much attention in recent years on the significance of global city regions in the new world economy (Brenner and Keil 2006) and while the governance and regulation of these regions has captured the imagination of academics and policymakers alike (Buck et al 2005; Harding 2005; Heinelt and Kübler 2005; Kantor and Savitch 2005; Scott 2001) , little has been said specifically about the growing pressures posed by the potential threat of infectious disease through the global network on urban governance. 2 For the area of urban planning and governance a more or less critical literature has begun to explore the spaces that cities have to maneuver in the rather open field of infectious disease preparedness planning and public health since the onset of the "new normal" after the attacks of 9/11 Malizia 2006; Matthew and Macdonald 2006) . doi = 10.1111/j.1467-8330.2007.00555.x id = cord-305130-vz72ldbo author = Keil, Shawn D. title = Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment date = 2020-05-14 keywords = SARS; plasma summary = title: Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment CONCLUSION: Riboflavin and UV light effectively reduced the titre of SARS‐CoV‐2 in both plasma and platelet products to below the limit of detection in tissue culture. The author of MERS-CoV study also indicated that they were not able to recover infectious virus from those patient samples using cell culture, suggesting that transfusion transmission is a low risk [15] . As with the plasma study, the virus titre was reduced to the limit of detection (≤0Á25 log PFU/ml) in all three donor platelet units. Riboflavin and UV light effectively reduced the titre of SARS-CoV-2 in both human platelet and plasma products to below the limit of detection using an in vitro plaque assay. Inactivation of Middle East respiratory syndrome coronavirus (MERS-CoV) in plasma products using a riboflavinbased and ultraviolet light-based photochemical treatment doi = 10.1111/vox.12937 id = cord-301744-rx7ywew5 author = Kelleni, Mina T. title = SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality date = 2020-08-15 keywords = SARS summary = title: SARS CoV-2 viral load might not be the right predictor of COVID-19 mortality have reported SARS-CoV-2 viral load at diagnosis as an independent predictor of mortality. In a trial to explain the apparent contradictory results found in different studies as well as the lack of a distinct boundary between the viral loads that might be associated with a higher mortality rate or a higher recover rate; the author would like to suggest that SARS CoV-2 viral load should be only considered as a personalized reflection to the immune response to COVID-19 as well as to the genetic polymorphisms in SARS CoV-2 receptors 3 . ACE2 polymorphisms might be a better field of study than SARS CoV-2 viral load wishing to develop a genetic test that might predict and exempt, if possible, from COVID-19 related duty those who are more vulnerable to complications and mortality 4 SARS-CoV-2 viral load predicts COVID-19 mortality doi = 10.1016/j.jinf.2020.08.018 id = cord-353599-cw29edwr author = Kelleni, Mina T. title = Early use of Non-steroidal anti-inflammatory drugs in COVID-19 might reverse pathogenesis, prevent complications and improve clinical outcomes date = 2020-11-04 keywords = COVID-19; SARS; patient summary = In this manuscript, we present a novel theory to explain the pathogenesis of COVID-19; lymphocyte distraction theory upon which the author has used, in a preprinted protocol, non-steroidal anti-inflammatory drugs (NSAIDs); diclofenac potassium, ibuprofen and ketoprofen, successfully to treat COVID-19 patients. It was previously suggested that SARS CoV induced lymphopenia is likely to be caused by indirect mechanisms such as an increase in cortisol levels that occurred as part of the body stress response to this severe respiratory viral infection or by an iatrogenic effect of glucocorticoids used to manage those patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1016/j.biopha.2020.110982 id = cord-337200-2qwty2jp author = Kempfle, J. S. title = Management von Patienten mit Tracheostoma während der COVID-19-Pandemie: Literaturüberblick und Demonstration date = 2020-06-08 keywords = Patienten; SARS; Tröpfchen; der; die; und summary = Die durch das neue Coronavirus, auch Severe-Acute-Respiratory-Syndrome-Coronavirus 2, kurz SARS-CoV-2 genannt, ausgelöste Erkrankung (COVID19) , zeichnet sich durch eine hohe Variabilität an Symptomen aus. Während eine große Anzahl an SARS-CoV-2-positiven Patienten keine oder nur leichte Symptome einer oberen Atemwegsinfektion hat, gibt es eine Gruppe von Patienten, die eine deutliche Einschränkung ihrer Lungenfunktion mit Pneumonie bis hin zur lebensbedrohlichen Variante mit akutem Lungenversagen ("acute respiratory distress syndrome", ARDS) entwickelt [18, 37, 40] . Eine kürzlich in Nature Medicine erschienene Studie, welche sich mit den Erkältungs-Coronaviren beschäftigte, konnte diese sowohl in der ausgeatmeten Luft über einen Zeitraum von 30 min als auch in erhöhter Konzentration in Aerosolen und Tröpfchen von wiederholt hustenden Patienten nachweisen [19] . Während erste Leitlinien sowohl in Deutschland als auch international vorläufige Empfehlungen zu Vorsichtsmaßnahmen bei In-und Extubationen oder Tracheotomien von beatmungspflichtigen COVID-19-Patienten aussprechen [1, 4, 12, 20, 22, 30, 35] , ist vergleichsweise wenig Information zum weiteren Umgang mit einem tracheotomierten SARS-CoV-2-positiven Patienten auf Station, ambulant oder während der Rehabilitation zu finden [10] . doi = 10.1007/s00106-020-00892-3 id = cord-329290-vqvujry3 author = Kempker, Russell R title = Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date = 2020-06-28 keywords = HCP; SARS summary = HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. doi = 10.1093/cid/ciaa877 id = cord-336488-opjjowcq author = Kenanidis, Eustathios title = Organizing an Orthopaedic Department During COVID-19 Pandemic to Mitigate In-Hospital Transmission: Experience From Greece date = 2020-06-17 keywords = SARS; covid-19; patient summary = The aim of this paper is to review the existing orthopaedic literature and to present the principles of management and care implemented in the orthopaedic departments of a tertiary academic hospital in Greece to operate during COVID-19 pandemic in order to mitigate the risk of in-hospital transmission of SARS-CoV-2 to the medical, nursing and administrative orthopaedic personnel. In addition, we presented the clinical indications to delineate orthopaedic patients who deserve emergency or urgent in-hospital care from those that can be treated in the outpatient setting, as well as from the day surgery clinics or could not be admitted in the hospital, in order to decrease the SARS-CoV-2 transmission load. The proposed principles of management and care are deployed below as (1) general management of the orthopaedic departments, (2) recommendations for the management of traumatic orthopaedic injuries, (3) hospital pathways for the admitted orthopaedic patients (4) workflow of the isolated and negative pressure COVID-19 operating theatre (COT) and (5) postoperative care of the COVID-19 infected patients. doi = 10.7759/cureus.8676 id = cord-023875-5mu5ra29 author = Keng, Choong-Tat title = Molecular and Biochemical Characterization of the SARS-CoV Accessory Proteins ORF8a, ORF8b and ORF8ab date = 2009-07-22 keywords = SARS summary = Epidemiological studies have revealed that the part of the viral genome that encodes for ORF8a and ORF8b showed major variations and the animal isolates contain an additional 29-nucleotide sequence which is absent in most of the human isolates. Although the mutations in the ORF8 region do not appear to have any adverse effect on the survival of the virus, it is conceivable that the ORF8a, ORF8b and ORF8ab proteins have different stabilities and/or functions, and hence would contribute differently to viral replication and/or pathogenesis in vivo. Since SARS-CoV grows well in cell culture, different groups also generated ORF8a and ORF8b specific antibodies in order to determine their expression during infection in vitro. As described above, the accessory proteins ORF8a and ORF8b are expressed during infection in vitro, but replacing them with ORF8ab does not affect SARS-CoV replication in cell culture or small animal models. doi = 10.1007/978-3-642-03683-5_12 id = cord-332196-03cklmm3 author = Kennedy, Amy J. title = Retesting for severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Patterns of testing from a large US healthcare system date = 2020-08-10 keywords = SARS summary = Often decisions on who to test are left to individual clinicians, which leads to questions about when and who to retest for COVID-19, how often false positives or negatives might occur, and the duration of positivity. This report describes patterns of SARS-CoV-2 nucleic acid polymerase chain reaction (PCR) retesting in inpatients and outpatients within a large US healthcare system. We performed a retrospective chart review of all inpatients and outpatients aged ≥18 years receiving care within the University of Pittsburgh Medical Center (UPMC) with ≥2 SARS-CoV-2 PCR tests with an initial test between March 3 and May 3, 2020, and a subsequent test before May 21, 2020. In this retrospective study of a large US healthcare system, we found that retesting for SARS-CoV-2 was uncommon and often resulted in multiple negative tests. Utility of retesting for diagnosis of SARS-CoV-2/COVID-19 in hospitalized patients: impact of the interval between tests doi = 10.1017/ice.2020.413 id = cord-260429-5wsj003j author = Kenyon, Chris title = Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study date = 2020-04-06 keywords = SARS; mask summary = title: Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV1. Methods At a country level, linear regression was used to assess the association between COVID19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID19 epidemic and testing intensity. Conclusion Whilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections. /2020 In this ecological study we found that countries that promoted widespread face mask 185 usage had lower cumulative numbers of COVID-19 diagnosed after controlling for 186 testing intensity and age of the epidemic. doi = 10.1101/2020.03.31.20048652 id = cord-316970-n2dly3oa author = Kerbaj, Jad title = COVID-19: The New Caledonia experience date = 2020-05-16 keywords = SARS summary = Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island''s hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. doi = 10.1093/cid/ciaa600 id = cord-305610-v1hn934x author = Kerslake, Rachel title = Co-expression of peripheral olfactory receptors with SARS-CoV-2 infection mediators: Potential implications beyond loss of smell as a COVID-19 symptom date = 2020-06-17 keywords = OR51E2; SARS; TMPRSS2 summary = Using Gene Expression Profiling Interactive Analysis, The Cancer Genome Atlas, Genotype-Tissue Expression, cBioPortal and Shiny Methylation Analysis Resource Tool, we highlight the expression of peripheral ORs in both healthy and malignant tissues, and describe their co-expression with key mediators of SARS-CoV-2 infection, such as ACE2 and TMPRSS2, as well as cathepsin L (CTSL; another cellular protease mediating SARS-CoV-2 infection of host cells). The present study aimed to identify, both in normal and cancer tissues, the co-expression profile of a number of ORs which are known to be expressed in peripheral tissues in relationship to key mediators of the SARS-coV-2 infection, namely AcE2, TMPRSS2 and cTSL. In conclusion, the present study offers new data regarding the expression of ORs in peripheral tissues and their co-expression pattern with key mediators of SARS-coV-2 cell entry and infection (i.e., AcE2, TMPRSS2, and cTSL). doi = 10.3892/ijmm.2020.4646 id = cord-287447-5lzzobl3 author = Keyaerts, Els title = In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date = 2004-10-08 keywords = PCR; SARS summary = Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Glycyrrhizin (an active component of liquorice roots), niclosamide (an antihelminthic drug), nelfinavir (a human immunodeficiency deficiency virus (HIV) protease inhibitor), and SNAP (a nitric oxide donor) were reported to have an antiviral effect against SARS-CoV [12] [13] [14] [15] . In this study we report the in vitro antiviral activity of chloroquine against SARS-CoV Frankfurt 1 strain infection. The IC 50 of chloroquine inhibition of SARS-CoV replication in Vero E6 cells, 8.8 lM, is below (1000-fold) the plasma concentrations of chloroquine that are reached in human plasma, following treatment with chloroquine (for acute malaria) at a dose of 25 mg/kg over three days [27] . Our results show that chloroquine inhibits the replication of SARS-CoV in Vero E6 cells. doi = 10.1016/j.bbrc.2004.08.085 id = cord-284038-93s3ffoy author = Keyhanian, Kiandokht title = SARS-CoV-2 and nervous system: From pathogenesis to clinical manifestation date = 2020-11-07 keywords = CNS; COVID-19; CSF; SARS; patient summary = Since the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a growing body of evidence indicates that besides common COVID-19 symptoms, patients may develop various neurological manifestations affecting both the central and peripheral nervous systems as well as skeletal muscles. Growing number of case reports and/or series indicate that a variety of neurological conditions and post-viral triggered autoimmune complications, as we discuss below, occur in association with SARS-CoV-2 infection which mainly include Guillain-Barré syndromes (GBSs) (table 2), myopathy and rhabdomyolysis (table 2) , encephalopathy, meningoencephalitis, encephalomyelitis, and myelitis (table 3) . Moreover, two cases of acute necrotizing encephalopathy (ANE) in patients with COVID-19 positivity from nasopharyngeal and oropharyngeal swab, but without CSF PCR for SARS-CoV-2 data, were reported in the literature (Poyiadji, Shahin, 2020 , Radmanesh et al. doi = 10.1016/j.jneuroim.2020.577436 id = cord-253862-jl1zhg13 author = Khalaf, Khalil title = SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date = 2020-10-06 keywords = ACE-2; COVID-19; CoV-2; IFN; RNA; SARS; cell; patient summary = Although this novel virus is less severe than the first SARS-CoV outbreak, human-to-human transmission remains very high and the number of cases continues to rise exponentially in major urban areas, highlighting the urgent need to develop new containment, diagnostic, and treatment protocols. In the case of SARS-CoV-2, viral evasion of the innate immune system leads to an increase in cytokine production and late CD4+/CD8+ response, which then leads to pathogenic inflammation in patients with high viral loads. (ChiCTR2000029308), involving severe SARS-CoV-2 cases, compared lopinavir/ritonavir treatment with standard care alone, and they showed that the antivirals yielded no clinical benefits. In an open-label control study conducted by Cai et al., the antiviral activity of favipiravir + IFN-α was compared to that of lopinavir/ritonavir + IFN-α in patients with confirmed SARS-CoV-2 infection. doi = 10.3389/fimmu.2020.570927 id = cord-301828-qux5hvcw author = Khalifa, Ibrahim title = Tannins inhibit SARS‐CoV‐2 through binding with catalytic dyad residues of 3CL(pro): An in silico approach with 19 structural different hydrolysable tannins date = 2020-08-11 keywords = 3CL; COVID-19; SARS summary = We therefore theoretically studied and docked the effects of 19 hydrolysable tannins on SARS‐CoV‐2 by assembling with the catalytic dyad residues of its 3CL(pro) using molecular operating environment (MOE 09). Likewise, tannin-type compounds, such as epiacutissimins A and B, castalin, vescalin, chebulagic acid, and punicalagin showed anti-herpesvirus activity via targeting viral glycoprotein-glycosaminoglycan binding to inhibit access and cell-to-cell feast (Lin et al., 2011; Aires, 2020 The current study was designed to find out a potent inhibitor against COVID-19 from 19 structural different hydrolysable tannins which could target the main protease of SARS-CoV-2 using in silico approaches (molecular docking and drug-likeness scan). Among these hydrolysable tannins, pedunculagin, strongly interacted with the catalytic dyad residues (Cys-145 and His-41) of SARS-CoV-2-3CL pro , with sense binding affinity, docking score, and ADMET properties. Herein, we screened the structural relationship activity of 19 hydrolysable tannins as potential antiviral components and we chose the top three hits that may inhibit the main protease of SARS-CoV-2 and hence virus copying. doi = 10.1111/jfbc.13432 id = cord-274459-781by93r author = Khalifa, Shaden A. M. title = Comprehensive Overview on Multiple Strategies Fighting COVID-19 date = 2020-08-11 keywords = COVID-19; China; Health; SARS; people summary = Our review aims to evaluate strategies of the most affected countries from different continents all over the world (China, Italy, Germany, France, Spain, America, Canada, Brazil, UK, India, Japan, Singapore, Iran, Korea, and Australia) for confronting the epidemic as it explains the best practices that could help other countries to overcome current or any upcoming pandemic. Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . Most countries were forced to announce emergency measures to protect vulnerable people and block ways of transmission due to the continuous increase in confirmed cases by time as reported in Figure 3 [11] [12] [13] [14] [15] [16] . doi = 10.3390/ijerph17165813 id = cord-322204-kc7dy2za author = Khalil, Asma title = SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date = 2020-08-08 keywords = SARS summary = title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of doi = 10.1093/cid/ciaa893 id = cord-252725-e3pazjdi author = Khalil, Ayman title = The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date = 2020-10-15 keywords = COVID-19; Fig; SARS; TNF; anti; virus summary = In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . doi = 10.1007/s13659-020-00271-z id = cord-316129-mjg3un0l author = Khamar, Pooja title = Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases date = 2020-07-13 keywords = SARS; droplet; microkeratome summary = title: Aerosol and droplet creation during oscillatory motion of the microkeratome amidst COVID-19 and other infectious diseases METHOD: In an experimental setup, flap creation was performed on enucleated goat''s eyes (n = 8) mounted on a stand using One Use-Plus SBK Moria microkeratome (Moria SA) to assess the spread of aerosols and droplets using high-speed shadowgraphy. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively. 13, 14 Therefore, we quantified the aerosol and droplet generation during flap creation using the Moria One Use-Plus SBK microkeratome (Moria SA) and assessed their trajectory using high-speed shadowgraphy and fluid mechanics principles. doi = 10.1097/j.jcrs.0000000000000326 id = cord-352322-tsjwnvkk author = Khamassi Khbou, Médiha title = Coronaviruses in farm animals: Epidemiology and public health implications date = 2020-09-25 keywords = China; MERS; SARS; coronavirus; porcine summary = As consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (TGEV) of swine and the bovine CoV (BCoV) likely originated from the closely related canine coronavirus (CCoV) (Pratelli, 2011) . Coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean CoVs were also considered, as marine mammals are a food source in many countries around the world. Since the first case of human infected by the MERS-CoV was identified in September 2012 in Saudi Arabia (World Health Organization, 2019), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (Omrani, Al-Tawfiq, & Memish, 2015) . Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Infection with a new porcine respiratory coronavirus in Denmark: Serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies doi = 10.1002/vms3.359 id = cord-278362-pwi48i20 author = Khan, Abbas title = Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) date = 2020-06-18 keywords = COV-2; SARS; Saquinavir; drug summary = title: Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro) Furthermore, results from molecular dynamics simulation and total binding free energy revealed that Saquinavir and TCM5280805 target the catalytic dyad (His41 and Cys145) and possess stable dynamics behavior. In this study, the protein of SARS-COV-2 (3CLpro, also named 3-chymotrypsin-like protease) was subjected to drug repurposing and virtual screening for potent drug identification followed by molecular dynamics simulation and binding free energy calculation. In the current study, the repurposing of anti-HIV drugs against the SARS-COV-2 main protease was carried out using structure-based screening methods. In this study, based on the results of bioinformatics analysis, we targeted 3CLpro from SARS-COV-2 using drugs repurposing (anti-HIV drugs) virtual drugs screening (TCM) approaches to shortlist the most potent compounds for the possible treatment. doi = 10.1080/07391102.2020.1779128 id = cord-300991-ipy24zxp author = Khan, Amira Sayed title = Obesity and COVID-19: Oro-Naso-Sensory Perception date = 2020-07-08 keywords = SARS; TNF; covid-19; obesity; olfactory summary = Through a recent upsurge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, the clinical assessment of most of the coronavirus disease 19 (COVID-19) patients clearly presents a health condition with the loss of oro-naso-sensory (ONS) perception, responsible for the detection of flavor and savor. Hence, obesity represents a great risk factor for SARS-CoV-2 infection, as it may hide the viral-associated altered ONS symptoms, thus leading to a high mortality rate in these subjects. Moreover, the number of immunosuppressive T-regulatory, Treg (CD4 + CD25 + Foxp3 + ) cells and concentrations of IL-6, IL-10, and C-reactive protein (CRP) were upregulated in patients with severe COVID-19 [18] , suggesting that SARS-CoV-2 infection may lead to "over-immunosuppression" in the case of obesity ( Figure 1 ). SARS-CoV-2 infection may further aggravate the ONS functions; mask the obesity-induced inflammation, including loss of taste and smell; and render the obese subjects more vulnerable and prone to severe pathophysiological consequences such as RTI, leading to death. doi = 10.3390/jcm9072158 id = cord-304792-8sdxqmkb author = Khan, Md. Abdullah-Al-Kamran title = SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date = 2020-05-08 keywords = CoV-2; SARS; figure summary = title: SARS-CoV-2 proteins exploit host''s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. We have utilized KEGG mapper tool (Kanehisa and Sato, 2020) for the mapping of 197 deregulated genes SARS-CoV-2 interacting host proteins in different cellular pathways. doi = 10.1101/2020.05.06.050260 id = cord-263874-q0egnzwf author = Khan, Md. Arif title = Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study date = 2020-07-22 keywords = Epirubicin; SARS; drug summary = Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. Also, researchers have currently reported using the drug repurposing approach based on the molecular docking and dynamics study where the key target proteins are 3CL protease, RNA dependent RNA polymerase (RdRp), and spike proteins (Elfiky, 2020b; Muralidharan et al., 2020; Smith & Smith, 2020; Tahir Ul Qamar et al., 2020; Yu et al., 2020) . In this ground, it is clearly seen that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions among the 23 potential inhibitors against SARS-CoV-19 main protease and those results pave the way in drug discovery although it has to be further validated by in vitro and in vivo investigations. doi = 10.1080/07391102.2020.1796813 id = cord-346819-11fkgzaa author = Khan, Mohd Imran title = Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date = 2020-09-03 keywords = CoV-2; Mpro; SARS; protein summary = title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. The genome analysis of the SARS-CoV-2 strains from 13 different countries showed a large number of mutations within the major structural proteins. This study provides a deeper insight into the emergence of these mutations within the major structural as well as nsp encoded by the SARS-CoV-2 genome from different countries. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations backbone RMSD was also noticed (Fig 4A) . doi = 10.1371/journal.pone.0238344 id = cord-304295-3mpymd8a author = Khan, Muhammad Muzamil title = Emergence of novel coronavirus and progress toward treatment and vaccine date = 2020-06-04 keywords = CoV-2; SARS; coronavirus summary = 10 Favipiravir was effectively used against influenza and has the potential to inhibit viral RNA synthesis and a new study also supports its activity against SARS-CoV-2. 15 In another recent study, Gao et al found that chloroquine phosphate reduced the symptoms of pneumonia in SARS-CoV-2 patients and shortening the duration of disease. 67 Different technologies are being utilized to F I G U R E 1 Mechanism of action of HCQ and CQ by blocking binding of virus with ACE-2 receptors and increasing endosomal pH and preventing fusion with the cell develop potential vaccine for SARS-CoV-2 including DNA and mRNAbased nanoparticles. Clinical study for safety and efficacy of favipiravir in the treatment of novel coronavirus pneumonia (COVID-19) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1002/rmv.2116 id = cord-333524-a6p6ma8r author = Khan, Pavana title = Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date = 2020-09-23 keywords = LAMP; PCR; RNA; SARS; dna summary = 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). doi = 10.1021/acssynbio.0c00359 id = cord-281501-ca9oxl7f author = Khan, Shumayila title = Neuropathogenesis of SARS-CoV-2 infection date = 2020-07-30 keywords = ACE2; SARS; covid-19 summary = Emerging reports of encephalopathies and similar ailments with the detection of the virus in the CSF has elicited an urgent need for investigating the possibility of neuroinvasiveness of the virus, which cannot be ruled out given the expression of low levels of ACE2 receptors in the brain. One study from Japan which described the first case of COVID-19-associated encephalitis where the patient was admitted for convulsions accompanied by unconsciousness reported that although the patient tested negative for SARS-CoV-2 in a nasopharyngeal swab, the viral RNA was surprisingly detected in the CSF, and the patient MRI exhibited abnormalities of the medial temporal lobe and hippocampus (Moriguchi et al., 2020) . The preliminary reports which hint towards the involvement of the CNS imply an urgent need for more studies, and a systematic collection and preservation of CSF samples along with associated clinical data, at least in patients displaying extrapulmonary or neurological symptoms, to examine the neuronal aspect of COVID-19. doi = 10.7554/elife.59136 id = cord-269553-d3hozs14 author = Khan, Suliman title = The spread of novel coronavirus has created an alarming situation worldwide date = 2020-04-30 keywords = China; SARS summary = The COVID-19 epidemic became a serious challenge for the healthcare authorities, scientific community, and the infections controlling agencies across China, in terms of spread, treatment, and prevention. In the current scenario of the outbreak in Wuhan, healthcare workers are at the highest risk of contracting an infection. This indicates that a large number of medical staffs is suspected to have contracted the infection and their confirmation may create an alarming situation for healthcare authorities. Therefore, the increasing numbers of infected and suspected doctors and nurses are creating an additional significant shortage of working medical staff, thus, increasing an additional working and mental pressure on the normal health workers [6] . The medical staff resisted to provide treatment services to the suspected individual, fearing the possible transmission of the infection. Beside this, hospitals in developing or underdeveloped countries should be equipped on urgent basis for providing effective services to the individuals infected by novel coronavirus. doi = 10.1016/j.jiph.2020.03.005 id = cord-276769-th7iou21 author = Khan, Suliman title = Coronaviruses disease 2019 (COVID-19): causative agent, mental health concerns, and potential management options date = 2020-07-25 keywords = MERS; SARS; covid-19 summary = Despite physical health consequences, COVID-19 pandemic has created stress and anxiety, as result there is an increased risk of mental illnesses both in the infected and normal individuals. Although bats are thought to be the source of origin for SARS-CoV-2, the intermediate animal that caused the transmission of virus to humans, is still unknown [3] . The individuals at higher risk of developing severe disease after contracting the infection should be give the priority for treatment and providing the mangeemtn and health servicesConsidering the importance of COVID-19 in the aspects of the asymptomatic spread of the virus and adverse health impacts, it is deemed necessary to investigate the factors associated with the rate of infectiousness and severity of symptoms. After originating in bats, SARS-CoV-2 emerged in Wuhan, spread all over the world through human to human transmission, and infected millions of individuals. doi = 10.1016/j.jiph.2020.07.010 id = cord-279443-2e4gz2bo author = Khan, Suliman title = Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns date = 2020-06-09 keywords = CoV-2; SARS; covid-19; transmission summary = To identify and select the papers in this review we searched the published research and review articles relevant to origin and outbreaks of three human coronaviruses, and features, transmission, spread, entry mechanisms, infectiousness, control strategies, and animals hosts for SARS-CoV-2. Although it is important to know about the symptoms'' appearance and severity, however, understanding the transmission of the infection to healthy individuals from COVID-19 patients and zoonotic sources can be of great importance in the aspects of developing strategies to prevent and control the spread of COVID-19. This outbreak was reported to be caused by SARS-CoV, originated from market civets before its transmission and infection in humans (17) . Early claims came FIGURE 2 | The SARS-CoV-2 transmission from bats via unknown intermediate to humans causes infectiousness known as COVID-19 disease. According to the CDC report on coronavirus disease, individuals with underlying chronic medical conditions are at higher risk for contracting COVID-19 infection. doi = 10.3389/fmed.2020.00310 id = cord-312350-klxw65qa author = Khan, Zafran title = Diagnostic approaches and potential therapeutic options for coronavirus disease (COVID-19) date = 2020-09-30 keywords = Khan; SARS summary = To date, more than 300 clinical trials have been conducted on various antiviral drugs, and immunomodulators are being evaluated at various stages of COVID-19. This review is aimed to collect and summarize a list of drugs used to treat COVID-19 for instance, dexamethasone, chloroquine, hydroxychloroquine, lopinavir/ritonavir, favipiravir, remdesivir, tociluzimab, nitazoxanide, and ivermectin. WHO 154 launches the "Solidarity" clinical trial for COVID-19 treatment to further evaluate remdesivir, 155 hydroxychloroquine/chloroquine, and lopinavir-ritonavir with and without interferon-beta [64] . Recently in Singapore, the five COVID-19 patients were subjected to treatment with lopinavir 258 and ritonavir within 1 to 3 days of desaturation, but evidence of clinical use is ambiguous. Clinical and 708 microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-709 19 patients with at least a six-day follow up: A pilot observational study. Effective treatment of severe COVID-749 19 patients with tocilizumab Antigen Detection Tests for Respiratory Syncytial Virus Infection: Systematic Review and Meta-779 analysis doi = 10.1016/j.nmni.2020.100770 id = cord-309138-44qpk2vf author = Khanna, Kanika title = Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date = 2020-10-03 keywords = ACE2; COVID-19; CoV-2; PAK1; SARS; infection summary = Moreover, AYUSH has recommended certain preventive and medicinal plants for prevention and prophylactic of COVID-19 including warm extracts of Tinospora cordifolia (advised for chronic fever), Andrograhis paniculata (advised for fever and cold), Cydonia oblonga, Zizyphus jujube and Cordia myxa (enhancing antioxidant, immune-modulatory, anti-allergic, smooth muscle relaxant, anti-influenza activity) and Ever since, has been elucidated that, PAK1 tends to cause cancers, viral diseases like HIV, Hepatitis, pappiloma, influenza, ebola, SARS and corona virus along with immune system suppression of hosts, henceforth, propolis would be quintessential in blocking COVID/coronavirus curbed fibrosis in respiratory tract and boosting the immunity of an individual (Maruta, 2014) . Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study Molecular mechanism of action of repurposed drugs and traditional Chinese medicine used for the treatment of patients infected with COVID-19: A systematic review Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective doi = 10.1016/j.phymed.2020.153361 id = cord-345999-iiw4cs8p author = Khare, Prashant title = Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date = 2020-09-24 keywords = SARS; Wen summary = Since it is a newly emerging viral disease and obviously there is a lack of anti-SARS-CoV-2 therapeutic agents, it is urgently required to develop an effective anti-SARS-CoV-2-agent.Through recent advancements in computational biology and biological assays, several natural compounds and their derivatives have been reported to confirm their target specific antiviral potential against Middle East respiratory syndrome coronavirus (MERS-CoV) or Severe Acute Respiratory Syndrome(SARS-CoV).These targets including an important host cell receptor, i.e., angiotensin-converting enzyme ACE2 and several viral proteins e.g. spike glycoprotein (S) containing S1 and S2 domains, SARS CoV Chymotrypsin-like cysteine protease (3CL(pro)), papain-like cysteine protease (PL(pro)), helicases and RNA-dependent RNA polymerase (RdRp). For the management J o u r n a l P r e -p r o o f of COVID-19 infection, various molecular targets playing important role in the SARS-CoV-2 life cycle including host cell receptor-Angiotensin-converting enzyme ACE2 (PDB ID 3D0G) and viral proteins such as S protein (containing S1 and S2 domains) (PDB ID 6XM0); various cysteine proteases such as papain-like cysteine protease (PL pro ) (PDB ID 6WX4) or Chymotrypsin like nprotease (3CL pro ) (PDB ID 1P9U), helicases and RNA-dependent RNA polymerase (RdRp) (PDB ID 6M71) could be evaluated . doi = 10.1016/j.virusres.2020.198169 id = cord-323061-0i5w7vm9 author = Kharel Sitaula, Ranju title = Unfolding COVID-19: Lessons-in-Learning in Ophthalmology date = 2020-09-28 keywords = ACE2; CoV-2; SARS; ocular summary = 10 Epiphora and Conjunctival redness had been the first manifestation of SARS-CoV-2 infection in 3 reported cases till date which includes a member of National expert on pneumonia during his visit to endemic areas of Wuhan and an anesthesiologist contracting the virus from a known patient of novel coronavirus pneumonia during intubation in Italy; similarly, it was reported in a nurse working in the emergency department of ophthalmology who presented with viral conjunctivitis and watering as a first sign. Hence, our knowledge and understanding about the SARS-CoV-2 virus, modes of entry to the eye, hypothesis on the interaction with the Renin-Angiotensin System (RAS) system and ACE2 receptor and ocular pathogenesis and RT PCR analysis from the ocular secretions have been summarized below using text, tables, diagrams, and flowcharts. doi = 10.2147/opth.s259857 id = cord-277679-sc9hugxr author = Khateb, Mohamed title = Coronaviruses and Central Nervous System Manifestations date = 2020-06-23 keywords = CNS; COVID-19; SARS summary = This minireview scans the literature regarding the involvement of the CNS in coronavirus infections in general, and in regard to the recent SARS-CoV-2, specifically. In December 2019, the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged in Wuhan, China. Accumulating evidence implies a possible link between infection with the novel SARS-CoV-2 and acute ischemic stroke (AIS). Accumulating evidence from the current SARS-CoV-2 pandemic, together with literature on other coronaviruses, suggest that infection with coronaviruses may be related to CNS manifestations or complications, including anosmia, acute ischemic strokes, viral meningoenchephalitis, acute necrotizing encephalopathy, acute flaccid paralysis, and other presumably post/para-infectious syndromes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome doi = 10.3389/fneur.2020.00715 id = cord-349226-xzlc1pni author = Khatiwada, Saroj title = Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date = 2020-08-05 keywords = COVID-19; SARS; lung; respiratory summary = To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease. doi = 10.1016/j.humic.2020.100073 id = cord-306581-g3d0lqxp author = Khattab, Mohamed H. title = Early detection of SARS-CoV-2 from staging PET-CT date = 2020-09-29 keywords = CoV-2; SARS summary = METHODS: Here, we present a case study of a mildly symptomatic patient with anal cancer diagnosed with SARS-CoV-2 from a staging PET-CT scan. Given the ongoing COVID-19 pandemic, a nasopharyngeal swab with polymerase chain reaction (PCR) was obtained and was confirmed positive for the potentially lethal SARS-CoV-2 viral infection. In geographic regions with a Fig. 1 Screening positron emission tomography fused with computed tomography demonstrating fluorodeoxyglucose-avid multifocal, rounded, peripheral ground-glass nodules, some demonstrating the reversed halo sign, within the right lower, right middle, and left lower lung lobes concerning for an infectious process significant and increasing COVID-19 case burden, routine PCR testing in the absence of clinical or radiologic findings may be indicated in patients undergoing chemoradiation or radiation, and it is our institutional practice to test all patients receiving any chemotherapy or greater than 10 days of radiation. In the setting of asymptomatic or mildly symptomatic patients with confirmed SARS-CoV-2 infection, multidisciplinary discussion with oncology and infectious disease teams is important to ascertain the risks and benefits of delaying cancer therapy. doi = 10.1007/s13566-020-00436-w id = cord-310803-iig414jg author = Khazeei Tabari, Mohammad Amin title = Applying Computer Simulations in Battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic date = 2020-10-17 keywords = COVID-19; SARS summary = COVID-19 is a disorder caused by SARS-CoV-2, which has CoV-2 genome sequencing demonstrated that ORF1a/b is closely similar to those from the bat, 4 civet, and other human SARS-CoVs, but the external sub-domain amino acid sequence of the 5 spike receptor-binding domain for this novel virus is only 40% similar to other SARS-related 6 coronaviruses. Nelfinavir was predicted to be a potential 5 inhibitor of 2019-nCov main protease by an integrative approach combining homology 6 modelling, molecular docking and binding free energy calculation Structural and molecular modelling studies 24 reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 25 infection Network-based drug repurposing 29 for novel coronavirus 2019-nCoV/SARS-CoV-2 Emodin blocks the SARS coronavirus 46 spike protein and angiotensin-converting enzyme 2 interaction Repurposing didanosine as a potential treatment for COVID-19 using scRNA-18 seq data Repurposing Didanosine as a Potential Treatment for COVID-19 Using Single-Cell 20 RNA Sequencing Data doi = 10.1016/j.imu.2020.100458 id = cord-337436-3xzgv370 author = Khider, Lina title = Curative anticoagulation prevents endothelial lesion in COVID‐19 patients date = 2020-06-18 keywords = SARS; covid-19 summary = METHODS: Study analyzed clinical and biological profiles of patients with suspected COVID‐19 infection at admission, including hemostasis tests and quantification of circulating endothelial cells (CECs). Circulating endothelial cells (CECs) are considered as relevant markers of Accepted Article 1 endothelial lesion or dysfunction (12) and were used to explore the potential vascular dysfunction 2 in COVID-19 patients. Among COVID-19 positive patients, 64% were above this threshold, suggesting a SARSThe originality of this study was to evidence an endothelial lesion during SARS-CoV-2 infection, 3 as witnessed by increased levels of CECs. Second, we show that this endothelial damage is 4 thwarted by curative anticoagulation. Interestingly, patients enrolled while they were treated with 6 curative anticoagulation had a significantly lower level of CECs, especially in the hypertensive 7 population treated with ACEi or ARBs. Increased mortality and/or morbidity of COVID-19 in 8 patients with hypertension has been described in China (3). doi = 10.1111/jth.14968 id = cord-031518-1w14wr0i author = Khodarahmi, Reza title = The ACE2 as a “rescue protein” or “suspect enzyme” in COVID-19: possible application of the “engineered inactive hrsACE2” as a safer therapeutic agent in the treatment of SARS-CoV-2 infection date = 2020-09-07 keywords = ACE2; COVID-19; SARS summary = The authors expressed that hrsACE2 can block early entry of SARS-CoV-2 infections in various host cells, especially alveolar epithelial type II cells, as a viral reservoir and stated that they cannot make any predictions with respect to the effect of the recombinant protein on the later stages of COVID-19 and, also, honestly mentioned the study limitations. Moreover, since ACE2 is expressed in various tissues including the heart, kidney tubules, the luminal surface of the small intestine and blood vessels [2] and references therein), SARS-CoV-2could also infect these tissues, so that clinically, SARS-CoV-2 has been found in the urine, and cardiovascular and renal dysfunctions have been reported for many patients with COVID-19. As mentioned above, patients with COVID-19 have significantly elevated levels of plasma angiotensin II compared to that of healthy individual and membrane-bound ACE2 (in addition to protecting from lung injury, based on its catalytic domain) is the critical in vivo SARS-CoV spike glycoprotein receptor. doi = 10.1007/s13738-020-02049-z id = cord-338680-wwlttymp author = Khonyongwa, K. title = Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date = 2020-07-30 keywords = COVID-19; RNA; SARS summary = Due to the high prevalence of infection during the peak of the outbreak, one of the suggested strategies to prevent healthcare transmission was to screen all patients on admission by a single combined nose and throat swab assessed for SARS-CoV-2 RNA to allow segregation into COVID-19 positive and non COVID-19 cohort wards. The latter included assessment of the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity, COVID-19 patients as sources of infection, self-reported COVID-19 sickness absence among hospital staff hospital bed occupancy, community incidence, and the incidence of other significant hospital-acquired infections. NHS England released its reporting criteria in May 2020 (written communication described in supplementary data) following which cases were also classified as per date of the SARS-CoV-2 RNA detection. Correlation between weekly incidence of HA-COVID-19 (including late indeterminate cases) and staff self-reported sickness absence, delayed RNA positive cases, community incidence and Trust COVID-19 bed occupancy is displayed in figure 3. doi = 10.1101/2020.07.24.20148262 id = cord-269408-6qncy0nd author = Khonyongwa, Kirstin title = Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date = 2020-10-13 keywords = COVID-19; SARS summary = AIMS: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a Teaching Hospital NHS Trust in London, England. Factors studied included the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity (DRP), selfreported COVID-19 sickness absence among hospital staff, total hospital bed occupancy, community incidence of COVID-19 (CIC19) and the change in incidence of other significant hospital-acquired bacterial infections (HAB). When a HA-COVID-19 case was identified, actions included staff refresher training for correct PPE usage, rapid transfer of patients to a COVID-19 positive cohort ward, deep cleaning (washing walls and carpets) followed by increasing the cleaning frequency until no further transmission was seen (defined as no new symptom onset within 2 weeks of last known case and in haematology and geriatrics a CNTS was tested for SARS-CoV-2 RNA twice weekly for all contacts up to 2 weeks from last positive case regardless of symptoms). doi = 10.1016/j.jhin.2020.10.006 id = cord-282371-39qo9afy author = Khulood, Daulat title = Convalescent plasma appears efficacious and safe in COVID-19 date = 2020-09-28 keywords = COVID-19; SARS summary = Convalescent plasma (CP) therapy is a classic adaptive immunotherapy which has been in use for more a century to prevent and treat infections including SARS, Middle East respiratory syndrome (MERS), and H1N1 pandemic. Despite its promising beneficial effects in patients severely ill with COVID-19, CP therapy requires further evaluation in randomized clinical trials (RCTs) as a lack of satisfactory efficacy data from this area certainly enhances the hesitancy with regard to employing this treatment. Although CP therapy showed satisfactory efficacy in treating patients with severe COVID-19, 41 this approach requires evaluation in randomized clinical trials (RCTs) 38 as lack of data from this area certainly enhances the hesitation with regard to employing this treatment. 46 Recently, the FDA has approved use of CP to treat critically ill patients while a clinical trial of plasma therapy for COVID-19 has been approved in the UK. Treatment with convalescent plasma for critically ill patients with SARS-CoV-2 infection. doi = 10.1177/2049936120957931 id = cord-315951-5gsbtfag author = Kiemer, Lars title = Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology date = 2004-06-06 keywords = SARS; cleavage; site summary = The general approach is still valid though, and we decided to apply this method to the problem of predicting the 3CL pro proteinase cleavage sites and identifying potential host cell target proteins. In this paper, we describe the development of a computational prediction method using artificial neural networks for predicting coronavirus 3CL pro proteinase cleavage sites. We discuss potential targets of 3CL pro proteinase, e.g. the cystic fibrosis transmembrane conductance regulator (CFTR) and translational and transcriptional factors, which may be involved in the molecular pathology of coronaviruses in general and SARS virus in particular. Another known target for viral infections is the microtubule-associated protein 4 (MAP-4) which is cleavable in HeLa cells by the poliovirus 3C pro proteinase [26, 27] . We have developed a neural network capable of identifying the cleavage site of the coronavirus proteinase 3CL pro and use this model to predict potential cleavage sites in host cell proteins. doi = 10.1186/1471-2105-5-72 id = cord-342983-7o0slu0z author = Killeen, G. F. title = A simple arithmetic rationale for crushing the epidemic curve of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) instead of flattening it date = 2020-05-10 keywords = SARS; figure summary = Here is presented a simple set of arithmetic modelling analyses that explain why preferable crush the "curve strategies", to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to "flatten the curve" strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. Here is presented a simple arithmetic rationale for why preferable crush the curve strategies, to eliminate transmission within months, would require only a modest amount of additional containment effort when compared to flatten the curve strategies that allow epidemics to persist at a steady, supposedly manageable level for years, decades or even indefinitely. 2 From this assumed starting point, a country that contains its epidemic sufficiently to flatten the curve to a plateau, so that the rate of incidence of new infections remains constant, would have achieved a controlled reproductive number (Rc) of exactly 1.0 ( Figure 1A ). doi = 10.1101/2020.05.06.20093112 id = cord-347128-6lyoz8nn author = Kim, Cheorl-Ho title = SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date = 2020-06-26 keywords = ACE2; CLQ; MERS; RNA; SARS summary = O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. In RNA viruses, the S glycoprotein (PDB: 6VSB) is the biggest protein, heavily glycosylated and its N-terminal domain (NTD) sequence binds to the host receptor to enter the ER of host cells. However, MERS-CoV does not have a similar enzyme and thus MER-CoV binding to SA receptors is mediated by energetically reversible interactions of the lipid rafts with increased SA receptors [75] , thus enhancing dipeptidyl peptidase 4 (DPP4) or carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) recognition power and viral entry [76] and membrane-associated 78-kDa glucose-regulated protein (GRP78) [77] . Entry of host cells needs binding of S glycoproteins to the CEACAM receptor, forming S-protein-mediated membrane fusion. For example, impairment of ACE2 receptor glycosylation does not influence S-glycoprotein-ACE2 interaction, however, SARS-CoV-2 virus entry into respiratory epithelial host cells was downregulated [133] . doi = 10.3390/ijms21124549 id = cord-346222-rzbzlnr4 author = Kim, Dae-Kyum title = A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions date = 2020-08-06 keywords = SARS summary = Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. SARS-CoV-2 coding sequence collection Gatewaycompatible TEV (tobacco etch virus) sequence A global pandemic of the coronavirus disease COVID-19, a severe respiratory illness caused by a novel virus from the family Coronaviridae (SARS-CoV-2), has infected millions and caused hundreds of thousands of deaths (World Health Organization 2020a). Broad availability of a collection of SARS-CoV-2 CDSs has the potential to enable many downstream biochemical and structural studies and thus a better understanding of processes within the viral life cycle, including scalable assays for screening drug candidates that could potentially disrupt these processes. However, to enable the subsequent removal of such N-terminal fusion tags, we generated an additional set of clones containing, at the N-terminus of the ORF, a recognition sequence for nuclear inclusion protease from tobacco etch virus (TEV). doi = 10.1534/g3.120.401554 id = cord-302020-ypsh3rjv author = Kim, Dongwan title = The Architecture of SARS-CoV-2 Transcriptome date = 2020-04-23 keywords = DRS; RNA; SARS; figure; read summary = In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. (A) Read counts from nanopore direct RNA sequencing of total RNA from Vero cells infected with SARS-CoV-2. We further discovered RNA modification sites and measured the poly(A) tail length of gRNAs and sgRNAs. To delineate the SARS-CoV-2 transcriptome, we first performed DRS runs on a MinION nanopore sequencer with total RNA extracted from Vero cells infected with SARS-CoV-2 (Be-taCoV/Korea/KCDC03/2020). To unambiguously investigate the modifications, we generated negative control RNAs by in vitro transcription of the viral sequences and performed a DRS run on these unmodified controls ( Figure S4A ). doi = 10.1016/j.cell.2020.04.011 id = cord-294698-mtfrbn87 author = Kim, H. K. title = Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date = 2016-05-23 keywords = B15; Bat; SARS summary = In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential. doi = 10.1111/tbed.12515 id = cord-015235-lv8mll28 author = Kim, Hyun title = Functional analysis of the receptor binding domain of SARS coronavirus S1 region and its monoclonal antibody date = 2014-04-16 keywords = ACE2; Fig; RBD; SARS summary = The receptor-binding domain (RBD) positioned in S1 can specifically bind to angiotensin-converting enzyme 2 (ACE2) on target cells, and ACE2 regulates the balance between vasoconstrictors and vasodilators within the heart and kidneys. Infection of SARS-CoV is initiated by binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) functional receptor expressed on target cells (Li et al. Our cellular enzyme-linked immunosorbent assay (ELISA) and competitive binding assay using a polyclonal ACE2 antibody indicated that our prepared recombinant RBD fusion protein binds to various tissues as well as NIH3T3 and HEK293 cells through ACE2. After washing with PBS, the RBD fusion protein was incubated for 1 h at room temperature to bind with the ACE2 molecules on the cell membranes. Next, we examined whether RBD binding was blocked by the ACE2 antibody in a Western blot using mouse tissue cell lysates with a pair of membranes. doi = 10.1007/s13258-014-0186-9 id = cord-262107-qso8ewi9 author = Kim, In-Cheol title = Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned date = 2020-05-22 keywords = SARS summary = title: Successful Heart Transplantation to a Fulminant Myocarditis Patient during COVID-19 Outbreak – Lessons Learned procurement team from the city (Daegu) where the COVID-19 outbreak was prevalent due to the concern of SARS-CoV-2 spread. Our procurement team decided to take a nasopharyngeal swab to prove negative of SARS-CoV-2 infection before the departure. Algorithm of the SARS-CoV-2 Test Strategy for the brain death donor and candidate for heart transplantation during COVID-19 outbreak. Brain death donors should be tested for SARS-CoV-2 infection (preferably rRT-PCR assay from upper and/or lower respiratory tract specimens). When the heart transplantation recipient has symptoms suggesting viral infection, unknown cause of fever, or close contact history with the SARS-CoV-2 infected patients prior 14 days, test for SARS-CoV-2 infection should be performed and proceed heart transplantation when the result is negative. Confirmation of the negative SARS-CoV-2 result need to be ensured according to the strategy of each hospital organ procurement organization. If the symptom of SARS-CoV-2 infection is highly suggested, repeated test need to be performed for the suspicious result. doi = 10.4070/kcj.2020.0177 id = cord-260310-0gkoanrg author = Kim, Jin Yong title = Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea date = 2020-02-20 keywords = LRT; SARS summary = In this patient, the initial test was performed on day 14 of symptom onset and SARS-CoV-2 was detected in both URT and LRT specimens. Although the viral load and CXR findings in these two patients may not represent the whole spectrum of SARS-CoV-2 illness, our report will provide many important findings and opportunity to understand this newly discovered virus infection in human. First, unlike SARS-CoV infection, 8 we found that viral load was highest during the early phase of the illness (3-5 days from first symptom onset, fever and myalgia were the only symptoms in Patient 1) and continued to decrease until the end of the second week. Second, even in a patient with mild disease, if visible infiltration on CXR is observed, virus is still detected in both URT and LRT specimens even at the end of second week after symptom onset. doi = 10.3346/jkms.2020.35.e86 id = cord-281487-x0a9qgjs author = Kim, Min Young title = General Approach to the Clinical Care of Solid Organ Transplant Recipients with COVID-19 Infection: Management for Transplant Recipients date = 2020-10-29 keywords = COVID-19; SARS; recipient; transplant summary = The coronavirus disease 2019 (COVID19) pandemic has led to unique challenges in solid organ transplantation as centers balance the risk of caring for immunosuppressed patients with the best timing and urgency of transplantation. Patients hospitalized with COVID-19 pneumonia were included Abbreviations: CHF, congestive heart failure; Because renal abnormalities are associated with a high risk of in-hospital death and appear to be more prevalent in transplant recipients [36] , serum creatinine and urinalysis should be monitored closely. Figure 1 shows a model for the management of solid organ transplant recipients during COVID-19 pandemic, based on recommendations of the Centers for Disease Control and Prevention (CDC) and the American Society of Transplantation (AST) [52, 61] . Transplant recipients with direct contact (< 6 ft for ≥ 15 min) with a COVID-19 infected individual should be quarantined for 14 days and consider testing for SARS-CoV-2 after exposure or if they develop symptoms [49, 52] . doi = 10.1007/s40472-020-00305-y id = cord-254825-c5d0wul9 author = Kim, Sei Won title = Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date = 2020-08-14 keywords = COVID-19; PCR; SARS summary = In this study, we retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing, contact history, and presence of respiratory symptoms in a single center with a healthcare-associated COVID-19 outbreak. We reviewed the history of patients to assess whether they visited China or other high-risk countries within two weeks prior to the outbreak of healthcare-associated COVID-19, or if they came into contact with confirmed COVID-19 cases. After SARS-CoV-2 infection was confirmed, the Seoul city government announced the closure of the hospital on February 21, 2020, to prevent a healthcare-associated outbreak. After the hospital staff member responsible for transporting patients was confirmed as the first COVID-19 case, people with contact history, fever, or respiratory symptoms were tested for SARS-CoV-2 infection with RT-PCR (Fig 2) . After the first case was reported, epidemiologists from KCDC and the infection control unit of our hospital reviewed electronic medical charts, CCTV, and personal movements to identify individuals with potential contact with confirmed COVID-19 patients. doi = 10.1371/journal.pone.0237692 id = cord-277564-x5qfxag3 author = Kim, Si-Hyun title = Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea date = 2020-10-24 keywords = COVID-19; SARS summary = title: Infection prevention and control practices for emergency surgery during the COVID-19 pandemic in a tertiary care hospital in South Korea Patients with findings suggestive of COVID-19 should be placed in a negative-pressure isolation room in the ED until the results of the rRT-PCR test for SARS-CoV-2 are confirmed as negative. However, patients requiring emergency surgery before confirmed negative SARS-CoV-2 rRT-PCR test results are evaluated for the risk of transmission by infectious disease specialists and the infection control team based on 3 criteria: clinical signs or symptoms, epidemiological risk, and chest radiological findings (Fig. 1 ). Patients who still have unconfirmed SARS-CoV-2 rRT-PCR test at the end of the surgery are transferred to the cohort ward, a single room, or a negative-pressure isolation room according to their risk. doi = 10.1016/j.ijso.2020.10.007 id = cord-257058-wf6oxzrk author = Kim, Sinae title = The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene date = 2020-10-26 keywords = Fig; SARS; d614 summary = The S gene of SARS-CoV, which encodes for the spike glycoprotein on the viral envelope, recognizes a receptor on the membrane of specific host cells. The present study with novel mutations in critical RBD of S gene may explain the high pathogenicity of SARS-CoV2 through precise biochemistry result with recombinant spike proteins as well as cell infectivity experiment. The alignment of four SARS-CoV2 spike amino acid sequences compared to the wild type sequence revealed that there are two additional mutations in the critical RBD and another mutation in subdomain (SD) 2, which is very close to the known mutation residue D614G (Figs. A recent study reported a single point mutation in which amino acid residue aspartic acid 614 replaced by glycine (D614G) in S gene, resulting in enhanced infectivity of SARS-CoV2 (18) . However, two novel mutations in S gene of Korean COVID-19 in the Korean patients were present in RBD (Fig. 6 , green bar), a site that is important for binding to ACE2 receptor on the host cell membrane. doi = 10.4110/in.2020.20.e41 id = cord-266869-fs8dn7ir author = Kim, So Young title = Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date = 2020-04-15 keywords = Fig; SARS; SGP summary = title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs might be involved in host cell entry of SARS-CoV-2. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. Using a modified version of Autodock Vina tuned for use with carbohydrates (Vina-Carb) [20, 21] , we performed blind docking on the trimeric SARS-CoV-2 SGP model to discover objectively the preferred binding GAG-binding sites on the SGP protein surface. doi = 10.1101/2020.04.14.041459 id = cord-295830-1sbnewog author = Kim, Sung-Jae title = A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? date = 2020-05-14 keywords = SARS summary = Therefore, we analyzed the S gene sequences of SARS-CoV-2 to better understand the antigenicity and immunogenicity of this virus in this study. The region containing this mutation point was confirmed as a B-cell epitope located in the S1 domain, and SARS-CoV-2b strains exhibited severe reduced antigenic indexes compared to SARS-CoV-2a in this area. Generally, several types of coronavirus are divided into subtypes depending on amino acid mutations in S gene sequences, and molecular analysis based on the S gene can provide insights into antigenicity, immunogenicity, or evolutionary trends [2, 4, 10, 12, 13] . Vaccines 2020, 8, 220 3 of 8 change alters the conformation of these immunogenic determinants; consequently, this region is expected to no longer act as a B-cell epitope in SARS-CoV-2b. The results of the antigenic index analysis showed severely reduced indexes of amino acids 615-617 in the SARS-CoV-2b strains compared to SARS-CoV-2a; it is predicted that the change of D614G affects the antigenicity of this region ( Figure 1F ). doi = 10.3390/vaccines8020220 id = cord-323449-r1gyjxei author = Kim, Uh Jin title = Air and Environmental Contamination Caused by COVID-19 Patients: a Multi-Center Study date = 2020-09-08 keywords = Hospital; SARS summary = BACKGROUND: The purpose of this study was to determine the extent of air and surface contamination of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in four health care facilities with hospitalized coronavirus disease 2019 (COVID-19) patients. CONCLUSION: Our data suggest that remote (> 2 m) airborne transmission of SARS-CoV-2 from hospitalized COVID-19 patients is uncommon when aerosol-generating procedures have not been performed. 10, 11 The objectives of the present study were 1) to investigate air and environmental contamination caused by COVID-19 patients in a variety of hospital settings; 2) to evaluate the effectiveness of environmental cleaning; and 3) to examine the potential for remote airborne transmission in the absence of aerosol-generating procedures. Despite extensive surface sampling, SARS-CoV-2 RNA was not detected in the room in Hospital B (AIIR with routine surface cleansing using disinfectant wipes the patient''s respiratory samples (Ct value 22.4-28.9) (Fig. 1B) . doi = 10.3346/jkms.2020.35.e332 id = cord-335443-iv2gs3kg author = Kim, Youngchang title = Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date = 2020-06-28 keywords = Nsp15; RNA; SARS; Tipiracil summary = Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme''s active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5''GAACU¯CAU¯GGACCU¯U¯GGCAG3'' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5''UMP, 3''UMP, 5''GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5''GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5''UMP complex. doi = 10.1101/2020.06.26.173872 id = cord-280621-tph5n7ak author = Kim, Yunjeong title = Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor date = 2016-03-30 keywords = FIPV; Fig; GC376; SARS; npi64 summary = Shifts in tissue or cell tropism and resulting changes in virulence have also been reported for coronaviruses; porcine respiratory coronavirus causes mild respiratory infection in pigs and presumably arose from transmissible gastroenteritis virus (TGEV), the etiologic agent of gastroenteritis in young pigs with a high fatality, by spontaneous mutations and/or deletions in its genome [9] . Effective treatment intervention for coronavirus infections with an immunopathological component, such as SARS, MERS and FIP, is speculated to involve the judicious use of immunomodulatory agents to enhance protective host immunity and decrease pathological immune responses and antiviral drugs to directly inhibit viral replication. These results on viral titers show that FIPV 3CLpro is a valid target for FIPV antiviral drugs and GC376 can effectively reduce the virus load in the macrophages from the ascites and the omentum of cats with FIP. doi = 10.1371/journal.ppat.1005531 id = cord-256537-axbyav1m author = Kimball, Ann Marie title = Emergence of Novel Human Infections: New Insights and New Challenges date = 2016-10-24 keywords = Health; MERS; SARS; human; new summary = In reviewing the new challenges posed by these emergent events, new technologies promise some answers; however, global health security against pandemic threats, particularly given the uneven distribution of global resources for prevention, detection, and response, remains a critical area of challenge. Specifically: (1) it is now well appreciated that influenza can migrate directly from avian sources to humans, and the appreciation of the actual directness of ''species jumping'' has moved forward; (2) new infections have also introduced uncertainty in transmission dynamics with emphasis on super-spreader events as well as nosocomial transmission; (3) infectious particles are not confined to those organisms which contain genetic material; (4) a new paradigm such as ''Planetary Health'' may be necessary for defining these trends; and (5) global preparedness and response is not in place for the next pandemic. To summarize, the recent episodes of respiratory infectious diseases related to influenza, SARS-CoV, and MERS-CoV have demonstrated increasingly direct links between animal and human infections, agile intercontinental geographic spread, and complex transmission dynamics including ''superspreader'' events. doi = 10.1016/b978-0-12-803678-5.00153-3 id = cord-316632-rr9f88oi author = Kimura, Yurika title = Society of swallowing and dysphagia of Japan: Position statement on dysphagia management during the COVID-19 outbreak date = 2020-07-23 keywords = PPE; SARS; covid-19 summary = On April 14, the Society of Swallowing and Dysphagia of Japan (SSDJ) proposed its position statement on dysphagia treatment considering the ongoing spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This statement is arranged into separate sections providing information and advice in consideration of the COVID-19 outbreak, including "terminology", "clinical swallowing assessment and examination", "swallowing therapy", "oral care", "surgical procedure for dysphagia", "tracheotomy care", and "nursing care". The current set of statements on dysphagia management in the COVID-19 outbreak is not an evidence-based clinical practice guideline, but a guide for all healthcare workers involved in the treatment of dysphagia during the COVID-19 epidemic to prevent SARS-CoV-2 infection. 48 This statement is arranged into separate sections provid-49 ing information and advice considering the COVID-19 out-50 break, including "clinical swallowing assessment and ex-51 amination", "dysphagia rehabilitation", "oral care", "nursing 52 care", "surgical procedure for dysphagia", and "tracheotomy 53 care". doi = 10.1016/j.anl.2020.07.009 id = cord-258019-njky7v5x author = Kinaret, Pia A.S. title = Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us date = 2020-08-10 keywords = SARS; covid-19 summary = However, similarities between the responses to SARS-CoV-2 and certain nanomaterials suggest fibrotic pulmonary disease as a concern for public health in the next future. Also rigid multi-walled carbon nanotubes (rMWCNT), among other nanomaterials, induce innate immune response by activation of NF-κB, STAT3 and HIF-1/2, and consequent cytokine cascade [15, 16] . As the Covid-19 disease progresses, massive damage of the pulmonary tissue occurs by induction of an uncontrolled innate immune response, mainly mediated by M1 pro-inflammatory macrophages and granulocytes. Moreover, up-regulation of antigen processing pathways, RIG-1 and several viral-induced human disease pathways have been reported consequently to carbon nanomaterial exposure, both in vitro [23] and in murine lung in vivo [19, 24] . On the other hand, certain nanoparticles might induce lung fibrosis by a combination of metabolic tissue damage and primary activation of the innate immune cells. Here we summarized noticeable cellular and molecular similarities between the acute responses to both SARS-CoV-2 infection and certain nanomaterials exposure. doi = 10.1016/j.nantod.2020.100945 id = cord-290744-m0vpizuh author = Kindler, E. title = Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date = 2016-09-09 keywords = IFN; MERS; RNA; SARS summary = Here, we will summarize the insights gathered so far on an important aspect of virulence and host adaptation, the interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells. The broad antiviral activity of IFNs occurs on several levels, namely virus entry, viral polymerase function, host cell translation, RNA availability, RNA stability, particle budding, apoptosis, or general boosting of innate and adaptive immune responses. Crystal structure of the middle east respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response doi = 10.1016/bs.aivir.2016.08.006 id = cord-285527-1mceq6v0 author = Kinloch, Natalie N title = Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date = 2020-06-28 keywords = PCR; SARS summary = To investigate suboptimal sample collection as a possible cause of false-negative test results, we quantified human DNA levels recovered on nasopharyngeal swabs submitted to a single laboratory for COVID-19 testing, hypothesizing that human DNA could serve as a stable molecular marker of specimen collection quality. Human DNA levels were quantified using droplet digital PCR (ddPCR), a technique where each sample is fractionated into 20,000 nanolitre-sized water-in-oil droplets prior to PCR amplification with sequence-specific primers and fluorescent probes, and where Poisson detection sensitivity compared to the original real-time RT-PCR assay, we re-tested the 40 suspected false-negative specimens by nested RT-PCR. Overall, we observed significantly lower human DNA levels in the suspected false-negative nasopharyngeal swab samples compared to a panel of consecutive samples submitted for testing during the same period, though overlap between groups was still substantial (Figure 1, p<0.001) . Our observations strongly support suboptimal biological sampling, but not PCR sensitivity for SARS-CoV-2 RNA detection, as a contributing cause of false-negative COVID-19 test results. doi = 10.1093/infdis/jiaa370 id = cord-266996-knwpkyg6 author = Kipkorir, Vincent title = Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test date = 2020-05-13 keywords = SARS summary = title: Prolonged SARS‐Cov‐2 RNA Detection in Anal/Rectal Swabs and Stool Specimens in COVID‐19 Patients After Negative Conversion in Nasopharyngeal RT‐PCR Test 2 Recently, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has also been isolated from anal/rectal swabs and stool specimens 3, 4 , raising concerns of potential alternative routes of viral transmission. Thereafter, a pooled analysis incorporating only cohort studies or case series with sample ≥10 patients was conducted to calculate pooled prevalence estimates (PPE) of prolonged SARS-CoV-2 RNA detection in anal/rectal swabs and stool samples after negative conversion in nasopharyngeal RT-PCR using the MetaXL (software Version 5.3, EpiGear International Pty Ltd., Sunrise Beach, Australia). In the pooled analysis of 8 cohort studies/ case series (n= 315), the pooled prevalence estimate (PPE) for prolonged rectal/anal/stool SARS-CoV-2 RNA was 32% (95% CI 22-44) (Figure 1 ). doi = 10.1002/jmv.26007 id = cord-273891-7w334xgt author = Kirchdoerfer, Robert N. title = Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date = 2018-03-31 keywords = RBD; SARS summary = The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. Subsequent studies of the highly pathogenic human coronavirus S proteins of SARS-64 CoV 15,22 and MERS-CoV 17,22 showed that these viral S1 RBD do indeed sample an ''up'' 65 conformation where the receptor-binding site is accessible. 70 To examine the hypothesized conformational transitions induced by proteolysis and 71 receptor binding, we used single-particle cryo-EM to determine structures of S in uncleaved, 72 S1/S2 cleaved and ACE2-bound states. Three-dimensional classification of the S1 RBD 73 positions and corresponding atomic protein models revealed that neither ACE2-binding nor 74 trypsin cleavage at the S1/S2 boundary induced substantial conformational changes in the CoV may use a distinct mechanism of FP2 membrane insertion. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein 381 reveal a prerequisite conformational state for receptor binding doi = 10.1101/292672 id = cord-319100-3gdawhfn author = Kirkland, P.D. title = The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date = 2020-06-10 keywords = RNA; SARS; VTM summary = authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). doi = 10.1101/2020.06.09.142323 id = cord-336775-d4hi9myk author = Kirtipal, Nikhil title = From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date = 2020-08-13 keywords = ACE2; CoV; Coronavirus; MERS; RNA; SARS summary = Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Hence, acute respiratory distress syndrome (ARDS) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of SARS-CoV-2 outbreak; similar observations were noted in case of SARS-CoV infection (Kumar et al., 2020) . When developing novel therapeutic strategies to check the immunoregulatory cytokines such as TNFβ and IL6, investigation should be considered on the viral strain and targeted organ specificity; for example, SARS-CoV-2 has more affinity to ACE2 which are scattering on different organs like lung and kidney while MERS-like CoV can even infect T-cells. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.1016/j.meegid.2020.104502 id = cord-314960-f4hj35dr author = Kissler, Stephen M title = Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period date = 2020-03-06 keywords = HKU1; OC43; SARS summary = To quantify the relative contribution of immunity versus seasonal forcing on the transmission dynamics of the betacoronaviruses, we adopted a regression model (22) that expressed the effective reproduction number for each strain (HKU1 and OC43) as the product of a baseline transmissibility constant (related to the basic reproduction number and the proportion of the population susceptible at the start of the season), the depletion of susceptibles due to infection with the same strain, the depletion of susceptibles due to infection with the other strain, and a spline to capture further unexplained seasonal variation in transmission strength (seasonal forcing). https://doi.org/10.1101/2020.03.04.20031112 doi: medRxiv preprint infection due to SARS-CoV-2, and autumn establishments and smaller seasonal fluctuations in transmissibility were associated with larger pandemic peak sizes. Peak simulated SARS-CoV-2 epidemic sizes, in units of percent influenza-like illness (ILI) x percent positive laboratory tests, by year for a representative set of cross immunities, immunity durations, and establishment times. doi = 10.1101/2020.03.04.20031112 id = cord-331520-o9e4qqn4 author = Kistler, Christine E. title = The Winter Respiratory Viral Season During the COVID-19 Pandemic date = 2020-10-26 keywords = COVID-19; SARS; respiratory summary = The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research. doi = 10.1016/j.jamda.2020.10.030 id = cord-254957-jqp1gto6 author = Klann, Kevin title = Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication date = 2020-08-11 keywords = GFR; SARS; cell; figure; protein summary = We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. Additionally, we found carbon 160 metabolism among the pathways showing significantly increased phosphorylation upon SARS-CoV-2 infection (Table S4 ) in addition to previously described changes of total protein levels of enzymes part of glycolysis and carbon metabolism (Bojkova et al., 2020 )( Figure S3 ). We mapped identified members of GFR signaling and their respective phosphorylation differences upon SARS-CoV-2 infection ( Figure 3C ) revealing an extensive overall increase in phosphorylation of the whole pathway, including related components for cytoskeleton remodeling and receptor endocytosis. Growth factor receptor signaling was highly activated upon infection and its inhibition prevented SARS-CoV-2 replication in cells. doi = 10.1016/j.molcel.2020.08.006 id = cord-338498-3238fz73 author = Kleen, Thomas-Oliver title = Mitigating Coronavirus Induced Dysfunctional Immunity for At-Risk Populations in COVID-19: Trained Immunity, BCG and “New Old Friends” date = 2020-09-04 keywords = BCG; CD4; CD8; COVID-19; SARS; cell; imm-101 summary = Bacterial "new old friends" such as Bacille Calmette-Guérin (BCG) or Mycobacterium obuense have the ability to elevate basal systemic levels of type 1 cytokines and immune cells, correlating with increased protection against diverse and unrelated infectious agents, called "trained immunity." Here we describe dysfunctional immune responses induced by coronaviruses, representing potentially difficult to overcome obstacles to safe, effective vaccine development for COVID-19, and outline how trained immunity could help protect high risk populations through immunomodulation with BCG and other "new old friends." One recent example of the need for continued vigilance is a study using Chinese macaques indicating cause for concern by showing that vaccine-induced, S-specific immunity in the form of anti-spike IgG resulted in severe ALI by skewing macrophage responses during subsequent, acute infection with closely related SARS-CoV (139) . doi = 10.3389/fimmu.2020.02059 id = cord-328042-e1is656g author = Klein, Steffen title = SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date = 2020-08-07 keywords = LAMP; RNA; SARS summary = The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] . doi = 10.3390/v12080863 id = cord-315931-kc8gnj6z author = Klempt, Petr title = Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis date = 2020-09-29 keywords = SARS; Table summary = During the first attempt, thirty libraries (including 4 positive and 2 negative controls) were prepared in three plexes (10 samples each, see Supplementary Table S1 ) employing NEBNext ® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) followed by capture-based workflow utilizing the Twist SARS-CoV-2 Research Panel (Twist Bioscience). Compare to NEB+TWIST the capture-based Illumina approach data showed in average a lower percentage of mapped reads (Supplementary Table S1 ), this consequence could be related to the lower specificity of Respiratory Oligo Viral Panel designed next to the SARS-CoV-2 also for other pathogens (see https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/ngsenrichment-coronavirus-app-note-1270-2020-002.pdf). Also, the viral load in a sample (corresponding to sample Ct value ≤ 23.29 or positive control value ≤ 25.84) showed to be the limiting factor in case of each workflow, samples with higher Ct value resulted in either poor genome coverage (NEB+Twist workflow and Illumina workflow) or in absence of expected library preparation product (Paragon workflow). doi = 10.3390/diagnostics10100769 id = cord-300968-dtaasxk1 author = Kliger, Yossef title = From genome to antivirals: SARS as a test tube date = 2005-03-01 keywords = CoV; HIV; SARS summary = Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. This strategy seems promising in developing anti-viral therapeutic peptides to other viruses that possess type 1 viral fusion proteins [e.g. measles virus and respiratory syncytial virus (RSV)], which share some structural motifs with HIV. Similar to HIV, binding of the viral spike glycoprotein to some receptor(s) on host cells is the first step in SARS-CoV infection. HIV entry involves the binding of the viral envelope glycoproteins (comprising gp120 and gp41, which are the homologous of SARS-CoV S1 and S2, respectively) to CD4 on the host cell plasma membrane. Following the rule: formation of the 6-helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoproteinmediated viral entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeatderived peptides doi = 10.1016/s1359-6446(04)03320-3 id = cord-307248-8e34ndn4 author = Klimek, Ludger title = Handling of allergen immunotherapy in the COVID‐19 pandemic: An ARIA‐EAACI statement date = 2020-04-24 keywords = AIT; SARS; immunotherapy summary = Allergen‐specific immunotherapy (AIT) is one of the most important treatment options for IgE‐mediated allergies and is based on immunological effects on the diseased patient Allergen-specific immunotherapy (AIT) is one of the most important treatment options for IgE-mediated allergies and is based on immunological effects on the diseased patient. The highest risk of healthcare-associated transmission occurs in the absence of standard precautions, when primary infection prevention and control measures for respiratory infections are not in place, and when handling patients whose COVID-19 diagnoses is yet to be confirmed. Eventhough it is well established that allergic airway diseases are associated with an Highly active antiretroviral treatment has improved the immune function and life expectancy in HIV-infected patients whose respiratory allergic incidence is similar to that of the general population (33) . In patients, who recovered from COVID-19 or who are found to have a sufficient SARS-CoV-2 antibody response after (asymptomatic) disease (14), AIT can be started or continued as planned. doi = 10.1111/all.14336 id = cord-307605-8zgyar7e author = Klimek, Ludger title = Management von Anaphylaxie-gefährdeten Patienten während der Covid-19-Pandemie: Ein Positionspapier des Ärzteverbandes Deutscher Allergologen (AeDA)A, der Deutschen Gesellschaft für Allergologie und klinische Immunologie (DGAKI)B, der Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)C und des Deutschen Allergie- und Asthmabundes (DAAB)D date = 2020-11-09 keywords = Anaphylaxie; Patienten; SARS; der; die; mit; und summary = Schlussfolgerung: Die Beratung, die Entwicklung von Strategien zur Expositionsprophylaxe und die Notfalltherapie von Patienten mit Anaphylaxie ist in der aktuellen Covid-19-Pandemie bei gefährdeten Patienten sehr wichtig. Die Selbstapplikation der Notfallmedikation ist gerade unter den Bedingungen einer möglichen Quarantäne oder Isolation zu bevorzugen und auch die Verordnung eines zweiten Adrenalin-Autoinjektors sollte großzügig Patientenindividuell geprüft werden. Der globale Ausbruch einer Pandemie von Infektionen mit dem neuartigen Coronavirus SARS-CoV-2 wurde als "Coronavirus-Krankheit 2019" ( Covid19) benannt und stellt die Gesundheitssysteme weltweit vor große Herausforderungen. Bei einer großen Zahl von Patienten führt die Infektion nach der Inkubationszeit zu einer Erkrankung der oberen und unteren Atemwege oder seltener anderer Organsysteme (NerAngiotensin-converting-enzyme-2 Fall zum Multiorganversagen und respiratorischer Insuffizienz führt, wie dies auch für andere Coronavirus-Infektionen (SARS-CoV-1, MERS-CoV) beschrieben wurde [4, 5, 6] . Unter Berücksichtigung der aktuellen Leitlinien zur Anaphylaxie-Behandlung wie auch der WHO-und RKI-Empfehlungen zu Covid-19 schlussfolgern wir, dass Anaphylaxie-Patienten mit vermuteter oder diagnostizierter SARS-CoV-2-Infektion weiterhin nach den aktuellen Richtlinien behandelt werden sollten. doi = 10.1007/s15007-020-2618-y id = cord-320831-owfnttqr author = Klimek, Ludger title = Allergen immunotherapy in the current COVID-19 pandemic: A position paper of AeDA, ARIA, EAACI, DGAKI and GPA: Position paper of the German ARIA Group(A) in cooperation with the Austrian ARIA Group(B), the Swiss ARIA Group(C), German Society for Applied Allergology (AEDA)(D), German Society for Allergology and Clinical Immunology (DGAKI)(E), Society for Pediatric Allergology (GPA)(F) in cooperation with AG Clinical Immunology, Allergology and Environmental Medicine of the DGHNO-KHC(G) and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date = 2020-05-28 keywords = AIT; COVID-19; SARS; patient summary = The highest risk of transmission for medical staff is present when standard precautions are missing, when primary infection prevention and control measures for respiratory infections are not undertaken, and when infected, potentially asymptomatic patients who are not yet tested positive for COVID-19 are treated without protective measures. The staff, including doctors, medical assistants, nutritional scientists, nursing and administrative staff, and all other staff at the facility with patient contact, should be made aware of: a) the current epidemiological situation of COVID-19 in Germany/Austria/ Switzerland and worldwide; b) known risk factors for infection; c) clinical signs and symptoms of COVID-19; d) recommended measures to prevent and contain infections in their region or country, including those mentioned in this document; e) procedures for reporting and transferring examined patients and probable/confirmed cases taking into account the appropriate regional regulations and specifications [36, 40] . doi = 10.5414/alx02147e id = cord-345381-9cckppk2 author = Klimek, Ludger title = Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date = 2020-09-07 keywords = CoV-2; SARS; covid-19; disease; infection; patient summary = title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontaneous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontane-ous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. doi = 10.5414/alx02166e id = cord-286038-a62k3lma author = Klimke, A. title = Hydroxychloroquine as an aerosol might markedly reduce and even prevent severe clinical symptoms after SARS-CoV-2 infection date = 2020-04-27 keywords = HCQ; SARS summary = The antimalarial drugs chloroquine phosphate (CQ) and hydroxychloroquine (HCQ) impair in vitro the terminal glycosylation of ACE2 without significant change of cell-surface ACE2 and, therefore, might be potent inhibitors of SARS-CoV-2 infections. We hypothesize that HCQ especially as an aerosol application will prevent or at least markedly reduce the replication rate of the SARS-CoV-2 virus in the early phase of the infection and subsequently substantially lower the number of severe pneumonias and casualties. This hypothesis is new since the major assumption in ongoing clinical studies and actual recommendations is that HCQ and CQ should be used in oral application form in patients with severe covid-19 pneumonia and only when other treatment strategies have failed. If our hypothesis is true, HCQ as an aerosol might not only reduce the side effect potential of the oral application form but can also be clinically used as an efficient antiviral agent in the early phase of COVID-19 and eventually lower the rate of severely ill patients and fatalities. doi = 10.1016/j.mehy.2020.109783 id = cord-312476-20ifwznd author = Kline, Jeffrey A. title = Crash Course in Decision Making date = 2008-01-08 keywords = SARS summary = in this month''s Academic Emergency Medicine shows how emergency physicians can use scientific method to ''''get it in gear'''' to produce a decision instrument, used in real time on huge numbers of patients, to render a major impact on public health. The Centers for Disease Control and Prevention (CDC) have issued specific recommendations for the diagnosis and evaluation of patients with suspected SARS. Curiously, at the time of this writing, no areas of the world are reporting ongoing SARS transmission, yet the CDC''s recommendation for infection control stated above were issued in September 2003, and are current and active. 2 Regardless of whether SARS returns to the public consciousness, the CDC''s recommendations for infection control of SARS have several major ramifications on the practice of emergency medicine. Numerous other contagious diseases that cause an ILI prodrome could emerge at any time and the CDC could issue similar infectious control recommendations. doi = 10.1111/j.1553-2712.2004.tb01431.x id = cord-321800-0h28pg3b author = Klingelhöfer, Doris title = Coronavirus: An insight into global research until outbreak of COVID-19 and its implications for the future date = 2020-09-23 keywords = MERS; SARS; USA; research summary = RESULTS: The trend in publication and citation numbers shows the strong influence of the past pandemics SARS and MERS with an untypical decline afterward. The current extremely rapid global spread of SARS-CoV-2 has led to the highly dangerous outbreak of the pandemic CoVID-19 with daily increasing numbers of new infections and deaths around the world. Additionally, socio-economic, scientific and epidemiological parameters were related to the publication numbers to obtain an even more meaningful picture of the global landscape of CoV research. The resulting scientific interest and the possible in-si-VIEWPOINTS RESEARCH THEME 1: COVID-19 PANDEMIC tu investigation of the cases caused the publication figures to rise at the beginning of the SARS disease and to fall rapidly thereafter. Here, the USA and China are the highest-ranking countries, demonstrating their overall interest in CoV research and also focusing on the MERS pandemic, despite the relatively low case numbers. doi = 10.7189/jogh.10.020508 id = cord-312560-onfabcfv author = Klingler, J. title = Role of IgM and IgA Antibodies to the Neutralization of SARS-CoV-2 date = 2020-08-21 keywords = Fig; RBD; SARS summary = The data demonstrate high prevalence of spike-and RBD-specific IgM and IgA, similar to that of IgG1, in plasma/serum from COVID-19 patients and their significant contributions to virusneutralizing activities. In Fig. 3 , comparing levels of total Ig with the different Ig isotypes showed a highly significant correlation with IgG1 for both Abs specific for spike and RBD indicating that IgG1 is the major isotype induced by SARS-CoV-2 infection. To ask directly to what extent Abs of different isotypes mediate neutralization, we evaluated the neutralization activities of IgM, IgG, and IgA fractions purified from plasma from five COVID-19-convalescent individuals (RP#1-5). Several SARS-CoV-2 vaccine candidates tested in animal models and humans were shown to induce IgG responses against spike and RBD as well as virus neutralizing activities, but in many of these studies, the induction of other Ig isotypes was not evaluated 46-49 . doi = 10.1101/2020.08.18.20177303 id = cord-267723-loj718vd author = Kloc, Małgorzata title = Macrophages in diabetes mellitus (DM) and COVID-19: do they trigger DM? date = 2020-10-17 keywords = SARS; T1DM summary = We also describe the DM-related changes in the monocyte/macrophages functions, how they could lead to the severe outcome of SARS-CoV-2 infection, and importantly, if and how they could initiate DM in DM-susceptible patients. Preclinical and clinical studies indicate that the increased numbers of innate immune cells, and produced by them inflammatory factors have causative and detrimental effects on the islets and β-cells in diabetes (Böni-Schnetzler and Meier 2019). As we wrote above, SARS-CoV-2 infects many types of cells expressing ACE2 receptors, including the macrophages and β-cell in the pancreas. One possibility is that, similar to the effect of SARS-CoV-2 in the lungs, the infection of pancreatic macrophages causes inflammatory cytokine and chemokines storm in the pancreas. Although, this scenario seemed the least likely because the direct damage to the pancreatic islets should result in higher than the reported incidence of COVID-19-induced diabetes, however, recent data presented in Nature News indicate that indead, the SARS-CoV-2 may cause direct damage to the insulin producing β-cells (Mallapaty 2020) . doi = 10.1007/s40200-020-00665-3 id = cord-336810-77wq9laa author = Klocperk, Adam title = Complex Immunometabolic Profiling Reveals the Activation of Cellular Immunity and Biliary Lesions in Patients with Severe COVID-19 date = 2020-09-17 keywords = COVID-19; SARS; figure; patient summary = Therefore, we observed a gradual increase of CRP, procalcitonin, ferritin, and serum IL-6 corresponding to the severity of the disease; however, these markers displayed a relative failure to upregulate in patients with a fatal course, who instead displayed high sIL2R and D-dimers ( Figure 1C ). Most markers of inflammation, the immune response, and liver damage presented in patients with a fatal course of COVID-19 so far seem mostly on par with those seen in patients with a moderate form of the disease, suggesting a weaker response to the infection compared to severely ill patients, which resulted in the patients'' deaths. In contrast, patients with fatal COVID-19 ( Figure 5B ) displayed a negative correlation between leukocytes and lymphocytes, and their inflammatory markers increased with markers of organ failure (liver enzymes, amylase, GGT, urea, and creatinine) and cytotoxic cellular immunity (activated CD38+ HLA-DR+ CD8 T cells) instead. doi = 10.3390/jcm9093000 id = cord-312005-9so3orib author = Klussmeier, Anja title = Etablierung der PCR-basierten SARS-CoV-2-Testung im Hochdurchsatz date = 2020-09-05 keywords = SARS summary = Eine entscheidende Maßnahme zur Eindämmung des SARS-CoV-2-Infektionsgeschehens ist die rechtzeitige Diagnose von Einzelfällen. Ende März 2020 war daher abzusehen, dass bei einem stark steigendem Infektionsgeschehen, wie es zu diesem Zeitpunkt in Italien oder Spanien beobachtet werden konnte, hohe Laborkapazitäten für die Diagnostik von SARS-CoV-2 in Deutschland benötigt werden würden. Das DKMS Life Science Lab ist das weltweit größte Labor für die HLA-Genotypisierung von Personen, die sich für eine Stammzellspende registrieren möchten. Pro Werktag werden hier rund 5.000 Proben im Hochdurchsatz bearbeitet: von der Annahme der Abstrichtupfer, über die DNA-Isolation, PCR und Sequenzierung bis hin zur Datenanalyse [2, 3] Der hier beschriebene Laborprozess zur Diag nostik von akuten SARS-CoV-2-Infektionen wurde in einem Zeitraum von etwa drei Monaten geplant, umgesetzt und validiert. 2016-2019 Spezialist für Labortechnik und Automation und seit 2019 Business Development Manager bei DKMS Life Science Lab GmbH in Dresden. Abteilungsleiter Labortechnik und seit 2016 Geschäftsführer (CTO) der DKMS Life Science Lab GmbH in Dresden doi = 10.1007/s12268-020-1431-1 id = cord-103837-iuvigqdx author = Knierman, Michael D. title = The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date = 2020-11-13 keywords = HLA; SARS; cluster; peptide summary = Mass spectrometry is used to identify 526 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The ability to automate and miniaturize the MAPPs assay enables facile identification of 1000''s of naturally processed and displayed HLA-II peptides from human DCs. Using this approach, we were able J o u r n a l P r e -p r o o f to determine the precise regions and sequences of peptides from SARS-CoV-2 spike glycoprotein ECD derived from a panel of healthy subjects presented for immune surveillance by T-cells. We observed a total of 526 unique peptide sequences contained within 73 clusters distributed across each segment of the SARS-CoV-2 spike glycoprotein ECD presented by human DCs (Figure 2 and Supplemental Table S2 ). doi = 10.1016/j.celrep.2020.108454 id = cord-331010-4phhz79k author = Knight, M. title = Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) date = 2020-05-12 keywords = SARS summary = title: Characteristics and outcomes of pregnant women hospitalised with confirmed SARS-CoV-2 infection in the UK: a national cohort study using the UK Obstetric Surveillance System (UKOSS) Objective: To describe a national cohort of pregnant women hospitalised with SARS-CoV-2 infection in the UK, identify factors associated with infection and describe outcomes, including transmission of infection, for mother and infant. Rates of maternal death, level 3 critical care unit admission, preterm birth, stillbirth, early neonatal death, perinatal death; odds ratios for infected versus comparison women. The incidence of hospitalisation with confirmed SARS-CoV-2 infection in pregnancy was calculated using denominator estimates based on the most recently available (2018) national maternity data for the constituent countries of the United Kingdom. The clinical data from this national surveillance study show black and minority ethnicity is significantly associated with admission with SARS-CoV-2 infection in pregnancy, along with preexisting co-morbidities, overweight and obesity and older maternal age. doi = 10.1101/2020.05.08.20089268 id = cord-339172-210dwhgj author = Knoops, Kèvin title = SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date = 2008-09-16 keywords = DMV; RNA; SARS; figure; membrane; virus summary = Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''''inner vesicles,'''' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. doi = 10.1371/journal.pbio.0060226 id = cord-314546-fbddxbhd author = Ko, Meehyun title = Comparative analysis of antiviral efficacy of FDA‐approved drugs against SARS‐CoV‐2 in human lung cells date = 2020-08-16 keywords = SARS; Vero summary = Although nafamostat mesylate and camostat mesylate were not selected as potent antiviral drug candidates in our earlier study, we compared the antiviral efficacy of these drugs at this time in between Vero and Calu-3 cells following the discovery that TMPRSS2, a host protease necessary for priming viral spike glycoprotein, could be a target for COVID-19 antiviral development. 11 The discrepancy in IC 50 was specifically remarkable with nafamostat mesylate; the IC 50 decreased by approximately 6000 folds when the drug was used in the SARS-CoV-2-infected Calu-3 cells perhaps due to the dominant role of TMPRSS2-dependent viral entry in the Calu-3 human lung epithelial cells. In summary, we compared antiviral efficacy of the potential antiviral drug candidates against SARS-CoV-2 in between Vero and Calu-3 cells and found that nafamostat mesylate is the most potent antiviral drug candidate in vitro. Comparative analysis of antiviral efficacy of FDA-approved drugs against SARS-CoV-2 in human lung cells doi = 10.1002/jmv.26397 id = cord-306748-i9ndb71n author = Kobia, Francis title = COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness? date = 2020-04-17 keywords = Africa; SARS; covid-19 summary = In fact, this strategy is being used by Senegal, which together with UK collaborators, is developing an affordable COVID-19 RDT (expected to cost $1 per test) for home use in African countries (Financial Times, 2020b). The authors contend that most African countries lack the capacity to administer mass screening to ascertain the extent of the disease spread, and call for support toward the development of homegrown RDTs and POCTs as a strategy to achieve mass screening of COVID-19 in Africa The present review by the authors provides important information on diagnostic challenges facing African countries in their combat against the ongoing COVID-19 pandemic. Specific to the present COVID-19 case, would it be faster and cheaper importing the diagnostic tools, as is already being done by some countries?The authors may wish to put " " section before " COVID-19 point of care testing strategies " section, for consistency with the conclusion. doi = 10.12688/aasopenres.13061.1 id = cord-151024-qe7c2uks author = Koca, Caglar title = Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date = 2020-11-07 keywords = ACE2; SARS; respiratory; virus summary = We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . doi = nan id = cord-298372-4pw1y404 author = Koch, Lionel title = Natural outbreaks and bioterrorism: How to deal with the two sides of the same coin? date = 2020-08-18 keywords = COVID-19; Ebola; SARS; disease; outbreak summary = The last Ebola outbreak in 2014 in West Africa was regarded as a paradigm of the issues caused by emerging infectious diseases nowadays: this extremely deadly pathogen has naturally emerged in a large new area, and its overwhelming spread has subsequently impacted Europe and the United States [3] . At the same time, some natural outbreaks were caused by naturally altered pathogens like the Escherichia coli O104:H4 in Europe in 2011, a strain that acquired and combined unusual virulence factor and drug resistance genes [25] or in 2003 the new human coronavirus (SARS-CoV) identified with surprise in front of severe acute respiratory syndrome cases [26] . Indeed, even if the substantial remaining risk in the case of an attack is the possibility of secondary actions aiming to maximise damages to the emergency infrastructure [38] , the real challenge for global safety remains the early detection, the accurate characterisation and the establishment of specific measures, whatever the outbreak origin [39, 40] . doi = 10.7189/jogh.10.020317 id = cord-277539-xt2nt11e author = Kochhar, Anuraj Singh title = Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date = 2020 keywords = COVID-19; SARS; dental; infection; patient summary = Despite the avalanche of information that has exploded in relation to this rapidly spreading disease, there is a lack of consolidated information to guide dentists regarding clinical management including precautions to take materials to use and postprocedure care, during and after the COVID-19 pandemic. This review aims to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan can be formulated and adapted to the circumstances of each dental practice during the pandemic and the times to follow. The purpose of this review is to provide a comprehensive summary from the available literature on COVID-19, its insinuation in dentistry, recommendations that have been published, and the actual in-practice implications, so a plan of measures can be formulated and adapted according to the circumstances of each dental practice during the pandemic and the times to follow. doi = 10.5005/jp-journals-10005-1782 id = cord-321933-cq0fa3hs author = Koff, Alan G. title = Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy date = 2020-10-07 keywords = SARS summary = title: Prolonged incubation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a patient on rituximab therapy The incubation period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rarely >14 days. We report a patient with hypogammaglobulinemia who developed coronavirus disease 2019 (COVID-19) with a confirmed incubation period of at least 21 days. [2] [3] [4] 6, 7 In the vast majority of cases, the incubation period is far less than 14 days, which has helped to inform the Centers for Disease Control and Prevention (CDC) recommendations for a 14-day quarantine period after a known coronavirus disease 2019 (COVID-19) exposure. This case demonstrates an objectively confirmed asymptomatic SARS-CoV-2 infection with symptom onset 21 days after her positive test. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application The difference in the incubation period of 2019 novel coronavirus (SARS-CoV-2) infection between travelers to Hubei and nontravelers: the need for a longer quarantine period doi = 10.1017/ice.2020.1239 id = cord-253851-27nt0op8 author = Koh, David title = SARS: health care work can be hazardous to health date = 2003-06-17 keywords = SARS; case summary = Health care workers (HCWs) are a high-risk group for SARS-CoV infection. As at 4 May, 41% of 203 SARS patients in Singapore and 22% of 1629 cases in Hong Kong [7] were HCWs. The majority of cases in Canada (74.4%) have been attributed to exposure in a hospital or health care setting [8] . That the cluster of cases included housekeepers is also significant-preventive measures need to target much broader groups of HCWs than just the doctors and nurses in direct contact with patients. This was the case in a Singapore hospital [11] , where the experience was reported as: ''We did not see any further transmission from this index patient after we implemented strict infection control measures involving use of N95 masks, gown, gloves, and handwashing before and after patient contact''. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.1093/occmed/kqg090 id = cord-276980-k8xi2zvh author = Koh, David title = Occupational Health Response to SARS date = 2005-01-17 keywords = SARS; specimen summary = detected severe acute respiratory syndrome-associated coronavirus (SARS-CoV) from throat wash and saliva specimens and suggested that these specimens have advantages over other specimens, including ease of procurement and safety for medical personnel (1) . To the Editor: Severe acute respiratory syndrome (SARS), an occupational disease risk for healthcare workers, warrants an occupational health response, as clearly described by Esswein et al. The occupational health audits included site inspections and reviews of work processes of those areas where actual transmission of SARS had occurred and where triage of febrile patients was taking place. Occupational health physicians subsequently served on hospital SARS debriefing committees that reviewed institutional shortcomings and recommended new measures for future outbreaks. Clinical specimens were retrieved, and RT-PCR was performed to specifically amplify a genomic segment of SARS-CoV encompassing the deletion site. Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) doi = 10.3201/eid1101.040637 id = cord-283116-ib5c3lbi author = Koh, David title = Occupational health responses to COVID‐19: What lessons can we learn from SARS? date = 2020-05-13 keywords = SARS; covid-19; health summary = Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. Among the insights gained from the past outbreaks were: outbreaks caused by viruses are hazardous to healthcare workers; the impact of the disease extends beyond the infection; general principles of prevention and control are effective in containing the disease; the disease poses both a public health as well as an occupational health threat; and emerging infectious diseases pose a continuing threat to the world. coronavirus, COVID-19, health care, occupational health, outbreaks, public health, SARS-CoV-2 confirmed cases and over 62 000 deaths spread over 200 countries and territories. doi = 10.1002/1348-9585.12128 id = cord-278759-pykihnup author = Koh, Yiwen title = Nurses'' perceptions of risk from emerging respiratory infectious diseases: A Singapore study date = 2012-03-21 keywords = H1N1; SARS; risk summary = Another significant finding of this study is that the government''s, organizations'' and nurses'' perceptions of new emerging respiratory infectious diseases were influenced by their previous experience with SARS. 16 It can be seen from this discussion that there is a substantial amount of research examining how HCWs perceive the risks of Emerging Acute Respiratory Infectious Diseases such as H1N1 and SARS; 17, 25 however, few studies have focused specifically on nurses. 41, 42 With the resurgence of emerging acute respiratory infectious diseases such as SARS and pandemic influenza in the 21st century, research investigating nurses'' risk perceptions towards their exposure is more than ever pertinent. The data show that the nurses in this study have similar concerns to previous research on HCW''s perceptions of risk from SARS and other emerging acute respiratory infectious diseases in that these nurses were concerned about risks to their personal health (from patients, from colleagues and visitors to the organization). doi = 10.1111/j.1440-172x.2012.02018.x id = cord-320560-yn3bbkdh author = Kohanski, Michael A. title = Review of indoor aerosol generation, transport, and control in the context of COVID‐19 date = 2020-07-24 keywords = SARS; aerosol; transmission summary = [5] [6] [7] [8] [9] The lack of studies within the otorhinolaryngology field assessing the aerosol-generating potential of procedures involving mucosal surfaces pre-COVID-19 made it challenging to understand in an evidence-based fashion the potential risks of SARS-CoV-2 transmission associated with instrumentation of the upper airway; that is, whether these procedures may be infectious AGPs. At the early stages of the pandemic, based on the risks of exposure to high viral load mucosal surfaces, 10, 11 as well as on the lack of any immunity to SARS-CoV-2 and of any vaccines or effective treatments, an array of practice changes to protect health-care workers and patients were recommended and instituted for otorhinolaryngology procedures involving upper airway mucosal surfaces. doi = 10.1002/alr.22661 id = cord-327920-51s4figy author = Kohler, Philipp P. title = Prevalence of SARS-CoV-2 antibodies among Swiss hospital workers: Results of a prospective cohort study date = 2020-10-08 keywords = CMIA; SARS summary = 5 The aims of this prospective cohort study were to assess seropositivity for SARS-CoV-2, to identify risk exposures, and to describe the spectrum of COVID-19 symptoms among hospital workers. Participants'' sera were analyzed for SARS-CoV-2 antibodies using 3 different tests: a lateral flow immunochromatographic assay (LFIA, Sugentech, Yuseong-gu, Daejeon, Republic of Korea), a chemiluminescence microparticle immunoassay (CMIA, Abbott Diagnostics, Lake Bluff, IL), and an electro-chemiluminescence immunoassay (ECLIA, Roche Diagnostics, Basel, Switzerland). At followup, 2 participants showed a positive LFIA (IgG) and ECLIA/ CMIA result in addition to the 8 samples confirmed at baseline, resulting in 10 of 1,012 true seropositives (1.0%) and 48 of 1,012 false seropositives (4.7%) (Fig. 1) . This finding is in line with data from the Infectious Diseases Society of America (IDSA) guideline on SARS-CoV serology testing showing a lower sensitivity of CMIA IgG compared to LFIA IgM early after infection. doi = 10.1017/ice.2020.1244 id = cord-351718-sf5zp5wg author = Kohli, Utkarsh title = COVID-19 pneumonia in an infant with a hemodynamically significant ventricular septal defect date = 2020-10-12 keywords = COVID-19; SARS summary = Reports thus far suggest a mild course for acute COVID-19 infection in children; however, its effects in vulnerable paediatric populations, including children with haemodynamically significant congenital heart disease, have rarely been reported. We therefore report on a 4-month-old Hispanic male with a moderate sized conoventricular ventricular septal defect and pulmonary overcirculation who presented with COVID-19-associated pneumonia. 6 Children with haemodynamically significant congenital heart disease are at an increased risk of decompensation and hospitalisation when concomitantly infected with other respiratory viruses such as respiratory syncytial virus and influenza, [12] [13] [14] lending credence to the notion that COVID-19 could run a more severe course in these children. Given the probable paucity of these patients at any single paediatric centre, there is a dire need for collaborative research efforts on a global scale to characterise the clinical features and outcomes of COVID-19 in children with haemodynamically significant congenital heart disease as well as other vulnerable paediatric populations. doi = 10.1017/s1047951120003303 id = cord-336535-r3a57m57 author = Kohmer, Niko title = Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays date = 2020-06-01 keywords = SARS summary = So far, there is limited data on how recently commercially available, high-throughput immunoassays, using different recombinant SARS-CoV-2 antigens, perform with clinical samples. Five follow-up samples of three individuals were only detected in either an S and/or N protein-based assay, indicating an individual different immune response to SARS-CoV-2 and the influence of the used assay in the detection of IgG antibodies. This study aims to provide a quick overview on some of these assays (two commercially available ELISA assays, four automated immunoassays and a plaque reduction neutralization test (PRNT)) focusing on the detection and neutralization capacity of IgG antibodies in follow up serum or plasma samples of individuals with PCR-diagnosed infections with SARS-CoV-2. The commercially available assays examined in our study, generated consistent results regarding the detection of SARS-CoV-2-IgG antibodies. Interestingly, in samples of three individuals with mild clinical course of COVID-19, examined in our study (1, 2, 3 in The automated immunoassays demonstrated a higher overall sensitivity than the ELISA based assays. doi = 10.1016/j.jcv.2020.104480 id = cord-340291-bah2ege0 author = Kohmer, Niko title = Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date = 2020-05-10 keywords = SARS summary = With exception of one sample, all positive tested samples in the analysed cohort, using the commercially available assays examined (including the in-house developed IFA), demonstrated neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-CoV-2. With exception of one sample, all positive tested samples in the analysed cohort, using the 37 commercially available assays examined (including the in-house developed IFA), demonstrated 38 neutralizing (protective) properties in the PRNT, indicating a potential protective immunity to SARS-39 there is an increasing demand in the detection of antibodies -especially of IgG antibodies. Currently there are many S 57 protein based commercially or in-house developed assays available, but there is limited data on how 58 these tests perform with clinical samples and if the detected IgG antibodies provide protective 59 doi = 10.1101/2020.05.08.085506 id = cord-308021-cnf4xljc author = Kohns Vasconcelos, Malte title = SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date = 2020-10-13 keywords = SARS; test summary = Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Paediatric departments of 23 mostly tertiary care hospitals in 12 European countries (Belgium, Germany, France, Italy, Poland, Portugal, the UK, the Netherlands, Greece, Spain, Lithuania and Switzerland) participated in the surveys (response rate 29%). This changed by April at all three sites, so that afterwards detection of another pathogen that could explain the respiratory symptoms no longer excluded a patient from being a suspect case and from undergoing SARS-CoV-2 testing. In the early stages of the COVID-19 pandemic, paediatric emergency departments implemented standardised case definitions, testing guidelines and infection control measures rapidly. doi = 10.1007/s00431-020-03843-w id = cord-288146-xqxznv1r author = Kohyama, Shunsuke title = Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date = 2009-09-11 keywords = CD8; CTL; HLA; SARS summary = title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a As shown in Fig. 2 , significant numbers of IFN-␥-producing CD8 + T cells (p < 0.01) were detected in mice immunized with syngeneic cells pulsed with each of nine pp1aderived peptides including pp1a-2187, -2207, -2340, -2546, -2755, -2990, -3444, -3687, and -3709 , suggesting that these nine peptides may be HLA-A*0201-restricted CTL epitopes derived from SARS-CoV pp1a protein. After HHD mice were immunized once with one of the nine liposomal peptides, spleen cells of them were prepared, stimulated with a relevant synthetic peptide, and stained for their expression of surface CD8 and intracellular IFN-␥. In summary, we have identified seven HLA-A*0201-restricted CTL epitopes derived from pp1a protein of SARS-CoV using computational algorithms, HLA-A*0201 transgenic mice and the surface-linked liposomal peptide. doi = 10.1016/j.antiviral.2009.09.004 id = cord-026099-97luq10a author = Kok, J title = Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus date = 2020-06-05 keywords = SARS summary = title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus We reported that the sensitivity, specificity, positive predictive value (PPV) and negative predictive value of the AusDiagnostics RUO assay was 100%, 92.16%, 55.56% and 100%, respectively when compared to our RT-PCR assay. Even if the specificity of the AusDiagnostics RUO assay was 99% (i.e. a 1% false positive rate), given the current prevalence of COVID-19 infection in NSW of 0.84%, the calculated PPV of the assay would be 54.15%, which is concordant with our findings. Cohen et al also estimated false positive rates of up to 7% in commercial diagnostics assays detecting SARS-CoV-2 [Cohen] . Furthermore, false positive RT-PCR results have also been reported from commercial kits that have been contaminated with SARS-CoV-2 sequences [Bustin] . Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus doi = 10.1016/j.jcv.2020.104484 id = cord-256458-3fyul3k2 author = Kolikonda, Murali Krishnan title = Association of Coronavirus Disease 2019 and Stroke: A Rising Concern date = 2020-08-13 keywords = COVID-19; SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) causes the coronavirus disease 2019 (COVID-19). Several chemical, mechanical, and/or inflammatory central nervous system pathologies are proposed to explain how this viral infection might induce acute cerebrovascular disease. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus 2019 (COVID19) disease, which quickly became a pandemic [1] . Beyond knowing that bacteria and viruses can be risk factors for cerebrovascular ischemia, the impact of this novel coronavirus on emergency medical issues like acute ischemic stroke remains to be clarified [2] . Although the exact mechanism of SARS-CoV-2 causing cerebrovascular pathology is unclear, there might be a neuroinvasive potential that increases the incidence of stroke, thromboses, and related neuropsychiatric conditions [10] [11] [12] . While coronavirus precautions are being relaxed, acknowledging COVID-19 associations to cerebrovascular disease helps plan health care services and should improve clinical outcomes. doi = 10.1159/000510134 id = cord-296619-uhhndp0a author = Kondo, Yuki title = Coinfection with SARS-CoV-2 and influenza A virus date = 2020-07-01 keywords = COVID-19; SARS summary = We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. We report a case of coinfection with SARS-CoV-2 and influenza A virus in a patient with pneumonia in Japan. The patient with both COVID-19 and influenza virus infection presented similar clinical characteristics with COVID-19 only. Initial considerations for this patient who presented acutely with fever and cough include infection with a common virus (rhinoviruses, non-SARS-CoV-2 coronaviruses and influenza virus) and communityacquired pneumonia. 3 The clinical characteristics of patients with both COVID-19 and influenza virus infection were similar to those of COVID-19 cases. ► There was no significant difference in rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with and without other pathogens. The clinical characteristics of pneumonia patients coinfected with 2019 novel coronavirus and influenza virus in Wuhan doi = 10.1136/bcr-2020-236812 id = cord-300466-sk9iilum author = Kong, Wen-Hua title = Serologic Response to SARS-CoV-2 in COVID-19 Patients with Different Severity date = 2020-07-23 keywords = SARS; covid-19 summary = According to the Chinese Centers for Disease Prevention and Control (CDC) report, among 72,314 COVID-19 cases in China''s mainland most of cases (81%) presented only mild illness or moderate pneumonia, yet 14% developed severe symptoms such as dyspnea, high respiratory frequency and low blood oxygen saturation, and another 5% were in critical conditions like respiratory failure, septic shock, and multiple organ dysfunction/failure (Epidemiology Working Group for NCIP Epidemic Response and Chinese CDC, 2020; Wu and McGoogan 2020) . In this study, we, compared the results of serologic tests and nucleic acid test (NAT) from a group of COVID-19 patients in Wuhan, and analyzed the serologic IgM and IgG antibody level of patients with different disease severity. In summary, this study supported the combination of serologic testing and NAT in routine COVID-19 diagnosis and provided evidence on the temporal profile of antibody response against SARS-CoV-2 in patients with different disease severity. doi = 10.1007/s12250-020-00270-x id = cord-305093-og4k3fc7 author = Konno, Yoriyuki title = SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant date = 2020-09-04 keywords = IFN; SARS; figure summary = Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Although 177 three additional ORF3b proteins of SARS-CoV-related viruses from bats (HKU3-2, 178 GX2013 and Yunnan2011) were shorter than 39 amino acids in length, they did not 179 exhibit anti-IFN-I activity, most likely because of their poor expression and/or 180 stability (Figures 2C and S2B) . mean values of three independent experiments with SEM are shown, 648 and statistically significant differences (P < 0.05) compared to the SeV-infected 649 empty vector-transfected cells (#) and the same amount of the SARS The mean values of three independent 753 experiments with SEM are shown, and statistically significant differences (P < 0.05) 754 compared to the SeV-infected empty vector-transfected cells (#) and the same 755 amount of the SARS-CoV-2 ORF3b WT doi = 10.1016/j.celrep.2020.108185 id = cord-316667-b1xabkzk author = Konopka, Kristine E. title = Diffuse Alveolar Damage (DAD) from Coronavirus Disease 2019 Infection is Morphologically Indistinguishable from Other Causes of DAD date = 2020-06-15 keywords = DAD; SARS summary = Additionally, to better understand if COVID-19 represents a histologic variant of DAD we systematically compare the pathologic findings of SARS-CoV-2-positive patients to uninfected controls. 11 Our autopsy databases were then searched from January 1, 2016 through December 31, 2019 for inpatient and nonhospitalized community cases diagnosed as "diffuse alveolar damage." Since these deaths occurred prior to the first reported case of COVID-19 in the United States, 12 they are considered SARS-CoV-2negative (further referred to as "control cohort"). To our knowledge, this is the first comparison of autopsy lung findings in SARS-CoV-2-positive medically managed inpatients and untreated, non-hospitalized decedents to uninfected historical control cases of DAD. Nonetheless, we think our SARS-CoV-2 positive cases are likely representative of the broader COVID-19 patient population, since both hospitalized and non-hospitalized decedents had underlying conditions previously identified as risk factors for severe disease, including diabetes, chronic lung disease, cardiovascular disease, 13 and obesity. doi = 10.1111/his.14180 id = cord-349745-zlhu1jit author = Konrad, Regina title = Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date = 2020-03-05 keywords = PCR; SARS summary = The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2 ), which complicated the evaluation of the qPCR result. The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. doi = 10.2807/1560-7917.es.2020.25.9.2000173 id = cord-345101-h0i5o0do author = Koo, Bon-Sang title = Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques date = 2020-08-03 keywords = SARS; figure summary = Using a reliable primate model is critical for developing therapeutic advances to treat humans infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The absence of a reliable preclinical animal model that recapitulates patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection poses a major limitation to the development of improved diagnostics and therapeutics. Studies reported that SARS-CoV-2 developed no severe clinical signs, but pulmonary pneumonia in 50% of cynomolgus macaques, recapitulating mild symptoms in humans [6] . The viral RNA was highest in the upper respiratory swab samples and lung tissues at the earliest phase of infection, and the viral antigen was present in the lungs ( Figure 1C and D) , suggesting the predominant site of the virus. Using a high viral titre administered through combined routes, virus assays, and histopathological changes suggests that both cynomolgus and rhesus macaques are permissive to infection of SARS-CoV-2 and recapitulate COVID-19-like disease in human. doi = 10.1093/infdis/jiaa486 id = cord-267770-ik1ib3zb author = Koo, Hyun Jung title = RadioGraphics Update: Radiographic and CT Features of Viral Pneumonia date = 2020-06-05 keywords = CoV-2; SARS summary = In this updated review, we expand on the information presented in our 2018 article (4) and focus on the clinical features and chest CT findings of SARS-CoV-2 pneumonia to help radiologists detect the disease at its early stage. A reverse transcription-polymerase chain reaction (RT-PCR) test of an upper respiratory tract specimen (obtained with nasopharyngeal swab and/or oropharyngeal swab) and/or sputum sample is the standard diagnostic tool for determining hospitalization and isolation of patients with SARS-CoV infection. After 13 days of conservative management, her respiratory symptoms ameliorated, and a negative RT-PCR test result for SARS-CoV-2 was obtained. On the basis of this suggestion and experience managing patients with COVID-19, we provide a brief clinical setting to show the use of chest CT to facilitate the diagnosis of SARS-CoV-2 pneumonia (Fig 5) . For the management of patients with respiratory symptoms in endemic areas, an RT-PCR test is the primary diagnostic tool used for discriminating SARS-CoV-2-positive cases. doi = 10.1148/rg.2020200097 id = cord-253238-ptmxkpae author = Kopel, Jonathan title = Clinical Insights into the Gastrointestinal Manifestations of COVID-19 date = 2020-05-23 keywords = COVID-19; MERS; SARS summary = Furthermore, testing stool after a patient has been infected with COVID-19 may be necessary to monitor any GI complications, and the potential for fecal-oral transmission after respiratory symptoms has resolved. Despite the limited information on COVID-19 and its GI symptoms, information from SARS-CoV and MERS-CoV provides some insights on the symptoms and disease severity from other CoVs. The MERS-CoV has shown to infect human primary intestinal epithelial cells, small intestine It is also found to transmit via the fecal-oral route [35] . Physicians should monitor for GI symptoms in COVID-19-infected patients and examine whether the virus continues to remain in their stools after their respiratory symptoms have resolved. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus doi = 10.1007/s10620-020-06362-8 id = cord-352577-h3652seb author = Kopić, Jasminka title = Expanding the Use of Noninvasive Ventilation During an Epidemic date = 2014-08-27 keywords = NIV; SARS; patient summary = 4 When appropriately indicated and promptly administered, NIV offers an alternative to tracheal intubation, sedation, risk of infection, and myriad complications associated with invasive ventilation, and it can promote rapid respiratory recovery, and reduce a patient''s dependence on critical care facilities. Rello et al described NIV use at ICU admission in 1 of 3 patients with H1N1 virus and respiratory failure, but 75% of them had an unfavorable clinical course and required tracheal intubation and invasive mechanical ventilation. In a position statement, the Australian Society for Infectious Diseases recommends "reserving negative-pressure ventilation rooms (if available) for intensive care patients, especially those receiving non-invasive ventilation." 31 The UK Department of Health, in "Guidance for infection control in critical care for pandemic influenza," approved the use of NIV under strict infection control measures. doi = 10.1017/dmp.2014.71 id = cord-277486-12uah5qi author = Kopp, Kristen title = Interdisciplinary Model for Scheduling Post-discharge Cardiopulmonary Care of Patients Following Severe and Critical SARS-CoV-2 (Coronavirus) Infection date = 2020-08-14 keywords = SARS; follow; patient summary = As Covid-19 can severely implicate the respiratory and cardiovascular systems, potential pulmonary, and/or cardiovascular sequelae may be anticipated in patients following severe and critical SARS-CoV-2 infection meriting coordinated post-discharge management to identify residual effects and to mitigate potential worsening of pre-existing conditions. The WHO report Interim Guidance: Clinical Management of Covid 19, released 27 May 2020 however anticipates potential sequelae in patients with severe and critical SARS-CoV-2 infection following treatment with mechanical ventilation, sedation, and/or prolonged bed rest based on evidence from general critical care populations. A coordinated post-discharge care concept for patients surviving Covid-19 is therefore warranted to identify any cardiopulmonary sequelae and to mitigate possible worsening of preexisting disease following severe and critical SARS-Cov-2 infection. Short, intermediate and long-term effects following severe and critical SARS-CoV-2 infection are unknown, and significant sequelae may be expected, especially in patient populations experiencing ARDS, sepsis, and/or multiple organ dysfunction, as well as patients with exacerbation or progression of preexisting pulmonary or cardiovascular disease. doi = 10.3389/fcvm.2020.00157 id = cord-311535-ppkwd1kp author = Korakas, Emmanouil title = Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes date = 2020-07-01 keywords = SARS; covid-19; obesity summary = The production of increased amounts of cytokines such as TNFα, IL-1, IL-6, and monocyte chemoattractant protein (MCP-1) lead to oxidative stress and defective function of innate and adaptive immunity, whereas the activation of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome seems to play a crucial role in the pathogenesis of the infection. Endothelial dysfunction and arterial stiffness could favor the recently discovered infection of the endothelium by SARS-CoV-2, whereas alterations in cardiac structure and function and the prothrombotic microenvironment in obesity could provide a link for the increased cardiovascular events in these patients. Chronic inflammation and oxidative stress, hypercytokinemia, immune dysregulation, endothelial dysfunction, and cardiovascular abnormalities are all possible mechanisms through which the excess in adipose tissue could lead to the acute hyperinflammatory state that characterizes severe SARS-CoV-2 infections and is responsible for its complications. doi = 10.1152/ajpendo.00198.2020 id = cord-280025-4hmecfi0 author = Korber, B title = Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date = 2020-05-05 keywords = Fig; G614; GISAID; SARS; Spike; d614 summary = We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. Over the past two months, the HIV database team at Los Alamos National Laboratory has turned to developing an analysis pipeline to track in real time the evolution of the SARS-CoV-2 Spike (S) protein in the COVID-19 pandemic, using the Global Initiative for Sharing All Influenza Data GISAID SARS-CoV-2 sequence database as our baseline (Sup. Item 1 is the GISAID acknowledgments table, listing all the groups who contribute sequences to this global effort) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017) . GISAID is the primary SARS-CoV-2 sequence database resource, and our intent is to complement what they provide with visualizations and summary data specifically intended to support the immunology and vaccine communities, and to alert the broader community to changes in frequency of mutations that might signal positive selection and a change in either viral phenotype or antigenicity. doi = 10.1101/2020.04.29.069054 id = cord-337896-mct29erg author = Kornbluth, Asher title = Management of Inflammatory Bowel Disease and COVID-19 in New York City 2020: The Epicenter of IBD in the First Epicenter of the Global Pandemic date = 2020-09-03 keywords = COVID-19; IBD; NYC; SARS; patient summary = A number of the major GI societies, the Crohn''s & Colitis Foundation, 3 British Society of Gastroenterology, 4 European Crohn''s and Colitis Organization, 5 The American Gastroenterology Association, 6 and the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) 7 have published guidelines regarding treating the IBD patient with SARS-CoV-2 and COVID-19. 8 The key features are that the patient without proven or suspected SARS-CoV-2 should continue on their current medications with aggressive attempts to reduce steroid usage because this is the only single agent that has been associated with increased poor outcomes with COVID-19, defined in the SECURE registry as a composite score of hospitalization, intubation, or death. 14 We are now participating in the development of a database that will follow patients after clearance of the SARS-CoV-2 virus to determine the courses and outcomes of the IBD and of any sequelae or recurrence of COVID-19 after any drug therapy has been suspended. doi = 10.1093/ibd/izaa212 id = cord-323905-ayufx3wv author = Kort, N. P. title = Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members date = 2020-08-18 keywords = CoV-2; SARS; arthroplasty summary = title: Recommendations for resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: the European Hip Society and European Knee Associates Survey of Members The April 2020 SARS-CoV-2 survey completed by EHS and EKA members in Europe has confirmed the impact of SARS-CoV-2: this pandemic has resulted in a tremendous reduction in primary hip and knee arthroplasty procedures as shown in the survey. The benefits of hip and knee arthroplasty should be carefully weighed against the risks of viral transmission and infection, complications and mortality in the mostly elderly population requiring joint arthroplasty Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: pre-operative phase 1. Is there a need for -Modification or reorganization of hospital wards (patient density, bed density, medical and nursing stuff density, etc.)?417 (81) 70 (14) Resuming elective hip and knee arthroplasty in the setting of the SARS-CoV-2 pandemic: post-operative phase 1. doi = 10.1007/s00167-020-06212-0 id = cord-280544-1rhu478r author = Korte, Wolfgang title = SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on date = 2020-08-25 keywords = SARS summary = title: SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on antibodies rapidly decline early on 1, 3 Wolfgang Korte*, 2,3 Marija Buljan, 2,3 Matthias Rösslein, 2,3 Peter Wick, 1 Valentina Golubov, 1 Jana Jentsch, 1 Michael Reut, 3, 4 Karen Peier, 3 Brigitte Nohynek, 3 Aldo Fischer, 3 Raphael Stolz, 3 This cohort study included patients with a history of a positive SARS-CoV-2 PCR test. Results of the antibody course in 159 participants (52·2% females, 47·8% males), effectively spanning the time frame of two to ten weeks after a positive SARS-CoV-2 PCR test, are provided. The decline is statistically significant for anti-SP and anti-NC IgG at weeks 8-10 ( Figure 1) ; this is remarkable, as a continued IgG response for more than 34 weeks was seen with the SARS-CoV(-1) outbreak 6 . Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1016/j.jinf.2020.08.032 id = cord-289599-7vsynfgn author = Kostoff, Ronald N. title = COVID-19 vaccine safety date = 2020-09-18 keywords = SARS; effect; vaccine summary = The present article examines whether short-term, mid-term, and long-term vaccine safety can be achieved under such an accelerated schedule, given the myriad vaccine-induced mechanisms that have demonstrated adverse effects based on previous clinical trials and laboratory research. It is uncertain as to whether any of the drugs, vaccines, foods or radiation exposures of our predecessors, which were not tested for transgenerational effects, are adversely affecting human life at present. Of note, the question remains whether humanity is currently willing to pass on potential devastating diseases to future generations due to the present need for the speedy development of a vaccine, bypassing adequate long-term and transgenerational safety testing. The vaccine costs in this discussion are the potential adverse health effects from a cOVId-19 vaccine, particularly for the mid-and long-term. This least vulnerable demographic population would have to bear the brunt of any potential mid-and long-term adverse health impacts that may result from a vaccine inadequately tested for these effects. doi = 10.3892/ijmm.2020.4733 id = cord-311332-n8tvglif author = Kostoff, Ronald N. title = Literature-related discovery: Potential treatments and preventatives for SARS() date = 2011-04-20 keywords = LRD; SARS; discovery; potential; type summary = The present paper presents a comprehensive approach to systematic acceleration of potential discovery and innovation, and demonstrates the generation of large amounts of potential discovery for prevention/treatment of an infectious disease: severe acute respiratory syndrome (SARS). Approximately four times as many records were retrieved from Medline when MeSH terms were included in the query compared to using only terms in the title or Abstract, due to the greater choice of potential discovery substances. To retrieve the directly related literature from which potential discovery would be extracted, this higher level functional query was applied to the search engines of three databases: SCI, Medline, and SD. This proximity form of the query (as contrasted to the Boolean form used in prior LRD studies) provided highly ''relevant'' retrievals, where ''relevant'' is defined as any article that contains a potential discovery or innovation candidate. doi = 10.1016/j.techfore.2011.03.022 id = cord-265022-p5cab562 author = Kotfis, Katarzyna title = COVID-19: ICU delirium management during SARS-CoV-2 pandemic date = 2020-04-28 keywords = COVID-19; ICU; SARS; delirium; patient summary = Indeed, patients with COVID-19 are at accelerated risk for delirium due to at least seven factors including (1) direct central nervous system (CNS) invasion, (2) induction of CNS inflammatory mediators, (3) secondary effect of other organ system failure, (4) effect of sedative strategies, (5) prolonged mechanical ventilation time, (6) immobilization, and (7) other needed but unfortunate environmental factors including social isolation and quarantine without family. Given early insights into the pathobiology of the virus, as well as the emerging interventions utilized to treat the critically ill patients, delirium prevention and management will prove exceedingly challenging, especially in the intensive care unit (ICU). Many hospitalized patients with COVID-19 will develop delirium, and given early insights into the pathobiology of this virus indicating invasion into the brain stem, as well as the emerging interventions utilized to treat these critically ill patients, delirium prevention and management may prove exceedingly challenging, especially in the intensive care unit (ICU). doi = 10.1186/s13054-020-02882-x id = cord-341819-emjg3dsw author = Kouznetsova, Valentina L. title = Potential COVID-19 papain-like protease PL(pro) inhibitors: repurposing FDA-approved drugs date = 2020-09-18 keywords = SARS summary = Using the crystal structure of SARS-CoV-2 papain-like protease (PL(pro)) as a template, we developed a pharmacophore model of functional centers of the PL(pro) inhibitor-binding pocket. In a previous report, we (Kouznetsova, Huang & Tsigelny, 2020 ) and others (Kandeel & Al-Nazawi, 2020; Arya et al., 2020; Plewczynski et al., 2007; Ton et al., 2020) have used molecular modeling studies to identify FDA-approved drugs and other compounds (Arya et al., 2020; Ton et al., 2020; Alamri, Tahir ul Qamar & Alqahtani, 2020) that are predicted to bind to 3CL pro . Based on the crystal structure of SARS-CoV-2 PL pro (PDB ID: 6W9C), we developed two pharmacophore models of the binding pocket of this protein. We developed a pharmacophore model of the binding pocket site S3/S4 of COVID-19 PL pro then conducted multi-conformational docking of these drug compounds to this site for ranging the potential inhibitors selected by pharmacophore-based search. Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs doi = 10.7717/peerj.9965 id = cord-334277-g3go3u02 author = Kovac, Marc title = EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA) date = 2020-08-14 keywords = ECLIA; ELISA; SARS summary = While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). It can thus be concluded that the anti-SARS-CoV-2 antibody results in whole blood corrected for hematocrit with weakly and moderately positive findings are comparable to those obtained from serum. doi = 10.3390/diagnostics10080593 id = cord-261111-g1qxo01i author = Kowalewski, Joel title = Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space date = 2020-08-06 keywords = SARS; chemical; figure; target summary = There are subsequently unmet needs in COVID-19 research, including identification of compounds that target the relevant SARS-CoV-2 human proteins from (1) approved drugs, (2) FDA registered chemicals or (3) a large repository of~14 million purchasable chemicals from the ZINC 15 database [18] , which we computed additional properties for such as mammalian toxicity, vapor pressure, and logP. For 65 human protein targets that SARS-CoV-2 interacts with that had publicly available bioassay and chemical data [6] , we first generated a database of predictions based on structural similarity to chemicals that interact with the targets and then machine learning models (34) . Accordingly, we used the machine learning models to predict activities of 100,000 FDA registered chemicals (UNII database) [19] as well as the DrugBank [20] and Therapeutic Targets [21, 22] databases, which include information on drug interactions, pathways, and approval status. doi = 10.1016/j.heliyon.2020.e04639 id = cord-355577-w1yhtbz8 author = Kowalski, Luiz Paulo title = Effect of the COVID-19 Pandemic on the Activity of Physicians Working in the Areas of Head and Neck Surgery and Otorhinolaryngology date = 2020-05-22 keywords = COVID-19; PPE; SARS summary = Conclusion The study demonstrated a direct impact of the COVID-19 pandemic on the clinical practice of specialties related to the treatment of patients with diseases of the head and neck region already in the beginning of the illness management in Brazil. Specifically, we collected data regarding the impact of de COVID-19 pandemic on: 1) the amount and type of outpatient appointments, surgeries and exams with the risk of generating aerosols; 2) availability of adequate PPE in different settings and practices; 3) the preparedness of the responder''s health institution in orienting their HCPs and developing strategies to manage COVID-19 suspected and confirmed patients. Although the pandemic is already in its 7 th week in Brazil, since the identification of the 1 st case, 45.3% and 48.8% of physicians in the private and public sectors, respectively, reported that they had not received face-to-face or distance training in the management of confirmed or suspected patients with COVID-19. doi = 10.1055/s-0040-1712169 id = cord-321624-z2mntwef author = Kowitdamrong, Ekasit title = Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date = 2020-10-09 keywords = CoV-2; SARS summary = AIM: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19. The objective of this study was to investigate the response of IgA and IgG antibodies to SARS--CoV-2 in serial blood samples collected from a population of Thai patients with confirmed COVID-19, and the association of these responses with the severity of the illness. The second subgroup included 49 plasma samples collected from May 1 to May 31, 2020, from patients under investigation (PUI) for COVID-19 with RT-PCR results that were negative for SARS-CoV-2. In the present study, 30% of COVID-19 patients developed positive IgA antibodies very early, within 3 days after the onset of symptoms. In the present study, 20% of the patients with mild symptoms did not develop any IgG antibodies specific to COVID-19, even after 2 weeks after the onset of symptoms. doi = 10.1371/journal.pone.0240502 id = cord-269234-8twdx4g2 author = Koyama, Takahiko title = Variant analysis of SARS-CoV-2 genomes date = 2020-07-01 keywords = China; SARS; d614; variant summary = OBJECTIVE: To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here we analysed the SARS-CoV-2 genome from 10 022 samples to understand the variability in the viral genome landscape and to identify emerging clades. Finally, we carefully Objective To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Given the evolving nature of the SARS-CoV-2 genome, drug and vaccine developers should continue to be vigilant for emergence of new variants or sub-strains of the virus. Variant analysis of SARS-CoV-2 genomes [data repository doi = 10.2471/blt.20.253591 id = cord-322807-b24ujorz author = Koyama, Takahiko title = Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment date = 2020-04-26 keywords = SARS summary = The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. Typically, surface proteins outside of the viral virion are selected for antigens so that antibodies generated from a vaccine-trained B-cell can bind to the virus for neutralization. This study''s objective is to interrogate currently identified sub-strains of SARS-CoV-2 and identify genetic drifts and potential immune recognition escape sites that would be integral for the development of a successful vaccine. In these countries, the majority of infected patients possess the variant; therefore, vaccine design and convalescent plasma antibody treatment might require further considerations to accommodate the drift. A spike glycoprotein peptide encompassing residues 604-625 derived from a convalescent SARS-CoV-1 patient was successfully able to elicit humoral immune response and prevent infection in non-human primates, underscoring the immunogenic importance of this region [10] . doi = 10.3390/pathogens9050324 id = cord-345730-bxwsup70 author = Kočar, Eva title = Cholesterol, lipoproteins, and COVID-19: basic concepts and clinical applications date = 2020-11-04 keywords = COVID-19; HDL; SARS; cholesterol summary = In vitro depletion of membrane-bound cholesterol from Angiotensin-Converting Enzyme 2 (ACE2)-expressing cells led to a reduced infectivity of CoVs, since the binding of the spike protein was reduced by half [44] . By participating in cholesterol outflow from the cell membrane to HDL particles, PON1 contributes to lowering the cholesterol levels within lipid rafts, thus modulating viral infection (Fig. 1c) . Therefore, it is intriguing to contemplate whether NAFLD patients without treatment are more J o u r n a l P r e -p r o o f susceptible for SARS-CoV-2 infection, or whether statin application may directly affect the entry of SARS-CoV-2 into the host cell by regulating cholesterol cell levels. As lipid lowering drugs, statins might thus significantly reduce the attachment and internalization of SARS-CoV-2 by lowering membrane cholesterol levels (Fig. 1c ) [37] . doi = 10.1016/j.bbalip.2020.158849 id = cord-340799-1awmtj52 author = Krajewska, Joanna title = Review of practical recommendations for otolaryngologists and head and neck surgeons during the COVID-19 pandemic: Recommendations for otolaryngologists during the COVID-19 pandemic date = 2020-06-06 keywords = ENT; Neck; PPE; SARS; covid-19; patient summary = Laryngectomy patients and individuals after tracheotomy with COVID-19 carry a particularly high risk of infecting ENT specialists and other members of medical staff as the way of breathing is these individuals is modified and enables the easy spread of SARS-CoV-2 containing aerosolized tracheal secretions [11] . In accordance with such high risk of infection, only emergency consultations and procedures should be performed by ENT specialists in times of COVID-19 pandemic in areas with confirmed SARS-CoV-2 cases [23, 28] . American Head and Neck Society, AAO-HNS, and the American Colleges of Surgeons, recommended that preoperative testing for SARS-CoV-2 presence should be performed in all individuals undergoing high-risk procedures [22, 30] . Patients with acute airway obstruction requiring tracheotomy should be considered as COVID-19 positive, as there is no time for SARS-CoV-2 testing in case of such urgent surgery [29] . doi = 10.1016/j.anl.2020.05.022 id = cord-296483-x95lwwnm author = Kranke, Peter title = Geburtshilfliche Anästhesie während der SARS-CoV-2-Pandemie: Übersicht der Handlungsempfehlungen date = 2020-04-09 keywords = SARS; covid-19; der; die summary = Diese Annahmen stützten sich möglicherweise auf den Umstand, dass die Morbidität Schwangerer bei saisonaler Influenza höher ist als in einem Vergleichskollektiv [4 -6] und im beschriebenen Kollektiv zu einer gegenüber einem Vergleichskollektiv überproportionalen Frühgeburtlichkeit von 24-25 % führte [7] . In Bezug auf die vertikale Übertragung (Übertragung von der Mutter auf das Kind prä-oder intrapartal) zeigen nahezu alle publizierten Fallberichte aus China keine Hinweise für eine Übertragung auf den Fetus [9, 15 -17] . Einschränkend sollte berücksichtigt werden, dass es sich bislang nur um einen einzigen Fallbericht handelt und es im Rahmen der systemischen Inflammation möglicherweise zu einem erhöhten Transfer von Antikörpern kommen könnte. Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 (23.03.2020). doi = 10.1055/a-1144-5562 id = cord-330031-c1n994j6 author = Kratzel, Annika title = Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date = 2020-03-17 keywords = SARS summary = title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-2 CoV-2) causing COVID-19 is a major burden for health care systems worldwide. We therefore determined the virucidal activity of two 5 alcohol-based hand rub solutions for hand disinfection recommended by the World 6 Hand Hygiene in Health Care'' suggests two alcohol-based formulations for hand 9 sanitization to reduce pathogen infectivity and spreading. doi = 10.1101/2020.03.10.986711 id = cord-333703-1ku3jc9s author = Kraus, Aurora title = A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date = 2020-11-08 keywords = ACE2; COVID-19; CoV-2; RBD; SARS; figure; zebrafish summary = Exposure of larvae to SARS-CoV-2 Spike (S) receptor binding domain (RBD) recombinant protein was sufficient to elevate larval heart rate and treatment with captopril, an ACE inhibitor, reverted this effect. In mice and humans, ace2 expression is detected in 121 sustentacular cells, olfactory stem cells known as horizontal and globose basal cells in the 122 olfactory epithelium, and vascular cells (pericytes) in the olfactory bulb (Brann et al., 2020 The present study reports for the first time that zebrafish larvae exposed to SARS-CoV-2 appear 134 to mount innate immune responses that resemble cytokine responses of mild COVID-19 patients. There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 doi = 10.1101/2020.11.06.368191 id = cord-319930-ymqnb54a author = Kremer, Stéphane title = Brain MRI Findings in Severe COVID-19: A Retrospective Observational Study date = 2020-06-16 keywords = COVID-19; MRI; SARS; patient summary = Eight distinctive neuroradiologic patterns (excluding ischemic infarcts) were identified in patients with severe COVID-19 infection with abnormal brain MRIs. In patients with COVID-19, the most frequent neuroimaging features were: involvement of the medial temporal lobe, non-confluent multifocal white matter hyperintense lesions on FLAIR with variable enhancement and hemorrhagic lesions, and extensive and isolated white matter microhemorrhages. Inclusion criteria were: (i) diagnosis of COVID-19 based on possible exposure history or symptoms clinically compatible, validated with a detection of SARS-CoV-2 by reverse transcriptase-polymerase chain reaction (RT-PCR) assays on the nasopharyngeal, throat or lower respiratory tract swabs; (ii) severe COVID-19 infection defined as requirement for hospitalization and oxygen therapy; (iii) neurologic manifestations; (iv) abnormal brain MRI with acute/subacute abnormalities. Among the eight groups of brain MRI features classification, three main neuroradiological patterns appeared more frequently in patient with severe COVID-19: signal abnormalities located in the medial temporal lobe, non-confluent multifocal WM hyperintense lesions on FLAIR and diffusion with variable enhancement, associated with hemorrhagic lesions, and extensive and isolated WM microhemorrhages. doi = 10.1148/radiol.2020202222 id = cord-015552-pm9kdqdw author = Kreuder-Sonnen, Christian title = China vs the WHO: a behavioural norm conflict in the SARS crisis date = 2019-05-01 keywords = China; IHR; SARS; health; norm summary = On the one hand, the established norm of sovereignty, particularly the principle of non-interference, had structured a regime for dealing with infectious disease outbreaks that provided ground rules of conduct but ascribed decision-making authority to member states alone. 33 This sediment of the unfinished IHR revision process reveals the limited degree to which the emerging norm of global health security had been accepted prior to the SARS outbreak: the powers conferred upon the WHO to deal with infectious disease outbreaks remained extremely limited and-apart from the outbreak information issue-mostly subject to member-state agreement. 35 This section of the article analyses the actions of China and the WHO during the SARS crisis as representing a behavioural norm conflict over the relative priority of sovereignty and global health security. doi = 10.1093/ia/iiz022 id = cord-103576-g5de4fwj author = Kriegel, M. title = Predicted Infection Risk via Aerosols date = 2020-10-12 keywords = PIRA; SARS; rate summary = 34 In order to perform an infection risk assessment for the airborne transmission in the far field 35 and to introduce appropriate preventive measures, it would be necessary to know the amount The so-called aerosols (liquid or solid particles in a dispersed phase with a fluid) as well as 50 droplets differ by size. In equation (3), the number of infectious persons (I), the quanta emission rate depending on 74 the activity (q), the pulmonary ventilation rate of exposed susceptible persons (Qb), the 75 duration of stay (t) and the volume flow of pathogen free air (Q) was used. To calculate the predicted 156 infection risk via aerosols (PIRA) in the far field of a room the concentration of quanta (c(t)) 157 and the respiratory rate (Qb) has to be known. To reduce the risk of infection via aerosols the necessary volume flow of virus-free air 327 depending on the exposure time can be seen in Figure 5 . doi = 10.1101/2020.10.08.20209106 id = cord-126015-zc7u3g34 author = Krieger, Elizabeth title = Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date = 2020-05-13 keywords = HLA; KIR; SARS; response summary = To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. The HLA genes exhibit extreme allelic polymorphisms and present viral peptides on host HLA molecules to T cells to trigger an adaptive immune response. A quantitative approach relating differences in cytokine levels and polymorphisms in the immune response pathways may help identify patients at risk of severe disease. doi = nan id = cord-318426-kv7aa0og author = Kritsotakis, Evangelos I. title = On the importance of population-based serological surveys of SARS-CoV-2 without overlooking their inherent uncertainties date = 2020-05-22 keywords = SARS summary = This brief note aims to explain the scope in conducting large-scale serological surveys of SARS-CoV-2 to define the landscape of population immunity, without overlooking the inherent uncertainty steaming from sampling design and diagnostic validity. The note completes with a succinct appendix of simple statistical methods for estimating prevalence from random population samples using imperfect diagnostic tests. They use serological tests to examine a large number of blood samples from people without a confirmed SARS-CoV-2 infection to detect signs that they were once infected with the virus. Available serological tests are not perfect but are acceptable for use in the context of surveying populations for SARS-CoV-2 antibodies, because survey estimates can be corrected for imperfect diagnostic performance. Large-scale seroprevalence surveys are an important tool in combating COVID-19 disease as they can provide much-needed estimates of the fraction of the population with antibodies against SARS-CoV-2. The quality of the antibody prevalence estimates depends on the sampling design and the diagnostic accuracy of serological tests. doi = 10.1016/j.puhip.2020.100013 id = cord-284862-nhihxog0 author = Kroemer, Marie title = COVID-19 patients display distinct SARS-CoV-2 specific T-cell responses according to disease severity date = 2020-08-25 keywords = SARS summary = Although the existence of SARS-CoV-2 specific T-cells has been described 2,3 , the frequency and the intensity of SARS-CoV-2 specific T-cell responses among mild illness and severe pneumonia convalescent COVID-19 patients remains to be investigated. In this prospective study, 60 patients who had COVID-19 were enrolled in a two cohorts study that were entitled mild illness (n=30) and severe pneumonia (n=30) at least 21 days after the first symptoms of ; Table 1 for CoV-N) might be explained by the sequence homology between structural proteins from various coronavirus suggesting the existence of cross reactive memory T-cells 5 . We observed that all patients with severe pneumonia had a positive serology index and most of them had at least one specific cellular response for SARS-CoV-2 proteins (28 out of 30). Specific T-cell responses for S, M and N proteins were simultaneously shown for 70.0% of severe pneumonia patients while only for 37.9% of mild illness patients (P=0.0191) (Fig. 1E) . doi = 10.1016/j.jinf.2020.08.036 id = cord-252873-4tazhf40 author = Kruglikov, Ilja L. title = The role of adipocytes and adipocyte‐like cells in the severity of COVID‐19 infections date = 2020-04-27 keywords = ACE2; SARS summary = Coronavirus disease‐2019 (COVID‐19), caused by the highly pathogenic virus SARS‐CoV‐2, demonstrates high morbidity and mortality caused by development of a severe acute respiratory syndrome connected with extensive pulmonary fibrosis (PF). Expression of angiotensin‐converting enzyme 2 (ACE2 ‐ the functional receptor for SARS‐CoV) ‐ is upregulated in adipocytes of obese and diabetic patients, which turns adipose tissue into a potential target and viral reservoir. Similar to the recently established adipocyte‐myofibroblast transition (AMT), pulmonary lipofibroblasts located in the alveolar interstitium and closely related to classical adipocytes, demonstrate the ability to transdifferentiate into myofibroblasts that play an integral part of PF. Recently it was shown that another anti-diabetic drug, metformin, accelerates resolution of pulmonary fibrosis by inducing trans-differentiation of myofibroblasts into lipofibroblasts (18) . Adipose tissue can serve as a viral reservoir, whereas transdifferentiation of pulmonary lipofibroblasts into myofibroblasts can contribute to the development of PF and thus is likely to influence the clinical severity of COVID-19. doi = 10.1002/oby.22856 id = cord-350753-qbm145tr author = Krüttgen, Alexander title = Determination of SARS-CoV-2 antibodies with assays from Diasorin, Roche and IDvet date = 2020-09-23 keywords = SARS summary = Using 75 sera from patients tested positive or negative by SARS-CoV-2 PCR, we investigated the sensitivity and specificity of the Liaison SARS-CoV-2 S1/S2 IgG assay (DiaSorin), the Elecsys Anti-SARS-CoV-2 assay (Roche), and the ID Screen SARS-CoV-2-N IgG indirect kit (IDVet). We and others have published results of the assessment of the first commercially available serological assays, such as the Anti SARS-CoV-2 ELISA (IgG) from Euroimmun (Krüttgen et al., 2020; Okba et al., 2020) . We therefore compared these three new assays with respect to their sensitivity and specificity to detect SARS-CoV-2 specific antibodies using a collection of serum samples employed previously for the analysis of four other assays. Our comparative approach to test in total seven different SARS-CoV-2 antibody assays with an identical collection of serum samples allowed for the first time the direct comparison of performance indicators of such a large number of automated assays. doi = 10.1016/j.jviromet.2020.113978 id = cord-291655-l7mg5a0z author = Ku, C. W. title = Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19 date = 2020-10-05 keywords = NPS; October; SARS summary = Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods. In order to validate the use of buccal swabs and saliva specimen as alternative diagnostic tests for SARS-CoV-2, our group performed a cross-sectional study of NPS, self-collected buccal swabs and saliva specimens collected concurrently in order to determine the positive percent agreement (PPA), negative percent agreement (NPA), overall agreement (OA), positive and negative predictive values. In this study, we have shown that saliva tests and buccal swabs were comparable to each other and were in moderate agreement with NPS for the detection of SARS-CoV-2, with PPA between 56 and 66% and PPV 95 to 100%. doi = 10.1101/2020.10.03.20205278 id = cord-024317-w1ep0wq8 author = Ku, Zhiqiang title = Antibody therapies for the treatment of COVID-19 date = 2020-04-30 keywords = COVID-19; CoV-2; SARS summary = Here, we discuss some of the most active areas of developing strategies to treat COVID-19, focusing on approaches to generate neutralizing antibodies against SARS-CoV-2 for prophylactic and therapeutic treatment of COVID-19. SIGNIFICANCE: Development of SARS-CoV-2 neutralizing antibodies with the desired efficacy and safety profile is a critical part of the toolbox of therapies for the treatment of COVID-19. The spike protein of SARS-CoV-2 plays an essential role in virus entry into host cells and is a primary target of neutralizing antibodies 5, 9 (Figures 1C,D) . Two MERS-CoV neutralizing mAbs, G2 and 7D10, target the S1-NTD region and function by blocking spike protein interaction with the host receptor DPP4 47, 48 . In the monkey study, researchers found that rhesus macaques infected with SARS-CoV-2 through the intratracheal route had mild illness, and their lungs showed signs of pneumonia similar to those in humans with COVID-19 58 . doi = 10.1093/abt/tbaa007 id = cord-337491-ztco6guw author = Kucharski, Adam J title = Using serological data to understand unobserved SARS-CoV-2 risk in health-care settings date = 2020-08-03 keywords = SARS summary = 1 Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), growing evidence of nosocomial transmission has been observed, but tracking such outbreaks is challenging because a substantial proportion of infected individuals might exhibit mild or no symptoms. Staff working in dedicated COVID-19 wards showed substantially higher rates of seropositivity (1·65 [1·34-2·03]; p<0·001) than other frontline health-care workers working in hospitals, reflecting increased risk for this group, a pattern that has also been reported in neighbouring Sweden. The results highlight the risk that SARS-CoV-2 can pose to health-care workers, particularly those in regular contact with patients with COVID-19, and the importance of understanding possible routes of exposure in hospitals. However, the prevalence of asymptomatic SARS-CoV-2 infections and COVID-19-like symptoms among seronegative staff illustrates the limitations of relying on symptom-based surveillance alone. Risk of COVID-19 in health-care workers in Denmark: an observational cohort study SARS-CoV-2 exposure, symptoms and seroprevalence in health care workers doi = 10.1016/s1473-3099(20)30579-x id = cord-290170-s6wjitfo author = Kuhrt, Katy title = Placental abruption in a twin pregnancy at 32 weeks’ gestation complicated by COVID-19, without vertical transmission to the babies. date = 2020-05-08 keywords = SARS summary = key: cord-290170-s6wjitfo title: Placental abruption in a twin pregnancy at 32 weeks'' gestation complicated by COVID-19, without vertical transmission to the babies. cord_uid: s6wjitfo Other coronavirus spectrum infections have been 31 associated with miscarriage, preterm birth, preeclampsia, caesarean delivery, perinatal death, 32 fetal growth restriction, and placental abruption. She gave a one-day history of cough, fever and 100 5 mild shortness of breath. An echocardiogram performed the same day showed a mild pericardial 102 effusion, and NT-BNP was 28pg/ml (normal <100pg/ml) (done to rule out cardiac failure or 103 cardiomyopathy). Outcome 186 of Coronavirus spectrum infections (SARS, MERS, COVID 1 -19) during 187 pregnancy: a systematic review and meta-analysis MERS-CoV Infection in a Pregnant Woman in Korea Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in 198 Possible Vertical Transmission 202 of SARS-CoV-2 From an Infected Mother to Her Newborn Placental 210 abruption in twin pregnancies, risk factors and perinatal outcomes doi = 10.1016/j.ajogmf.2020.100135 id = cord-256146-d599uera author = Kuiken, Thijs title = Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date = 2003-07-26 keywords = CoV; PCR; SARS; macaque summary = METHODS: We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARSCoV, human metapneumovirus, and other respiratory pathogens. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. . Serial dilutions of the SARS-CoV virus stock and SARS-CoV-infected Vero cells from patient 5688 were made and tested with the NP and polymerase-specific RT-PCRs. Samples from the respiratory tract (nasal swabs, pharyngeal swabs, postmortem trachea, and lung samples) were also monitored for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E), and human metapneumovirus with use of essentially the same RT-PCR methods but with specific primers. Virological examinations of nasal and pharyngeal swabs, and tracheal and lung samples from all four macaques by RT-PCR for influenza A and B virus, respiratory syncytial virus A and B, rhinovirus, coronavirus (OC43 and 229E) and human metapneumovirus were negative. doi = 10.1016/s0140-6736(03)13967-0 id = cord-325113-sou8xyld author = Kuiper, Johannes W. P. title = Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date = 2020-11-02 keywords = PCR; RNA; SARS summary = The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. doi = 10.1371/journal.pone.0241740 id = cord-301292-yaii6e16 author = Kuk, Anthony Y. C. title = The estimation of SARS incubation distribution from serial interval data using a convolution likelihood date = 2005-07-12 keywords = SARS summary = By constructing a convolution likelihood based on the serial interval data, we are able to estimate the incubation distribution which is assumed to be Weibull, and justifications are given to support this choice over other distributions. The indirect estimate obtained using the method of convolution likelihood is validated by means of comparison with a direct estimate obtained directly from a subset of patients for whom the incubation time can be ascertained. Despite its name, the proposed indirect estimate is actually more precise than the direct estimate because serial interval data are recorded for almost all patients, whereas exact incubation times can be determined for only a small subset. By constructing a convolution likelihood based on the serial interval data in Singapore, we are able to estimate the incubation distribution parametrically. It is possible to obtain a combined estimate that makes use of the incubation times for the 50 patients in the ascertained subset and the serial intervals for the remaining 148 cases. doi = 10.1002/sim.2123 id = cord-269454-9gthf2jl author = Kulkarni, Rajesh title = Early-onset symptomatic neonatal COVID-19 infection with high probability of vertical transmission date = 2020-08-02 keywords = SARS summary = RESULTS: A COVID-19 suspected mother, who tested negative by RT-PCR for COVID, but tested positive for SARS-CoV-2 by serology, delivered a term baby. CONCLUSION: This report highlights a very strong possibility of vertical transmission of COVID-19 from a mildly symptomatic, RT-PCR negative but antibody-positive mother with significant symptomatic, early—onset neonatal infection. This report describes the clinical course and laboratory findings in a neonate born in Pune, India in whom infection with SARS-CoV-2 very likely occurred via vertical transmission. NPA from baby, cord stump, and placenta (which were collected as per national guidelines at birth) were reported as positive for SARS-CoV2 at 12 h of life. Two neonates with positive RT-PCR testing as early as 30 h after delivery have been reported; however, these cases lacked sufficient clinical data or precise information regarding isolation methods, and perinatal transmission could not be ruled out [7, 8] . doi = 10.1007/s15010-020-01493-6 id = cord-346998-01i6zxv8 author = Kulkarni, Spoorthy title = COVID-19 and hypertension date = 2020-05-20 keywords = ACE2; COVID-19; SARS summary = COVID-19 seems to follow a pattern seen with influenza and previous severe acute respiratory syndrome coronavirus (SARS-CoV) outbreaks: that the severity and mortality of the infection is higher in the elderly age group. The controversy regarding continuing or discontinuing angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) in COVID-19 patients arose after it became apparent that SARS-CoV uses angiotensin-converting enzyme 2 (ACE2) to gain entry in host cells. 12 Consequently, the increased expression of ACE2 would facilitate an increased rate or susceptibility to infection with SARS-CoV-2 and further hypothesis that this may increase the risk of developing severe and fatal COVID-19. The study tested the hypothesis of an increased risk of severe illness in COVID-19 with hypertension with ACEi use (on ACEi n=37; not on ACEi n=168) in admitted patients. Effect of angiotensin converting enzyme gene I/D polymorphism and its expression on clinical outcome in acute respiratory distress syndrome doi = 10.1177/1470320320927851 id = cord-277443-mv7sk5aa author = Kumaki, Yohichi title = Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol(®) (Poly IC:LC), in a lethal SARS-CoV-infected BALB/c mouse model date = 2016-12-09 keywords = BALB; Hiltonol; IL-6; PSS; SARS summary = Hiltonol(®) at 5, 1, 0.5 or 0.25 mg/kg/day by intranasal (i.n.) route resulted in significant survival benefit when administered at selected times 24 h prior to challenge with a lethal dose of mouse-adapted severe acute respiratory syndrome coronavirus (SARS-CoV). In other studies, treatment with an interferon inducer, polyriboinosinicpolyribocytidylic acid stabilized with poly-L-lysine and carboxymethyl cellulose (poly IC:LC), given by the intranasal route, was effective in protecting mice against a lethal infection with mouseadapted SARS-CoV and reduced viral lung titers (Kumaki et al., 2010) . These treated, SARS-CoVinfected mice receiving the various Hiltonol ® dosing regimens were also significantly protected against weight loss due to virus infection (Table 1 , p < 0.05-p<0.001) from days 0e3 post virus exposure when the greatest weight loss occurred in this mouse model. doi = 10.1016/j.antiviral.2016.12.007 id = cord-275111-38hgg0jz author = Kumar, Abhishek title = Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients date = 2020-10-06 keywords = COVID-19; SARS summary = title: Pattern of liver function and clinical profile in COVID-19: A cross-sectional study of 91 patients AIM: To analyse the liver function in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. 91 patients admitted with confirmed SARS-CoV-2 infection were included in this study and divided into asymptomatic, mild, moderate and severe groups. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. CONCLUSION-Liver injury is common in SARS-CoV-2 infection and is more prevalent in the severe disease group. In this study, we aimed to analyse the liver function abnormalities in patients with COVID-19 and their association with respect to age, sex, severity of disease and clinical features. [16, 21, 22] In our study, the levels of AST and ALP between different groups of disease severity was highly significant which is consistent with a previous report. doi = 10.1016/j.dsx.2020.10.001 id = cord-272241-2fwz8z8n author = Kumar, Amit title = Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach date = 2020-09-09 keywords = SARS; TLR-3; protein; vaccine summary = title: Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach Hence, in this study, we have used immunoinformatic approaches to predict highly antigenic epitopes from SARS-CoV-2 structural proteins that would evoke a strong immune response in humans. For this purpose, we have used the structural proteins: Spike, Envelope, and nucleocapsid to predict B-cell, cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes for construction of vaccine. We have also performed the docking and molecular dynamic simulations (MDS) between the vaccine and human Toll-like Receptor-3 (TLR-3) to study their binding stability. The VaxiJen 2.0 server predicts the antigenicity of the multi-epitope vaccine peptide based on the physicochemical properties of the input protein. Whereas, ANTIGENpro server predicts the antigenicity of the multi-epitopic vaccine based on the protein microarray data analysis of the target organism. Three structural proteins (spike glycoprotein, nucleocapsid, and envelope) were selected to construct a multi-epitope vaccine, which is capable of eliciting the humoral and cell-mediated immune response. doi = 10.1080/14760584.2020.1813576 id = cord-287091-a3nieh5p author = Kumar, Anuj title = Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches date = 2020-06-04 keywords = COVID-19; SARS summary = In the current study, we report novel natural metabolites namely, ursolic acid, carvacrol and oleanolic acid as the potential inhibitors against main protease (M(pro)) of COVID-19 by using integrated molecular modeling approaches. Besides the uses of various FDA-approved antiviral compounds as mentioned above, there are many in-silico studies have been performed to screen the novel phytochemical molecules as a potential inhibitors of main protease of SARS-CoV-2 or develop new drugs against COVID-19 (Adem et al., 2020; Chandel et al., 2020; Gentile et al., 2020; Gonzalez-Paz et al., 2020; Khaerunnisa et al., 2020; Khan et al., 2020; Qamar et al., 2020; Sharma & Kaur, 2020; Sun et al., 2020) . In the present study, we have targeted the protease of SARS-CoV-2 virus using available molecular modelling based methods and studied the interactions with selected natural compounds (ursolic acid, carvacrol and oleanolic acid) by molecular docking and molecular dynamics simulations followed by molecular mechanic/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) validation. doi = 10.1080/07391102.2020.1772112 id = cord-353716-gxgvhhv1 author = Kumar, Ashutosh title = SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients date = 2020-09-30 keywords = ACE2; SARS summary = title: SARS-CoV-2 cell entry receptor ACE2 mediated endothelial dysfunction leads to vascular thrombosis in COVID-19 patients Based on the circumstantial evidence present in the literature, we propose a SARS-CoV-2 cell entry receptor ACE2 based mechanism for vascular thrombosis in COVID-19 patients. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative pathogen for COVID-19 has been shown to bind to angiotensin converting enzyme 2 (ACE2) protein in human epithelial cells, which facilitates its entry in the organ and mediate tissue specific pathogenesis (4,5). SARS-CoV-2 binding to the cell entry receptor ACE2 downregulates receptor expression that in turn induces vascular endothelial dysfunction, which activates prothrombotic cascade and eventually leads to vascular thrombosis observed in COVID-19 patients. doi = 10.1016/j.mehy.2020.110320 id = cord-317037-1qydcc5e author = Kumar, Asit title = Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date = 2020-08-13 keywords = Exosomes; Extracellular; HIV; RNA; SARS; Vesicles; viral summary = Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. doi = 10.3390/v12080887 id = cord-319797-455ldhiy author = Kumar, Deepali title = COVID‐19: A global transplant perspective on successfully navigating a pandemic date = 2020-04-12 keywords = SARS; donor summary = The impact has not been just restricted to issues pertaining to donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. Here we provide a personal viewpoint representing different jurisdictions from around the world in order to outline the impact of the current COVID-19 pandemic on organ transplantation. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. Based on our collective experience, we discuss mitigation strategies such as donor screening, resource planning, and a staged approach to transplant volume considerations as local resource issues demand. The impact has not been just restricted to issues around donors or recipients, but also health-care resource utilization as the intensity of cases in certain jurisdictions exceeds available capacity. doi = 10.1111/ajt.15876 id = cord-301641-epr1sct6 author = Kumar, Durgesh title = Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures date = 2020-05-04 keywords = 23b; COVID-19; SARS summary = Herein, MM-GBSA method was to calculate the change in enthalpy and the change in free energy for the formation of complex, number of hydrogen bonds (HBs) are determined to study the binding of the hit molecule with the protease of SARS-CoV-2 for COVID-19. However, the designed molecules were filtered against the protease of SARS-CoV-2 for COVID-19 based on total energy or binding energy (kcal/mol) of drug-target complex using iGEMDOCK Singh et al., 2019; Zhao et al., 2019) . Herein, MM-GBSA method is used to determine the change in enthalpy and change in free energy for the formation of complex, number of HBs to understand the binding of screened noscapines with the protease of SARS-CoV-2 of COVID-19 (Al-Anazi et al., 2018; Chaudhari & Pahelkar, 2019; Chinnasamy et al., 2019; Du et al., 2011) . Further, the detailed analysis of newly formed drug-target complex through root-mean-square fluctuation (RMSF) versus the residue number of protease of coronavirus for COVID-19 for top hit molecule is represented in Figure 7 . doi = 10.1080/07391102.2020.1752310 id = cord-353392-rqeultbq author = Kumar, Govindarajan Venkat title = A short review on antibody therapy for COVID-19 date = 2020-04-20 keywords = CoV-2; SARS summary = Abstract The beginning of the novel SARS-CoV-2 human coronavirus in Wuhan, China, has triggered a worldwide respiratory disease outbreak (COVID-19). The third outbreak of severe illness caused by the novel SARS-CoV-2 coronavirus (COVID-19) that emerged in the Wuhan city, China, is pandemic and spread to more than 200 countries [5, 6, 7] . Based on the previous studies and reports in treating other coronaviruses such as SARS and MERS, the early administration of convalescent plasma from patients that contains raised antibodies can possibly reduce the spreading of infection and mortality [19, 20, 21, 22] . reported that the convalescent plasma transfusion may be beneficial in the treatment of critically ill patients with SARS-CoV-2 infections. After getting approval from the ethical committee, Shenzhen, Third People''s Hospital, they administrated convalescent plasma containing neutralizing antibodies to 5 critically ill patients with SARS-CoV-2. doi = 10.1016/j.nmni.2020.100682 id = cord-329710-vqorb6j7 author = Kumar, Krishna title = Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date = 2020-05-27 keywords = RNA; SARS; viral summary = We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. doi = 10.1021/acsmedchemlett.0c00254 id = cord-275565-xerr4vki author = Kumar, Manish title = Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date = 2020-09-15 keywords = CoV-2; RNA; SARS summary = For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. Thus, there still remains questions pertaining to: i) capability of conventional WWTPs to reduce the abundance of SARS-CoV-2 RNA, ii) better understanding of the protocol, virus J o u r n a l P r e -p r o o f Journal Pre-proof precipitation through PEG and filtration which one is better methods for concentrating the samples before RNA isolation. Appraising the genetic loading reduction through Upflow Anaerobic Sludge Blanket (UASB) systems, and iii) Comparing the performances between PEG and filtration as virus concentration methods in terms of SARS-CoV-2 RNA sensitivity and inhibition removal. doi = 10.1016/j.scitotenv.2020.142329 id = cord-292045-pnid9dmq author = Kumar, Manish title = First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date = 2020-07-28 keywords = India; RNA; SARS summary = While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. Consistency between abundance of SARS-CoV-2 genetic materials and number of confirmed cases was observed in the previous reports in Australia, France, Italy, Spain and Japan Further, referring to the limitations of the present study owing to lockdown scenario, we recommend that although based MPC analysis, the efficiency of RNA extraction and RT-PCR is considered high for all the wastewater samples collected for this study, the efficiency of PEG method could have been better established. The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 doi = 10.1016/j.scitotenv.2020.141326 id = cord-296986-8fuj072z author = Kumar, Manish title = A chronicle of SARS-CoV-2: Part-I - Epidemiology, diagnosis, prognosis, transmission and treatment date = 2020-05-15 keywords = COVID-19; China; CoV-2; SARS summary = The review explicitly covers the aspects like genome and pedigree of SARS-CoV-2; epidemiology, prognosis, pathogenesis, symptoms and diagnosis of COVID-19 in order to catalog the right information on transmission route, and influence of environmental factors on virus transmissions, for the robust understanding of right strategical steps for proper COVID-19 management. We have explicitly highlighted several useful information and facts like: i) No established relationship between progression of SARS-CoV-2 with temperature, humidity and/or both, ii) The underlying mechanism of SARS-CoV-2 is not fully understood, iii) Respiratory droplet size determines drop and airborne-based transmission, iv) Prognosis of COVID-19 can be done by its effects on various body organs, v) Infection can be stopped by restricting the binding of S protein and AE2, vi) Hydroxychloroquine is believed to be better than chloroquine for COVID-19, vii) Ivermectin with Vero-hSLAM cells is able to reduce infection by ~5000 time within 2 days, and viii) Nafamostat mesylate can inhibit SARS-CoV-2 S protein-initiated membrane fusion. Outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): increased transmission beyond China-fourth update doi = 10.1016/j.scitotenv.2020.139278 id = cord-320935-3n157yl4 author = Kumar, Manish title = Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date = 2020-09-12 keywords = COVID-19; CoV-2; RNA; SARS; virus summary = This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. doi = 10.1007/s40726-020-00161-5 id = cord-252389-xrdbmosj author = Kumar, Mukesh title = Neurological manifestations and comorbidity associated with COVID-19: an overview date = 2020-10-14 keywords = CNS; COVID-19; CoV-2; SARS summary = In this article, we have reviewed the neurological characteristic features of COVID-19 patients, latent neurotropic mechanisms of SARS-CoV-2 involvement in the comorbidity associated with CNS disorders, and neurological manifestations associated with COVID-19. Therefore, exploring the neurologic manifestations associated with COVID-19 is urgently required for better understanding the SARS-CoV-2 brain infections, inhibiting the additional spread and treating patients affected by this pandemic. The neuronal cells infected with virus, immune systems (microphase, T cells, and monocytes) triggered, and inflammatory system activated leads to cytokine storm, oxidative stress, and associated neurological manifestations neuroinvasiveness of SARS-CoV-2 [11, 35] . In a recent review [51] , authors have categorized the reported neurological findings related to COVID-19 into three categories: a) Central (headache, dizziness, impaired consciousness, acute cerebrovascular disease, ataxia, seizures, and special senses) b) Peripheral (hypogeusia, hyposmia) c) Musculoskeletal (ischemic or hemorrhagic) Apart from the above, increasing evidence indicated that coronaviruses may invade the CNS, causing neurological disorders. doi = 10.1007/s10072-020-04823-6 id = cord-324166-6ydn2bvy author = Kumar, Neeraj title = Antitussive noscapine and antiviral drug conjugates as arsenal against COVID-19: a comprehensive chemoinformatics analysis date = 2020-08-20 keywords = Hcq; Mpro; Nos; SARS; drug summary = We found that Noscapine-Hydroxychloroquine (Nos-Hcq) conjugate has strong binding affinity for the main protease (Mpro) of SARS-CoV-2, which performs key biological function in virus infection and progression. Also, dynamical residue cross-correlation map with principal component analysis depicted the stable binding of Nos-Hcq conjugate to Mpro domains with optimal secondary structure statistics of complex dynamics. Similar binding sites were employed for performing the molecular docking of the noscapine conjugations with the target Mpro of coronavirus using the Hex 8.0 and SwissDock servers. With these significant results, it can be attributed that Nos-Hcq conjugate has a high potential to bind the target Mpro enzyme and further can be used as effective therapeutics for SARS-CoV-2. We report the efficient combinatorial therapy by conjugating the noscapine (antitussive drug) with potential hydroxychloroquine (Nos-Hcq) against the SARS-CoV-2, through the computational assays with insights into the experimental results. doi = 10.1080/07391102.2020.1808072 id = cord-265418-yqe9vdj1 author = Kumar, Nilesh title = Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date = 2020-04-11 keywords = CSI; Fig; SARS; Supplementary summary = Integrated interactome-transcriptome analysis to generate Calu-3-specific humanIt is likely that the outcome of SARS-CoV-2 infection can largely be determined by the interaction patterns of host proteins and viral factors. By integrating this Calu-3 co-expression network with SIPs-derived PPI subnetwork, we generated Calu-3-specific human-SARS-CoV-2 Interactome (CSI) that contains 214 SIPs interacting with their first and second neighbors make a network of 4,123 nodes and 14,650 edges (Fig. 1c, Supplementary Data 1) . We showed that CSI follows a power law degree distribution with a few nodes harboring increased connectivity, and thus exhibits properties of a scale-free network (r 2 = 0.91; (Fig. 1d , Supplementary Data 1), similar to the previously generated other human-viral interactomes 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . In conclusion, we generated a human-SARS-CoV-2 interactome, integrated virusrelated transcriptome to interactome, discover COVID-19 pertinent structural and functional modules, identify high-value viral targets, and perform dynamic transcriptional modeling. doi = 10.1101/2020.04.09.033910 id = cord-336604-2auhkxce author = Kumar, Pramod title = Integrated genomic view of SARS-CoV-2 in India date = 2020-08-03 keywords = India; Kumar; SARS summary = Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). A total of 127 laboratory-confirmed cases of COVID-19 from targeted testing and available samples at NCDC which represent different geographic locations or states and travel history from different countries during the early phase of the outbreak (Table 1 and Extended data, Supplementary figure S1 [Kumar et al., 2020b] ). We also compared SARS-CoV-2 mutation sites with other six coronavirus sequences (Extended data, Supplementary figure S5b [Kumar et al., 2020b] ). doi = 10.12688/wellcomeopenres.16119.1 id = cord-339329-8yvre7qc author = Kumar, Prashant title = Could fighting airborne transmission be the next line of defence against COVID-19 spread? date = 2020-05-23 keywords = SARS summary = Abstract The World Health Organization declared the infectious spread of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) an epidemic during its initial outbreak in Wuhan (China) and has since declared it a pandemic and, more recently, an endemic infection that may remain in our communities. While these measures have worked well under lockdowns, the potential of airborne transmission of COVID-19 under the eased restrictions has not been considered important enough. Social distancing, self-isolation, handwashing, provision of hand sanitisers in public buildings, frequent disinfection of high-touch surfaces and the use of face masks have been recommended as effective mitigation measures against the spread of COVID-19 by the SARS-CoV-2 virus. Another study has reported a high concentration of viral RNA peaks in sub-and super-micrometre particle ranges and highlighted the potential transmission of SARS-CoV-2 via aerosols inside two Wuhan hospitals [3] . This work highlighted the probability of a much higher COVID-19 infection rate in closed environments with re-circulated air, and substantiates our below point regarding airborne transmission. doi = 10.1016/j.cacint.2020.100033 id = cord-311214-eqwxkwqa author = Kumar, Roshan title = Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date = 2020-04-16 keywords = CoV-2; SARS; USA summary = Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-β, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. A manually annotated reference database was generated using the Genbank 128 file of Severe acute respiratory syndrome coronavirus 2 isolate-SARS-CoV-129 2/SH01/human/2020/CHN (Accession number: MT121215) and open reading frames (ORFs) 130 were predicted against the formatted database using prokka (-gcode 1) [22] . All these isolates 189 were found to harbor 9 open reading frames coding for ORF1a (13218 bp) and ORF1b (7788 190 bp) polyproteins, surface glycoprotein or S-protein (3822 bp), ORF3a protein (828 bp Our analysis revealed that strains of human infecting SARS-CoV-2 are novel and highly 201 identical (>99.9%). In this study, the analysis was 358 performed on the genomes of the novel SARS-CoV-2 isolates recently reported from different 359 countries to understand viral pathogenesis. doi = 10.1101/2020.03.25.006213 id = cord-262550-oip5m9br author = Kumar, S. Udhaya title = The Rise and Impact of COVID-19 in India date = 2020-05-22 keywords = COVID-19; India; SARS summary = The coronavirus disease (COVID-19) pandemic, which originated in the city of Wuhan, China, has quickly spread to various countries, with many cases having been reported worldwide. The Ministry of Health and Family Welfare of India has raised awareness about the recent outbreak and has taken necessary actions to control the spread of COVID-19. The recent outbreak of COVID-19 in several countries is similar to the previous outbreaks of SARS and Middle East respiratory syndrome (MERS) that emerged in 2003 and 2012 in China and Saudi Arabia, respectively (8) (9) (10) . A recent study reported that affected family members had not visit the Wuhan market in China, suggesting that SARS-CoV-2 may spread without manifesting symptoms (21) . The Ministry of Health and Family Welfare (MOHFW), India, has raised awareness about the recent outbreak and taken necessary action to control COVID-19. The impacts on health, society, and economy of SARS and H7N9 outbreaks in China: a case comparison study doi = 10.3389/fmed.2020.00250 id = cord-296917-yk574m99 author = Kumar, Sathish title = Aerosol‐mediated transmission of SARS‐Cov‐2 or COVID‐19 in the cardiac surgical operating room date = 2020-07-11 keywords = SARS summary = The coronavirus disease-2019 (COVID-19) virus spreads predominantly through droplet and aerosol routes and blood-borne infection is not considered a major source of transmission. As a result, while contact is necessary for droplet infections and thereby handwashing and gloves are highly effective against contact transmission, viral particles transmitted though aerosol is absorbed via the respiratory mucosa and potentially across the conjunctivae, other measures are required to prevent transmission. However, because of the smaller size, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 as it is popularly known as, can spread across larger areas and has been shown to remain viable in aerosols even at 3 hours. 7 The highest viral load of the virus causing COVID-19 is in sputum and upper airway secretions and endotracheal intubation is the commonest and most relevant aerosol-generating procedure in cardiac surgery. Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review doi = 10.1111/jocs.14728 id = cord-279180-xad53zht author = Kumaravel, Santhosh Kumar title = Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies date = 2020-08-17 keywords = Artificial; COVID-19; China; Fig; Health; India; Intelligence; SARS summary = The COVID-19 is a respiratory disease that spreads at a maximum rate through droplets of the infected people through the air (World Health Organisation 2020a). • In addition, the incorporation of lockdown with other treatment and prevention measures such as school closures, travel restrictions, and social distancing has had a greater impact on spread prevention, cases requiring critical care beds, and deaths compared with quarantine alone. Machine learning has the potential to support clinicians'' work processing and management of large amounts of medical data contained in electronic health records and used in clinical applications which includes recognizing high-risk patients in need of ICU, the identification of early signs of lung cancer, determination of patient''s respiratory status from X-rays in the chest, such deep learning approaches employ neural networks to predict the input-output data relationship. doi = 10.1007/s13205-020-02382-3 id = cord-277841-7sp8ftbc author = Kumari, Pratibha title = Potential diagnostics and therapeutic approaches in COVID-19 date = 2020-08-12 keywords = COVID-19; CoV-2; RNA; SARS; detection summary = Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. COVID-19 is a contagious disease, caused by a novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2). In this article, we evaluated literature for reports informing various diagnostic methods, potential antiviral chemical therapeutics, and effective treatment strategies towards clinical management of COVID-19 patients. Molecular diagnostic methods target to detect either specific regions of the viral genome or RNA-dependent RNA polymerase (RdRP) and/or structural proteins of SARS-CoV-2 (Table 1) . Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2. Table 2: Primers and probes for targeting SARS-Cov-2 genes in an RT-PCR test for COVID-19 diagnosis. doi = 10.1016/j.cca.2020.08.013 id = cord-294696-pm6pfeeb author = Kunz, Y. title = Was sollte ein Urologe zu SARS-Cov-2 wissen? Risikoanalyse für urologische Operationen und Handlungsempfehlungen im klinischen Alltag date = 2020-10-13 keywords = COVID-19; Coronavirus; SARS; der; eine; und summary = Ausgelöst wird diese Infektionskrankheit durch das Virus SARS-CoV-2 ("severe acute respiratory syndrome coronavirus 2"), das zur Familie der β-Coronaviridiae bzw. Das SARS-CoV-2 wird im Wesentlichen via Tröpfcheninfektion -und somit über Aerosole -von symptomatischen COVID-19-Patienten übertragen. Es wurde eine Literatursuche in PubMed, bioRxiv und medRxiv sowie den Datenbanken der WHO und des CDC über SARS-CoV-2 und chirurgisches Prozedere bei infizierten Patienten durchgeführt. Das Prostatagewebe scheint demgegenüber nicht von SARS-CoV-2 befallen zu werden, zumindest konnte eine chinesische Gruppe in einer kleinen Studie keine Virus-RNA im Prostatasekret nachweisen [29] . Da basierend auf der oben angesprochenen Studienlage eine SARS-CoV-2-Übertragung mittels Urin denkbar ist, muss bei COVID-19-Patienten und unklaren Verdachtsfällen zusätzlich zur gängigen Schutzkleidung im Operationssaal auf FFP-2-Masken und Schutzbrillen zurückgegriffen werden. Da Aerosole nicht nur während der Operation, sondern bereits zuvor im Rahmen einer OP-Einleitung entstehen können, sollte laut aktuellen Empfehlungen unbedingt auf FFP-2-Masken im Falle eines zu behandelnden Patienten mit Verdacht auf oder einer bestätigten COVID-19-Infektion zurückgegriffen werden. doi = 10.1007/s00120-020-01264-z id = cord-343808-uqhiyj56 author = Kuo, Hsiao-I. title = Assessing impacts of SARS and Avian Flu on international tourism demand to Asia date = 2008-01-07 keywords = ARMAX; Avian; Flu; SARS summary = In order to estimate the impacts of epidemic diseases including SARS and Avian Flu on tourism demand in most Asian affected countries, the methodology of the ARMAX model is adopted in our study. The monthly data for international tourist arrivals are collected from statistical datasets for each country, and the probable numbers of SARS-infected patients and the confirmed human cases of Avian Flu are obtained from the World Health Organization (WHO, 2006 Furthermore, the ARMA and ARMAX models are estimated by using nonlinear least squares estimators, while dynamic panel models are implemented by using the panel GMM technique. Table 3 presents the results of the ADF tests for the three series, including tourism demand, namely, international tourist arrivals, the probable SARS-infected patients and the number of confirmed cases of Avian Flu. The ADF test statistics are compared with the critical values from the nonstandard Dickey-Fuller distribution at the 5% significance level. doi = 10.1016/j.tourman.2007.10.006 id = cord-340240-dk48pdqa author = Kuo, Tsun-Yung title = Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date = 2020-08-11 keywords = S-2P; SARS summary = title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 S-2P was combined with various adjuvants, including CpG 1018, and administered to mice to test its effectiveness in eliciting anti-SARS-CoV-2 neutralizing antibodies. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of spike-specific antibodies in sera of immunized mice. In this study, we present data from preclinical studies aimed at developing a COVID-19 candidate subunit 84 vaccine using CHO cell-expressed SARS-CoV-2 S-2P antigen combined with various adjuvants. We have 85 shown that S-2P, when mixed with CpG 1018 and aluminum hydroxide adjuvants, was most effective in 86 inducing antibodies that neutralized pseudovirus and wild-type live virus while minimizing Th2-biased 87 responses with no vaccine-related adverse effects. Previous studies showed that the lung-infiltrating eosinophils were a common 308 indication of Th2-biased immune responses seen in animal models testing SARS-CoV vaccine candidates [22] . doi = 10.1101/2020.08.11.245704 id = cord-354685-oggtmum4 author = Kurup, Drishya title = Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2 date = 2020-10-16 keywords = CORAVAX; Cat; RABV; SARS summary = This study reports that both a live and an inactivated rabies virus containing the SARS-CoV-2 spike S1 protein induces potent virus-neutralizing antibodies at much higher levels than seen in the sera of convalescent patients. To assess the correct confirmation of the chimeric S1 incorporated into CORAVAX, we first analyzed the binding of the recombinant human ACE-2 receptor-Fc chimera (human IgG) protein (Fig. 2a) and a SARS-COV-2 receptor binding domain (RBD) directed mouse monoclonal antibody (Fig. 2b) . After blocking, the membrane was incubated overnight with a human monoclonal 4C12 specific for the RABV glycoprotein (hybridoma kindly provided by Dr. Scott Dessain) or rabbit serum against the S1 subunit of SARS-CoV-2 Spike protein (Invitrogen, ThermoFisher Scientific, Cat# PA5-81798) at a dilution of 1:1000 in PBS containing 5% BSA. The cells were then stained for 2 h at RT with mouse polyclonal antiserum against the S1 subunit of SARS-CoV-2 Spike protein and a human monoclonal antibody 4C12 against RABV glycoprotein (2 µg/ ml). doi = 10.1038/s41541-020-00248-6 id = cord-341543-gcnph9gf author = Kuryntseva, P. title = A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia date = 2020-09-23 keywords = COVID-19; SARS summary = The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of wastewater samples and their serial dilutions but the approach excludes usage of concentration techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. 30 In the present study, a modified approach for detection of COVID-19 infection rate using 31 wastewater analysis has been developed. In the modelling experiment with the excreta of ten COVID-19 235 patients, it was demonstrated that the minimal rate of infected people in the community that can 236 be detected by this method is 10-2%. doi = 10.1101/2020.09.21.20197244 id = cord-293578-yu2i0u2h author = Kusadasi, Nuray title = A Pathophysiological Perspective on the SARS-CoV-2 Coagulopathy date = 2020-08-10 keywords = CoV-2; FXII; SARS summary = The potential role of plasma kallikrein in case of SARS-CoV-2 infection may be summarized as (1) the activation of FXII with the end-product thrombin (coagulation system) (2) the generation of bradykinin with subsequent vascular permeability and leakage (kallikrein-kinin system), (3) the activation of the renin-angiotensin system through conversion of renin from pre-renin leading to a pro-inflammatory state through increased angiotensin 1 receptor activation and (4) the activation of C5, in part through activation of C1 via FXII and in part through activation of C3 via plasmin (complement system). 54, 55 Since prekallikrein is seen as a potential regulator in the fibrin clot formation through FXII activation and is involved in the pathogenesis of thrombosis, there might be an important role for controlling the hypercoagulable state of the patients infected with SARS-CoV-2 as a therapeutic target. Taken together, all these mechanisms may contribute to the complex hypercoagulable state of the critically ill patients infected with SARS-CoV-2 having severe hypoxia and ongoing endothelial activation. doi = 10.1097/hs9.0000000000000457 id = cord-345689-5ns1onkw author = Kusters, Inca C. title = Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date = 2009-01-30 keywords = SARS; Vero; phase; vaccine; virus summary = doi = 10.1016/b978-0-12-369408-9.00011-1 id = cord-263764-2ewz8ok4 author = Kutter, Jasmin S title = Transmission routes of respiratory viruses among humans date = 2018-01-17 keywords = SARS; respiratory; transmission; virus summary = We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . doi = 10.1016/j.coviro.2018.01.001 id = cord-314937-jrxu65bl author = Kuwelker, K. title = High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date = 2020-11-04 keywords = November; PCR; SARS summary = The secondary attack rate of SARS-CoV-2 from index cases to household contacts reflects the natural spread of infection in immunologically naive populations with limited preventive measures to control transmission. Here, we estimated the secondary household attack rate of SARS-CoV-2 and identified the determinants of household transmission by measuring SARS-CoV-2-specific antibodies in household members of RT-PCR confirmed cases during the first month of the COVID-19 pandemic in Norway. Our study was specifically designed to assess household attack rates as measured by seropositivity in household members 6-8 weeks after onset of symptoms in the index case, with low prevalence of SARS-CoV-2 virus in the community. We calculated attack rates based on SARS-CoV-2-specific antibodies in household members, whereas the majority of previous studies have ascertained transmission based on RT-PCR, with estimates of 7·6% to 38% (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . doi = 10.1101/2020.11.02.20224485 id = cord-301946-erzh30mt author = Kwak-Kim, Joanne title = COVID-19 and immunomodulation treatment for women with reproductive failures date = 2020-06-12 keywords = COVID-19; RFI; SARS; TNF summary = With the Coronavirus Disease 2019 (COVID-19) pandemic, patient care has been significantly challenged not only for the COVID-19 cases but for the others, including pregnant women with a history of reproductive failures (RF), such as recurrent pregnancy losses (RPL), repeated implantation failures (RIF), with immune etiologies including autoimmune diseases, cellular immune dysfunction, and rheumatic conditions. SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus), which caused the SARS outbreak in 2003, infects macrophages and T cells (Perlman and Dandekar 2005) and induces various cytokines, such as type I IFN, TNF-α, IL-1, etc., and B cell-related antibodies (Prompetchara et al. With the currently available data, it is unlikely that the use of IVIg in patients with RFI will impact the chances of contracting the disease or negatively affect the clinical course in women with COVID-19 infection during pregnancy. doi = 10.1016/j.jri.2020.103168 id = cord-284037-nj5jo1ev author = Kwee, Thomas C. title = Chest CT in COVID-19: What the Radiologist Needs to Know date = 2020-10-23 keywords = COVID-19; PCR; SARS summary = Chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available. According to the Fleischner Society consensus statement, chest imaging is indicated in patients with moderate to severe respiratory symptoms (ie, presence of significant pulmonary dysfunction or damage) and any pretest probability of COVID-19 infection, when RT-PCR test results are negative, and in any patient for whom an RT-PCR test is not performed or not readily available (59) . In cases of clinical worsening, chest imaging is advised to assess for COVID-19 progression or secondary cardiopulmonary complications such as acute respiratory distress syndrome (ARDS), PE, superimposed pneumonia, or heart failure that can potentially be secondary to COVID-19-induced cardiac injury (59) . doi = 10.1148/rg.2020200159 id = cord-261750-6b1y7yxg author = Kwek, Seow-Khee title = Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge date = 2006-05-31 keywords = SARS; SF-36 summary = title: Quality of life and psychological status in survivors of severe acute respiratory syndrome at 3 months postdischarge Method Postal survey comprising Health-Related Quality of Life (HRQoL) questionnaires and anxiety and depression measures was sent to them at 3 months'' postdischarge. Hence, in this study, we undertook to ascertain systematically the quality of life and psychological well-being of SARS survivors 3 months'' postdischarge from the acute episode. The responders and the nonresponders were comparable on demographic parameters, duration of hospital stay, preillness health status, as well as the proportion of patients admitted to the intensive care unit ( Table 2 ). The health care workers appeared to be more adversely affected than nonstaff based on both the HRQol SF-36 scores (Fig. 1 , see staff-SARS) and the mean scores for IES, and the HADS Depression and Anxiety scores, although these were not significant. doi = 10.1016/j.jpsychores.2005.08.020 id = cord-333121-kt6t41ff author = Kwenandar, Felix title = Coronavirus Disease 2019 and Cardiovascular System: A Narrative Review date = 2020-06-03 keywords = COVID-19; SARS summary = At the end of 2019, a viral pneumonia disease called coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2), emerged in Wuhan, China. Although this infective disease is mostly characterized by respiratory tract symptoms, increasing numbers of evidence had shown considerable amounts of patients with cardiovascular involvements and these were associated with higher mortality among COVID-19 patients. Cardiovascular manifestation in COVID-19 patients include myocardial injury (MI), arrhythmias, cardiac arrests, heart failure and coagulation abnormality, ranging from 7.2% up to 33%. [2] With the increasing number of confirmed cases and the accumulating clinical data, in addition to the common clinical presentation of respiratory failure caused by COVID-19, the cardiovascular manifestations induced by this viral infection has generated considerable concern. Although the exact pathophysiological mechanism underlying myocardial injury caused by COVID-19 is not fully understood, a previous report showed that in 35% of the patients infected, the SARS-CoV genome was positively detected in the heart. doi = 10.1016/j.ijcha.2020.100557 id = cord-267566-gdjl0qmu author = Kweon, Oh Joo title = Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date = 2020-10-22 keywords = COVID-19; PSO; SARS summary = This study aims to assess the serologic profiles and time kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with COVID-19 using two immunoassays. METHODS: A total of 97 samples serially collected from 17 patients with COVID-19 and 137 negative control samples were analyzed for IgM and IgG against SARS-CoV-2 using the AFIAS COVID-19 Ab (Boditech Med Inc., Chuncheon, Republic of Korea) and the EDI(™) Novel Coronavirus COVID-19 ELISA Kit (Epitope Diagnostics, Inc., San Diego, CA). The diagnostic sensitivities of IgM/IgG for ≤14d PSO were 21.4%/35.7~57.1% and increased to 41.2~52.9%/88.2~94.1% at >14 d PSO with specificities of 98.5%/94.2% for AFIAS COVID-19 Ab and 100.0%/96.4% for EDI(™) Novel Coronavirus COVID-19 ELISA Kit. Among 137 negative controls, 12 samples (8.8%) showed positive or indeterminate results. doi = 10.1371/journal.pone.0240395 id = cord-017995-azqjvxtu author = Kwong, Kim-hung title = Spatial Components in Disease Modelling date = 2010 keywords = Hong; Kong; SARS summary = Modelling of infectious diseases could help gain further understanding of their diffusion processes that provide knowledge on the detection of epidemics and decision making for future infection control measures. This research made an attempt to map different phases of the spatial diffusion of SARS in Hong Kong to identify the underlying spatial factors attributing to its transmission patterns. Socio-economic factors found statistically significant against SARS incidence included the following: c) percentage of population aged over 65, g) average number of rooms per household, and h) net residential density ( Table 1 ). Certain socio-economic factors (i.e., average number of rooms per household, percentage of elderly population, and net residential density) were found to correlate positively with the occurrence of SARS in Hong Kong, indicating their potential influence in the disease transmission. This research mapped different development phases of the SARS epidemic in Hong Kong and employed the Pearson''s correlation to isolate environmental factors and socio-economic factors of significant pertinence to the disease. doi = 10.1007/978-3-642-12156-2_30 id = cord-104500-m0kfom0x author = Kyriakopoulos, Anthony M. title = The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review date = 2020-09-21 keywords = COV-2; COVID-19; Coronavirus; MERS; SARS; SSE summary = A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20(th) of August 2020. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. Following this initial selection stage, further screening was performed by all reviewers, using the previously described search items to identify parameters determining the global impact of COVID-19 due to SSEs. Identified parameters included the global impact of immunity and vaccination, the holy cup and religion transmission, and the austerity caused by COVID-19 and other coronavirus epidemics due to restrictions applied. doi = nan id = cord-298227-av1ev8ta author = Kähler, Christian J. title = Fundamental protective mechanisms of face masks against droplet infections date = 2020-06-28 keywords = SARS; droplet; filter; infection; mask summary = Many governments have instructed the population to wear simple mouth-and-nose covers or surgical face masks to protect themselves from droplet infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in public. First of all, we show that the masks protect people in the surrounding area quite well, since the flow resistance of the face masks effectively prevents the spread of exhaled air, e.g. when breathing, speaking, singing, coughing and sneezing. Thirdly, we show that even simple mouth-and-nose covers made of good filter material cannot reliably protect against droplet infection in contaminated ambient air, since most of the air flows through gaps at the edge of the masks. However, if the distance rules cannot be observed and the risk of inhalation-based infection becomes high because many people in the vicinity are infectious and the air exchange rate is small, improved filtration efficiency masks are needed, to take full advantage of the three fundamental protective mechanisms these masks provide. doi = 10.1016/j.jaerosci.2020.105617 id = cord-296605-p67twx7a author = LAU, Arthur Chun-Wing title = Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date = 2004-03-10 keywords = SARS; acute; patient; respiratory; severe summary = title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS) doi = nan id = cord-320787-dwyyjq6o author = La Rosa, Giuseppina title = First detection of SARS-CoV-2 in untreated wastewaters in Italy date = 2020-05-23 keywords = PCR; SARS summary = Italy is among the world''s worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Herein we report the results of the screening for SARS-CoV-2 presence in sewage samples collected between the end of February and the beginning of April 2020 from WWTPs in Milan (Northern Italy) and Rome (Central Italy). In the absence of a standardized method for SARS-CoV-2 detection in environmental samples, RNAs were tested for the presence of SARS-CoV-2 using three different nested RT-PCR assays and one real-time qPCR assay (Table 1 and Figure 1 b) a newly designed primer set specific for SARS-CoV-2. doi = 10.1016/j.scitotenv.2020.139652 id = cord-298321-8871aifz author = Laamarti, Meriem title = Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date = 2020-07-01 keywords = SARS; Tunisia summary = The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes. Our recent study (13) based on the analysis of 30,983 genomes of SARS-CoV-2 variants belonging to 80 countries, revealed 5.67% of total mutations with a frequency greater than 1% of all the sequences analyzed suggesting that this virus is not yet adapted to its host. In all Moroccan SARS-CoV-2 genomes, the analysis of genetic variants revealed 61 mutations compared to the reference sequence (Fig 1) , including 29 non-syn(Fig 2A) . doi = 10.1101/2020.06.30.181123 id = cord-346331-d0s028wl author = Lackey, Kimberly A. title = SARS‐CoV‐2 and human milk: What is the evidence? date = 2020-05-30 keywords = MERS; SARS; human; milk summary = Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. • Limited, weak evidence suggests that some coronaviruses (including SARS-CoV-2) may be present in human milk, but these studies do not report methods of sample collection and validation of reverse transcription polymerase chain reaction (RT-PCR) assays for human milk. Of particular interest in this context are (1) the potential role that breastfeeding could play in vertical transmission of SARS-CoV-2 from women to infants via human milk and (2) the potential protective effects of targeted antibodies and other immunoprotective components in human milk against COVID-19. Milk was submitted to the CDC, where it was analysed using reverse transcription polymerase chain reaction (RTSearch terms, databases and preprint servers used to identify existing literature reporting the possibility of vertical transmission of coronaviruses from mother to infant during breastfeeding as of 17 April 2020 The infant in this study was never tested for SARS-CoV infection. doi = 10.1111/mcn.13032 id = cord-326965-xrnhkcsv author = Lacout, Carole title = A new diagnosis of systemic capillary leak syndrome in a patient with COVID-19 date = 2020-09-17 keywords = SARS; capillary summary = SIR, With the coronavirus disease 2019 (COVID-19) pandemic, we are discovering that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has properties to induce a dysregulated immune response that exceed the simple respiratory infection [1] . Systemic capillary leak syndrome is a rare immune disorder that evolves with repeated episodes of pseudoshock that can occur spontaneously or can be triggered by viral infections. Systemic capillary leak syndrome is a rare disorder that can be secondary to blood malignancies, immune disorders, toxics, medication, infections or idiopathic (Clarkson''s disease) [4] . In conclusion, we think that it is not a coincidence that a first episode of systemic capillary leak syndrome, which is a very rare disease, occurred simultaneously with a respiratory infection caused by SARS-CoV-2. Idiopathic systemic capillary leak syndrome (Clarkson disease) SARS-CoV-2 induces acute and refractory relapse of systemic capillary leak syndrome (Clarkson''s disease) doi = 10.1093/rheumatology/keaa606 id = cord-287653-69nfi379 author = Lacy, J. Matthew title = COVID-19: POSTMORTEM DIAGNOSTIC AND BIOSAFETY CONSIDERATIONS date = 2020-04-24 keywords = COVID-19; PPE; SARS summary =  Prosect cases in negative pressure isolation suite with at least 6-12 air changes per hour  Doff contact and droplet precaution PPE, as well as N95 respirator or PAPR  Limit personnel in the isolation suite to the minimum necessary to perform the examination  Employ splash and aerosol reduction techniques during prosection; oscillating saws are discouraged but if used should have vacuum shroud attachment  Use caution when handling sharps; allow only one person to prosect at a given time  Ensure a technician is outside isolation room to monitor procedure and provide support as needed  Procure synthetic nasopharyngeal (+/-lung) respiratory swabs in sterile tubes of 2-3 ml of viral transport media for SARS-CoV-2 testing as needed  Carefully decontaminate morgue surfaces and outer body bag following autopsy  Ensure body is fully enclosed in a secure bag, tag as infectious and ensure funeral home is informed  Consider modifying release procedures to prevent bag being opened in morgue for identification  Perform hand hygiene after doffing PPE A C C E P T E D doi = 10.1097/paf.0000000000000567 id = cord-286919-fny060vk author = Lahfaoui, M title = Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson date = 2020-04-27 keywords = SARS summary = Les auteurs déclarent ne pas avoir de liens d''intérêts Syndrome de détresse respiratoire aiguë secondaire à une infection à SARS-COV-2 chez un nourrisson L''émergence et la propagation d''un nouveau coronavirus (SARSCoV-2) à partir de Wuhan, en Chine, sont devenues une urgence de santé publique de portée internationale, désignée par l''Organisation mondiale de la santé [1]. Nous rapportons un cas d''un nourrisson, de sexe féminin âgée de 17 mois, de Berkan, Maroc, admis initialement pour prise en charge d''une anémie, puis un tableau de sepsis sévère, le body-scan a objectivé des lésions pulmonaire bilatérale d''allure virale, le RT-PCR a confirmé le diagnostic de SARS-COV-2, la patiente a été décédé après 24H suite à un syndrome de détresse respiratoire aigüe. A la date du 10 mars 2020, ce nouveau coronavirus (SRAS-CoV-2) est déjà responsable de plus de 110000 infections et de 4 000 décès dans le monde, mais les données concernant les caractéristiques épidémiologiques et cliniques des enfants doi = 10.1016/j.rmr.2020.04.009 id = cord-253704-y0t30xw3 author = Lahiri, Durjoy title = COVID-19 Pandemic: A Neurological Perspective date = 2020-04-29 keywords = COVID-19; SARS; neurological; patient summary = Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to principally affect the respiratory system, neurological involvements have already been reported in some published work. Neurological manifestations can further be subdivided into the central nervous system (headache, dizziness, alteration of the sensorium, ataxia encephalitis, stroke, and seizures) and peripheral nervous system (skeletal muscle injury and peripheral nerve involvement including hyposmia and hypogeusia) symptomatology. Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to mainly affect the respiratory system, neurological involvements have already been reported in some published work. In the present paper, we have reviewed the recently published or pre-print original articles, case reports, and existing open-source data-sets in order to delineate the spectrum of neurological disorders in SARS-CoV-2 positive cases. Another report from China describes a case of acute myelitis, possibly affecting the cervical spinal cord, as evidenced by the clinical features, in a known patient of SARS-CoV-2 infection [22] . doi = 10.7759/cureus.7889 id = cord-303665-l57e54hu author = Lahrich, S. title = Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date = 2020-09-10 keywords = PCR; SARS; virus summary = Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. doi = 10.1016/j.scitotenv.2020.142325 id = cord-016405-86kghmzf author = Lai, Allen Yu-Hung title = Impact of Disasters and Disaster Risk Management in Singapore: A Case Study of Singapore’s Experience in Fighting the SARS Epidemic date = 2014-06-13 keywords = MOH; SARS; SCDF; Singapore; disaster; public; risk summary = doi = 10.1007/978-4-431-55022-8_15 id = cord-336066-n9yq8enz author = Lai, Chien‐Chen title = Proteomic analysis of up‐regulated proteins in human promonocyte cells expressing severe acute respiratory syndrome coronavirus 3C‐like protease date = 2007-04-04 keywords = Fig; SARS summary = Functional classification of identified up-regulated proteins indicated that protein metabolism and modification, particularly in the ubiquitin proteasome pathway, was the main biological process occurring in SARS CoV 3CLpro-expressing cells. Interestingly, analysis of apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Table 3 ). Confocal imaging of the stained cells revealed that the release of apoptosis-inducing factor from mitochondria was found in the SARS CoV 3CLpro-expressing cells (Fig. 7A, right) , but not in mock cells (Fig. 7A, left) . Interestingly, analysis of the apoptosis signaling pathway revealed that the mitochondrial apoptogenic apoptosisinducing factor (Spot ID 55) was up-regulated and antiapoptogenic heat shock cognate 71-kDa protein (HSP70) (Spot ID 83) was down-regulated in 3CLpro-expressing cells (Figs. doi = 10.1002/pmic.200600459 id = cord-304388-pth2d40p author = Lai, Chih-Cheng title = Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths date = 2020-03-04 keywords = COVID-19; China; SARS summary = Abstract Since the emergence of coronavirus disease 2019 (COVID-19) (formerly known as the 2019 novel coronavirus [2019-nCoV]) in Wuhan, China in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more than 75,000 cases have been reported in 32 countries/regions, resulting in more than 2000 deaths worldwide. 11, 15 Similarly, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team in China reported that 66.7% (n Z 29,798) of 44,672 cases of COVID-19 of varying degrees of severity were between 20 and 60 years of age. First, the clinical manifestation of COVID-19 ranges from the asymptomatic carrier state to severe pneumonia; however, most early reports only showed the findings of SARS-CoV-2 pneumonia, in which the ratio of male patients was much larger than that of female patients, there were no pediatric cases, and the mortality rate was high. doi = 10.1016/j.jmii.2020.02.012 id = cord-305763-160heazx author = Lai, Chih-Cheng title = Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date = 2020-10-09 keywords = COVID-19; SARS summary = One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. doi = 10.1016/j.ijid.2020.10.011 id = cord-332080-923jpec0 author = Lai, Chih-Cheng title = In vitro diagnostics of coronavirus disease 2019: technologies and application date = 2020-06-05 keywords = CoV-2; SARS summary = Abstract Laboratory-based diagnostic measures including virological and serological tests are essential for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, serological tests cannot confirm SARS-CoV-2, and results will be false-negative when antibody concentrations fall below detection limits. (Hangzhou Bigfish Bio-tech Co., Ltd., Zhejiang, China) was recently registered 127 as a CE-IVD for detecting SARS-CoV-2 ORF-1ab and N genes in 128 nasopharyngeal swabs, sputum, and BAL fluids. The 145 performance of the Xpress SARS-CoV-2 test was clinically evaluated in 146 patients with respiratory illnesses from whom contrived nasopharyngeal swab 147 samples were collected into viral transport media. Serological tests that can detect SARS-CoV-2 IgG-IgM antibodies are simpler 248 than rRT-PCR, and do not require complicated equipment and protocols 249 (Table 3) . During the previous SARS 251 epidemic, the IgM antibody was the first line of defense during viral infections 252 and was detectable in blood samples from patients after 3 -6 days. Dynamics of 617 anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients doi = 10.1016/j.jmii.2020.05.016 id = cord-269383-1tyorrb0 author = Lai, Christopher K C title = Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19) date = 2020-08-01 keywords = DTS; SARS summary = METHODS: We performed a prospective study in two regional hospitals in Hong Kong RESULTS: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep-throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. International authorities recommend laboratory diagnosis of SARS-CoV-2 infection should base on real-time PCR (RT-PCR) detection of viral RNA in respiratory specimens [2, 3] . In another study by the same research group [23] , they tested archived nasopharyngeal swabs and posterior oropharyngeal saliva specimens from 58 confirmed COVID-19 patients using Xpert® Xpress SARS-CoV-2 assay. To date, our current study provides the largest number of patients with prospectively collected saliva specimens throughout the clinical course and with head-to-head comparison of DTS to both upper and lower tract respiratory samples. DTS contains lower viral RNA concentration and is less sensitive in detecting SARS-CoV-2 infection than sputum and pooled NP and throat swabs. doi = 10.1093/infdis/jiaa487 id = cord-323038-hmi061vn author = Lai, Christopher K C title = Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy date = 2020-06-30 keywords = China; SARS summary = title: Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy METHODS: We performed an epidemiological study using government information covering the first 100 confirmed cases to examine the epidemic curve, incidence, clusters, reproduction number (R(t)), incubation period and time to containment. [8] [9] [10] The key measures included: (i) emergency arrangements according to a Preparedness and Response Plan that stipulated the Government''s actions against novel infectious diseases, (ii) mandatory quarantine for people at risk of carrying the infection, (iii) promoting ''social distancing'' including a work-from-home policy and school closure, (iv) implementing border control, (v) increasing the supply of surgical masks, and (vi) transparent communication with the public. We controlled for age (in four age strata: 0-24, 25-44, 45-64 and !65 years), gender, source of infection (local vs imported), case identification (self vs by others) and whether the patient had attended any healthcare services before admission to hospital. doi = 10.1093/ije/dyaa106 id = cord-314025-h9gj814e author = Lai, Mary Y. Y. title = Survival of Severe Acute Respiratory Syndrome Coronavirus date = 2005-10-01 keywords = SARS; TCID summary = SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. doi = 10.1086/433186 id = cord-352379-q5inrxcm author = Lai, Michael M. C. title = SARS virus: The beginning of the unraveling of a new coronavirus date = 2003-10-17 keywords = MHV; RNA; SARS; coronavirus; virus summary = Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1007/bf02256318 id = cord-313415-5qrpucr4 author = Lai, Rongtao title = Sentinel surveillance strategies for early detection of coronavirus disease in fever clinics: experience from China date = 2020-08-25 keywords = SARS; covid-19 summary = During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. During SARS period in 2003, fever clinics emerged in many cities in mainland China with the purpose to screen the suspected SARS patients and to transfer the confirmed cases to designated hospitals for professional management. It is employed for discerning patients with suspected symptoms and signs, for timely isolation, for effectively blocking disease transmission during the early outbreak period before the pathogen has been identified, and for determining effective therapeutic methods; this strategy was used during the severe acute respiratory syndrome (SARS) epidemic in 2003 [2] . In the early outbreak period, the use of the sentinel surveillance strategy in fever clinics can provide benefits in terms of identifying patients with suspected symptoms, effectively blocking disease transmission, and protecting vulnerable populations. doi = 10.1017/s0950268820001892 id = cord-319273-ok2p1h9f author = Lai, Yu-Ju title = Severe acute respiratory syndrome coronavirus-2 and the deduction effect of angiotensin-converting enzyme 2 in pregnancy date = 2020-08-17 keywords = ACE2; COVID-19; SARS summary = Angiotensin-converting enzyme 2 (ACE2) has transient overexpression and increased activity during pregnancy, which is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. The management strategy includes monitoring fetal heart rate and uterine contractions; early oxygenation if O(2) saturation is less than 95%; empiric antibiotics for prevention of secondary infection; corticosteroid to treat maternal SARS-CoV-2 disease routinely is not suggested, only for fetal lung maturation in selected cases; and consideration of delivery is according to the obstetric indication, gestational age, and severity of the disease. 40 But a study indicated that angiotensin-converting enzyme 2 (ACE2), which is the receptor of SARS-CoV-2, was highly expressed in maternal-fetal interface cells, suggesting the possibility of vertical transmission. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes doi = 10.1097/jcma.0000000000000362 id = cord-342177-iqt3ghc0 author = Laine, Roger A title = The case for re-examining glycosylation inhibitors, mimetics, primers and glycosylation decoys as antivirals and anti-inflammatories in COVID19 date = 2020-08-21 keywords = SARS summary = 1974) and in 1976 showed that tunicamycin, which inhibits the formation of N-acetylglucosamine-lipid intermediates in N-linked glycan synthesis (Lennarz 1975) , suppressed glycoprotein synthesis in Semliki Forest, influenza and avian sarcoma virus (Schwarz et al. The "peplomeric glycoprotein E2 was not detectable upon tunicamycin treatment," indicating its synthesis was interdicted or its degradation was facilitated by lack of N-linked glycosylation and was improperly processed (Holmes et al. (1982) showed swainsonine, an α-mannosidase inhibitor, to inhibit processing of oligosaccharides on influenza viral hemagglutinin, and in 1983 showed its effect on vesicular stomatitis virus (Kang and Elbein 1983) . It seems a reasonable approach that interfering with host glycosylation systems hijacked by SARS COV2, plus interfering with the ACE2 receptor glycosylation may combine to 1) interdict infectivity and 2) glycosylation interference with Sialyl LeX can inhibit E-selectin-based inflammatory responses, mitigating the Covid19 ARDS pathology. Antiviral effect of alpha-glucosidase inhibitors on viral morphogenesis and binding properties of hepatitis C virus-like particles doi = 10.1093/glycob/cwaa083 id = cord-274508-nigru1o8 author = Lally, Michelle title = Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 date = 2020-10-26 keywords = SARS summary = title: Metformin is associated with Decreased 30-day Mortality among Nursing Home Residents Infected with SARS-CoV2 Design Retrospective cohort study Setting and Participants: 775 nursing home residents infected with SARS-CoV-2 who resided in one of the 134 Community Living Centers (CLC) of the Veterans Health Administration (VHA) during March 1, 2020 to May 13, 2020 were included. Results Relative to those not receiving diabetes medications, residents taking metformin were at significantly reduced hazard of death (adjusted HR 0.48, 95%CI 0.28, 0.84) over the subsequent 30 days from COVID-19 diagnosis. Conclusions and Implications Our data suggests a reduction in 30-day mortality following SARS-CoV-2 infection in residents who were on metformin-containing diabetes regimens. These findings suggest a relative survival benefit in nursing home residents on metformin, potentially through its mTOR inhibition effects. A recent focus on potential treatment for SARS-CoV-2 42 infection includes a pathway not usually considered for its "antiviral" property, the mammalian 43 target of rapamycin (mTOR) pathway. doi = 10.1016/j.jamda.2020.10.031 id = cord-316705-3wzurnfp author = Lalmuanawma, Samuel title = Applications of Machine Learning and Artificial Intelligence for Covid-19 (SARS-CoV-2) pandemic: A review date = 2020-06-25 keywords = SARS; covid-19 summary = A new novel model, that forecast and predicting 1-3 to 6 days ahead of total Covid-19 patient of 10 Brazilian states, using stacking-ensemble with support vector regression algorithm on the cumulative positive Covid-19 cases of Brazilian data was proposed, thus augmenting the short-term forecasting process to alert the healthcare expert and the government to tackle the pandemic [38] . A Canadian based forecasting model using time-series was developed employing Deep learning algorithm for the long-short-term-memory network, the studies found out a key factor intended for predicting the course with an ending point estimation of the current SARS-CoV-2 epidemic in Canada and all over the globe [40] . Since the outbreak of the novel SARS-CoV-2, scientists and medical industries around the globe ubiquitously urged to fight against the pandemic, searching alternative method of rapid screening and prediction process, contact tracing, forecasting, and development of vaccine or drugs with the more accurate and reliable operation. doi = 10.1016/j.chaos.2020.110059 id = cord-284925-vy2li9lz author = Lam, Dennis Shun Chiu title = COVID-19: Special Precautions in Ophthalmic Practice and FAQs on Personal Protection and Mask Selection date = 2020-04-29 keywords = COVID-19; N95; SARS; mask summary = We also endeavor to answer the key frequently asked questions in areas of the coronaviruses, COVID-19, disease transmission, personal protection, mask selection, and special measures in ophthalmic practices. Ophthalmologists are at risk of COVID-19 infection, since routine ophthalmic examinations are usually performed in a setting with close doctor-patient contact. We have also shared the precautions and strategies that we have implemented in our ophthalmic practice, based on our previous and current successful experiences in preventing severe acute respiratory syndrome (SARS) in 2003 and the current COVID-19 outbreaks in Hong Kong. For healthcare workers, surgical masks should be worn when performing sterile procedures, or as general protection against droplets infections. The close proximity of patients and doctors during eye examination, the presence of tears and liquids for anesthesia and dilation, or the potential aerosol or droplets from "air puff" tonometry, all pose a high risk for infective transmission. Interim infection prevention and control recommendations for patients with suspected or confirmed Coronavirus Disease 2019 (COVID-19) in healthcare settings doi = 10.1097/apo.0000000000000280 id = cord-263471-u3su9loz author = Lam, Meylin Caballeros title = Cardiac magnetic resonance characterization of COVID-19 myocarditis date = 2020-07-04 keywords = CMR; SARS summary = 1 Myocardial injury may occur at different phases of COVID-19 disease (ie, viral, pulmonary, inflammatory, and recovery phase), even late after the onset of symptoms. SARS-CoV-2 viral particles have been identified by real-time polymerase chain reaction (PCR) testing in cardiac tissue, providing evidence that direct cardiotoxicity might occur. Since more than 7.5% of myocardial cells have positive ACE2 expression, this could mediate SARS-CoV-2 entry into cardiomyocytes and cause direct cardiotoxicity. The CMR study performed on a 1.5T system (Magnetom Aera, Siemens Healthineers, Erlangen, Germany) showed normal biventricular function, no regional wall motion abnormalities, slightly increased T2 (54 ms, normal < 52 ms) and native T1 values (1110 ms, CMR allows targeting of several features of myocarditis, such as contractile dysfunction, inflammatory edema, and necrosis, and has become the gold standard for the noninvasive assessment of the disease. The role of cardiovascular imaging for myocardial injury in hospitalized COVID-19 patients doi = 10.1016/j.rec.2020.06.018 id = cord-288824-sygnmiun author = Lam, SD title = SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date = 2020-08-19 keywords = ACE2; SARS; Supplementary; TMPRSS2 summary = To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We correlated changes in the energy of the complex with changes in the structure of ACE2, chemical properties of residues in the binding interface, and experimental COVID-19 infection phenotypes from in vivo and in vitro animal studies. We used multiple methods to assess the relative change in binding energy (ΔΔG) of the SARS-CoV-2 S-protein:ACE2 complex following mutations in DC residues and DCEX residues that are likely to influence binding. Irrespective of host, the SARS-CoV-2 spike receptor binding domain is conserved (Fig. 4b) across tested human and animal associated SARS-CoV-2, suggesting mutations in the RBD are not required for infections observed in non-human species to date. doi = 10.1101/2020.05.01.072371 id = cord-342539-o004ggon author = Lam, Tommy Tsan-Yuk title = Tracking the genomic footprints of SARS-CoV-2 transmission date = 2020-05-28 keywords = SARS summary = [1], conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains. Several studies using mathematical modelling of the COVID-19 incidence and other coronavirus infections have suggested the effectiveness of disease control such as social distancing and city lockdown [6, 7] , but these methods seldom assess individual transmission It is evident in literature that genomic information of pathogens provide valuable empirical information about their transmission histories [2] , such as the identification of transmission chains through phylogenetic analysis of the genome sequences as illustrated in the work done by Lu et al. In addition to revealing the evolutionary process of the pathogen and acting as a proxy of disease transmission history, phylogenetic trees also serve as versatile frameworks for comparative analysis of virus genetics and phenotypes, disease epidemiology and clinical manifestations, and population demography and environment, thus facilitating identification of a possible interplay between these various aspects in disease dynamics ( Figure 1 ). doi = 10.1016/j.tig.2020.05.009 id = cord-355356-g7lvb8b4 author = Lamb, Yvette N. title = Remdesivir: First Approval date = 2020-09-01 keywords = COVID-19; SARS; remdesivir; simple summary = Having demonstrated potent antiviral activity against coronaviruses in preclinical studies, remdesivir emerged as a candidate drug for the treatment of the novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, during the current global pandemic. Based on preliminary results from the randomized, double-blind, placebo-controlled, multinational phase III ACTT-1 trial (NCT04280705) in patients with COVID-19, remdesivir significantly reduced time to recovery relative to placebo (median 11 days vs 15 days; rate ratio for recovery 1.32; 95% CI 1.12-1.55; p < 0.001) [primary endpoint] [41] . Among pregnant women (n = 67) and postpartum women (n = 19) who received compassionate use remdesivir for severe COVID-19, rates of clinical improvement were 96% and 89%, respectively, at day 28 [45] . In paediatric patients (aged 0-17 years) with severe COVID-19 treated with compassionate use remdesivir (n = 77), the clinical improvement rate was 88% at day 28 [46] . doi = 10.1007/s40265-020-01378-w id = cord-350618-rtilfnzi author = Lambelet, Valentine title = Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date = 2020-05-26 keywords = COVID-19; SARS; infection; pregnancy; pregnant; woman summary = College of Obstetricians and Gynaecologists (RCOG), pregnant women with moderate symptoms should self-isolate, unless they attend a maternity unit where patients in the 2 nd or 3 rd trimester meeting PHE criteria ( ≥ 1 of: (1) Clinical/radiological evidence of pneumonia, (2) Acute Respiratory Distress Syndrome (ARDS), (3) Fever ≥37.8 and at least one of acute persistent cough, hoarseness, nasal discharge/congestion, shortness of breath, sore throat, wheezing or sneezing) should be tested for COVID-19 and treated as infected until results are available. Past coronavirus epidemics were associated with adverse outcomes for the fetus and/or newborns including miscarriages (57%), preterm birth, fetal distress and FGR with SARS-CoV-1 infection during the 2 nd and 3 rd trimesters. In this review, we found that of 142 cases of SARS-CoV-2 infections in pregnancy, 28% experienced preterm birth and 14% had adverse fetal/neonata l outcomes (FGR, fetal/neonatal demise, severe symptoms at birth). doi = 10.1002/pd.5759 id = cord-294856-eeh2a0t8 author = Lambert, Paul-Henri title = Consensus Summary Report for CEPI/BC March 12-13, 2020 Meeting: Assessment of Risk of Disease Enhancement with COVID-19 Vaccines date = 2020-05-25 keywords = MERS; SARS; disease; vaccine summary = Therefore, CEPI and the Brighton Collaboration Safety Platform for Emergency vACcines (SPEAC) convened a scientific working meeting https://brightoncollaboration.us/brighton-collaboration-cepi-covid-19-web-conference/) on March 12 and 13, 2020 of experts in the field of vaccine immunology and coronaviruses to discuss current knowledge that could form the basis for the assessment of the risk of enhanced disease during SARS-CoV-2 vaccine development. Ferret models of SARS-CoV-1 also demonstrate virus replication in respiratory tracts with induction of a neutralizing antibody response but also demonstrated little evidence of clinical disease [13] . Efficacy of several SARS-CoV-1 vaccines was evaluated in these models with spike (S) protein based vaccines demonstrating neutralizing antibody and protection against pulmonary replication of the challenge virus in mice and hamsters [16] . There is evidence for disease enhancement in vaccinated animals after challenge with live virus in multiple studies with SARS-CoV-1 vaccine candidates as summarized in Table. Chinese macaques immunized with a modified vaccinia virus expressing S protein then challenged with SARS-CoV-1 did not develop clinical disease, but histopathology showed lung injury. doi = 10.1016/j.vaccine.2020.05.064 id = cord-320087-iu4ulxtu author = Lampe, Anne title = Guillain-Barré syndrome and SARS-CoV-2 date = 2020-07-08 keywords = GBS; SARS summary = Since January 2020, after Chinese health authorities identified a new type of coronavirus (SARS-CoV-2), the virus has spread throughout China and consecutively throughout the whole world. This article presents the case of a 65-years old man who was presumptively infected with SARS-CoV-2 during his ski vacation in Austria in March 2020 and acutely presented with typical symptoms of Guillain-Barré syndrome. We herein report about a COVID-19 patient who was admitted to the emergency department of our hospital with typical symptoms of Guillain-Barré syndrome (GBS). The interval between the onset of symptoms of SARS-CoV-2 infection and first symptoms of GBS was only 1 day in the case presented here. A case study of 5 patients with SARS-CoV-2 infection and GBS was published a few weeks ago [14] . The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Guillain-Barre syndrome associated with SARS-CoV-2 infection: Causality or coincidence? doi = 10.1186/s42466-020-00066-0 id = cord-267782-4pjfnund author = Lan, Fan-Yun title = Association between SARS-CoV-2 infection, exposure risk and mental health among a cohort of essential retail workers in the USA date = 2020-10-30 keywords = COVID-19; CoV-2; SARS summary = Therefore, we conducted this study aiming to investigate: 1) SARS-CoV-2 infection rate, transmission and exposure risks among grocery retail employees, 2) their use of personal protective equipment (PPE) and perception on COVID-19 and 3) their mental health state during the COVID-19 pandemic. ► This is the first study to demonstrate the significant asymptomatic infection rate, exposure risks and associated psychological distress of grocery retail essential workers during the pandemic, which supports the policy recommendations that employers and government officials should take actions on implementing preventive strategies and administrative arrangements, such as methods to reduce interpersonal contact, repeat and routine SARS-CoV-2 employee testing, to ensure the health and safety of essential workers. 13 14 In fact, a pioneering study conducted in the Table 3 Characteristics of retail essential employees in a single grocery store in Massachusetts, USA presented for SARS-CoV-2, the virus causing COVID-19, RT-PCR assay testing by Patient Health Questionnaire-9 (PHQ-9) screening score for depression These are in contrast to positions mainly dealing with consumer goods or the environment, such as stocker, backroom, receiving and maintenance. doi = 10.1136/oemed-2020-106774 id = cord-291360-z19ri377 author = Lan, Fan-Yun title = COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date = 2020-06-26 keywords = PCR; SARS summary = Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system''s estimated total HCW population (n = 4600). doi = 10.1371/journal.pone.0235460 id = cord-329102-2y49kcwu author = Lan, Tammy C. T. title = Structure of the full SARS-CoV-2 RNA genome in infected cells date = 2020-06-30 keywords = FSE; RNA; SARS; figure; structure summary = We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. doi = 10.1101/2020.06.29.178343 id = cord-267136-1abp6oom author = Lan, Yu-Ching title = Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan date = 2004-12-07 keywords = CUHK; SARS; Taiwan summary = Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. To better understand evolutionary relationships between SCoVs isolated in Taiwan and those isolated in other parts of the world, we constructed phylogenetic trees with two different methods using full-length genomic sequences from 45 human (12 Taiwanese) and two civet SCoVs. Tree topologies were consistent for the NJ (Fig. 1a) and Pars (Fig. 1b) methods. Pairwise comparison methods were used to analyze nucleotide sequence variation within the full-length genomes of 20 human SCoVs (7 from early epidemic and 13 from late epidemic) (Fig. 2) . doi = 10.1016/j.meegid.2004.08.005 id = cord-322585-5gio6ruj author = Lanari, Marcello title = Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date = 2020-06-25 keywords = SARS summary = The possible role of children in the COVID-19 viral disease pandemic is also commented. However, the current available data on severe acute respiratory syndrome 31 coronavirus 2 (SARS-CoV-2) show that, from the beginning of the outbreak until now, there is a 32 low attack rate in paediatrics worldwide. Particularly, in Madrid region (Spain), individuals <18 33 years-old accounted for 0.8% of the laboratory-confirmed cases during the first 2 weeks of the Finally, the lockdown imposed until recently by some governments, along with the growing fear of 103 going to hospitals, has led to a significant reduction in the circulation of the other respiratory pathogens and in the number of Paediatric ER visits. Screening 158 and severity of Coronavirus Disease 2019 (COVID-19) in children in Paediatric inflammatory multisystem 163 syndrome and SARS-CoV-2 infection in children -15 A Case Series of children with 2019 novel 180 coronavirus infection: clinical and epidemiological features doi = 10.1016/j.cmi.2020.06.017 id = cord-292733-dya40tln author = Lancman, Guido title = Severe COVID-19 virus reactivation following treatment for B cell acute lymphoblastic leukemia date = 2020-10-02 keywords = SARS summary = She was initially hospitalized with COVID-19 in April and developed a high antibody titer with two negative nasal polymerase chain reaction (PCR) swabs for SARS-CoV-2 on discharge. She developed a severe COVID-19 pneumonia with lymphopenia, high inflammatory markers, and characteristic bilateral ground-glass opacities on chest CT, requiring high-flow nasal cannula and transfer to the intensive care unit. Given the short time frame from leukemia treatment to PCR positivity and the low case rate in mid-June in New York City, reinfection appears to have been unlikely and SARS-CoV-2 reactivation is a possible explanation. This case illustrates the risks of treating recently recovered COVID-19 patients with immunosuppressive therapy, particularly lymphocyteand antibody-depleting therapy, and raises new questions about the potential of SARS-CoV-2 reactivation. Here, we report a case of severe COVID-19 virus reactivation following chemotherapy, including rituximab, cytarabine, and dasatinib for B cell acute lymphoblastic leukemia (B-ALL). doi = 10.1186/s13045-020-00968-1 id = cord-332404-va3rxy5p author = Landeros, A. title = An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic date = 2020-08-06 keywords = SARS; child; figure summary = Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence. Given transmission of SARS-CoV-2 occurs through respiratory droplets, any reopening policy must adequately reduce crowded environments at school to protect children, teachers, staff, and ultimately communities. A recent study on the effects of school closure in March in the U.S. suggests that it reduced COVID-19 cases in states with low cumulative incidence [2] , yet education researchers worry that teachers will face lagging educational development of children once schools reopen due to the extended period of remote learning [11] . Our simulations with a single cohort indicate that a 5% percent threshold policy can shift infections in children from 80% to 55% over a 6 month period when child-to-child transmission rates in school are high ( Figure 3C ). doi = 10.1101/2020.08.05.20169086 id = cord-260402-9b1ltcf1 author = Lang, Adam Edward title = More Than Meets the Eye: The Similarities Between COVID-19 and Smoking date = 2020-08-11 keywords = SARS summary = To the Editor: Research shows that cigarette smoking upregulates ACE2, the receptor by which SARS-CoV-2 gains entry to the host resulting in COVID-19, in the lungs and therefore potentially leads to increased morbidity [1] . As part of a tobacco treatment campaign implemented at the beginning of the pandemic at McDonald Army Health Center, the authors performed a literature search and found that SARS-CoV-2 and smoking both contribute to myocarditis, thrombosis, immune impairment, and increased inflammation. SARS-CoV-2 and smoking upregulate this cytokine release and lead to an increased risk of coagulopathy [4, 5] . The upregulation of ACE2 in smokers may predispose this population to an increased risk of SARS-CoV-2 infection. The host cell transmembrane protease, serine 2 (TMPSRSS2), which primes the SAR-CoV-2 S protein for entry, may also be upregulated in smokers [6] , which would further increase the odds of viral infectivity. Smoking-Mediated Upregulation of the Androgen Pathway Leads to Increased SARS-CoV-2 Susceptibility doi = 10.1016/j.mayocp.2020.08.008 id = cord-308071-1bk3xuwf author = Lang, Christian title = Lung transplantation for COVID-19-associated acute respiratory distress syndrome in a PCR-positive patient date = 2020-08-25 keywords = SARS; lung; patient summary = Herein, we report the first case of lung transplantation for a patient with a persistently positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR test result. This decision was based on the following considerations: (1) virus culture was negative and real-time RT-PCR Ct values were high; (2) it was more than 5 weeks since the start of the SARS-CoV-2 infection; (3) no alternative treatment options were available; (4) the case was a single-organ failure in a young patient; (5) it was a preseptic condition originating from the lungs; and (6) there were no other obvious barriers for long-term recovery. To our knowledge, available evidence for lung transplant ation in COVID-19 is limited to two preliminary reports from China, suggesting that this treatment might be an option for SARS-CoV-2 PCR-negative patients. 11, 12 The case we present here extends the reports from China by showing that lung transplantation can be done in patients with positive RT-PCR results, provided that Vero cell cultures confirm non-infectivity. doi = 10.1016/s2213-2600(20)30361-1 id = cord-325958-1v1pg2z0 author = Lange, Clemens title = Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date = 2020-05-06 keywords = ACE2; RNA; SARS summary = In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. Since the outbreak, many studies described ACE2 expression across human tissues, including lung, stomach, ileum, colon, liver and kidney 8, 9 , supporting the clinical observation that SARS-CoV-2 can infect multiple organs. To obtain information on transcription of ACE2 and associated molecules required for cell entry by SARS-CoV-2, existing datasets of 38 conjunctival samples from 38 patients were included in this study. This study shows that ACE2, which is the main receptor for SARS-CoV-2 6 , is not significantly expressed in healthy and diseased human conjunctival samples. doi = 10.1002/jmv.25981 id = cord-343836-daqrym0b author = Lange, Clemens title = Welche Bedeutung hat die Bindehaut als möglicher Übertragungsweg für eine SARS-CoV-2-Infektion? date = 2020-06-22 keywords = ACE2; SARS summary = Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV‑2 via these mediators unlikely. Es ist derzeit nicht eindeutig geklärt, ob Zellen der Augenoberfläche ACE2 oder TMPRSS2 exprimieren und damit für eine SARS-CoV-2-Infektion anfällig sind. The current body of evidence indicates that SARS-CoV-2 requires the membrane-bound angiotensinconverting enzyme 2 (ACE2) and the membrane-bound serine protease TMPRSS2 to enter cells. Recent studies suggest that COVID-19 patients rarely exhibit viral RNA in tear film and conjunctival smears and that, ACE2 and TMPRSS2 are only expressed in very small amounts in the conjunctiva, making conjunctival infection with SARS-CoV-2 via these mediators unlikely. ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection doi = 10.1007/s00347-020-01150-1 id = cord-303692-py908dt8 author = Langley, Caroline title = Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement date = 2019-01-01 keywords = SARS; isg15 summary = title: Structure of interferon-stimulated gene product 15 (ISG15) from the bat species Myotis davidii and the impact of interdomain ISG15 interactions on viral protein engagement davidii ISG15, we use this protease as a biochemical tool; specifically, as a tool to illuminate the importance of the hydrophobic interdomain interface of ISG15 and how residue variation in this region between different species of ISG15s leads to biochemical differences in ISG15-protein engagement. With the exception of Pro38, which is a histidine residue in hISG15, all of these positions are conserved between bISG15 and the ISG15s from mice and humans. Taking the ITC data as a whole, the impact of mutations at Phe40 in bISG15 and its counterparts highlights the importance of ISG15 interdomain interactions in the effective binding of ISG15 by a protein that engages more than one domain of ISG15. doi = 10.1107/s2059798318015322 id = cord-331541-u0xm9a89 author = Lankes, Heather A title = Biospecimen Collection During the COVID-19 Pandemic: Considerations for Biobanking date = 2020-09-25 keywords = COVID-19; SARS; biospecimen summary = METHODS: Centers for Disease Control and Prevention and World Health Organization severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interim biosafety guidelines continue to be updated. Additional CDC SARS guidance recommended that laboratory personnel have a baseline serum sample collected prior to working with SARS-CoV biospecimens and stored for future reference. Testing of banked biospecimens collected in late 2019 may help define asymptomatic (or mildly symptomatic) circulation of SARS-CoV-2 prior to the presentation of severe cases in December; however, until a more accurate date is defined, use of October 1, 2019, as the start of the pandemic window is reasonable. Per CDC and WHO SARS-CoV-2 interim biosafety guidance 48, 49 and reported COVID-19 experience, 57 biobanks handling pandemic window biospecimens must: SARS-CoV-2 is the highly transmittable respiratory virus that causes COVID-19, a disease hallmarked by asymptomatic infection in some, and severe symptoms, including death, in others. doi = 10.1093/ajcp/aqaa171 id = cord-323394-osx7llte author = Lanser, Lukas title = Evaluating the clinical utility and sensitivity of SARS-CoV-2 antigen testing in relation to RT-PCR Ct values date = 2020-11-13 keywords = SARS summary = We compared the SARS-CoV-2 antigen detection in nasopharyngeal swab samples by the Panbio™ COVID-19 Ag Rapid test (Abbott, Chicago, Illionis) with the simultaneous routinely conducted RT-PCR analysis of SARS-CoV-2 orf1 RNA detection with the cobas ® analyzer (Roche Diagnostics GmbH, Mannheim, Germany). Among 51 RT-PCR SARS-CoV-2 positive patients, the Pan-bio™ COVID-19 Ag Rapid test was positive in 31 subjects depicting a poor sensitivity of 60.8% (95% CI 46.1-74.2%), compared to 93.3% in the manufacturer''s information. In the 14 patients with a Ct-value ≤ 25, being indicative for higher viral loads, the sensitivity for the Panbio™ COVID-19 Ag Rapid test was at a level of 85.7% (95% CI 57.2-98.2%, Table 1 ). Although our results are quite encouraging regarding the use of antigen test as point-of-care diagnostic which may contribute to a better control of the pandemic, we need longitudinal studied which larger patient cohorts to corroborate our results and to develop algorithms or to identify those subjects who are contagious but not detected by that test. doi = 10.1007/s15010-020-01542-0 id = cord-329877-vish6v8e author = Lapinsky, Stephen E. title = ICU management of severe acute respiratory syndrome date = 2003-05-09 keywords = SARS; patient; respiratory summary = BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ). doi = 10.1007/s00134-003-1821-0 id = cord-309091-te15ahvw author = Larson, Derek title = A Case of Early Re-infection with SARS-CoV-2 date = 2020-09-19 keywords = SARS summary = A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus doi = 10.1093/cid/ciaa1436 id = cord-326017-qw4qynqv author = Laskar, Partha title = “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date = 2020-08-06 keywords = COVID-19; China; CoV-2; Coronavirus; PCR; RNA; SARS; disease; patient summary = Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Overall, real-time RT-PCR based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against COVID-19 in clinical settings [39] . Another newly developed method, SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), was found to perform simultaneous reverse transcription and isothermal amplification by (i) RT-LAMP for RNA extracted (for nasopharyngeal or oropharyngeal swabs), (ii) Cas12 detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [56] . doi = 10.3390/diseases8030030 id = cord-274409-4ugdxbmy author = Laskar, Rezwanuzzaman title = Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date = 2020-10-19 keywords = Disease; SARS; site summary = title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India Further, constitution of ''Disease'' mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2. With a definitive possibility of India becoming the most affected country by SARS-CoV-2 in near future and the demographic burden involved, its pertinent to be analyze the accumulating variations in the genome accounting for possible changes in protein and their potential to alter the virus in any manner. Herein we extend our study using the same congregation of sequences to analyze the nature and composition of the observed mutations and their impact on proteins of SARS-CoV-2. The distribution of Disease and Neutral variants across the different genes of SARS-CoV-2 has been shown in Table 4 and Supplementary file 5. doi = 10.1101/2020.10.19.345066 id = cord-287156-3plpi6i9 author = Lassandro, Giuseppe title = Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date = 2020-07-01 keywords = COVID-19; East; MERS; Middle; SARS; respiratory summary = Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission doi = 10.4084/mjhid.2020.042 id = cord-349744-8cg5yj20 author = Lassaunière, Ria title = Evaluation of nine commercial SARS-CoV-2 immunoassays date = 2020-04-10 keywords = ELISA; SARS summary = The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. While the four POC tests evaluated according to illness duration were often weakly positive or detected only IgG or IgM during the early phase (data not shown), their sensitivities were comparable to the Wantai Total Ab ELISA and Euroimmun IgA ELISA in all three phases. In the present study, three SARS-CoV-2-specific commercial ELISA assays and six POC rapid tests were evaluated using sera from hospitalized adult patients with PCR-confirmed diagnoses for SARS-CoV-2 and a collection of control serum samples taken before the emergence of the virus in China in December 2019. Overall, the Wantai Total Ab ELISA had superior sensitivity and specificity compared to both Euroimmun IgA and IgG ELISAs. The POC tests varied notably, with the best performance observed for the test produced by AutoBio Diagnostics, followed by the tests produced by Dynamiker Biotechnology and CTK Biotech. doi = 10.1101/2020.04.09.20056325 id = cord-294704-prizmksg author = Lateef, Fatimah title = New paradigm for protection:: The emergency ambulance services in the time of severe acute respiratory syndrome date = 2004-06-16 keywords = EAS; SARS; Singapore summary = Severe acute respiratory syndrome (SARS) is a newly emerging and highly infectious form of atypical pneumonia with a high rate of transmission, especially among health care workers. With SARS, certain policies had to be implemented rapidly by the emergency ambulance services and the Ministry of Health to support and protect all personnel adequately. The authors hope to share their experience in the implementation of these strategies by the Singapore Civil Defence Force and stress the importance of the psychological preparedness of the paramedics and prehospital care providers worldwide in this era of SARS. To date, a total of seven probable and five suspected cases were conveyed by the EAS out of a total of 204 patients with SARS-like signs and symptoms. With the declaration of the SARS outbreak in Singapore, the Ministry of Health designated Tan Tock Seng Hospital (TTSH), one of the public hospitals, as the ''''SARS hospital.'''' All suspected and probable cases were sent and managed there. doi = 10.1016/j.prehos.2003.12.016 id = cord-257169-1lk737lw author = Lau, C. S. title = Performance of an automated chemiluminescence SARS-COV-2 IG-G Assay date = 2020-09-08 keywords = Abbott; COI; SARS summary = Methods We assessed assay precision, sensitivity, specificity, positive/negative predictive values (PPV/NPV), cross-reactivity (influenza/dengue/hepatitis B and C/rheumatoid factor/anti-nuclear/double-stranded DNA/syphilis) and sample throughput in samples from real-time polymerase chain reaction (RT-PCR) positive patients/healthcare workers (HCWs)/pre-pandemic samples. A lower COI limit for reactivity (≥0.55, using the 99th percentile COI of our controls and ROC analysis) improved diagnostic sensitivity, especially at 0-6 days POS (45.9% to 55.8%), with a small decrease in specificity (98.9%). We report on our evaluation of the Abbott Architect chemiluminescent immunoassay for SARS-CoV-2-IgG including deriving an optimised cut-off index that may be useful in testing early Covid-19 samples. An optimized COI limit for reactive samples (COI ≥0.55) (concordant values between 99th percentile of healthy controls and ROC analysis) improved the sensitivity of the assay in early infection (45.9% to 55.8% in subjects 0-6 days POS) but with a small decrease in specificity (99.8% to 98.9%). doi = 10.1016/j.cca.2020.09.005 id = cord-338054-n2r4pzan author = Lau, Joseph TF title = Anticipated and current preventive behaviors in response to an anticipated human-to-human H5N1 epidemic in the Hong Kong Chinese general population date = 2007-03-15 keywords = Hong; SARS summary = Respondents were asked how likely they would be to adopt the following preventive behaviors if a local human-to-human H5N1 outbreak (defined as "if 2-3 new human-to-human transmission of H5N1 cases were to be reported in Hong Kong") were to occur: face mask use in public venues, increased frequency of handwashing, avoidance of eating poultry, declaration of influenzalike illness (ILI) symptoms at border health checkpoints, the seeking of medical consultation immediately with the onset of a fever, face mask use in public venues when having ILI symptoms and compliance with any quarantine policies. Respondents were asked about perceptions related to human-to-human H5N1 transmission, including perceived modes of transmission (whether human-to-human transmission of the H5N1 virus could occur via respiratory droplets, bodily contact, contaminated objects, eating well-cooked poultry), perceived susceptibility to H5N1 in different groups of people (self, family members, children, adults, older people, health care workers, food handlers, food vendors and the general public), perceived chance of having a major outbreak in Hong Kong in the next 12 months and perceived efficacy of various prevention measures (quarantine of infected people, face mask use in public venues, frequent handwashing, home disinfection, mass extermination of poultry). doi = 10.1186/1471-2334-7-18 id = cord-270964-kxze0470 author = Lau, Kwok-Kwong title = Possible Central Nervous System Infection by SARS Coronavirus date = 2004-02-17 keywords = PCR; SARS summary = On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). In our patient, the occurrence of generalized convulsion with a positive RT-PCR for SARS-CoV in the CSF suggests possible infection of the central nervous system by SARS-CoV. The findings from our patient are not compatible with multiple sclerosis, and the PCR result suggests that the central nervous system (CNS) is affected by SARS-CoV. The possibility also remains that infection of the CNS never occurred, as suggested by the lack of focal neurologic deficit, normal CSF pressure, cell count, and biochemistry. Besides involvement of the lungs and possibly the CNS, no good alternative explanation exists for acute renal failure in this patient. Renal failure could possibly be caused by SARS-CoV involving the kidneys. Additionally, our patient had diarrhea from day 3 to day 20, with positive RT-PCR for SARS-CoV in stool specimens, suggesting involvement of the gastrointestinal tract as well. doi = 10.3201/eid1002.030638 id = cord-284702-reu77suz author = Lau, Suet-Ting title = Tachycardia amongst subjects recovering from severe acute respiratory syndrome (SARS) date = 2005-04-08 keywords = SARS summary = This study to identify the possible causes for the tachycardia excluded active disease, thyroid dysfunction, haematological, cardiac, autonomic and significant pulmonary defect at 2 months from onset of disease. Possible causes are deconditioning [2] , impaired pulmonary function, impaired cardiac function, cardiac arrhythmia, thyroid dysfunction, anaemia, autonomic dysfunction [3] and anxiety state. Chest radiography findings, haemoglobin level, length of hospital stay, time elapsed after discharge, presence of complications, WHO Quality of Life (QOL) score and Monitored Functional Task Evaluation (MFTE) score [4] are shown in Table 2 . Mild residual CXR changes, minor lung function impairment and normal blood gas makes pulmonary defect unlikely to be a significant cause of sinus tachycardia during normal activity. Deconditioning and anxiety state causes tachycardia in the daytime but not at night, and is compatible with the pattern observed in this cohort. In the absence of significant cardiac, pulmonary, thyroid and haematological dysfunction, we believe that sinus tachycardia is attributable to physical deconditioning and contributed by impaired psychological well-being. doi = 10.1016/j.ijcard.2004.06.022 id = cord-267587-hag6qydb author = Lau, Susanna K.P. title = Engineering Coronaviruses to Evaluate Emergence and Pathogenic Potential date = 2016-04-16 keywords = SARS; WNV summary = A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. A recent study provides a platform for generating infectious coronavirus genomes using sequence data, examining their capabilities of replicating in human cells and causing diseases in animal models, and evaluating therapeutics and vaccines. [1] and another similar study in Nature Medicine published in December 2015 by the same group [2] reported the use of existing sequence data with reverse genetics to engineer SARS-related CoVs and evaluate their potential of emergence and pathogenicity. In order to predict whether a SARS-related bat CoV, named WIV1-CoV, discovered in Chinese horseshoe bats in Yunnan [6] , had the potential to emerge in humans, Menachery et al. employed can be used for evaluating the emergence and pathogenic potential of other CoVs. Before the SARS epidemic, fewer than 10 CoVs with complete genome sequences were available. doi = 10.1016/j.tim.2016.04.001 id = cord-332557-qm3qfvry author = Lau, Susanna K.P. title = SARS Coronavirus Detection Methods date = 2005-07-17 keywords = SARS summary = Using clinical samples from patients with severe acute respiratory syndrome, we showed that the sensitivities of a quantitative reverse transcription–polymerase chain reaction (80% for fecal samples and 25% for urine samples) were higher than those of the polyclonal (50% and 5%) and monoclonal (35% and 8%) antibody-based nucleocapsid antigen capture enzyme-linked immunosorbent assays. Specimens were tested with polyclonal and monoclonal antibody-based capture ELISAs for SARS-CoV nucleocapsid protein and realtime qRT-PCR. Among the 40 fecal samples from SARS patients, 32 (80%) were positive by qRT-PCR, which was significantly higher than that of the polyclonal (50%) and monoclonal (35%) antibody-based ELISAs (McNemar test, p<0.005 and p<0.001, respectively). Of the 133 urine samples from SARS patients, 33 (25%) were positive by qRT-PCR, which was also significantly higher than that of the polyclonal (5%) and monoclonal (8%) antibody-based ELISAs (McNemar test, p<0.001 for both comparisons). doi = 10.3201/eid1107.041045 id = cord-270533-s2d3q4ob author = Lau, Yu-Lung title = SARS: future research and vaccine date = 2004-11-05 keywords = CoV; SARS; severe summary = Severe acute respiratory syndrome (SARS), a newly emerged infectious disease of humans in the 21st century, appeared in Guangdong Province in Southern China in November 2002 and spread to 26 countries on five continents along international air travel routes, causing large scale outbreaks in Hong Kong, Singapore and Toronto in early 2003. This novel CoV has satisfied Koch''s postulates for causation by its consistent isolation from SARS patients, viral isolation, reproduction of disease in non-human primates after inoculation and the presence of specific antibody response against the virus in both patients and experimentally infected primates 8 . Indeed, sporadic reemergence of cases have been reported in Guangdong Province as well as from research laboratories Summary Severe acute respiratory syndrome (SARS) is a new infectious disease of the 21st century that has pandemic potential. The high morbidity and mortality of this potentially pandemic infection demands a rapid research response to develop effective antiviral treatment and vaccine. doi = 10.1016/j.prrv.2004.07.005 id = cord-274707-mxh38hwd author = Laureano, Ana Flávia Santarine title = The different tests for the diagnosis of COVID-19 - A review in Brazil so far date = 2020 keywords = COVID-19; PCR; SARS; dna summary = The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor''s Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis doi = 10.5935/1518-0557.20200046 id = cord-283779-mudwcypl author = Lauretani, Fulvio title = Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date = 2020-05-11 keywords = ARDS; COVID-19; SARS; clinical; infection; old; patient; phase summary = The chronic increase in inflammatory cytokines, augmented by COVID-19 infection, may explain the higher tendency for "the cascade leading to pulmonary fibrosis and insufficiency and activation of clotting" and poorer clinical prognosis, especially in multimorbid older persons (4) . In case of persistent fever, higher than 37.5°C for a time longer than 3 days and peripheral oxygen level lower than 95% after starting therapy, we should consider and proceed to hospitalization especially in multimorbid older patients with cardiac, respiratory diseases and diabetes. First, patients at risk for poor outcomes and higher mortality following infection with SARS-CoV-2, namely older adults and multimorbid individuals, should be checked for malnutrition through screening and assessment. Older patients infected by COVID-19 often experience atypical and less severe symptoms in older persons, side-effects of the drugs and require specific nutritional and motor treatment for avoiding disability and death. doi = 10.23750/abm.v91i2.9629 id = cord-270510-z6qg48nz author = Lauro, A. title = Emergency Endoscopy During the SARS-CoV-2 Pandemic in the North of Italy: Experience from St. Orsola University Hospital—Bologna date = 2020-04-22 keywords = SARS; endoscopy summary = We report our experience with emergency endoscopies in the COVID-19 era; the goal was to sustain a full emergency endoscopic capability despite the hospital overload due to SARS-CoV-2-infected patients. Instead, emergency endoscopies were performed on SARS-CoV-2-negative and positive patients; a negative-pressure room outside the endoscopy department was planned, but, at the beginning of the pandemic, the only practical possibility was to create a separate suite for SARS-CoV-2-positive patients needing Editor''s Note: This report is one of a series documenting the impact of the pandemic caused by the SARS-CoV-2 virus with resultant morbidity and mortality due to COVID-19. In our hospital, trainees are essential to the management of the burden among patients infected by SARS-CoV-2, but, regarding endoscopy, our policy was to stop training in the urgent endoscopy suite in order to reduce the numbers of inside operators and their use of PPE. doi = 10.1007/s10620-020-06270-x id = cord-324752-t50bg7pq author = Lavery, Michael Joseph title = Cutaneous manifestations of COVID-19 in children (and adults): A virus that does not discriminate date = 2020-11-01 keywords = COVID-19; SARS; child summary = COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a beta coronavirus with a characteristic S-glycoprotein ''spike'' on the cell surface.(1) Initial reports did not include cutaneous manifestations as a feature of COVID-19; however, there is a growing repertoire of reports demonstrating an array of dermatologic manifestations on the skin in children and adults. Dermatologic afflictions have been summarized into different categories several times, with the most recent analysis identifying six clinical patterns: urticaria, maculopapular-morbilliform eruption, papulovesicular exanthem, chilblain-like acral pattern, livedo reticularis-livedo racemose pattern, and purpuric ''vasculitic'' pattern.(2) In children, the dermatologic features appear to occur before or concomitantly with other COVID-19 manifestations. 24 Recently, nail changes have been identified in patients with COVID-19 manifesting as a convex half-moon shaped erythematous band at the distal margin of the lunula and coined ''the red half-moon nail sign.'' 25, 26 In the United Kingdom (UK), researchers analyzed data from users of the COVID Symptom Study application and noted 8.8% of 336,847 users, with a positive SARS-CoV-2 viral swab, reported a skin eruption. doi = 10.1016/j.clindermatol.2020.10.020 id = cord-302902-34vftqt9 author = Law, Brenda Hiu Yan title = Effect of COVID-19 Precautions on Neonatal Resuscitation Practice: A Balance Between Healthcare Provider Safety, Infection Control, and Effective Neonatal Care date = 2020-08-18 keywords = PPE; SARS; covid-19 summary = Adaptations have been proposed for resuscitation of infants born to women with COVID-19, to protect health care providers, maintain infection control, and limit post-natal transmission. Changes especially impact respiratory procedures, personal protective equipment (PPE) use, resuscitation environments, teamwork, and family involvement. Adaptations have been proposed for resuscitation of infants born to women with suspected or confirmed COVID-19, to protect health care providers (HCPs), limit post-natal transmission, and maintain infection control (7) . Neonatal resuscitation may be especially impacted by changes in (i) respiratory support, (ii) personal protective equipment (PPE), (iii) resuscitation environment, (iv) team-based activities, and (v) family involvement ( Table 1) . Modifications to ventilation practices during neonatal resuscitation have been proposed to protect HCPs during AGPs, based on limited evidence on vertical transmission and aerosolization of SARS-CoV-2 (7, 9) . General COVID-19 resuscitation guidelines recommend the use of viral filters on mask ventilation devices to decrease risks to HCPs (9) . doi = 10.3389/fped.2020.00478 id = cord-296602-19noki6p author = Law, Helen KW title = Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells date = 2009-06-08 keywords = CoV; SARS; TRAIL summary = In this study, we focussed on the gene expression of toll-like receptors (TLRs), chemokine receptors (CCRs) and death receptor ligands in SARS-CoV infected DCs. We also compared adult and cord blood (CB) DCs to find a possible explanation for the age-dependent severity of SARS. There was also strong induction of TNF-related apoptosis-inducing ligand (TRAIL), but not Fas ligand gene expression in SARS-CoV infected DCs. Interestingly, the expressions of most genes studied were higher in CB DCs than adult DCs. CONCLUSION: The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. Interestingly, the SARS-CoV infected DCs showed low expression of antiviral cytokines (IFN-α, IFN-β, IFN-γ and IL-12p40), moderate upregulation of proinflammatory cytokines (TNF-α and IL-6) but significant upregulation of inflammatory chemokines (macrophage inflammatory protein (MIP)-1α/CCL3, regulated upon activation, normal T cell expressed and secreted (RANTES)/CCL-5, interferon-inducible protein of 10 kD (IP-10)/CXCL10 and monocyte chemotactic protein (MCP)-1/CCL2. doi = 10.1186/1471-2172-10-35 id = cord-299308-gza1pwx6 author = Laxminarayan, Ramanan title = Is Gradual and Controlled Approach to Herd Protection a Valid Strategy to Curb the COVID-19 Pandemic? date = 2020-05-06 keywords = COVID-19; SARS summary = Most pandemics in the twentieth and twentyfirst centuries have been caused by virusesinfluenza, chikungunya, HIV/AIDS and now the coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients reportedly acquire COVID-19 either through close contact with infected family members (89%), exposure to endemic areas (33%), or both (22%); with the majority (53%) showing moderate symptoms and no severe or critical cases [2] . We do not endorse the idea of letting the epidemic a free hand in order to create sufficient herd immunity to end the epidemic;as it would entail an enormous burden on the healthcare system -United Kingdom, at first, considered a different approach -of unrestricted spread of disease without any brakes applied, but public health experts were able to convince the government to accept the more reasonable mitigation approach. The proportion of the population that should be exposed to the virus for herd immunity to be effective is calculated as 1-1/Ro. In the absence of serological studies, the true extent of spread of SARS-COV-2 in India is unknown. doi = 10.1007/s13312-020-1844-4 id = cord-316712-1ngcwdln author = Laxminarayan, Ramanan title = India’s Battle against COVID-19: Progress and Challenges date = 2020-08-24 keywords = COVID-19; India; SARS summary = The first reported case of infection with the SARS-CoV-2, the virus that causes COVID-19, in India was reported on January 30, 2020 in an Indian student evacuated from Wuhan, and the first death was reported on March 12, 2020. Model-based estimates 8 produced in March 2020 had indicated that a national lockdown could reduce the number of infections at the peak of the pandemic-expected in early May-by 70-80%, depending on the degree of public compliance with physical distancing. Mortality rates (based on reported cases and deaths) appear to be low in India, as they are in most countries in the region, perhaps indicative of both limited testing and other unexplained factors. 12 At the current time, India has conducted approximately 18,000 tests per million population, a rate that is a third that of South Africa, about 60% that of Nepal, and among the lowest of any large country. doi = 10.4269/ajtmh.20-0992 id = cord-308740-06jr58kz author = Lazaridis, Charalampos title = Involvement of Cardiovascular System As The Critical Point in Coronavirus Disease 2019 (COVID-19) Prognosis and Recovery date = 2020-06-10 keywords = ACE2; COVID-19; SARS summary = All cases were linked to a seafood market in the same city 2 and were confirmed to be associated with a novel RNA betacoronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3,4 . A recent study in patients with heart failure found that circulating levels of ACE2 were higher in men than in women, suggesting increased ACE2 tissue expression which could contribute to susceptibility to SARS-CoV-2 infection and disease progress 49 . Remarkably, severe COVID-19 has been associated with hypokalemia and higher blood pressure, supporting suggestions of decreased ACE2 function and augmented levels of angiotensin II after SARS-CoV-2 infection 96 . The participation of ACE2 in the pathogenesis of COVID-19, acting as a cell receptor for SARS-CoV-2 13 has caused increasing concern about the role of antihypertensive therapy with angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II Chloroquine, an antimalarial agent with known anti-viral effects 141 Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan doi = 10.1016/j.hjc.2020.05.004 id = cord-023488-jf2xl3vl author = Le Duc, James W. title = Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date = 2016-02-12 keywords = Africa; Ebola; SARS; disease; human; virus summary = doi = 10.1016/b978-0-12-800964-2.00016-1 id = cord-304418-k9owyolj author = Le Maréchal, M. title = COVID-19 in clinical practice: a narrative synthesis date = 2020-09-29 keywords = COVID-19; China; CoV-2; SARS; Wuhan; patient summary = Plasmatic detection of SARS-CoV-2 has been reported but only with low viral titers, and mainly in clinically severe cases [44] ; bloodstream infectivity has yet to be demonstrated. The first large clinical trial published on LPV/RTV on SARS-CoV-2 compared 99 patients receiving the antiviral vs 100 receiving SoC alone [124] ; there was no difference between the 2 groups regarding the primary end point (time to improvement) (15 vs 16 days, p=0.09). Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China doi = 10.1016/j.medmal.2020.09.012 id = cord-349794-mhviub6e author = Le, Brian L. title = Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date = 2020-10-23 keywords = COVID-19; SARS; drug; signature summary = We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. By infecting human adenocarcinomic alveolar basal epithelial cells with SARS-CoV-2 and comparing to controls, the authors generated a list of 120 differentially expressed genes. Here, we applied our existing computational drug repositioning pipeline to identify drug profiles with significantly reversed differential gene expression compared to predicted inhibitors (including one tested in Calu-3) were incubated with SARS-CoV-2 infected human embryonic kidney 293T cells overexpressing ACE2 (293T-ACE2) with viral replication determined using an immunofluorescence-based assay. In this study, we applied our drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available RNA-seq data ( Figure 1 ). Here, we used a transcriptomics-based drug repositioning pipeline to predict therapeutic drug hits for three different input SARS-CoV-2 signatures, each of which came from distinct human cell or tissue origins. doi = 10.1101/2020.10.23.352666 id = cord-259558-remrzrq1 author = LeBlanc, Jason J. title = A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2 date = 2020-05-16 keywords = SARS summary = Low viral loads are known to occur in the early and late stages of COVID-19 illness [4] [5] [6] [11] [12] [13] [14] [15] [16] [17] [18] [19] , and false negative results can arise from differences in analytical sensitivity between methods (Table S1 ) [20, 21] , the variability in specimen collection, or factors influencing specimen stability or recovery of SARS-CoV-2 RNA during specimen transport, storage or processing. [4, 13] For example, three different SARS-CoV-2 targets were detected between the various PCR methods used for testing of J o u r n a l P r e -p r o o f specimens from patient 1, yet high Ct values were observed for these targets (Table 1) . doi = 10.1016/j.jcv.2020.104442 id = cord-255069-9xueqdri author = Leary, Shay title = Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date = 2020-04-11 keywords = HLA; SARS summary = The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . doi = 10.1101/2020.04.10.029454 id = cord-316646-rd3zl9qz author = Lebedin, Y. S. title = Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia date = 2020-09-25 keywords = SARS summary = The article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia In this report, we evaluate the SARS-CoV-2 nucleocapsid antigen (N-Ag) and respective antibodies as diagnostic markers and demonstrate the total prevalence of N-Ag seroconversion in SARS-CoV-2-associated pneumonia patients. The immunoassay-based detection of serum N-Ag in combination with its respective antibodies confirmed COVID-19 in 280 patients (59%) of the studied cohort. The results indicate high relevance of combined serological tests for SARS-CoV-2 N-Ag and the antibodies to SARS-CoV-2 antigens as applied to the infectious pneumonia emergency patients at the admission, since: According to the results of the study, hospitalization of the patients with SARS-CoV-2associated pneumonia at the height of pandemic most frequently occurred before the onset of seroconversion (i.e. against the background of detectable serum N-Ag concentrations). doi = 10.1101/2020.09.24.20200303 id = cord-324557-4u8dja0n author = Leblanc, Jean‐François title = Risk of Transmission of Severe Acute Respiratory Syndrome Coronavirus‐2 by Transfusion: A Literature Review date = 2020-08-15 keywords = COVID-19; CoV-2; SARS summary = Complementary searches have identified reports demonstrating that the correlation between the presence of viral RNA in a biological sample and infectivity requires a minimal RNA load, which is rarely, if at all observed, in blood components. More specifically, PubMed was interrogated with a series of queries aimed at identifying references that relate to COVID-19/SARS-CoV-2 and the detection of viral genomic material in blood, plasma, or serum. From this screen, 23 references reporting any data or stating any information on the detection of SARS-CoV-2 genomic material in human blood, plasma, or serum, were selected ( Table 2) . An exhaustive search strategy led to the identification of 23 references reporting data on the detection of SARS-CoV-2 genomic material in blood components (Table 2) . doi = 10.1111/trf.16056 id = cord-304031-poh3te9j author = Leder, K. title = Respiratory infections during air travel date = 2005-01-13 keywords = SARS; air summary = Issues regarding cabin air quality and the potential risks of transmission of respiratory infections during flight have been investigated and debated previously, but, with the advent of severe acute respiratory syndrome and influenza outbreaks, these issues have recently taken on heightened importance. Confined space, limited ventilation, prolonged exposure times and recirculating air, all common to air travel, are demonstrated risk factors for the transmission of upper respiratory tract infections in other settings and create the potential for the spread of respiratory pathogens during flight. Aspects of the aircraft cabin environment that influence the potential transmission of respiratory pathogens on airplanes will be outlined here and then the Internal Medicine Journal 2005; 35: 50-55 evidence for the occurrence of outbreaks of respiratory illness among airline passengers will be reviewed. The majority of patients (68%) had recently completed a series of commercial aircraft flights, and the authors concluded that air travel played a role in the transmission of disease among the 60 infected persons. doi = 10.1111/j.1445-5994.2004.00696.x id = cord-263719-a9mnjr3s author = Lee, A. title = Wuhan novel coronavirus (COVID-19): why global control is challenging? date = 2020-02-29 keywords = SARS; health summary = At this stage, the global spread of COVID-19 acute respiratory disease continues to grow, and the full extent and severity of this outbreak remains to be seen. 7 Once the pathogen has landed in a new country, the likelihood of contagion and spread is dependent on local transmission pathways and the strength of local health protection systems. 8 High-income countries such as the United States and United Kingdom have well-developed health protection systems to detect and respond to communicable disease threats. The other component of well-developed health protection systems are strong infectious disease surveillance systems. The current concerns then regarding the 2019-nCoV outbreak must be for low-and middle-income countries where health protection systems tend to be weaker. In these settings, laboratory resources may be lacking, notification of infectious diseases are often not timely or complete, and their public health infrastructure is often weak. Global infectious disease surveillance and health intelligence doi = 10.1016/j.puhe.2020.02.001 id = cord-274521-u8p5lz9o author = Lee, Abby C. title = Tobacco, but Not Nicotine and Flavor-Less Electronic Cigarettes, Induces ACE2 and Immune Dysregulation date = 2020-07-31 keywords = ACE2; SARS; covid-19 summary = In this study, we mined three independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. Both smoking and use of nicotine and flavor-containing e-cigs led to upregulation of pro-inflammatory cytokines and inflammasome-related genes. Current data indicate that patients who have cardiovascular and chronic respiratory conditions, including those caused by tobacco use, are at higher risk of developing severe COVID-19 symptoms and have significantly increased fatality [1] . The GSE138326 dataset, from Song et al., details gene expression in the bronchial epithelial cells of patients who smoked flavor-less and nicotine-less e-cigs vs. The GSE112073 dataset, from Corbett et al., details gene expression in bronchial cells of patients who smoked nicotine-containing e-cigs of any flavor vs. The upregulation of a significant number of inflammatory cytokines in smokers and nicotine/flavor-containing e-cig users and the association of smoking with IL-1B prompted us to examine inflammasome activation in smokers and e-cig users ( Table 2 ). doi = 10.3390/ijms21155513 id = cord-279105-e2zjxjox author = Lee, Cheryl Yi-Pin title = Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control date = 2020-04-24 keywords = CoV-2; SARS; antibody summary = With the limitations of qRT-PCR, immunoassays may offer another FIGURE 2 | Schematic illustration on the window period of detection for either viral RNA or antibodies in SARS-CoV-2-infected individuals. However, interestingly, one study demonstrated that longitudinal profiling of both antibodies in a population of 63 COVID-19 patients showed no specific chronological order in terms of IgM and IgG seroconversion (10) , which was also observed in patients infected with SARS-CoV and another human coronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV) (22, 23) . These findings on SARS-CoV-2-specific antibodies seroconversion against the S viral protein suggest the importance to test for both IgM and IgG antibodies to confirm a positive infection. With the availability of immunoassays utilizing various coronavirus structural proteins, the use of more than one different antigen-based serological approach may be essential to establish a true positive SARS-CoV-2 infection. doi = 10.3389/fimmu.2020.00879 id = cord-293826-2p7dqacd author = Lee, Cheryl Yi-Pin title = Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date = 2020-10-09 keywords = SARS summary = Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. Overall, our study shows that the D614G mutation on the S protein does not 150 impact SARS-CoV-2 neutralization by the host antibody response, nor confer viral 151 resistance against the humoral immunity. doi = 10.1101/2020.10.08.332544 id = cord-284028-l0r7f9sr author = Lee, Chi-Wei title = A loophole in international quarantine procedures disclosed during the SARS crisis date = 2004-12-30 keywords = Hong; Kong; SARS summary = This phenomenon revealed a loophole in the control mechanisms of international quarantine procedures, letting travelers carrying a highly contagious virus slip by undetected and causing possible multi-country outbreaks of communicable diseases. Reasons for its rapid global spread were the highly contagious nature of the virus with its air-borne route of infection, the busy links between affected countries, and probably inadequacies in international quarantine procedures. As shown in Tables 1 and 2, although none of the six patients were eventually diagnosed wild SARS, this observed phenomenon disclosed a very important loophole in the control aspect of international quarantine procedures: the inability to prevent persons with a highly contagious virus from slipping past undetected and thus preventing the further spread of epidemics like SARS on international travel routes. In this study, we identified that there were loopholes in the international quarantine system for controlling the international spread of contagious disease like SARS, especially when travelers lack a strong motivation to cooperate with national health authorities. doi = 10.1016/j.tmaid.2004.10.002 id = cord-338723-3vm23fgy author = Lee, In-Hee title = A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date = 2020-08-26 keywords = ACE2; SARS; TMPRSS2 summary = title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. SARS-CoV-2 is an enveloped and positive single-stranded RNA (ssRNA) virus and initiates human cell entry by binding of spike (S) protein present on the viral envelope to angiotensin converting enzyme 2 (ACE2) receptor on the host cells (Zhou et al., 2020b) . Here we surveyed the genetic variants in functional residues of ACE2, TMPRSS2, CTSB/L (CatB/L), and TLR3/7/8 to investigate the difference in the genetic predisposition to the susceptibly of SARS-CoV-2 infection and the initiation of innate immune response. The list of reported genetic variants in the genes and their allele frequencies (AFs) were ACE2 is highly conserved with few nonsynonymous variants in the interacting domain with the SARS-CoV-2 RBM (Lan et al., 2020) . doi = 10.1016/j.meegid.2020.104507 id = cord-332071-bqvn3ceq author = Lee, Jeong Seok title = Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 date = 2020-07-10 keywords = Fig; IFN; SARS; TNF; covid-19 summary = In a murine model of SARS-CoV infection, a delayed, but considerable type I IFN (IFN-I) response CORONAVIRUS Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19 (Page numbers not final at time of first release) 2 promotes the accumulation of monocytes-macrophages and the production of pro-inflammatory cytokines, resulting in lethal pneumonia with vascular leakage and impaired virusspecific T-cell responses (10) . To examine the host immune responses in a cell type-specific manner, we subjected 59,572 cells to t-distributed stochastic neighbor embedding (tSNE) based on highly variable genes using the Seurat package (17) and identified 22 different clusters unbiased by patients or experimental batches of scRNA-seq (Fig. 1A, Fig. S1D ). First, we combined both mild and severe COVID-19 as a COVID-19 group and identified disease-specific changes in genes for each cell type compared to the healthy donor group using model-based analysis of single cell transcriptomics (MAST) (18) . doi = 10.1126/sciimmunol.abd1554 id = cord-258360-fqrn02lr author = Lee, Jimmy title = No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date = 2020-06-19 keywords = SARS summary = In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ''upstream'' market chain samples suggests that these detections in ''downstream'' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. Our negative findings across five viral families associated with emerging and re-emerging zoonotic diseases in recent decades contrast with reports of the detection of parainfluenza virus (Wang et al., 2018) , coronaviruses and Sendai virus (Liu et al., 2019; Zhang et al., 2020) , and SARSr-CoVs (Lam et al., 2020; Xiao et al., 2020) in Sunda pangolins. We therefore conclude that the detections of SARS-CoV-2 related viruses in pangolins are more plausibly a result of their exposure to infected people, wildlife or other animals after they entered the trade network. doi = 10.1101/2020.06.19.158717 id = cord-266903-lxtxqdst author = Lee, Jong-Hwan title = A novel rapid detection for SARS-CoV-2 spike 1 antigens using human angiotensin converting enzyme 2 (ACE2) date = 2020-10-15 keywords = SARS summary = In this study, we designed and developed a novel rapid detection method for SARS-CoV-2 spike 1 (S1) protein using the SARS-CoV-2 receptor ACE2, which can form matched pairs with commercially available antibodies. ACE2 and S1-mAb were paired with each other for capture and detection in a lateral flow immunoassay (LFIA) that did not cross-react with SARS-CoV Spike 1 or MERS-CoV Spike 1 protein. To decrease the non-specific interaction between capture probes in test lines and 20 detection probes, the nitrocellulose membrane was treated with the blocking solution (10 mM 2-21 amino-2-methyl-1-propanol (pH 9.0), 0.5% BSA, 0.5% β-Lactose, 0.05% Triton X-100, 0.05% 22 sodium azide) for 1 hour in a vacuum oven (37°C). -The human ACE2 and commercial antibody were paired with each other as capture and detection probes in a lateral flow immunoassay that was not cross-reactive with SARS-CoV S1 and MERS-CoV S1 proteins. doi = 10.1016/j.bios.2020.112715 id = cord-333929-oprpgcyr author = Lee, Justin title = Impact of Severe Acute Respiratory Syndrome on Patient Access to Palliative Radiation Therapy date = 2005-01-31 keywords = SARS summary = Abstract This study evaluated the impact of the severe acute respiratory syndrome (SARS) epidemic on access and utilization of palliative radiation therapy (RT) at a single institution using a retrospective chart review. 2, 3 Recent studies have demonstrated the negative impact of the SARS epidemic on access to health care services such as emergency room visits, cardiac surgery, lumpectomy/mastectomy, and chemotherapy procedures. The primary objective of the study was to identify any significant change in the number of patients seen and/or treated by the Rapid Response Radiotherapy Program (RRRP) at our center. A retrospective chart review was used to evaluate all patients who attended the RRRP at the Toronto Sunnybrook Regional Cancer Centre between January 1 and May 31, 2002, and the same time period in 2003. There was a significant decrease in the waiting times of patients seen during the SARS epidemic compared with the previous year ( Table 3 ). doi = 10.3816/sct.2005.n.004 id = cord-287742-y1j9x5ne author = Lee, Kai Wei title = Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis date = 2020-10-06 keywords = COVID-19; SARS; patient; stroke; study summary = Therefore, we performed a systematic review and meta-analysis of currently available epidemiological, clinical, and laboratory data related to both stroke and COVID-19 infection. We, therefore, performed a systematic review and metaanalysis involving the epidemiological, clinical presentation, imaging characteristics, and laboratory finding related to both stroke and COVID-19 infection. The following data were extracted from every study: the last name of the first author, year of publication, country, severity status, study design, patient characteristics (ethnicity composition, gender, and mean age), comorbidities (diabetes, hyperlipidemia, hypertension, ischemic heart disease, heart failure, previous stroke, chronic kidney disease/end-stage renal disease, number of stroke patients per overall participants, any information relevant to strokes such as the location of stroke [arterial or venous]), types of stroke (ischemic or haemorrhagic), classification of stroke, mortality rate, and blood parameters. The aim of this current study is to perform a systematic review and meta-analysis concerning the epidemiological, clinical presentation, imaging characteristics, and laboratory findings related to both stroke and COVID-19 infection. doi = 10.3389/fneur.2020.579070 id = cord-330583-ltkpt80u author = Lee, Kyu-Myoung title = Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date = 2019-04-22 keywords = Korea; MERS; SARS; factor; response summary = Following the 2003 the severe acute respiratory syndrome (SARS) and the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to explore and examine the factors influencing the response to infectious diseases, which encompasses both communicable and non-communicable diseases. As the results conducted meta-analyses to comprehensively analyze the correlations of factors influencing disaster response from a Korean context, the findings show that the legislative factor had direct and indirect influence on the overall process of infectious disease response and that Leadership of the central government, establishment of an intergovernmental response system, the need for communication, information sharing and disclosure and onsite response were identified as key factors influencing effective infectious disease response. However, there is also need for comprehensive discussions that include the establishment of laws; regulations; resources; information on infectious disease response from administrative and policy perspectives; information sharing system; and the establishment of an international cooperation system and national response system involving the central government, the regional government, private organizations and the public for effective response when an actual infectious disease outbreak occurs. doi = 10.3390/ijerph16081432 id = cord-325070-583innd7 author = Lee, Lennard Y.W. title = Utility of COVID-19 Screening in Cancer Patients date = 2020-07-24 keywords = SARS summary = We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care in the era of COVID-19. Patients with cancer are at increased risk of contracting SARS-CoV-2 and have a high mortality rate from COVID-19 (Lee et al., 2020) . A number of national and international cancer guidelines now advise the screening of every patient undergoing chemotherapy to enable early identification and isolation of patients with asymptomatic SARS-CoV-2 infections to prevent hospital transmission (https://www.idsociety.org/practice-guideline/covid-19-guidelinediagnostics/; https://www.rcr.ac.uk/sites/default/files/guidance-covid19-testing-asymptomatic-hcw-patientsoncology.pdf; https://www.asco.org/sites/new-www.asco.org/files/content-files/2020-ASCO-Guide-Cancer-COVID19.pdf). Our cohort demonstrates that uptake for screening of SARS-CoV-2 through nasopharyngeal testing is high in cancer patients. We conclude that where the incidence of asymptomatic infection is low and patients can be identified early, screening enables the confidence to safely deliver effective cancer care; this will be monitored as the pandemic evolves. Screening for COVID-19 in asymptomatic patients with cancer in a hospital in the United Arab Emirates doi = 10.1016/j.ccell.2020.07.009 id = cord-308142-3x3n6cpt author = Lee, Nelson title = Chikungunya Fever, Hong Kong date = 2006-11-17 keywords = IFN; SARS summary = aureus isolated from active lesions were not available for testing, the recovery of identical PVL-positive organisms from nasal cultures strongly suggests the presence of a pathogenic clone that probably caused the recurrent infections in the 6 affected family members. Serum specimens taken on days 2 and 6 were positive for chikungunya virus RNA by in-house reverse transcription (RT)-PCR at the Public Health Laboratory Service (PHLS) (targeting the nonstructural protein-1 [NSP-1] gene) and PWH laboratory (targeting both NSP-1 and the envelope glycoprotein [E1] gene). The most striking finding from the cytokine analysis (Table) is the high level of interferon-γ (IFN-γ)-inducible protein-10 (IP-10/CXCL-10), up to 26 and 16 times the upper limit of the normal range at days 2 and 6 after disease onset, respectively. In severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (4, 5) and H5N1 influenza (6) infections, very high blood levels of CXCL10 and moderately high CCL2, CXCL9, and CXCL8 concentrations, or their enhanced expressions in vitro, have been reported. doi = 10.3201/eid1211.060574 id = cord-334628-axon4jdc author = Lee, Saemi title = Genetic Characteristics of Coronaviruses from Korean Bats in 2016 date = 2017-07-19 keywords = Bat; MERS; SARS summary = In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. Given the import of MERS into South Korea [14] and the presence of SARS in the relatively close geographic location of China [9] (Fig. 3) , together with the fact that bats are a reservoir for coronaviruses, the prevalence of coronavirus infection in Korean bat species should provide valuable information. Oral swabs and other samples (n = 60) were obtained from three species of bats, Rhinolophus ferrumequinum, Miniopterus schreibersii, and Myotis macrodactylus, but coronaviruses were only detected in samples from R. Thirteen sequences from oral swabs were clustered with Bat-CoV B15-21, which was detected in fecal bat samples collected from an abandoned mine in Gangwon province. doi = 10.1007/s00248-017-1033-8 id = cord-333606-5z3kumu9 author = Lee, SangJoon title = Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines date = 2020-10-15 keywords = MERS; SARS summary = title: Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. Despite these limitations, significant work has been done to molecularly characterize the innate immune pathways involved in detecting and controlling CoV infections. patients with severe or critical COVID-19 also found that reduced amounts of type I IFNs in the blood during SARS-CoV-2 infection were associated with increased viral load in the blood, and exacerbation of the inflammatory response [38] . Pyroptosis and necroptosis are similar in that they are lytic forms of cell death driven by the GSDMD pore and MLKL channel, respectively, that release proinflammatory cytokines and other cellular factors to alert the surrounding cells of danger and to recruit innate and adaptive inflammatory cells [54, 55].  Specific CoV infections can activate inflammatory cell death (PANoptosis), thereby inducing cytokine release. doi = 10.1016/j.it.2020.10.005 id = cord-341502-jlzufa28 author = Lee, Sungyul title = The SARS-CoV-2 RNA interactome date = 2020-11-02 keywords = OC43; Probe; RNA; RNP; SARS; figure summary = The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). doi = 10.1101/2020.11.02.364497 id = cord-286537-7ri2p5b8 author = Lee, Ting-Wai title = Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide date = 2005-11-11 keywords = SARS; ape; pro summary = authors: Lee, Ting-Wai; Cherney, Maia M.; Huitema, Carly; Liu, Jie; James, Karen Ellis; Powers, James C.; Eltis, Lindsay D.; James, Michael N.G. title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide The crystal structures of the Mpro:APE complex in the space groups C2 and P212121 revealed the formation of a covalent bond between the catalytic Cys145 Sγ atom of the peptidase and the epoxide C3 atom of the inhibitor, substantiating the mode of action of this class of cysteine-peptidase inhibitors. In contrast, in protomer A of the M pro CAðK1Þ :APE complex, the benzyl group of APE squeezes into and thereby widens the S4 specificity pocket of the peptidase, so that it is snugly accommodated in this enlarged pocket now formed by the residues 165 to 168, Phe185, Gln192 and the main-chain atoms of Val186 (Figures 3(b) and 4(c)). doi = 10.1016/j.jmb.2005.09.004 id = cord-339019-vgnxhksv author = Lee, Ting-Wai title = Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase date = 2007-02-23 keywords = A(-1; SARS; ape summary = We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M+A(-1) pro), both at a resolution of 2.00 Å, in space group P43212: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). 25 We have now grown crystals of M pro in the same space group (P2 1 with the same unit-cell constants) at pH 6.0 under slightly different conditions; the active sites and the S1 specificity pockets of both protomers are in the catalytically competent conformation (Figures 2(a) and (b), 3(a) and (b), 4(a) and (b)). Active sites and substrate-binding regions of the unbound SARS-CoV M +A(-1) pro We have reported the crystal structure of the SARS-CoV M +A (-1) pro :APE complex in space group P2 1 2 1 2 1 , whose asymmetric unit contains both protomers of the M +A(-1) pro dimer. doi = 10.1016/j.jmb.2006.11.078 id = cord-267744-asjvf123 author = Lee, Yu-Ching title = Chicken single-chain variable fragments against the SARS-CoV spike protein date = 2007-07-23 keywords = SARS; antibody summary = Following the immunization of chickens with these recombinant spike proteins, two single-chain variable fragment (scFv) antibody libraries were established with short or long linkers to contain 5 × 10(7) and 9 × 10(6) transformants, respectively. In a comparison of nucleotide sequences with the chicken germline gene, we found that all clones varied in the complementarity-determining regions, that two scFv antibodies reacted significantly with SARS-CoV-infected Vero cells, and that those two specific scFv antibodies recognized the same region of the spike protein spanning amino acid residues 750–1000. The current study aimed to show that monoclonal IgY scFv antibodies which bind specifically to the S protein and SARS-CoV-infected Vero cells can be isolated from chickens immunized with Escherichia coli-derived S proteins. Cellular lysates containing single-chain variable fragment (scFv) antibodies from various Ssc (A) and Lsc (B) library clones were examined for their binding to SARS-CoV-infected cell lysates using a commercially available kit. doi = 10.1016/j.jviromet.2007.06.010 id = cord-308123-eu0azqfu author = Lee, Yun Young title = Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm date = 2020-10-23 keywords = COVID-19; DNase-1; Fig; SARS summary = title: Long-acting nanoparticulate DNase-1 for effective suppression of SARS-CoV-2-mediated neutrophil activities and cytokine storm Our findings suggest that exogenously administered long-acting nanoparticulate DNase-1 can effectively reduce cfDNA levels and neutrophil activities and may be used as a potential therapeutic intervention for life-threatening SARS-CoV-2-mediated illnesses. We showed that an intravenous administration of DNase-1-coated polydopamine-poly (ethylene glycol) nanoparticulates, named long-acting DNase-1 (Scheme 1), effectively inhibited NETosis factors in blood samples of patients with COVID-19 and also improve survival in a sepsis model. We also observed markedly reduced NET levels, MPO activity, and NE levels in neutrophils of COVID-19 patients with sepsis upon treatment of the DNase-1 formulations (Fig. 4C-E) . patients with sepsis, the long-acting DNase-1 significantly reduced cfDNA levels and increased the activity of the DNase-1 ( Fig. S6A and B) . (C) NET ratio of SARS-CoV-2 Sepsis patient PBMCs was suppressed after free DNase-1 or long-acting DNase-1 treatment. doi = 10.1016/j.biomaterials.2020.120389 id = cord-321797-2xhusfth author = Lee‐Baggley, Dayna title = Coping with the threat of severe acute respiratory syndrome: Role of threat appraisals and coping responses in health behaviors date = 2004-03-11 keywords = SARS; behavior; health; threat summary = Hierarchical linear regression indicated that the use of wishful thinking in response to the threat of SARS was related to both avoiding public places and avoiding people perceived to be possible carriers of the SARS virus, but was not associated with the use of more adaptive health behaviors, such as using disinfectants and hand washing. Perception of SARS threat was significantly related to reports of both coping (wishful thinking and support seeking) and health behaviors (avoidant behavior, avoiding people perceived to be at risk for SARS and taking precautions). In sum, multivariate analyses controlling for differences in perceived threat of SARS, state anxiety and other ways of coping indicated that both wishful thinking and empathic responding were significantly associated with specific SARS-related health behaviors. 4 Controlling for differences in perceived threat of SARS, state anxiety and other ways of coping, support seeking was not significantly related to the SARS-related health behaviors examined in the present study. doi = 10.1111/j.1467-839x.2004.00131.x id = cord-311599-m400cal3 author = Lehmann, Christian title = A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses date = 2008-05-31 keywords = HKU1; OC43; SARS summary = Here, we report the development of a serologic assay for detection of antibodies to human coronaviruses (HCoVs) based on recombinant nucleocapsid (N) proteins of all known pathogenic strains (229E, NL63, OC43, HKU1, SARS). Here, we describe the establishment of a line immunoassay for rapid and simultaneous detection of antibodies directed against the 5 known HCoVs (229E, NL63, OC43, HKU1, and SARS) in human sera based on recombinant viral N proteins. Table 2 Reactions of clinically defined sera with HCoV nucleocapsids In sera taken during acute phase of HCoV infection, no OC43-or 229E-specific antibodies could be detected, whereas samples collected after convalescence strongly reacted with the corresponding antigens. Consistently, all available human sera sampled from convalescent patients (tested positive for HCoVs 229E, OC43, or SARS-CoV by microneutralization experiments, Western blotting, ELISA, or IF) reacted with their respective antigens as expected, indicating an excellent sensitivity of our line immunoassay. doi = 10.1016/j.diagmicrobio.2007.12.002 id = cord-276316-7ot9ds34 author = Lei, Chunliang title = Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China date = 2020-10-14 keywords = COVID-19; SARS summary = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in respiratory tract, blood samples and digestive tract was detected and lymphocyte subsets were tested periodically. 270 patients were detected for SARS-CoV-2 RNA in anal swabs and/or blood samples, and the overall positive rate was 23.0 % (62/270), higher in severe/critical cases than in mild/moderate cases (52.0 % vs. Detectable SARS-CoV-2 RNA in anal swabs and/or blood samples, as well as higher CD4/CD8 ratio were independent risk factors of respiratory failure and ICU admission. A total of 270 patients were detected for SARS-CoV-2 RNA in anal swabs J o u r n a l P r e -p r o o f 8 / 25 and/or blood samples, and the overall positive rate was 23.0% (62/270), higher in severe/critical cases than in mild/moderate cases (52.0% vs. doi = 10.1016/j.jcv.2020.104661 id = cord-329876-4cgrjnjo author = Lei, Jian title = Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin date = 2016-05-30 keywords = MERS; SARS; pro summary = title: Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. The substrate-binding site of MERS-CoV PL pro features significant differences from those of the corresponding SARS-CoV enzyme and human ubiquitin-specific proteases (USPs, such as, USP14) (Hu et al., 2005; Chou et al., 2014; Ratia et al., 2014) . Hence, we crystallized the ubiquitin (Ub) complex of a MERS-CoV PL pro variant that had the active-site Cys111 replaced by serine (C111S) and determined the structure at 3.16 Å ( Figure 1A ). Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression doi = 10.1007/s12250-016-3742-4 id = cord-279569-289fu2yb author = Lei, Yu title = Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area date = 2020-03-13 keywords = SARS; Wuhan summary = title: Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area Abstract Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in Epidemiological, clinical laboratory and radiological characteristics, chronic medical histories, clinical symptoms, treatment and outcome data were obtained from electronic medical records and analysed by two independent researchers. With advancing time, the medical history associated with case exposure to SARS-CoV-2 infected patients from Wuhan has become less obvious. In conclusion, imported cases of SARS-CoV-2 infection in Tibetan patients were generally mild in this high-altitude area. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan doi = 10.1101/2020.03.09.20033126 id = cord-310396-jitao9k0 author = Lei, Yu title = MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date = 2009-03-07 keywords = Fig; IFN; MAVS; SARS; cell summary = The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. Currently, there are no reports of viral proteins targeting MAVS for inhibition of virus-induced cell death responses. In this report, we describe a novel function of MAVS in mediating virus-induced apoptosis, and identify viral proteins as inhibitors of this response. In addition, the involvement of proteins on IFN axis in virusinduced host cell apoptosis has been implicated in another previous report, in which MAVS has been shown to be critical for reovirus-triggered caspase-3/7 activation in HEK293T cells [46] , however, the study did not evaluate whether MAVS mediates virus-induced apoptosis and what roles type 1 IFNs play in MAVS-mediated apoptosis. doi = 10.1371/journal.pone.0005466 id = cord-265366-vmuqbpkk author = Leibowitz, Jill title = Comparison of Clinical and Epidemiologic Characteristics of Young Febrile Infants with and without SARS-CoV-2 Infection date = 2020-10-09 keywords = CoV-2; SARS; infant summary = 7, 8, 9, 10, 11, 12, 13 The largest case series to date describes 18 infants younger than 90 days of age who tested positive for SARS-CoV-2, 14 of whom were febrile. 9 The objective of this study was to compare the clinical and demographic characteristics and hospital course of febrile infants who presented to Cohen Children''s Medical Center (CCMC) during March and April of 2020, the time period of peak COVID-19 incidence in our region, to febrile infants treated in CCMC during March and April of previous years. The key findings of our study are that during the peak of the COVID-19 pandemic in New York, SARS-CoV-2 was the predominant pathogen identified among febrile infants younger than 57 days of age, and the disease was self-limited in all infants with COVID-19. 26 Infants with COVID-19 presented with lethargy and feeding difficulty more with SARS-CoV-2 infection among infants younger than 90 days of age. doi = 10.1016/j.jpeds.2020.10.002 id = cord-289476-8wh3hn0n author = Leiker, Brenna title = COVID - 19 BRIEF INTRODUCTION IN MENTAL HEALTH CONSIDERATIONS FOR HEALTH CARE WORKERS AND PATIENTS date = 2020-07-28 keywords = CDC; COVID-19; SARS summary = This document describes five categories of people for SARS-CoV-2 testing with viral tests (i.e., nucleic acid or antigen tests) [the following are hot links to CDC resources]:  Testing individuals with signs or symptoms consistent with COVID-19  Testing asymptomatic individuals with recent known or suspected exposure to SARS-CoV-2 to control transmission  Testing asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification in special settings  Testing to determine resolution of infection (i.e., test-based strategy for Discontinuation of Transmission-based Precautions, HCP Return to Work, and Discontinuation of Home Isolation)  Public health surveillance for SARS-CoV-2 Generally, viral testing for SARS-CoV-2 is considered to be diagnostic when conducted among individuals with symptoms consistent with COVID-19 or among asymptomatic individuals with known or suspected recent exposure to SARS-CoV-2 to control transmission, or to determine resolution of infection. Testing is considered to be surveillance when conducted among asymptomatic individuals without known or suspected exposure to SARS-CoV-2 for early identification, or to detect transmission hot spots or characterize disease trends. doi = 10.1016/j.disamonth.2020.101059 id = cord-307502-vuju89lc author = Leipe, J. title = SARS-CoV-2 & Rheuma: Konsequenzen der SARS-CoV-2-Pandemie für Patienten mit entzündlich rheumatischen Erkrankungen. Ein Vergleich der Handlungsempfehlungen rheumatologischer Fachgesellschaften und Risikobewertung verschiedener antirheumatischer Therapien date = 2020-08-26 keywords = COVID-19; Patienten; SARS; update summary = V. (DGRh) bereits zu Beginn der COVID-19-Pandemie im März 2020 erste Handlungsempfehlungen zum Management von Patienten mit entzündlich rheumatischen Erkrankungen (ERE) unter dem Aspekt der SARS-CoV-2/COVID-19-Bedrohung herausgegeben hat [13] , wurden diese im Juli 2020 durch ein Update aktualisiert und erweitert (im Folgenden DGRh-Update) [14] . Bezüglich der Risikoeinschätzung für schwere COVID-19-Verläufe wurde in den Empfehlungen der DGRh, EULAR und ACR postuliert, dass Patienten mit ERE kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 oder eines schweren Verlaufes für COVID-19 aufweisen. a. basierend auf teilweise kurz davor publizierten Daten, davon aus, dass auch die medikamentöse antirheumatische Therapie kein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt, mit Ausnahme von Glukokortikoiden in einer Dosierung von 10 mg Prednisolonäquivalent/Tag und mehr [4] . Im DGRh-Update wurde, basierend auf aktuell publizierten Daten zu SARS-CoV-2 und Erkenntnissen aus früheren Studien zum allgemeinen Infektionsrisiko, von einem erhöhten Risiko für einen schweren COVID-19-Verlauf bei unzureichend eingestellten ERE ausgegangen [3] . doi = 10.1007/s00393-020-00878-0 id = cord-310051-bl8l4bgo author = Leitner, Thomas title = Where did SARS-CoV-2 come from? date = 2020-07-06 keywords = SARS summary = Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastro-intestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. While it is possible that a bat coronavirus jumped directly to a human, the closest known bat virus, RaTG13 found in a Rhinolophus affinis bat , shows 96% genomic similarity to SARS-CoV-2. Canine coronaviruses were not the only viruses with CpG patterns similar to those observed in SARS-CoV-2. Therefore, reduced genomic CpG content alone cannot predict the zoonotic origin of SARS-CoV-2, even though Xia (2020) (Pollock et al. Identification of the zoonotic origin of SARS-CoV-2 may be particularly challenging, as coronaviruses frequently recombine and are found in many different host species in the wild (Graham and Baric 2010) . doi = 10.1093/molbev/msaa162 id = cord-348636-qqcb85uk author = Lekone, Phenyo E. title = Bayesian Analysis of Severe Acute Respiratory Syndrome: The 2003 Hong Kong Epidemic date = 2008-07-09 keywords = Hong; SARS summary = This paper analyzes data arising from a Severe Acute Respiratory Syndrome (SARS) epidemic in Hong Kong in 2003 involving 1755 cases. Applying the method to SARS data from Hong Kong, a value of 3.88 with a posterior standard deviation of 0.09 was estimated for the basic reproduction number. A reduction in the transmission parameter during the course of the epidemic forced the effective reproduction number to cross the threshold value of one, seven days after control interventions were introduced. These parameters were obtained using maximum likelihood estimation methods assuming a gamma distribution for each period with allowance for censoring due to incomplete observation. A simple model that captures the form of distributions of epidemiological determinants has been introduced to estimate the basic reproduction number and to assess the effect of control interventions introduced during the course of the epidemic. doi = 10.1002/bimj.200710431 id = cord-309193-v8lphej4 author = Lemriss, Sanaâ title = Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco date = 2020-07-02 keywords = SARS summary = title: Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19). Phylogenetic tree of the complete nucleotide sequence of hCoV-19_Morocco_OUA677_19_2020 and 54 other global strains obtained from the GISAID database, associated with a table representing single-nucleotide polymorphisms (SNPs). Phylogenetic analysis of this virus genome compared with 54 selected sequences showed that it was grouped in SARS-CoV-2 clade G, which includes strains from Asia, Europe, North America, Australia, and Africa (Fig. 1) . We are currently sequencing and analyzing more complete genomes from different regions of Morocco to understand the virus dispersion and to associate this information with epidemiological data. doi = 10.1128/mra.00633-20 id = cord-324888-oak27okj author = Leng, Ling title = Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis date = 2020-04-18 keywords = ACE2; SARS; figure summary = title: Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. Therefore, we wonder whether there are some key local microenvironment proteins specifically expressed on the surface of airway EpC that makes the virus prefer airway EpCs. In some cases, additional cell surface molecules or co-receptors are required for sufficient viral entry into host cells. We used the human protein atlas (HPA) database [16] to extract the protein expression level of 65 receptors involved in "virus receptor activity" (GO:0001618) of EpCs and epithelial or epithelial-derived cells from 14 organs (16 cell types) ( Figure 1A and Supplementary Materials and Methods). doi = 10.1101/2020.04.16.045799 id = cord-280408-0ze1lfnf author = Leon, A. title = SARS-CoV-2 infection may mask another infection date = 2020-05-16 keywords = SARS summary = key: cord-280408-0ze1lfnf authors: Leon, A.; Debry, C.; Renaud, M. title: SARS-CoV-2 infection may mask another infection date: 2020-05-16 journal: Eur Ann Otorhinolaryngol Head Neck Dis DOI: 10.1016/j.anorl.2020.05.005 sha: doc_id: 280408 cord_uid: 0ze1lfnf nan Brain CT, axial scan with bone window setting. Presence of a bone defect of the lateral wall of the left sphenoid sinus (arrow). MRI, gadolinium-enhanced T1-weighted sequence, coronal section through the cavernous sinus. Intense enhancement of the fluid-filled sphenoid sinus (solid arrow) and the walls of the lateral sellar compartment (*) with inflammatory stenosis of the intracavernous segment of the internal carotid arteries (dotted arrow). Neurological Complications of Acute and Chronic Sinusitis Neurologic Features in Severe SARS-CoV-2 Infection Incidence of thrombotic complications in critically ill ICU patients with COVID-19 European Position Paper on Rhinosinusitis and Nasal Polyps Intraoperative bacterial analysis in nasal polyposis: Clinical and functional impact doi = 10.1016/j.anorl.2020.05.005 id = cord-338928-y5l7cf31 author = Leonardi, Matilde title = Neurological manifestations associated with COVID-19: a review and a call for action date = 2020-05-20 keywords = COVID-19; SARS summary = While the epidemic of Coronavirus disease 2019 (COVID-19) continues to spread globally, more and more evidences are collected about the presence of neurological manifestations and symptoms associated with it. The review shows that although more and more papers are reporting neurological manifestations associated with COVID-19; however, many items remain unclear and this uncertainty calls for a global action that requires close coordination and open-data sharing between hospitals, academic institutions and the fast establishment of harmonised research priorities and research consortia to face the NeuroCOVID-19 complications. Reports are emerging from China and Italy and increasingly from several countries of neurological symptoms associated with SARS-CoV-2, which may be worsening clinical pictures, respiratory outcomes and mortality rates in patients with COVID-19. Observations from Italy have confirmed Chinese data noting a high number of patients with hyposmia, anosmia and varying patterns of possibly centrally mediated symptoms including respiratory manifestations. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice doi = 10.1007/s00415-020-09896-z id = cord-324345-j43rpvwk author = Leong, Hoe Nam title = SARS – My personal battle date = 2010-11-19 keywords = SARS; Singapore; day summary = I vividly remember the time when I first saw the index patient with Severe Acute Respiratory Syndrome (SARS) in Singapore. The index patient was admitted to Tan Tock Seng Hospital (TTSH) on Saturday, (1st March 2003), and an infectious disease consult was sought on the following Monday. It was an exceedingly busy day for me as I had to attend to new referrals, run an outpatient clinic, and subsequently draft a clinical summary of these two patients by the early evening. Eventually, the patient''s fever defervesced on day 14 of illness. I wasn''t scheduled to perform the ward round that day, but I returned to visit the patient that Sunday morning. My wife and I telephoned a colleague in Singapore and we concurred to have a full blood count test done at the clinic the next day. My wife eventually joined me when she developed fever at the end of the second day of arrival. With that news, my days as a patient in isolation continued. doi = 10.1016/j.tmaid.2010.10.007 id = cord-355718-7dafsxp9 author = Leong, Hoe‐Nam title = Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 date = 2004-08-10 keywords = SARS summary = title: Investigational use of ribavirin in the treatment of severe acute respiratory syndrome, Singapore, 2003 We performed a retrospective cohort study assessing the effectiveness of ribavirin use in our patients with SARS. We compared the results of clinical and laboratory investigations at the start of ribavirin treatment with correspondent parameters of patients who did not receive ribavirin on day 6 of illness. * Parameters taken on start of treatment for those on ribavirin, and day 6 for the control group. Most patients received this combination therapy but no comparative efficacy data from treatment and control groups were available. After correcting for steroid use, the hazard ratio of death for patients treated with ribavirin was 1.03 (95% CI: 0.44-2.41, P ¼ 0.939). Our study was a retrospective analysis with two groups of patients being treated at different times of the epidemic. doi = 10.1111/j.1365-3156.2004.01281.x id = cord-334210-lhadzo7o author = Lepak, Alexander J title = Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date = 2020-08-27 keywords = PUI; SARS summary = Key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible COVID-19 or for asymptomatic screening. CONCLUSIONS: In a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. In this paper we report the findings of a retrospective observational study to examine results of repeat SARS-CoV-2 RT-PCR testing for patients who were suspected of having COVID-19 (persons under investigation, or PUI) and asymptomatic patients and how the results may inform diagnostic stewardship within our academic medical center in Wisconsin. We believe the biggest lesson learned for our institution is that we found no cases of conversion from a negative to a positive result for inpatients undergoing a repeat PUI test or a repeat asymptomatic screen test. doi = 10.1093/ofid/ofaa388 id = cord-268935-4obwu75u author = Lepak, Alexander J. title = Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) date = 2020-10-12 keywords = SARS summary = title: Implementation of infection control measures to prevent healthcare-associated transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) Adoption of the infection control bundle described may be helpful to prevent SARS-CoV-2 spread within healthcare institutions. Notably, repeated inpatient testing of individuals was, in general, directed toward those undergoing procedures, those in whom signs or symptoms suggested possible COVID-19, those with acute changes in status requiring intensive care unit (ICU) or intermediate (IMC) care, and/or based on provider judgment. For the single positive inpatient without a prior history of SARS-CoV-2, chart review revealed that this adult patient lived in a community setting, had mild symptoms (sinus congestion, eye pain, and cough) that started 10 days prior to admission, and was self-isolating at home. We believe that infection was present from community exposure prior to admission; therefore, we did not find any laboratory-confirmed cases suggestive of possible nosocomially acquired SARS-CoV-2 infection despite a substantial inpatient population with and without COVID-19. doi = 10.1017/ice.2020.1262 id = cord-310419-s3qkscw7 author = Lephart, Paul R. title = Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() date = 2020-09-03 keywords = SARS summary = title: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type() The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. Within a few weeks, additional SARS-CoV-2 NAAT options emerged that were specifically designed for rapid testing of patients in the point of care setting: the Cepheid Xpert Xpress SARS-CoV-2 (Xpert) assay, which could provide results in 45 minutes, and the Abbott ID NOW COVID-19 (ID NOW) assay, ultimately approved for direct nasal, nasopharyngeal and throat swab testing only, with results in 5-15 minutes. This comparative analysis of SARS-CoV-2 NAATs utilizing the m2000, Simplexa, Xpert and ID NOW assays demonstrated that significant performance deficits were found in the ID NOW assay when tested in a mixed patient population using both NP and nasal specimens. doi = 10.1016/j.diagmicrobio.2020.115200 id = cord-355439-eqtk51q3 author = Lesko, Catherine R title = HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date = 2020-07-22 keywords = HIV; PLWH; SARS summary = Surveillance data, such as those available from South Africa or Wuhan, will provide the most complete picture of COVID-19 risk among PLWH (e.g., by not restricting to PLWH who are in care and who are more likely to have wellcontrolled HIV disease); however clinical data, such as those from Madrid, may provide the most depth (e.g., by allowing examination of the role of comorbidities, medications, and COVID-19 treatments) as long as potential selection bias is considered. Despite some good telehealth outcomes for some PLWH, telehealth has the potential to exacerbate disparities in care for people with lower socio-economic status: lack of necessary technology and services, technology literacy, and safe, confidential surroundings to participate fully in telehealth may be barriers to engagement in care (32 distancing restrictions if they need to go outside their homes to access alcohol or other drugs, or critically, medication assisted treatments (such as methadone or buprenorphine). doi = 10.1093/aje/kwaa158 id = cord-298886-xidaim04 author = Leszczyński, Piotr title = COVID-19: a short message to rheumatologists date = 2020-06-29 keywords = COVID-19; SARS summary = In the treatment of cytokine storm in COVID-19, there is a possibility of using a TNF alpha inhibitor (adalimumab) or IL-6 receptor inhibitors (tocilizumab, sarilumab) [6] [7] [8] , which are currently being studied in randomized clinical trials in SARS-CoV-2 infected patients with signs and symptoms of rapidly progressing pneumonia. Our own experience with the combined use of chloroquine and azithromycin or ceftriaxone (n = 34) and tocilizumab (n = 1) in the treatment of severe pneumonia in the course of COVID-19 disease is very good, although it should only be considered as a series of cases (Figs. In accordance with some clinical concerns of rheumatologists, patients with rheumatic diseases treated with disease-modifying drugs (DMARDs) should have a higher risk of SARS-CoV-2 infection. Patient with pharmacologically treated rheumatic disease after close contact (staying at a distance of less than 2 m, for more than 15 minutes, in the last 7 days) with a person with confirmed SARS-CoV-2 infection without clinical symptoms of COVID-19: doi = 10.5114/reum.2020.96685 id = cord-269465-3fdjqnhb author = Leth-Larsen, Rikke title = The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages date = 2007-05-15 keywords = SARS summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) infects host cells with its surface glycosylated spike-protein (S-protein). Macrophages, DCs, 293T and Vero cells were harvested, incubated for 30 min with 20% (v/v) goat serum, and then stained for 45 min on ice with a mouse monoclonal anti-ACE2 antibody. Cells were washed twice with the binding buffer and then incubated with the myc antibody followed by goat anti-mouse IgG and analyzed by flow cytometry as above. To examine whether S-protein expressed in this study is recognized by ACE2, Vero cells were incubated with the purified S-protein and bound S-protein was detected by flow cytometry using a myc antibody. Blocking of Binding of S-protein to macrophages and DCs: (A) macrophages and DCs were cultured from monocytes and, upon washing, incubated with a mouse anti-human ACE2 monoclonal antibody (solid lines) or, as a control, isotype IgG (solid histograms). doi = 10.1016/j.imbio.2006.12.001 id = cord-253502-v2hh3w3r author = Leung, C.W. title = Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date = 2004-11-05 keywords = PCR; SARS; acute; child; respiratory; severe summary = authors: Leung, C.W.; Chiu, W.K. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children [5] [6] [7] [8] [9] [10] [11] Superspreading events including a major hospital outbreak, in-flight transmission on board commercial PAEDIATRIC RESPIRATORY REVIEWS (2004) Summary Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. doi = 10.1016/j.prrv.2004.07.010 id = cord-277735-a9gkath5 author = Leung, Danny Tze Ming title = Antibody Response of Patients with Severe Acute Respiratory Syndrome (SARS) Targets the Viral Nucleocapsid date = 2004-07-15 keywords = ELISA; SARS summary = We examined serum samples obtained from 46 patients with SARS, 40 patients with non-SARS pneumonia, and 38 healthy individuals, by use of Western blotting (WB), enzyme-linked immunoassay (ELISA), and immunofluorescence assay, using both native and bacterially produced antigens of the virus. Both the humoral and cellular arms of the adaptive immune response are presumed to be important in controlling 2 or preparation U reacted with a serum sample from a patient with SARS showing the highly reactive antigens-nucleocapsid (N) 1, N2, and N3-in the former. Second, we made a recombinant antigen of the N-terminal half of the N protein (rNa), and, when it was used in an IgG ELISA, we found results almost identical to those found with the crude viral extract (89% sensitivity and 94%-95% specificity), including 4 negative cases in common ( figure 2) . doi = 10.1086/422040 id = cord-310651-pxfwe67t author = Leung, Gabriel M. title = SARS-CoV Antibody Prevalence in All Hong Kong Patient Contacts date = 2004-09-17 keywords = Hong; SARS summary = A total of 1,068 asymptomatic close contacts of patients with severe acute respiratory (SARS) from the 2003 epidemic in Hong Kong were serologically tested, and 2 (0.19%) were positive for SARS coronavirus immunoglobulin G antibody. Serologic surveys can be based on a random sample from the total population with appropriate stratification, on serum collected for other reasons (e.g., blood donors, all hospital admissions), or on surveys of persons who resided in sites of superspreading events or who have had close contact with a confirmed SARS patient. During the epidemic, close contacts were prospectively identified by the Hong Kong Special Administrative Region Government Department of Health through standardized telephone interviews with all 1,755 confirmed SARS patients within 1 week of hospital admission (February 15-June 22, 2003). doi = 10.3201/eid1009.040155 id = cord-275858-46jzw94p author = Leung, Janice M. title = COVID-19 and COPD date = 2020-08-13 keywords = COPD; COVID-19; SARS summary = Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study Risk factors associated with clinical outcomes in 323 COVID-19 hospitalized patients in Wuhan, China Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: a retrospective single center analysis A preliminary study on serological assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 238 admitted hospital patients Epidemiological, clinical, and virological characteristics of 465 hospitalized cases of coronavirus disease 2019 (COVID-19) from Zhejiang province in China. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China doi = 10.1183/13993003.02108-2020 id = cord-330093-asba80bi author = Leung, Janice M. title = Smoking, ACE-2 and COVID-19: ongoing controversies date = 2020-07-16 keywords = ACE-2; COVID-19; SARS summary = Both research teams are reporting increased angiotensin-converting enzyme 2 (ACE-2) expression in airways of current smokers and those with COPD, with important implications for coronavirus disease 2019 (COVID-19) patients. Since ACE-2 has been shown to be the main receptor utilised by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to enter the host cells [2] , the authors conclude that nicotine is a risk factor for COVID-19. Here, we bring to the discussion whether the increased susceptibility and virulence of SARS-CoV-2 via α7-nAChR and the upregulation of small airway ACE-2 expression may also be relevant for those who vape using nicotine-based e-cigarettes. While smoking may not necessarily increase one''s risk for contracting COVID-19, the biological and inflammatory cascade that occurs upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may be particularly devastating for a smoker. doi = 10.1183/13993003.01759-2020 id = cord-291149-j70b7kyi author = Leuzinger, K. title = Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures date = 2020-09-23 keywords = NOPS; Roche; SARS summary = Aim: To cross-validate manual and automated high-throughput (Roche-cobas6800-Target1/Target2) testing for SARS-CoV-2-RNA, to describe detection rates following lockdown and relaxation, and to evaluate SARS-CoV-2-loads in different specimens. As comprehensive real-life data are scarce, we analyze the epidemiology of SARS-CoV-2detection following lockdown and relaxation measures and investigate the quantitative relationship of the different assays and explore SARS-CoV-2-loads in follow-up NOPS and in time-matched lower respiratory fluids, and in plasma samples. Basel-S-gene RT-QNAT was used for SARS-CoV-2 genome quantification in 936 follow-up NOPS from 261 patients with a positive Roche-Cobas-Target1/Target2 screening result, in 95 NOPS and time-matched lower respiratory fluids (tracheal aspirates, bronchial-alveolar lavage, or sputum) or in 259 NOPS and time-matched plasma samples from COVID-19 patients. To follow the SARS-CoV-2-detection rates after introducing more stringent lockdown measures in Switzerland in calendar week 12 (https://www.bag.admin.ch/bag/en/home/dasbag/aktuell/medienmitteilungen.msg-id-78454.html), we identified all NOPS from 12''363 symptomatic adults and children tested for SARS-CoV-2 from calendar week 14 to 24 (Follow-up cohort-1; Table 1 ) including 270 (2%) confirmed infections ( Figure 3A) . doi = 10.1101/2020.09.22.20198697 id = cord-018106-5giapmcf author = Levin, Jacqueline title = Mental Health Care for Survivors and Healthcare Workers in the Aftermath of an Outbreak date = 2019-05-16 keywords = SARS; healthcare; patient; worker summary = Similar findings have been reported in multiple studies indicating acute and persistently elevated stress levels as well as other emotional sequelae of healthcare workers during and after pandemic disease outbreaks [10] [11] [12] . A study of the psychological impact of the 2003 SARS outbreak on healthcare workers in Singapore found that support from supervisors and colleagues was a significant negative predictor for psychiatric symptoms and PTSD, in addition to clear communication of directives and precautionary measures which also helped reduce psychiatric symptoms [15] . Providing psychiatric care to survivors and healthcare workers in the aftermath of a pandemic outbreak is a complicated, but crucial, imperative in the service of reducing the burden of human suffering. doi = 10.1007/978-3-030-15346-5_11 id = cord-252005-3ld5e7f5 author = Lewis, Nathaniel M title = Household Transmission of SARS-CoV-2 in the United States date = 2020-08-16 keywords = SARS; household summary = The Centers for Disease Control and Prevention collaborated (CDC) with state and local health departments in the Milwaukee, Wisconsin, and Salt Lake City, Utah, metropolitan areas to identify persons with laboratory-confirmed SARS-CoV-2 infection captured by public health surveillance during March 22-April 25, 2020. The investigation team defined persons identified by local health departments as "index patients." Households were selected by convenience sampling and considered eligible if the index patient was not hospitalized at the time, lived with ≥1 additional person, and tested positive for SARS-CoV-2 rRT-PCR from a nasopharyngeal (NP) swab collected ≤10 days prior to enrollment. One study from China estimated a 28% SIR for spouses of primary patients and 4% for household contacts aged A c c e p t e d M a n u s c r i p t 10 <18 years by SARS-CoV-2 rRT-PCR testing [6] . doi = 10.1093/cid/ciaa1166 id = cord-256497-kyer0zjx author = Leyendecker, Pierre title = Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients date = 2020-08-27 keywords = AAI; SARS summary = title: Acute adrenal infarction as an incidental CT finding and a potential prognosis factor in severe SARS-CoV-2 infection: a retrospective cohort analysis on 219 patients OBJECTIVES: To retrospectively investigate the incidence of acute adrenal infarction (AAI) in patients who underwent chest CT for severe SARS-CoV-2 infection and to correlate findings with prognosis. Consequently, the purpose of this study is to retrospectively investigate the incidence of AAI in patients with severe SARS-CoV-2 infection and to correlate findings to prognosis data. (a) Severe or critical lung parenchyma lesion characteristics of COVID-19, i.e., involving at least 50% of the total lung parenchyma [10] ; (b) Presence of both entire adrenal glands in the inferior part of the volume of acquisition; (c) Positive RT-PCR for SARS-CoV-2 at the time of chest CT. To conclude, our work demonstrated a high incidence of acute adrenal infarction on initial chest CT of severe COVID-19 (51/219, 23%), which might be a sign of a poorer prognosis. doi = 10.1007/s00330-020-07226-5 id = cord-320882-cr0ccsnp author = Li Volti, Giovanni title = Smoking and SARS-CoV-2 Disease (COVID-19): Dangerous Liaisons or Confusing Relationships? date = 2020-05-02 keywords = ACE2; SARS summary = Keywords: COVID-19; SARS-Cov-2; smoking; angiotensin-converting enzyme-2 We read with great interest the article by Brake SJ and colleagues [1] investigating the relationship between smoking and angiotensin-converting enzyme-2 (ACE-2) and the potential implication for COVID-19. The authors present findings linking ACE-2 expression to smoking in a variety of experimental models together with observations of their own; immunohistochemistry data showing an increased expression of ACE-2 in a series of biopsies from a group of current smokers with chronic obstructive pulmonary disease when compared to a control group. The authors then venture into reporting existing Chinese case reports to support their hypothesis that smoking could increase the risk of COVID-19 via upregulation of ACE-2 expression, a known cellular entry gateway for SARS-CoV-2 [2] . Smoking upregulates angiotensin-converting enzyme-2 receptor: A potential adhesion site for novel coronavirus SARS-CoV-2 (Covid-19) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target doi = 10.3390/jcm9051321 id = cord-338403-mfde6juv author = Li, Bo title = Prevalence and impact of cardiovascular metabolic diseases on COVID-19 in China date = 2020-03-11 keywords = SARS; icu summary = METHODS: A meta-analysis of eligible studies that summarized the prevalence of cardiovascular metabolic diseases in COVID-19 and compared the incidences of the comorbidities in ICU/severe and non-ICU/severe patients was performed. Inclusion criteria are as follows: (1) comparative studies: randomised controlled trials RCTs or non-RCTs published in English; (2) study population: more than ten participants were included in the study; (3) study intervention: patients in the studies should be confirmed to have been infected by 2019 novel coronavirus; (4) parameters: the comorbidities of cardiovascular metabolic diseases and the outcome of cardiac injury should be given. Systematic analysis of studies that described the epidemiological and clinical features of COVID-19 cases and reported the prevalence of cardiovascular metabolic diseases as well as the impact on cardiac injury in the infectious disease, has identified six reports with 1527 patients ( Table 1 ). doi = 10.1007/s00392-020-01626-9 id = cord-338205-sy91rnse author = Li, Chenxi title = Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date = 2020-07-02 keywords = COVID-19; CoV-2; PCR; SARS summary = With limited understanding of COVID-19, it is difficult to exclude SARS-CoV-2 infection based on a single negative PCR result, especially when testing was used for upper respiratory tract specimens. The study found that SARS-CoV-2 could be detected in all primer-probe sets applied in the qRT-PCR tests, but significant discrepancy was observed in the detection limit and the ability to identify negatives and positives with a lower viral load. Compared with the qRT-PCR kit, nested RT-PCR analysis showed higher sensitivity and specificity, indicating that it is more suitable for clinical application to detect SARS-CoV-2 in cases with low viral load. In cases where RT-PCR assays are negative and there is a strong epidemiological link to SARS-CoV-2 infection, paired serum samples (in the acute and convalescent-phase) could support diagnosis once validated serology tests are available with the initial samples collected in the first week of COVID-19 and the second collected after 2-4 weeks [28] . doi = 10.1016/j.cca.2020.06.045 id = cord-325124-0hxan9rw author = Li, Chenyu title = Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date = 2020-05-18 keywords = Fig; PCR; SARS summary = However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. doi = 10.1101/2020.03.12.988246 id = cord-334228-n69iewmx author = Li, Chunmei title = Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity date = 2016-02-16 keywords = GLRQ; SARS summary = Like other known CoV-3CLpro structures, such as TGEV, hCoV-229E, hCoV-HKU1, and IBV 2-5 , SARS-3CLpro has a highly conserved three-dimensional structure, dimer interface, catalysis dyad, and substrate binding site, but an extremely low homology with cellular proteases. Ser139 and Phe140 are two key residues that not only contribute to interactions between the two protomers in the parent dimer but also maintain the correct conformation of the S1 subsite in the substrate-binding pocket. Other residue mutations, which are neither on the dimer interface nor key to catalysis, can also influence enzyme activity and dimer association-dissociation of SARS-3CLpro via long-range interactions 15, 16 . Our molecular dynamics simulations showed that Ser139-Leu141 maintains a stable 3 10 -helix conformation in the inactive monomer structure and a well-defined loop conformation in the active protomer of the dimer structure. Although SARS-3CLpro uses the dimer structure to maintain its enzyme activity, our study shows that the monomer can also be evolved into an active enzyme via mutations. doi = 10.1038/srep20918 id = cord-300322-koqm5yxq author = Li, Fang title = Interactions Between Sars Coronavirus and its Receptor date = 2006 keywords = ACE2; SARS summary = The SARS-CoV RBD is sufficient for tight binding to ACE2, and thus it is the most important determinant of virus-receptor interactions, viral host range, and tropism. 8 The final model of the complex contains the N-terminal peptidase domain of human ACE2 (residues 19-615) and the spike RBD of human SARS-CoV (residues 323-502, missing residues 376-381). The structure reveals important residue changes at the binding interface that determine the species specificity of SARS-CoV. 6, 7 Detailed structural analysis sheds light on the significance of these residues in virus-receptor interactions (Figure 4 ). Rat ACE2 does not support SARS-CoV Leu472 on the RBD has a hydrophobic interaction with Met82 on ACE2. On rat ACE2, residue 82 is glycosylated, preventing the binding of SARS-CoV. In summary, the crystal structure of SARS-CoV spike RBD in complex with ACE2 has revealed detailed interactions between the virus and its receptor. Structure of SARS coronavirus spike receptor-binding doi = 10.1007/978-0-387-33012-9_38 id = cord-274528-mr81o9cu author = Li, Fei title = Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date = 2020-09-12 keywords = Data; Fig; SARS; TMPRSS2 summary = Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Notably, in addition to prostate, other essential 40 organs, including lung, kidney and liver, which are permissive for SARS-CoV-2 infection in human, were 41 characterized with Tmprss2-postive epithelial cells ( Fig. 1b and Extended Data Fig. 1c ). Consistently, 25 enzalutamide significantly decreased TMPRSS2 expression and inhibited SARS-CoV-2 infection in human 26 prostate cancer cells (Fig. 2) . doi = 10.1101/2020.09.11.293035 id = cord-251961-g0n85kxz author = Li, Guoming title = Safety and efficacy of Artemisinin-Piperaquine for treatment of COVID-19: an open-label, non-randomized, and controlled trial date = 2020-11-02 keywords = COVID-19; SARS summary = CONCLUSIONS: In patients with mild to moderate COVID-19, the time to reach undetectable SARS-CoV-2 was significantly shorter in the AP group than that in the control group. According to the "China''s Novel Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Seventh Edition) ", COVID-19 patients are usually categorized into mild, moderate, severe, and critical based on their symptoms. Initially, this trial was an open-label randomized parallel-group controlled trial intended to compare the efficacy and safety of AP tablets in comparison with hydroxychloroquine to treat patients with mild to moderate COVID-19. And the rate of patients to undetected SARS-CoV-2 by RT-PCR at day 7, 10, 14, 21, and 28 during drug administration, the CT images results within ten days, the abnormal laboratory index and adverse events would be compared between the two treatments. doi = 10.1016/j.ijantimicag.2020.106216 id = cord-349645-6o8773c5 author = Li, He title = Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date = 2020-06-02 keywords = SARS; covid-19 summary = METHODS: A retrospective study is conducted to study whether air quality index (AQI), four ambient air pollutants (PM(2.5), PM(10), NO(2) and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26(th) to Feb 29(th) in 2020. In this retrospective study, we attempted to conduct an exploratory analysis looking at the association between environment conditions (including ambient pollutants and meteoroidal parameter) and COVID-19 incidence/mortality in Wuhan, given a city-wide lockdown and varying pollution/meteorological data throughout the entire study period. In the current study, although the NO 2 level was constantly lower than the US EPA standards (United States Environmental Protection Agency, 2016), our data revealed that COVID-19 incidence were highly correlated with the ambient NO 2 concentration. The correlation between the COVID-19 incidence and three ambient air pollution along with five meteorological parameters Jan 26 th to Feb 29 th in 2020 in Wuhan and XiaoGan, China. doi = 10.1016/j.ijid.2020.05.076 id = cord-338901-1kzy7rts author = Li, Heng title = Overview of therapeutic drug research for COVID-19 in China date = 2020-06-17 keywords = COVID-19; RNA; SARS; chinese summary = According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. In these 155 pooled clinical trials, a number of approved chemical and biomacromolecule drugs have been used in COVID-19 treatment clinical trials for drug repurposing, most of which are nucleotide analogs and protease inhibitors against other viral pathogens, including influenza virus, HIV and HCV. In vitro studies have shown that lopinavir/ritonavir can inhibit the replication of MERS-CoV and SARS-CoV and exert antiviral effects [22] [23] [24] [25] . In the latest "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia", it is recommended to use ribavirin at a dose of 500 mg each time for adults and in combination with interferon or lopinavir/ritonavir, with 2-3 intravenous infusions daily. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) doi = 10.1038/s41401-020-0438-y id = cord-316814-9fv9xrln author = Li, Hong-Ye title = Use of GFP to Investigate Expression of Plant-Derived Vaccines date = 2009 keywords = GFP; SARS summary = Agroinfiltration is a more recent technique that can be applied to investigate transient expression in plant cells by which an Agrobacterium liquid culture is infiltrated into intact plant leaves (7) . By simple infiltration of Agrobacterium cells carrying appropriate gene constructs into tobacco plants leaves, transient expression assays can be performed within 3 days without using expensive instruments or complicated procedures. Two days after agroinfiltration, expression and subcellular localization of the GFP fusion proteins in tobacco leaves can be determined by simple observation under fluorescence or confocal laser scanning microscopy. 7. Generate plasmid pCV12 (Fig. 1 ) or similar nuclear transformation vector for expression of a fusion protein consisting of the SARS-CoV S1 and GFP. Production of tobacco leaves transiently expressing a protein fusion consisting of the SARS-CoV S1 protein fused with the GFP was carried out using Agrobacterium-mediated transformation with plasmid pCV12. doi = 10.1007/978-1-59745-559-6_19 id = cord-208426-wz3jan5d author = Li, Hongying title = Airborne dispersion of droplets during coughing: a physical model of viral transmission date = 2020-08-05 keywords = SARS; droplet; figure summary = Using realistic air flow simulation, we model droplet dispersion from coughing and study the transmission risk related to SARS-CoV-2. Notably, numerical methods, such as Computational Fluid Dynamics (CFD) based on Reynolds Averaged Navier-Stokes (RANS) turbulence models 31 produce high resolution flow fields and concentration data, 32 which not only compensate for slow instrumental speeds of analytical techniques, 25 but are also adaptable to different environments and scenarios, such as passengers in an aircraft cabin, 33 and more recently, a cough dispersion study in an outdoor environment under significant wind speeds, 34 whose results are useful in integrated transmission modeling. As detailed in the Supplementary Information, the model cough is inclined downwards at an average of 27·5°, 37 follows a characteristic air flow pattern 33,37 at breath temperature of 36°C, and emits a cluster of droplets with a standard size distribution 11, 38 and viral loading 39 doi = nan id = cord-341254-xnj6slby author = Li, Hua title = A new and rapid approach for detecting COVID‐19 based on S1 protein fragments date = 2020-06-05 keywords = CoV-2; SARS summary = Based on it, the detection of IgM/IgG in blood became an optional approach to improve the diagnosis, especially for the COVID-19 patient with negative nucleic acid test result. 2. Colloidal gold-labeled mouse-antihuman lgM/lgG antibody was manufactured by SAIYA Hebei Biotechnology Co., Ltd. To obtain the well-performance antibody, the antibody was selected for functional test including the positive and negative coincidence rates, minimum test threshold, and accelerated stability. Due to only around 50% positive rate of SARS-CoV-2 nucleic acid test 8, 12 under various condition of sample collection and storage, viral infection regions, RNA extraction methods, the quality of nucleic acid detection kit, and so on, 13 detection of IgM/IgG became a powerful approach for the early diagnosis of COVID-19 and could help identify the patients with negative nucleic acid but with obvious clinical symptoms. Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis doi = 10.1002/ctm2.90 id = cord-295846-quhnesbr author = Li, Huan title = Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis date = 2020-05-05 keywords = MERS; SARS summary = In conclusion, corticosteroid use in subjects with SARS-CoV-2, SARS-CoV, and MERS-CoV infections delayed virus clearing and did not convincingly improve survival, reduce hospitalization duration or ICU admission rate and/or use of mechanical ventilation. Because of the overlapping genetic and clinical feature of SARS-CoV-2, SARS-CoV, and MERS-CoV, we performed a meta-analysis of safety and efficacy of corticosteroid use in these coronavirus infections. Our meta-analysis focus on the effects of corticosteroids on virus clearing and mortality in persons infected with SARS-CoV-2, SARS-CoV, or MERS-CoV. Inclusion criteria included: (1) research articles including observational studies and clinical trials but excluding reviews or case reports on the use of corticosteroids in persons with SARS-CoV-2, SARS-CoV, and MERS-CoV infections; (2) reported outcomes of virus clearance and/or death; and (3) published in English and/or Chinese. To test impact of corticosteroid use on duration of hospitalization we included 3 studies [12, 13, 16] involving 828 subjects (SARS, N = 519; MERS, N = 309). doi = 10.1038/s41375-020-0848-3 id = cord-298067-awo3smgp author = Li, Huanjie title = Transmission Routes Analysis of SARS-CoV-2: A Systematic Review and Case Report date = 2020-07-10 keywords = CoV-2; Jinan; SARS; patient summary = Through associating infection symptoms with the transmission routes of virus and the patient course of the disease, we expect to provide guidelines for clinical diagnosis and the basis for suppressing the spread of the virus and antiviral treatment. On February 1, 2020, respiratory samples of four patients were confirmed SARS-CoV-2 infections by real-time PCR in Jinan Central Hospital, Shandong province, China. Summarizing the published articles, including SARS-CoV and SARS-CoV-2, we combined with epidemiological and clinical data to analyze the possible routes of asymptomatic patients with virus infection in order to provide the basis for suppressing the spread of the virus, and antiviral treatment and advice for the protection of medical staff. The study found that the detection of SARS-CoV-2 nucleic acid positive in a few feces of patients with confirmed COVID-19 cases indicated the presence of a live virus. doi = 10.3389/fcell.2020.00618 id = cord-274313-mrvk9r4w author = Li, Hui title = SARS-CoV-2 and viral sepsis: observations and hypotheses date = 2020-04-17 keywords = COVID-19; SARS summary = With evidence collected from autopsy studies on COVID-19 and basic science research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV, we have put forward several hypotheses about SARS-CoV-2 pathogenesis after multiple rounds of discussion among basic science researchers, pathologists, and clinicians working on COVID-19. Whether SARS-CoV-2 is able to directly attack vascular endothelial cells expressing high levels of ACE2, 13 and then lead to abnormal coagulation and sepsis, still needs to be explored. On the basis of observations from COVID-19 patients, we hypothesise that in mild cases, resident macrophages initiating lung inflammatory responses were able to contain the virus after SARS-CoV-2 infection; both innate and adaptive immune responses were efficiently established to curb the viral replication so that the patient would recover quickly. Meanwhile, the direct attack on other organs by disseminated SARS-CoV-2, the immune pathogenesis caused by the systemic cytokine storm, and the microcirculation dysfunctions together lead to viral sepsis (figure). doi = 10.1016/s0140-6736(20)30920-x id = cord-264461-nzvuugls author = Li, Jing title = Puzzle of highly pathogenic human coronaviruses (2019-nCoV) date = 2020-02-22 keywords = SARS summary = The immunosuppressive drug CsA prevents the nucleocapsid protein of the virus from binding to cyclophilin A (CypA) of the host cell, which has a peptidyl prolyl cis/trans isomerase (PPIase) activity, and a combination of interferon and CsA has been shown previously to significantly inhibit the replication and tissue damage caused by coronavirus infection in bronchi and lungs of humans. reported a mathematical model for simulating the transmission of the novel Wuhan Coronavirus, which is a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source to the humans (Chen et al., 2020a) . They estimated the transmissibility of 2019-nCoV via the basic reproduction number based on only the data from the early stages of the outbreak (Zhao et al., 2020a) . From SARS-CoV to Wuhan 2019-nCoV outbreak: similarity of early epidemic and prediction of future trends Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin doi = 10.1007/s13238-020-00693-y id = cord-291361-2vn1o7ag author = Li, Jing title = Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China date = 2020-07-06 keywords = SARS; family summary = title: Epidemiological and clinical characteristics of three family clusters of COVID-19 transmitted by latent patients in China The epidemiological and clinical characteristics of the family cluster patients were analysed and compared with those of 43 contemporaneous sporadic cases. In terms of epidemiological characters and clinical symptoms, no significant differences were observed between the family cluster and sporadic cases. In this study, we aimed to investigate the epidemiological and clinical characteristics of these three family clusters of COVID-19 cases by comparing them with sporadic cases, which would provide insights for epidemic control in the context of the current serious situation worldwide. This study revealed that sporadic cases had lower levels of albumin and lymphocyte counts than family cluster cases; otherwise, there were no significant differences in terms of other epidemiological characters and clinical features between the two groups. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1017/s0950268820001491 id = cord-294275-pp0vlaye author = Li, Jingjing title = Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date = 2020-06-03 keywords = Flongle; SARS summary = Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. Here, we use nanopore Flongle workflow combined with LAMP reaction to propose a faster and more convenient method to detect SARS-CoV-2 and other respiratory viruses in two hours. This study presents a LAMP based method combined with nanopore Flongle rapid realtime sequencing workflow to detect COVID-19 as low as 3.25×10^2 copies/mL of SARS-CoV-2 in both laboratory and wild-caught environment. To test the limit of detection, the amplification products of dilution gradient 3.25×10^4, 3.25 × 10^3, 1.1 × 10^3, 6.5 × 10^2, 3.25 × 10^2 copies/mL and negative control total 12 samples were constructed another barcoding library (Oxford Nanopore, SQK-RBK004) as described above and sequenced using a PromethION flowcell to achieve more data. The study design ( Figure 2 ) for SARS-CoV-2 detection is based on LAMP rapid amplification of specific genes and sequenced by nanopore Flongle workflow. doi = 10.1101/2020.06.03.131474 id = cord-029547-9ei1ram3 author = Li, Jingwei title = The epidemiology and therapeutic options for the COVID-19 date = 2020-05-28 keywords = COVID-19; China; CoV-2; SARS; clinical; patient summary = According to the Diagnosis and Treatment Program of Novel Coronavirus Pneumonia, only a suspected case has one of the pieces of evidence of etiology or serology, such as positive nucleic acid, confirmation of gene sequencing, and virus specific antibody, to be confirmed to be COVID-19 patient, 55 and the suspected cases were identified by a comprehensive analysis of epidemiological history and clinical manifestations. 64 There have been tens of clinical trials to confirm the safety and efficiency of chloroquine in treating COVID-19 patients, and its mechanism can be described as interfering with the glycosylation of ACE2 or alkalizing the phagolysosome to inhibit viral replication, 65, 66 which prevents the SARS-Cov-2 entering the host cells. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial doi = 10.1093/pcmedi/pbaa017 id = cord-300604-xx2d1s41 author = Li, Juyi title = Association between ABO blood groups and risk of SARS‐CoV‐2 pneumonia date = 2020-05-26 keywords = SARS summary = In December, 2019, a cluster of acute respiratory illness caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred in Wuhan, China.1,2 Epidemiological, clinical characteristics, risk factors for mortality of patients infected with SARS-CoV-2, and risk factors in the susceptibility to SARS-CoV-2 included age and chronic disease have been reported. 32Á2 %, P < 0Á01) in blood group A was much higher than that in the control group; however, there is currently no literature supporting that hypertension and hepatitis increase the risk of infection of SARS-CoV-2. 7 We still find that the proportion of blood group A in patients infected with SARS-CoV-2 was significantly higher than that in healthy controls (38Á0 % vs. 32Á2 %, P < 0Á001), while the proportion of blood group O in SARS-CoV-2 infected patients was significantly lower than in healthy controls (25Á7 % vs. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.1111/bjh.16797 id = cord-330887-q5i8lpan author = Li, K. title = The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19 date = 2020-05-21 keywords = COVID-19; SARS summary = By comprehensively analyzing the laboratory findings of 1,850 patients, we describe the dynamic changes of the total antibody, spike protein (S)-, receptor-binding domain (RBD)-, and nucleoprotein (N)specific IgM and IgG levels during SARS-CoV-2 infection and recovery. Our results indicate that the S-, RBD-, and Nspecific IgG generation of severe/critical COVID-19 patients is one week later than mild/moderate cases, while the levels of these antibodies are 1.5-fold higher in severe/critical patients during hospitalization (P<0.01). To explore the temporal dynamics of immune response after SARS-Cov-2 infection, we analyzed the antibody levels at different time points after symptoms onset, and the timing and level were compared between mild/moderate and severe/critical COVID-19 Results showed that total IgG, S-, RBD-, and N-specific IgG levels of the severe/critical COVID-19 patients were lower than that of the mild/moderate patients on admission, but these levels sharply increased during hospitalization and on discharge ( Figure 1 , Table 1 ). doi = 10.1101/2020.05.18.20105155 id = cord-315046-ltmuw6f8 author = Li, Keying title = SARS‐CoV‐2 infection‐induced immune responses: friends or foes? date = 2020-05-23 keywords = SARS; cell summary = 6-7 SARS-COV-2-infected patients were observed to have massive accumulation of inflammatory cytokines and aberrant T cell responses compared to healthy individuals, providing evidence that COVID-19 may be an immune interrelated disease. [12] [13] So, viral RNA and S protein of SARS-related coronaviruses may have evolved as major PAMPs which can mediate innate immune signaling cascades, initiating an antiviral state in infected-cells. All rights reserved SARS-CoV-2-induced respiratory distress syndrome may involve deranged innate immune effector molecule production, abnormal elevation of inflammatory immune cells and cytokine storms. Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Cell Responses Are Required for Protection from Clinical Disease and for Virus Clearance in Severe Acute Respiratory Syndrome Coronavirus-Infected Mice▿ Response of Memory CD8+ T Cells to Severe Acute Respiratory Syndrome (SARS) Coronavirus in Recovered SARS Patients and Healthy Individuals doi = 10.1111/sji.12895 id = cord-262841-nr42rs8f author = Li, Lanjuan title = SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date = 2003-12-31 keywords = RNA; SARS summary = Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, "replicative intermediates") and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Although the virus has been identified Abbreviations: BNIBernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany; BSL3biosafety level 3; CoVcoronavirus; MHVmouse hepatitis virus; PCRpolymerase chain reaction; minus -RNAreplicative negative-stranded RNA; plus -RNApositive-stranded genomic RNA; RTreverse transcription; SARSsevere acute respiratory syndrome; SCAsodium citrate anticoagulant. In order to evaluate (i) whether SARS-CoV can infect peripheral blood mononuclear cells (PBMCs) of infected persons, (ii) whether the virus can replicate in their PBMCs, and (iii) to reveal any dynamic changes to the virus during the course of the disease, we carried out follow-up investigations on the plusand minus-RNA forms in SARS patients. doi = 10.1016/s1386-6532(03)00195-1 id = cord-305582-3hmsknon author = Li, Lei title = Therapeutic strategies for critically ill patients with COVID-19 date = 2020-04-20 keywords = COVID-19; MERS; SARS; patient; treatment summary = In the present article, we have summarized the promising drugs, adjunctive agents, respiratory supportive strategies, as well as circulation management, multiple organ function monitoring and appropriate nutritional strategies for the treatment of COVID-19 in the ICU based on the previous experience of treating other viral infections and influenza. According to the latest version of diagnosis and treatment guidelines, confirmed cases infected with 2019-nCoV are classified to have severe illness once complying with one of the following symptoms: (1) anhelation, respiratory rate ≥ 30 times/min; (2) oxygen saturation at rest ≤ 93%; (3) PaO2/FiO2 ≤ 300 mmHg; and classified to be the critical/life-threatening illness once complying with one of the following symptoms: (1) respiratory failure, mechanical ventilation needed; (2) shock; (3) other organ dysfunction syndrome and requirement of intensive care unit admission. doi = 10.1186/s13613-020-00661-z id = cord-262735-xj9md751 author = Li, Lian Yong title = Digestive system involvement of novel coronavirus infection: Prevention and control infection from a gastroenterology perspective date = 2020-05-12 keywords = SARS; coronavirus summary = In this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of COVID‐19; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of SARS‐CoV‐2 infection in the digestive endoscopy room. Gastrointestinal manifestation in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection above, by adopting single-cell RNA-sequencing technology from two cohort samples, a recent study has shown that ACE2 is highly expressed in cholangiocytes rather than the hepatocytes or other interstitial cells. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1111/1751-2980.12862 id = cord-348178-6bjimde4 author = Li, Ling title = Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date = 2005-09-15 keywords = BSL-3; SARS; area summary = title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) doi = 10.1086/432720 id = cord-284008-vlwdtjbe author = Li, Na title = The Application of Corticosteroids in COVID-19: A Two-edged Sword date = 2020-06-25 keywords = COVID-19; SARS; corticosteroid summary = Their study revealed that proper corticosteroid treatment resulted in lower mortality and shorter hospitalization stay in patients with critical SARS with an oxygenation index (OI) of <300 mm Hg, and it was not associated with significant secondary lower respiratory infection and other complications. [21] described the effect of different doses of adjuvant corticosteroid therapy on 30-or 60-day mortality of patients with influenza A (H1N1) pdm09 viral pneumonia through a retrospective analysis. The results of stratified analysis based on the doses of corticosteroids showed that only treatment with low-to moderate-dose corticosteroid could reduce 30-and 60-day mortality of patients with severe infection with PaO2/FiO2 <300 mm Hg. However, corticosteroids at any dose increased the 60-day mortality of patients with mild infection with PaO2/FiO2 >300 mm Hg. Cao et al. [25] reported the clinical characteristics and treatment of patients with COVID-19 with ARDS in a study available on the medRxiv preprint server. doi = 10.2478/jtim-2020-0011 id = cord-353862-7xe3fvd5 author = Li, Na title = Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date = 2020-03-30 keywords = SARS; Wuhan; covid-19 summary = METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. doi = 10.1093/cid/ciaa352 id = cord-287054-zmxpuynv author = Li, Ning title = Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date = 2020-08-25 keywords = China; PCR; SARS; detection summary = Since March 3, 2020, three methods have been used for the diagnosis of novel coronavirus pneumonia: i) Detection of positive 2019-nCoV nucleic acids by RT-PCR; ii) viral gene sequencing to detect known 2019-nCoV sequences; and iii) the identification of positive 2019-nCoV-specific IgM and IgG antibodies in serum (15) . The China National Medical Products Administration has approved a gene sequencing system (ultra-high-throughput sequencer DNBSEQ-T7), supporting analysis software and nucleic acid detection kits (Table Ⅲ ), which can identify and diagnose coronaviruses, including 2019-nCoV and other infectious respiratory pathogens and enable rapid detection of viral sequences (22) . The clinical application of the total antibody detection can improve limitations, including slow speed of nucleic acid detection in suspected patients, complex sampling, low sensitivity and the requirement for high-level biosafety measures for the control and prevention of the current 2019-nCoV epidemic (74) . doi = 10.3892/etm.2020.9142 id = cord-291790-z5rwznmv author = Li, Qianqian title = The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity date = 2020-07-17 keywords = RBD; SARS; d614 summary = We first tested the infectivity of 106 pseudotyped viruses (80 natural variants and 26 129 glycosylation mutants) in 293T-hACE2 cells, where a difference by 4 -fold in RLU compared 130 with the reference Wuhan-1 strain (GenBank: MN908947) was deemed as being significant 131 ( Figure S1 ). Notably, some RBD variants such as A475V 283 and F490L have been confirmed to have decreased sensitivity to both human sera and multiple 284 neutralizing mAbs. A475V reduced the sensitivity to 6 mAbs out of the 13 mAb used in this study, 285 while F490L reduced the sensitivity to neutralization by 3 mAbs. It is possible that antibodies in 286 14 convalescent sera are able to neutralize these critical epitopes targeted by these mAbs that are 287 known to disrupt the binding of the S protein to hACE2 receptor (Ju et Serial dilutions of mAb preparations were pre-incubated with the pseudotyped viruses at 37°C for 355 one hour before they were added to Huh-7 cells. doi = 10.1016/j.cell.2020.07.012 id = cord-310680-klywz85w author = Li, Qihan title = The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect date = 2005-04-06 keywords = SARS; cell; protein summary = The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The pathological analysis of the lung tissue from the deceased patients revealed severe Abbreviations: SARS-CoV, severe acute respiratory syndrome coronavirus; BTF3, basic transcription factor-3; ATF5, activation transcription factor-5; NADH, nicotinamide adenine dinucleotide dehydrogenase; FBS, fetal bovine serum; DMEM, double minimal essential media; QDO, quartdrop-out; NC, nitrocellulose; HE, hematoxyline and eosin method; GFP, green fluorescence protein; GST, glutathione S-transferase * Corresponding author. To further investigate the contribution of this interaction to the cytopathic effect of SARS-CoV, a detection series of mitochondrial function and the activity of the oxido-reductase system in the human embryo lung fibroblast transfected with the nsp10 gene was performed. doi = 10.1016/j.jcv.2004.12.019 id = cord-024989-0o6agnrc author = Li, Qihao title = Prediction and analysis of key protein structures of 2019-nCoV date = 2020-05-12 keywords = ACE2; SARS; protein summary = Aim: The purpose of this study was to predict and analyze the structure and function of 2019-novel Coronavirus (nCoV) key proteins. Differential key protein structure analysis of 2019-nCoV Although some amino acids were inserted in two positions of nsp3 in orf1ab [23] , the insertion sites were in the nsp3b and nsp3c regions, which are mainly related to the binding reaction of nucleic acids. Back-mutating mutant amino acids to study the functional change of RBD of S protein In order to study the effect of interactional amino acid changes in 2019-nCoV-ACE2 binding region RBD, we mutated the changed three amino acid residues (Glu 470 , Gln 484 and Asn 487 ) within the RBD structure back to the original amino acids. • We elaborated the sequence and structure differences in each key protein of 2019-nCoV and other bat SARS coronaviruses (CoVs). doi = 10.2217/fvl-2020-0020 id = cord-270622-aofva2ab author = Li, Qizhang title = Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 date = 2020-08-26 keywords = SARS; TMPRSS2; drug summary = title: Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2 Based on the "steric-clashes alleviating receptor (SCAR)" strategy developed in our lab recently, we screened the library of clinic and investigational drugs, and identified nine drugs that might be repurposed as covalent inhibitors of the priming proteases (cathepsin B, cathepsin L, and TMPRSS2) of the spike protein of SARS-CoV-2. After careful filtering and 79 evaluation, we identified five (trapoxin B, neratinib, HKI-357, domatinostat and (Z)-dacomitinib) 80 potential covalent inhibitors for CatB, three (neratinib, HKI-357 and (Z)-dacomitinib) for CatL Although the docked poses 160 were slightly different on these two proteins, the warheads of these drugs were also at the positions 161 suitable for covalent bonding (Figure 3F-H) Taken together, using our SCARdock protocol, we identified nine drugs that might be repurposed as 229 the covalent inhibitors of the priming proteases of the S protein of SARS-CoV-2. doi = 10.1016/j.csbj.2020.08.016 id = cord-326882-bbn1tfq5 author = Li, Quan title = Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date = 2020-04-14 keywords = ACE2; SARS summary = We set out to examine genetic differences in the human angiotensin-converting enzyme 2 (hACE2) gene, as its receptor serves as a cellular entry for SARSCoV-2. To explore the variability in genetic polymorphisms and expression in human ACE2 (hACE2), we set out to determine if there were any differences between the Asian and Caucasian populations for ACE2 polymorphisms and compare the variability of hACE2 expression in peripheral blood among eight different populations. In order to investigate whether differences in genetic variations exist between Caucasians and Asians and if these variants can influence the efficiency of cell entry of SARS-CoV-2, we retrieved the variants in the hACE2 from gnomAD v2.1 exomes13. Asians and Other Races Express Similar Levels of and Share the Same Genetic Polymorphisms of the SARS-CoV-2 Cell-Entry Receptor doi = 10.1101/2020.04.14.041434 id = cord-293180-f1ulk9ce author = Li, R W K title = Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs date = 2004-08-14 keywords = SARS; aerosol; dental; patient summary = Special management protocols and modified measures that regulate droplet and aerosol contamination in a dental setting have to be introduced and may include the reduction or avoidance of droplet/aerosol generation, the disinfection of the treatment field, application of rubber dam, pre-procedural antiseptic mouthrinse and the dilution and efficient removal of contaminated ambient air. In the first part of this two-part article an account of the epidemiology, virology, pathology and management of Severe Acute Respiratory Syndrome (SARS) was provided together with public health issues and general aspects of infection control. On the other hand smaller droplets (or aerosols, generally under 10 µm in size) or small-particle residue of evaporated droplets are usually airborne and are entrained in the air for a lengthy period • SARS is a highly infectious disease and dental personnel are likely to be at risk because of the nature of their profession, working in close proximity to the patient. doi = 10.1038/sj.bdj.4811522 id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 keywords = IFN; PEDV; RNA; SARS; protein; rig; virus summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. doi = 10.3390/pathogens9050367 id = cord-301626-7ow1jja4 author = Li, Shih-Wen title = SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6 date = 2016-05-05 keywords = SARS; TLR7; figure summary = Severe acute respiratory syndrome coronavirus (SARS-CoV) papain-like protease (PLPro) reportedly inhibits the production of type I interferons (IFNs) and pro-inflammatory cytokines in Toll-like receptor 3 (TLR3) and retinoic acid-inducible gene 1 (RIG-I) pathways. The decrease in the activated state of TRAF3 and TRAF6 correlated with the inactivation of TBK1 in response to IMQ by PLPro. The results revealed that the antagonism of SARS-CoV PLPro on TLR7-mediated innate immunity was associated with the negative regulation of TRAF3/6-TBK1-IRF3/NF-κB/AP1 signals. To examine whether SARS-CoV PLPro modulates the TLR7 signaling pathway, stable transfected promonocyte cells expressing PLPro and vector control cells were established, treated with TLR7 agonist (imiquimod (IMQ)), then further analyzed for activation of type I IFN production ( Figure 1 ). To examine the inhibitory mechanism of TLR7 antagonism by SARS-CoV PLPro, differential profiles of ubiquitin-conjugated proteins in the vector control and PLPro-expressing cells in the absence or presence of IMQ were analyzed using immune-precipitation ( Figure 5A,B) . doi = 10.3390/ijms17050678 id = cord-273764-itu39mln author = Li, Taisheng title = Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date = 2006-12-20 keywords = CTL; SARS summary = In this report, we have sequentially monitored 30 recovered patients over a two-year period to characterize temporal changes in SARS-CoV-specific antibody responses as well as cytotoxic T cell (CTL) responses. As show in Fig. 1 , recovered patients clearly experienced two distinct phases of cell restoration in the peripheral blood; an initial rapid phase for all the cell populations studied in the first 3 months after the onset of symptoms followed by a significant slower phase during the subsequent months. To study the sequential changes in CTL responses against SARS-CoV, we used ELISPOT-based technique to quantify the number of INF-c releasing cells in the peripheral blood against peptide pools covering the entire N protein derived from the Urbani strain [3] . We have shown for the first time that recovered patients have persistent and robust binding as well as neutralizing antibody and CTL responses throughout the study period with a moderate decline one year after the onset of symptoms. doi = 10.1371/journal.pone.0000024 id = cord-297942-6wdwrttn author = Li, Taisheng title = Diagnosis and clinical management of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection: an operational recommendation of Peking Union Medical College Hospital (V2.0): Working Group of 2019 Novel Coronavirus, Peking Union Medical College Hospital date = 2020-03-14 keywords = Medical; SARS summary = To standardize the clinical diagnosis and treatment, Peking Union Medical College Hospital (PUMCH) has established a working group and formulated the following operational recommendation regarding "Diagnosis and Clinical Management of Severe Acute Respiratory Syndrome Coronavirus 2 Infection" (V2.0). According to the definition of the National Health Commission [1] , patients in accordance with one of the following standards should be hospitalized and transferred to Beijing designated medical institution as soon as possible; (1) respiratory rate increased (≥30 per min) or dyspnoea; (2) oxygen saturation ≤ 95% when breathing ambient air, or arterial oxygen tension (PaO₂) over inspiratory oxygen fraction (FIO₂) of less than 300 mm Hg (1 mm Hg equals to 0.133 kPa); (3) lung imaging indicating multilobular lesions or progression of lesions over 50% within 48 h; (4) quick sequential organ failure assessment (qSOFA) score ≥2; (5) community-acquired pneumonia-65 (CURB-65) score ≥ 1; (6) combined pneumothorax; (7) other clinical conditions that require hospitalization. doi = 10.1080/22221751.2020.1735265 id = cord-321455-ooouqna7 author = Li, Tao title = Characteristics of laboratory indexes in COVID-19 patients with non-severe symptoms in Hefei City, China: diagnostic value in organ injuries date = 2020-07-01 keywords = SARS; covid-19 summary = In the peripheral blood system of non-severe symptom COVID-19 patients, lymphocytes, eosinophils, basophils, total procollagen type 1 amino-terminal propeptide, osteocalcin N-terminal, thyroid-stimulating hormone, growth hormone, and insulin-like growth factor–binding protein 3 significantly decreased, and total protein, albumin, alanine transaminase, alkaline phosphatase, γ-glutamyl transferase, activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer, fibrinogen degradation products, human epididymal protein 4, serum ferritin, and C-reactive protein were elevated. In the process of continuous monitoring, the expression of CRE in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, and 7th days of admission, and showed an overall downward trend (Fig. 3a) . The expression of Ca 2+ in patients with COVID-19 were significantly lower than those in the controls on the 1st, 4th, 7th and 10th days of admission, and showed an overall upward trend (Fig. 3d ). doi = 10.1007/s10096-020-03967-9 id = cord-328484-4iptwc3n author = Li, Tao title = Clinical Characteristics of 312 Hospitalized Older Patients with COVID-19 in Wuhan, China date = 2020-07-15 keywords = COVID-19; SARS; patient summary = Although some case series have been published, no previous studies focused on older patients exclusively (Novel Coronavirus Pneumonia Emergency Response Epidemiology Team, 2020; Fu et al., 2020; . Further regression analysis suggested that age(OR 1.59, 95%CI 1.13-2.08), SOFA score(OR 5.89, 95%CI 3.48-7.96), APACHEⅡ score(OR 3.13, 95%CI 1.85-5.62), platelet count＜125×10 9 /L(OR 2.36, 95%CI 1.03-4.14), d-dimer(OR 4.37, 95%CI 2.58-7.16), creatinine＞133μmol/L(OR 1.85, 95%CI 1.12-3.04), interleukin-6(OR 4.32, 95%CI 2.07-7.13), and lung consolidation(OR 1.94, 95%CI 1.45-4.27) on admission were independent risk factors for severe COVID-19 (Table 3) . This study compared clinical characteristics between non-severe and severe COVID-19 cases among older patients, and identified several risk factors for severe cases. This study identified several risk factors for severe COVID-19 cases among older patients. Age, SOFA score, APACHEⅡ score, platelet count＜125×109/L, d-dimer, creatinine＞ 133μmol/L, interleukin-6, and lung consolidation on admission were independent risk factors for severe cases among older patients with COVID-19. doi = 10.1016/j.archger.2020.104185 id = cord-012045-1cqqj84n author = Li, Tiao title = The Role of Deubiquitinating Enzymes in Acute Lung Injury and Acute Respiratory Distress Syndrome date = 2020-07-08 keywords = ALI; ARDS; CYLD; SARS; regulate summary = doi = 10.3390/ijms21144842 id = cord-332134-88wfcc3y author = Li, Tingting title = A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date = 2020-09-24 keywords = Fig; RBD; SARS summary = title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection Molecular mechanism for neutralization 157 Structure alignment of SR4-, MR17-and ACE2-RBD 4 showed that both sybodies 158 engage with RBD at the receptor-binding motif (RBM) ( Fig. 2A, 2B) . Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. As LR5 showed 209 higher affinity and neutralization activity than LR1 (Fig. 1A) , we fused this non-210 competing sybody to the N-terminal of MR3 with various length of GS linkers ranging 211 from 13 to 34 amino acids (Extended Data Table S1 ). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with 803 doi = 10.1101/2020.06.09.143438 id = cord-264051-ps0x2es1 author = Li, Wei title = Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date = 2020-11-05 keywords = HEK293; RNA; SARS; covid-19 summary = Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Besides, these virus fragments containing HIS can increase the H3K27 acetylation (H3K27ac) enrichment at their corresponding regions of the human genome in different mammalian cells and activate the expression of adjacent and distant genes associated with inflammation. Collectively, we identified HIS in SARS-CoV-2 genome, and the targeted human genome loci enriched with cytokines genes suggested that HIS may underly the clinical characteristics of COVID-19 patients and serve as a vital player in the pathological progression. doi = 10.1101/2020.11.04.361576 id = cord-300847-ycuiso0g author = Li, Wei title = Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date = 2020-06-02 keywords = Fig; RBD; SARS summary = We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. By using phage display we have previously identified a number of potent fully human mAbs (m396, m336, m102.4) against emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV) (4) , Middle East respiratory syndrome coronavirus (MERS-CoV) (5) and henipaviruses (6, 7) , respectively, which are also highly effective in animal models of infection (8) (9) (10) (11) ; one of them was administered on a compassionate basis to humans exposed to henipaviruses and successfully evaluated in a clinical trial (12) . Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak. doi = 10.1101/2020.05.13.093088 id = cord-332469-zegawla5 author = Li, Wei title = The characteristics of household transmission of COVID-19 date = 2020-04-17 keywords = SARS; household summary = Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. doi = 10.1093/cid/ciaa450 id = cord-339093-mwxkvwaz author = Li, Wei title = High potency of a bivalent human VH domain in SARS-CoV-2 animal models date = 2020-09-04 keywords = -fc; ACE2; RBD; SARS; ab8; figure summary = It potently neutralized mouse adapted SARS-CoV-2 in wild type mice at a dose as low as 2 mg/kg and exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection, possibly enhanced by its relatively small size. To identify potent neutralizing V H s against SARS-CoV-2, we panned our large (10 11 clones) and diverse phage-displayed human V H antibody library against recombinant RBD. One of those V H s, ab8, in an Fc (human IgG1, crystallizable fragment) fusion format, showed potent neutralization activity and specificity against SARS-CoV-2 both in vitro and in two animal models. They also suggest that the double mutations Q498T/P499Y on RBD did not influence V H -Fc ab8 binding and contribute to the validation of the mouse adapted SARS-CoV-2 model for evaluation of neutralizing antibody efficacy. In conclusion, we identified a fully human antibody V H domain that shows strong competition with ACE2 for binding to RBD and potent neutralization of SARS-CoV-2 in vitro and in two animal models. doi = 10.1016/j.cell.2020.09.007 id = cord-340472-9ijlj4so author = Li, Wenhui title = Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 date = 2005-03-24 keywords = ACE2; RBD; SARS summary = Figure 3B -D shows three views of the crystal structure of human ACE2, in which residues that convert rat ACE2 to an efficient SARS-CoV receptor are shown in red, and additional residues whose alteration interferes with S1-Ig association are shown in yellow. (C) Murine leukemia viruses (MLV) expressing green fluorescent protein (GFP), lacking its endogenous envelope glycoprotein (MLV-GFP), and pseudotyped with the S protein of SARS-CoV (TOR2 isolate) were incubated with HEK293T cells transfected with plasmids encoding the indicated human or rat ACE2 variants. We have shown that entry is the primary barrier to SARS-CoV infection of murine Surface plasmon resonance experiments in which the indicated RBD-Ig TOR2 variants shown in Figure 6B bound to immobilized anti-human antibody were assayed for association with soluble human ACE2. S-protein alterations at residues 479 and 487 are important for high-affinity association with human ACE2, and for efficient infection of cells expressing this receptor. doi = 10.1038/sj.emboj.7600640 id = cord-269087-f9hyntvf author = Li, X. title = A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19 date = 2020-04-04 keywords = COVID-19; SARS; child; patient summary = Results: We included 25 published literature references related to the epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. The risk factors which may suggest severe or critical progress for children are: Fast respiratory rate and/or; lethargy and drowsiness mental state and/or; lactate progressively increasing and/or; imaging showed bilateral or multi lobed infiltration, pleural effusion or rapidly expending of lesions in a short period of time and/or; less than 3 months old or those who underly diseases. To help better understand how it would affect children and what is the latest specific clinical and research finding on children with it, we provide a mini-review based on 25 literature references covering the fields of epidemiology, clinical manifestation, accessary examination, treatment, and prognosis of pediatric patients with COVID-19. According to the current literature on the pediatric cases, children confirmed with COVID-19 mostly had good prognosis, with considerably less severe to critical progress (5.9%) as compared to adult patients (18.5%). doi = 10.1101/2020.03.30.20044545 id = cord-252910-7qvnj6c8 author = Li, Xin title = The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date = 2020-09-21 keywords = ORF8; SARS; figure summary = In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Different from these studies, we previously reported several other findings on SARS-CoV-2 for the first time, including the following in particular: (1) the alternative translation of Nankai coding sequence (CDS) that characterize the rapid mutation rate of betacoronavirus at the nucleotide level [2] ; (2) a furin cleavage site (FCS) "RRAR" in the junction region between S1 and S2 subunits (junction FCS) of SARS-CoV-2 that may increase the efficiency of viral entry into cells [3] ; and (3) the use of 5'' untranslated-region (UTR) barcoding for the detection, identification, classification and phylogenetic analysis of-though not limited to-CoVs [4] . Using the insertions and deletions (InDels) at six sites, we identified two recently detected betacoronavirus strains RmYN01 and RmYN02 from a bat [6] and discovered that RmYN02 was a recombinant SARS2-like CoV strain. doi = 10.1101/2020.07.22.213926 id = cord-342947-dhe31r3a author = Li, Xin title = Preliminary recommendations for lung surgery during COVID‐19 epidemic period date = 2020-04-14 keywords = SARS summary = After SARS-CoV-2 infection has been excluded and space-occupying lesions in the lungs confirmed by computed tomography (CT) scan, they could be transferred to thoracic surgery for further diagnosis and treatment. • For peripheral solid nodules with a diameter of less than 3 cm considered as malignant lesions by PET-CT or percutaneous pulmonary puncture biopsy, short-term regular follow-up (once a month) can be recommended during the outbreak prevention and control period. 3 Therefore, we suggest that during the epidemic prevention and control period, whether the patient has pure GGNs, mixed GGNs or multiple GGNs (SARS-CoV-2 infection should be excluded for multiple GGNs), follow-up re-examination should be the main recommendation, and surgery should not be carried out. For patients undergoing emergency thoracic surgery, if the symptoms mentioned above occur, isolation measures should be taken during the operation, and the possibility of SARS-CoV-2 latent infection should be eliminated without delay. Preliminary recommendations for lung surgery during 2019 novel coronavirus disease (COVID-19) epidemic period doi = 10.1111/1759-7714.13423 id = cord-253905-zknmfgsh author = Li, Xingguang title = Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 date = 2020-03-11 keywords = CoV-2; SARS; figure summary = To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. Homology plot analysis of "dataset_6" also revealed that BetaCoV/bat/Yunnan/ RaTG13/2013 was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378), consistent with phylogenetic analysis ( Figure S5 ). 46, 47 Bayesian analyses with the tip-dating method using a strict clock as well as constant size coalescent tree prior indicated that SARS-CoV-2 is evolving at a rate of 1.24 × 10 −3 substitutions per site per year (Table 1 ), in accordance with our prior research 46, 47 and similar to that found for other human F I G U R E 4 Estimated maximum-clade-credibility tree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using tip-dating method. doi = 10.1002/jmv.25731 id = cord-298902-afek8kgr author = Li, Xingguang title = Transmission dynamics and evolutionary history of 2019‐nCoV date = 2020-02-14 keywords = SARS; figure summary = To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019‐nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. 19 In the present study, we investigated the time origin and genetic diversity of 2019-nCoV in humans based on 32 genomes of virus strains sampled from China, Thailand, and the USA with known sampling dates between 24 December 2019 and 23 January 2020. Likelihood-mapping analysis of "dataset_14" revealed that 100% of the quartets were distributed in the center of the triangle, indicating a strong star-like topology signal reflecting a novel virus, which may be due to exponential epidemic spread ( Figure 1A) . Of note, the strong star-like signal (100% of quartets were distributed in the center of the triangle) from "dataset_14" at the beginning of the virus outbreak suggests that 2019-nCoV initially exhibited low genetic divergence, with recent and rapid human-tohuman transmission. doi = 10.1002/jmv.25701 id = cord-262000-k32cb9ym author = Li, Xue-Ting title = Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 date = 2020-09-07 keywords = ACE2; SARS summary = title: Letter to the Editor: Increased plasma ACE2 concentration does not mean increased risk of SARS-CoV-2 infection and increased fatality rate of COVID-19 Angiotensin converting enzyme 2 (ACE2) has garnered widespread interest as the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19 pandemic, providing a critical link among COVID-19, inflammatory storm, ACE2 and cardiovascular disease 1,2 . Remarkably, recombinant human ACE2 (rhACE2), sACE2, ACE2-Fc, and ACE2-Ig are thought to be promising therapeutic approaches for COVID-19 patients with SARS-CoV-2 infection through competitive inhibiting the binding of viral Spike protein to mACE2 4 . Intriguingly, circulating Ang II level was obviously elevated in COVID-19 patients with lung injury (Table 1) 9 which further upregulates ADAM-17 activity by interacting with AT1 receptors, leading to more shedding of ACE2 and thereby accelerating renin-angiotensin-aldosterone system (RAAS)-mediated injury including severe cardiopulmonary damage (Fig. 1) (Table 1) 10 . doi = 10.1016/j.apsb.2020.09.003 id = cord-355943-bezpprrk author = Li, Y. title = Urine Proteome of COVID-19 Patients date = 2020-05-06 keywords = SARS; covid-19; figure summary = In this study, we performed proteomic profiling of urine samples from 32 healthy control individuals and 6 COVID-19 positive patients (3 mild and 3 severe). We found that urine proteome samples from the mild and severe COVID-19 patients with comorbidities can be clearly differentiated from healthy proteome samples based on the clustering analysis. We identified and quantified 1380 and 1641 proteins in urine samples from COVID-19 and two recovery person in total, which was significantly lower than that of healthy controls ( Figure 2B and 2C , Tables S2 and S3 ). The molecular features used to distinguish the patient type (M and S) in our classifier ( Figure 5B and 5D, Tables S4-5) contain several potential biomarkers which were highly associated with the clinical characteristics of mild and severe COVID-19. . https://doi.org/10.1101/2020.05.02.20088666 doi: medRxiv preprint dysregulated proteins in the COVID-19 patients. doi = 10.1101/2020.05.02.20088666 id = cord-320717-wk4zxmz9 author = Li, Yang title = Lack of Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2, China date = 2020-06-17 keywords = SARS summary = We report a pregnant woman with confirmed SARS-CoV-2 infection who underwent cesarean section delivery of a SARS-CoV-2-negative infant in Zhejiang Province, China. On days 4 and 5 of hospitalization, the woman''s sputum tests were negative for SARS-CoV-2, and she remained afebrile. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. A woman with coronavirus disease in her 35th week of pregnancy delivered an infant by cesarean section in a negative-pressure operating room. In conclusion, we report a pregnant woman with SARS-CoV-2 infection who delivered a healthy infant, suggesting that mother-to-child transmission is unlikely for this virus. Because our conclusions are limited by our sample size of 1, we cannot definitively state whether cesarean section is better than vaginal delivery for preventing transmission from a pregnant mother with SARS-CoV-2 infection. doi = 10.3201/eid2606.200287 id = cord-251986-ajlpb9li author = Li, Yan‐Chao title = The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date = 2020-03-11 keywords = SARS; respiratory summary = This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients doi = 10.1002/jmv.25728 id = cord-305640-tgowzrqo author = Li, Yong-Hua title = Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: Comparison with results of other viral markers date = 2005-07-15 keywords = SARS summary = A capture enzyme-enhanced chemiluminescence immunoassay (ECLIA) based on three specific monoclonal antibodies to detect the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in the serial serum samples from SARS patients was developed. The N protein is an extensively phosphorylated, highly basic protein, which interacts with viral RNA and makes up the viral core and nucleocapsid (Lai, 2003 the diagnosis of SARS depends basically upon detecting SARS-CoV RNA by RT-PCR and/or testing specific antibodies directed against SARS-CoV by assays based on cultured virus or recombinant viral antigens. In the present study, a capture ECLIA was developed based on three monoclonal antibodies directed against the N protein of SARS-CoV, and the N protein in the longitudinal serum samples from the SARS patients were detected with this method. The detection of the N protein of SARS-CoV in serum samples by ECLIA appears to be superior to the detection of the viral RNA by RT-PCR in rapid diagnosis of SARS patients. doi = 10.1016/j.jviromet.2005.06.001 id = cord-336394-1xf2sxtv author = Li, Yu title = The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date = 2020-05-13 keywords = SARS summary = Here, bioinformatics approaches combining human-virus protein interaction prediction and protein docking based on crystal structures have revealed the high affinity between human dipeptidyl peptidase 4 (DPP4) and the spike (S) receptor-binding domain of SARS-CoV-2. The atomic interaction details of the 145 binding interface showed that almost all of the contacting residues of DPP4 with 146 SARS-CoV-2-S RBD were consistent with those for binding with MERS-CoV-S 147 RBD (Table S1 ) (Song et al., 2014) . In addition, the models evaluated the 228 binding potential, interface residues and structures that were consistent with those 229 Comparison of the key residues between human and pangolin DPP4 protein 471 Identification of residues on human receptor DPP4 critical for MERS-CoV binding 401 and entry Structure of MERS-CoV spike receptor-binding domain 417 complexed with human receptor DPP4 SARS-CoV-2 spike receptor-binding domain has a potentially high affinity with DPP4 doi = 10.1016/j.isci.2020.101160 id = cord-348752-bbghqy1a author = Li, Yuguo title = Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant date = 2020-04-22 keywords = April; SARS; preprint summary = We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions. Methods: We collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Results: Three families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Year''s Eve (January 24, 2020) at three neighboring tables. healthy) of each person at non-A tables as the dependent variable and applied a binary logistic regression model to investigate the association between the measured concentrations of trace gas and infection probability. doi = 10.1101/2020.04.16.20067728 id = cord-253438-k8iqv1jb author = Li, Yujun title = SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig date = 2020-10-27 keywords = ACE2; Fig; RBD; SARS summary = We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. The RBD of Bat-CoV RaTG13 then showed a binding profile significantly different and narrower than the other three RBDs. Note that human ACE2 and ACE2 orthologs of some domestic animals, including camels, cattle, horses, goats, sheep, cats, and rabbits, support efficient binding to all the four tested RBDs, suggesting that these ACE2 orthologs might be generally functional for supporting cell entry of the four tested viruses. doi = 10.1128/jvi.01283-20 id = cord-297989-4grwa4ab author = Li, Yunjin title = Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID‐19/SARS‐CoV‐2 date = 2020-07-08 keywords = ACE2; SARS summary = Since the expression profile of ACE2, a crucial cell entry receptor for SARS‐CoV‐2, could indicate the susceptibility to SARS‐CoV‐2 infection, here we systematically dissected ACE2 expression using large‐scale multi‐omics data from 30 organs/tissues, 33 cancer types and some common chronic diseases involving >28 000 samples. Furthermore, the patients with common chronic diseases regarding angiocardiopathy, type 2 diabetes, liver, pneumonia and hypertension were also with higher ACE2 expression compared to related controls, which were validated using independent data sets. Collectively, our study may reveal a novel important mechanism that the patients with certain cancers and chronic diseases may express higher ACE2 expression compared to the individuals without diseases, which could lead to their higher susceptibility to multi‐organ injury of SARS‐CoV‐2 infection. Here, we systematically analysed ACE2 expression using largescale multi-omics data from a variety of organs/tissues and cancer types, as well as the common chronic diseases of heart, liver, diabetes, pneumonia and hypertension involving a total of >28 000 samples. doi = 10.1111/jcmm.15607 id = cord-257135-xt4w0baw author = Li, Zhengqian title = The brain, another potential target organ, needs early protection from SARS-CoV-2 neuroinvasion date = 2020-03-31 keywords = China; SARS summary = Based on the existing evidence and lessons from SARS outbreak in 2003, our attention should not be confined to the general organs whose dysfunctions were relatively easy to be observed or examined such as lung, kidney, and liver; at the same time, the brain should not be neglected due to the potential neuroinvasion of SARS-CoV-2, which prompts us to keep an alert on the onset of neurological symptoms, early diagnostics, and neuroprotection. So far, no direct evidence of entry of SARS-CoV-2 into the CNS has been reported in any international peer-reviewed journal, although some researchers have proposed that the neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients . Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients doi = 10.1007/s11427-020-1690-y id = cord-351031-e8suoeim author = Liang En Ian, Wee title = Containing COVID-19 outside the isolation ward: the impact of an infection control bundle on environmental contamination and transmission in a cohorted general ward date = 2020-06-26 keywords = COVID-19; RSW; SARS summary = In these general wards, termed as respiratory surveillance wards (RSWs), an infection control bundle was implemented comprising infrastructural enhancements, improved personal-protective-equipment (PPE), and social distancing between patients, in order to mitigate the risk of a potential COVID-19 case initially admitted outside of an AIIR. The main finding of our study was that an infection control bundle comprising infrastructural enhancements, improved PPE and social distancing mitigated the risk of environmental contamination and transmission in a cohorted general ward setting. In conclusion, over a 3-month period, our institution implemented a bundle of interventions to reduce risk of intra-hospital transmission of COVID-19 in a multi-bedded cohorted general ward setting, through the implementation of an infection control bundle comprising infrastructural enhancements, improved PPE, and social distancing between patients. doi = 10.1016/j.ajic.2020.06.188 id = cord-312664-tgpaidhp author = Liang, Julia title = Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex date = 2020-05-28 keywords = CoV-2; SARS summary = title: Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes an illness known as COVID-19, which has been declared a global pandemic with over 2 million confirmed cases and 137,000 deaths in 185 countries and regions at the time of writing (16 April 2020), over a quarter of these cases being in the United States. Further, molecular dynamics simulations highlight the stability of the interaction of the α-ketoamide 13b ligand with the SARS-CoV-2 M(pro) (ΔG = -25.2 and -22.3 kcal/mol for protomers A and B). Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . Here, we performed molecular docking and molecular dynamics simulations to further characterize the interaction of α-ketoamide 13b with the active site of the SARS-CoV-2 M pro . doi = 10.1016/j.compbiolchem.2020.107292 id = cord-276394-s9y11oep author = Liang, W. title = Hindsight: A re-analysis of the severe acute respiratory syndrome outbreak in Beijing date = 2007-10-31 keywords = Beijing; SARS summary = Summary Objective To review the severe acute respiratory syndrome (SARS) epidemic in Beijing using basic epidemiological principles omitted from the original analysis. Previously excluded cases were included for plotting on an epidemic curve, and basic spot mapping for distribution of cases was used from attack rates recalculated for age, gender, occupation, residential location, date of onset of illness and demographics. If a spot map of incidence density rates was used during the early phase of the outbreak, the inner city might have been identified as a major risk factor requiring rapid quarantining. 8 Re-analysis included an epidemic curve for ''probable'' SARS cases only and calculations of the Beijing population-based rate, stratified by age and sex, using the Fifth General Census of China (version 2000). The import phase of the Beijing epidemic occurred rapidly, between 1 and 10 March, with 14 cases admitted with an acute pneumonia of unknown cause without history taken for exposure to a case of respiratory illness or environmental contact. doi = 10.1016/j.puhe.2007.02.023 id = cord-332348-yi85sfks author = Liang, Yujie title = Neurosensory dysfunction: a diagnostic marker of early COVID-19 date = 2020-06-29 keywords = COVID-19; SARS summary = Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. doi = 10.1016/j.ijid.2020.06.086 id = cord-340746-icuzy3vp author = Liang, Yunfei title = Comprehensive Antibody Epitope Mapping of the Nucleocapsid Protein of Severe Acute Respiratory Syndrome (SARS) Coronavirus: Insight into the Humoral Immunity of SARS date = 2005-08-01 keywords = Fig; SARS; epitope; protein summary = We identified the immunodominant antigenic sites responsible for the antibodies in sera from SARS patients and antisera from small animals and differentiated the linear from the conformational antibody-combining sites comprising the natural epitopes by use of yeast surface display. The full-length SARS-CoV N protein (amino acids 1-422) was expressed on the yeast cell surface, as indicated by reactivity of the Xpress epitope tag with the anti-Xpress antibody (Fig. 2) . We used heat denaturation of the fusion proteins tethered to the EBY100 yeast cell surface to categorize the specific linear and conformational SARS-CoV N protein mAb epitopes (35, 36 ) . Our subsequent determination of the antigenic structures of the N protein responsible for antibodies in polyclonal antisera from immunized mice and sera from convalescent SARS patients demonstrated the immunogenic specificity of 3 conformational (amino acids 1-69, 68 -213, and 337-422) and 3 linear (amino acids 1-69, 121-213, and 337-422) epitopes (Fig. 1C) . doi = 10.1373/clinchem.2005.051045 id = cord-296227-dm1wkpnv author = Liao, L. title = Can N95 respirators be reused after disinfection? And for how many times? date = 2020-04-07 keywords = N95; SARS; UVGI summary = We found that heating (<100 {degrees}C) under various humidities (up to 100% RH at 75 {degrees}C) and ultraviolet (UV) irradiation were the most promising candidates for mask reuse in the modern hospital infrastructure (up to 20 cycles), when tested on a fabric with particle filtration efficiency [≥]95%. For dangerous airborne particulates, including viral aerosols during the current COVID-19 pandemic, the United States Centers for Disease Control and Prevention (CDC) recommends the usage of N95 filtering facepiece respirators (FFR) as personal protective equipment for healthcare professionals [18] [19] [20] . We applied these treatments (see methods for details) to a meltblown fabric (20 g/m 2 ) that has an initial efficiency of ≥95%, which may be integrated into N95 FFRs. We evaluated the filtration efficiency and pressure drop of these treated fabrics via industry standard equipment, Automated Filter Tester 8130A (TSI), with a flow rate of 32 L/min. doi = 10.1101/2020.04.01.20050443 id = cord-335446-8l1vfsbc author = Liao, M. title = The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing date = 2020-02-26 keywords = CD8; SARS; covid-19 summary = Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. To characterize the immune microenvironment of the SARS-CoV-2-infected lung, we performed scRNA-seq analysis of single cells in the lung BALF (37, 820 cells) using the 10X Genomics platform, from 3 of recovered mild cases and 3 of severe cases ( Figure 1A , Table 1 ). Our data indicated that the monocytes are recruited from circulation (FCN1 + ) to the lung to fuel the inflammation during severe diseases, and some monocytes may further go through the differentiation process into the SPP1 + populations and eventually the FABP4 + AMs. robust and early T cell response played crucial roles in viral clearance during acute respiratory infections [14] . doi = 10.1101/2020.02.23.20026690 id = cord-271930-9a18h2tr author = Licari, Amelia title = Allergy and asthma in children and adolescents during the COVID outbreak: What we know and how we could prevent allergy and asthma flares date = 2020-05-28 keywords = SARS; covid-19 summary = The Center for Disease Control and Prevention (CDC) initially proposed that patients with chronic lung diseases, including moderate-severe asthma, and allergy may have a higher risk of developing severe COVID-19 than otherwise healthy people (https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/asthma.html). Allergic children had a significantly higher (P < .0001) eosinophil count than COVID-19 patients. However, it has been recently commented that chronic respiratory diseases, including COPD and asthma, seem to be underrepresented in the comorbidities of COVID-19 patients. On the other hand, children and adolescents with allergy and asthma should be adequately managed during this COVID-19 pandemic, also considering the restrictive rules released by governmental authorities that impose a strict limitation on movements. 10 In summary, the rapid spread of SARS-CoV-2 infection and the lack of specific antiviral therapies and vaccines currently require additional medical efforts to prevent COVID-19 and mostly protect patients with chronic diseases. Association of respiratory allergy, asthma, and expression of the SARS-CoV-2 receptor, ACE2 Do chronic respiratory diseases or their treatment affect the risk of SARS-CoV-2 infection? doi = 10.1111/all.14369 id = cord-298866-dzatps7b author = Licskai, Christopher title = Key highlights from the Canadian Thoracic Society’s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic date = 2020-05-28 keywords = COVID-19; SARS summary = title: Key highlights from the Canadian Thoracic Society''s Position Statement on the Optimization of Asthma Management during the COVID-19 Pandemic In general, asthma maintenance and exacerbation management should continue according to national and international guidelines during the COVID-19 pandemic, however treatment decisions should be individualized based on patient characteristics. 6, 7, 8 Are patients with asthma at risk of having an exacerbation triggered by SARS-CoV-2 (COVID 19)? The Centers for Disease Control identify people with asthma as a group that may be at higher risk for severe illness from COVID-19. No. Asthma patients should restart or continue their prescribed inhaled corticosteroid or inhaled corticosteroid steroid plus long-acting beta 2 -agonist maintenance therapy to improve disease control and to reduce the severity of exacerbations, including exacerbations that may be caused by SARS-CoV-2. Yes. There is no evidence that inhaled corticosteroids increase the risk of acquiring COVID-19 or that inhaled corticosteroids increase the severity of infection. doi = 10.1016/j.chest.2020.05.551 id = cord-318909-h5b7mncf author = Liguori, Claudio title = Subjective neurological symptoms frequently occur in patients with SARS-CoV2 infection date = 2020-05-19 keywords = COVID-19; SARS; patient summary = 7 A large retrospective analysis carried out in China on 214 patients affected by SARS-CoV2 infection confirmed that hospitalized patients complained of subjective neurological symptoms (sNS) in a 36 .4% of cases, including headache, disturbed consciousness, and paresthesia as the most frequent. This observational study, carried out in 103 patients affected by SARS-CoV2 infection, documented the high prevalence of sNS during the course of the disease, even immediately after admission to the Hospital. Although the involvement of nervous system during SARS-CoV2 infection has been extensively proposed, [10] [11] [12] few studies focused the investigation on neurological symptoms in patients with 7 The largest study examining the neurological manifestations of hospitalized patients with COVID-19 was a retrospective analysis achieved by reviewing patients'' clinical charts. 15 In the present study, we performed a prospective observation in patients with non-severe respiratory form of SARS-CoV2 by using an anamnestic interview designed to better determinate the occurrence and type of sNS over the course of the disease. doi = 10.1016/j.bbi.2020.05.037 id = cord-334012-b2akycst author = Liguori, Claudio title = Sleep and wake impairment in patients with SARS-CoV2 infection date = 2020-07-17 keywords = SARS summary = Coronavirus Disease 2019 (COVID-19) is unquestionably a worldwide life-threatening condition causing severe acute respiratory distress; 1 however, pauci-symptomatic or non-severe forms of pneumonia currently represent the more frequent manifestations of the infection. [3] [4] Our NeuroCOVID-19 group performed a prospective observational study focused on the occurrence of subjective neurological symptoms in hospitalized patients with a non-severe respiratory form of COVID-19. 4 Here, we present data deriving from a secondary analysis of the previous study with the aims to emphasize and deepen the characteristics of sleep and wake impairment in patients with SARS-CoV2 infection and their relationships with the other neurological symptoms, white blood cells (WBC), C-reactive protein (CRP), and days of hospitalization. Considering patients with sleep impairment, they had higher CRP serum levels, more frequent dysgeusia, headache, and dizziness, and more concomitant neurological symptoms than patients without sleep alteration ( Table 1) . Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection doi = 10.1016/j.sleep.2020.06.036 id = cord-336366-2y68n8s0 author = Liguori, Claudio title = Depressive and anxiety symptoms in patients with SARS-CoV2 infection date = 2020-09-14 keywords = SARS summary = 5 Based on the study protocol, all patients underwent an anamnestic interview requiring a dichotomized answer (YES/NO) about 13 neurological symptoms (hyposmia, dysgeusia, auditory dysfunction, headache, confusion, dizziness, numbness/paresthesia, fatigue, daytime sleepiness, sleep impairment, muscle ache, depression, and anxiety). In this secondary analysis derived from this previous investigation, 5 we aimed at primarily focusing on the occurrence of depressive and anxiety symptoms in patients with COVID-19, also considering the possible correlation of these symptoms with the other neurological symptoms investigated and the demographic, clinical, and laboratory data achieved. 6 Depression, anxiety, and post-traumatic stress symptoms were more frequent in patients with COVID-19 compared to volunteers not affected by SARS-CoV2 infection. This result can be explained by a higher psychological burden in patients with several neurological symptoms, or by a more severe nervous system involvement also producing depression and anxiety. Subjective Neurological Symptoms Frequently Occur in Patients With SARS-CoV2 Infection doi = 10.1016/j.jad.2020.09.042 id = cord-281536-8y7yxcp4 author = Lim, Hocheol title = Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method date = 2020-10-08 keywords = FMO; RBD; SARS summary = title: Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method In this work, to find common hot spot amino acids on the interfaces between the RBD domain and hACE2 of the three complexes, RBD-SARS-CoV-2/hACE2 (twelve experimental structural data), RBD-SARS-CoV-1/ hACE2 (four experimental structural data), and RBD-HCoV-NL63/hACE2 (one experimental structural data), we performed FMO-DFTB3/D/PCM calculations. Consequently, we summarized the FMO-DFTB3/D/PCM/3D-SPIEs results as interaction maps and found the hot spot regions in RBD-SARS-CoV-2 and hACE2 at a QM level. In order to narrow down the hot spot regions between hACE2 and RBD-SARS-CoV-1, we performed FMO calculations on four RBD-SARS-CoV-1/antibody complexes (Supplementary Table S14-S19). In order to find common hot spot amino acids in RBD-SARS-CoV-1 against hACE2 and SARS-CoV-1 antibodies, we illustrated the FMO results with a 3D-SPIEs-based map. doi = 10.1038/s41598-020-73820-8 id = cord-352925-abry6oz3 author = Lim, Jia Yin title = Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic date = 2020-05-21 keywords = SARS summary = title: Hardware versus heartware: The need to address psychological well-being among operating room staff during the COVID-19 pandemic Months into the coronavirus disease (COVID-19) pandemic, healthcare workers continue the fight against an increasing disease burden worldwide. This requires mental resilience and perseverance to function under challenging working conditions, sometimes with limited resources and risking personal safety. [1] What often gets overlooked is the "heartware", such as addressing burnout, anxiety of perceived risks, moral injury [2] and the resultant long-term psychological impact that may impair performance and compromise staff and patient safety. [4] In this current pandemic, a considerable proportion of healthcare workers in China reported symptoms of depression, anxiety, insomnia, and distress, signifying the need for psychological support or interventions. [5] With these in mind, we recognized the need to prepare our anesthesia department staff for the threat and associated challenges when managing COVID-19 patients. Managing mental health challenges faced by healthcare workers during covid-19 pandemic doi = 10.1016/j.jclinane.2020.109891 id = cord-298696-rsifxvtj author = Lim, Meng-Kin title = Global response to pandemic flu: more research needed on a critical front date = 2006-10-13 keywords = Health; SARS; air summary = Given that air transportation is the one feature that most differentiates present day transmission scenarios from those in 1918, our present inability to prevent spread of influenza by international air travel, as reckoned by the World Health Organization, constitutes a major weakness in the current global preparedness plan against pandemic flu. Alas, the 2005 WHO report Avian influenza: assessing the pandemic has dismally concluded that "If only a few countries are affected, travel-related measures, such as exit screening for persons departing from affected areas, might delay international spread somewhat, but cannot stop it. Against a conservatively estimated US$800 billion a year that a human pandemic of avian influenza could cost the global economy [24] , not to mention the incalculable cost in terms of human lives [25] , it seems incredible that the aviation lessons of SARS have not led to an acceleration of scientific research and health policy evaluation aimed at strengthening public health defenses on the air transportation front. doi = 10.1186/1478-4505-4-8 id = cord-295514-vhymj0rw author = Lim, Peter A title = Impact of a viral respiratory epidemic on the practice of medicine and rehabilitation: Severe acute respiratory syndrome date = 2004-08-01 keywords = PPE; SARS; Singapore; patient; rehabilitation summary = Severe acute respiratory syndrome (SARS) is a new respiratory viral epidemic that originated in China but has affected many parts of the world, with devastating impact on economies and the practice of medicine and rehabilitation. Rehabilitation was significantly affected by SARS, because strict infection control measures run counter to principles such as multidisciplinary interactions, patients encouraging and learning from each other, and close physical contact during therapy. Rehabilitation medicine was increasingly affected by everstricter infection control measures regarding close contacts and interactions between health care workers. Rehabilitation medicine was directly affected when the entire neurology ward, including patients and health care staff, were transferred out to TTSH for isolation and observation because of suspicious clusters of fevers that involved both patients and staff. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.1016/j.apmr.2004.01.022 id = cord-329308-ipui7lo6 author = Lim, Soo title = Proper Management of People with Obesity during the COVID-19 Pandemic date = 2020-06-30 keywords = ACE2; COVID-19; SARS; angiotensin; obesity summary = During the COVID-19 pandemic, people have tended to gain weight because of environmental factors imposed by quarantine policies, such as decreased physical activity and increased consumption of unhealthy food. The common medications used to treat people with obesity, such as glucagon-like peptide-1 analogues, statins, and antiplatelets agents, should be continued because these agents have anti-inflammatory properties and play protective roles against cardiovascular and all-cause mortality. 54 A cumulative effect of chronic inflammation and hypercytokinemia seems to bring about a hyperinflammatory response through macrophage active syndrome, especially in patients with severe COVID-19 (Fig. 2) . Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Letter to the Editor: obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease doi = 10.7570/jomes20056 id = cord-264012-q2quyijg author = Lim, Su Bin title = ACE2-expressing endothelial cells in aging mouse brain date = 2020-07-11 keywords = ACE2; SARS summary = Further, scRNA-seq dataset specifically derived from brain vasculature in young adult and aged mice (T3) confirms the elevated ACE2 expression in subsets of the three identified cell types, which consist of 32.8% of the cell populations ( Fig. 1 C) . While our study provides a foundation for a more refined level of analysis of EC and vascular PC, a cell type that remains poorly understood despite its key roles in immune response and microvascular stability [17] , our analyses are limited only to the normal aging mouse and human brains, lacking the context of COVID-19 neuropathology. Despite the works that failed to identify direct signs of SARS-CoV-2 infection in the brains of COVID-19 patients [12, 13] , other lines of evidence support the neurotropism of the virus, as evidenced by experimental platforms leveraging human induced pluripotent stem cell (iPSC)derived dopaminergic neurons [22] and an organotypic brain model [23] . doi = 10.1101/2020.07.11.198770 id = cord-256808-lxlerb13 author = Lim, W.S title = Hospital management of adults with severe acute respiratory syndrome (SARS) if SARS re-emerges—updated 10 February 2004 date = 2004-06-02 keywords = Health; SARS summary = Severe Acute Respiratory Syndrome (SARS) is a potentially severe and highly infectious disease to which healthcare workers involved in the management of cases are particularly vulnerable. These guidelines briefly summarise optimal and safe practice for clinicians involved in the emergency care of patients with probable or confirmed SARS. During 2003 Severe Acute Respiratory Syndrome caused by a novel coronavirus (SARS-CoV) emerged as an infectious disease with a significant inhospital mortality and posed a considerable occupational risk for healthcare workers. Please discuss the classification of SARS patients with the Health Protection Agency''s Communicable Disease Surveillance Centre (CDSC) Duty doctor (Tel.: 0208-200-6868) and complete a standard SARS report form and fax to your local Consultant in Communicable Disease Control (CCDC) and CDSC (details at: http://www.hpa.org.uk/infections/ topics_az/SARS/forms.htm). Inform the local Health Protection Team/CCDC regarding the hospital discharge of patients to ensure follow-up in the community. Severe acute respiratory syndrome (SARS): infection control doi = 10.1016/j.jinf.2004.04.001 id = cord-319864-t6ql9hz2 author = Lima, Amorce title = Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens date = 2020-11-11 keywords = CDC; SARS summary = In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. In this study, we sought to describe a modified CDC SARS-CoV-2 assay validation and compare its performance and workflow to that of the NeuMoDx SARS-CoV-2 and DiaSorin Simplexa Covid-19 Direct assays using respiratory specimens. The primer/probe sets used in this validation were selected from regions of the SARS-CoV-2 virus nucleocapsid (N) gene and were described in the CDC EUA protocol for COVID-19 diagnostic testing (7) . Of the 43 samples used for comparison between modified CDC SARS-CoV-2 assay and Simplexa Covid 19 Direct assay, 37 samples were run within 2 days and 6 were run within 5 days of first testing. The clinical performance comparison between NeuMoDx SARS-CoV-2 assay, Simplexa Covid-19 Direct assay, and the modified CDC SARS-CoV-2 assay showed an overall agreement of 100%. doi = 10.1016/j.jcv.2020.104688 id = cord-338734-laeocs3j author = Lima, Amorce title = Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date = 2020-06-30 keywords = CDC; SARS summary = In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. A 149 series of two-fold dilutions of SARS-CoV-2 strain USA_WA1/2020 RNA were spiked in pooled 150 sputum at concentrations of 800 copies/ml to 0.05 copy/ml in order to determine the limit of 151 detection (LoD) of the assay. On the other hand, the average Ct values difference between 235 samples run within 2 days between DiaSorin Simplexa Covid 19 Direct assay and the modified 236 CDC SARS-CoV-2 assay was -2.42, and -6.0 between samples run within 5 days. In this study, we validated a modified CDC SARS-CoV-2 assay and compared its 263 performance to two commercial automated sample-to-answer assays for the detection of SARS-264 The difference is even greater 286 in samples that were run 5 days after the routine testing on the modified CDC SARS-CoV-2 287 assay. doi = 10.1101/2020.06.29.179192 id = cord-274834-24v2b509 author = Lima, Rosiane title = Establishment of a pediatric COVID-19 biorepository: unique considerations and opportunities for studying the impact of the COVID-19 pandemic on children date = 2020-09-11 keywords = COVID-19; CoV-2; MIS; SARS; child summary = Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. METHODS: A COVID-19 biospecimen collection study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. Specific questions that must be addressed revolve around the role children play in viral transmission, differences in pediatric viral susceptibility and immune responses, which could guide potential therapies for adults, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the development of severe hyperinflammatory shock and cardiac damage seen in Multisystem Inflammatory Syndrome in Children (MIS-C). In order to capture the full range of SARS-CoV-2 infection in the pediatric population, a COVID-19 biospecimen collection study was designed and implemented, including patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2-infected mothers, and asymptomatic children. doi = 10.1186/s12874-020-01110-y id = cord-276630-qci7khki author = Lima, William Gustavo title = The potential of drug repositioning as a short-term strategy for the control and treatment of COVID-19 (SARS-CoV-2): a systematic review date = 2020-06-08 keywords = COVID-19; CoV-2; SARS summary = Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus. doi = 10.1007/s00705-020-04693-5 id = cord-350401-suefuurq author = Lima-Setta, Fernanda title = Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() date = 2020-11-09 keywords = MIS; SARS; patient summary = title: Multisystem inflammatory syndrome in children (MIS-C) during SARS-CoV-2 pandemic in Brazil: a multicenter, prospective cohort study()()() From March 25 to August 23, 2020, pediatric patients (age range: 1 month -19 years) were consecutively included if they met the CDC case definition[8] for MIS-C: 1) fever > 38.0°C for ≥ 24 hours (objective or subjective); 2) laboratory evidence of inflammation, including, but not limited to, one or more of the following: high values of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), fibrinogen, procalcitonin, d-dimer, ferritin, lactic acid dehydrogenase (LDH), or interleukin 6 (IL-6); elevated neutrophils, reduced lymphocytes, and low albumin; 3) no alternative plausible diagnosis; 4) current or recent SARS-CoV-2 infection diagnosed by a positive reverse transcription polymerase chain reaction (RT-PCR) or positive serological tests (IgM, IgG or IgA), or exposure to a suspected or confirmed COVID-19 case within the four weeks prior to the onset of symptoms. doi = 10.1016/j.jped.2020.10.008 id = cord-328073-bqeffvzl author = Limonta, Daniel title = Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date = 2020-11-06 keywords = NOD2; SARS summary = The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. A drug that targets NOD2 was shown to have potent broad-spectrum antiviral activity against other flaviviruses, alphaviruses and SARS-CoV-2, the causative agent of COVID-19. Next, we demonstrated that the NOD2 inhibitor GSK717 blocks infection by and 205 spread of ZIKV in human fetal brain and cell lines. Similarly, the work here which demonstrated the antiviral activity of NOD2 and RIPK2 inhibitors using tissue explants, 216 primary cells and cell lines, support the potential clinical use of these compounds in mono or co-217 infections by arboviruses as well as coronavirus infections at early and/or advanced stages. Calu-3 and Huh7 cells infected with SARS-CoV-2 (MOI=0.1) were also treated with GSK583 for 24 hours before collecting the cell supernatants for viral titer determination. doi = 10.1101/2020.11.05.370767 id = cord-323105-gqqzekfk author = Lin, Chen-Si title = Enhancement of anti-murine colon cancer immunity by fusion of a SARS fragment to a low-immunogenic carcinoembryonic antigen date = 2012-02-03 keywords = CEA; SARS summary = Oral vaccination of an attenuated Salmonella typhimurium strain transformed with plasmids encoding CEA-SARS-CoV fusion gene into BALB/c mice elicited significant increases in TNF-α and IL-10 in the serum. For achieving simple administration of drugs and enhancement of host immunity, an oral DNA vaccine vector, Salmonella typhimurium (SL3261) [7] , was used as a carrier to deliver the SARS-CoV-CEA fusion genes. By combining SARS-CoV epitope, a tumor unrelated antigenic fragment, with CEA, we finally demonstrated this could be a promising anti-cancer strategy through effectively increasing both Th1 and Th2 cytokines and decreasing tumor volume. In comparison with the negative control group, no significant differences in tumor volume were observed in mice immunized with CEA alone, while the tumor volume was found to be smaller in the pCEA-SARS-CoV group in the protection and therapy assays (Figure 3 &4) . doi = 10.1186/1480-9222-14-2 id = cord-354780-yzyixucr author = Lin, Chih-Yen title = Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date = 2020-06-13 keywords = SARS; Taiwan summary = title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan Conclusion This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. This novel coronavirus was initially named 2019-novel coronavirus (2019-nCoV), however, currently the name has been established as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); with the disease being named as coronavirus disease 2019 (COVID-19) (Coronaviridae Study Group of the International Committee on Taxonomy of, 2020) Since the first reported case, there has been a rapid increase in the number of cases, with outbreaks being reported in countries all over the world. Accordingly, we suggest that the constant importation of SARS-CoV-2 infection is the major risk factor leading the COVID-19 epidemic in Taiwan. doi = 10.1016/j.ijid.2020.06.031 id = cord-300950-ag0sql4i author = Lin, John title = Potential therapeutic options for coronavirus disease 2019: using knowledge of past outbreaks to guide future treatment date = 2020-06-05 keywords = MERS; SARS summary = Several case reports including the first report of SARS outbreak described the use of the anti-viral drug ribavirin and a corticosteroid in patients with contradictory clinical outcomes. In several studies, lopinavir/ritonavir was shown to have anti-CoV effects in vitro, in MERS-infected primate models, and in SARS-infected humans. Furthermore, in a single MERS patient, a triple-combination therapy of ribavirin, IFN and lopinavir/ ritonavir resolved viremia in 2 days following initiation of treatment. [7] [8] [9] In two reports from China and Korea, the use of lopinavir/ritonavir in patients with COVID-19 improved recovery and reduced viral load. [7, 8] However, Chen et al [9] showed that lopinavir/ ritonavir and the anti-influenza treatment Arbidol had no clinically significant improvement in 134 people with mild COVID-19. [17] In an effort to combat inflammation and improve clinical outcome, corticosteroid use has been described in SARS, MERS, and COVID-19. doi = 10.1097/cm9.0000000000000816 id = cord-343850-p4bbb6vm author = Lin, Meng-Hsuan title = Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain date = 2020-09-18 keywords = ADPR; SARS; domain; figure; macro summary = SARS-CoV-2 encodes the conserved macro domain within nonstructural protein 3, which may reverse cellular ADP-ribosylation and potentially cut the signal of a viral infection in the cell. Herein, we report that the SARS-CoV-2 macro domain was examined as a poly-ADP-ribose (ADPR) binding module and possessed mono-ADPR cleavage enzyme activity. After confirming the ADPR binding ability via a biophysical approach, the X-ray crystal structure of the SARS-CoV-2 macro domain was determined and structurally compared with those of other viruses. This study provides structural, biophysical, and biochemical bases to further evaluate the role of the SARS-CoV-2 macro domain in the host response via ADP-ribose binding but also as a potential target for drug design against COVID-19. Virus macro domains were reported to have multiple functions, including a ADP-ribose (ADPR) 8−10 or poly-ADPR 9 interaction, adenine-rich RNA 11 binding, enzyme activities of ADPR-1″ phosphohydrolase, 7, 9 and the removal of mono(ADP-ribose) from protein. doi = 10.1021/acsinfecdis.0c00441 id = cord-329959-4yecwdlo author = Lin, Min-Han title = Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes date = 2017-12-28 keywords = Fig; MERS; SARS summary = Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL(pro)s) of MERS-CoV and SARS-CoV. The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL(pro) by disulfiram, while synergistic inhibition of MERS-CoV PL(pro) by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. For the inactivation studies, SARS-CoV PL pro (0.05 μM in 20 mM phosphate buffer, pH 6.5) was incubated with different concentrations of disulfiram and peptide substrate, and enzymatic activity was traced for 5 min. On the other hand, the results of kinetic assays, continued inactivation after the removal of disulfiram, reactivation by reductant, and the phenomenon of slow-binding inhibition suggest that disulfiram may act at the active site of SARS-CoV PL pro , forming a covalent adduct with residue Cys112. doi = 10.1016/j.antiviral.2017.12.015 id = cord-312741-0au4nctt author = Lin, Panpan title = Coronavirus in human diseases: Mechanisms and advances in clinical treatment date = 2020-10-01 keywords = East; MERS; Middle; RNA; SARS; coronavirus; protein; respiratory; syndrome summary = 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein doi = 10.1002/mco2.26 id = cord-272603-nbosceoz author = Lin, Qiuyuan title = Microfluidic Immunoassays for Sensitive and Simultaneous Detection of IgG/IgM/Antigen of SARS-CoV-2 within 15 min date = 2020-07-02 keywords = CoV-2; SARS summary = Facing the emergence of this pandemic, we established a portable microfluidic immunoassay system for easy-to-use, sensitive, rapid (<15 min), multiple, and on-site detection of IgG/IgM/Antigen of SARS-CoV-2 simultaneously. This integrated method was successfully applied for detecting SARS-CoV-2 IgM and IgG antibodies in clinical human serum as well as SARS-CoV-2 antigen in pharyngeal swabs from 26 patients with COVID-19 infection and 28 uninfected people. 26 To meet the challenge of the large epidemic, we describe the development of a point-of-care microfluidic platform integrating a homemade fluorescence detection analyzer ( Figure 1A ), SARS-CoV-2 diagnostic microchips ( Figure 1B) , and multiple immunoassays ( Figure 1C ) for detecting three biomarkers (IgG, IgM, and antigen). This robust microfluidic immunoassay system can provide a useful tool for SARS-CoV-2 diagnosis in public health laboratories as well as for timely screening potentially infected patients to monitor and prevent the epidemic owning to its capability of easy, fast, cost-effective, and point-of-care detection. doi = 10.1021/acs.analchem.0c01635 id = cord-300300-jqi4ylrx author = Lin, Ray Junhao title = From SARS to COVID‐19: the Singapore journey date = 2020-05-31 keywords = COVID-19; SARS; Singapore summary = The 2003 severe acute respiratory syndrome (SARS) outbreak challenged the nation''s public health system and now the coronavirus disease 2019 (COVID-19) pandemic is presenting a greater challenge. This framework serves as the foundation for the national responses to any outbreak and is divided into four levels of incremental severity (green, yellow, orange and red), based on risk assessment of the public health impact of the disease and the current disease situation in Singapore (Box 1). Workers who tested positive were transferred to community isolation facilities if they had mild symptoms, or to the NCID and public hospitals for further treatment and isolation. Health care workers in direct contact with COVID-19 patients who developed fever or symptoms of acute respiratory infection were encouraged to declare their symptoms to their superiors and present themselves to the screening centre, to be managed based on their exposure risk (Box 4). doi = 10.5694/mja2.50623 id = cord-339521-qfnu319w author = Lin, Shiming title = Surface ultrastructure of SARS coronavirus revealed by atomic force microscopy date = 2005-08-08 keywords = AFM; Fig; SARS summary = Here, we used AFM to determine the surface ultra structure of each single SARS-CoV virion and observe the surface characteristics and their topography and phase changes after treatments with hydroxyoctanoic acid or protease. The higher-resolution image shows that many individual spherical protrusions exist on the surface and the corresponding cursor profile (Fig. 1 a ) clearly reveals the presence of SARS-CoV particles and each single particle is readily distinguishable. The corresponding cursor profile provides quantitative measurements of the heights for the SARS-CoV particles on the surface. It was found that from the contour map (Fig. 5C ) 15 spike proteins (arrowheads) surround the envelope of a single SARS-CoV virion. The phase image provides a measure of sample heterogeneity and also indicates that the small spherical particles (arrowheads) come from the SARS-CoV virion itself (Fig. 6B) . doi = 10.1111/j.1462-5822.2005.00593.x id = cord-314572-1pou702r author = Lin, Ya-Hui title = Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date = 2016-10-14 keywords = PRF; RNA; SARS; Switch-1; figure summary = Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. In a first step to constructing a ligand-responsive −1 PRF stimulator, we designed Switch-0 RNA with a theophylline aptamer replacing the stem 3 of SARS-PK ( Figure 1A and C). We rationalized that such an engineered switch hairpin of reasonable stability (predicted free energy of −12.7 kcal/mole (37)) would be the dominant conformation that could interfere with the formation of pseudoknot stem 2 in the absence of theophylline (Supplementary Figure S2A) . To improve the dynamic range of ligand response and to see if theophylline aptamers can be functional while existing in both positive and negative regulators of −1 PRF, we fused previously designed theophylline-dependent upstream attenuator, theoOFF2 (24) with Switch-1 ( Figure 5A ) and examined theophylline-dependent −1 PRF activity in vitro. doi = 10.1093/nar/gkw718 id = cord-282177-8l7zukg4 author = Lin, Yi-Chun title = A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date = 2020-05-26 keywords = SARS summary = title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 doi = 10.1016/j.ijid.2020.05.070 id = cord-352156-sa8cvyuw author = Lindeman, Robbert-Jan title = Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries date = 2020-05-06 keywords = COVID-19; SARS summary = title: Preventing spread of SARS-CoV-2 and preparing for the COVID-19 outbreak in the surgical department: perspectives from two Scandinavian countries In both countries, the first weeks of preparation has seen a strong reduction in elective surgery, with several implemented principles to mitigate SARS-CoV-2 spread and prepare for surgical care for COVID-19 diseases as needed. Norway, that initially started with aggressive testing of subjects with symptoms or returning from high-endemic areas in order to get control over the spread pattern and asymptomatic COVID-19 patients, needed to restrict its activity later in March. An early effect of the initially suboptimal test routines for healthcare workers (HCW) was experienced in Norway, when one HCW returning from central Europe, was confirmed positive to SARS-CoV-2 only after having spent several days at work on the advice from the hospital. The acute threat of the COVID-19 epidemic to global healthcare has led to forced reorganization of surgical care in Norway and Sweden. doi = 10.1093/jscr/rjaa131 id = cord-142389-t5swlp04 author = Linden, Matthias title = The foreshadow of a second wave: An analysis of current COVID-19 fatalities in Germany date = 2020-10-12 keywords = IFR; SARS; age; case summary = We investigated this apparent discrepancy using age-stratified case and death reports [3] , and an age-dependent infection fatality rate (IFR). From this age-dependent IFR we predict the temporal evolution of the COVID-19associated deaths by delaying each age group''s observed weekly cases by two weeks and multiplying by the IFR (see supplementary material). The observed number deaths (black) in each age group matches well the predicted deaths calculated from the case numbers (color) using an age-dependent infection-fatality rate from a metaanalysis [4] . b. IFR calculation The overall goal is to estimate death numbers from past reported cases per age group and compare them to the observed number of deaths. c. Estimating the number of deaths from the reported SARS-CoV-2 cases The number of deaths is estimated by multiplying the published weekly number of reported cases in 5-years-wide age groups by the associated IFR (equation (2)). doi = nan id = cord-261619-31jk1vh6 author = Lindholm, David A title = Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date = 2020-07-17 keywords = SARS; drive summary = Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. Mitigation of the coronavirus disease 2019 (COVID-19) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] . During the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (PPE) use [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . The electronic medical record was reviewed (1) for comorbid conditions in positive cases and (2) for additional SARS-CoV-2 testing and BAMC hospital admission within 14 days of screening for all patients. Nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. However, none of the screen-only patients later tested positive or were hospitalized for COVID-19 within 14 days. doi = 10.1093/ofid/ofaa306 id = cord-261180-w62mynqb author = Ling, L. title = Infection control in non‐clinical areas during the COVID‐19 pandemic date = 2020-04-19 keywords = SARS summary = SARS-CoV-2 is easily transmissible as each person with COVID-19 infects approximately 2.2 close contacts, and asymptomatic transmission has been reported [2,3]. Therefore, we believe non-clinical areas are potentially high-risk for transmission between healthcare workers, and often neglected by infection prevention and control protocols. To alert others to this risk and how it may be reduced, we describe our non-clinical workplace infection prevention and control measures that have been modified from those originally developed during the 2003 severe acute respiratory syndrome epidemic [5] . Infographics are displayed on walls as reminders to perform hand hygiene when entering offices, after contact with respiratory secretions, before and after eating or drinking, and donning and doffing of masks. Designated bins for mask disposal are placed in communal areas. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Transmission of SARS to healthcare workers. doi = 10.1111/anae.15075 id = cord-007560-nck4f5ny author = Ling, Lowell title = COVID-19: A critical care perspective informed by lessons learnt from other viral epidemics date = 2020-02-20 keywords = China; ICU; SARS summary = Infection control Outbreak SARS-CoV-2 strategies during mechanical ventilation and prevention of hospital acquired infections is likely to contribute to improved outcomes in critically ill patients. If full airborne precautions are not possible due to limited facilities or overwhelming numbers of cases, other measures that may decrease risk of nosocomial transmission include cohorting of patients in dedicated wards, or physical separation, supported by disciplined use of PPE, universal contact and droplet precautions and adequate ward ventilation [15, [19] [20] [21] . Within the ICU, and with HCW protected by high-level PPE (including an N95 mask), non-invasive ventilation (NIV) and HFNO use during SARS-CoV and 2009 influenza epidemic was not clearly associated with an increased risk in HCW [24, 25] . Anyone who develops symptoms that could suggest a coronavirus infection are encouraged to call a single emergency number and if COVID-19 is suspected, they are managed at their location by a specialised medical team equipped with PPE to prevent viral contamination, and when necessary, hospitalised in an intensive care unit. doi = 10.1016/j.accpm.2020.02.002 id = cord-311585-h4holhit author = Ling, R. title = Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China date = 2020-06-19 keywords = SARS; Wuhan summary = Background The seroprevalence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. This retrospective study estimated the seroprevalence of IgM and IgG and compared the epidemiological characteristics of asymptomatic SARS-CoV-2-infected population. Hubei province including IgM and IgG tests for SARS-CoV-2 antibody, nucleic acid tests from March 26 to April 28, 2020 among people aged 16-64 years who went back to work. Clinical data were collected from March 26 to April 28, 2020, including serum IgG positivity and IgM positivity or negative results for SARS-CoV-2 antibodies, nucleic acid testing, clinical symptoms, previous medical history, and chest CT. . https://doi.org/10.1101/2020.06.16.20132423 doi: medRxiv preprint study, the IgG seroprevalence was higher in females than in males, indicating that women were more likely to have asymptomatic infections. doi = 10.1101/2020.06.16.20132423 id = cord-320428-sg3srt8r author = Ling, Zhoukun title = Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings date = 2020-03-12 keywords = SARS summary = title: Asymptomatic SARS-CoV-2 infected patients with persistent negative CT findings In this family, a 10-year-old child had no clinical symptoms, but showed ground glass lung opacification on CT, subsequently, the patient presented positive for the SARS-CoV-2 nucleic acid by real time polymerase chain reaction (RT-PCR). Therefore, these findings indicated the clinical symptoms were not essential components of SARS-CoV-2 infection. In our observation, we found that four patients with SARS-CoV-2 infection, showed no clinical symptoms or abnormal chest CT images. It is worth noting that, the clinical symptoms and radiological abnormalities are not the essential components of SARS-CoV-2 infection. If some people have a history of exposure to infected areas or contact with patients, regardless of radiological manifestations or clinical symptoms, medical observation and home isolation or SARS-CoV-2 nucleic acid tests are quite important to rule out infection. SARS-CoV-2 viral load in upper respiratory specimens of infected patients doi = 10.1016/j.ejrad.2020.108956 id = cord-269130-zsem29ss author = Lingappan, K. title = Understanding the age divide in COVID-19: why are children overwhelmingly spared? date = 2020-07-01 keywords = ACE2; COVID-19; SARS summary = The differences in the clinical course are highlighted by the lack of progression of the SARS-CoV-2 infection beyond mild symptoms in a majority of children, whereas in adults the disease progresses to acute lung injury and an acute respiratory distress syndrome (ARDS)-like phenotype with high mortality. The pathophysiological mechanisms leading to decreased lung injury in children may involve the decreased expression of the mediators necessary for viral entry into the respiratory epithelium and differences in the immune system responses in children. On the other hand, the heightened immune response to the virus in many adult patients can lead to the worsening of lung disease with SARS-CoV-2 infection (37) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice doi = 10.1152/ajplung.00183.2020 id = cord-326341-egtnqlov author = Liotti, Flora Marzia title = Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date = 2020-09-23 keywords = SARS summary = title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus doi = 10.1016/j.cmi.2020.09.030 id = cord-304013-nzigx0k0 author = Lipinski, Tom title = Review of ventilation strategies to reduce the risk of disease transmission in high occupancy buildings date = 2020-09-13 keywords = COVID-19; Natural; SARS; Ventilation; air; system; transmission summary = This paper will discuss the factors affecting air particle properties in-terms of flow dynamics and critically analyse current ventilation strategies and mechanisms and identify areas for improvement in the search for the reduction of indoor infections. The study by the University of Oregon [54, 58] observed that Natural Ventilation with a plentiful supply of fresh air dilutes and removes contaminated air much more effectively than fan driven, recirculated air movement, significantly reducing the risk of infection, as shown in Figure 17 . Displacement ventilation with a generously sized natural inlet is preferred as it can move stale, contaminated air directly to the exhaust of the room in a laminar fashion whilst the concentration of small droplets and airborne particles in the indoor air is significantly reduced. doi = 10.1016/j.ijft.2020.100045 id = cord-319749-je0l22l5 author = Lippi, Alice title = SARS‐CoV‐2: At the Crossroad Between Aging and Neurodegeneration date = 2020-04-24 keywords = Parkinson; SARS summary = Here, we posit that severe acute respiratory distress syndrome coronavirus 2 infection may, in the long-term, lead to accelerated aging phenotypes in survivors, not only in affected tissues but also in other organs, including the brain. 1, 2 As the causative agent of coronavirus disease 2019 (COVID19) , the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) is now responsible for the third coronavirus-associated pandemic in recent human history. SARS-CoV-2 proteins with human proteins from several aging-related pathways, like vesicle trafficking (Nsp6, Nsp7, Nsp10, Nsp13, Nsp15, Orf3a, E, and Orf8), lipid modifications (Spike), RNA processing and regulation (Nsp8, N), ubiquitin ligases (Orf10), and mitochondrial activity (Nsp4, Nsp8, and Orf9c). Moreover, Hsp40-NP interaction plays a role at the late stages of infection by inhibiting protein kinase R (PKR) activation, essential in the antiviral response of the host. 25 The infection with SARS-CoV induces the unfolded protein response (UPR) in the host cell. doi = 10.1002/mds.28084 id = cord-270116-r2rnnsfh author = Lippi, Giuseppe title = Current laboratory diagnostics of coronavirus disease 2019 (COVID-19) date = 2020-05-11 keywords = COVID-19; CoV-2; SARS summary = As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized especially by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. Recent studies have also been published on the possibility to use rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for SARS-CoV-2 detection, but additional evidence is needed at this point in time for validating their routine usage in COVID-19 diagnostics (38, 39) . As concerns serological testing, promising information can be garnered from preliminary investigations, showing that the vast majority of COVID-19 patients seem to develop a sustained immune response against the virus, characterized by emergence of anti-SARS-CoV-2 IgG and IgA, 1 to 2 weeks after the onset of fever and/or respiratory symptoms. doi = 10.23750/abm.v91i2.9548 id = cord-256233-k9hdq3z8 author = Lipsky, Martin S. title = Men and COVID-19: A Pathophysiologic Review date = 2020-09-16 keywords = ACE2; SARS; covid-19 summary = The plausible theories underlying these observations include sex-related differences in angiotensin-converting enzyme 2 receptors, immune function, hormones, habits, and coinfection rates.In this review we examine these factors and explore the rationale as to how each may impact COVID-19. Epidemiological evidence from influenza outbreaks and pandemics also reveals a higher morbidity and mortality for menthan that for women in some age groups (Klein et al., 2012) .In animal studies, male animals have poorer immune responses when exposed to the coronavirus and experience more damage to their lungs (Vermillion et al., 2018) .For both SARS and the MERS coronavirus outbreaks, men fared worse than women did. A recent German study found that that critically ill male COVID-19 patients suffer from severe testosterone and dihydrotestosterone deficiencies and concluded that androgens are required to mount a strong antiviral immune response to combat infection in men (Schroeder et al., 2020) . doi = 10.1177/1557988320954021 id = cord-271174-886xc1n3 author = Lipworth, Brian title = Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection date = 2020-04-18 keywords = COPD; SARS; covid-19 summary = High-risk patients requiring hospitalization for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are those over 60 years old, males, obese, smokers, and those with common comorbidities including hypertension, cardiovascular disease, diabetes, and chronic lung disease. The cytokine cascade resulting from acute severe SARS-CoV-2 infection, with downstream IL-6 activation considered to be a hallmark feature in terms of progression of COVID-19 pneumonia to hyperinflammation and ARDS. Also shown are the putative mechanisms of action for bromhexine and hydroxychloroquine in attenuating upstream SARS-CoV-2 tissue binding, the effect of antivirals on replication, azithromycin as an antiviral and immunomudulator, nonspecific cytokine suppression by corticosteroids, together with the selective downstream effect of IL-6 blockade with tocilizumab or sarilumab and effects of anti-TNF and interferon beta-1-a. Patients with eosinophilic asthma and COPD should continue to use ICS-containing therapy to maintain optimal control and protect against viral insults including SARS-CoV-2 infection. doi = 10.1016/j.jaip.2020.04.014 id = cord-334773-yw2qgv13 author = Lisco, Giuseppe title = Hypothesized mechanisms explaining poor prognosis in type 2 diabetes patients with COVID-19: a review date = 2020-08-10 keywords = COVID-19; CoV-2; SARS; clinical; diabetes; patient summary = This concern has been further confirmed by the results of a cohort study among 85 fatal cases of COVID-19 in Wuhan, hence defining DM as a potentially harmful comorbidity predisposing to worse clinical course or death once SARS-CoV-2 infection occurred [49] . Different hypothesis should be considered for explaining this clinical phenomenon, including glucose control at baseline and during the infection course, pathophysiology and immune system response in SARS-CoV-2 infected patients with T2D, diabetes-related comorbidities and concomitant medications. In conclusion, diabetic patients especially elderly individuals and those with worse baseline glucose control may exhibit immune system dysregulation that predispose them to a less effective response against SARS-CoV-2 and to a dysfunctional inflammation that requires to be carefully monitored in confirmed cases of COVID-19, for preventing or avoiding a harmful progression of the disease. Immune response and systemic inflammation play a crucial role in SARS-CoV-2 infection, particularly in case of severe clinical course of the disease. doi = 10.1007/s12020-020-02444-9 id = cord-345371-pjbviagq author = Lisi, Lucia title = Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date = 2020-07-23 keywords = ACE2; COVID-19; CoV-2; RNA; SARS; clinical; patient; severe summary = The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. Here, we review the recently published literature on the pharmacological treatments used so far and/or undergoing evaluation in clinical trials, with focus on the biochemical mechanisms of action of repurposed or investigational drugs, classified as agents directly targeting the virus ( Figure 1 and Table 1 ) and those used to treat the respiratory distress and inflammation associated with the cytokine release syndrome ( Figure 2 and Table 2 ). doi = 10.1016/j.bcp.2020.114169 id = cord-340201-ai4apr4w author = List, Wolfgang title = Occurrence of SARS-CoV-2 in the intraocular milieu date = 2020-09-28 keywords = SARS summary = All individuals were previously positive in nasopharyngeal swabbing and cause of death was respiratory failure due to SARS-CoV-2 infection. (Chen et al., 2020; Siedlecki et al., 2020; Wu et al., 2020; Xia et al., 2020; Zhang et al., 2020) In this study, we tested for SARS-CoV-2 in the aqueous humor and the vitreous representing the intraocular milieu. In sixteen individuals with confirmed SARS-CoV-2 infection samples from the vitreous and aqueous humor were taken during postmortem examinations. PCR was negative for all aqueous humor and vitreous samples for SARS-CoV-2. (Table 1) In this case series, SARS-CoV-2 could not be found in the aqueous humor and in the vitreous. In these patients, SARS-CoV-2 might be found in the aqueous humor and/or vitreous. In conclusion, this case series did not find SARS-CoV-2 in aqueous humor and vitreous samples during postmortem examinations of 16 patients with cause of death by SARS-CoV-2 infections. doi = 10.1016/j.exer.2020.108273 id = cord-282738-aqc9gxlw author = Liu, Anding title = Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date = 2020-10-23 keywords = SARS summary = key: cord-282738-aqc9gxlw authors: Liu, Anding; Li, Ying; Wan, Zhengce; Wang, Wenjie; Lei, Xiaomei; Lv, Yongman title: Seropositive Prevalence of Antibodies Against SARS-CoV-2 in Wuhan, China date: 2020-10-23 cord_uid: aqc9gxlw This cross-sectional study examines the seropositive prevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, by sex and age group. Nasal swab specimens were obtained to test for SARS-CoV-2 by real-time RT-PCR. Total RNAs from nasal swab specimens was extracted by a viral nucleic acid kit The 95% CI of the seroprevalence was calculated from binomial probabilities using Wilson''s methods. Chisquare test was used for comparison of seroprevalence between groups, and logistic Association of Public Health Interventions With the Epidemiology of the COVID-19 Outbreak in Wuhan, China Antibody responses to SARS-CoV-2 in patients with COVID-19 Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely correlated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients doi = 10.1001/jamanetworkopen.2020.25717 id = cord-327405-xgtqfwyn author = Liu, Bing title = Reduced numbers of T cells and B cells correlates with persistent SARS-CoV-2 presence in non-severe COVID-19 patients date = 2020-10-19 keywords = SARS summary = 37 non-severe patients with persistent SARS-CoV-2 presence that were transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to the PP (persistently positive) group, which was further allocated to PPP group (n = 19) and PPN group (n = 18), according to their testing results after 7 days (N = negative). Finally, paired results of these lymphocyte subpopulations from 10 PPN patients demonstrated that the number of T cells and B cells significantly increased when the SARS-CoV-2 tests turned negative. These results indicated that non-severe COVID-19 patients (PA group) have already dysregulated immune system at disease onset, and those with persistent SARS-CoV-2 shedding could restore this abnormality to certain level. Together, these results indicated that the abnormalities in adaptive immune cells, but not symptoms and laboratory indicators, were associated with SARS-CoV-2 viral RNA detection in non-severe COVID-19 patients. doi = 10.1038/s41598-020-73955-8 id = cord-348065-0tkx7aas author = Liu, Bing title = Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients date = 2020-03-30 keywords = SARS summary = Methods 37 non-severe patients with persistent SARS-CoV-2 presence transferred to Zhongnan hospital of Wuhan University were retrospectively recruited to PP (persistently positive) group, which was further allocated to PPP group (n=19) and PPN group (n=18), according to their testing results after 7 days (N=negative). Conclusion Persistent SARS-CoV-2 presence in non-severe COVID-19 patients is associated with reduced numbers of adaptive immune cells. Next, we determined the abnormalities for each parameters Lymphopenia was observed at illness onset in 72.8% of non-severe COVID-19 patients (the PA group) in our study, which is similar to those reported by Zhang et al [15] (75.4%), Mo et al [17] (73.5%), Wang et al [27] (70.3%), and Guan et al [2] (83.2%), suggesting the involvement of lymphocytes in the early phase of SARS-CoV-2 infection. Together, these results suggest that measurement of these lymphocyte subpopulations could be used to distinguish non-severe patients with persistent viral presence from healthy subjects and those turned negative, and thus have clinical relevance for discharge management. doi = 10.1101/2020.03.26.20044768 id = cord-343818-pj1oludh author = Liu, Chan title = Children with COVID-19 behaving milder may challenge the public policies: a systematic review and meta-analysis date = 2020-09-01 keywords = COVID-19; SARS; child summary = We searched PubMed, Google Scholar, Web of Science, and several Chinese databases for studies presenting characteristics of children confirmed with Coronavirus Disease 2019 (COVID-19) from December 12, 2019 to May 10, 2020. The studies included in this meta-analysis should meet the following criteria: (1) all types of studies either retrospective or prospective (e.g. cohort, cross-sectional study, case report, case series); (2) studies reporting information regarding COVID-19; (3) studies describing clinical characteristics of pediatric patients (0-19 years) diagnosed by RT-PCR; (4) clinical data of more than five cases can be drawn from the articles. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study Clinical features of children with SARS-CoV-2 infection: an analysis of 13 cases from Changsha Clinical features of coronavirus disease 2019 in children aged <18 years in Jiangxi, China: an analysis of 23 cases doi = 10.1186/s12887-020-02316-1 id = cord-294861-inlaz4od author = Liu, Chen title = Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series date = 2020-09-15 keywords = COVID-19; SARS summary = title: Six Gynecological Cancer Patients Infected With SARS-CoV-2 After Surgery or Radio-/Chemo-Therapy Treatment: Case Series METHODS: We retrospectively analyzed the diagnosis and treatment of six gynecological cancer patients infected with SARS-CoV-2 in Tongji Hospital in Wuhan from January 30 to March 25, 2020. RESULTS: We observed a high rate of nosocomial SARS-CoV-2 infection among these six gynecological cancer patients, who were in a low immune state. reported a case in which a lung cancer patient infected with SARS-CoV-2 recovered from pneumonia while continuing initial targeted therapy (10) . After antivirus and anti-infection treatment, combined with G-CSF (Recombinant Human Granulocytestimulating Factor) and immunity enhancing drugs, she was finally discharged from hospital after 35 days (Figure 1) . Moreover, cancer patients showed a state of low immunity after surgery or radio-/chemo-therapy treatment, so they became more susceptible to COVID-19 (12) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.3389/fonc.2020.01606 id = cord-322329-zqjiiy4l author = Liu, Chunyu title = Establishment of a reference panel for the detection of anti-SARS-CoV antibodies date = 2007-06-30 keywords = SARS summary = In this study, we have expressed and purified severe acute respiratory syndrome (SARS) structural proteins and their fragments and developed indirect enzyme-linked immunosorbent assays (ELISAs) that detect antibodies against the SARS N, N1, N2, S1, SC, S2, and M proteins as well as the human coronavirus OC43 and 229E N proteins. In this study, SARS N and S proteins and their fragments were expressed and purified, and samples from convalescent SARS patients and blood donors were screened with enzyme-linked immunosorbent assays (ELISAs) that were developed with these proteins. IgG and IgM immunoglobulin were detected in the 58 SARS convalescent plasma specimens using an indirect ELISA developed with entire virus antigens. In this study, the indirect ELISAs were developed with different fragments of SARS structure proteins and used to detect antibodies in 58 SARS plasma specimens donated by convalescent patients 3 months after onset of SARS. doi = 10.1016/j.biologicals.2006.11.001 id = cord-335916-fh28qrt7 author = Liu, Cuiwei title = COVID-19 in cancer patients: risk, clinical features, and management date = 2020-08-15 keywords = COVID-19; SARS; patient summary = Cancer patients are regarded as a highly vulnerable population to SARS-CoV-2 infection and development of more severe COVID-19 symptoms, which is possibly due to the systemic immunosuppressive state caused directly by tumor growth and indirectly by effects of anticancer treatment. Another cohort study of 28 COVID-19 cancer patients reported that patients with Stage IV disease accounted for a higher percentage of infected patients (35.7%), suggesting that later stage cancer patients may be more susceptible to SARS-CoV-2 5 . Notably, a retrospective study of 28 COVID-19 cancer patients found that anti-cancer treatment within 14 days before COVID-19 diagnosis was more frequently associated with severe clinical events due to SARS-CoV-2 infection 5 . The higher proportion of COVID-19 patients with cancer requiring oxygen therapy and mechanical ventilation may be related to more severe disease and an immunosuppressive state in cancer patients, who are more susceptible to secondary lung infection with other pathogens. doi = 10.20892/j.issn.2095-3941.2020.0289 id = cord-350309-j4oh1z8m author = Liu, D. X. title = Coronavirus envelope protein: A small membrane protein with multiple functions date = 2007-05-29 keywords = SARS; protein summary = The E proteins from infectious bronchitis virus (IBV) and mouse hepatitis virus (MHV) are translated from the third and second ORFs of mRNA 3 and 5 of the respective viruses by a cap-independent, internal ribosomal entry mechanism [6] [7] [8] [9] [10] [11] [12] . This modification is unique to SARS-CoV E protein, and it is still unknown whether the modification can also be detected in virus-infected cells and in virions. However, the membrane topologies of SARS-CoV E protein in virions and in virusinfected cells are still unknown. Similar to other viroporins [46] , expression of SARS-CoV and MHV E protein enhanced the membrane permeability of bacterial and mammalian cells [47, 48] . These results indicate that the ion channel activity of coronavirus E protein is important for virus replication, especially in the case of some coronaviruses, such as MHV. Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells doi = 10.1007/s00018-007-7103-1 id = cord-277253-vy0mvzeb author = Liu, Hongbo title = Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date = 2020-04-11 keywords = CoV-2; SARS summary = title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors. Inspired by the previous studies, several covalent inhibitors were experimentally identified to inhibit the 3CL pro activity and viral replication of SARS-CoV-2, and some of the complex crystal structures were solved [14, 15] . baicalensis inhibits SARS-CoV-2 3CL pro activity and the most active ingredient baicalein exhibits an IC50 of 0.39 M. We also identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CL pro activity at microM concentration. baicalensis and tested its inhibitory activity against SARS-CoV-2 3CL pro . baicalensis extract at different concentrations on SARS-CoV-2 3CL pro activity were 6 shown in Figure 1A . doi = 10.1101/2020.04.10.035824 id = cord-253513-zn87f1lk author = Liu, Jia title = Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro date = 2020-03-18 keywords = HCQ; SARS summary = Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Jia Liu 1 , Ruiyuan Cao 2 , Mingyue Xu 1,3 , Xi Wang 1 , Huanyu Zhang 1,3 , Hengrui Hu 1,3 , Yufeng Li 1,3 , Zhihong Hu 1 , Wu Zhong 2 and Manli Wang 1 Dear Editor, The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/2019-nCoV) poses a serious threat to global public health and local economies. To better compare the antiviral activity of CQ versus HCQ, the dose-response curves of the two compounds against SARS-CoV-2 were determined at four different multiplicities of infection (MOIs) by quantification of viral RNA copy numbers in the cell supernatant at 48 h post infection (p.i.). Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment (Supplementary Fig. S2 ). doi = 10.1038/s41421-020-0156-0 id = cord-343362-4u2re1cu author = Liu, Jianjun title = SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis date = 2005-02-22 keywords = SARS summary = METHODS AND FINDINGS: The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. We present here a novel application of mass spectrometry (MS)-based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore. The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. A further application of MS-based viral sequence variation analysis in tracking the virus strain and thus the transmission of SARS-CoV was demonstrated by our confirmation of the Singapore origin of a SARS-CoV isolate from a German patient. doi = 10.1371/journal.pmed.0020043 id = cord-307044-4czeehkq author = Liu, Jiaye title = Longitudinal Changes of Liver Function and Hepatitis B Reactivation in COVID‐19 Patients with Pre‐existing Chronic HBV Infection date = 2020-08-06 keywords = COVID-19; HBV; SARS summary = However, to the best of our knowledge, no studies had been carried out on the impact of chronic HBV infection on the disease progression and liver function changes of COVID-19 patients, and how the SARS-CoV-2 infection in turn affects the course of chronic HBV infection. 16 The factors for propensity score calculation include age, gender, body mass index (BMI), time intervals between COVID-19 onset to hospital admission, number of comorbidities except for CHB, liver biochemistries (ALT, AST, GGT, TBIL), PaO2/FIO2 ratio, chest CT score, CRP, lymphocyte count, and platelet count at baseline. As the median of testing/assessing time intervals and follow-up durations were 3 days and 14 days for liver biochemistries (ALT, AST, GGT, TBIL), we compared the dynamic levels of these indicators within/between the two groups at baseline, 3, 6, 9, 12, 15 days during hospitalization. The median levels of liver biochemistries over time were no significant difference between two groups ( Figure 3 ; Wilcoxon signed-rank test, ALT: p=0.56, AST: p=0.58, GGT: p=0.43, TBIL: p=0. doi = 10.1111/hepr.13553 id = cord-352030-hnm54k4r author = Liu, Jie title = Epidemiological, Clinical Characteristics and Outcome of Medical Staff Infected with COVID-19 in Wuhan, China: A Retrospective Case Series Analysis date = 2020-03-13 keywords = COVID-19; China; SARS; Wuhan summary = These included age, sex, occupation (doctor, or nurse), body mass index (BMI ≥ 24, or <24 kg/m 2 ), current smoking status (yes, or no), disease severity (non-severe, or severe), date of symptom onset, symptoms before hospital admission (fever, cough, fatigue, sore throat, myalgia, sputum production, difficulty breathing or chest tightness, chill, loss of appetite, diarrhea, and chest pain), coexisting conditions (e.g. hypertension, diabetes, etc.), laboratory testing indicators on admission (leucocyte count, lymphocyte count, platelet count, D-dimer, creatinine, creatine kinase, lactose dehydrogenase, alanine aminotransferase, aspartate aminotransferase, hemoglobin, ferritin, C-reactive protein, Amyloid A, total bilirubin, procalcitonin, erythrocyte sedimentation rate, interleukin-6 (IL-6) and lymphocyte subsets, etc.), radiologic assessments of chest CT (lung involvement, lung lobe involvement, predominant CT changes, predominant distribution of opacities, etc.), treatment measures (antibiotics agents, antiviral agents, traditional Chinese medicine, immune globulin, thymosin, corticosteroids and oxygen therapy), and complications (e.g. pneumonia, acute respiratory distress syndrome, acute cardiac injury, acute kidney injury, shock, etc.). doi = 10.1101/2020.03.09.20033118 id = cord-268254-1mg7a17c author = Liu, Li title = High neutralizing antibody titer in intensive care unit patients with COVID-19 date = 2020-07-20 keywords = ICU; SARS; patient summary = This study determined the seroprevalence of 733 non-COVID-19 individuals from April 2018 to February 2020 in the Hong Kong Special Administrative Region and compared the neutralizing antibody (NAb) responses of eight COVID-19 patients admitted to the intensive care unit (ICU) with those of 42 patients not admitted to the ICU. In this study, the absence of NAb in the serum of over 733 HKSAR residents indicates that SARS-CoV-2 is unlikely to have spread silently in Hong Kong before its emergence in COVID-19 patients. During our manuscript revision, a preprint paper indicated that SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease [26] . Neutralizing antibodies responses to SARS-CoV-2 in COVID-19 inpatients and convalescent patients. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. doi = 10.1080/22221751.2020.1791738 id = cord-266052-rcuzi70u author = Liu, Lilong title = Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19 date = 2020-10-29 keywords = China; SARS; covid-19 summary = As pit latrines and the use of untreated excreta as fertilizer were common in rural China, we surveyed 27 villages of Jiangxi and Hubei provinces and found that pit latrines could be a potential source of SARS-CoV-2 water pollution. Another study showed that infectious SARS-CoV-2 virus were successfully isolated from 2 of 3 patients with viral RNA-positive, indicating that infectious virus in feces was a common manifestation of COVID-19 and confirmed the potential of fecal-oral or fecal-respiratory transmission (Xiao et al., 2020b) . Coupled with the fact that villagers usually use untreated excreta as agricultural fertilizer, we believe that the use of pit latrines in rural China and other low-income countries increases the possibility of SARS-CoV-2 contaminating the surrounding natural environment and ultimately harms human health. We proposed this hypothesis to illustrate the mechanism that SARS-COV-2 might spread from the excreta of infected humans in pit latrines to potential animal hosts and then become a sustainable source of infection in rural China and other low-income countries. doi = 10.1016/j.scitotenv.2020.143283 id = cord-030923-r0lfot3w author = Liu, Lixin title = Subunit Nanovaccine with Potent Cellular and Mucosal Immunity for COVID-19 date = 2020-08-18 keywords = MPLA; SARS summary = [Image: see text] To combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we formulated the S1 subunit of the virus with two adjuvants, amphiphilic adjuvant monophosphoryl lipid A for Toll-like receptor 4 and CpG oligodeoxynucleotide for Toll-like receptor 9, into cationic liposomes to produce a potent, safer, and translatable nanovaccine. NANOVACCINE MPLA/CpG-loaded liposome particle, p(M+C), was produced via a thin-film hydration approach by using cationic 1,2dioleoyl-3-trimethylammonium-propane (DOTAP), helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and cholesterol as carrier materials. Previous research on vaccines using the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) as the subunit showed that the antibodies could effectively prevent the coronavirus from binding to the cell and undergoing membrane fusion, neutralizing the virus during infection. Moreover, MPLA/CpG-loaded liposomes alone can be used as nanoparticulate adjuvants of a coronavirus vaccine with different antigens to enhance an innate immunity and thus a cellular immune response. doi = 10.1021/acsabm.0c00668 id = cord-288357-3mqoexcr author = Liu, Pei title = Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds date = 2020-08-01 keywords = 3CL; SARS summary = title: Potent inhibitors of SARS-CoV-2 3C-like protease derived from N-substituted isatin compounds We identified several N-substituted isatin compounds as potent SARS-CoV-2 3C-like protease inhibitors. [4, [9] [10] [11] [12] To date, several potential SARS-CoV-2 3CL pro inhibitors have been reported from compound library screening, [8] rational design [8, 13] , [14] and testing of ingredients from traditional Chinese medicine. Previously, we reported a series of N-substituted 5-carboxamide-isatin compounds as inhibitors of SARS CoV 3CL pro . [12] Apparently, the isatin scaffold with derivatization may also provide a good starting point for SARS CoV-2 3CL pro inhibitor development, because the two proteases share high sequence identity and the same active site. In conclusion, we have tested the inhibition activity of 29 N-substituted isatin derivatives against SARS-CoV-2 3CL pro . Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors substituted isatin compounds are potent SARS-CoV-2 3C-like protease inhibitors. doi = 10.1016/j.ejmech.2020.112702 id = cord-309970-jkmjiika author = Liu, Qin title = From SARS to COVID-19: What lessons have we learned? date = 2020-08-21 keywords = COVID-19; China; SARS summary = On December 1, 2019, the first case of coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), was reported in Wuhan, China, and CoVs returned to public view. In this review, we systematically compare COVID-19 and SARS in terms of epidemiology, pathogenesis and clinical characteristics and discuss the current treatment approaches, scientific advancements and Chinese experience in fighting the epidemic to combat the novel coronavirus pandemic. As the virus continued to spread, on March 11, 2020 , the WHO declared that COVID-19 is a pandemic disease, making this the first time that a coronavirus infection has been regarded as a global pandemic, in contrast to SARS in 2002, which did not reach this level. This paper summarizes the differences in the epidemiology, clinical manifestations, and treatment of SARS and COVID-19 during the two outbreaks, summarizes the lessons learned, and provides a comprehensive reference for the global epidemic prevention and treatment of reported in China and resulted in a large number of infections. doi = 10.1016/j.jiph.2020.08.001 id = cord-301167-101lnq4f author = Liu, Quanjun title = Microarray-in-a-Tube for Detection of Multiple Viruses date = 2007-02-01 keywords = PCR; SARS; dna summary = Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube. doi = 10.1373/clinchem.2006.071720 id = cord-333381-wz70o9tt author = Liu, Shao title = Providing pharmacy services during the coronavirus pandemic date = 2020-03-28 keywords = China; SARS; drug summary = Chinese pharmacists have acted swiftly in the public health response in China, such as drafting professional service guidance to pharmacists and pharmacies, establishing emergency drug formularies, monitoring and resolving drug shortages, establishing remote pharmacy services to prevent human-to-human infections, providing event-driven pharmaceutical care, educating the public on infection prevention and disease management, and participating in clinical trials and drug evaluation. Specifically, pharmacy needs to work with other healthcare organizations, professionals, and government agencies to address the following seven service needs: (1) drafting professional service guidances to pharmacists and pharmacies, (2) establishing emergency drug formularies based on treatment guidelines, (3) coordinating with drug companies and distributors to ensure adequate supply, storage and transport of identified formulary drugs, (4) providing event-driven pharmaceutical care, (5) establishing remote pharmacy services to reduce the incidence of human-to-human infections, (6) educating the public with a focus on infection prevention and disease management, and (7) involving in clinical trial research to screen, evaluate and develop antiviral medications in line with national and international guidelines [4] . doi = 10.1007/s11096-020-01017-0 id = cord-272292-k0ugjb6f author = Liu, Shih-Jen title = Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates date = 2006-04-12 keywords = ISA; SARS summary = The recombinant nucleocapsid (rN) protein of the coronavirus (CoV) responsible for severe acute respiratory syndrome (SARS) was cloned and expressed in Escherichia coli, extracted from cell lysates containing 6 M urea, then purified by Ni(2+)-affinity chromatography. To identify the B-cell immunodominant epitopes of the rN protein in the mouse and monkey, the reactivities of antisera raised against purified rN proteins formulated in ISA-51/CpG were tested with a panel of overlapping synthetic peptides covering the entire N protein sequence. We also only observed that peptides corresponding to residues 336–350 were capable of stimulating IFN-γ production in T-cell cultures derived from peripheral blood mononuclear cells (PBMCs) of macaques immunized with the rN protein emulsified in ISA/CpG adjuvant. doi = 10.1016/j.vaccine.2006.01.058 id = cord-035307-r74ovkbd author = Liu, Shuchang title = Attitudes towards Wildlife Consumption inside and outside Hubei Province, China, in Relation to the SARS and COVID-19 Outbreaks date = 2020-11-11 keywords = COVID-19; Hubei; SARS summary = Our study results indicate over the period between the SARS epidemic to the outbreak of the COVID-19 pandemic, attitudes towards the consumption of wildlife in China have changed significantly. Therefore, our aim in this study was to determine changes in attitudes towards wildlife consumption in Chinese adults in relation to the SARS and COVID-19 outbreaks with a particular focus on Hubei Province. doi = 10.1007/s10745-020-00199-5 id = cord-284464-avriske3 author = Liu, Tao title = Recurrent positive SARS‐CoV‐2: Immune certificate may not be valid date = 2020-06-09 keywords = SARS summary = key: cord-284464-avriske3 cord_uid: avriske3 The presence of SARS-CoV-2 in COVID-19 patients is usually confirmed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) method.2 This article is protected by copyright. Statistical analyses were conducted using SAS software version 9.4 (SAS Institute; Carey, NC). A two-sided P < .05 was considered statistically significant. Among 150 patients who were recovering from COVID-19, 11 (7.3%, 95% confidence interval: 3.1%-11.6%) tested positive again for SARS-CoV-2 in throat swabs. Positive rates for SARS-CoV-2 did not differ by sex or age. There were no differences in the prevalence of IgM or IgG to SARS-CoV-2 ( Figure S1 ) or serum levels of these antibodies (Table 1) Detection of SARS-CoV-2 in different types of clinical specimens Positive RT-PCR test results in patients recovered from COVID-19 Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis doi = 10.1002/jmv.26074 id = cord-258242-xblxjlb5 author = Liu, Tengwen title = Systems Pharmacology and Verification of ShenFuHuang Formula in Zebrafish Model Reveal Multi-Scale Treatment Strategy for Septic Syndrome in COVID-19 date = 2020-09-15 keywords = COVID-19; SARS; SFH; target summary = Recent studies reported that many critically ill COVID-19 patients developed typical septic syndrome, including inflammatory injury, immune dysfunction, coagulation disorder, and multiple organ failure (Bellinvia et al., 2020; Coronado et al., 2020; . Current studies reported that severe COVID-19 patients with septic syndrome mainly showed abnormal pathological features, including virus infection and tissue damage, excessive inflammation in early stage but immune suppression in late stage, and coagulation dysfunction . Since the data of systems pharmacology illustrated that SFH may regulate several key targets and biological processes of sepsis, such as PPARG in inflammatory response, GSK3b and MAPK14 in cell proliferation, and PTGS2 in coagulation, we hypothesized that SFH improves the condition of critically ill COVID-19 patients with septic syndrome by ameliorating lung injury, suppressing excessive inflammation but enhancing the capacity of pathogen phagocytosis and killing, and improving the function of blood coagulation. doi = 10.3389/fphar.2020.584057 id = cord-258630-mvz2l3yj author = Liu, Tiantian title = A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date = 2020-11-10 keywords = Fig; SARS; SNV summary = We compared seven different library construction protocols and specifically evaluated the cross-protocol performance in sequencing read mappability, viral genome coverage percentage and uniformity, effect of sequence depth, SNV calling concordance (reproducibility), precision (positive predictive value), and sensitivity (proportion of consensus variants identified at different sequencing depths and viral copy number inputs) across protocols. Here, we compared seven WGS protocols for SARS-CoV-2 using clinical samples from infected patients, benchmarking the performances of these protocols in several aspects including the sequencing read mappability, genome coverage (percentage and uniformity, minimum sequences required); sample storage condition; effects of viral input, sequencing depth, length and platform; sensitivity, reproducibility and precision of SNV calling and related assay factors (e.g., amount of viral input, sequencing depth and bioinformatics pipeline). doi = 10.1101/2020.11.10.375022 id = cord-023463-vr6uaw3a author = Liu, Wei title = Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date = 2009-06-05 keywords = SARS; infection summary = Objective To evaluate possible severe acute respiratory syndrome (SARS) infection associated risk factors in a SARS affected hospital in Beijing by means of a case control study. Results Multivariate analysis confirmed the strong role of performing chest compression (or intubation, which is highly correlated), contact with respiratory secretion, and emergency care experience as risk factors to acquire SARS infection. Measures to prevent nosocomial infection included establishing isolation wards for triage SARS patients; training and monitoring hospital staff in infection-control procedures; active and passive screening of HCWs; enforcement of droplet and contact precautions; and compliance with the use of PPE. In summary, this study identified exposure to high-risk procedures (such as chest compression), and contact with respiratory secretions to be significant risk factors for SARS infection among HCWs in a hospital in Beijing. doi = 10.1111/j.1365-3156.2009.02255.x id = cord-271188-ewlxy5po author = Liu, Wei title = Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date = 2020-04-20 keywords = HIV-1; RNA; SARS; iron summary = Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 doi = 10.1007/s40588-020-00140-w id = cord-343870-g2v7ihud author = Liu, Wei title = Virus-, host-, immune-based targets for COVID-19 therapy date = 2020-10-06 keywords = SARS; covid-19 summary = Anti-viral agents against different targets had exhibited profound therapeutic effect on SARS-CoV-2 through which the clinicians were able to control the COVID-19 outbreak. Clinicians worldwide have been voraciously seeking for a potential anti-COVID-19 drug of all modules such as vaccines; targetspecific monoclonal antibodies; viral oligonucleotide-based peptide drugs; interferons and other small bio-actives [2] . S protein being the crucial protein facilitating the SARS-CoV-2 entry into the host has been preferred as a potential therapeutic target of interests as it could be spliced into two individual peptides by the furin-like proteases [5] . The other novel drug-like K22 that inhibits the viral-dependent RNA synthesis exhibited strong anti-replicative activity against the coronaviruses in an in-vitro set-up. Stimulation of innate immune response is crucial for controlling the SARS-CoV-2 replication and its virulence on the infected hosts [8] . doi = 10.1016/j.drudis.2020.10.001 id = cord-258902-h0wrs01h author = Liu, Xianglei title = Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice date = 2020-09-22 keywords = 293T; RBD; SARS summary = title: Enhanced Elicitation of Potent Neutralizing Antibodies by the SARS-CoV-2 Spike Receptor Binding Domain Fc Fusion Protein in Mice The cell-cell fusion assay results correlated well with the virus neutralization potency and could be used for high-throughput screening of large panels of anti-SARS-CoV-2 antibodies and vaccines without the requirement of live virus infection in BSL3 containment. Based on its highly homology to SARS-CoV, SARS-CoV-2 RBD is corroborated to contain immune dominant epitopes capable of eliciting antibodies that can neutralize viral infection and block viral entry by competing hACE2 Pseudovirus neutralization assay was then performed by incubation of SARS-CoV-2 pseudovirus with serially diluted mice serum for 1h at 37 °C, followed by addition of the mixture into pre-seeded 293T-ACE2 cells. On day 0 (pre-immunization), day 13 and day 27, mouse sera were collected and analyzed for RBD binding, pseudovirus and live virus neutralization, and cell-cell fusion inhibition. doi = 10.1016/j.vaccine.2020.09.058 id = cord-273505-pcsw3vmx author = Liu, Xiaosheng title = High-Dose Intravenous Immunoglobulins in the Treatment of Severe Acute Viral Pneumonia: The Known Mechanisms and Clinical Effects date = 2020-07-14 keywords = SARS; cell; covid-19; ivig summary = Based on the previous clinical experience in China, it was proposed that early initiation of high-dose intravenous immunoglobulins (IVIg) and low-molecular-weight heparin might be effective in improving the prognosis of severe and critically ill COVID-19 patients (16, 17) . The substantial increase in IgG concentration may saturate FcRn and reduce the half-life of pathogenic antibodies, contributing to the anti-inflammatory mechanism of high-dose IVIg. A balance between activating and inhibitory FcγRs is critical for a well-regulated immune response, and a disbalance markedly influences immunopathology in autoimmune and infectious diseases. Based on these potential supportive F(ab) ′ 2 and Fc mediated mechanisms and the known clinical effects in treating severe virus pneumonia such as SARS, MERS, influenza, and RSV disease, the early application of high-dose IVIg therapy may be considered in the management of severe COVID-19 patients. doi = 10.3389/fimmu.2020.01660 id = cord-348729-kejlm425 author = Liu, Xiaoyu title = Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date = 2020-05-04 keywords = ACE2; SARS; figure summary = SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. These determined infection mechanisms indicated that blocking the interaction of SARS-CoV-2-RBD and ACE2 would cause a direct neutralizing effect against virus. This information suggests that the ACE2 interface of SARS-CoV-2-RBD might have high immunogenicity, which would be a suitable targeting epitope to develop SARS-CoV-2-specific antibodies with potent neutralizing function by in vitro screening. We performed site-directed antibody screening by phage display and finally obtained one IgG antibody and three single domain antibodies with potent neutralizing activities for SARS-CoV-2. Notably, the eluted phage exhibited a stronger binding signal on SARS-CoV-2-RBD compared to that on SARS-CoV-2-RBD mut, especially those from the domain antibody library ( Figure 2C ), indicating an expected precleaning effect during selection. doi = 10.1101/2020.05.03.074914 id = cord-341976-yts6pzn3 author = Liu, Xintian title = Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China date = 2020-07-06 keywords = COVID-19; SARS summary = title: Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China We conducted a single-center, retrospective, cohort study to investigate the relationship between serum immunoglobulin G (IgG) and IgM and clinical outcomes in severe/critical patients with COVID-19. Specific serum immunoglobulin G (IgG) and IgM against SARS-CoV or Middle East Respiratory Syndrome-coronavirus (MERS-CoV) became detectable in patients as early as 11-15 days post illness onset [11, 12] . AGING Additionally, the titers of IgM and IgG were significantly correlated with viral load in patients infected by SARS-CoV-2 in a recent finding [14] , which promoted the hypothesis that specific antibody against virus might be associated with disease progression in COVID-19. In this retrospective cohort study, IgG and IgM against SARS-CoV-2 in severe/critical patients with COVID-19 were profiled, and relationship between antibody titers AGING and outcomes was also assessed. doi = 10.18632/aging.103417 id = cord-353484-q7d0ysbo author = Liu, Xue title = COVID-19: Progress in diagnostics, therapy and vaccination date = 2020-06-19 keywords = COVID-19; CoV-2; Coronavirus; RNA; SARS; patient summary = Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] . doi = 10.7150/thno.47987 id = cord-324902-18h0maxi author = Liu, Xuemei title = Patterns of IgG and IgM antibody response in COVID-19 patients date = 2020-06-09 keywords = SARS summary = As shown in Figure 1 , anti-SARS-CoV-2 S-specific IgG and IgM antibodies were not detectable in the very early days of infection (from day 0 to day 3). Anti-SARS-CoV-2 S-specific IgG antibodies were identifiable from day 7 onwards, peaking at approximately day 25, as shown in Figure 1(A) . Figure 1(B) shows a typical IgG and IgM antibody response in a 65-year-old woman with COVID-19 (supplementary materials, Table 1 ). As shown in Figure 1 (C), serum IgG antibody levels were not significantly correlated with clinical severity in the early stage of infection. Severe cases of COVID-19 tended to have a more vigorous IgG response against SARS-CoV-2 compared with mild cases. Our results also showed that mild cases tended to develop faster peak anti-SARS-CoV-2 S-specific IgM responses (approximately 17 days after symptom onset) compared with severe cases (approximately 21 days after symptom onset). doi = 10.1080/22221751.2020.1773324 id = cord-266564-imj1lcy9 author = Liu, Yangli title = Clinical manifestations and outcome of SARS-CoV-2 infection during pregnancy date = 2020-03-05 keywords = SARS summary = Given the maternal physiologic and immune function changes in pregnancy [2] , pregnant individuals might face greater risk of getting infected by SARS-CoV-2 and might have more complicated clinical events. We described epidemiological, clinical characteristics, pregnancy and perinatal outcomes of all hospitalized pregnant patients diagnosed with COVID-19 in China. We identified all hospitalized pregnant patients with laboratory-confirmed SARS-CoV-2 infection between December 8, 2019, and February 25, 2020 officially reported by the central government, in areas outside Wuhan, China. We reported 13 pregnant COVID-19 patients in China, indicating pregnant women also susceptible to SARS-CoV-2. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China doi = 10.1016/j.jinf.2020.02.028 id = cord-320169-dtv7to3l author = Liu, Yen-Chin title = COVID-19: the First Documented Coronavirus Pandemic in History date = 2020-05-05 keywords = RNA; SARS summary = The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. The spike glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) in human and Chinese horseshoe bats, civet for cell entry, that is also dependent on S protein priming by the serine protease TMPRSS2. Domestic animals can suffer from disease as intermediate hosts that cause virus transmission from natural hosts to humans; for example, SARS-CoV and MERS-CoV crossed the species barriers into masked palm civets and camels, respectively [30, 31] [ Table 1 ]. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. doi = 10.1016/j.bj.2020.04.007 id = cord-034481-zi9q96lj author = Liu, Yongjian title = Stability of SARS-CoV-2 on environmental surfaces and in human excreta date = 2020-11-01 keywords = SARS summary = Although close exposure to respiratory droplets from an infected patient is the main transmission route of SARS-CoV-2, touching contaminated surfaces and objects might also contribute to transmission of this virus. Here, we provide a report of our study of the stability of SARS-CoV-2 on various environmental surfaces and in human excreta (feces and urine). SARS-CoV-2 was more stable in urine than in feces, and infectious virus was detected up to 3 days in two adult urine and 4 days in one child urine. Prior to our study, two research teams had just reported the stability of SARS-CoV-2 on different material surfaces [4, 5] . In comparison with the above two studies, our data displayed a prolonged survival time of this virus on environmental surfaces. In Chin''s study, a five microliters of virus stock with the infectious titer of 10 6.8 TCID 50 /ml was deposited on the surface. doi = 10.1016/j.jhin.2020.10.021 id = cord-266616-boeb1xcp author = Liu, Yu title = Regulatory T cells: A potential weapon to combat COVID‐19? date = 2020-08-06 keywords = CD4; SARS; Treg summary = This review discusses the clinical and pathological features of COVID‐19, the roles of immune cells in pathological processes, and the possible avenues for induction of immunosuppressive T regulatory cells attenuating lung inflammation due to viral infection. 13, 19, 37, 38 In a mouse model study by Fulton et al, 38 evaluating the balance between virus clearance and immunopathology, Foxp3 + CD4 + regulatory T cells were shown to accumulate in mediastinal lymph nodes and the lungs of infected animals and to reduce immunopathology by regulating the responses of CD8 effector T cell during infection of respiratory syncytial virus. 38 IL-10 and TGF-β, antiinflammatory cytokines, could suppress the activity of NK cells, macrophage, cytotoxic CD8 T cells, and T helper cells 1 to reduce inflammatory storm caused by those during virus infection (Figure 1 ). Current pathology reports have revealed that the lung tissues in people infected with SARS-CoV-2 were prominently infiltrated with multinucleated giant cells and inflammatory cells. doi = 10.1002/mco2.12 id = cord-305054-4d84b2g6 author = Liu, Yuan title = The selection of reference genome and the search for the origin of SARS-CoV-2 date = 2020-08-11 keywords = SARS; Wuhan summary = The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts. Zhang, Wu, and Zhang [13] re-analyzed the RNA-Seq reads from two pangolins carrying coronavirus using reference-guided de novo assembly method, with Wuhan-Hu-1 as the reference genome. They also performed RNA sequencing in five archived pangolins samples from Guangdong, and assembled the genomes using WIV04, another SARS-CoV-2 genome from human, as reference genome. Using de novo assembly method, they obtained viral genome that showed 90.32% and 90.24% of whole genome identify to Wuhan-Hu-1and Bat-CoV RaTG13, respectively. RaTG13, which is a bat CoV, had 1,287 reads mapped to it, and the resulting assembly has total length of 21,925 and N50 of 1,428. doi = 10.1101/2020.08.10.245290 id = cord-349015-5oisrm5s author = Liu, Zhe title = Identification of a common deletion in the spike protein of SARS-CoV-2 date = 2020-04-02 keywords = SARS summary = In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. By sequencing the whole genome of SARS-CoV-2, we identified two variants having deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. To investigate whether these deletions described above are random mutations occasionally identified in a strain or would commonly occur after cell passages, we performed whole genome sequencing on the other 21 SARS-CoV-2 viral strains collected after 2 rounds of cell passage in Vero-E6 or Vero cells (Supplemental Table) . doi = 10.1101/2020.03.31.015941 id = cord-299480-mehwd0dk author = Liu, Zheng-Xue title = Identification of single-chain antibody fragments specific against SARS-associated coronavirus from phage-displayed antibody library date = 2005-04-08 keywords = HRP; SARS; sa59b summary = Abstract To develop early diagnostic reagents, effective vaccines, and even drugs against SARS-associated coronavirus (SARS-CoV), the human single fold single-chain antibody fragments, (scFv) libraries I+J (Tomlinson I+J) were used to identify novel scFvs, which can specifically bind to SARS-CoV. Interestingly, two scFvs (B5 and B9) exhibited higher binding specificity to SARS-CoV with the OD450 value 0.608 and 0.545, respectively, and their coding sequences shared the identical sequence composed of VH gene (351bp) and VL gene (327bp), so the two scFvs were uniformly named as SA59B and chosen for further analysis. Hence, single-chain antibody fragments specific against SARS-CoV from phage-displayed antibody library have potential for exploitation as diagnostic or even antiviral therapeutic reagents. The ELISA plates coated with purified SARS-CoV lysate, positive and negative sera were provided by Military Medical Science Academic and HuaDa Gene Company (Beijing, China). The panning procedure was performed on a 96-well flexible assay plate coated with purified SARS-CoV lysate, which was blocked directly with MPBS (PBS containing 4% skimmed milk powder) at room temperature for 2 h. doi = 10.1016/j.bbrc.2005.02.003 id = cord-161674-nk0wie0w author = Liu, Zhi title = Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date = 2020-04-10 keywords = SARS; figure; miRNA; virus summary = Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). doi = nan id = cord-103872-yzqic5vt author = Liu, Zhijin title = Global view on virus infection in non-human primates and implication for public health and wildlife conservation date = 2020-05-13 keywords = NHP; SARS summary = Research has revealed that SARS-CoV-2 and other coronaviruses have been transmitted from animals to humans and vice versa, and across animal species, and hence, attracted public attention concerning host-virus interactions and transmission ways. We suggest epidemiological investigations in NHPs, specifically in Old World monkeys with close contact to humans, and other effective measures to prevent this potential circular transmission. First, we generated a summary statistics of worldwide reported VI-NHPs. We then 61 identified and predicted NHP species with a high risk of virus transmission from humans and 62 predicted geographic locations where disease outbreaks are likely to occur. Since centrality in primate-virus networks could assess the potential for the 72 circulation of viruses among NHPs and humans, we estimated the centrality using four metrics: 73 strength degree centrality, eigenvector centrality, betweenness centrality, and closeness centrality 74 implemented in the R package "igraph" and UCINET 6. Centrality in primate-parasite networks 225 reveals the potential for the transmission of emerging infectious diseases to humans doi = 10.1101/2020.05.12.089961 id = cord-351835-1s2zsqoq author = Liu, Zhixin title = Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 date = 2020-03-11 keywords = ACE2; SARS summary = title: Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 In this study, we used systematic comparison and analysis to predict the interaction between the receptor‐binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin‐converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans. FP, fusion peptide; HR, heptad repeat 1 and heptad repeat 2; RBD, receptor-binding domain, contains core binding motif in the external subdomain; SP, signal peptide Phylogenetic reconstruction determines the evolutionary relationship and host selection between spike glycoproteins in the human-close beta coronaviruses. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2 doi = 10.1002/jmv.25726 id = cord-314072-av3r7it7 author = Liu, Zhuoming title = Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date = 2020-11-08 keywords = SARS summary = title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans. To select for SARS-CoV-2 S variants that escape neutralization, we used VSV-SARSas we isolated this mutation alone, and acquisition of the L517R substitution appeared to 141 increase viral fitness as judged by plaque morphology (Fig S2) . doi = 10.1101/2020.11.06.372037 id = cord-302912-aqutzlx4 author = Liu, Ziteng title = The Inhibitory Effect of Curcumin on Virus-Induced Cytokine Storm and Its Potential Use in the Associated Severe Pneumonia date = 2020-06-12 keywords = SARS; curcumin summary = The development of coronavirus-evoked pneumonia is associated with excessive inflammatory responses in the lung, known as "cytokine storms," which results in pulmonary edema, atelectasis, and acute lung injury (ALI) or fatal acute respiratory distress syndrome (ARDS). Therefore, in this review, we summarize the mounting evidence obtained from preclinical studies using animal models of lethal pneumonia where curcumin exerts protective effects by regulating the expression of both proand anti-inflammatory factors such as IL-6, IL-8, IL-10, and COX-2, promoting the apoptosis of PMN cells, and scavenging the reactive oxygen species (ROS), which exacerbates the inflammatory response. As part of a robust immune response in severe cases, the virus triggers overaction of immune systems, producing a large number of inflammatory factors, which causes severe damage to the lung and manifests acute respiratory distress syndrome (ARDS), resulting in high mortality. Such an inflammatory response, including overproduction of immune cells and pro-inflammatory cytokines, is defined as the cytokine storm that usually occurs in viral infection and causes acute lung injury (ALI) and ARDS. doi = 10.3389/fcell.2020.00479 id = cord-297209-84gs67bn author = Livanos, A. E. title = Gastrointestinal involvement attenuates COVID-19 severity and mortality date = 2020-09-09 keywords = Fig; SARS; September; covid-19 summary = In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first time in vivo but failed to obtain culturable virus. . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint (nausea, vomiting and diarrhea) was associated with less severe disease (p<0.02 Fisher''s exact 188 test) and lower mortality (p<0.001 Fisher''s exact test) (Fig. 1a) . . https://doi.org/10.1101/2020.09.07.20187666 doi: medRxiv preprint CoV-2 nucleocapsid protein in small intestinal enterocytes of COVID-19 patients ( Fig. 4i,n, CD8 + T cells, the dominant IEL 388 population, showed an increase (2.6-fold) in COVID-19 cases compared to controls but the 389 difference did not reach statistical significance (p=0.4) ( Supplementary Table 12a ), likely owing 390 to inter-patient variability, also observed by light microscopy. doi = 10.1101/2020.09.07.20187666 id = cord-342139-t2tukk0z author = Livingston, Gill title = Prevalence, management, and outcomes of SARS-CoV-2 infections in older people and those with dementia in mental health wards in London, UK: a retrospective observational study date = 2020-10-05 keywords = COVID-19; SARS; patient; trust summary = For individuals, the following data were collected: demographic data (age, sex, ethnicity); mental health clinical details (ie, dementia or other diagnosis); Mental Health Act 1983 or Mental Capacity Act 2005 status 31 (these are legislative frameworks for those with mental illness, including an absence of decisional capacity, which in defined circumstances allow people to be detained in a hospital without giving consent); physical comorbidities; and COVID-19-related details, which were COVID-19 clinical diagnosis (date of clinical suspicion of COVID-19 and SARS-CoV-2 RT-PCR test result or results, if retested), possible COVID-19 symptoms (first symptom noted, presence of new persistent cough, shortness of breath [respiratory rate >20 breaths per min], temperature ≥37·8°C, new loss of smell or taste, sore throat, gastrointestinal symptoms, fatigue, loss of appetite, asymptomatic, duration of symptoms [days]), change to mental state related to COVID-19 (increased cognitive impairment or delirium, increased or new mood disturbance or psychosis); and manage ment (do not attempt resuscitation status; whether the patient was receiving vitamin D treatment; isolation of patients and duration [days] if applicable; whether venous thromboembolism [VTE] prophylaxis was given before the patient became symptomatic; whether VTE prophylaxis was given after symptoms developed; whether antipsychotic medication had been stopped, started, or increased during SARS-CoV-2 infection and treatment, and new antipsychotic sideeffects; whether prophylactic antibiotics were prescribed for community-acquired pneumonia or hospital-acquired pneumonia; whether oxygen therapy was administered on the ward; and whether the patient was transferred to a medical ward in a general hospital). doi = 10.1016/s2215-0366(20)30434-x id = cord-319194-ukuia48s author = Liò, Pietro title = Phylogenomics and bioinformatics of SARS-CoV date = 2004-02-04 keywords = CoV; RNA; SARS; s1b summary = Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Figure 1 shows the maximum likelihood tree produced using a set of homologous replicases from five SARS-CoV strains, 12 other coronaviruses representing both groups 1 and 2 of the genus [2, 3] , one torovirus (Breda virus) and one okavirus [yellow head (YH) virus], which were determined to most closely represent the consensus coronavirus sequence by a PSI-Blast search [12] . doi = 10.1016/j.tim.2004.01.005 id = cord-326643-obfvi3ms author = Lo Giudice, Roberto title = The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in Dentistry. Management of Biological Risk in Dental Practice date = 2020-04-28 keywords = COVID-19; SARS; patient summary = Considering the virus'' route of transmission, a specific protocol should be applied to reduce the risk of infection in addition to measures that prevent the spread of infection from a patient to another person or medical tools and equipment (cross-infection). Due to the transmission route, in addition to measures that prevent diffusion of the infection from a patient to another person or medical tools and equipment (cross-infection), it is advisable to add further airborne and contact precautions to the routine standard hygienic procedures in order to reduce the risk of SARS-CoV-2 transmission. The use of personal protective equipment (PPE) such as gloves, masks, visors, goggles, dental uniform, and surgical gown and shoes (see section on PPEs below). To reduce the risk of SARS-CoV-2 infection, given how the disease spreads and the current health crisis, the following prevention measures are suggested in addition to what is already generally performed: doi = 10.3390/ijerph17093067 id = cord-337137-0ey40gzw author = Lo, Anthony WI title = How the SARS coronavirus causes disease: host or organism? date = 2005-12-17 keywords = SARS; acute; respiratory; severe summary = Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection doi = 10.1002/path.1897 id = cord-334849-8rblgq9b author = LoPresti, Marissa title = The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature date = 2020-08-12 keywords = ACE2; COVID-19; SARS; genetic; study summary = 1 As with many complex diseases, the reality for most individuals likely involves a combination of genetic -including viral and host genetics -and non-genetic Relative to other coronaviruses, SARS-CoV-2 has unique biological properties and related clinical impact, but data regarding other coronaviruses may be relevant. This can help populate lists of genes that -along with data from related biological studies -may bear scrutiny in the developing and important large-scale host genetic 6 and porcine epidemic diarrhea virus (PEDV)in pigs. In various species, efforts have focused on genes encoding the relevant coronavirus receptor, including effects of viral and host genetic changes and how these may impact the disease process. 30 In humans (see Tables 1 and S2 and Figures 3 and 4 for details on human studies of these genes, including specific references), studies of specific ACE2 polymorphisms have not shown significant associations with SARS-CoV-1 susceptibility or outcome. doi = 10.1016/j.ajhg.2020.08.007 id = cord-334049-r3rlykli author = Lobo-Galo, Naún title = FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication date = 2020-05-14 keywords = DSF; SARS summary = Our inclusion criteria for the selection of drugs for potential COVID-19 therapy were: (1) The drug is a FDA-approved that can potentially be repurposed as an ready-to-use therapeutic antiviral; (2) Its use has been extensively studied, and there is sufficient literature on its pharmacology; (3) The drug has few side effects in long-term administration, with not known direct fatalities associated to it, and not additional extensive toxicological studies are needed; (4) Drug can interact with active site of SARS-CoV-2 main protease and reacts with thiol group of its catalytic cysteine, producing an irreversible covalent-inhibition; (5) Administered drug shows efficient distribution through multiple organs, as recent publications suggest the possibility that SARS-CoV-2 has tropism for multiple tissues, beyond the pneumocytes, including heart and blood vessels, liver, intestine, neural cortex and brain stem (Wadman et al., 2020); (6) Drug penetrates the cell membrane, as its antiviral target, the protease acts early during replication in the host cytoplasm; and (7) When administered, drug is metabolized and excreted slowly; and possible metabolites have also potential inhibitory activity. doi = 10.1080/07391102.2020.1764393 id = cord-338317-ro041w5l author = Lockhart, Sam M. title = When two pandemics meet: Why is obesity associated with increased COVID-19 mortality? date = 2020-06-29 keywords = SARS; covid-19; insulin; obesity summary = Thus, the association of obesity with worse 105 outcomes in acute lung infection or widespread alveolar damage of other types, appears to be 106 strongest and most consistent with COVID-19 and pandemic H1N1 influenza. In addition to being lower in obesity and most insulin 168 resistant states it is worth noting that adiponectin levels have been reported to be significantly 169 lower in many of the COVID-19 "at risk" groups e.g. Male < Females 20 and South Asians < White 170 is secreted from adipose tissue, associated with insulin resistance and likely contributes to 197 thrombotic risk in obesity by impairing fibrinolysis 23 . In summary, we have applied insights into the pathophysiology of the adverse consequences of 279 obesity and emerging evidence regarding the pathological mechanisms in COVID-19 to suggest 280 possible routes whereby obesity can exacerbate the tissue damage associated with infection by the 281 SARS-CoV-2 virus. doi = 10.1016/j.medj.2020.06.005 id = cord-302228-n5o6jfs2 author = Lodise, Thomas P. title = COVID‐19: Important Therapy Considerations and Approaches in this Hour of Need date = 2020-05-05 keywords = SARS; covid-19 summary = A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients.1-3 However, optimal drug therapy decisions for those with moderate to severe COVID-19 infections are extremely challenging at this time as evidence is limited. A number of novel and repurposed therapies agents with activity against SARS-CoV-2 have been identified, and most institutions have developed clinical pathways to operationalize their use in appropriate COVID-19 patients. If data are amassed on COVID-19 patients, it is important that detailed information is collected on the outcomes associated with the treatment strategies used at our respective institutions. Despite data suggesting that lopinavir-ritonavir was active against SARS-CoV-2 infection, no benefit was observed with lopinavir-ritonavir treatment versus standard care in a study of hospitalized adult patients with severe COVID-19. doi = 10.1002/phar.2396 id = cord-266987-ikt8r2o1 author = Loeffelholz, Michael J. title = Laboratory diagnosis of emerging human coronavirus infections – the state of the art date = 2020-03-30 keywords = China; CoV-2; MERS; SARS summary = The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. It must be appreciated that no matter how accurate and fast laboratory testing methods are, the diagnosis of viral pneumonias such as caused by SARS-CoV-2 involves collecting the correct specimen from the patient at the right time. The authors recommended to use serology to facilitate the diagnosis of SARS-CoV-2 infections when an NP swab specimen was collected inappropriately and the molecular assays were performed unsatisfactorily [42] . Several RT-PCR protocols for detection of SARS-CoV-2 RNA have been posted by the World Health Organization at https://www.who.int/emergencies/ diseases/novel-coronavirus-2019/technical-guidance/ laboratory-guidance. Considering the increased levels of mortality and infectivity associated with three novel-coronavirus outbreaks, these random-access, safe and simple tests, which offer fast and accurate detection and identification, are likely to have an immediate impact on prompt clinical and epidemiological decisions [7, 63] . doi = 10.1080/22221751.2020.1745095 id = cord-291315-y40s45iv author = Logunov, Denis Y title = Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia date = 2020-09-04 keywords = SARS; covid-19; day; vaccine summary = title: Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). INTERPRETATION: The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong humoral and cellular immune responses in participants. These findings of two open, phase 1/2 non-randomised studies of a heterologous prime-boost COVID-19 vaccine based on recombinant adenoviral vectors rAd26-S and rAd5-S show that the vaccine is safe, well tolerated, and induces strong humoral and cellular immune responses in 100% of healthy participants. In our study, despite formation of neutralising antibodies to recombinant adenoviruses after vaccination with rAd26 and rAd5, formation of a humoral immune response to target antigen (SARS-CoV-2 glycoprotein S) in vaccinated volunteers was not affected. doi = 10.1016/s0140-6736(20)31866-3 id = cord-283984-jch0ja1o author = Loizzo, Monica R. title = Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species date = 2008-03-20 keywords = SARS summary = title: Phytochemical Analysis and in vitro Antiviral Activities of the Essential Oils of Seven Lebanon Species oxycedrus oil, in which α‐pinene and β‐myrcene were the major constituents, revealed antiviral activity against HSV‐1 with an IC (50) value of 200 μg/ml and a SI of 5. In this study, we report the antiviral activity of seven essential oils obtained from berry, fruits, and leaves of different species collected in Lebanon. nobilis berries oil exhibited an IC 50 value of 120 mg/ml against SARS-CoV with a selectivity index (SI; TC 50 /IC 50 ) of 4.2. oxycedrus oil exhibited the highest activity against HSV-1 with a IC 50 value of 200 mg/ml and a SI of 5. P. palaestina essential oil was inactive against SARS-CoV (IC 50 > 1000 mg/ml) and less active against HSV-1 (IC 50 500 mg/ml). nobilis oil against SARS-CoV, and we also reported the interesting anti-herpetic activity of J. doi = 10.1002/cbdv.200890045 id = cord-270495-2u072mtp author = Lokida, Dewi title = Diagnosis of COVID-19 in a Dengue-Endemic Area date = 2020-08-05 keywords = DENV; SARS summary = When SARS-CoV-2 is negative and clinical indication is present (at least fever and thrombocytopenia), DENV NS1 antigen and/or IgM/IgG antibody testing may be performed. Clinicians from Singapore reported two COVID-19 cases that were misdiagnosed as dengue among patients who presented with clinical manifestations and hematology profiles, suggesting dengue infection and false-positive DENV IgM antibody using a rapid diagnostic test (RDT). COVID-19 cases were defined as inpatients who met the COVID-19 criteria based on a predetermined combination of symptoms, laboratory testing, imaging, and risk exposure at Tangerang District Hospital, Indonesia (see Supplemental Table 1 ), and had a positive nasopharyngeal or oropharyngeal real-time RT-PCR for SARS-CoV-2. None of the 42 subjects was positive for dengue NS1 or showed seroconversion or increasing DENV IgM and IgG index values, suggesting no acute DENV infection among these COVID-19 cases. The third patient did not recall having a fever before acute COVID-19 illness, suggesting asymptomatic or mild dengue, the most common presentation of DENV infection. doi = 10.4269/ajtmh.20-0676 id = cord-263481-w5ytp1q7 author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date = 2020-06-02 keywords = CoV-2; RBD; SARS summary = MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. doi = 10.1016/j.meegid.2020.104389 id = cord-343517-vf32wxkx author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date = 2020-04-11 keywords = CoV-2; SARS; spike summary = However, SARS-CoV-2 has emerged with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. The evolutionary distances showed that all the SARS-CoV-2 spike proteins cluster in the same node of the phylogenetic tree confirming the sequences are similar to Refseq YP_009724390 (Fig. 2) . doi = 10.1101/2020.04.07.030924 id = cord-309737-u960ftdm author = Lolachi, Sanaz title = Macrophage activation syndrome as an unusual presentation of paucisymptomatic severe acute respiratory syndrome coronavirus 2 infection: A case report date = 2020-08-07 keywords = MAS; SARS summary = PATIENT CONCERNS: We describe the unique case of young man who developed MAS as the sole manifestation of an otherwise paucisymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. DIAGNOSES: Clinical and biological criteria led to the diagnosis of MAS; cytokine profile was highly suggestive reverse transcription polymerase chain reaction for SARS-CoV-2 in nasopharyngeal swabs was negative, but serum anti-SARS-CoV-2 immunoglobulin A and immunoglobulin G resulted positive leading to the diagnosis of SARS-CoV-2 infection. [2] Aims and scope of the report: to describe the unique case of a patient who developed MAS as the sole manifestation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and to highlight that even paucisymptomatic COVID-19 patients can develop life-threatening complications. Rapid clinical deterioration with high, sustained fever, cytopenias, rising transaminases and ferritin, and evolving coagulopathy prompted us to suspect a MAS (or secondary hemophagocytic lymphohistiocytosis, HLH) in the context of SARS-CoV-2 infection. doi = 10.1097/md.0000000000021570 id = cord-298441-77w86l8q author = Lombardi, Andrea title = Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date = 2020-06-20 keywords = SARS; test summary = To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca'' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). doi = 10.1016/j.cmi.2020.06.013 id = cord-336026-x02f7byo author = Lommatzsch, Marek title = COVID‐19 in a patient with severe asthma treated with Omalizumab date = 2020-06-27 keywords = SARS summary = 1, 3, 4 This is supwith asthma following Omalizumab treatment is primarily mediated by a downregulation of the high-affinity IgE receptor on pDCs. 8, 9 Thus, we hypothesize that the patient described in this case report might have been protected from an asthma exacerbation or pneumonia during COVID-19, either because of the underlying disease (allergic asthma) or because of the antibody used for treatment (Omalizumab), or both. Therefore, studies are needed to characterize the precise interaction of chronic airway diseases (such as asthma) and of biologics (such as Omalizumab) with SARS-CoV-2 infections in humans. We report a case of a 52-year-old man with severe allergic asthma treated with Omalizumab with no evidence of an asthma exacerbation, loss of asthma control or pneumonia during symptomatic COVID-19 disease. We hypothesize that the underlying disease (allergic asthma) or the antibody used for treatment (Omalizumab), or both, might have exerted protective effects. doi = 10.1111/all.14456 id = cord-262904-0b0ljjq1 author = Lon, Jerome Rumdon title = Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2 date = 2020-10-29 keywords = SARS; epitope; protein summary = It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. On this basis, we predicted the linear and conformational B cell epitopes, analyzed the conservation of the epitopes, the adaptability and other evolutionary characteristics of the surface protein, which provided a theoretical basis for the vaccine development and prevention of SARS-CoV-2. With the amino acid sequences of the surface protein of SARS-CoV-2 of NC_045512.2 as templates, we predicted the 3D structure of E and M protein through the online server SWISS-MODEL [10] based on homology modeling method, selected the optimal structure based on the template identity and GMQE value [10] , and the rationality of the structure was evaluated by Ramachandran plot [11] with PDBsum server. doi = 10.1186/s12985-020-01437-4 id = cord-353133-tsqb6pa8 author = Long, Dustin R. title = Considerations for Assessing Risk of Provider Exposure to SARS-CoV-2 after a Negative Test date = 2020-05-26 keywords = SARS summary = Recent publication of data suggesting imperfect clinical sensitivity of reverse transcription polymerase chain reaction assays for SARS-CoV-2 3 could lead healthcare providers to intuitively question the wisdom of a strategy that relies on a negative SARS-CoV-2 test, particularly when planning high-risk procedures such as endotracheal intubation. To help providers and clinical leaders grapple with this dynamic uncertainty, we have developed an online tool (https://covid-airway-npv.info) that enables the user to examine the impact of different assumptions regarding SARS-CoV-2 reverse transcription polymerase chain reaction test characteristics and disease prevalence on the potential risk of provider exposure during airway management. Uncertainty is modeled by asking the user to provide the most likely, minimum, and maximum value of the parameter (here, SARS-CoV-2 testing characteristics and COVID-19 community prevalence), using a Project Evaluation and Review Techniques distribution. doi = 10.1097/aln.0000000000003392 id = cord-334313-v2syspu6 author = Long, S. Wesley title = Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date = 2020-05-03 keywords = CoV-2; Houston; SARS; covid-19 summary = We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. Because in vitro resistance of SARS-CoV to remdesivir has been reported to be caused by either of two amino acid replacements in RdRp (Phe476Leu and Val553Leu), we interrogated our data for polymorphisms in the nsp12 gene. doi = 10.1101/2020.05.01.072652 id = cord-321670-f2d4bykp author = Longardt, Ann Carolin title = Perinatale Aspekte der SARS-CoV-2 Infektion date = 2020-08-24 keywords = Coronavirus; Frauen; SARS; der; die summary = In einer Studie aus den 50 Kliniken in Wuhan wurden 118 Frauen mit COVID-19 zwischen Dezember 2019 und März 2020 erfasst; 109 zeigten einen milden Verlauf und 9 (8 %) einen schweren Verlauf mit Hypoxämie, eine hiervon wurde beatmet. Abgesehen davon, dass das Virus selten im Blut detektiert wurde, stellt sich auch die Frage nach der Expres sion des SARS-CoV-2-Rezeptors ACE2 im Bereich der maternofetalen Grenzfläche beziehungsweise in der Plazenta. Gesichert ist der Infektionsweg durch eine SARS-CoV-2-Übertragung über die Muttermilch damit jedoch nicht. Anzunehmen ist aber auch die Weitergabe von SARSCoV2Antikörpern über die Muttermilch an das Kind, was den klinischen Verlauf einer kindlichen Infektion positiv beeinflussen könnte, ähnlich wie es bei der SARS-Epidemie 2002/2003 berichtet wurde [42] . Vertical Transmission of Coronavirus Disease 19 (COVID-19) from Infected Pregnant Mothers to Neonates: A Review An Analysis of 38 Pregnant Women with COVID19, Their Newborn Infants, and MaternalFetal Transmission of SARS CoV2: Maternal Coronavirus Infections and Pregnancy Outcomes doi = 10.1055/a-1192-7437 id = cord-320673-4guarm0k author = Lopera, E. title = Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes date = 2020-04-25 keywords = ACE2; SARS; TMPRSS2; covid-19 summary = title: Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes While large-scale genetic studies of COVID-19 patients are being assembled, such as those coordinated by the COVID host genetics consortium (https://www.covid19hg.com/), it is worthwhile to evaluate the effects of genetic variants in genes involved in SARS-CoV-2 infection on human phenotypes, including quantitative traits, taking advantage of already existing cohorts. Therefore, understanding the role of genetic variants at genes essential for SARS-CoV-2 infection in human quantitative phenotypes is important to explain the observed variability in infection susceptibility and severity of COVID-19 and this understanding may suggest potential treatments. In conclusion we carried out an extensive screening of potential genetic associations at common and low frequency variants in the ACE2 and TMPRSS2 genes, and found a lack of substantial effect in human quantitative phenotype variation in the general population. doi = 10.1101/2020.04.22.20074963 id = cord-335270-edga753o author = Lopez-Alvarez, Diana title = Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing date = 2020-06-25 keywords = Cali-01; SARS summary = title: Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing We report the genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a patient with symptoms of coronavirus disease 2019 (COVID-19) who was infected in Cali, Colombia. We report the coding-complete genome sequence of SARS-CoV-2 isolate Cali-01, obtained from a Colombian patient with no recent record of international travel. First, for quality control and filtering of reads (fragments of 400 to 700 bp), we used the gupplyplex script of the ARTIC Network bioinformatics protocol (https://artic.network/ncov-2019/ncov2019-bioinformatics -sop.html), followed by a reference assembly with minimap2 (6) and Pilon (7), using the sequence of the Wuhan-Hu-1 isolate (GenBank accession number MN908947.3). The genome sequence of SARS-CoV-2 isolate Cali-01 was deposited in GISAID and GenBank under accession numbers EPI_ISL_445219 and MT470219, respectively. The sequencing work was carried out at the Virology Laboratory, Department of Microbiology, of the Universidad del Valle, in Cali. doi = 10.1128/mra.00573-20 id = cord-314369-o4nis91y author = Lopez-Lopes, G. I. S. title = Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date = 2020-08-01 keywords = RNA; SARS summary = Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. During the initial months of the COVID-19 swabs and other collection methods were used by LHW in the institute to identify SARS-Cov-2 RNA in upper respiratory tract, but occasionally throat wash (TW) was alternatively used. We compared the CT obtained at this survey to results generated from contemporary swab collections, sent as routine testing at the institute, that provide SARS-CoV-2 rtPCR testing to clinical services. The study did not compare the rate of positivity in paired samples, and only one individual was documented that performed both a swab test (negative) and a positive throat wash collection at a same day. The study suggests that throat wash may be a valid alternative to the detection of SARS-CoV-2 RNA. doi = 10.1101/2020.07.29.20163998 id = cord-287658-c2lljdi7 author = Lopez-Rincon, Alejandro title = Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date = 2020-09-10 keywords = CoV-2; RNA; SARS; sequence summary = The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets'' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. doi = 10.1101/2020.03.13.990242 id = cord-330536-q8zr0mkl author = Lopinto, Julien title = Severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection date = 2020-09-14 keywords = SARS summary = We report here a case of severe hemoptysis in post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and managed in a referral center. CASE PRESENTATION: A 58-year-old man was admitted to our intensive care unit for severe hemoptysis with history of post-tuberculosis bronchiectasis. CONCLUSIONS: To our knowledge, this is the first case of acute exacerbation of bronchiectasis related to SARS-CoV-2 infection and complicated by severe hemoptysis. Since the beginning of SARS-CoV-2 outbreak in China, severe acute respiratory syndrome has been widely descripted [1] [2] [3] and hemoptysis has rarely been observed in this condition [1, 2, 4, 5] . We report here a case of acute exacerbation of posttuberculosis bronchiectasis precipitated by SARS-CoV-2 infection complicated by severe hemoptysis and managed in a referral center. To our knowledge, this is the first case reported of acute exacerbation of post-tuberculosis bronchiectasis precipitated by SARS-CoV-2 infection and complicated by severe hemoptysis. doi = 10.1186/s12890-020-01285-6 id = cord-317233-k3wuqwyu author = Lorenzo-Redondo, Ramon title = A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways date = 2020-11-11 keywords = Chicago; Illinois; March; SARS; clade summary = INTERPRETATION: These results show that multiple variants of SARS-CoV-2 were circulating in the Chicago area in mid-March 2020 that differed in their relative viral loads in patient upper airways. While the predominant virus genotype in Washington state was most closely related to viruses in China in the early epidemic, the predominant virus genotype in New York was more closely related to viruses from Europe [12] .The latter viruses carry a mutation in their Spike protein (D614G) that has not only become more common worldwide over time, but that has also been associated with higher viral loads in COVID-19 patients. Furthermore, this study supports a correlation between SARS-CoV-2 clade and relative viral load in the upper airways of infected patients. In this study, we report the phylogenetic and phylodynamic analyses of 88 SARS-CoV-2 genomes from COVID-19 patients in Chicago, Illinois, US, which largely fall into three major clades. doi = 10.1016/j.ebiom.2020.103112 id = cord-290209-gkx57lyq author = Losurdo, Pasquale title = Impact of lockdown for SARS-CoV-2 (COVID-19) on surgical site infection rates: a monocentric observational cohort study date = 2020-09-14 keywords = COVID-19; SARS; SSI; surgical summary = At multivariate analysis, the measures to reduce the SARS-CoV-2 spread (OR 0.368; p 0.05) were independently associated with the reduction for total, superficial and deep SSIs. Moreover, the presence of drains (OR 4.99; p 0.009) and a Type III–IV of SWC (OR 1.8; p 0.001) demonstrated a worse effect regarding the primary endpoint. The presence of a drain and a contaminated or dirty type of surgery (according to SWC) could increase the overall rate of SSIs, but the presence of a drain did not demonstrate an increased risk of superficial and/or deep SSIs. On the other hand, protection with surgical masks for both patient and surgeon during the post-operative period in the surgical unit and the absence of visitors, dramatically reduced superficial and deep SSIs. These two simple precautions emerged as independently associated with the reduction of both superficial and deep SSIs. Quality improvement initiatives aimed at reducing SSI rates are often hindered by limited or even conflicting evidence for proposed interventions to reduce SSI [33] . Surgery and the postoperative management of surgical wound carries a non-negligible risk of SSIs. In this study, we provided important insights into the superficial and deep surgical site infection risk assessment for patients who underwent surgery. doi = 10.1007/s13304-020-00884-6 id = cord-341176-83khavoh author = Lotfi, Melika title = CRISPR/Cas13: A potential therapeutic option of COVID-19 date = 2020-09-17 keywords = CRISPR; Cas13; RNA; SARS summary = In contrast to traditional vaccines and therapies, which rely on priming the human immune system to identify viral proteins and components and reduce viral entrance into cells (12) , the CRISPR-based system has focused on identifying and degrading the intracellular viral genome and its resulting viral mRNAs. Thus, for using CRISPR as a therapeutic option, it is critical to identify the SARS-CoV-2 molecular characteristics. They found that the two highly-conserved regions in SARS-CoV-2 genome, which can be appropriate to be targeted by PAC-MAN as a potential pan-coronavirus inhibition strategy are respectively the RNA-dependent RNA polymerase (RdRP) gene in the open reading frame1a/b or ORF1a/b region, which maintains the proliferation of all coronaviruses, and the Nucleocapsid (N) gene at the 3'' end of the genome, which encodes the capsid protein for viral packaging (13) . doi = 10.1016/j.biopha.2020.110738 id = cord-314051-dr27bsvt author = Lother, Sylvain A. title = Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date = 2020-06-23 keywords = CoV-2; PCR; SARS summary = If viral carriage is not detected by testing, patients may proceed with elective surgery whereby signs and symptoms of coronavirus disease (COVID-19) may arise in the postoperative period, leading to adverse outcomes. 3 While screening with RT-PCR may detect some presymptomatic preoperative patients, the window of diagnostic utility is small, and careful interpretation of negative and positive test results must be considered prior to altering the course of therapy. A positive RT-PCR result identifies a group of patients who may be infected with SARS-CoV-2 and should have elective surgeries delayed. Si la présence virale n''est pas dépistée par un test, les patients peuvent aller de l''avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d''une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. doi = 10.1007/s12630-020-01746-w id = cord-280003-ndpuezpo author = Lou, Bin title = Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date = 2020-03-27 keywords = RNA; SARS summary = Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. In order to answer some of the questions, we investigated the characteristics of antibody responses in 80 Covid-19 patients during their hospitalization periods, through detecting total antibody, IgM and IgG using immunoassays. A total of 80 Covid-19 patients and 100 to 300 healthy people were tested for antibodies against SARS-CoV-2 using different immunoassays. The present data showed that the sensitivity of total antibody detection was higher than that of IgM and IgG (p<0.001) while the specificities are overall comparable when the same testing technic (ELISA, CLMA or LFIA) is used. doi = 10.1101/2020.03.23.20041707 id = cord-256556-1zea3wa1 author = Lou, Yan title = Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: An Exploratory Randomized, Controlled Trial date = 2020-10-25 keywords = COVID-19; SARS; patient summary = The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir marboxil, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. Then, an exploratory single center, open-label, randomized, controlled trial was conducted to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). This trial was an exploratory single center, open-label, randomized, controlled trial to evaluate the efficacy and safety of adding baloxavir marboxil or favipiravir to the current standard antiviral treatment in patients confirmed as COVID-19 who are still positive for the SARS-CoV-2 (ChiCTR2000029544). The activity against SARS-CoV-2 was tested in vitro for the antiviral drugs used in this trial, including arbidol, ritonavir, lopinavir, darunavir, baloxavir acid, and favipiravir. doi = 10.1016/j.ejps.2020.105631 id = cord-317468-pnxni1x5 author = Louie, Philip K. title = Early Peri-operative Outcomes Were Unchanged in Patients Undergoing Spine Surgery During the COVID-19 Pandemic in New York City date = 2020-09-15 keywords = SARS; patient; surgery summary = The purpose of this study was to describe the peri-operative outcomes of patients undergoing spine surgery for spine pathology during the heights of the COVID-19 pandemic in New York City, including particular attention to the development of SARS-CoV-2 symptoms, post-operative complications, and patient monitoring following hospital discharge during the early post-operative period. The surgical dates also encompass a period of time in which the institution (1) followed state directives to suspend elective surgery and instead utilize strict criteria to define essential surgical cases (Table 1) , (2) dispensed personal protective equipment to medical personnel, (3) selectively performed post-admission SARS-CoV-2 testing (Cepheid Xpert Xpress SARS-CoV-2 RT-PCR, Sunnyvale, CA, USA) following patient assessment by a multidisciplinary team, (4) initiated a telehealth service for post-operative follow-up, and (5) began a progressively intensive patient screening process (Fig. 1) . doi = 10.1007/s11420-020-09797-x id = cord-334858-wxexl0qy author = Lozada-Nur, Francina title = Dysgeusia in COVID-19: possible mechanisms and implications date = 2020-06-27 keywords = SARS; taste summary = A European multi-center epidemiological study 6 analyzing the prevalence of olfactory and gustatory dysfunctions as a clinical presentation in a cohort of 417 laboratory-confirmed cases of COVID-19 with mild-to-moderate disease presentation reported that 88.8% of patients population had gustatory disorders. 18, 19 It may be quite plausible that SARS-Cov-2 binds to ACE2 receptors present in oral mucosa, triggering an inflammatory response that leads to cellular and genetic changes which could alter taste. It is possible that zinc chelation through immune mechanisms and molecules known to increase in concentration with inflammatory processes may result in acute hypozincemia 27 or a more localized change in cellular zinc homeostasis of oral gustatory cells due to infection with SARS-Cov-2. We hypothesize that changes in localized cellular zinc homeostasis in oral gustatory cells due to immune responses to SARS-Cov-2 viral replication, may result in dysgeusia which may or may not be accompanied by hypozincemia. doi = 10.1016/j.oooo.2020.06.016 id = cord-329794-msxrdhb3 author = Lu, Aili title = Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date = 2004-06-20 keywords = RDRP; RNA; SARS summary = Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. doi = 10.1016/j.virol.2004.03.031 id = cord-296661-6ndn2qxc author = Lu, Dingnan title = Primary concentration – The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review date = 2020-07-25 keywords = SARS; peg summary = This review provides new insights into the primary concentration methods that have been adopted by the eighteen recently reported COVID-19 wastewater detection studies, along with a brief discussion of the mechanisms of the most commonly used virus concentration methods, including the PEG-based separation, electrostatically charged membrane filtration, and ultrafiltration. The PEG-based separation is the most used technique (7 out of 18) among all concentration methods, and all four studies that adopted this concentration method showed positive results regarding the SARS-CoV-2 detection in wastewater samples (Bar Or et al., 2020; Hata et al., 2020; La Rosa et al., 2020b; Wu et al., 2020) . As previously mentioned, using electrostatically charged membranes filtration to concentrate viruses from turbid water, such as raw wastewater, can be subject to a significant reduction of virus recovery efficiency due to the presence of organic matter and high turbidity, which can lead to a preferential attachment to the charged filters and raise the risk of detrimental clogging. doi = 10.1016/j.scitotenv.2020.141245 id = cord-273893-3nd6ptrg author = Lu, Guangwen title = Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 date = 2013-07-07 keywords = CD26; MERS; RBD; SARS summary = Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition. doi = 10.1038/nature12328 id = cord-275357-yx8lsfdv author = Lu, J. title = Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting date = 2020-05-15 keywords = NPS; SARS summary = The Limits of Detection of two sets of RT-PCR assays, the TaqPath Multiplex RT-PCR COVID-19 Kit (Thermo) and the PrimerDesign COVID-19 assay, were determined using different viral RNA and reaction volumes ( Supplementary Table 1 ). In the Helix lab, a miniaturized 5 uL input RNA (10 uL total reaction volume) TaqPath assay was performed on a Quantstudio 7 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 6.25 viral copies. In the UCSD lab, a miniaturized 2 uL input RNA (3 uL total reaction volume) TaqPath assay was performed on a Quantstudio 5 qRT-PCR instrument (Thermo), and the limit of detection was determined to be 3.125 viral copies. RNA was extracted from the NPS VTM and Saliva samples and analyzed using the PrimerDesign and TaqPath assays at the sites shown in Table 2 (full dataset with Ct values for each viral target sequence and internal control sequences are shown in Supplementary Table 2 ). doi = 10.1101/2020.05.11.20092338 id = cord-342361-eu3rry7p author = Lu, Jiatao title = ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China date = 2020-02-23 keywords = COVID-19; SARS; international summary = title: ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan, China Our current study was conducted aiming to characterize the clinical features of either confirmed or suspected COVID-19 patients who were hospitalized in a COVID-19-designated hospital in Wuhan, and to develop a mortality risk index, as an evaluation tool used for establishing a COVID-19 hierarchical management system in highly endemic areas. To our knowledge, this is the first-ever study to compare the clinical characteristics of pneumonia patients who were either positive or negative for SARS-CoV-2 by RT-PCR assay, and to develop a first-ever COVID-19 mortality risk index derived from patients in highly endemic areas during early stage of outbreak. doi = 10.1101/2020.02.20.20025510 id = cord-319964-ju9japd8 author = Lu, Jing title = Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China date = 2020-04-04 keywords = China; Guangdong; SARS summary = Highlights: 1) 1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020; 2) Virus genomes can be recovered using a variety of sequencing approaches from a range of patient samples. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint To understand the genetic diversity of the SARS-CoV-2 epidemic in Guangdong we performed phylogenetic analyses using maximum likelihood and Bayesian molecular clock approaches. https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint Our analyses of the genomic epidemiology of SARS-CoV-2 in Guangdong province indicate that, following the first COVID-19 case detected in early January, most infections were the result of virus importation from elsewhere, and that chains of local transmission were limited in size and duration. doi = 10.1101/2020.04.01.20047076 id = cord-326282-uxn64olw author = Lu, Maolin title = Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date = 2020-09-13 keywords = RBD; SARS summary = To measure conformational dynamics of the SARS-CoV-2 S trimer on the surface of virus particles, we established two types of particles, lentiviral pseudoparticles carrying S, as well as coronaviruslike particles generated by expression of S, membrane (M), envelope (E) and nucleocapsid (N) 15 protein (S-MEN)(24, 25) (Fig. 1, A and B ). Analyses of smFRET data from ligand-free S protein on lentiviral particles revealed that the SARS-CoV-2 S protein is dynamic, sampling at least four distinct conformational states To identify the receptor-bound conformation of the SARS-CoV-2 S protein by smFRET, we measured the conformational consequences of soluble, monomeric hACE2 binding. Addition of 5 the monomeric hACE2 receptor to surface-immobilized virus particles lead to increased occupancy of the low-(~0.1) FRET S protein conformation (Fig. 2E) , which was observed at both the single-molecule and population level (Fig. 2F ). Relative state-occupancy and fitting parameters in each of four FRET-defined conformational states of SARS-CoV-2 spike protein on the surface of virus particles. doi = 10.1101/2020.09.10.286948 id = cord-016312-u47mb2h0 author = Lu, Pu-Xuan title = Introduction of Emerging Infectious Diseases date = 2015-07-25 keywords = SARS; disease summary = Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specific preventive or control measures. Due to their uncertainty and unpredictability, EIDs could result in high mortality and great impacts on social stability and economic development as people are unable to react immediately and take specifi c preventive or control measures. Cases in point are the epidemics of SARS in 2003 and H7N9 avian infl uenza around 2006, which have eloquently demonstrated their great threats to human health, society, and economy. Such contagious diseases did not exist in the past and newly emerge due to new pathogens such as AIDS, severe acute respiratory syndrome (SARS), human infection with highly pathogenic avian infl uenza H5N1, infl uenza A (HlN1), and human infection with avian infl uenza H7N9. revealed that 60.3 % EIDs were zoonotic, with 71.8 % caused by wild animals, such as human avian infl uenza and Ebola virus. doi = 10.1007/978-94-017-7363-8_1 id = cord-310657-04pp0o74 author = Lu, Renfei title = A Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date = 2020-04-18 keywords = LAMP; SARS summary = Using a mismatch-tolerant amplification technique, we developed a simple, rapid, sensitive and visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection based on its N gene. In this study, we applied the mismatch-tolerant technique to develop novel real-time fluorescent and visual RT-LAMP assays for the rapid and sensitive detection of SARS-CoV-2 RNA, and evaluated the novel assays using clinical samples. The novel RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies per reaction, and shows no cross-reactivity with 17 common human respiratory viruses, including four other human coronaviruses (OC43, 229E, HKU-1 and NL63). In view of a mean viral load of 1.4 × 10 6 copies/mL in nasal swabs of COVID-19 patients, the novel assay is sufficiently sensitive for the detection of SARS-CoV-2 at an early stage of infection using nasal swab specimens. The RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies of SARS-CoV-2 RNA per 25 µL reaction, and good specificity regarding common respiratory viruses. doi = 10.3390/ijms21082826 id = cord-333195-m4gvpsf8 author = Lu, Renfei title = Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 date = 2020-04-01 keywords = SARS summary = title: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2 Here, we present a novel visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid and sensitive detection of SARS-CoV-2 using mismatch-tolerant technique. The RdRp primers showed higher amplification efficiency, and were selected to establish the SARS-CoV-2 detection assay using the mismatch-tolerant RT-LAMP method Zhou et al. For the POCT diagnosis of SARS-CoV-2 infection in the resource-poor settings, we developed the assay into a visual detection using WarmStart Colorimetric LAMP 2 9 Master Mix (New England Biolabs, Beverly, MA, United States). The sensitivity of the colorimetric RT-LAMP assay for SARS-CoV-2 was 30 copies per reaction, slightly lower than the real-time monitoring (Fig. 1E) . The evaluation with 24 clinical samples showed that all 17 COVID-19 patients in Nantong city were positive for SARS-CoV-2 by both the RT-LAMP and the RT-qPCR assays, showing a full consistence. doi = 10.1007/s12250-020-00218-1 id = cord-256961-935r7w01 author = Lu, S. title = Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis date = 2020-04-22 keywords = COVID-19; SARS summary = We included RCTs and cohort studies evaluating the effectiveness and safety of glucocorticoids in children and adults with COVID-19, SARS and MERS, and conducted meta-analyses of the main indicators that were identified in the studies. We used the following search: ("COVID-19" OR "SARS-CoV-2" OR "2019 novel coronavirus" OR "2019-nCoV" OR "Wuhan coronavirus" OR "novel coronavirus" OR "Wuhan seafood market pneumonia virus" OR "Wuhan virus" OR "MERS" OR "SARS" OR "Severe Acute Respiratory Syndrome" OR "Middle East Respiratory Syndrome Coronavirus" OR "Influenza") AND ("adrenal cortex hormones" OR " betamethasone valerate " OR " glucocorticoids" OR " methylprednisolone" OR "Cortisone" OR "Dexamethasone" OR "Cortodoxone" OR "Hydrocortisone"). Five cohort studies (one on COVID-19, three on SARS, one on severe MERS) with a total of 5872 patients assessed the duration of hospital stay (29, 31, 35, 37, 41 Figure 9 ). doi = 10.1101/2020.04.17.20064469 id = cord-328585-1rkrrx8a author = Lu, Shuai title = The immunodominant and neutralization linear epitopes for SARS-CoV-2 date = 2020-08-27 keywords = SARS summary = To investigate the spectrum of antibodies in COVID-19 patients, we detected the binding of the 155 early convalescent sera of 8 imported (Europe) cases which infected SARS-CoV-2 in early April, 156 2020 and 12 domestic (China) cases in early February, 2020 to various epitopes ( Table 1) K203R204/G189R203G204/R203G204/R203G204S344 in N protein, respectively (Table 1) , 172 resulting in different immunodominant epitopes of different virus sub-strains which provide the 173 bases for the differential diagnosis. The predicted epitopes induce neutralization antibody production 175 SARS-CoV-2 pseudo-virus neutralization assay is a well-accepted method to detect the ability of 176 vaccine to inhibit SARS-CoV-2 infection . To assess 8 neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with 178 D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT 179 cells which stably expressed ACE2. doi = 10.1101/2020.08.27.267716 id = cord-273645-czh3zfb3 author = Lu, Shuaiyao title = Comparison of SARS-CoV-2 infections among 3 species of non-human primates date = 2020-07-17 keywords = SARS summary = In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Here, to establish the COVID-19 model, two families including 3 species of non-human primates, which are widely used for animal models with their own advantages and disadvantages, were experimentally infected with SARS-CoV-2, followed by comparisons of clinical symptoms, hematology, biochemical indexes, immunology and histopathology among 3 species. Given that host factors may be involved in viral pathogenesis, we designed an experiment in the present study to investigate whether host genetics, age and gender affect SARS-CoV-2 infection in non-human primates ( Figure 1 ). To know dynamics of viral replication and virus shedding, samples of nasal swabs, throat swabs, anal swabs, feces, blood and tissues were collected at the indicated time points, and SARS-CoV-2 genomes were quantitated by RT-qPCR. doi = 10.1101/2020.04.08.031807 id = cord-303027-r2jgu2be author = Lu, Yen-Ta title = Viral load and outcome in SARS infection: The role of personal protective equipment in the emergency department date = 2006-01-24 keywords = HRCT; SARS; non summary = Both specific droplet and rigorous universal precautions were thus recommended for healthcare workers (HCWs) taking care of patients with severe acute respiratory syndrome (SARS) (4) . We designed this study to explore the relationship between personal protective equipment (PPE) used by HCWs and the clinical course, outcome, and viral load in both HCWs and non-HCWs involved in a SARS cluster stemming from exposure to a single index case in our Emergency Department. Differences between the quantitative RT-PCR values for SARS-CoV in nasopharyngeal swab and HRCT scores in HCWs and non-HCWs were tested for significance using the Mann-Whitney U test. We have described a better clinical outcome after SARS in 4 HCWs compared with 12 non-HCWs; despite all having been involved in a cluster related to one index patient, with 13 apparently directly infected by that patient and 3 others by secondary transmission. doi = 10.1016/j.jemermed.2005.03.011 id = cord-326956-oz047qmf author = Lu, Yiping title = Cerebral Micro-Structural Changes in COVID-19 Patients – An MRI-based 3-month Follow-up Study date = 2020-08-03 keywords = GMV; SARS; covid-19 summary = COVID-19 patients had statistically significantly higher bilateral gray matter volumes (GMV) in olfactory cortices, hippocampi, insulas, left Rolandic operculum, left Heschl''s gyrus and right cingulate gyrus and a general decline of MD, AD, RD accompanied with an increase of FA in white matter, especially AD in the right CR, EC and SFF, and MD in SFF compared with non-COVID-19 volunteers (corrected p value <0.05). We found that these recovered COVID-19 patients were more likely to have enlarged olfactory cortices, hippocampi, insulas, Heschl''s gyrus, Rolandic operculum and cingulate gyrus, and a general decline of Mean Diffusivity (MD), Axial Diffusivity (AD), Radial Diffusivity (RD) accompanied with an increase of Fractional Anisotropy (FA) in white matter, especially AD in the right Coronal Radiata (CR), External Capsule (EC) and Superior Frontal-occipital Fasciculus (SFF), and MD in SFF compared with non-COVID-19 volunteers. doi = 10.1016/j.eclinm.2020.100484 id = cord-277705-6lgt2i7f author = Luan, Junwen title = A potential inhibitory role for integrin in the receptor targeting of SARS-CoV-2 date = 2020-04-10 keywords = SARS summary = An RGD motif (403-405) was identified in SARS-CoV-2 S protein ( Figure 1A ). These results suggested that RGD/KGD integrin-binding motif is conserved in several coronaviruses including SARS-CoV-2 and SARS-CoV. To investigate whether RGD/KGD motif in S proteins from SARS-CoV-2 We identified a KGD motif in 353-355 of ACE2 (BAB40370.1), which is a key region for binding S protein ( Figure 1F ). Integrin associates with ACE2 through its KGD motif including K353, which is one of key AAs for S protein recognition. Integrin associates with S protein by its RGD/KGD motif, which would shield the space of RBM for contacting with ACE2. Because RGD recognized a broader spectrum of integrins than KGD, more integrins could block receptor binding of SARS-CoV-2 S than that of SARS-CoV S. In conclusion, we identified an RGD/KGD integrin-binding motif in S proteins from SARS-CoV-2 and SARS-CoV. doi = 10.1016/j.jinf.2020.03.046 id = cord-344949-9zyz4hll author = Luban, Jeremy title = The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date = 2020-08-05 keywords = COVID-19; DHODH; PTC299; SARS summary = a Selectivity index is the ratio of CC50 to EC50 b values are mean ± standard deviation (SD) Abbreviations: CC50, compound concentration at which cell number is reduced by 50%; EC50, compound concentration at which viral replication on a linear scale is inhibited by 50%; GFP, green fluorescent protein; HCV, hepatitis C virus replicon genotype 1b; PIV-3, Parainfluenza type 3; RSV, respiratory syncytial virus; RT-qPCR, quantitative reverse transcription PCR; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TCID50, tissue culture infectious dose 50%. In the BT co-cell culture system, which models chronic inflammatory conditions driven by B cell activation and antibody production, incubation of cells with 10 nM PTC299 resulted in a significant reduction in the levels of soluble (s)IgG, sIL-17A, sIL-17F, sIL-6, and sTNFα released from the cells after 72 hours of stimulation (range, 49% to 68%) (all p values <0.01) ( Figure 4 and Table 2 ). doi = 10.1101/2020.08.05.238394 id = cord-269521-vq2m4c8q author = Lucchese, Guglielmo title = Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons date = 2020-05-01 keywords = SARS summary = Brainstem involvement has been proposed as a possible cause of respiratory failure in SARS-CoV-2 infection, given that the virus appears to have potential for inducing neurological damage, a number of neurological symptoms have been described, and SARS-CoV has been reported to massively infect the brainstem in both patients and experimental animals [3] . Indeed, the proteome of the virus (https://www.ncbi.nlm.nih.gov/nuccore/ MN908947) shares three sequences of six amino acids (GSQASS, LNEVAK, and SAAEAS) with three proteins, namely DAB1, AIFM, and SURF1 (as catalogued at www.uniprot.org) that are present in the human brainstem preBötC (Table 1 ) and are part of experimentally validated epitopes [10] . In the context of this peptide sharing between the preBötc, and SARS-CoV-2, it appears possible that immunological targeting of DAB1, AIFM1, and SURF1 might contribute to brainstem-related respiratory failure in COVID-19 patients and that a therapeutic benefit might come from immunomodulatory agents. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients doi = 10.1016/j.autrev.2020.102556 id = cord-319728-d0kf9gme author = Lucchini, Matteo title = Is serological response to SARS-CoV-2 preserved in MS patients on ocrelizumab treatment? A case report date = 2020-06-22 keywords = COVID-19; SARS summary = We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. We present the case of a MS patient with mild COVID-19 who developed SARS-CoV-2 specific IgA without IgG ten weeks after infection. Few case reports of multiple sclerosis (MS) patients receiving ocrelizumab who contracted COVID-19 with a benign course have recently been published (Novi et al., 2020; Suwanwongse and Shabarek, 2020) . Forty days before COVID-19 onset, the patient performed routine blood tests including cell blood count (CBC), lymphocyte subtypes, immunoglobulin dosage and liver and kidney function showing CD19+ complete depletion (normal CD4+ and CD8+) and IgG at lower limit (700 mg/dl, normal range 700-1600). Despite an optimal recovery from COVID-19, our patient did not develop a full serological response against SARS-CoV-2 as demonstrated by the absence of specific IgG production. doi = 10.1016/j.msard.2020.102323 id = cord-304574-03s404s5 author = Luciani, Lorenzo G. title = Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. Urinary Frequency as a Possible Overlooked Symptom in COVID-19 Patients: Does SARS-CoV-2 Cause Viral Cystitis? Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection date = 2020-06-12 keywords = SARS summary = key: cord-304574-03s404s5 authors: Luciani, Lorenzo G.; Gallo, Fabrizio; Malossini, Gianni title: Re: Jan-Niclas Mumm, Andreas Osterman, Michael Ruzicka, et al. https://doi.org/10.1016/j.eururo.2020.05.013: Severe Involvement of the Urinary Tract During COVID-19 Infection journal: Eur Urol DOI: 10.1016/j.eururo.2020.06.006 cord_uid: 03s404s5 Mumm et al [1] reported that urinary frequency might be a symptom of SARS-CoV-2. This assumption is based on the finding that the bladder urothelium, as well as the kidney, harbors cells expressing ACE2, the receptor for the viral spike protein [2,3]. Our experience appears to confirm their suspicion, further suggesting that the urinary tract may become the target of life-threatening involvement by SARS-CoV-2. We report three cases of gross hematuria admitted to two hospitals in Northern Italy between The authors have nothing to disclose. Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Urinary frequency as a possible overlooked symptom in COVID-19 patients: does SARS-CoV-2 cause viral cystitis? Eur Urol Eur Urol doi = 10.1016/j.eururo.2020.06.006 id = cord-259619-sco0d5cc author = Ludvigsson, Johnny title = Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society date = 2020-09-30 keywords = COVID-19; SARS; vulnerable summary = title: Corona Pandemic: Assisted Isolation and Care to Protect Vulnerable Populations May Allow Us to Shorten the Universal Lock-Down and Gradually Re-open Society We suggest here that more selective assisted isolation of vulnerable populations would reduce the predictable increase in hospital admissions and more rapidly alleviate the fallout from total lockdown measures. Even though COVID19 sometimes leads to need for treatment at intensive care units (ICU) also for younger individuals, the virus appears most dangerous for a selected group of the most vulnerable people. We must consider diverting our major efforts to protect the vulnerable-elderly and patients with preexisting comorbidities-by providing safe and assisted isolation and care; not least now that lockdown rules start to be relaxed. However, these measures have isolated subjects at risk, but have not increased immunization of the population with so called herd immunity through the transient infection of the less vulnerable. doi = 10.3389/fpubh.2020.562901 id = cord-337572-kx5hihnr author = Ludwig, Stephan title = Coronaviruses and SARS-CoV-2: A Brief Overview date = 2020-04-20 keywords = COVID-19; China; SARS summary = The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 . Here we provide a short background on coronaviruses and their origin, and we describe in more detail the novel SARS-CoV-2 and the efforts thus far to identify effective therapies against COVID-19. The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). The virus was later denominated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19). 19 SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 At the end of December 2019, China reported the increasing occurrence of pneumonia in the city of Wuhan, Hubei province. Identification of a novel coronavirus in patients with severe acute respiratory syndrome doi = 10.1213/ane.0000000000004845 id = cord-319164-wbrnhpgs author = Luellen, E. title = A Machine Learning Explanation of Incidence Inequalities of SARS-CoV-2 Across 88 Days in 157 Countries date = 2020-06-08 keywords = SARS summary = Because the SARS-CoV-2 (COVID-19) pandemic viral outbreaks will likely continue until effective vaccines are widely administered, (1) new capabilities to accurately predict incidence rates by location and time to know in advance the disease burden and specific needs for any given population are valuable to minimize morbidity and mortality. In this study, a random forest of 9,250 regression trees was applied to 6,941 observations of 13 statistically significant predictor variables targeting SARS-CoV-2 incidence rates per 100,000 across 88 days in 157 countries. One key finding is an algorithm that can predict the incidence rate per day of a SARS-CoV-2 epidemic cycle with a pseudo-R2 accuracy of 98.5% and explain 97.4% of the variances. In this study, machine learning -a robust statistical version of artificial intelligence -was applied to a data set of 6,941 observations to identify the relative importance of 13 demographic, economic, environmental, and public health factors in modulating the incidence rate per 100,000 population of SARS-CoV-2 across 88 days in 157 countries. doi = 10.1101/2020.06.06.20124529 id = cord-261405-n05wjimk author = Lui, Grace title = Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19 date = 2020-04-18 keywords = SARS summary = reported in this journal that viral shedding of SARS-CoV-2 in nasal swabs was longer in intensive care unit (ICU) patients compared with non-ICU patients with Coronavirus Disease 2019 (COVID-19). 3 We collected serial upper (pooled nasopharyngeal and throat swabs, N=75) and lower respiratory tract samples (sputum and tracheal aspirate, N=43), peripheral blood plasma (N=50), urine (N=43) and stool (N=43) samples from all participants, and monitored SARS-CoV-2 viral loads in these samples. In all five participants with severe/critical and three with moderate disease, viral loads in respiratory tract samples continued to rise and peaked in the second week of illness (range 5.57-9.66 log copies/mL). In this study of patients with COVID-19 across a wide spectrum of severity, we observed that viral shedding in the respiratory tract lasting longer than 14 days was common. In more severe disease, viral load appeared to peak in the second week of illness in both upper and lower respiratory tract. doi = 10.1016/j.jinf.2020.04.014 id = cord-273859-tr4s5i7h author = Luis García Garmendia, José title = DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date = 2020-04-29 keywords = PCR; SARS summary = En las formas clínicas menos graves, la detección de ARN viral es máxima durante las dos primeras semanas desde el inicio de los síntomas(4), y a partir de los 7-10 días se produce respuesta inmunológica de IgM y después de IgG (5) . El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). A estos pacientes se les hicieron 2 determinaciones de rRT-PCR de Coronavirus a partir de 21 días del inicio de síntomas, separadas por 24 h, para comprobar si persistía eliminación del virus. La detección del ARN viral mediante técnicas de rRT-PCR parece ser una forma adecuada de determinar la necesidad de aislamiento de los pacientes con SARS-CoV-2(8, 12). Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. doi = 10.1016/j.medin.2020.04.014 id = cord-289490-u0f0zyad author = Lumba, Rishi title = Neonate Born to a Mother with a Diagnosis of Suspected Intra-Amniotic Infection versus COVID-19 or Both date = 2020-07-18 keywords = COVID-19; SARS summary = In this report, we detail a case of a newborn born to a mother with a clinical diagnosis of intra-amniotic infection with maternal fever and fetal tachycardia, who was then found to be SARS-CoV-2 positive on testing. Due to the varying presentation of COVID-19, this case illustrates the low threshold needed to test mothers for SARS-CoV-2 in order to prevent horizontal transmission to neonates and to healthcare providers. e current recommendations made by the American College of Obstetricians and Gynecologists (ACOG) are that the diagnosis of suspected intraamniotic infection be made on clinical criteria, which include maternal intrapartum fever and one or more of the following: maternal leukocytosis, purulent cervical drainage, or fetal tachycardia. Although a clinical diagnosis of Triple I was made by the obstetrics team, given maternal fever, testing for SARS-CoV-2 was included as well. doi = 10.1155/2020/8886800 id = cord-277669-uujny2dm author = Lumpuy-Castillo, Jairo title = Cardiovascular Damage in COVID-19: Therapeutic Approaches Targeting the Renin-Angiotensin-Aldosterone System date = 2020-09-04 keywords = ACE2; Ang-(1; Angiotensin; COVID-19; SARS summary = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can differentially infect multiple tissues (i.e., lung, vessel, heart, liver) in different stages of disease, and in an ageand sex-dependent manner. In particular, treatments with angiotensin-converting enzyme inhibitors (ACEi) and angiotensin-receptor blockers (ARB) may help to reduce hyperinflammation and viral propagation, while infusion of soluble ACE2 may trap plasma viral particles and increase cardioprotective Ang-(1–9) and Ang-(1–7) peptides. SARS-CoV-2 infection initiates in the respiratory system, when the S protein of its external layer binds the angiotensin-converting enzyme-2 (ACE2) at the plasma membrane of host cells [5] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . It was originally suggested that elevation of ACE2 might favor SARS-CoV-2 infection and replication in COVID-19 patients with underlying CV disease and ACEi/ARB treatment [92] . doi = 10.3390/ijms21186471 id = cord-323383-dmzhywb9 author = Lundon, DJ title = Early Mortality Risk Stratification after SARS-CoV-2 Infection date = 2020-07-04 keywords = SARS summary = While the majority of those who test positive for SARS-CoV-2 will not require hospital admission, intensive care or mechanical ventilation, some will (data from our institution suggest ~13% of those hospitalized due to COVID-19 underwent mechanical ventilation). Using the Mount Sinai Health Systems'' database of all SARS-Co-V-2 positive patients with an encounter in New York City, we developed a prediction model to identify those patients most likely to succumb to the disease thin 7 days (the median time to death of those who died) from the onset of COVID-19 symptoms. The risk probability of death within 7 days for patients was calculated from a model developed in 80% of this cohort, using the 3 demographic and 4 clinical variables listed above. This model demonstrates the significant role that both clinical and social determinants play in predicting the clinical outcome for patients infected with SARS-CoV-2 and tested positive for COVID-19. doi = 10.1016/j.medin.2020.06.011 id = cord-310062-mmlh9i1o author = Luo, Haibin title = In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS date = 2004-12-01 keywords = Fig; SARS summary = Both the thermal and chemical denaturant-induced denaturation analyses showed that oligomeric SARS_NP unfolds and refolds through a two-state model, and the electrostatic interactions among the charge groups of SARS_NP made a significant contribution to its conformational stability. In addition, the unfolding and refolding characterizations of SARS _ NP dimer caused by thermaland chemical denaturant-induced denaturations were also inspected by fluorescent and CD spectral investigation, it is found that SARS _ NP exhibits its most stable conformation near pH 9.0, and its oligomer dissociation and protein unfolding seem to be of coinstantaneous occurring events. The fluorescent intensity was found to decrease with increase of temperature accompanied by a shift in emission k max from 333 to 343 nm ( Fig. 4A and C) , whereas far-UV CD spectral information suggested the loss of secondary structure for SARS _ NP during its thermal-induced denaturation (Fig. 4B and D) . doi = 10.1016/j.bpc.2004.06.008 id = cord-297599-y4lu8m4k author = Luo, Hua title = Anti-COVID-19 drug screening: Frontier concepts and core technologies date = 2020-10-28 keywords = ACE2; COV-2; COVID-19; SARS; TCM; chinese summary = This paper thoroughly summarizes interdisciplinary notions and techniques, including disease model, biochip, network pharmacology, and molecular docking technology, etc., providing a reference for researchers in the screening of drugs for COVID-19 prevention and treatment. Some researchers are currently using mice as an animal model to test drugs and vaccines and to investigate the nature of the infection of SARS-CoV-2 [49] [50] [51] . In fact, in a study led by Qin Chuan on SARS, engineered mice that could express human ACE2 protein was successfully established, leading this Chinese team pioneered the establishment of a SARS-CoV-2 infected hACE2 transgenic mouse model [54] . For example, an effective and convenient novel mouse model in evaluating in vivo protective capacity of the SARS-CoV-2 vaccines was developed through stitching the human gene for ACE2 into an adenovirus by Perlman et al. doi = 10.1186/s13020-020-00393-z id = cord-313215-diqfmitr author = Luo, Lei title = Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date = 2020-07-09 keywords = SARS; covid-19 summary = title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. To address this question, in this study, we sampled total of 641 surfaces 63 environmental and air specimens among 39 cases in Guangzhou, China, to explore the 64 surrounding environmental surfaces and air contamination by SARS-CoV-2 in non-65 health care settings. A total of 641 157 environmental surfaces and air specimens were collected among 39 COVID-19 cases, 158 and 20 specimens (20/641, 3.1%) were positive by RT-PCR testing from 9 COVID-19 159 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic 160 cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases 161 ( of SARS-CoV-2 (Table 2) . doi = 10.1101/2020.07.09.195008 id = cord-347804-kxhasabe author = Luo, Ruibang title = Tracking cytosine depletion in SARS-CoV-2 date = 2020-10-26 keywords = SARS summary = Results We built a website to track the composition change of mono-, di-, and tri-nucleotide of SARS-CoV-2 over time. Using 137,315 SARS-CoV-2 strains collected in ten months, we observed cytosine depletion at a rate of about one cytosine loss per month from the whole genome. We built an interactive website at http://www.bio8.cs.hku.hk/sarscov2 to show the mono-, di-, and tri-nucleotide composition trends of the whole genome and single genes. In Table 1 , we first compared the composition of nucleotides in multiple coronaviruses, including SARS-CoV-2 (an average of 76 strands collected from Dec 20, 2019 to Feb 15, 2020), SARS, MERS, and four that causes a common cold. Compared to SARS-CoV-2, which we assumed a relative mortality level of 3, the percentage of cytosine is lower in almost all of the eleven genes in the four common cold coronaviruses with a lower mortality level 1. The results are available on an interactive website at http://www.bio8.cs.hku.hk/sarscov2. doi = 10.1101/2020.10.26.354787 id = cord-279158-dsnniuo6 author = Luo, Y. title = Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study date = 2020-05-22 keywords = COVID-19; SARS; patient summary = title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study Through a systematic review, meta-analysis and retrospective cohort study, we found that the low blood sodium population may significantly increase the risk and severity of SARS-CoV-2 infection. In this study, we aimed to find a key risk factor for SARS-CoV-2 epidemic by investigating the relationship between the blood sodium concentration and the severity of patients with COVID-19 through a systematic reviews, meta-analysis and retrospective cohort study. For the systematic review and meta-analysis, median or mean values of serum sodium, chloride and potassium concentrations from each report were considered as an independent variable for statistical analysis, and an unpaired t-test was used to compare the differences between the groups related to the severity of disease. In this study, we found that the patients infected by SARS-CoV-2 on admission have presented the low blood sodium levels (hyponatremia) that were related to the disease severity. doi = 10.1101/2020.05.18.20102509 id = cord-318006-9op556q2 author = Luo, Y. R. title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-08-02 keywords = SARS summary = Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. Given that SARS-CoV-2 specific IgG avidity is strong in ICU patients after 1 month, this suggests that antibody-mediated immune enhancement triggered by suboptimal antibodies may not play a role in COVID-19 disease progression and severity. . https://doi.org/10.1101/2020.07.30.20165522 doi: medRxiv preprint Further studies are needed to determine if the antibody response, both IgG concentration and avidity, correlate with virus neutralization and persist over time. doi = 10.1101/2020.07.30.20165522 id = cord-334945-lxowaacg author = Luo, Yi title = Asymptomatic SARS-CoV-2 Infection in Household Contacts of a Healthcare Provider, Wuhan, China date = 2020-08-17 keywords = SARS; covid-19 summary = We describe the case of a physician in Wuhan, China, who had mildly symptomatic COVID-19 and the subsequent asymptomatic SARS-CoV-2 infection in all 5 of his household contacts. All 5 household contacts of patient 1 had laboratory evidence of SARS-CoV-2 infection but remained asymptomatic throughout the period of observation (February 11-March 1) (Figure, panel A) . An early report from China on 72,314 COVID-19 cases found that only 1% of SARS-CoV-2 infections were asymptomatic; however, asymptomatic close contacts were not routinely tested in that study (7) . In summary, this single-household study found a high attack rate for asymptomatic SARS-CoV-2 infection among the immediate family members of a symptomatic COVID-19 case-patient. Moreover, our experience indicates that screening symptomatic contacts with a single throat swab test for SARS-CoV-2 might lead to an underestimate of the rate of infection and that asymptomatic persons can repeatedly revert between positive and negative PCR results on throat specimens. doi = 10.3201/eid2608.201016 id = cord-327862-zcg3baym author = Luo, Yiqi Ruben title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-09-14 keywords = SARS summary = The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity doi = 10.1093/cid/ciaa1389 id = cord-276013-8dhqa2gj author = Luo, Yung-Hung title = Overview of coronavirus disease 2019: Treatment updates and advances date = 2020-08-17 keywords = China; SARS; covid-19 summary = 7, 11 Patients with severe symptoms may have unfavorable disease Abstract: In late December 2019, several cases of pneumonia with unknown cause were reported in Wuhan, China, and this new type of pneumonia spread rapidly to across provinces during the subsequent weeks. Clinical trials on baricitinib demonstrated at least some effects in selective patient populations with COVID-19 acute respiratory disease. On March 17, 2020, the National Medical Products Administration of China approved favipiravir as the first coronavirus drug with evidence from clinical trials showing efficacy for the treatment of COVID-19 infection. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1097/jcma.0000000000000367 id = cord-271504-t3y1w9ef author = Luo, Zichao title = Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date = 2020-06-16 keywords = COVID-19; CRISPR; China; LAMP; MERS; PCR; RNA; SARS; dna summary = A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . doi = 10.34133/2020/6925296 id = cord-297747-kifqgskc author = Lupala, Cecylia S. title = Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date = 2020-03-27 keywords = ACE2; RBD; SARS summary = Using homology modeling and molecular dynamics (MD) simulation methods, we report here the detailed structure of the ACE2 in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The simulation data further revealed critical residues at the complex interface and provided more details about the interactions between the SARS-CoV-2 RBD and human ACE2. When this study was started, neither the crystal structure of the SARS-CoV-2 spike protein nor the RBD segment were determined, so the homology modeling approach was applied to construct the model of the SARS-CoV-2 spike RBD in complex with the human ACE2 binding domain (denoted as CoV2-RBD/ACE2 in the following). Although the crystal structure and the predicted model of the CoV2-RBD/ACE2 complex provide important information about the binding interactions at the molecular interfaces, MD simulations can extend the knowledge to a dynamics regime in a fully solvated environment. doi = 10.1101/2020.03.24.005561 id = cord-285852-ocu69od2 author = Luqman, Zubair title = Disinfection of corona virus in histopathology laboratories date = 2020-06-25 keywords = SARS summary = Severe acute respiratory syndrome (SARS CoV‐2/COVID‐19) is a highly contagious and deadly disease caused by a virus belonging to the coronaviridae family. Researchers working in histopathology laboratories, dealing with morbid samples, are particularly vulnerable to infection unless they have very strong immunity. The current review highlights the biological and physical agents that can be used to inactivate the virus and disinfect the surrounding environment in the laboratory. Severe acute respiratory syndrome, also termed SARS-CoV, was first (Lim et al., 2004; Rachael, 2004; World Health Organization [WHO], 2003 , 2006 . Severe acute respiratory syndrome (SARS CoV-2/COVID-19) is a highly communicable and lethal virus (WHO, 2020). Scientists working in histopathology laboratories, handling morbid samples, can be infected with this dangerous virus and are more likely to be susceptible to it regardless of well-functioning immune systems. Severe Acute Respiratory Syndrome (SARS) Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Laboratory-acquired severe acute respiratory syndrome doi = 10.1002/ca.23636 id = cord-297451-p5rlquym author = Luz María Trujillo, G title = Relación Entre Covid-19 Y Síndrome De Guillain-Barre En Adultos.Revisión Sistemática date = 2020-07-24 keywords = Barré; Guillain; SARS summary = Se han reportado varios casos en distintos centros de salud, de ingreso de pacientes que presentan Síndrome de Guillain-Barré (SGB) y son COVID-19 positivo activos o cursaron con la enfermedad, por lo que se ha planteado la asociación entre ambas patologías. Encefalopatía infecciosa Aguda/tóxica, descrita como síndrome de disfunción cerebral reversible causado por cuadros tóxicos sistémicos, trastornos metabólicos e hipoxia durante un período de infección aguda; y por último, la Enfermedad cerebrovascular aguda (Ataque cerebrovascular) que en los últimos meses ha sido ampliamente atribuida al SARS-CoV-2, debido a que este virus causa una cascada de citoquinas proinflamatorias, encontrándose también niveles elevados de Dímero-D y bajos niveles de plaquetas, pudiendo presentarse un Ataque cerebrovascular 4 . Los estudios analizados demuestran una clara tendencia de asociación entre ambas patologías, donde el virus SARS-CoV-2, sería el potencial gatillador del SGB. Guillain-Barré Syndrome associated with SARS-CoV-2 infection Guillain-Barré Syndrome associated with SARS-CoV-2 infection doi = 10.1016/j.nrl.2020.07.004 id = cord-279260-tdvb0fhv author = Lv, Huibin title = COVID‐19 vaccines: knowing the unknown date = 2020-05-21 keywords = SARS; vaccine summary = It is also important to note that T-cell immunity was found to be elicited by SARS-CoV or MERS-CoV DNA vaccines (both express trimeric spike protein) [7, 9] . Determining which adjuvants can enhance protective vaccine response to SARS-CoV-2 will be important. For example, the MF59-adjuvanted influenza vaccine, Fluad, is only licensed and approved for adults aged 65 years and older, to elicit a higher protective immune response in the elderly This article is protected by copyright. To accelerate vaccine development, animal infection models for SARS-CoV-2 are needed. Although macaques show COVID-19-like disease upon SARS-CoV-2 infection, the non-human primate model is usually not readily accessible to most laboratories [27] . Expressing hACE2 through adenoviral transduction may provide another possible approach to generate a mouse model for SARs-CoV-2 infection. For example, a conserved CD4 T-cell epitope can mediate cross-reactive protection between SARS-CoV and MERS-CoV [38] . doi = 10.1002/eji.202048663 id = cord-317042-dll3qt4g author = Lv, Jun title = Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date = 2020-06-19 keywords = PCR; SARS summary = title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. In this study, we aimed to 1) determine the concentration of SARS-Cov-2 present on the object surfaces and personal protective equipment after the nucleic acid test, 2) identify the risk areas and operation behaviors that may cause contamination, and 3) provide reference basis for the targeted formulation of laboratory disinfection programs and personal operating specifications. The SARS-CoV-2 test results of object surface samples from nucleic acid detection laboratory were shown in Table 1 . In this study, all objects in nucleic acid detection laboratory that tested positive for SARS-CoV-2 were directly or indirectly contacted by the operator''s gloved hands. doi = 10.1016/j.scitotenv.2020.140370 id = cord-346957-bmajkabp author = Lv, Yanbo title = Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date = 2009-12-03 keywords = CTL; HLA; SARS summary = RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. doi = 10.1186/1471-2172-10-61 id = cord-336057-tj9qcuf8 author = Lv, Yantian title = No intrauterine vertical transmission in pregnancy with COVID-19: a case report date = 2020-08-05 keywords = COV-2; SARS summary = The data of status of pregnant women and neonates after infection of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is limited. We report a case of pregnant woman in her third trimester with critical COVID-19, and amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were retained during cesarean section. Amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were collected during the operation and tested for the SARS-COV-2 nucleic acid, and the mother and infant were separated after the operation. In addition, not only SARS-COV-2 nucleic acid test results were negative in 4 times pharyngeal swabs, but also the anal swab, amniotic fluid, umbilical cord blood, placenta, and neonatal gastric fluid were negative. Li 9 also reported a 35-week pregnant woman with COVID-19, whose amniotic fluid, cord blood and placenta, breast milk samples as well as neonates swab SARS-COV-2 nucleic acid were all negative. doi = 10.1016/j.jiac.2020.07.015 id = cord-298327-j04nyg5y author = Lv, Zhihua title = Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study date = 2020-05-18 keywords = COVID-19; SARS summary = Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Additionally, stepwise multivariable regression 13 analysis suggested that co-infection, lymphocyte count and levels of D-dimer were associated 14 with severity of COVID-19.These findings provide crucial clues for further identification of 15 the mechanisms, characteristics and treatments of patients with COVID-19. Preliminary analysis indicated that higher white blood cell and 129 neutrophil counts, as well as higher levels of D-dimer, IL-6, IL-10, CRP and PCT were found 130 in male patients compared to those of females, which was similar to patients in critical and 131 severe groups compared with those of mild groups (Table 2) . Higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, IL-6, 155 IL-10, CRP and PCT were observed in patients co-infected with other respiratory pathogens 156 than those of infected with SARS-CoV-2 homogeneously (Table 2) . doi = 10.1016/j.micinf.2020.05.007 id = cord-292600-mgvrbfzd author = Ly, T. D. A. title = Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020. date = 2020-05-11 keywords = SARS; preprint summary = In March-April, we enrolled 411 homeless individuals, 77 asylum-seekers, 58 people living in precarious conditions, and 152 employees working in these accommodation centres and collected nasal samples. In this study, we present the results of SARS-CoV-2 screening campaigns conducted among sheltered homeless individuals, in comparison with asylum-seekers, other persons living in precarious conditions, and employees working in the accommodation centres. . https://doi.org/10.1101/2020.05.05.20091934 doi: medRxiv preprint Table 3 shows SARS-CoV-2 positivity rates among homeless people according to the time of screening, demographics and housing facility, using univariate analysis. We found an overall 7.0% SARS-CoV-2 positivity rate, with most infected individuals among homeless people and employees working in homeless facilities, while no cases were found in asylum-seekers and in other people also living in precarious conditions. Grey cells: four groups in study : Homeless people (N=411); other specific population living in precarious conditions (N=58), asylum seekers (N=77), and employees (N=152) and SARS-CoV-2 prevalence in each group. doi = 10.1101/2020.05.05.20091934 id = cord-325598-gy809ee0 author = Lyne, Cloutier title = Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study date = 2020-08-21 keywords = SARS; asymptomatic summary = title: Asymptomatic carriers of COVID-19 in a confined adult community population in Quebec: a cross-sectional study In our cross-sectional study, 1.82% of 330 asymptomatic confined individuals living in the community carried SARS-CoV-2 despite no contact with declared cases, raising concerns about unnoticed transmission. Cloutier, Lyne 1 ; Merindol, Natacha 2,3 ; Pépin, Geneviève 4 ; Marcoux-Huard, Caroline 5 ; Vasil, Pier-Alexandre 5 ; Houle, Claudia 6, 7 ; Todkar, Shweta 1 ; Lehoux, Marie-Claude 3 ; Houle, Nathalie 1 ; Germain, Hugo 2,3 ; Danylo, Alexis 6  SARS-CoV-2 may spread asymptomatically in a population under social distancing restrictions. Studies conducted on individuals from the same households have convincingly shown that pre-symptomatic or asymptomatic SARS-CoV-2 carriers might transmit to their family members [8] [9] [10] . Transmission potential of asymptomatic and paucisymptomatic SARS-CoV-2 infections: a three-family cluster study in China. doi = 10.1016/j.ajic.2020.08.015 id = cord-310008-hwpn7ti1 author = Lyons-Weiler, James title = Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity date = 2020-04-09 keywords = SARS summary = Failure of SARS and MERS vaccines in animal trials involved pathogenesis consistent with an immunological priming that could involve autoimmunity in lung tissues due to previous exposure to the SARS and MERS spike protein. In this study, I present the likely human epitopic targets of biomimicry-induced autoimmunological components of morbidity and mortality caused by SARS-CoV-2 infection. This is achieved via bioinformatics analysis of the homology between highly immunogenic SARS-CoV-2 epitopes and human proteins to promote comprehension of the etiologies of pathogenesis of SARS-CoV-2 in COVID-19. A list of human peptides with high local homology was compiled and their roles in the pathogenesis of COVID-19 from SARS-CoV-2 infection noted. Remarkably, over 1/3 (11/27) of the immunogenic proteins in SARS-CoV-2 have potentially problematic homology to proteins that are key to the human adaptive immune system (emboldened in Table 1 ). doi = 10.1016/j.jtauto.2020.100051 id = cord-258533-gds7sdc9 author = Lytras, Theodore title = High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries date = 2020-04-16 keywords = SARS summary = title: High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries Passengers on repatriation flights to Greece from the UK, Spain and Turkey were screened with oropharyngeal swabs on arrival for SARS-CoV-2 infection. Despite almost all passengers being asymptomatic, many tested positive (3.6% from UK, 6.3% from Spain and 6.3% from Turkey), indicating widespread transmission of SARS-CoV-2 in these countries. Even more remarkably, the infection prevalence in these passengers was much higher than in the repatriation flights from Wuhan during the peak of the epidemic there, which was reported as <1%. Estimating infection prevalence in Wuhan City from repatriation flights Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries Estimating the ascertainment rate of SARS-CoV-2 infection in Wuhan, China: implications for management of the global outbreak doi = 10.1093/jtm/taaa054 id = cord-278271-rpq62xhl author = Lyu, Jinglu title = Reflection on lower rates of COVID-19 in children: does childhood immunizations offer unexpected protection? date = 2020-05-15 keywords = COVID-19; SARS; cell summary = The frequent childhood vaccinations and repeated pathogens infections might be resulting in trained immunity of innate immune cells, immune fitness of adaptive immune cells or cross-protection of antibodies in the children. Candida isolated from 4 airway specimens in a case report of patients with new coronavirus pneumonia Compared with adult cases, children tend to have milder symptoms, shorter disease course and generally better prognosis. found that memory lymphocytes can also mediate longer-term cross-protection as a byproduct of adaptive immunity: CD8 + memory T cells can be activated by cytokines (IL-12 and IL-18) in early stages of infection in an antigen-independent manner, leading to the production of IFN-γ and enhanced response to subsequent infectious agents (45) . Equipping confirmed COVID-19 patients with these vaccinations as emergent prophylaxis may prevent severe illness caused by secondary infection, in the meantime, it may mobilize the host''s lymphocyte response to the opposite direction in response to SARS-CoV-2. doi = 10.1016/j.mehy.2020.109842 id = cord-253968-jtr0p930 author = López, Verónica title = Recomendaciones en el manejo de la pandemia por coronavirus SARS-CoV-2 (Covid-19) en pacientes con trasplante renal date = 2020-04-03 keywords = COVID-19; SARS summary = Manejo clínico del COVID-19: tratamiento médico, del 19 de marzo de 2020), los pacientes receptores de un trasplante renal en los que haya sospecha de infección por SARS-CoV-2 tienen indicación de test diagnóstico y valoración de ingreso si el resultado es positivo, así como de inicio de tratamiento específico. Por tanto, dada la escasa experiencia acumulada y la alta probabilidad de evolución tórpida del cuadro clínico en un breve periodo de tiempo, con desarrollo de fracaso multiorgánico y necesidad de soporte ventilatorio, la estrategia inmunosupresora recomendada a priori, al menos en los casos más graves de pacientes trasplantados renales con neumonía por COVID-19, debe consistir en la interrupción temporal de los inmunosupresores e inicio de metilprednisolona a dosis bajas entre 20 y 40 mg/día, para conferir la adquisición en un corto periodo de tiempo de la inmunidad celular necesaria para controlar la infección y evitar así la progresión de la misma y sus complicaciones vitales. doi = 10.1016/j.nefro.2020.03.002 id = cord-330369-75cotmn2 author = López, Verónica title = Recommendations on management of the SARS-CoV-2 coronavirus pandemic (Covid-19) in kidney transplant patients date = 2020-04-06 keywords = COVID-19; SARS; patient; transplant summary = In kidney transplant recipients, due to their status of immunosuppression, the clinical manifestations, treatment, and prognosis of COVID-19 pneumonia may differ from the general population, hence the importance of early diagnosis by SARS-CoV-2 screening, in those cases where the infection is suspected. Currently there is no evidence from controlled clinical trials to recommend a specific treatment for the SARS-CoV-2 coronavirus in the general population in patients with suspected or confirmed COVID19. 7 Therefore, given the limited experience accumulated and the high probability of torpid evolution in a short period of time, with the development of multi-organ failure and the need for respiratory support, the immunosuppressive strategy recommended a priori, at least in the most severe cases of kidney transplant patients with COVID-19 pneumonia, should involve the temporary interruption of immunosuppressants and the start of methylprednisolone at low doses between 20 and 40 mg/day, to confer the rapid acquisition of the necessary cellular immunity to control the infection and thus prevent vital complications. doi = 10.1016/j.nefroe.2020.03.017 id = cord-287100-xkp8a9b9 author = López-Díaz, Álvaro title = COVID-19 Infection During Pregnancy and Risk of Neurodevelopmental Disorders in Offspring: Time for Collaborative Research date = 2020-10-31 keywords = COVID-19; SARS summary = Cohorts of COVID-19-infected pregnant women may currently provide biological (e.g., umbilical cord and placenta samples) and clinical (e.g., maternal serum samples and neonatal filter paper blood samples) data that would enable the acquisition of very valuable genetic, metabolic, and immunological information. Such information would help determine the extent to which maternal infection, in addition to genetic vulnerability, contributes to an increased risk of neuropsychiatric disturbance in the offspring, and would improve our understanding of the role of immune-inflammatory mechanisms during pregnancy in the etiology of neurodevelopmental disorders (10). Such populationbased birth cohort studies of SARS-CoV-2-infected pregnant women should involve detailed systematic clinical and biological examinations during pregnancy and delivery along with an extended follow-up of the offspring, including neurocognitive, neuroimaging, and electrophysiological examination. Large-scale and long-term prospective population-based birth cohort studies of COVID-19-infected and unaffected pregnant women are needed to unravel the complex interactions between maternal infection and risk of neurodevelopmental disorders in offspring. doi = 10.1016/j.biopsych.2020.09.011 id = cord-344979-ngujhhp6 author = Lübke, Nadine title = Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials date = 2020-08-05 keywords = SARS summary = OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. Ct values of 91 SARS-CoV-2 positive samples analyzed in direct comparison by RT-qPCR using different primary materials and extracted RNA showed a significant correlation. doi = 10.1016/j.jcv.2020.104579 id = cord-196265-mvnkkcow author = M''esz''aros, B''alint title = Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications date = 2020-04-21 keywords = ACE2; RGD; SARS; Spike; integrin; motif; protein summary = We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. Proximity-based mass spectrometry on the MHV replication complex further revealed that the RTC environment repurposes components from the host autophagy, vesicular trafficking and translation machineries (V''kovski et al., 2019) In the present work, we identify a set of conserved SLiM candidates in the ACE2 and integrin proteins, which are likely to act in the cell entry system of SARS-CoV-2. The C-terminal tail of both subunits share a high degree of sequence similarity, and similarly to ACE2, contain several known and candidate SLiMs (see Table 1 and Figure 6 ) that propagate signals in the cytoplasm and regulate integrin activity not just through intracellular pathways, but also changing the structural state of the ectodomains determining ligand binding capacity (Anthis and Campbell, 2011) . doi = nan id = cord-301484-y9l2hmqf author = MASSAROTTI, Claudia title = Asymptomatic SARS‐CoV‐2 infections in pregnant patients in an Italian city during complete lockdown date = 2020-08-25 keywords = SARS summary = Data from both New York and London report a high prevalence of the asymptomatic SARS‐CoV‐2 infection in pregnant patients admitted for delivery, raising questions on the possible correlated dangers (i.e. contacts with healthcare workers; the possible creation of an intra‐hospital outbreak at birth; conflicting evidences on vertical transmission). For this study, results from SARS‐CoV‐2 screening via nasopharyngeal swab from maternity wards of the four hospitals of Genoa, Italy were collected during a month of complete lockdown, from April 1 to April 30, 2020. Early detection and isolation of asymptomatic SARS-CoV-2 positive patients is a crucial public safety action [1] , but a screening of the entire population is difficult to be This article is protected by copyright. The incidence of positive SARS-CoV-2 nasopharyngeal swabs in asymptomatic pregnant women were 13.5 and 6.2% in two reported screened cohort in New York and London [2, 3] . Since the implementation of the universal screening, all pregnant women admitted for delivery were tested for SARS-CoV-2. doi = 10.1002/jmv.26458 id = cord-279316-xz7aawem author = MIZUTANI, T. title = Signal Transduction in SARS‐CoV‐Infected Cells date = 2007-04-23 keywords = SARS; Vero summary = Recent studies regarding SARS and SARS‐CoV have clarified that activation of mitogen‐activated protein kinases (MAPKs) plays important roles in upregulation of cytokine expression and apoptosis both in vitro and in vivo. For example, mitogen-activated protein kinases (MAPKs) are well-known signal transducers that respond to extracellular stimulation by cytokines, growth factors, viral infection, and stress, and in turn regulate cell differentiation, proliferation, survival, and apoptosis. Extracellular signal-regulated kinase (ERK) 1/2 was phosphorylated in SARS-CoV-infected Vero E6 cells, 27 whereas ERK1/2 was downregulated in N protein-expressing COS-1 cells as described below. Activation of the p38 MAPK signaling pathway and dephosphorylation of STAT3 via p38 MAPK induced by SARS-CoV infection have partially proapoptotic roles in Vero E6 cells. Importance of Akt signaling pathway for apoptosis in SARS-CoV-infected Vero E6 cells doi = 10.1196/annals.1408.006 id = cord-033951-77tfhm5b author = Ma, Chunlong title = Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors date = 2020-10-09 keywords = A71; DTT; SARS summary = In this study, we investigated the mechanism of action of six previously reported M(pro) inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12, using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. 31 Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin were recently reported as SARS-CoV-2 M pro inhibitors with IC 50 values ranging from 0.67 to 21.39 μM in the FRET-based enzymatic assay. Collectively, our results showed that in the absence of DTT, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 nonspecifically inhibit all six viral cysteine proteases including SARS-CoV-2 M pro . Collectively, the enzymatic assay results suggest that ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are promiscuous cysteine protease inhibitors that inhibit not only M pro but also five other related and unrelated viral cysteine proteases including SARS-CoV-2 PL pro and EV-A71 and EV-D68 2A pro and 3C pro in the absence of DTT, and the doi = 10.1021/acsptsci.0c00130 id = cord-305587-xtqvtleb author = Ma, Cuiqing title = From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development date = 2020-05-11 keywords = CoV; SARS summary = Identification and characterization of novel neutralizing epitopes in the 506 receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic determinants in inactivated 507 SARS-CoV vaccine Intranasal vaccination of recombinant adeno-associated virus 533 encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces 534 strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of SARS-CoV spike protein induces highly 556 potent neutralizing antibodies: implication for developing subunit vaccine Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies 613 primarily targeting the receptor binding region Receptor-binding domain of severe acute respiratory syndrome coronavirus 621 spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies. Cross-neutralization of human and palm civet severe acute 636 respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein doi = 10.1016/j.micinf.2020.05.004 id = cord-324970-yty7aajj author = Ma, Di title = Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea date = 2020-05-07 keywords = ACE2; SARS; TMPRSS2 summary = title: Expression of SARS-CoV-2 receptor ACE2 and TMPRSS2 in human primary conjunctival and pterygium cell lines and in mouse cornea PURPOSE: To determine the expressions of SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS2) genes in human and mouse ocular cells and comparison to other tissue cells. The expression of ACE2 and TMPRSS2 genes was determined in human primary conjunctival and pterygium cells, human ocular and other tissue cell lines, mesenchymal stem cells as well as mouse ocular and other tissues by reverse transcription-polymerase chain reaction (RT-PCR) and SYBR green PCR. Herein, this study aimed to determine the expressions of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human and mouse ocular cells and tissues. In summary, this study revealed the expression of SARS-CoV-2 receptor ACE2 and serine protease TMPRSS2 genes in human conjunctival and pterygium cells as well as mouse cornea tissue. doi = 10.1038/s41433-020-0939-4 id = cord-333754-copxoyqu author = Ma, Hsin-Chieh title = Expression and membrane integration of SARS-CoV M protein date = 2008-04-09 keywords = Fig; SARS summary = Full-length SARS-CoV M gene fragment was cloned and expressed as a recombinant protein (221 a.a.) with a C-terminal V5-His tag (29 a.a.) in Vero E6 cells (Fig. 1a) . In addition to the glycosylated and un-glycosylated SARS-CoV M proteins, two smaller protein products (marked by thick line and thin line, respectively) were also detected when M gene was expressed in Vero E6 cells ( Fig. 1a and b) . The protein translated in-frame from the third Met (amino acid 83) could still be detected when the authentic 5 0 -untranslated region of SARS-CoV M gene was included in the expression vector (lane 3 in supplement Fig. 2 ). In this study, SARS-CoV M gene fragment was cloned and expressed as a recombinant protein fused with a C-terminal V5 tag in Vero E6 cells (Fig. 1) . Two other expressed SARS-CoV M protein products with smaller size than the full-length one were also detected in Vero E6 cells (Figs. doi = 10.1007/s11373-008-9235-1 id = cord-300784-4jeaqqn9 author = Ma, Huan title = COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay date = 2020-04-22 keywords = RBD; SARS summary = Here, we aimed to develop a more quantitative and sensitive serological test for COVID-19 diagnosis, monitoring and clinical investigation, based on the detection of antigen-specific IgA as well as IgM and IgG in blood in response to SARS-CoV-2 infection. Methods In this investigation, we report the development of a set of validated diagnostic kits for detecting serum IgA, IgM, and IgG specific to SARS-CoV-2 nucleocapsid protein (NP) and receptor-binding domain (RBD) of the spike protein by chemi-luminescence immuno-analysis. . https://doi.org/10.1101/2020.04.17.20064907 doi: medRxiv preprint Based on the clinical RT-qPCR diagnosis results of SARS-CoV-2 infection, receiver operating 208 characteristic (ROC) analysis was conducted using MedCalc software to determine the optimal cut-off 209 value (criterion) and evaluate the diagnostic value of NP-or RBD-specific IgA, IgM, and IgG kits. Nonetheless, we showed that our serological kits based on SARS-CoV-2 spike 322 protein RBD as an immobilized antigen provide a high sensitivity and specificity for detecting IgA, IgM, 323 and IgG in a quantitative manner. doi = 10.1101/2020.04.17.20064907 id = cord-298343-nvuc1j7t author = Ma, J. title = Exhaled breath is a significant source of SARS-CoV-2 emission date = 2020-06-02 keywords = SARS; covid-19 summary = Here, 35 COVID-19 subjects were recruited; exhaled breath condensate (EBC), air samples and surface swabs were collected and analyzed for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). COVID-19 patients were shown to exhale SARS-CoV-2 into the air at an estimated rate of 103-105 RNA copies/min; while toilet and floor surfaces represented two important SARS-CoV-2 reservoirs. Surface swabs from the cell phone and hands of one patient(ITA-YL1) tested negative for the virus, but the SARS-CoV-2 was present on the toilet pit surface in that patient''s hotel room (Fig. 1C ). Although EBC samples from two patients (ITA-YW2 and UK-YJ1) were shown to 20 contain SARS-CoV-2, surface swabs from their cell phones, hands, and toilet surfaces were negative for the virus. . https://doi.org/10.1101/2020.05.31.20115154 doi: medRxiv preprint Out of 242 surface swab samples, 13 were positive for SARS-CoV-2 ( Fig. 3 and Table S4 ). doi = 10.1101/2020.05.31.20115154 id = cord-284449-z7r4n0w7 author = Ma, L. title = Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study date = 2020-03-24 keywords = COVID-19; SARS summary = This study provides the first direct evidence about the influence of medical condition of COVID-19 on male sex hormones, alerting more attention to gonadal function evaluation among patients recovered from SARS-CoV-2 infection, especially the reproductive-aged men. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. In this study, we compared the sex-related hormones between reproductive-aged men with SARS-CoV-2 infection and age-matched healthy men, and found serum luteinizing hormone (LH) was significantly increased, but the ratio of testosterone (T) to LH and the ratio of follicle stimulating hormone (FSH) to LH were dramatically decreased in male with COVID-19. doi = 10.1101/2020.03.21.20037267 id = cord-310027-846vp7ii author = Ma, Lin-Lu title = Coronavirus Disease 2019 Related Clinical Studies: A Cross-Sectional Analysis date = 2020-09-02 keywords = COVID-19; SARS; clinical; study summary = METHODS: We did an electronic search of COVID-19 related clinical studies registered between December 1, 2019 and February 21, 2020 (updated to May 28, 2020) from the ClinicalTrials.gov, and collected registration information, study details, recruitment status, characteristics of the subjects, and relevant information about the trial implementation process. We extracted the following information from registered studies: registration number, registration date, registration title, primary sponsor, funding source, study type, study phase, study objectives, study design, length of the study, intervention, countries of recruitment and research settings, recruiting status, allocation, sample size, participant age, gender, masking, the time and method of sharing individual participant data (IPD), data management committee. Among the 943 interventional studies, 416 studies (44.1%) explored the effectiveness and/or safety of drugs commonly used in preventing and treating COVID-19, such as hydroxychloroquine (HCQ), chloroquine (CQ), immunotherapy (including stem cell therapy, monoclonal antibody, immunoregulation), lopinavir/ritonavir, glucocorticoids, interferon, targeted therapy (Baricitinib, Ruxolitinib, Imatinib), favipiravir, and Remdesivir. doi = 10.3389/fphar.2020.540187 id = cord-322009-0cwljo0c author = Ma, Ling title = Coinfection of SARS-CoV-2 and Other Respiratory Pathogens date = 2020-08-26 keywords = SARS; covid-19; patient summary = Although the number of confirmed global cases of COVID-19 now exceeds 16 million, as of July 29, and several retrospective observational studies have noted that coinfection with other respiratory pathogens is relatively common, [1] [2] [3] [4] the clinical features of coinfection and its impact on patient outcomes, is yet to be clarified. All these patients were tested for SARS-CoV-2, respiratory syncytial virus, influenza A virus, influenza B virus, adenovirus, Chlamydia pneumoniae, and Mycoplasma pneumoniae, using sputum or nasopharyngeal swab specimens collected in the interval between the onset of symptoms, and up to seven days after their hospital admission. Routine laboratory tests, including tests for SARS-CoV-2 and other common respiratory viral and atypical bacterial pathogens, routine blood investigations, coagulation studies, organ function tests and inflammatory biomarkers, such as c-reactive protein (CRP) and procalcitonin (PCT), were taken at the time of patient presentation, while the serum interleukin (IL)-2, IL-4, IL-6, IL-10, TNF-α and IFN-γ levels were obtained on the 2nd day of admission. doi = 10.2147/idr.s267238 id = cord-310691-6danlh8h author = Ma, Simin title = Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date = 2020-05-26 keywords = SARS; covid-19 summary = title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. doi = 10.1016/j.ijid.2020.05.068 id = cord-193893-rzurz5bj author = Ma, Zhanshan title = Spatiotemporal fluctuation scaling law and metapopulation modeling of the novel coronavirus (COVID-19) and SARS outbreaks date = 2020-03-08 keywords = SARS; Taylor summary = Another TPL parameter (M0) (i.e., infection critical threshold) depends on virus kinds (COVID-19/SARS), time (disease-stages), space (regions) and public-health interventions (e.g., quarantines and mobility control). While TPL can be harnessed to investigate the spatiotemporal fluctuations of coronaviruses, specifically, the scaling (changes) law of coronaviruses infections over space and time, we also aim to understand the spread of the virus infections from both local contagion (endemic) and external migration (epidemic and pandemic) perspectives. Overall, this study sets two primary objectives: (i) to investigate the spatiotemporal fluctuation scaling law and (ii) to obtain an educated guess for the local contagion spread and global migration parameters of the COVID-19 infections. At the community level, the four Taylor''s power law extensions (TPLE), can be used to measure the community spatial (temporal) heterogeneity ( on both the general principle of TPL (explained above) and system-or data-specific information (such as the biology of COVID or SARS). doi = nan id = cord-354582-fniymnmf author = Ma, Zhiqian title = Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date = 2020-06-30 keywords = MERS; RNA; SARS; virus summary = In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . doi = 10.1016/bs.aivir.2020.06.003 id = cord-308996-tf0v2ojk author = Maas, Angela HEM title = The Coronavirus Disease 2019 Outbreak Highlights the Importance of Sex-sensitive Medicine date = 2020-08-24 keywords = COVID-19; SARS summary = The novel coronavirus disease 2019 (COVID-19) pandemic has revealed important differences between the sexes in epidemiology, risk factors, clinical course, mortality and socioeconomic dimensions of the disease in all populations worldwide. The role of the TMPRSS2 protease in SARS-CoV-2 needs to be further investigated, but information on other diseases points towards sexspecific differences. 34 Sex differences in the binding of SARS-CoV-2 to the ACE2 receptor have been identified as an important contributor to the initiation and course of the disease. 27, 35, 36 Sex differences regarding potential protective effects of renin-angiotensin-aldosterone system inhibitors in SARS-CoV-2 infections are as yet unknown. Sex-specific SARS-CoV-2 mortality: among hormone-modulated ACE2 expression, risk of venous thromboembolism and hypovitaminosis D The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Gender differences in patients with COVID-19: focus on severity and mortality doi = 10.15420/ecr.2020.28 id = cord-269289-6uog10j4 author = Mabillard, Holly title = Electrolyte Disturbances in SARS-CoV-2 Infection date = 2020-07-22 keywords = CoV-2; RAS; SARS; patient summary = These include additional respiratory complications (pulmonary fibrosis -reported in 21% of those hospitalised with SARS-CoV-2 9 months post-discharge in one study 3 ) 7 , cardiovascular complications (acute cardiac injury (7% 8 ), cardiomyopathy (1/3 patients 9 ), cardiac tamponade, heart failure, dysrhythmias (17% 8 ) and venous thromboembolic events (20% 10 )) 11 , neurological complications (myopathy, acute stroke (5.7% of those with severe infection 12 ), Guillain-Barre syndrome (0.4% hospitalised patients 11 ) and encephalopathy) 13 , acute liver and/or pancreatic injury (29% and 17% respectively in one cohort) 14 , cytokine storm syndrome, septic shock, DIC, diarrhoea, Kawasaki-like disease 14 and renal complications (acute tubular injury, rhabdomyolysis, proteinuria, secondary focal segmental glomerulosclerosis and possible renin-angiotensinaldosterone system activation) 15 . The study reported that the degree of hypokalaemia correlated with severity of SARS-CoV-2 symptoms and they suggested that hypokalaemia can be difficult to correct as seen in two patients because the renal potassium wasting persists until clinical recovery from the virus. doi = 10.12688/f1000research.24441.2 id = cord-336142-jmetfa6x author = MacDougall, Heather title = Toronto’s Health Department in Action: Influenza in 1918 and SARS in 2003 date = 2006-10-11 keywords = Hastings; Health; Ontario; Public; SARS; TPH; Toronto; disease summary = This article compares the Toronto Health Department''s role in controlling the 1918 influenza epidemic with its activities during the SARS outbreak in 2003 and concludes that local health departments are the foundation for successful disease containment, provided that there is effective coordination, communication, and capacity. 3 By comparing and contrasting the way in which public health authorities in Toronto managed the 1918 influenza pandemic and SARS in 2003, we can see how a century of medical advances had conditioned the public and health care professionals to expect prompt control of communicable diseases, speedy development of a prophylactic vaccine, and effective exchange of information at the provincial, national, and international levels. For Toronto''s medical officer and its Local Board of Health (LBH), this presented a challenge, because influenza was not a reportable disease under the 1912 Ontario Public Health Act, and most doctors were hoping that the outbreak would be similar to the one in 1889-90 that had attacked primarily the elderly and apparently provided some immunity to those who survived. doi = 10.1093/jhmas/jrl042 id = cord-343476-0chuwvg6 author = MacLean, Oscar A. title = Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date = 2020-05-29 keywords = SARS summary = Here we contrast the role of positive selection and recombination in the Sarbecoviruses in horseshoe bats to SARS-CoV-2 evolution in humans. While methods can detect some evidence for positive selection in SARS-CoV-2, we demonstrate these are mostly due to recombination and sequencing artefacts. For all but two of the ten positive selected codons, this signal was being driven by apparent convergent evolution (or homoplasy) in the tree, with the same mutation occurring in parallel across the phylogeny. To investigate whether this observation was truly due to independent events or because of recombination signatures in the SARS-CoV-2 outbreak tree, we firstly determined if the samples with these convergent mutations were geographically correlated. The Spike V367F signal was driven by apparent convergent evolution between four french samples sequenced in January and a Hong Kong sample 412028, which shows shared variation either side of the homoplasy suggesting it is not a recombinant (Supplementary figure 3C) . doi = 10.1101/2020.05.28.122366 id = cord-278406-n5e3a09i author = Macauley, Precious title = CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date = 2020-08-21 keywords = COVID-19; SARS summary = Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). doi = 10.1016/j.ijid.2020.08.051 id = cord-015613-ls9qus8y author = Macdonald, David W. title = Infectious disease: Inextricable linkages between human and ecosystem health date = 2006-06-06 keywords = SARS; disease; human summary = Several papers, including those on rabies in Ethiopian wolves, Canis simensis (Randall et al., 2006) , and African wild dogs, Lycaon pictus (Vial et al., 2006) , disease in Island foxes, Urocyon littoralis (Clifford et al., 2006) , squirrel parapox virus (SQPV) in red squirrels, Sciurus vulgaris (Gurnell et al., 2006) , and devil facial tumour disease (DFTD) in Tasmanian devils, Sarcophilus harrisii (Hawkins et al., 2006) examine this theme. The importance of reservoir identification is classically illustrated by a range of papers in this Special Issue, for example the ongoing dilemma facing bovine tuberculosis control , the diseases emerging from bats (Breed et al., 2006) , phocine distemper virus (PDV) in northern seal population (Hall et al., 2006) and the canid pathogens threatening Island foxes (Clifford et al., 2006) . doi = 10.1016/j.biocon.2006.05.007 id = cord-319158-n8e2n30b author = Mackenzie, John S title = COVID-19: a novel zoonotic disease caused by a coronavirus from China: what we know and what we don’t date = 2020-03-17 keywords = China; SARS summary = Based on established practice, the new virus was named SARS-CoV-2 by the Coronavirus Study Group of the International Committee for the Taxonomy of Viruses 10 , and the disease it causes as COVID-19 by WHO 11 . Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Estimating the unreported number of novel coronavirus (2019-nCoV) cases in China in the first half of January 2020: a data-driven modelling analysis of the early outbreak Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China SARS-CoV-2 viral load in upper respiratory specimens of infected patients A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan (2020) The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) -China doi = 10.1071/ma20013 id = cord-339459-z22a5yzo author = Mackey, Katherine title = Risks and Impact of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers on SARS-CoV-2 Infection in Adults: A Living Systematic Review date = 2020-05-15 keywords = ARB; COVID-19; SARS summary = PURPOSE: To evaluate, on an ongoing basis, whether use of ACEIs or ARBs either increases risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or is associated with worse COVID-19 disease outcomes, and to assess the efficacy of these medications for COVID-19 treatment. STUDY SELECTION: Observational studies and trials in adults that examined associations and effects of ACEIs or ARBs on risk for SARS-CoV-2 infection and COVID-19 disease severity and mortality. Three studies (33, 36, 37) , which included a total of 8766 patients with COVID-19 and presented analyses adjusted for important confounding factors, had consistent results and provide moderate-certainty evidence that ACEIs or ARBs are not associated with a higher likelihood of positive SARS-CoV-2 test results among symptomatic patients ( Table 1) . Risks and Impact of ACEIs or ARBs in Adults With SARS-CoV-2 Infection REVIEW Annals.org Annals of Internal Medicine other U.S. study included patients with COVID-19 in the New York University health system and examined ICU admission, assisted ventilation, and death as outcomes (37) . doi = 10.7326/m20-1515 id = cord-256374-l492w2i2 author = Mackler, Niklas title = Will First-Responders Show Up for Work During a Pandemic? Lessons From a Smallpox Vaccination Survey of Paramedics date = 2007-05-22 keywords = SARS; duty summary = Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. Even if protective gear was available but the vaccine was unavailable, only 39% of respondents would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. If no vaccine was available and paramedics had no protective gear, 4 (4%) answered that they probably would remain on duty. The results of this survey indicate that in the event of an outbreak of a contagious disease like smallpox or pandemic influenza, a significant number of paramedics might be unwilling to remain on duty to care for patients without adequate protection against infection. 2, 5 Several recent studies have addressed public health worker and basic and paramedic emergency medical technician (EMT) perceptions about coming to work during a contagious outbreak. doi = 10.1016/j.dmr.2007.02.002 id = cord-305134-s7h6bpof author = Mackman, Nigel title = Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses date = 2020-07-13 keywords = H1N1; MERS; SARS; covid-19; patient summary = It is likely that multiple systems contribute to thrombosis in COVID-19 patients, such as activation of coagulation, platelet activation, hypofibrinolysis, endothelial cell dysfunction, inflammation, neutrophil extracellular traps, and complement. 60, 82 Taken together, these results indicate that most COVID-19 patients have an activated coagulation system that is associated with increased levels of d-dimer; however, it is unlike classic DIC since there is little change in PT and the thrombocytopenia is generally mild. [95] [96] [97] [98] [99] There is clear evidence for activation of different cell types, such as lung epithelial cells, macrophages, neutrophils, endothelial cells, and platelets, as well as different systems, such as coagulation, inflammation, and complement, in the lungs of COVID-19 patients (Figure) . We found that plasma levels of extracellular vesicle TF activity were increased in severe influenza virus patients and were associated with mortality. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infects lung epithelial cells and endothelial cells (ECs), which leads to the recruitment of a variety of immune cells, such as macrophages and neutrophils. doi = 10.1161/atvbaha.120.314514 id = cord-303022-9hqoq7tf author = Madapusi Balaji, Thodur title = Oral cancer and periodontal disease increase the risk of COVID 19? A mechanism mediated through furin and cathepsin overexpression date = 2020-06-01 keywords = SARS summary = In addition to furin, another protease cathepsin L is also elevated in chronic periodontitis and oral cancer, which in turn could be a result of the interleukin 6 mediated activation of the caveolin -1 mediated JNK-AP-1 signaling pathway [8] [9] [10] . 3) Following binding of the S1 subunit to the ACE-2 receptors, the virus fuses with the host cell in two mechanisms: (a) endosomal fusion which is mediated by cysteine proteases cathepsin B/L and (b) plasma membrane fusion mediated by the serine protease TMPRSS2. Based on the above-mentioned data, it can be hypothesized that the increased protease levels in chronic periodontitis and oral cancer could potentially increase the risk of an oral mucosa mediated SARS-corona virus-2 infection (figure 1). In addition to increasing proteases, chronic periodontitis, and oral cancer patients have also reported having a low melatonin level [14, 15] . doi = 10.1016/j.mehy.2020.109936 id = cord-026803-p1o4qc1h author = Maddury, Jyotsna title = Need of the Hour— COVID-19 for Cardiologists date = 2020-04-16 keywords = SARS; covid-19 summary = The most distressing pandemic at present is coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial studies showed low association of chronic cardiac diseases (10%) in COVID-19 patients along with the acute cardiac injury accounting to 23%. These reports with new information urge cardiologists to warn patients about the potential risk and encourage them to practice "additional, reasonable precautions" for those with underlying heart disease. As SARS-CoV-2 and MERS-CoV have similar pathogenicity, myocardial injury caused due to SARS-CoV-2 infection may be immune mediated through the ACE2 receptor or cytokine storm and/or hypoxia due to acute respiratory distress syndrome (ARDS). As there is an increased risk of secondary infections with COVID-19, patients are advised to remain current with vaccinations, including the pneumococcal vaccine and influenza vaccine in accordance with current ACC/American Heart Association (AHA) guidelines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges doi = 10.1055/s-0040-1709950 id = cord-274648-e0daf8w6 author = Madeddu, Paolo title = Cardiovascular complications of COVID-19: evidence, misconceptions, and new opportunities date = 2020-06-08 keywords = ACE2; SARS summary = The virus binds with its spike protein to the surface receptor angiotensin converting enzyme 2 (ACE2) to unlock human cells and begin infection. Likewise, it remains to be established whether repeated exposures or a single contact with massive doses of the virus, like in the case of clinical staff caring patients who are not known to be infected, can increase the risk of developing severe forms of the disease. The binding of SARS-CoV-2 to ACE2 is stronger than previous coronaviruses, due to difference in key amino acid residues allowing for enhanced interactions between the virus and human cells. Therefore, when considering severity of COVID-19, the low ACE2 levels observed in elderly people and those with cardiovascular disease seem to facilitate rather than protect from the disease (9) . The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts doi = 10.1530/vb-20-0008 id = cord-340942-oatf59k0 author = Magalhães, Jurandy Júnior Ferraz de title = Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil date = 2020-09-21 keywords = Brazil; SARS; covid-19 summary = METHODS: In this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for SARS-CoV-2 living in Pernambuco state, Northeast Brazil. Here, we describe for the first time the clinical, epidemiological and demographic features of the first 557 laboratory-confirmed COVID-19 cases in Pernambuco state, Northeast Brazil, who were diagnosed between March 12 and April 22, 2020. Patient epidemiological information, demographic and clinical characteristics, including medical history, signs and symptoms, laboratory findings, underlying co-morbidities, and date of disease onset were obtained from electronic medical records of the Pernambuco Central Public Health Laboratory (LACEN) and analyzed. Regarding the distribution of COVID-19 cases in the different household income ranges (Fig. 1B) , we found that SARS-CoV-2 infections occurred in neighborhoods with greater purchasing power. Here, we described for the first time the epidemiological and clinical characteristics of the first 557 consecutive patients diagnosed with SARS-CoV-2 in the state of Pernambuco between 12 March and April 22, 2020. doi = 10.1016/j.tmaid.2020.101884 id = cord-270635-l8380adr author = Maggi, Enrico title = COVID-19: unanswered questions on immune response and pathogenesis date = 2020-05-08 keywords = SARS summary = It is generally accepted that only achieving a better understanding of the interactions between the virus and host immune response and of the pathogenesis of infection is crucial to identify valid therapeutic tools to control virus entry, replication and spread as well as to impair its lethal effects. On this basis, we also touch important aspects regarding the immune response in asymptomatic subjects, the immune-evasion of SARS-CoV-2 in severe patients and differences in disease severity by age and gender. This implies to be able to answer many questions on the virus itself, on the pathogenesis of infection, on the 81 host immune response and to identify therapeutic tools to control virus entry into the cells, its replication and 82 spread as well as its lethal effects. Humoral Immune Responses SARS-CoV 3 -Seroconversion few days after the disease onset and specific IgG detectable in most patients by 14 days. doi = 10.1016/j.jaci.2020.05.001 id = cord-342391-arp07mck author = Magiorkinis, G. title = Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions date = 2004-09-14 keywords = Group; SARS summary = Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. Bayesian scanning and subsequent phylogenetic analysis revealed that the SARS-CoV sequence was related more closely to Group II than the other two groups in most of its genome (e.g., at the region spanning amino acid positions 4309-5612 in reference to the murine hepatitis virus ORF1ab gene) (Fig. 1) . This clustering was supported by high quartet puzzling support values and high posterior probabilities under various substitution models, thus suggesting that 80% of the SARS-CoV genomic sequence is related more closely to coronaviruses Group II than any other members of this family. doi = 10.1002/jmv.20187 id = cord-303330-zh8wzza5 author = Magleby, Reed title = Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date = 2020-06-30 keywords = COVID-19; SARS; viral summary = In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. doi = 10.1093/cid/ciaa851 id = cord-285806-363ivs67 author = Magro, Giuseppe title = SARS-CoV-2 and COVID-19: is interleukin-6 (IL-6) the ''culprit lesion'' of ARDS onset? What is there besides Tocilizumab? SGP130Fc date = 2020-05-14 keywords = COVID-19; IL-6; SARS; signal summary = In a humanized transgenic mouse MERS-CoV infection model, Remdesivir (a drug already being used against SARS-CoV-2 in patients with severe and moderate disease, GS-US-540-5773/4 Studies) showed more activity and efficacy in prophylactic and therapeutic use then the combination of Lopinavir/Ritonavir and Interferon beta 9 , this points towards the necessity to explore other options regarding immune system modulation and how control of viraemia is also essential. More evidence suggests that critically ill patients with severe respiratory failure and SARS-CoV-2 have either immune dysregulation or macrophage-activation syndrome, both of which are characterized by pro-inflammatory cytokines. This is another evidence of the pro-inflammatory role of the trans-signaling pathway and it could also be the explanation as to why some patients show a higher inflammatory response mediated by IL-6, similarly to what is happening with SARS-CoV-2 infection. doi = 10.1016/j.cytox.2020.100029 id = cord-287256-hgqz1bcs author = Magurano, Fabio title = SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date = 2020-11-05 keywords = SARS summary = title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID 50 viral titre of 0,67 and 0,25 log10 respectively. doi = 10.1016/j.cmi.2020.10.034 id = cord-281141-ouno4jpl author = Mahajan, Swapnil title = Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date = 2020-11-05 keywords = CD8; HLA; SARS summary = A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . doi = 10.1101/2020.11.03.367375 id = cord-025623-1v9614f8 author = Mahapatra, Pallab Sinha title = Surface Treatments to Enhance the Functionality of PPEs date = 2020-05-29 keywords = PPE; SARS; coating summary = This paper focuses on improving PPE functionality in a scalable manner by surface treatment and coating with appropriate materials and other functional enhancements, such as exposure to UV rays or other sterilizing agents (e.g., hydrogen peroxide). Surface treatments to enhance resistance against diseasecausing microbes, i.e., antimicrobial coatings, have the potential to improve PPE functionalities dramatically. Hydrophobic coatings make it difficult for droplets/particles to adhere on surfaces and are known to provide antimicrobial characteristics, which are retained after multiple washes; antibacterial and antifungal properties were demonstrated by Mukherjee et al. Klibanov''s group at MIT has shown extended functionality of hydrophobic coating characteristics against influenza viruses, which get transmitted through respiratory droplets, like SARS-CoV-2; Halder et al. Scalable surface treatment strategies that combine antiviral action with liquid-repelling properties are one of many possible approaches to enhance the functionality of PPEs, thereby serving to satisfy their high demand in the healthcare industry and other fronts where the COVID-19 pandemic is being fought. doi = 10.1007/s41403-020-00110-0 id = cord-344934-m0q7rm6z author = Mahapatra, Sovesh title = Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking date = 2020-04-07 keywords = April; SARS; drug summary = Here, we report the ML model based on the Naive Bayes algorithm, which has an accuracy of around 73% to predict the drugs that could be used for the treatment of COVID-19. Bioactivity datasets which are available from the numerous high throughput screens deliver useful means for machine learning classifiers as they contain binary information (active/inactive) as well as numerical values to classify different compounds under consideration 22, 23 . These drugs were downloaded in the form of SDFs and after processing, the descriptions generated were taken as the test model for developing the train model which was made on the basis of a database containing the inhibitors of the SARS coronavirus. Around 178 drugs were predicted by our ML model which can be effective for the treatment of diseases caused by SARS-Cov-2. doi = 10.1101/2020.04.05.20054254 id = cord-297859-p57pl45i author = Mahlke, Lutz title = Chirurgie in der SARS-CoV-2-Pandemie: Empfehlungen zum operativen Vorgehen date = 2020-06-02 keywords = SARS; der; die summary = authors: Mahlke, Lutz; Flohé, Sascha; Matthes, Gerrit; Paffrath, Thomas; Wagner, Frithjof; Wölfl, Christoph Die Virusinfektion mit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ist hochkontagiös, daher besteht auch für die Mitarbeiter des Krankenhauses ein hohes Risiko [1] . Über die persönliche Schutzausrüstung (PSA) für Mitarbeiter der Anästhesie sind in einer kürzlich erschienenen Publikation sehr detailliert das Vorgehen und das notwendige Equipment beschrieben worden [2] , sodass hier v. Sofern es Personalschlüssel und Ausbildungsstand der Abteilung erlauben, ist die Schaffung von speziell geschulten "COVID-19"-OP-Teams sinnvoll. Auch die bisherigen Virusnachweise im Darm und im Stuhl lassen keine hohe Viruslast erkennen [13] , zumal unklar ist, ob es sich hierbei noch um ein infektiöses Virus handelt [14] . Even patients infected by SARS-CoV-2 or COVID-19 may need operative procedures. Empfehlungen des RKI zu Hygienemaßnahmen im Rahmen der Behandlung und Pflege von Patienten mit einer Infektion durch SARS-CoV-2 doi = 10.1007/s00113-020-00830-6 id = cord-270015-5gtxfkoz author = Mahmood Shah, Sayed Mustafa title = Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health date = 2020-08-20 keywords = SARS summary = title: Pandemics and prayer: The impact of cattle markets and animal sacrifices during the muslim Eid festival on COVID‐19 transmission and public health 6 This comes at a time when many Muslim majority countries are stilling struggling with the public health crisis posed by COVID-19, with variable success in controlling the transmission of the virus. 7 A structural analysis of ACE-2 receptor in vertebrates has shown artiodactyl mammals (which include domesticated cattle, sheep and goats) express ACE-2 receptors and were classified as medium score for binding to SARS-CoV-2 Spike protein. 7 This finding has been reiterated in a comparative x-ray structural analysis of SARS-CoV-2 spike protein receptor binding domain to ACE-2 receptors in humans and putative intermediate hosts. Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts SARS-CoV-2: structural diversity, phylogeny, and potential animal host identification of spike glycoprotein doi = 10.1002/hpm.3040 id = cord-291595-8241pjpe author = Mahmudpour, Mehdi title = COVID-19 cytokine storm: The anger of inflammation date = 2020-05-30 keywords = ACE2; Ang; COVID-19; SARS summary = The virus-mediated down-regulation of ACE2 causes a burst of inflammatory cytokine release through dysregulation of the renin-angiotensin-aldosterone system (ACE/angiotensin II/AT1R axis), attenuation of Mas receptor (ACE2/MasR axis), increased activation of [des-Arg9]-bradykinin (ACE2/bradykinin B1R/DABK axis), and activation of the complement system including C5a and C5b-9 components. Because Ang-(1-7) exerts a critical role in counteracting the pro-inflammatory effect of RAAS, protecting from endothelial cell activation and resulting lung damage from inflammatory mediators in the cytokine storm, the administration of Ang-(1-7) or one of its similar agents to patients with COVID-19 pneumonitis has been suggested [35, 66] . We suggested ACE2/Bradykinin/DABK may be involved in the inflammatory response of SARS CoV-2; therefore, blockade of this axis by inhibiting BKB1R may ameliorate a part of the cytokine storm which occurs in COVID-19 infection. doi = 10.1016/j.cyto.2020.155151 id = cord-335302-6wsx0jby author = Mahy, Brian W.J. title = The diversity of viruses infecting humans date = 2011-12-12 keywords = SARS; human summary = Other new viruses have been recognized because of a new disease they caused in humans, such as the severe acute respiratory syndrome (SARS) coronavirus . Studies on the origin of the SARS coronavirus are still ongoing: there is recent evidence of a zoonotic origin of the human disease, perhaps from palm civets, but the true natural reservoir of the virus seems most likely to be in a bat species, probably Chinese horseshoe bats (Lau et al. This was the only known human parvovirus until very recently, when a new parvovirus was discovered to be the cause of lower respiratory tract infections in children. 2006 ) and elsewhere (unpublished) have revealed a significant number of children whose lower respiratory tract disease appears to be caused by human bocavirus infection. New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children doi = 10.1080/14888386.2006.9712792 id = cord-272573-wxqly479 author = Maia Chagas, Andre title = Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date = 2020-04-24 keywords = COVID-19; FOSH; RNA; SARS; open summary = Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. Community and commercial open source efforts in diagnostic technology to date have focused on four areas: i) open platforms for scaling reactions as exemplified by Opentrons ( Fig 3A) [28] , an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona; ii) trying to fill gaps where less attention is being paid by clinical diagnostics companies, such as Chia Bio''s Open qPCR (Fig 3B) environmental test kit for surveillance via surface swabs [111] ; iii) distributed reproduction of rapidly-published, lab-scale protocols, seen within the OpenCOVID initiative hosted by Just One Giant Lab [39] which involves many community labs worldwide; iv) initiatives such as the Open Enzyme Collection [93] , Free Genes [94] and Biomaker Challenge [112] which are investigating new approaches to foundational technologies such as reagents and instrumentation, with a view to building capacity and resources or global science and medicine to face a future pandemic. doi = 10.1371/journal.pbio.3000730 id = cord-257310-wqu7t44n author = Maideniuc, Catalina title = Acute necrotizing myelitis and acute motor axonal neuropathy in a COVID-19 patient date = 2020-08-09 keywords = CSF; SARS summary = A 61-year-old woman with COVID 19 infection developed acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. Here we present a unique case of COVID 19 patients with acute necrotizing myelitis (ANM) and acute motor axonal neuropathy (AMAN), a rare variant of Guillain-Barré syndrome (GBS) without systemic signs of infection. However, MRI Cervical spine showed patchy T2 hyperintensities within the central cord extending from below the foreman magnum, proximal Electronic supplementary material The online version of this article (https ://doi.org/10.1007/s0041 5-020-10145 -6) contains supplementary material, which is available to authorized users. The patient had a spinal fluid analysis that showed a hemorrhagic tap (red blood cells 312/mm 3 ) with normal white blood cells (3/mm 3) elevated protein (87 mg/ dl) and glucose (73 mg/dl). Acute necrotizing encephalitis, myelitis and variants of GBS such as axonal, demyelinating, and Miller Fisher Syndrome have been reported with the COVID 19 [2] [3] [4] [5] . doi = 10.1007/s00415-020-10145-6 id = cord-314109-wb45naw2 author = Maiese, Kenneth title = The Mechanistic Target of Rapamycin (mTOR): Novel Considerations as an Antiviral Treatment date = 2020-06-17 keywords = AMPK; COVID-19; SARS; mTOR summary = One such avenue that may prove to be exceedingly fruitful and offer exciting potential as new antiviral therapy involves the mechanistic target of rapamycin (mTOR) and its associated pathways of mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK). Recent work has shown that mTOR pathways in conjunction with AMPK may offer valuable targets to control cell injury, oxidative stress, mitochondrial dysfunction, and the onset of hyperinflammation, a significant disability associated with COVID-19. Considering that one of the mechanisms that can lead to severe disability and death during infection with SARS-CoV-2 is an exaggerated activation of the host''s immune system that results in systemic hyperinflammation with the elevation of multiple pro-inflammatory cytokines, it is interesting to note that mTOR pathways have been tied to immune system modulation [40, 54, 55] . • The mechanistic target of rapamycin (mTOR) and its associated pathways with mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), and AMP activated protein kinase (AMPK) offer new avenues of opportunity for the development of innovative antiviral treatment strategies. doi = 10.2174/1567202617666200425205122 id = cord-342996-honeavwj author = Mair-Jenkins, John title = The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis date = 2015-01-01 keywords = CFR; SARS; convalescent summary = title: The Effectiveness of Convalescent Plasma and Hyperimmune Immunoglobulin for the Treatment of Severe Acute Respiratory Infections of Viral Etiology: A Systematic Review and Exploratory Meta-analysis We conducted a systematic review and exploratory meta-analysis to evaluate the clinical effectiveness of convalescent plasma, serum, or hyperimmune immunoglobulin for the treatment of severe acute respiratory infections (SARIs) of viral etiology, to help inform clinical management of MERS-CoV infection. Four observational studies [24, 30, 37, 48] and 1 systematic review [22] reported data on severe cases of influenza A(H1N1)pdm09 infection treated with convalescent plasma (Table 3 and Supplementary Table 3 ). A case-comparison study at moderate risk of bias [30] reported no significant difference in length of hospital stay between treatment and control patients with severe pandemic influenza A (H1N1) infection who required ECMO ( Table 3) . doi = 10.1093/infdis/jiu396 id = cord-296147-yfcp0xf2 author = Mairesse, Antoine title = High clinical performance and quantitative assessment of antibody kinetics using a dual recognition assay for the detection of SARS-CoV-2 IgM and IgG antibodies date = 2020-08-25 keywords = SARS summary = This study aims at assessing the analytical and clinical performances of the iFlash® anti-SARS-CoV-2 chemiluminescence assay for the detection of both IgM and IgG antibodies. The determination of anti-SARS-CoV-2 IgG antibodies from 28 days since symptom onset was associated with high sensitivity, especially using optimized cut-offs (i.e. 100%). The aim of this study was to evaluate the analytical and clinical performances of the iFlash ® SARS-CoV-2 antibodies (IgM and IgG) chemiluminescence assay (CLIA). Clinical sensitivity for SARS-Cov-2 serological test depending on the onset of COVID-19 symptoms was carried out with the manufacturer''s cut-off (>10 AU/mL for both IgM and IgG) and with ROC curve adapted cut-offs (2.81 AU/mL for IgM; 4.86 AU/mL for IgG). The aims of the present study were to evaluate the analytical and clinical performances of the iFlash ® anti-SARS-CoV-2 CLIA assay for IgM and IgG antibodies with a large cohort of COVID-19 patients, to provide an external validation of this test and to evaluate the antibody kinetics since symptom onset. doi = 10.1016/j.clinbiochem.2020.08.009 id = cord-300458-jeuwaj50 author = Maisch, Bernhard title = COVID-19—What we know and what we need to know: There are more questions than answers date = 2020-04-23 keywords = SARS; patient summary = COVID-19-What we know and what we need to know: There are more questions than answers This collection of short statements from the editors of HERZ/Cardiovascular Diseases is a strong signal to the readers of our journal in critical times. But we also fear that with a low herd immunity a second wave of infection might follow, since no proven antiviral treatment for COVID-19 exists and vaccination is not yet available [3] . Pulmonology demonstrates with every ventilated patient that COVID-19 is a potentially lethal lung disease. The first reported Chinese patient with suspected myocarditis from SARS-CoV-2 was treated with ventilation, methylprednisolone, i.v. immunoglobulins and inotropics and survived [4] . A total of 55 authors (!) have described in an observational study with 66 COVID-19 patients without a control group a beneficial effect in the New England Journal of Medicine [5] . 2020) compassionate use of remdesivir for patients with severe Covid-19 doi = 10.1007/s00059-020-04929-9 id = cord-025948-6dsx7pey author = Maitra, Arindam title = Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date = 2020-06-04 keywords = India; RNA; SARS; mutation; sequence summary = Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. We have initiated a study on sequencing of SARS-CoV-2 genome from swab samples obtained from infected individuals from different regions of West Bengal in Eastern India and report here the first nine sequences and the results of analysis of the sequence data with respect to other sequences reported from the country until date. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. We have also detected emergence of mutations in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. doi = 10.1007/s12038-020-00046-1 id = cord-258312-3v5t4k8d author = Majachani, Nicole title = A Case of a Newborn Baby Girl Infected with SARS-CoV-2 Due to Transplacental Viral Transmission date = 2020-10-25 keywords = CoV-2; SARS summary = Patient: Female, 31-year-old Final Diagnosis: COVID-19 • SARS-CoV-2 Symptoms: Asymptomatic Medication:— Clinical Procedure: — Specialty: Pediatrics and Neonatology OBJECTIVE: Unusual clinical course BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious virus and is responsible for the current pandemic. CASE REPORT: 31-year-old Hispanic woman in the final week of pregnancy developed mild respiratory symptoms of COVID-19 pneumonia and tested positive for SARS-CoV-2 infection. In response to the potential risks to both the mother and fetus, the American College of Obstetricians and Gynecologists, the American Academy of Pediatrics, and the Centers for Disease Control have developed guidelines which provide a framework for detecting infections early and preventing potential transmission of SARS-CoV-2. Although similar viruses like severe acute respiratory syndrome coronavirus 1 have not demonstrated the ability to cause fetal infection, SARS-CoV-2 is able to bind ACE2 with much higher affinity [11] , thus increasing the probability of transplacental transmission. doi = 10.12659/ajcr.925766 id = cord-263844-ixgejst2 author = Majdic, Gregor title = Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? date = 2020-06-09 keywords = ACE2; SARS summary = title: Could Sex/Gender Differences in ACE2 Expression in the Lungs Contribute to the Large Gender Disparity in the Morbidity and Mortality of Patients Infected With the SARS-CoV-2 Virus? If there is a sex difference in the expression of ACE2 in the lung, this could theoretically explain the gender disparity in COVID-19 disease. Epidemiological data show that a much larger number of men are severely affected by the disease, and there is an even more substantial gender difference in the mortality of patients with COVID-19. Here, I propose a novel hypothesis that not only addresses the significant gender differences in morbidity and mortality due to COVID-19 but also potentially tackles the low morbidity and especially the low mortality in children infected by the SARS-CoV-2 virus. Therefore, I propose the hypothesis that the expression of ACE2 protein is different between males and females and that this sex difference contributes to the gender disparity in morbidity and mortality from the COVID-19 disease. doi = 10.3389/fcimb.2020.00327 id = cord-344217-kci4uw7u author = Majid, Sabhiya title = Managing the COVID-19 Pandemic: Research Strategies Based on the Evolutionary and Molecular Characteristics of Coronaviruses date = 2020-08-25 keywords = ACE2; COVID-19; MERS; SARS; coronavirus summary = Coronavirus disease 2019 (COVID-19), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses (CoVs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-CoV (SARS-CoV) in 2002–2003, Middle East respiratory syndrome-CoV (MERS-CoV) in 2012, and currently this devastating COVID-19. Beta coronaviruses are a subgroup of the coronavirus family, large enveloped positive-sense singlestranded RNA (+ssRNA) viruses able to infect a wide variety of mammals and avian species, causing mainly respiratory or enteric diseases [2] . The disease caused by SARS-CoV-2 has been named COVID-19, a highly transmittable and pathogenic respiratory infection, which has become a public health emergency of international concern as no clinically approved antiviral drug or vaccine is available-though few broad spectrum antiviral drugs and drug combinations in clinical trials have resulted in clinical recovery [23] [24] [25] [26] [27] . doi = 10.1007/s42399-020-00457-z id = cord-274474-u2fdicgz author = Majumder, Joydeb title = Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus date = 2020-10-13 keywords = NLC; SARS; cancer; delivery; drug; lung; nanoparticle summary = The present review summarizes recent advances in the development of nanocarrier based therapeutics for local and targeted delivery of drugs, nucleic acids and imaging agents for diagnostics and treatment of various diseases such as cancer, cystic fibrosis, and coronavirus. [1, 2] Therefore, methods of developing new therapeutic solutions as well as improving the current therapies for the common lung diseases such as asthma, cystic fibrosis, chronic obstructive pulmonary disease, lung cancer, and coronavirus infections remain the main focus in the fields of targeted drug delivery. In this review, we will summarize recent reports on the development of lipid and polymer based nanocarriers for targeted delivery of drugs and nucleic acids for the treatment of lung cancer. In a similar study, we used a complex liposomal drug delivery system containing anticancer drug doxorubicin and both MRP1 and BCL2 targeting antisense oligonucleotides for inhalation treatment in lung cancer cells. doi = 10.1002/adtp.202000203 id = cord-307853-m1q1sjr4 author = Majumder, Satyabrata title = Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model date = 2020-10-16 keywords = MERS; SARS summary = title: Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model In this study we have examined the intrinsic dynamics of the prefusion, lying state of trimeric S protein of these viruses through Normal Mode Analysis using Anisotropic Network Model. MERS-CoV spike shows unique dynamical motion compared to the other two S protein indicated by low RMSIP, spectral overlap and cosine correlation value. A detailed study to explore the intrinsic dynamical motion of the prefusion lying state spike protein trimer is needed for proper understanding of its function from conformation perspective. RMSIP computes quantitative comparison value between the sets of normal modes and expressed as: Structural alignments of the models were done using PyMol. We have computed the eigenvalues of first hundred non-zero normal modes of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike (S) proteins in the lying state ( Fig. 1 ). doi = 10.1016/j.jmgm.2020.107778 id = cord-300018-3uzau7if author = Mak, Gannon C.K. title = The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date = 2020-07-24 keywords = SARS summary = authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong In an attempt to understand the relevance of D614G substitution among COVID-19 patients in Hong Kong, full length S gene sequences from severe and non-severe cases were examined. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 The SARS-CoV-2 Spike Protein D614G doi = 10.1016/j.jcv.2020.104550 id = cord-337799-mc1oqhf4 author = Mak, Gannon CK title = Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus date = 2020-10-29 keywords = RAD; SARS summary = STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using PCR as a reference method. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. Besides RT-PCR, rapid antigen detection (RAD) kits for qualitative determination of SARS-CoV-2 antigen are available. The purpose of this evaluation is to assess analytical sensitivity of the three SARS-CoV-2 RAD kits by means of limit of detection (LOD) using a set of serial tenfold dilution samples; and It means that if we set a cut off by means of ≤day X after symptom onset for performing RAD kits, we will miss another group of specimens having a similar high viral load. doi = 10.1016/j.jcv.2020.104684 id = cord-325213-e6i6buow author = Mak, Ivan Wing Chit title = Risk factors for chronic post-traumatic stress disorder (PTSD) in SARS survivors date = 2010-09-15 keywords = AVN; PTSD; SARS; factor summary = BACKGROUND: Post-traumatic stress disorder (PTSD) is one of the most prevalent long-term psychiatric diagnoses among survivors of severe acute respiratory syndrome (SARS). Previous reported predictors of acute psychiatric complications include sociodemographic variables [e.g., being a health care worker (HCW)] [11] [12] [13] ; illness-related variables [e.g., the severity of disease and the administration of high-dose corticosteroids [11] , lowest level of arterial oxygen saturation (SaO 2 ) during hospitalisation] [14] ; and psychosocial variables including social support, cognitive appraisal and coping style [13, 15] . In the univariate analysis, variables significantly associated with current PTSD in the predictor block included female gender (P=.019), being a HCW(P=.031), pre-SARS chronic medical illness (P=.044) and having AVN as a complication (P=.035) ( Table 1) . Logistic regression of predictor and association factor block Multivariate logistic regression analysis showed that being of the female gender (P=.003), the presence of chronic medical illness before SARS (P=.014) and having AVN as a physical complication (P=.01) were predictors of PTSD at 30 months post-SARS (Table 3) . doi = 10.1016/j.genhosppsych.2010.07.007 id = cord-278649-ge9ike2c author = Makaronidis, Janine title = Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study date = 2020-10-01 keywords = COVID-19; SARS; smell summary = title: Seroprevalence of SARS-CoV-2 antibodies in people with an acute loss in their sense of smell and/or taste in a community-based population in London, UK: An observational cohort study The study aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a community-based population with acute loss of smell and/or taste and to compare the frequency of COVID-19 associated symptoms in participants with and without SARS-CoV-2 antibodies. • Recruited participants completed online questionnaires regarding demographics, their loss of smell and/or taste, and other COVID-19 symptoms, before they had a telemedicine consultation with a healthcare professional who confirmed the history of their symptoms and supervised a test to find out if they had SARS-CoV-2 antibodies. In this community-based cohort study, undertaken during the peak of the COVID-19 outbreak in London, the seroprevalence of SARS-CoV-2 antibodies in participants with new onset loss of sense of smell and/or taste, was 77.6%. doi = 10.1371/journal.pmed.1003358 id = cord-258307-nsdhvc8w author = Maki, Dennis G. title = SARS Revisited: The Challenge of Controlling Emerging Infectious Diseases at the Local, Regional, Federal, and Global Levels date = 2011-10-20 keywords = Hong; Kong; SARS; acute; severe summary = The most recent and perhaps most fearsome emerging infections are the appearance of West Nile virus encephalitis in New York City in 1999 and its rapid spread westward 6 ; inhalation anthrax, deriving from use of Bacillus anthracis spores as a biologic weapon against the US civilian population in 2001 7 ; the global outbreak of severe acute respiratory syndrome (SARS) in 2003 8 ; and the looming threat of pandemic influenza, especially global disease caused by the highly virulent avian subtype A (H5N1). If it is not, the effort will not have been wasted because it is likely that all the planning and resource allocation will prove invaluable for controlling the spread of natural emerging pathogens, such as SARS-CoV or a new strain of influenza virus, which are probably far more likely to pose a serious threat to human and animal health in the United States and worldwide. doi = 10.4065/79.11.1359 id = cord-292152-gmru83ac author = Makrinioti, Heidi title = Intussusception in two children with SARS-CoV-2 infection in children date = 2020-08-08 keywords = CoV-2; SARS summary = This report compares intussusception as likely associated with SARS-CoV-2 infection in infants that presented in Wuhan and London. Based on the data so far, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in children is shown to run a milder course with lower reported mortality rates (1, 2) . However, as the definition of suspected cases does not include presentations with gastrointestinal symptoms only, there is still no clear answer to the question "should we screen for SARS-CoV-2 infection in children who require admission to hospital with gastrointestinal symptoms?". In addition to the fact that most of the presentations of the infection in children are atypical, there is very recent evidence showing that the highest viral shedding is taking place 2 to 3 days before onset of symptoms (https://www.nature.com/articles/s41591-020-0869-5). This brief report describes two cases of intussusception in infants found to be positive with SARS-CoV-2. This report describes two infants with intussusception and SARS-CoV-2 infection. doi = 10.1093/jpids/piaa096 id = cord-277585-evw3pu87 author = Malavolta, Marco title = Exploring the Relevance of Senotherapeutics for the Current SARS-CoV-2 Emergency and Similar Future Global Health Threats date = 2020-04-08 keywords = SARS; SASP; cell; senescence summary = Drugs targeting IL-6 have been included among the potential strategies to inhibit the deleterious consequences of the senescence-associated secretory phenotype (SASP), the secretome produced by senescent cells [31, 32] . The evidence that patients with cancer, hypertension or with smoking habits (conditions associated with a pathological role of cellular senescence) experienced worse outcomes from COVID-19 [71] , further supports the hypothesis that an accumulation of senescent cells may favor the development of severe events during SARS-CoV-2 infection. In the case of dengue virus infection, cellular senescence seems to exert an anti-viral function [64] but other viruses, such as IFV, have evolved mechanisms to increase replication in senescent cells [68] . Clarifying the role of cellular senescence in SARS-CoV infection may additionally provide a strong rationale for the use of senotherapeutics, such as SASP inhibitors, in the management of elderly patients affected by COVID-19. doi = 10.3390/cells9040909 id = cord-346281-sma6e891 author = Maldonado, Valente title = Repositioning of pentoxifylline as an immunomodulator and regulator of the renin-angiotensin system in the treatment of COVID-19 date = 2020-06-09 keywords = Ang; COVID-19; PTX; SARS summary = Pentoxifylline (PTX) is a phosphodiesterase inhibitor that increases cyclic adenosine monophosphate levels, which in turn activate protein kinase, leading to a reduction in the synthesis of proinflammatory cytokines to ultimately influence the renin-angiotensin system (RAS) in vitro by inhibiting angiotensin 1 receptor (AT1R) expression. The rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19 by helping reduce the production of the inflammatory cytokines without deleterious effects on the immune system to delay viral clearance. 5 Overall, the rheological, anti-inflammatory, and renin-angiotensin axis properties of PTX highlight this drug as a therapeutic treatment alternative for patients with COVID-19, which can help reduce the production of the inflammatory cytokines TNF-α, IL-6, IFN-γ, and IL-17 and increase the anti-inflammatory cytokine IL-10. doi = 10.1016/j.mehy.2020.109988 id = cord-289216-g4kqi560 author = Malecki, M. title = Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date = 2020-09-23 keywords = PCR; SARS summary = title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. In this study, two diagnostic laboratories of a tertiary care hospital equipped with different PCR systems validated the available kits on the respective systems for SARS-CoV-2 testing. In order to evaluate the performance of analytical components used for SARS-CoV-2 diagnostic we compared three commercially available RT-PCR kits, six extraction kits and four PCR cyclers in all possible combinations using predefined EQA samples. doi = 10.1101/2020.09.18.20185744 id = cord-344003-oul2hdyq author = Maleki Dana, Parisa title = An Insight into the Sex Differences in COVID-19 Patients: What are the Possible Causes? date = 2020-06-18 keywords = ACE2; SARS; covid-19 summary = Moreover, it is observed that men have a higher risk of developing a severe form of the disease compared to women, highlighting the importance of disaggregated data of male and female COVID-19 patients. ACE2: angiotensin converting enzyme-2 ADAM-17: ADAM metallopeptidase domain-17 AR: androgen receptor CCL: chemokine (C-C motif) ligand cFT: calculated free testosterone CRP: C-reactive protein CXCL: chemokine (C-X-C motif) ligand E2: estradiol ESR: estrogen receptor ICU: intensive care unit IL: interleukin mACE2: myocardial angiotensin converting enzyme-2 NHBE: normal human bronchial epithelial RICU: respiratory intensive care unit sACE2: soluble angiotensin converting enzyme-2 SARS: Severe Acute Respiratory Syndrome SARS-CoV: Severe Acute Respiratory Syndrome Coronavirus TMPRSS2: transmembrane serine protease-2 TT: total testosterone with the virus will die in comparison with men (1.7%/2.8%). Studies of COVID-19 patients have shown that men have a higher risk of developing to the severe form of the disease compared to women. doi = 10.1017/s1049023x20000837 id = cord-328704-m2seavg6 author = Malfertheiner, Peter title = COVID-19: Don''t Neglect the Gastrointestinal Tract! date = 2020-04-29 keywords = GIS; SARS summary = There are 2 main aspects of concern: one being related to gastrointestinal symptoms (GIS) and their influence on the course of disease; the other being related to excretion of the virus (or its RNA fragments) in the patient''s faeces and a possible role for faecal-oral transmission. To prevent faecal SARS-CoV-2 transmission, a group of experts proposed assessing potential donors for the presence of typical COVID-19 symptoms within 30 days prior to donation. It certainly demands for studies on (a) the pathogenesis and impact of direct viral damage of the whole digestive system; and (b) factors contributing to COVID-19-associated diarrhoea with special emphasis on the gut microbiome and anti-diarrhoea management.A special focus should be directed on the role of the digestive system in transmitting the infection, on how to reduce the length of infectiousness, and on which precautions to be taken with regard to this matter. Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms doi = 10.1159/000508289 id = cord-263179-uvq3hzga author = Malik, Zohra R title = A Case of a COVID-19-positive Patient date = 2020-04-09 keywords = China; SARS summary = Virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) or the 2019 novel coronavirus (2019-nCoV) belong to the broad family of coronaviruses (subgenus Sarbecovirus). The HCoV (human coronavirus) is responsible for up to 10% -30% of the upper respiratory tract infections globally [2] . Historically, HCoV''s were only responsible for mild infections until 2002, with the emergence of the severe acute respiratory syndrome (SARS) that started in the Guangdong province of China. Based on available data of SARS and MERS, the Centers for Disease Control and Prevention (CDC) has estimated an incubation period for the COVID-19 to be between two and 14 days [6] . There have been reported cases involving large populations showing people with varying incubation periods and the severity of symptoms based on age and immune status. The patient was placed on airborne, droplet, and contact isolation because of the high suspicion of coronavirus infection. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease doi = 10.7759/cureus.7608 id = cord-293481-bmfj50fb author = Malin, Jakob J. title = Remdesivir against COVID-19 and Other Viral Diseases date = 2020-10-14 keywords = COVID-19; EBOV; MERS; RNA; SARS; remdesivir summary = Remdesivir or GS-5734 is a prodrug of a nucleoside analog with direct antiviral activity against several single-stranded RNA viruses, including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, preliminary data from a randomized placebo-controlled clinical trial showed that remdesivir reduces the time to recovery in patients with COVID-19 (5) , leading to an emergency-use authorization (EUA) by the U.S. Food and Drug Administration (FDA) only 2 days after the first press release from the National Institute of Allergy and Infectious Diseases (NIAID) (6) . There were strong arguments for the antiviral effect of remdesivir against coronaviruses emerging from multiple cell-based in vitro models, including primary human airway epithelial (HAE) cell cultures (25) , and, for MERS-CoV, from a mouse model of pulmonary infection (28) . After the outbreak of SARS-CoV-2 in January 2020, remdesivir was rapidly tested in a Vero E6 cell-based model that made use of direct viral quantification by rtPCR along with the antimalaria and immune-modulating drug chloroquine and known antivirals such as ribavirin and penciclovir. doi = 10.1128/cmr.00162-20 id = cord-270866-olc5r2yx author = Mallet, Jasmina title = Addictions in the COVID-19 era: Current evidence, future perspectives a comprehensive review date = 2020-08-12 keywords = COVID-19; SARS summary = RESULTS: Overall, pathophysiological data showed an increased risk of infections for individuals with Substance Use Disorders (SUD) and a possible protective role of nicotine. An electronic search was conducted in Medline (PubMed interface), using the MESH (Medical Subject Headings) search terms ("coronavirus 2019" OR "COVID-19" OR "2019-nCoV" OR "SARS-CoV-2") AND "substance use" OR "SUD" OR "tobacco smoking" OR "cigarette "OR "smoking" OR "nicotine" / "alcohol" / "cannabis" OR "THC" /"opiates" OR "opioid"; between 2019 and the present time (i.e., June 4, 2020), with language restriction (English or French). Heavy alcohol use (assessed several years before) was not associated with an increased risk of COVID-19 infection or COVID-19 related hospitalization (OR=1.12 (0.93-1.35)). Finally, as all past economic crises were associated with increased long-term alcohol-related problems (especially for men and low socio-economic strata) (de Goeij et al., 2015) , we might expect important effects of the COVID-19 pandemic in the next decade. Prevalence, Severity and Mortality associated with COPD and Smoking in patients with COVID-19: A Rapid Systematic Review and Meta-Analysis doi = 10.1016/j.pnpbp.2020.110070 id = cord-346859-r1v6ir8u author = Mallett, Sue title = At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date = 2020-11-04 keywords = IPD; PCR; SARS summary = BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. Because testing is pivotal to management and containment of COVID-19, we performed an individual participant data (IPD) systematic review of emerging evidence about test accuracy by anatomical sampling site to inform optimal sampling strategies for SARS-CoV-2. Previous studies have established that in COVID-19 infection, viral loads typically peak just before symptoms and at symptom onset [4] and estimated false negative test results over time since exposure from upper respiratory tract samples [2] . • Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). doi = 10.1186/s12916-020-01810-8 id = cord-266983-hpwebkbi author = Mallhi, Tauqeer Hussain title = Risks of Zoonotic Transmission of COVID-19 During Eid-Ul-Adha in Pakistan date = 2020-07-27 keywords = SARS summary = P akistan is expected to celebrate Eid-ul-Adha, an annual religious festival during which millions of farm animals, including sheep, goats, cows, buffalo, and camels are sacrificed, in the end of July or early August this year. 2 Since a recent investigation found the potential of zoonotic transmission of coronavirus disease (COVID-19) by farm animals, 3 we felt inclined to underscore the risks of virus transmission from humans to animals due to various activities surrounded by the festive celebration in Pakistan. It is pertinent to mention that ACE2s in animals, which are abundantly sacrificed during the Eid-Ul-Adha, have the ability to contract SARS-CoV-2, like humans. We believe that risks of zoonotic transmission of COVID-19 should be considered during the preparation of festive celebrations, and immediate measures must be taken to avoid any possible surge in COVID-19 cases during the Eid-Ul-Adha. doi = 10.1017/dmp.2020.278 id = cord-291624-fod0eyuj author = Malone, Robert W. title = COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms date = 2020-06-22 keywords = COVID-19; SARS; cell; famotidine; histamine; patient summary = We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H (2) activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. Patients with COVID-19 disease can present with a range of mild to severe non-speci c clinical signs and symptoms which develop two to fourteen days after exposure to SARS-CoV-2. The most likely mechanisms of actions include: via antiviral activity, via novel human targets, or via the on-target mechanism described in the current FDA market authorization-famotidine is a histamine receptor H 2 antagonist (and inverse agonist). To assess the possibility that famotidine may inhibit SARS-CoV-2 infection by other routes, a Vero E6 cell-based assay was performed to compare median tissue culture infectious doses (TCID50/mL) of famotidine, remdesivir, and hydroxychloroquine ( Figure 2 ). In both of these studies, the observed non-in ammatory edema in early-stage COVID-19 pulmonary disease is consistent with histamine release by mast cells. doi = 10.21203/rs.3.rs-30934/v2 id = cord-130351-w9mij6c6 author = Mamidala, Estari title = In silico identification of clinically approved medicines against the main protease of SARS-CoV-2, causative agent of covid-19 date = 2020-04-25 keywords = COVID-19; SARS; drug summary = In the present study, we report the potential inhibitory activity of some FDA approved drugs against SARS-CoV-2 main protease by molecular docking study to investigate their binding affinity in protease active site. Docking studies revealed that drug Oseltamivir (anti-H1N1 drug), Rifampin (anti-TB drug), Maraviroc, Etravirine, Indinavir, Rilpivirine (anti-HIV drugs) and Atovaquone, Quinidine, Halofantrine, Amodiaquine, Tetracylcine, Azithromycin, hydroxycholoroquine (anti-malarial drugs) among others binds in the active site of the protease with similar or higher affinity. 11 The free energy (DG) binding of SARS-CoV-2 viral protease with the selected FDA approved drugs was created by means of this molecular docking package. Oseltamivir and Zanamivir, two FDA approved drugs docked with SARS-CoV-2 main protease and obtained binding energy is −7.39 kcal/mol and -3.88 kcal/mol respectively (Table-2 Figure 2 ). doi = nan id = cord-319664-gyktrd36 author = Mancini, Fabiola title = Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date = 2020-06-18 keywords = RNA; SARS summary = Finally, to evaluate the performance of molecular assays a standard curve was generated by 10-fold dilutions of SARS-CoV-2 RNA, isolated and extracted at Istituto Superiore di Sanità in Rome, Italy, and quantified by a well-established copy number of RNA synthetic E gene (Wuhan coronavirus, EVAg, www. All specimens were also manually extracted and tested for the presence of SARS-CoV-2 by in-house rt-Realtime PCR and the 2019-nCoV TaqMan RT-PCR Kit. In particular, we investigated the RNA availability and virus detection using both the purified and thermal/non-extractive procedures also with this commercial kit because it is based on the same primers, probes and assays developed by the CDC and used in the inhouse molecular method. This study corroborates our results for in-house rt-Real Time PCR, showing a lower sensitivity of the heat treatment (range ΔCT value of 0.5-1.0) when compared with purified samples, but, dissimilar to our findings, a total inhibition was found by the commercial kit RealStar SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), where all positive samples failed in the detection of Sars-CoV-2 [14] . doi = 10.1080/22221751.2020.1775500 id = cord-312971-r9sggqh8 author = Mancino, Enrica title = A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 date = 2020-04-29 keywords = SARS; child summary = title: A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020 We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Key words: Community Acquired Pneumonia, SARS-CoV-2, COVID-19, virus Community Acquired Pneumonia (CAP) remains the leading cause of mortality and morbidity in children worldwide [1] . Surprisingly, only a small number of cases of COVID-19 has been described in children, suggesting that SARS-CoV-2 infection in the paediatric population is unusual [6] . Our aim was to describe viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children under 14 years of age. However, the clinical severity score was higher in RSV patients and hRV was found in 9/17 cases (53%) in coinfection, consistent with the notion that hRV is very frequently detected in respiratory infections J o u r n a l P r e -p r o o f during childhood. doi = 10.1016/j.jcv.2020.104385 id = cord-268085-vpzrk8u7 author = Mandal, Amrendra title = Gastrointestinal Manifestations in COVID-19 Infection and Its Practical Applications date = 2020-06-21 keywords = SARS; covid-19 summary = This outbreak is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is also commonly known as COVID-19. We reviewed the mechanisms, clinical manifestation, impact on pre-existing liver diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. This article aims to review the mechanisms, clinical manifestation, impact on pre-existing digestive diseases, and recommendations endorsed by the several GI societies for the management and prevention of its transmission. Clinical characteristics of hospitalized patients with SARS-CoV-2 and hepatitis B virus co-infection Exploring the mechanism of liver enzyme Abnormalities in patients with novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. doi = 10.7759/cureus.8750 id = cord-293655-2ab7wdsk author = Mandic-Rajcevic, S. title = Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy) date = 2020-05-08 keywords = SARS; covid-19; symptom summary = Objective To study the source, symptoms, and duration of infection, preventive measures, contact tracing and their effects on SARS-CoV-2 epidemic among healthcare workers (HCW) in 2 large hospitals and 40 external healthcare services in Milan (Italy) to propose effective measures to control the COVID-19 epidemic among healthcare workers. Most prominent symptoms include fever, dry cough, headache, sore throat and sneezing, although a growing number of reports underline asymptomatic and patients with mild symptoms having the same viral load as symptomatic patients and spreading the infection in the general population and among healthcare workers (HCW) (2) (3) (4) (5) . A much smaller sample of workers (N=10), commonly found among close contacts but absent from the hospital for other reasons, reported their daily symptoms even in the days leading to the positive NF swab. doi = 10.1101/2020.05.03.20082818 id = cord-297630-eabtzfd0 author = Manganaro, Marco title = First considerations on the SARS-CoV-2 epidemic in the Dialysis Units of Piedmont and Aosta Valley, Northern Italy date = 2020-04-10 keywords = Aosta; SARS summary = No SARS-COV-2 cases were observed in the only Paediatric Nephrology Unit in the Region (having in charge 4 hemodialysis, 4 peritoneal dialysis, and 35 transplanted The members of the Working group of the Piedmont and Aosta Valley Section of the SIN are listed in "Acknowledgements" section. In adults, 156 SARS-COV-2 cases were recorded: 130 RRT patients including 98 in hemodialysis, 4 in peritoneal dialysis, 26 transplanted, and 2 waiting for transplantation, and 26 health care workers (6 physicians, 18 nurses and 2 members of auxiliary staff). This is much higher than the rates for the general population in Piedmont and Aosta Valley (7782 subjects affected by SARS-CoV-2, i.e., 0.17% of the population), with an odds ratio of 13.43, 95% CI 11.27 to 16.00; z score p < 0.0001 for RRT patients, and of 12.80 (95% CI 8.67 to 18.89; z score p < 0.0001) for staff. doi = 10.1007/s40620-020-00732-1 id = cord-299024-jkqdzt87 author = Mangner, Norman title = Paraneoplastic syndrome and SARS-CoV-2 – incremental effect of two thrombogenic conditions? date = 2020-10-21 keywords = SARS; patient summary = We present the case of a patient with a non-bacterial thrombotic aortic valve endocarditis experiencing severe thromboembolic complications and an acute right internal carotid artery occlusion in the context of a paraneoplastic syndrome and an asymptomatic SARS-CoV-2 infection, despite treatment with different and overlapping anticoagulant medication. This case describes a patient with non-bacterial thrombotic aortic valve endocarditis that developed despite treatment with a factor-Xa-inhibitor and who subsequently suffered a myocardial infarction and two strokes within a short period of time in the context of a paraneoplastic syndrome and asymptomatic SARS-CoV-2 infection. Paraneoplastic syndromes are often linked to increased thrombogenicity; however, non-bacterial thrombotic aortic valve endocarditis is rare even in the situation of cancer. 3 This case highlights the many-sided effects of paraneoplastic syndromes and SARS-CoV-2 infection in patients being already at increased risk for thrombotic complications due to underlying disease. doi = 10.1016/j.cjco.2020.10.010 id = cord-274715-dcs1rgd0 author = Mani Mishra, Pushpendra title = Serum albumin-mediated strategy for the effective targeting of SARS-CoV-2 date = 2020-04-24 keywords = SARS; covid-19 summary = Novel coronavirus (NCoV-19), also known as SARS CoV-2, is a pathogen causing an emerging infection that rapidly increases in incidence and geographic range, is associated with the ever-increasing morbidity and mortality rates, and shows sever economic impact worldwide. We are suggesting here a strategy for the COVID-19 treatment that could be effective in curing the patients in the current scenario when no efficient medicine or Vaccine is currently available, and Clinicians solely depend upon the performing trials with drugs with known antiviral activities. If the albumin is used to stabilize and deliver the EGCG and Curcumin for targeting the intracellular virus components in combination with the drug that could block the virus fusion and/or entry to a cell, this strategy might represent an effective way of treating the SARS CoV-2 infection. doi = 10.1016/j.mehy.2020.109790 id = cord-278939-z6kiee09 author = Mani, Janice S. title = Natural product-derived phytochemicals as potential agents against coronaviruses: a review date = 2020-04-30 keywords = EC50; MERS; SARS; antiviral summary = As previous work has highlighted the potential of traditional Chinese medicines as a source of potential novel drugs (Ling, 2020) , we have not included details on such studies investigating the antiviral activity of remedies comprising portions of numerous plant species in this review. (2020) virtually screened 83 compounds found in Chinese traditional medicines for activity against the RNA-dependent RNA polymerase of SARS-CoV-2, identifying theaflavin, an antioxidant polyphenol, as a potential inhibitor. Several authors have utilised virtual computer docking models to screen for potential compounds that could bind to and inhibit key proteins present in SARS-CoV (Liu and Zhou, 2005; Toney et al., 2004; Wang et al., 2007) , highlighting the potential antiviral activity of compounds such as sabadinine and aurantiamide acetate. Several large in vitro screening studies searching for inhibitory activity of naturally occurring compounds against SARS-CoV have been performed, mainly on Chinese medicinal herbs (Li et al., 2005; Wang et al., 2003) . doi = 10.1016/j.virusres.2020.197989 id = cord-313427-6y4zvrmn author = Mani, Nandita S title = Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date = 2020-06-16 keywords = COVID-19; SARS summary = Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. doi = 10.1093/cid/ciaa761 id = cord-278509-k62bsk9b author = Manikandan, Natesan title = Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? date = 2020-09-12 keywords = SARS summary = title: Are social distancing, hand washing and wearing masks can mitigate the transmission of COVID-19? 7 In a new modeling study in Singapore, Joel R Koo and colleagues found that the combined approach of physical distancing interventions, quarantine, school closure, and workplace distancing, is the most effective at reducing the transmission of SARS-CoV-2. 8 A report from the United States suggested that social distancing interventions can give communities vital time to mitigate the spread of COVID-19 pandemic. Nevertheless, to overcome this global threat, combination of preventive measures like social distancing, hand washing and wearing face masks are the important key practices to mitigate the transmission of COVID-19 in the community. The role of community-wide wearing of face mask for control of Coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2 Impact of self-imposed prevention measures and short-term governmentimposed social distancing on mitigating and delaying a COVID-19 epidemic: A modelling study doi = 10.1016/j.vacun.2020.09.001 id = cord-274008-p3st70u3 author = Mann, E. R. title = Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis date = 2020-06-16 keywords = COVID-19; June; SARS; patient; preprint summary = Here we report the outcome of a longitudinal immune profiling study in hospitalised patients during the peak of the COVID-19 pandemic in the UK and show the relationship between immune responses and severity of the clinical presentation. Although, as reported previously 4 , a higher neutrophil to lymphocyte ratio (NLR) on hospital admission was observed in those patients whose disease trajectory was ultimately severe, whereas there were no appreciable differences observed in monocytes (figure 1A, 1B and table 1). Longitudinal analysis revealed that in the majority of patients (70%) (irrespective of severity) T cell frequencies in whole blood increased prior to hospital discharge, while neutrophil frequencies reciprocally decreased (figure 1E). Severe COVID-19, on the other hand, was associated with monocytes displaying increased expression of the cell cycle marker, Ki67 (normally <5% in healthy peripheral blood), irrespective of whether monocytes were stimulated or not (figure 3C and appendix 6C), which strongly correlated with hospital data for CRP (figure 3C). doi = 10.1101/2020.06.13.20127605 id = cord-033334-p7szd86k author = Mann, Jaclyn Kelly title = The potential of lactoferrin, ovotransferrin and lysozyme as antiviral and immune-modulating agents in COVID-19 date = 2020-10-08 keywords = COVID-19; SARS; bovine; effect; lactoferrin; lysozyme summary = Enhanced phagocytic activity as well as cytokine production of macrophages Enhanced intestinal immune responses: dendritic cell maturation, Th1/Th2 balance restored and humoral immunity promoted [77, 78] Peptides Anti-inflammatory Downregulates IL-6 and TNF-␣ and myeloperoxidase activity in peritonitis Binds to angiotensin II receptor type 1 to inhibit angiotensin II pro-inflammatory activity ACE inhibitory activity (antihypertensive) [79] [80] [81] [82] Intact Iron-binding activity* Sequestering free iron [83] Intact and peptides Antioxidant* Sequestering free iron Free radical scavenging [79, 84] Lysozyme Intact and peptides Antiviral Inhibits viral entry by binding to cell receptors or virus -cationic and hydrophobic nature is required rather than enzymatic activity Binds nucleic acids Inhibits virus-induced cell fusion Affects cell signaling, including NF-B pathway, to influence susceptibility to infection [85] [86] [87] [88] Intact and/or peptides Antibacterial Hydrolyzes cell wall of gram-positive bacteria (enzyme activity) Insert into and form pores in negatively charged bacterial membranes [40] † Specific anticoronavirus activity has been demonstrated: inhibits SARS-CoV cell entry by binding to HSPGs; inhibits entry and postentry steps of SARS-CoV-2 replication and elevates interferon-stimulated genes in SARS-CoV-2-infected cells. doi = 10.2217/fvl-2020-0170 id = cord-293732-rxd1lyi7 author = Manoj, M.G. title = Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date = 2020-08-01 keywords = COVID-19; SARS; virus summary = Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. doi = 10.1016/j.envres.2020.110001 id = cord-322388-c2nymio9 author = Manopo, Ivanus title = Evaluation of a safe and sensitive Spike protein-based immunofluorescence assay for the detection of antibody responses to SARS-CoV date = 2005-01-31 keywords = IFA; SARS; Spike summary = To study the diagnostic potential of our Spike protein-based immunoassay based on protein C expressed by recombinant baculovirus in Sf-9 cell, a panel of sera containing 21 SARS-positive samples collected 7-76 days after the onset of SARS symptom, 42 non-SARS serum samples, and 100 normal serum samples were subjected to our Spike protein-based IFA test. The immunoblot showed a 32-kDa band, indicating that protein C expressed in a baculovirus system is antigenic for antibody detection of SARS-CoV infection (represented by Fig. 1a) . Fig. 2 shows representative IFA results in the detection of positive serum samples using our Spike protein-based IFA, compared to the conventional IFA performed by SGH and the commercial SARS IFA kit (EUROIMMUN). In this study, we are the first to show that the immunogenic protein C-based IFA is a sensitive and specific method for detecting SARS-CoV infection. doi = 10.1016/j.jim.2004.10.012 id = cord-258548-1u7v1nlr author = Mansueto, Gelsomina title = Can COVID 2019 disease induces a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? date = 2020-06-26 keywords = ACE2; COVID-19; SARS; cardiovascular; disease; patient summary = Only one case of cardiac tamponade in a 47-year-old man SARS-CoV-2 infected without cardiovascular risk is reported in the literature as a complication of myocarditis and pericarditis (29) . Large and more recent studies have reported that previous myocardial infarction, diabetes, J o u r n a l P r e -p r o o f dyslipidaemias, hypertension, and other cardiovascular risk factors can predispose to an acute ischemic event in respiratory virus infections such as recently reported during the pandemic COVID-19 disease (34, 35, 36) . It is known that patients with cardiovascular disease have a higher risk of a thrombo-embolic event as it is known that all viral infections have a potential role in disseminated intravascular coagulation J o u r n a l P r e -p r o o f (DIC) The endothelial damage, the blood flow turbulence, and hypercoagulability are the basis of the mechanism. There is no substantial data to say that anti-RAAS, ACE inhibitors, statins increase the risk of cardiovascular damage in COVID patients. doi = 10.1016/j.prp.2020.153086 id = cord-318492-uu1p1rgi author = Mansueto, Gelsomina title = COVID-19: Brief Check Point Through The Pathologist''s Eye (autopsy archive) date = 2020-08-28 keywords = COVID-19; Coronavirus; SARS summary = The autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (DAD), myocarditis, acute myocardial infarction (AMI), and disseminated intravascular coagulation (DIC); these aspects are not only in COVID-19 but also in other viral infections and associated sepsis. In this brief summary, I would like to induce the reader''s reflection to the fact that coronavirus appears already before the pandemic in many texts of medical doctrine and that the pathological findings related to lung and multi-organ damage are described similar to those induced by other viral pathogens both from the same or different family. The autopsy pathologists can confirm that many deaths are due to complications from viral infections especially in subjects with comorbidities and they can also confirm that the aspects often observed are diffuse alveolar damage (DAD), cardiac damage from myocarditis or acute myocardial infarction (AMI), or even disseminated intra-vascular coagulation (DIC); these findings are also present in sepsis associated with various viral infections. doi = 10.1016/j.prp.2020.153195 id = cord-298075-lzuxlzb0 author = Mao, Kang title = Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology? date = 2020-03-23 keywords = SARS summary = However, an alternative method utilizing wastewater-based epidemiology (WBE), may provide an effective approach to predict the potential spread of the infection by testing for infectious agents in wastewater, which has been approved as an effective way to trace illicit drugs, and obtain information on health, disease, and pathogens. Therefore, it is critical to develop efficient transportable and robust analytical tools to accurately and quickly trace low-level SARS-CoV-2 sources through WBE to confirm these suspected cases and screen asymptomatic infected cases without centralized laboratories. We believe that in the case of asymptomatic infections in the community or people are not sure whether they are infected or not, rapid and real-time community sewage detection through paper analytical devices can determine whether there are SARS-CoV-2 carriers in the area in a timely manner to enable rapid screening, quarantine, and prevention. The potentially infected patient will also benefit from paper analytical device tracing SARS-CoV-2 sources with WBE, providing information for the correct and timely treatment of COVID-19. doi = 10.1021/acs.est.0c01174 id = cord-272423-o5yinjcz author = Mao, Xiao-Yuan title = iPSCs-Derived Platform: A Feasible Tool for Probing the Neurotropism of SARS-CoV-2 date = 2020-08-25 keywords = SARS summary = In a recent article, Yuen and colleagues present the first experimental evidence of SARS-CoV-2 infection in the human central nervous system using induced pluripotent stem cells (iPSCs)-derived platform including human neural progenitor cells, neurospheres, and three-dimensional brain organoids (Yuen, K.Y., and Huang, J.D. et al. Recently, Yuen and colleagues used induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and three-dimensional (3D) brain organoids for evaluation of SARS-CoV-2 infection in the brain. provided the first experimental evidence showing that SARS-CoV-2 could replicate in hNPCs and neurospheres and also the novel virus could productively infect cortical neurons and NPCs in 3D brain organoids ( Figure 1 ). In summary, the data provided by Yuen and colleagues offer useful experimental evidence supporting that SARS-CoV-2 can infect the human brain using an iPSCs-derived platform including hNPCs, neurospheres, and 3D human organoids. doi = 10.1021/acschemneuro.0c00512 id = cord-292650-i95upz10 author = Marafini, Irene title = LOW FREQUENCY OF COVID-19 IN INFLAMMATORY BOWEL DISEASES date = 2020-06-13 keywords = SARS summary = The risk of infection or death due to Covid-19 in patients with inflammatory bowel diseases (IBD) is unknown at this stage. We here examined the frequency of symptoms/signs suggestive of Covid-19 in IBD patients and assessed the risk of SARS-CoV-2 infection in IBD. Cumulative incidence of SARS-CoV-2 infection in IBD was calculated dividing the positive cases by the overall population of IBD patients enrolled for the study. Although, we need more robust epidemiological data to draw a conclusion regarding the incidence rate of Covid-19 in IBD, our findings suggest that IBD patients are not at increased risk of Covid-19 as compared with the general population. It is likely that the incidence of SARS-CoV-2 infection in our IBD population is underestimated as the majority of the patients did not underwent rhino-pharyngeal swab. published recently by Norsa and colleagues, who reported no case of SARS-CoV-2 infection in a cohort of IBD patients living in a high-risk area of Northern Italy (7). doi = 10.1016/j.dld.2020.06.007 id = cord-340085-ywg4rhnn author = Maras, J. S. title = Multi-Omics integration analysis of respiratory specimen characterizes baseline molecular determinants associated with COVID-19 diagnosis. date = 2020-07-07 keywords = July; SARS; covid-19 summary = Quantitative proteomics identified significant increase in 6 SARS-CoV-2 proteins along with ACE2 in the respiratory specimen of COVID-19 positive patients compared to negative patients (p<0.05, Figure 1C , H1N1 samples did not enrich any or associated proteins). /2020 Diagnostic accuracy: Amongst the identified DEP''s, mean decrease in the accuracy (calculated by random forest; 1000 trees) was highest for MX1 (MX Dynamin like GTPase 1) and WARS (Tryptophan--tRNA ligase) making them the most important proteins for segregating COVID-19 positive patients from negative or H1N1 patients ( Figure Together these findings showed that COVID-19 positive patients have virus mediated hyper immune activation involving monocytes and neutrophils, deregulated oxygen transport, increased fluid shear stress, bacterial invasion of the epithelial cells and glucose metabolism. Viral infection are also known for metabolic reprograming of host (Thaker et al., 2019) and proteome analysis of the respiratory specimen showed that there is significant increase in proteins associated to glucose metabolism suggesting that SARS-CoV-2 induces energy metabolism (Supplementary Figure 18 ). doi = 10.1101/2020.07.06.20147082 id = cord-352365-b9cmviny author = Marchetti, Monia title = COVID-19-driven endothelial damage: complement, HIF-1, and ABL2 are potential pathways of damage and targets for cure date = 2020-06-24 keywords = ARDS; SARS; covid-19; endothelial summary = This review also highlights potential targets for prevention and therapy of COVID-19-related organ damage and discusses the role of marketed drugs, such as eculizumab and imatinib, as suitable candidates for clinical trials. Also, C3a complement fraction plays a relevant role in the pathogenesis of infection-related lung injury: high serum C3a predicts evolution to ARDS [9, 10] , while both C3a and C5a increase endothelial permeability and activate endothelial cells, thereby increasing the expression of adhesion molecules and cytokines [11, 12] , and the distal complement activation product C5 b-9 triggers intracellular fluxes of calcium in epithelial and endothelial cells. Apoptosis of human pulmonary microvascular endothelial cell may be chronically triggered by inflammation, such as in COPD, or acutely induced by ARDS; the latter is mediated by Bruton kinase (BTK), IL-17, and macrophage stimulating-1, while IL-35 seems protective [41] [42] [43] [44] . doi = 10.1007/s00277-020-04138-8 id = cord-330465-16j5vm7h author = Marciniec, Krzysztof title = Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date = 2020-08-05 keywords = BVM; HIV-1; SARS; compound; figure summary = The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. In order to check the potential toxic properties of the compounds 3-5, docking study of phosphate betulin derivatives to cellular proteins was carried out. According to the results of docking (Table S1 ) obtained from AutoDock Vina, four potential SARS-CoV-2 inhibitors (BVM, betulinic acid, and compounds 4 and 6) were selected based on a lower negative dock energy value. doi = 10.3390/biom10081148 id = cord-354972-nc496v6s author = Margolin, Emmanuel title = Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date = 2020-09-10 keywords = Africa; BCG; COVID-19; HIV-1; SARS; South; vaccine summary = As of 8 August 2020, there have been over 1.2 million confirmed cases of COVID-19 in Africa, with 29,833 deaths reported (Africa CDC) There is concern that the pandemic may pose an even greater risk to countries in Africa owing to their weak health-care infrastructure, large burden of co-infections, including HIV-1 and tuberculosis, and ongoing outbreaks of emerging and re-emerging infections such as Ebola virus (Democratic Republic of Congo) and Lassa haemorrhagic fever (Nigeria) that will divert much-needed resources away from the fight against COVID-19 (ref. Given the optimistic development timeline of 12-18 months before any vaccines could be available for widespread use, it is clear that these efforts will not Box 1 | Potential impact of climate on SArS-coV-2 dissemination the comparatively low incidence of coronavirus disease-2019 (COviD19) in africa has raised the possibility that climate could influence the spread of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2). doi = 10.1038/s41579-020-00441-3 id = cord-353551-un4jw7aw author = Margoni, Monica title = Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic date = 2020-10-12 keywords = SARS summary = title: Natalizumab safety in paediatric-onset multiple sclerosis at the time of SARS-Cov-2 pandemic The authors, considering the impact of MS on brain atrophy and the high risk POMS have to develop cognitive impairment and evolve in the secondary progressive disease phase, recommend to keep in mind that MS in children/teens is a severe, highly active form of disease, and suggest the early use of highly effective second-line disease modifying drugs rather than the first-line injectable ones. May these drugs expose POMS to a greater risk of SARS-Cov-2 infection as well as to a symptomatic and potentially more severe COVID-19 or to longterm autoimmune severe adverse events? NTZ treatment does not seem not to expose POMS to a higher risk of SARS-Cov-2 infection. No evidence of disease activity including cognition (NEDA-3 plus) in naive pediatric multiple sclerosis patients treated with natalizumab Disease Modifying Therapies and COVID-19 Severity in Multiple Sclerosis doi = 10.1177/2055217320966346 id = cord-353576-f29kmtot author = Maricic, T. title = A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date = 2020-06-26 keywords = RNA; SARS summary = We then tested 1 l of mouthwash from each of the 20 individuals using two RT-qPCR kits advertised to allow direct detection of SARS-CoV-2 from nasopharyngeal swabs: Luna Universal Probe (NEB, Ipswich, USA) and PrimeDirect (Takara, Kyoto, Japan) as well as another kit, SuperScript III with Platinum Taq (Invitrogen, Waltham, USA). To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations. In the first scheme, the samples were tested individually using the direct RT-qPCR protocol and the results were evaluated and reported back to the facility by 7 p.m. To detect any inhibition that the mouthwash samples may introduce into the RT-qPCR reactions, we added a synthesized control RNA that was quantified in parallel with SARS-CoV-2 by a probe . doi = 10.1101/2020.06.24.20139501 id = cord-324265-j3v3i8vm author = Marietta, Marco title = COVID-19, coagulopathy and venous thromboembolism: more questions than answers date = 2020-07-11 keywords = COVID-19; LMWH; SARS; VTE summary = The severity of the derangement of coagulation parameters in COVID-19 patients has been associated with a poor prognosis, and the use of low molecular weight heparin (LMWH) at doses registered for prevention of venous thromboembolism (VTE) has been endorsed by the World Health Organization and by Several Scientific societies. In these patients, low molecular weight heparin (LMWH) or unfractionated heparin (UFH) at doses registered for prevention of venous thromboembolism (VTE) seemed to be associated with a lower risk of death [10] and is currently recommended by the World Health Organization [11] and by several scientific societies [12] [13] [14] [15] [16] [17] [18] (Table 1) . doi = 10.1007/s11739-020-02432-x id = cord-326833-boxgt4kb author = Marimuthu, Janakiram title = HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date = 2020-07-07 keywords = HIV; SARS summary = We conducted a retrospective, record based case series including three males, 2 females and 1 transgender PLHA co‐infected with SARS CoV‐2 in the Indian state of Tamil Nadu. Through literature search in PubMed and World Health organization'' (WHO) database on COVID-19, we obtained 5 case reports, and 5 case series on PLHA infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). Hence, we conducted a retrospective, record based case series on the PLHA who were infected with SARS CoV-2, in the Indian state of Tamil Nadu. 5 Our study reports that the clinical features of COVID-19 co-infection among PLHA in South India is mild, and the clinical outcomes are favorable. Further studies including greater number of patients should be done, to better understand the epidemiology, clinical outcomes and appropriate treatment modalities in the HIV-COVID 19 co-infection. COVID-19 in patients with HIV: clinical case series doi = 10.1002/jmv.26271 id = cord-315696-43wmazxa author = Marinaki, Smaragdi title = A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients’ Lives and Allografts date = 2020-09-16 keywords = SARS; covid-19; patient; recipient summary = title: A Systematic Review of COVID-19 Infection in Kidney Transplant Recipients: A Universal Effort to Preserve Patients'' Lives and Allografts Kidney transplant (KTx) recipients have been recently classified by the Center for Disease Control and Prevention (CDC) as a high-risk group for severe COVID-19 [2] . All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. All major adverse outcomes (O) of COVID-19 infection, i.e., hospitalization, intensive care unit (ICU) admission, mechanical ventilation (MV), acute kidney injury (AKI), acute respiratory syndrome (ARDS), and death, were recorded as were recovery and discharge. A Case Report of Oligosymptomatic Kidney Transplant Patients with COVID-19: Do They Pose a Risk to Other Recipients? doi = 10.3390/jcm9092986 id = cord-254079-pvl44u4d author = Marinella, Mark A. title = COVID-19 pandemic and the stethoscope: don''t forget to sanitize date = 2020-04-11 keywords = SARS summary = Indirect pathogen transmission from inanimate objects is of potential concern not only for the general public, but also for healthcare professionals whose hands come into frequent contact with hard surfaces. Viral pathogens have also been isolated on hard surfaces in the healthcare setting, 3,4 but have not received as much attention as a risk for nosocomial and person-to-person transmission until very recently with the COVID-19 pandemic. 4 The severe fever with thrombocytopenia syndrome (SFTS) virus, an emerging fatal viral hemorrhagic fever in East Asia, has been recovered from stethoscopes and other hard surfaces in patient rooms who were diagnosed with SFTS, also raising concern for nosocomial transmission of highly pathogenic viruses. Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination doi = 10.1016/j.hrtlng.2020.03.017 id = cord-275336-lnhkux0m author = Marino Gammazza, Antonella title = Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 date = 2020-08-04 keywords = COVID-19; SARS summary = title: Human molecular chaperones share with SARS-CoV-2 antigenic epitopes potentially capable of eliciting autoimmunity against endothelial cells: possible role of molecular mimicry in COVID-19 Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the cause of COVID-19 disease, has the potential to elicit autoimmunity because mimicry of human molecular chaperones by viral proteins. We compared viral proteins with human molecular chaperones, many of which are heat shock proteins, to determine if they share amino acid-sequence segments with immunogenic-antigenic potential, which can elicit cross-reactive antibodies and effector immune cells with the capacity to damage-destroy human cells by a mechanism of autoimmunity. We identified the chaperones that can putatively participate in molecular mimicry phenomena after SARS-CoV-2 infection, focusing on those for which endothelial cell plasma-cell membrane localization has already been demonstrated. We compared the amino acid sequences of all the SARS-CoV-2 proteins with the sequences of human chaperones to determine if they share segments with immunogenic-antigenic potential that might be causing autoimmunity. doi = 10.1007/s12192-020-01148-3 id = cord-289076-8iymevqm author = Marjanovic, Zdravko title = The relevance of psychosocial variables and working conditions in predicting nurses’ coping strategies during the SARS crisis: An online questionnaire survey date = 2007-08-31 keywords = SARS; nurse summary = Three multiple regression analysis revealed that the model we evolved—including higher levels of vigor, organizational support, and trust in equipment/infection control initiative; and lower levels of contact with SARS patients, and time spent in quarantine—predicted to lower levels of avoidance behavior, emotional exhaustion, and state anger. We hypothesized that greater vigor, organizational support, and trust in equipment/infection control, and less contact with SARS patients and time spent in quarantine, would predict to lower levels of emotional exhaustion, state anger, and avoidance behavior. The five independent measures (predictors) were three psychosocial variables, vigor, organizational support, and trust in equipment/ infection control initiatives; and two working conditions variables, contact with SARS patients, and time spent in quarantine. State anger was positively correlated to avoidance behavior, contact with SARS patients, and greater time in quarantine; and negatively related to vigor, organizational support, and trust in equipment/ infection control initiatives. doi = 10.1016/j.ijnurstu.2006.02.012 id = cord-255170-bp3irxlh author = Mark, John title = SARS coronavirus: Unusual lability of the nucleocapsid protein date = 2008-12-12 keywords = SARS; pro; tein summary = The exper i ments used prep a ra tions of recombinant N-pro tein from which the His-tag had not been enzy mat i cally removed; thus, cal cu la tion of the resul tant pro tein/ pep tide masses must take into con sid er ation the pres ence of the His-tag (an addi tional 11 amino acid sequence). A spe cific pro te ol y sis assay was then devel oped using pep tides con tain ing the SR-rich region cor re spond ing to the SARS N-pro tein cleav age site. Taken together, the results from the FITC-labelled casein, the refold ing, and the FRET (EDANS/DAB CYL) detec tion exper i ments strongly sug gest that the SR-spe cific cleav age of N-pro tein is not the result of a con tam i nat ing pro te ase activ ity. Cell type-spe cific cleav age of nucle o cap sid pro tein by effec tor casp as es dur ing SARS coro na vi rus infec tion doi = 10.1016/j.bbrc.2008.09.153 id = cord-320663-xypg6evo author = Market, Marisa title = Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies date = 2020-06-23 keywords = IFN; MERS; SARS; cell; covid-19; infection; natural; patient summary = A common feature of coronavirus infections is that significant morbidity and mortality is associated with lung injury and acute respiratory distress syndrome resulting from an exaggerated immune response, of which NK cells are an important component. Natural Killer (NK) cells are a key component of the innate immune system and are critical in the response to many viral infections in humans and animal models (1) (2) (3) . Altogether these studies show that during acute CoV infection, inflammatory monocyte-macrophages and neutrophils accumulate in the lungs and produce cytokines and chemokines that induce the activation and migration of lymphocytes, including NK cells, to the lungs, where they could be one of the main producers of IFN-γ (148). Studies have reported that patients infected with SARS-CoV-2 have lower levels of circulating NK cells and these express a greater level of inhibitory receptors (e.g., NKG2A) while producing less IFN-γ (127, 129, 130) . doi = 10.3389/fimmu.2020.01512 id = cord-310753-sv88b0dt author = Marks, M. title = Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study date = 2020-10-27 keywords = SARS; covid-19 summary = By the time of performing this search, various 57 authors had reported on retrospective analyses of clusters of index cases and their corresponding contacts, 58 as well as series of patients who developed symptomatic Covid-19 disease after PCR positive result. The objective of this study was to evaluate transmission dynamics of SARS-CoV-2 in the context of a trial 109 of post-exposure prophylaxis and evaluate the influence of baseline variables-including viral load of the 110 index cases and exposed contacts-to transmission, development of symptomatic disease, and the 111 incubation period. Also, after excluding 215 contacts who were PCR positive at the first study visit, we found no association between the viral load of 216 the index case and the time to onset of incident SARS-CoV-2 infection (HR 1.01 95% CI 0.83-1.23). doi = 10.1101/2020.10.27.20220277 id = cord-263970-9w6ciglv author = Marquez-Miranda, Valeria title = Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date = 2020-10-22 keywords = SARS; cavity; ion summary = SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. Here we used this dimeric structure to perform full atom molecular dynamic simulations and electrostatic potential calculations to ask questions concerning the dimers'' stability and whether ions could be populating specific regions of the channel. To assess the impact of the ion occupancies described above, we obtained the electrostatic potential maps for the ORF3a channel for the initial configuration, and the last frame, at the end of a trajectory of 500 ns of the molecular dynamics simulations, by employing the Poison-Boltzmann approach implemented in the APBS package [12] . This analysis shows that the entry of Cl-ions through the inter-subunit tunnel into the central polar cavity and the accumulation of K+ ions at the cytosolic domain''s surface changed the channel''s electrostatic profile. doi = 10.1101/2020.10.22.349522 id = cord-273913-xem3alih author = Marraha, Farah title = A Review of the Dermatological Manifestations of Coronavirus Disease 2019 (COVID-19) date = 2020-08-11 keywords = COVID-19; SARS; case; patient summary = In this review, we discuss these various cutaneous manifestations and skin problems related to personal protective equipment, as well as different cutaneous anti-COVID-19 drug-associated reactions. e first case infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was reported in Wuhan, China, in late November 2019. ese skin lesions can guide clinicians for diagnosis if the patients present other COVID-19 symptoms; however, viral infection cannot be the only cause; mediated inflammatory responses and drug reactions can also be suspected. e aim of our literature review is to report the various cutaneous manifestations described to date associated with COVID-19, the skin problems related to personal protective equipment, and the different cutaneous anti-COVID-19 drug reactions [6, 7] . e frequency of the skin lesions associated with COVID-19 infection varies according to the series; in a Chinese study of 1099 positive cases, the incidence was only 0.2%, while in an Italian series of 88 patients it was 20.4% [42] . doi = 10.1155/2020/9360476 id = cord-252761-ro5tj0tx author = Marriott, Deborah title = Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date = 2020-08-25 keywords = SARS summary = title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent''s Hospital and associated screening clinics, Sydney, NSW. Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. We report the prevalence of SARS-CoV-2 and other respiratory pathogens including co-infection, and evaluate the A c c e p t e d M a n u s c r i p t 4 temporal pattern of respiratory infections alongside the introduction, and subsequent relaxation, of physical distancing measures. Limited data have been reported on co-infection between SARS-CoV-2 and other respiratory viruses. In conclusion, the introduction of multiple public health measures to minimise SARS-CoV-2 transmission in Australia from mid to late-March 2020 had a major impact on the prevalence of all respiratory viral infections highlighting the effectiveness of this approach. doi = 10.1093/cid/ciaa1256 id = cord-335122-8s3bcyo8 author = Marshall, Steve title = COVID-19: What do we know? date = 2020-09-21 keywords = COVID-19; CoV-2; N95; SARS summary = 44, 45, [47] [48] [49] The amount of viable SARS-CoV-2 in droplet nuclei remains unclear, but in subjects infected with other respiratory viruses, such as influenza, experiments comparing coughing and breathing suggest an equivalent production of viral RNA and replication-competent virus, detected at close range (< 12 inches). 78 In situations where healthcare workers wearing personal protective equipment (PPE) attend to patients with COVID-19 and do not perform medical AGPs, direct airborne transmission of replicationcompetent SARS-CoV-2 has not been confirmed. 79 The results of hospital studies evaluating aerosolization of body fluids and respiratory droplets of SARS-CoV-1 infected patients generated during certain medical AGPs (tracheal intubation, non-invasive ventilation, bronchoscopy, etc.), suggest that airborne transmission of SARS-CoV-2 may be possible during these procedures. Currently there are no studies reporting airborne viable (replication-competent) SARS-CoV-2 virus J o u r n a l P r e -p r o o f in hospital settings where infected patients are cared for, but not subjected to medical AGPs, by healthcare workers wearing surgical masks. doi = 10.1016/j.ajodo.2020.08.010 id = cord-266536-4frv2vb7 author = Martel, Jan title = Could nitric oxide help to prevent or treat COVID-19? date = 2020-05-06 keywords = SARS; nitric summary = In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. In view of the pandemic caused by the novel coronavirus (SARS-CoV-2), clinical trials have been designed to examine the effects of inhaled nitric oxide in COVID-19 subjects. During the 2002-2003 severe acute respiratory syndrome (SARS) epidemic, also caused by a coronavirus, inhaled NO was tested in six SARS patients, producing beneficial effects that include decreased pulmonary hypertension, improved arterial oxygenation, and reduced spread and density of lung infiltrates [5] . In addition, limiting the lifestyle factors that reduce endogenous NO levels in the airways-such as mouth breathing and smoking-may also help to reduce SARS-CoV-2 viral load and symptoms of COVID-19 pneumonia by promoting more efficient antiviral defense mechanisms in the respiratory tract. doi = 10.1016/j.micinf.2020.05.002 id = cord-270645-tzctvs9q author = Martelletti, Luigi title = Air Pollution and the Novel Covid-19 Disease: a Putative Disease Risk Factor date = 2020-04-15 keywords = SARS summary = This study analyzed the correlation between the increment of the API (Air Pollution Index) and the rate of fatality due to SARS across 5 regions in China. In 2017, Ciencewicki and Jaspers conducted an epidemiological analysis regarding air pollution and respiratory viral infections which noted positive correlation between the high level of particulate matter (PM) in some urban areas and mortality due to cardiovascular and respiratory conditions. A recent study from the SIMA (Società Italiana di Medicina Ambientale) reported that the specificity of the high spread of the contagious virus in some areas of Northern Italy is likely to be linked to air pollution conditions. The above studies show that air pollutants, such as particulate matter, nitrogen dioxide, and carbon monoxide, are most likely direct to facilitate the longevity of virus particles in favorable climate conditions. Air pollution and case fatality of SARS in the People''s Republic of China: an ecologic study doi = 10.1007/s42399-020-00274-4 id = cord-299810-e57pwgnx author = Martelloni, Gabriele title = Modelling the downhill of the Sars-Cov-2 in Italy and a universal forecast of the epidemic in the world date = 2020-07-01 keywords = Italy; Sars summary = Finally we study the behavior of the ratio infected over swabs for Italy, Germany and USA, and we show as studying this parameter we recover the generalized Logistic model used in [1] for these three countries. The parameters r 0 represents the rates of growth of epidemic, K is the carrying capacity for the classical logistic model, α is a constant in order to have a power low initial growth before LD, β is the exponent of the second term of equation 1 that represents the influence of asymptomatic; δ,a correction of the quadratic term of logistic, and γ are the constant parameters considering the influence of the government measures 1 , K f is a proportionality constant between deaths and total number of infected, while t d and t r are the delays of deaths and recoveries respect to infected respectively; the constant A represents the contribution of asymptomatic people as introduced in [1] and finally t 0 is the time of LD start. doi = 10.1016/j.chaos.2020.110064 id = cord-342013-k54u2q0d author = Martenot, Antoine title = Favorable outcomes among neonates not separated from their symptomatic SARS-CoV-2-infected mothers date = 2020-11-03 keywords = COVID-19; SARS summary = 1, 2 Although neonates born of mothers infected with SARS-CoV-2 during pregnancy are seemingly vulnerable to infection, studies have found that they were not at a high risk for severe infection and were very rarely affected by COVID-19. This strategy involved preservation of continuous mother-infant proximity with specific hygienic measures, breast milk as the main source of feeding, early discharge with home isolation, and a structured follow-up with hospital-assisted home care. Breastfeeding may protect against the horizontal transmission of SARS-CoV-2, as specific antibodies against this virus have been found in the breast milk of a COVID-19-infected mother. 19 Our results support early postnatal proximity, despite many mothers worldwide being separated from their newborn infants during the COVID-19 pandemic. Even during the COVID-19 pandemic, safely maintaining familycentered perinatal care and continuing the promotion of bonding between neonates and their SARS-CoV-2-positive mothers appear possible, as these newborns are very rarely infected and, if infected, show only mild symptoms. doi = 10.1038/s41390-020-01226-3 id = cord-140318-xtx8hl14 author = Martin, Alexandra title = High-sensitivity COVID-19 group testing by digital PCR date = 2020-06-03 keywords = PCR; SARS summary = Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. The results for SARS-CoV-2 detection by RT-dPCR in groups of 8 samples, detailed in Tables 1 and 2 , are in concordance with the reference individual RT-PCR testing for 52 groups (corresponding for 416 samples), out of which 32 were RT-PCR negative groups and 20 groups contained at least one RT-PCR+ sample. In this work, we assessed the sensitivity and specificity of group testing combined with digital PCR for SARS-CoV-2 detection. doi = nan id = cord-286343-s8n1ldol author = Martin, Javier title = Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date = 2020-10-09 keywords = England; PCR; RNA; SARS summary = We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory (data not shown). doi = 10.3390/v12101144 id = cord-307227-x6xketcn author = Martin, William R. title = Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 date = 2020-09-10 keywords = COVID-19; SARS; protein; toremifene summary = Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19. 2, 3 In our initial network-based drug repurposing study, 4 we identified toremifene, another selective estrogen receptor modulator (SERM), as a strong candidate for the potential treatment of COVID-19. A drug repurposing study for SARS-CoV-1 5 indicated a low 50% effective concentration (EC 50 ) for toremifene, and noted that estrogen signaling may not be involved in the inhibitory pathway, similar to that of inhibition of Ebola. Future work will be needed to confirm these results; optimally, the determination of a cocrystal structure with Journal of Proteome Research pubs.acs.org/jpr Article NSP14 and/or the spike glycoprotein from SARS-CoV-2 with toremifene would be solved. doi = 10.1021/acs.jproteome.0c00397 id = cord-307109-nz8qvuw6 author = Martinez, Miguel Angel title = Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus date = 2020-04-21 keywords = LPV; MERS; SARS summary = The previous epidemics of infections by high-morbidity human coronaviruses, such as SARS-CoV in 2003 and the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, prompted the characterization of compounds that could be potentially active against the currently emerging novel coronavirus, SARS-CoV-2. In addition, a combination of the human immunodeficiency virus type 1 (HIV-1) protease inhibitors lopinavir/ritonavir and interferon beta (LPV/RTV–IFN-β) was shown to be effective in patients infected with SARS-CoV. To predict new zoonotic coronavirus jumps across species and to understand the rate of virus spread among people, it is crucial to determine whether SARS-CoV-2 is mutating to improve its binding to human receptors for infection. Clinical observations in animals and humans showed that MERS-CoV infections were mediated by both virus replication and host inflammatory responses. However, therapeutic treatment with human monoclonal antibodies did not protect against the severe disease or the loss of lung function induced by MERS-CoV in animal models (20) . doi = 10.1128/aac.00399-20 id = cord-303745-wx3udkee author = Martinez-Fleta, P. title = SARS-Cov-2 cysteine-like protease (Mpro) is immunogenic and can be detected in serum and saliva of COVID-19-seropositive individuals date = 2020-07-18 keywords = July; Mpro; SARS summary = Using ELISA tests, coating several SARS-CoV-2 proteins produced in vitro, we describe that COVID-19 patients make high titre IgG, IgM and IgA antibody responses to the Cys-like protease from SARS-CoV-2, also known as 3CLpro or Mpro, and it can be used to identify individuals with positive serology against the coronavirus. Since this study evaluated, for the first time, whether coronavirus-infected individuals could 121 generate an antibody response against the Cys-like protease, MPro, other SARS-CoV-2 122 proteins, commonly used in serology tests, were produced, for comparison. 1101 individuals with high specificity and sensitivity 153 A cohort of 36 COVID-19 patients (PCR+) and 33 healthy donors was recruited at La Princesa 154 University Hospital, Madrid (Table 1 ) and ELISA assays were performed to detect Mpro-, as 155 well as RBD-and NP-, specific antibodies of the IgG, IgA and IgM subclasses in sera ( Figure 156 3). doi = 10.1101/2020.07.16.20155853 id = cord-349313-2gupfqnl author = Martinez-Perez, Clara title = Citation Network Analysis of the Novel Coronavirus Disease 2019 (COVID-19) date = 2020-10-21 keywords = COVID-19; China; Coronavirus; SARS; publication summary = This study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. Methods: The search for publications was carried out through the Web of Science database using terms such as "COVID-19" and "SARS-CoV-2" for the period between January and July 2020. The search of publications was carried out using the Web of Science (WOS) database with the following search terms: "COVID-19", "SARS-CoV-2", "The Coronavirus Disease 2019" and "Corona Virus Disease 2019". Moreover, the most common keywords used in Chinese journals were "COVID-19", "SARS-CoV-2", "Prevention and control", "Traditional Chinese Medicine", "Computed tomography", "Epidemic", "Public health", "MERS", "Pneumonia" and "Male". In this group, the different articles analyze the viral transmission of SARS-CoV-2, the most frequent symptoms (fever, cough, diarrhea, etc.) and experimental treatment methods such as chloroquine phosphate (Figure 7 ). doi = 10.3390/ijerph17207690 id = cord-326393-gxy1w0qk author = Martino, Marcello Di title = CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD date = 2020-04-29 keywords = COVID-19; SARS summary = title: CIRUGÍA ELECTIVA DURANTE LA PANDEMIA POR SARS-CoV-2 (COVID-19): ANÁLISIS DE MORBIMORTALIDAD Y RECOMENDACIONES SOBRE PRIORIZACIÓN DE LOS PACIENTES Y MEDIDAS DE SEGURIDAD Desde que se produjeron los primeros casos de infección por SARS-CoV-2 (COVID-19) a finales de diciembre de 2019 en Wuhan (China), el crecimiento exponencial de esta enfermedad ha llevado a una pandemia, declarada como tal por la Organización Mundial de la Sanidad (OMS) el 11 de marzo J o u r n a l P r e -p r o o f 2020 (1, 2) . Se analizaron la edad, sexo, estado funcional definido según la escala ECOG (21), antecedentes personales, diagnóstico, tipo de intervención quirúrgica, momento en que se confirmó la infección por SARS-CoV-2, el tratamiento requerido para la misma (Tabla 1), la gravedad de la infección respiratoria según la BRCSS (20) y las complicaciones postoperatorias según la clasificación de Dindo-Clavien (19) . doi = 10.1016/j.ciresp.2020.04.029 id = cord-334688-0i1pu8wc author = Martos Pérez, F. title = Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date = 2020-08-19 keywords = COVID-19; PCR; SARS summary = Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. In this study, we describe the first cases of COVID-19 in patients hospitalized in a general hospital and analyze the characteristics upon admission associated with in-hospital death. Our model shows that a medical history of cardiopathy, LDH levels ≥345 IU/L upon admission, and age ≥65 years are associated with greater in-hospital mortality due to COVID-19. Predictors of Mortality for Patients with COVID-19 Pneumonia Caused by SARS-CoV-2: A Prospective Cohort Study Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. doi = 10.1016/j.rceng.2020.05.010 id = cord-343845-suoy3ojr author = Martín, Vicente title = Prevalencia de la Infección por SARS-CoV-2 en médicos y enfermeras de Atención Primaria y Residencias de Ancianos del Área de Salud de León y Factores asociados date = 2020-06-06 keywords = COVID-19; SARS summary = ABSTRACT Objective: To evaluate the prevalence and associated factors with SARS-CoV-2 infection in general practitioners and nurses of primary care centers and nursing homes in the health area of León (Spain). The aim of this study is to evaluate the prevalence and factors associated with SARS-CoV-2 infection in General Practitioners and Nurses of primary care centers and nursing homes in the health area of León. The most relevant results of this study indicate that the observed prevalence of SARS-CoV-2 infection in the health workers analyzed is 5.9% (CI95% 4.4%-8.0%), being higher in nursing home workers compared to primary care centers (9.5% vs. Our results indicate that a high number of professionals remain susceptible to SARS-CoV-2 infection and therefore protective measures should be taken, not only in primary care, as the main contact with the health system, but also in nursing homes. doi = 10.1016/j.semerg.2020.05.014 id = cord-291436-cu5o8ipw author = Martínez-Hernández, Fernando title = Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals date = 2020-10-05 keywords = ACE2; CoV-2; SARS; TMPRSS2 summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect animals, however, the whole range of potential hosts is still unknown. This work makes an assessment of wildlife susceptibility to SARS-CoV-2 by analyzing the similarities of Angiotensin Converting Enzyme 2 (ACE2) and Transmembrane Protease, Serine 2 (TMPRSS2) —both recognized as receptors and protease for coronavirus spike protein— and the genetic variation of the viral protein spike in the recognition sites. Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is causing the biggest pandemic 52 of this century, and could potentially infect between 30 to 40% of the world''s populations (De 53 Soto et al., 2020) . Due to its high transmission rate and mortality, researches around the world 54 are trying to get some insight about its origin through the analysis of related-virus genes 55 sequences in humans and animals (Lu R et al., 2020) , and looking for Angiotensin-Converting 56 doi = 10.1016/j.pecon.2020.09.008 id = cord-313571-umcbulcw author = Martínez-Murcia, Antonio title = In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date = 2020-05-05 keywords = SARS summary = title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. As the number of genomes available rapidly expanded during last January, the GPS™ CoVID-19 230 dtec-RT-qPCR Test was based on a more specific target for SARS-CoV-2 detection, being this 231 company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. doi = 10.1101/2020.04.27.065383 id = cord-269045-i7vijtol author = Martínez‐Murcia, A. title = Comparative in silico design and validation of GPS™ CoVID‐19 dtec‐RT‐qPCR test date = 2020-07-29 keywords = GPS; SARS summary = An illustration of the mismatching of primers/probe sequences of the GPS CoVID-19 dtec-RT-qPCR Test, respect of the SARS-CoV-2, Bat SARS-like-CoV, SARS-CoV, Bat-CoV, and Pangolin-CoV groups is shown in Fig. 2 . Finally, the results obtained in the diagnostic validation of the GPS TM CoVID-19 dtec-RT-qPCR Test, carried out by the Instituto de Salud Carlos III (ISCIII), are shown in Table 3 . As the number of genomes available rapidly expanded during last January, the GPS TM CoVID-19 dtec-RT-qPCR test was based on a more specific target for SARS-CoV-2 detection, being this company one of the pioneers marketing a PCR-kit for the CoVID-19 worldwide. Finally, the kit GPS TM COVID-19 dtec-RT-qPCR Test showed the highest number of mismatches (i.e. 19-48) for all coronavirus sequences described so far, including these of Pangolin-CoV, which showed a range of 19-31 mismatches. doi = 10.1111/jam.14781 id = cord-308424-crvnzr44 author = Mascarenhas, Victor Hugo Alves title = Care recommendations for parturient and postpartum women and newborns during the COVID-19 pandemic: a scoping review date = 2020-08-10 keywords = COVID-19; SARS; woman summary = Normal childbirth: • Mild clinical conditions; • There are no contraindications, especially due to a lack of evidence on vertical transmissions; • If pregnant women infected with SARS-CoV-2* present spontaneous labor and good cervical conditions, normal childbirth is advised, provided that the health service has the apparatus necessary to promote appropriate precautions; • To shorten the duration of the second stage of labor, directed pushing is recommended and parturient women are supposed to wear a surgical mask. This decision should be taken together with the mother and health workers involved in care delivery; • There is a risk of mothers transmitting SARS-CoV-2* to their NB † through respiratory droplets at the time of breastfeeding, even when wearing a surgical mask; • Women who opt not to breastfeed during the period of the disease should be encouraged to express breast milk to feed their NB † ; doi = 10.1590/1518-8345.4596.3359 id = cord-304280-2a84u4tm author = Masic, Izet title = Public Health Aspects of COVID-19 Infection with Focus on Cardiovascular Diseases date = 2020-03-17 keywords = COVID-19; Health; SARS; patient summary = METHODS: We used method of descriptive analysis of the published papers with described studies about Corona virus connected with CVD, and, also, Guidelines proposed by World Health Organization (WHO) and European Society of Cardiology (ESC), and some other international associations which are included in global fighting against COVID-19 infection. Early COVID-19 case reports suggest that patients with underlying conditions are at higher risk for complications or mortality -up to 50% of hospitalized patients have a chronic medical illness (40% cardiovascular or cerebrovascular disease). The clinical effects of pneumonia have been linked to increased risk of CVD up to 10-year follow-up (11) and it is likely that cases infected via respiratory virus outbreaks will experience similar adverse outcomes. The European Medicines Agency (EMA) has issued a statement advising that patients continue treatment with angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs), despite widely circulated reports that the agents could worsen coronavirus disease (20) . doi = 10.5455/msm.2020.32.71-76 id = cord-282853-l0c69uul author = Massad, Eduardo title = Forecasting versus projection models in epidemiology: The case of the SARS epidemics date = 2005-03-30 keywords = SARS summary = In this work we propose a simple mathematical model for the analysis of the impact of control measures against an emerging infection, namely, the severe acute respiratory syndrome (SARS). The model provides a testable hypothesis by considering a dynamical equation for the contact parameter, which drops exponentially with time, simulating control measures. In contrast, with control measures, which reduce the contact rate to about 25% of its initial value, the expected final number of cases is reduced to 1778 in Hong Kong and 226 in Toronto (Canada). The aim of this work is to provide a projection of what would have happened with the course of severe acute respiratory syndrome (SARS) epidemic if the universal procedures to reduce contact were not implemented in the affected areas. The model projects that, in the absence of control, the final number of cases would be 320,000 in Hong Kong and 36,900 in Toronto (Canada). doi = 10.1016/j.mehy.2004.09.029 id = cord-345033-guisyj11 author = Massarotti, Claudia title = SARS‐CoV‐2 in the semen: where does it come from? date = 2020-06-13 keywords = SARS summary = This finding re‐opened the discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and safety of fertility treatments during the pandemic period [1]. 2 A recent report by Li et al., described the presence of SARS-CoV-2 in semen samples of six patients, 3 including two subjects who were recovering from the clinical disease. This finding re-opened the 4 discussion on possible male genital tract infection, virus shedding in semen, sexual transmission and 5 safety of fertility treatments during the pandemic period [1] . Regarding Coronaviruses, there is evidence that 35 MERS-CoV binds to the host cell receptor dipeptidyl peptidase 4 (DPP4), which is broadly expressed 36 on prostate cells [12] . The ACE2 Expression in Sertoli cells and Germ cells may cause male reproductive disorder after SARS-CoV-2 Infection. Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues doi = 10.1111/andr.12839 id = cord-340590-7jql1ftj author = Massullo, Domenico title = Mountain Rescue During the COVID-19 Outbreak: Considerations and Practical Implications date = 2020-09-23 keywords = SARS summary = The COVID-19 pandemic causes several issues during rescue 48 operations in the wilderness environment due to concern for viral contagiousness during prolonged 49 close interaction between rescuers and victims. The key points during rescues are the protection of operators and patients from 59 infection and disinfection of materials and vehicles used during outdoor operations. In addition, each rescuer, before giving their availability to participate in 65 rescue operations, should perform a self-check through a COVID-19 screening questionnaire 66 ( Figure 1 ). In conclusion, during the COVID-19 pandemic, protocols for mountain rescue services should be 85 reassessed in order to protect both rescuers and victims from possible contagion. Characteristics of and important lessons from the coronavirus disease 144 2019 (COVID-19) outbreak in China: summary of a report of 72 SARS-CoV-2 in patients with COVID-19 Protection 155 and disinfection policies against SARS-CoV-2 (COVID-19) doi = 10.1016/j.wem.2020.09.003 id = cord-313957-hviv5zar author = Masucci, Maria Grazia title = Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection date = 2020-08-01 keywords = BPLF1; IFN; SARS; dna; isg15; rig summary = UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. UbL-specific proteases can reverse the modification, supplementing the cellular pools of free UbLs. The attachment of a Ub moiety to the N-terminal Met1 or to an internal Lys residue of the previous Ub (K6, K11, k27,K29,K33,K48 or K63) results in the formation of topologically different poly-Ub chains that, upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. doi = 10.3390/biom10081137 id = cord-255290-p64apuk1 author = Matheeussen, Veerle title = International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 date = 2020-07-09 keywords = EQA; SARS summary = title: International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020 We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. Between 6 April and 20 May 2020, each participating laboratory received a blinded panel of eight samples, with five samples containing serial 10-fold dilutions (2.30-5.30 dPCR log10 RNA copies/mL, one duplicated) of non-infectious SARS-CoV-2-positive supernatant obtained from Vero cell culture, two samples with cell culture-derived common human coronavirus (HCoV-NL63, HCoV-OC43) and one negative control with transport medium only. In parallel with the EQA study, laboratories were surveyed to assess their challenges in implementing and executing molecular testing capacity and throughput for SARS-CoV-2 detection, also in April and May 2020. doi = 10.2807/1560-7917.es.2020.25.27.2001223 id = cord-274708-w6gmscv4 author = Mathewson, Alison C. title = Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2 date = 2008-11-17 keywords = SARS summary = Although in different groups, the coronaviruses severe acute respiratory syndrome-coronavirus (SARS-CoV) and NL63 use the same receptor, angiotensin converting enzyme (ACE)-2, for entry into the host cell. (2007) showed that incubation of a tagged form of the RBD with cell lines expressing a number of natural and synthetic ACE-2 variants indicated that the ACE-2 contact residues critical for binding both SARS-CoV and NL63 S overlap (Li et al., 2007) . To investigate CoV S protein binding to ACE-2 in a unified format, we produced soluble and cell-bound versions of the two S proteins through the use of baculovirus expression vectors designed for secretion of proteins as Fc-tagged fusion proteins (Chen et al., 2007) or, separately, displayed on the insect cell surface following tagging with the VSV G protein transmembrane (TM) domain (Chapple & Jones, 2002 ) (see Supplementary Fig. S1 , available in JGV Online). Identification of residues in the receptor-binding domain (RBD) of the spike protein of human coronavirus NL63 that are critical for the RBD-ACE2 receptor interaction doi = 10.1099/vir.0.2008/003962-0 id = cord-288271-p074ffpt author = Mathies, D. title = A Case of SARS‐CoV‐2‐pneumonia with successful antiviral therapy in a 77‐year‐old male with heart transplant date = 2020-04-21 keywords = COVID-19; SARS; patient summary = In this report, we present a 77‐year old patient with a heart transplant under relevant immunosuppressive therapy who was tested positive for SARS‐CoV‐2 after several days of dyspnoea, dry cough and light general symptoms. All rights reserved Diagnosis: SARS-CoV-2-Infection with viral pneumonia in a patient with heart transplant due to coronary artery disease with ischemic cardiomyopathy In this case the combination of radiologic signs of viral pneumonia and the supposed high-risk state of severe immunosuppression led to the decision to start an antiviral therapy immediately after receiving the positive rtPCR-results although the patient presented only mild symptoms. [13] A second question is whether patients with a solid organ transplant who receive immunosuppressive medication are at greater risk for a severe manifestation of a SARS-CoV 2-Infection or might even benefit from a reduced immunologic reaction. For SARS-CoV 2 we found two cases of patients with a heart transplant of which one had only mild manifestations and one required mechanical ventilation but survived [9] . doi = 10.1111/ajt.15932 id = cord-269377-ylgyvxtd author = Matos, Ana R. title = COVID-19 Associated Central Nervous System Vasculopathy date = 2020-06-02 keywords = SARS; review summary = Stroke in the setting of viral vasculopathy has been described with other viruses, such as varicella zoster virus (VZV) or 1 ; more recently, it has also been associated with other coronavirus, namely, Middle East respiratory syndrome coronavirus, during the outbreak in Saudi Arabia in 2012. The imaging presentation of multiple lesions involving deep and subcortical white matter, as well as deep gray nuclei, with marked restricted diffusion of some, has been described in the setting of VZV vasculopathy. Primary angiitis of the central nervous system was also considered, but the absence of obvious large vessel irregularities, normal CSF cellular count, and concomitant SARS-CoV-2 infection led us consider a COVID-19-related vasculopathy as the most probable diagnosis, potentially induced by misdirected immune mediated-vasoconstriction of medium-/ small-sized arteries; we believe this represents a new imaging presentation of a SARS-CoV-2-related complication. doi = 10.1017/cjn.2020.109 id = cord-302115-r39ser2c author = Matricardi, Paolo Maria title = The first, holistic immunological model of COVID‐19: implications for prevention, diagnosis, and public health measures date = 2020-05-02 keywords = COVID-19; SARS; patient; severe summary = We propose here the first model, explaining how the outcome of first, crucial 10‐15 days after infection, hangs on the balance between the cumulative dose of viral exposure and the efficacy of the local innate immune response (natural IgA and IgM antibodies, Mannose Binding Lectin ). The delayed and strong adaptive immune response (high affinity IgM and IgG antibodies) that follows, causes severe inflammation and triggers mediator cascades (complement, coagulation, and cytokine storm) leading to complications often requiring intensive therapy and being, in some patients, fatal. All rights reserved We focused on humoral components and, in particular on natural antibodies and MBL, to ascertain whether these players of the innate immunity fit all the epidemiological and clinical pre-conditions presented in the last three months by SARS-CoV-2. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for Accepted Article This article is protected by copyright. doi = 10.1111/pai.13271 id = cord-277873-4819g00y author = Matson, M. Jeremiah title = Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum date = 2020-09-17 keywords = SARS summary = We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. We describe SARS-CoV-2 stability in human nasal mucus and sputum under different environmental conditions. The t 1/2 we report here for SARS-CoV-2 in surface nasal mucus and sputum at 21°C/40% (Table) is considerably shorter than what we found in culture media under similar conditions (t 1/2 6.8 [95% CI 5.6-8.2] hours) (3). Nevertheless, with our experimental protocol and initial titer, we predicted that SARS-CoV-2 would remain infectious in nasal mucus and sputum on surfaces for >10-12 hours even in warm, humid conditions. In addition, reduced surface stability of SARS-CoV-2 in human nasal mucus and sputum in warmer and more humid conditions might result in decreased virus transmission, and climatic influence on SARS-CoV-2 transmission rates might eventually drive seasonal outbreak dynamics in a postpandemic period (7) , similar to other respiratory viruses (e.g., influenza A virus or human coronavirus OC43). doi = 10.3201/eid2609.202267 id = cord-318934-dxipu00r author = Matsuyama, Shutoku title = Enhancement of SARS-CoV Infection by Proteases date = 2006 keywords = CoV; SARS summary = Moreover, SARS-CoV entry from the cell surface mediated by proteases was a 100-fold more efficient infection than entry through endosomes. However, no S2 band was detected in SARS-CoV infected cells treated with proteases that failed to induce fusion. 3 stated that SARS-CoV is able to enter cells directly from their surface, if receptor-bound virus is treated with trypsin and other proteases that induce fusion. Treatment of VeroE6 cells with bafilomycin was shown to suppress SARS-CoV infection via the endosomal pathway to less than 1/100 (Fig. 2) . Pseudotype VSV bearing SARS-CoV S protein infection was also facilitated in bafilomycin-treated VeroE6 cells after treatment with proteases that induce fusion of SARS-CoV infected cells. These observations suggest that proteases that facilitate SARS-CoV entry from the cell surface support efficient SARS-CoV infection. Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry doi = 10.1007/978-0-387-33012-9_42 id = cord-336793-9bbyu1qx author = Matsuyama, Shutoku title = The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date = 2020-08-24 keywords = SARS summary = title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells We screened steroid compounds to obtain a drug expected to block host inflammatory responses and MERS-CoV replication. Ciclesonide, an inhaled corticosteroid, suppressed replication of MERS-CoV and other coronaviruses, including SARS-CoV-2, the cause of COVID-19, in cultured cells. Eight consecutive passages of 43 SARS-CoV-2 isolates in the presence of ciclesonide generated 15 resistant mutants harboring single amino acid substitutions in non-structural protein 3 (nsp3) or nsp4. These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. In the present study, we found that an inhaled corticosteroid, ciclesonide suppresses replication of coronaviruses, including beta-coronaviruses (MHV-2, MERS-CoV, SARS-CoV, and SARS-CoV-2) and an alpha-coronavirus (HCoV-229E) in cultured cells. The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral doi = 10.1101/2020.08.22.258459 id = cord-319248-ynoxec7k author = Matsuyama, Toshifumi title = An aberrant STAT pathway is central to COVID-19 date = 2020-10-09 keywords = COVID-19; Fig; IFN; ORF6; PAI-1; SARS; STAT3 summary = In SARS-CoV-2-infected cells, a positive feedback loop established between STAT3 and plasminogen activator inhibitor-1 (PAI-1) may lead to an escalating cycle of activation in common with the interdependent signaling networks affected in COVID-19. After a careful review of the scientific literature, we realized that the SARS-CoV-2-mediated inhibition of IFN and STAT1, and the subsequent shift to a STAT3dominant signaling network (see below), could result in almost all of the clinical features of COVID-19. Molecular patterns derived from SARS-CoV-2-associated molecules, such as ssRNA, dsRNA, and viral proteins, bind to host PRRs and trigger the activation of signal transducers and transcription factors that drive the production of IFN-I and proinflammatory cytokines and chemokines. Therefore, in COVID-19, EGFR signaling may become an alternative pathway that activates STAT3 specifically when the lung is damaged while the production of IFN-I is severely impaired by SARS-CoV-2 infection [12] . doi = 10.1038/s41418-020-00633-7 id = cord-281113-t450ccnq author = Mattar, Rejane title = Breath tests for gastrointestinal diseases - will it be safe to conduct breath tests after the COVID-19 pandemic? date = 2020-06-16 keywords = SARS summary = Viral RNA was detected in respiratory droplets and aerosols from coronavirus-, influenza virus-, and rhinovirus-infected patients (9) . The test carries risks of contamination to the healthcare worker collecting the breath samples and to the patients, as the ultrafine aerosol droplets may also carry SARS-CoV-2 and remain airborne for long periods, and could be inhaled (5) . pylori infection diagnosis, the patient blows into a plastic mouthpiece attached to an aluminized bag. Although the test lasts 20 minutes, it carries the risk of contamination by SARS-CoV-2 in the aerosol droplets generated by the exhaled air (5) . Other analytical assays for SARS-CoV-2 diagnosis include antigen detection by lateral flow assays that are fast and low cost; nonetheless, these tests lack good sensitivity early in the infection stage (11) . Digestive Symptoms in COVID-19 Patients With Mild Disease Severity: Clinical Presentation, Stool Viral RNA Testing, and Outcomes doi = 10.6061/clinics/2020/e2092 id = cord-346246-2phtdgh4 author = Mattar, Shaikh Abdul Matin title = Subacute thyroiditis associated with COVID-19 date = 2020-08-25 keywords = COVID-19; SARS; thyroiditis summary = doi = 10.1136/bcr-2020-237336 id = cord-302983-3v5bc80z author = Matterne, Uwe title = Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review date = 2020-10-10 keywords = Health; MERS; SARS summary = title: Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: Rapid scoping review OBJECTIVE: The aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). METHODS: We searched major databases and included publications of quantitative and qualitative studies in English and German on any type of research on the functional, critical and communicative domains of HL conducted in the context of the three outbreaks in the general population. Therefore, the aim of this rapid scoping review, for which only studies from the general population were considered, was to describe the extent of existing research on HL in the context of previous coronavirus outbreaks (SARS-CoV-1, MERS-CoV and SARS-CoV-2). doi = 10.1016/j.pec.2020.10.012 id = cord-029419-b0w9nomq author = Matthews, Adam title = Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date = 2020-07-20 keywords = Honigsbaum; SARS; covid-19; virus summary = Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to ''fix'' ourselves and the planet, including new viral outbreaks. doi = 10.1007/s42438-020-00170-z id = cord-308093-m40czdsr author = Matthews, M. M. title = COVID-19 serological survey using micro blood sampling date = 2020-10-13 keywords = October; SARS; preprint summary = During August 2020, we carried out a serological survey among students and employees at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, testing for the presence of antibodies against SARS-CoV-2, the causative agent of COVID-19. We used a FDA-authorized 2-step ELISA protocol developed by the Krammer Lab in combination with at-home self-collection of blood samples using a custom low-cost finger prick-based capillary blood collection kit. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. Among our controls, we found 26 strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in 27 the anti-SARS-CoV-2-S ELISA. . https://doi.org/10.1101/2020.10.09.20209858 doi: medRxiv preprint 48 Serological surveys which detect the presence of antibodies against SARS-CoV-2 49 antigens can provide important information to the government for issuing health care 50 guidelines. doi = 10.1101/2020.10.09.20209858 id = cord-266022-aco5kpaj author = Matusiak, Magdalena title = Expression of SARS-CoV-2 entry receptors in the respiratory tract of healthy individuals, smokers and asthmatics date = 2020-09-29 keywords = ACE2; SARS summary = We analyzed publicly available RNA microarray datasets for SARS-CoV-2 entry receptors and cofactors ACE2, TMPRSS2, BSG (CD147) and FURIN. Furthermore, respiratory epithelia were negative for ACE-2 and TMPRSS2 protein expression while positive for BSG and furin, suggesting a possible alternative entry route for SARS-CoV-2. First, by plotting the first 2 principal components computed on ACE2, TMPRSS2, BSG and FURIN expression across smokers'' and asthmatics'' datasets, we verified that there were no detectable batch effects within each of the six microarray datasets we sought to analyze (Figs. We next examined four RNA microarray datasets for ACE2, TMPRSS2, BSG and FURIN expression in airway epithelia from patients with a common respiratory disease, asthma. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; COVID-19: Coronavirus disease 2019; ACE-2: Angiotensin I converting enzyme 2; TMPRSS2: Transmembrane serine protease 2; BSG: Basigin; XIST: X inactive specific transcript; RPS4Y1: Ribosomal protein S4 Y-linked 1 SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues doi = 10.1186/s12931-020-01521-x id = cord-328499-d6cvaxm9 author = Matzkies, Lucie-Marie title = Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date = 2020-07-08 keywords = SARS summary = RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. The aim of this study was to evaluate the analytical and the clinical performance 20 of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results 21 with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. Clinical Evaluation of 179 the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the VIASURE SARS-CoV-2 S-gene Real Time PCR Detection Kit doi = 10.1016/j.cmi.2020.06.036 id = cord-103914-ppgx7mci author = Maughan, Elizabeth F. title = Cell-intrinsic differences between human airway epithelial cells from children and adults date = 2020-04-20 keywords = RNA; SARS; basal; cell; figure summary = Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). doi = 10.1101/2020.04.20.027144 id = cord-263224-osf0tkzr author = Maunder, Robert G. title = Long-term Psychological and Occupational Effects of Providing Hospital Healthcare during SARS Outbreak date = 2006-12-17 keywords = Hamilton; SARS; Toronto summary = To identify factors that might explain variance in adverse outcome, between-group differences in traumatic stress symptoms, psychological distress, and burnout were tested for the following categories: gender; duration of healthcare experience; job type; regular work during the SARS outbreak in emergency department, intensive care unit, or SARS isolation unit; indicators of the frequency and intensity of contact with SARS patients; and exposure to quarantine. For this analysis, the functional impact of SARS experience was operationalized as the number of adverse outcomes experienced by a person (from 0 to 7) of the following 7 outcomes: posttraumatic stress (IES >26); psychological distress (K10 >16); burnout (MBI-EE >27); decrease in face-to-face patient contact since SARS; decrease in work hours since SARS; increase in smoking, alcohol, or other problematic behavior since SARS; and >4 shifts missed because of stress or illness in the 4 months before the survey. doi = 10.3201/eid1212.060584 id = cord-318786-qd0k8174 author = Mauriz, Elba title = Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date = 2020-08-22 keywords = LSPR; SARS; SERS; detection; figure; virus summary = Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. doi = 10.3390/s20174745 id = cord-315604-a6fvsd45 author = Maurya, Santosh K. title = Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 date = 2020-06-01 keywords = NSP10; SARS; anti summary = title: Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2 We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. HIGHLIGHTS: NSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs. Hydrophobic interaction successfully delineates specific functional groups that may be responsible for the hydrophobic generating effect of these compounds with strong binding affinity against target proteins and may play a highly influencing against SARS-CoV-2 infection All the compounds showed good binding free energy with their respective proteins of SARS-CoV-2. In this study, it has been shown that selected screened compounds have good docking score, high DG binding free energy as well as strong hydrophobic interactions, and follows the Lipinski rule of five. doi = 10.1080/10799893.2020.1772298 id = cord-317413-w2xfdwea author = Maurya, Vimal K. title = Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection date = 2020-10-19 keywords = ACE2; COVID-19; Inactive; SARS; constituent summary = Therefore, we have planned to investigate the active constituents present in these medicinal plants for possible antiviral activity against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor using structure-based drug design method. Besides these active constituents, molecules such as 6-gingerol, glycyrrhetic acid, piperine, sawertiamarine, magnoflorine, scopolamine, atropine, eupafolin, and hyoscyamine also have strong binding affinity towards spike glycoprotein and may be developed potential candidates against SARS-CoV-2 infection (supplementary Figures 1 and 2 ). The active constituents present in selected plants were evaluated for the prediction of potential attachment inhibitors against SARS-CoV-2 via targeting spike glycoprotein as well as its host receptor ACE2. Structure-based drug designing for potential antiviral activity of selected natural products from Ayurveda against SARS-CoV-2 spike glycoprotein and its cellular receptor doi = 10.1080/07391102.2020.1832577 id = cord-327086-u3l8nr73 author = Mauvais-Jarvis, Franck title = Estradiol, Progesterone, Immunomodulation, and COVID-19 Outcomes date = 2020-07-30 keywords = SARS; covid-19 summary = Abbreviations: COVID-19, coronavirus disease-2019; E2, 17β-estradiol; ER, estrogen receptor; HCC, hepatocellular carcinoma; IL-1β, interleukin-1β; IL-6, interleukin-6; ISARIC, International Severe Acute Respiratory and Emerging Infections Consortium; MERS-CoV, Middle East respiratory syndrome coronavirus; MHT, menopausal hormone therapy; P4, progesterone; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SERM, selective estrogen receptor modulator; TNF-α, tumor necrosis factor α; Tregs, regulatory T cells. In most experimental human or rodent models, the anti-inflammatory actions of E2 on innate immunity includes the suppression of the production of proinflammatory cytokines, for example, IL-6, IL-1β, and TNF-α, by monocytes and macrophages (a major factor in the COVID-19 cytokine storm) and a strong inhibition of CCL2, thus preventing innate immune cells migration into inflamed areas, particularly neutrophils and monocytes. Taken together, these findings suggest that E2 and related SERMs have 2 potential protective mechanisms of action against SARS-CoV-mediated pneumonias in mice: 1) an estrogen-dependent decrease in the deadly innate immune response and cytokine storm in the lungs, thus preventing respiratory failure, and 2) specific to SERMs, an off-target direct inhibition of SARS-CoV replication and cytopathic effects. doi = 10.1210/endocr/bqaa127 id = cord-331193-33cyvidx author = Mawhinney, Jamie A title = Neurotropism of SARS-CoV-2: COVID-19 presenting with an acute manic episode date = 2020-06-14 keywords = COVID-19; CoV-2; SARS summary = Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. Psychiatric assessment found features consistent with acute mania, and he was detained under the Mental Health Act. This case indicates the need to consider COVID-19 in a wider series of clinical presentations and to develop a validated assay for SARS-CoV-2 in the cerebrospinal fluid. [9] [10] [11] [12] This article outlines a case of COVID-19 presenting with an acute manic episode necessitating emergency intubation and discusses potential mechanisms for the development of neuropsychiatric disease. ► The neuroinvasive potential of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (neurotropism) has been reported, but the pathophysiology remains unclear with uncertainty over its long-term consequences. doi = 10.1136/bcr-2020-236123 id = cord-259907-yqmi0cqy author = Maxwell, Cynthia title = Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 date = 2009-10-31 keywords = Health; SARS; patient summary = title: Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS) No. 225, April 2009 Labour triage and antenatal hospital admission Actions • Assessment is made as to whether the patient has suspected or probable SARS [1, 14] • Upon arrival in the labour and delivery triage unit, pregnant patients presenting with fever N38°C and respiratory symptoms and one of the associated symptoms (cough, unexplained hypoxia, shortness of breath, or dyspnea) and history of an exposure to an individual with probable SARS are immediately transferred to the designated isolation room, which is equipped with negative pressure ventilation. • Parents and family are counselled to look for symptoms and signs of SARS in the mother and newborn, especially in the first 10 days following delivery, and to report to any findings to the health care team Summary SARS, a life-threatening respiratory illness caused by a novel coronavirus, was responsible for a worldwide outbreak in 2003. doi = 10.1016/j.ijgo.2009.05.006 id = cord-332610-t99l3zii author = Mayer, J.D. title = Emerging Diseases: Overview date = 2008-08-26 keywords = AIDS; Africa; HIV; SARS; States; United; disease summary = The potential for new diseases to emerge in the United States was there, and it took just a few years until this happened, catching the medical and public health communities by surprise. The issue at the time was whether legionnaires disease and toxic shock syndrome were anomalies, whether the assumption of the conquest of infectious diseases had clearly been erroneous, or whether these two outbreaks were harbingers of a new stage in ''epidemiologic history''a historical period during which emerging infections would become common and would catch the attention of the public, the public health community, the medical community, and government agencies. Severe acute respiratory syndrome (SARS) proved to be of great import in both the public awareness of emerging infectious diseases and in the testing and real-time construction of both domestic and international systems of public health surveillance and response. doi = 10.1016/b978-012373960-5.00453-6 id = cord-265855-zf52vl11 author = Mayor-Ibarguren, Ander title = A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date = 2020-07-10 keywords = IL-6; RNA; SARS; covid-19; zinc summary = Zinc deficiency may increase ACE-2 receptor activity on type 2 pneumocytes and other cells that are infected by SARS-COV-2, mainly in the lower respiratory tract. Although there are no specific data regarding zinc in this pathway for SARS-CoV-2, zinc may limit infection through upregulation of IFN-alpha production and an increase in its antiviral activity (77, 78) . Thus, patients with IL-6-174 GG polymorphism (C-carriers) may be susceptible to developing a severe infection due to SARS-CoV-2, leading to an increase in IL-6 levels that produce a cytokine storm related to impaired zinc homeostasis. We believe there is enough evidence to further investigate how zinc status or homeostasis is involved in the pathogenesis of severe illness produced by SARS-CoV-2 infection, and its potential role as an active treatment should be assessed in clinical trials. doi = 10.3389/fimmu.2020.01736 id = cord-254094-ed1epul1 author = Mayoral, Eduardo Pérez-Campos title = Factors related to asymptomatic or severe COVID-19 infection date = 2020-09-24 keywords = COVID-19; SARS summary = In particular, we refer to the TMPRSS2 expression profile, balance of androgen and estrogen, blood group-A and/or B, nonsynonymous mutations in ORF3, and proteins NS7b and NS8 in SARS-CoV-2. In the first months of the COVID-19 pandemic, most authors focused their attention on features such as the high expression of ACE2 in the salivary glands in asymptomatic infection [4] , and the maturity and binding capacity of ACE2 [5, 6] . A higher 2D:4D ratio is associated with COVID-19 severity in men [14] , this means that sex hormones play a role in protection, thus, causing women to develop less serious complications or an asymptomatic COVID-19 Infection [12] . An in-depth study of the factors associated with asymptomatic subjects can provide information to limit severe COVID-19 as much as possible. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated doi = 10.1016/j.mehy.2020.110296 id = cord-296388-ayfdsn07 author = Maziarz, Mariusz title = Agent‐based modelling for SARS‐CoV‐2 epidemic prediction and intervention assessment: A methodological appraisal date = 2020-08-21 keywords = ABM; SARS; mechanism; model summary = CONCLUSIONS: Given this, we claim that the best epidemiological ABMs are models of actual mechanisms and deliver both mechanistic and difference‐making evidence. While the 2009 swine flu pandemic was the motivation for constructing AceMod, the model was not intended to accurately represent the outbreak of the H1N1 strain, but rather as a generalized framework for studying how an infectious disease spreads through the social interactions of Australians. In cases like the current pandemic, effective interventions may best be aimed at the societal level and therefore mechanistic models that integrate social factors, human behaviour and biological aspects (something that the ABM discussed here attempts to do) are arguably best suited for providing understanding and suggesting policy decisions. 10 Our claim that AceMod calibrated for SARS-CoV-2 bears similarity to the actual mechanism of the epidemic depends on the accuracy of the empirical results used as an input for this model. Agent-based modelling for SARS-CoV-2 epidemic prediction and intervention assessment: A methodological appraisal doi = 10.1111/jep.13459 id = cord-320127-55h4hhm3 author = Mazingi, Dennis title = Mitigating the impact of COVID-19 on children''s surgery in Africa date = 2020-06-10 keywords = Africa; COVID-19; SARS summary = 13 The COVID-19 pandemic has placed unprecedented strain on health services around the world, and paediatric surgical services are no exception. During the 2003 severe acute respiratory syndrome-related coronavirus (SARS-CoV)-1 outbreak in Toronto, stringent restrictions on non-essential surgical services were thought to have aggravated precipitous declines in surgical volume, with only small increases in surge capacity for the outbreak. 42 Paediatric care in Africa is typically characterised by significant involvement by guardians and other family members who support the child during hospital admission, assist the overburdened healthcare workforce and act as care advocates. A recent global review of paediatric surgical workforce density showed that a minimum of four paediatric surgeons per million children under 15 years of age would be required to achieve a survival of >80% for a group of four bellwether paediatric surgical conditions. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review doi = 10.1136/bmjgh-2020-003016 id = cord-256109-dkp0fwe3 author = Mazzulli, Tony title = Severe Acute Respiratory Syndrome–associated Coronavirus in Lung Tissue date = 2004-01-17 keywords = SARS; patient summary = Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). All patients who met the current World Health Organization case definition of probable SARS and who underwent a postmortem examination in Canada during the March-April 2003 outbreak were included in this study. The clinical description and RT-PCR results for the 11 patients with probable SARS from whom postmortem lung tissue samples were examined are summarized in Table 1 . By using a standardized RT-PCR assay, SARS-CoV has been unequivocally identified in the lung tissue of all patients who died with probable SARS but not in any of the controls. doi = 10.3201/eid1001.030404 id = cord-261952-xq6qney7 author = Mazzulli, Tony title = Proteomics and Severe Acute Respiratory Syndrome (SARS): Emerging Technology Meets Emerging Pathogen date = 2005-01-01 keywords = SARS; TOF summary = This approach was hampered, however, by the fact that clinical and laboratory features did not distinguish patients with SARS from those with other respiratory illnesses and that there was no reliable rapid diagnostic test (1) (2) (3) . Characterizing the proteins that make up SELDI-TOF profiles in this manner not only provides insight into the pathophysiology of the disease, but may also lead to the development of more direct diagnostic tools and novel therapeutic targets relevant to SARS-CoV. In addition, in both studies (7, 8 ) , the patients with SARS were well characterized in terms of timing of specimen collection and severity of disease. (8 ) chose to apply SELDI-TOF to the diagnosis of SARS, there are many other, more common infectious diseases, such as influenza, that would also benefit from more rapid and reliable diagnostic and prognostic tests. doi = 10.1373/clinchem.2004.041574 id = cord-292742-mio4przi author = McAloose, Denise title = From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date = 2020-10-13 keywords = CoV-2; Fig; PCR; SARS; Tiger; animal summary = KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4). doi = 10.1128/mbio.02220-20 id = cord-313795-jr3n3uo9 author = McAuley, Julie L. title = Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date = 2020-11-02 keywords = SARS; chalk summary = We investigated whether liquid chalk is an antiseptic against highly pathogenic human viruses including, SARS-CoV-2, influenza virus and noroviruses. We observed that addition of chalk before or after virus contact lead to a significant reduction on recovery of infectious SARS-CoV-2 and influenza but had little impact on norovirus. To further our study, we also tested the antiviral effect of Liquid Chalk against another 155 highly infectious and pathogenic respiratory viral pathogen IAV. 157 As can be observed in Figure 2 , all four Liquid Chalk products were effective in restricting the 158 recovery of IAV compared to SARS-CoV-2. transmission of SARS-CoV-2 (the 52 causative agent of the COVID-19 pandemic), influenza A virus (H1N1) (IAV) and norovirus, 53 using the surrogate model of mouse norovirus As a comparator, we also investigated the ability of Liquid Chalk to inactivate another 178 highly infectious viral pathogen, norovirus. doi = 10.1101/2020.11.02.364661 id = cord-290993-bsnja161 author = McAuliffe, Josephine title = Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date = 2004-12-05 keywords = SARS; TCID; virus summary = Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. doi = 10.1016/j.virol.2004.09.030 id = cord-256737-ptjng78b author = McBride, Corrin E. title = Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein date = 2010-09-01 keywords = CoV; SARS summary = The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Importantly, we show that SARS-CoV S palmitoylation is not necessary for efficient interaction with SARS-CoV M, which differs from published experiments for MHV (Thorp et al., 2006) and suggests a significant difference between the two viruses that may have important implications for virus assembly and infectivity. To determine if SARS-CoV S becomes palmitoylated in a pre-medial Golgi compartment, HEK293T cells exogenously expressing SARS-CoV S were labeled for 30 min with 35 S-methionine/ cysteine to measure total protein expression or 3 H-palmitic acid to measure palmitoylated protein. Although both SARS-CoV S and S PN were present at the cell surface, it is possible that there could be a difference in the amount of protein at the plasma membrane at steady state if palmitoylation affects a post-Golgi trafficking step. doi = 10.1016/j.virol.2010.05.031 id = cord-321013-8pkrg0mx author = McBride, Ruth title = The Coronavirus Nucleocapsid Is a Multifunctional Protein date = 2014-08-07 keywords = CTD; RNA; SARS; protein summary = The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA doi = 10.3390/v6082991 id = cord-319580-awtp0mpg author = McCartney, Stephen A. title = Obesity as a contributor to immunopathology in pregnant and non‐pregnant adults with COVID‐19 date = 2020-08-11 keywords = COVID-19; SARS; obesity; woman summary = The synergistic effects of obesity‐associated delays in immune control of COVID‐19 with mechanical stress of increased adipose tissue may contribute to a greater risk of pulmonary compromise in obese pregnant women. The expression of ACE2 by adipocytes and immune cells also suggests the possibility that adipose tissue may represent a potential reservoir for viral infection and may lead to increased viral burden or persistence; however, no studies to date have demonstrated that adipocytes can be directly infected with SARS-CoV-2. Maternal obesity has emerged as a key risk factor increasing susceptibility of pregnant women to severe COVID-19 disease. There is also an urgent need to focus research on how risk factors, like obesity, alter the immune response to SARS-CoV-2 and influence disease pathogenesis of COVID-19 (Box 1). What is the mechanism of increased risk for severe COVID-19 disease in obese nonpregnant and pregnant women? doi = 10.1111/aji.13320 id = cord-280062-1qrav1d5 author = McClenaghan, Elliot title = The global impact of SARS-CoV-2 in 181 people with cystic fibrosis date = 2020-11-04 keywords = SARS summary = Whilst outcomes in this large cohort are better than initially feared overall, possibly due to a protective effect of the relatively younger age of the CF population compared to other chronic conditions, SARS-CoV-2 is not a benign disease for all people in this patient group. The characteristics of the 149 people in the non-transplant cohort were; median age 24 years (range 0-74 years), 48% male, 36% were homozygous and 37% were heterozygous for F508del, 24% had CFrelated diabetes (CFRD), 43% were taking CFTR modulator therapy, and median best FEV 1 prior to infection was 73% predicted, (range 18-123%) ( Table 1) . One of the seven deaths, in a non-transplant patient, was reported by the clinical team as being related to advanced cystic fibrosis, not SARS-CoV-2. In the non-transplant cohort, 4 deaths were recorded, 2 of which had a best FEV1 the year prior to infection of <40% predicted and 2 with 40-70% predicted. doi = 10.1016/j.jcf.2020.10.003 id = cord-354453-uze6ze8o author = McCloskey, Brian title = SARS to novel coronavirus – old lessons and new lessons date = 2020-02-05 keywords = China; SARS summary = By 26 January also, almost 50 million people in Wuhan and neighbouring cities had effectively been placed in quarantine while the WHO had determined that the event should not yet be declared as a Public Health Emergency of International Concern (PHEIC) [2] and had recommended no specific travel restrictions. There was extensive criticism of China for its perceived failure to share information about the emerging SARS infection early enough in the outbreak to allow countries to prepare and respond. The rapid sharing of information in this outbreak and the speed of the coordinated response both in the country and internationally suggest that lessons have been learned from SARS that improve global capacity. The global media response to the unfolding events has been relatively balanced and informed but the nuances of the evolving situation have not been critically examined in partnership with the media and as a result the public perception of the risk may be exaggeratedalthough it of course remains possible that the outbreak will develop in a way that matches up to the perceived risk. doi = 10.1017/s0950268820000254 id = cord-279334-j0i9ozsz author = McCreary, Erin K title = Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date = 2020-03-23 keywords = COVID-19; China; LPV; SARS summary = Most existing preclinical and clinical data on antiviral therapy are derived from other viruses, including SARS-CoV-1 (first reported in 2003), Middle East respiratory syndrome coronavirus ([MERS-CoV] first reported in 2012), and non-coronaviruses (eg, Ebola virus disease). The use of 500 mg of chloroquine by mouth twice daily as the reference for efficacy is rational given initial reports from China [16] , but it is important to note that this dosing still requires validation, and the improved R LTEC values reported are largely driven by the finding that hydroxychloroquine was 7.6 times more potent than chloroquine in vitro. Given this finding, the small numbers in this study, the lack of clinical outcomes presented, the potential for additive toxicity with hydroxychloroquine and azithromycin, and the desperate need to practice good antimicrobial stewardship during the COVID-19 pandemic, we would caution clinicians against using these data to support combination therapy. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1093/ofid/ofaa105 id = cord-342857-vj6sw2ne author = McCullough, Peter A. title = Pathophysiological Basis and Rationale for Early Outpatient Treatment of SARS-CoV-2 (COVID-19) Infection date = 2020-08-07 keywords = COVID-19; SARS; patient summary = In the absence of clinical trial results, physicians must use what has been learned about the pathophysiology of SARS-CoV-2 infection in determining early outpatient treatment of the illness with the aim of preventing hospitalization or death. Thus, in the context of present knowledge, given the severity of the outcomes and the relative availability, cost, and toxicity of the therapy, each physician and patient must make a choice: watchful waiting in self-quarantine or empiric treatment with the aim of reducing hospitalization and death. (10) For the ambulatory patient with recognized early signs and symptoms of COVID-19, often with nasal real-time reverse transcription or oral antigen testing pending, the following four principles could be deployed in a layered and escalating manner depending on clinical manifestations of COVID-19 like illness(11) and confirmed infection: 1) reduction of reinoculation, 2) combination antiviral therapy, 3) immunomodulation, 4) antiplatelet/antithrombotic therapy. doi = 10.1016/j.amjmed.2020.07.003 id = cord-255446-wddj6hrv author = McDade, T. W. title = High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date = 2020-06-02 keywords = DBS; June; SARS summary = To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. 7 We adapted this ELISA to measure IgG antibodies to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in DBS samples. . https://doi.org/10.1101/2020.06.01.20119602 doi: medRxiv preprint Participants who previously tested positive for SARS-CoV-2 virus were recruited from the community through direct contact. Seroprevalence in 202 samples collected from the community, which includes health care workers and first responders, none of which were confirmed SARS-CoV-2 viral positive. doi = 10.1101/2020.06.01.20119602 id = cord-346089-u31n0qxa author = McDade, Thomas W. title = High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date = 2020-08-14 keywords = SARS; dbs summary = title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. In addition, we demonstrate the feasibility and utility of quantifying SARS-CoV-2 antibodies in self-collected DBS with results from a community-based sample enriched with health care workers. We have validated a DBS assay to facilitate large-scale serological testing of SARS-CoV-2 IgG antibodies, and results from our feasibility study document a high rate of household transmission. doi = 10.1371/journal.pone.0237833 id = cord-350029-1y5ex4d5 author = McDade, Thomas W. title = Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies date = 2020-08-09 keywords = COVID-19; SARS; antibody summary = Serological testing is a complementary approach that detects the presence of antibodies against SARS-CoV-2 in blood samples from exposed individuals (World Health Organization, 2020). If sufficient time has passed since the initial infection, the presence of IgM antibodies against SARS-CoV-2 antigens can be used to confirm a clinical case of COVID-19. In developing a low-cost ELISA for SARS-CoV-2 antibodies, our hope is that others can draw on the longstanding tradition of methodological innovation in human biology to promote community-based research on COVID-19. Human biologists are also well-positioned to consider a life course perspective on variation in outcomes in response to SARS-CoV-2 infection. Human biologists are uniquely positioned to make important contributions to our understanding of COVID-19, and methods that facilitate research in community-based settings globally will be central to that effort. Enzyme immunoassay for SARS-CoV-2 antibodies in dried blood spot samples: A minimally-invasive approach to facilitate community-and population-based screening doi = 10.1002/ajhb.23483 id = cord-262020-ygl8xlhk author = McDermott, Aoibhinn title = Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection date = 2020-05-16 keywords = SARS summary = authors: McDermott, Aoibhinn; O''Kelly, John; de Barra, Eoghan; Fitzpatrick, Fidelma; Little, Dilly M.; Davis, Niall F. title: Perioperative Outcomes of Urological Surgery in Patients with SARS-CoV-2 Infection To date, many urological centres have prioritised their patients for urgent surgical intervention because of a reduction in operating theatre availability and the risk of hospital-acquired SARS-CoV-2 infection [1, 2] . Here we present our perioperative outcomes for patients undergoing urological surgery during the initial stage of the SARS-CoV-2 pandemic in Ireland (between March 16 and May 1, 2020, inclusive). Our hospital has an onsite microbiology laboratory that performs daily SARS-CoV-2 realJ o u r n a l P r e -p r o o f Elective surgery was prioritised according to recent European guidelines and patients were then placed on a centralised departmental theatre waiting list [1] . doi = 10.1016/j.eururo.2020.05.012 id = cord-286472-pqtem19t author = McFee, R.B. title = MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date = 2020-07-28 keywords = East; MERS; Middle; SARS; respiratory summary = This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol doi = 10.1016/j.disamonth.2020.101053 id = cord-007049-02p8ug67 author = McGeer, Allison title = Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date = 2004-07-15 keywords = SARS; hospital summary = In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants doi = 10.1086/421784 id = cord-339386-sxyeuiw1 author = McIntosh, Kenneth title = 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date = 2015-12-31 keywords = MERS; OC43; SARS; human; respiratory; virus summary = The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. doi = 10.1016/b978-1-4557-4801-3.00157-0 id = cord-329010-n0mz098o author = McKee, Dwight L. title = Candidate drugs against SARS-CoV-2 and COVID-19 date = 2020-04-29 keywords = ACE2; COVID-19; CoV-2; MERS; SARS summary = Further, chloroquine and hydroxychloroquine, and off-label antiviral drugs, such as the nucleotide analogue remdesivir, HIV protease inhibitors lopinavir and ritonavir, broad-spectrum antiviral drugs arbidol and favipiravir as well as antiviral phytochemicals available to date may prevent spread of SARS-CoV-2 and morbidity and mortality of COVID-19 pandemic. Drugs that have recently been shown to target MERS-CoV in mice [15] , and to inhibit Ebola virus RdRP and SARS-CoV-2 proteases in humans, such as remdesivir and ritonavir/lopinavir, also constitute candidate drugs against SARS-CoV-2 and are now investigated for their therapeutic efficacy in COVID-19 patients in 2 international clinical trials (SOLIDARITY Trial and DisCoVeRy Trial). The emergence of the novel beta coronavirus SARS-CoV-2 from Wuhan, Hubei province, China in December 2019 rapidly led to a pandemic involving more than 2,500,000 infected persons and more proven drugs such as camostat mesilate which prevents virus host cell entry by inhibiting TMPRSS2 [8] , and chloroquine phosphate which inhibits terminal phosphorylation of ACE2, or hydroxychloroquine which is metabolized in vivo to chloroquine [44] . doi = 10.1016/j.phrs.2020.104859 id = cord-282732-qym6wji7 author = McLaughlin, Katie-May title = COVID-19-Related Coagulopathy—Is Transferrin a Missing Link? date = 2020-07-30 keywords = SARS; covid-19 summary = To identify gene products that may contribute to COVID-19-related coagulopathy, we analyzed the expression of genes associated with the Gene Ontology (GO) term "blood coagulation" in the Genotype-Tissue Expression (GTEx) database and identified four procoagulants, whose expression is higher in males and increases with age (ADAMTS13, F11, HGFAC, KLKB1), and two anticoagulants, whose expression is higher in females and decreases with age (C1QTNF1, SERPINA5). Thus, gene products that (1) are involved in coagulation, (2) change with age, (3) differ in their levels between females and males, and (4) are regulated in response to SARS-CoV-2 infection represent candidate factors that may contribute to COVID-19-related coagulopathy and disease severity. To identify such candidate factors that may be involved in COVID-19-related coagulopathy, we here performed a combined analysis of a proteomics dataset derived from SARS-CoV-2-infected cells [10] , of a dataset of host cell proteins found to bind to SARS-CoV-2 proteins [11] , and of human gene expression data from the Genotype-Tissue Expression (GTEx) database [12] . doi = 10.3390/diagnostics10080539 id = cord-017224-naromr0a author = McLeish, Caitriona title = Evolving Biosecurity Frameworks date = 2016-12-06 keywords = AIDS; Health; SARS; Security; disease summary = The relationship between infectious disease and security concerns has undergone an evolution since the end of the Cold War. What was previously seen as two separate domains – public health and national security – have, through various events and disease outbreaks in the last 15 years, become intertwined and as a result biosecurity policies now need to address a spectrum of disease threats that encompass natural outbreaks, accidental releases and the deliberate use of disease as weapons. Calling it niche is not to say that bioterrorism had not been considered a security threat prior to 2001many commentators had noted the potential (see for example Stern, 1993; Tucker, 1996 Tucker, , 2000 Moodie and Roberts, 1997; Smithson and Levy, 2000) ; table top exercises had been conducted, domestic preparedness programmes initiated (Guillemin, 2011, p7) , and in countries such as the US, policy directives had been crafted that gave the highest priority to "developing effective capabilities to detect, prevent, defeat and manage the consequences of nuclear, biological or chemical materials or weapons use by terrorists" (United States, 1995) . doi = 10.1057/978-1-137-53675-4_4 id = cord-260048-yis26g81 author = McNamara, Ryan P. title = High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date = 2020-10-20 keywords = CoV-2; SARS; U.S. summary = The 154 number of reads aligned varied depending on the viral load, as determined by real-time qPCR using 155 CDC primer N1, but not total RNA, as determined using RNAse P, of the samples ( Figure 1B) . At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 158 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 159 and coverage was more variable. This data is consistent with the 187 astonishingly high reported genome copy numbers of SARS-CoV-2 in some cases 188 and demonstrates the principal suitability of "testing by sequencing" as a diagnostic option for SARSCoV-2 and other rapidly evolving viruses. In sum, this study generated exhaustive SNV information representing the introduction and 276 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 277 from symptomatic cases and the majority of genomes clustered with variants that predominate the 278 outbreak in the U.S., rather than Europe or China. doi = 10.1016/j.celrep.2020.108352 id = cord-314445-4cb4a9r5 author = McNamara, Ryan P. title = High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date = 2020-06-19 keywords = CoV-2; SARS; U.S. summary = This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S. The current COVID-19 pandemic is an urgent public health emergency with over 112,000 deaths in the United States (U.S.) alone. At a CP ≥35 most positive samples still yielded reads that mapped to the target genome 227 and thus allowed detection of SARS-CoV-2 sequences; however, the results were less consistent, 228 and coverage was more variable. In sum, this study generated exhaustive SNV information representing the introduction and 325 spread of SARS-CoV-2 across a suburban low-density area in the Southern U.S. All samples were 326 from symptomatic cases and the majority of genomes clustered with variants that predominate the 327 outbreak in the U.S., rather than Europe or China. doi = 10.1101/2020.06.19.161141 id = cord-331283-bfyoavon author = Meca-Lallana, Dra. Virginia title = COVID-19 IN 7 MULTIPLE SCLEROSIS PATIENTS IN TREATMENT WITH ANTI-CD20 THERAPIES date = 2020-06-15 keywords = SARS summary = We describe our experience in seven cases of patients with multiple sclerosis who have been affected by SARS-COV-2 (with a clinical/serological diagnosis or PCR diagnosis) and who were being treated with anti-CD20+ monoclonal antibodies. CONCLUSIONS: Patients treated with anti-CD20+ have adequate resolution of COVID-19 despite the fact that the presence of antibodies against SARS-CoV-2 was not detected in all cases. Ocrelizumab is associated with decreased levels of IgM (and to a lesser degree for IgA and IgG), and serious infections occurred, but their incidence was low in clinical trials and extended phases 4 In this work, we report our experience in MS patients with anti-CD20+ antibodies who have 2. We have found antibodies against SARS-CoV-2 in patients treated with ocrelizumab, but in patients who previously used rituximab this immunity is not achieved or we are not able to detect it. doi = 10.1016/j.msard.2020.102306 id = cord-295274-gzkfy70s author = Mecham, Jeffrey C. title = Utility of Tracheostomy in Patients With COVID‐19 and Other Special Considerations date = 2020-05-12 keywords = COVID-19; SARS; tracheostomy summary = METHODS: We explore current literature and recommendations for tracheostomy in patients with COVID‐19 and look back at previous data from severe acute respiratory syndrome coronavirus 1 (SARS‐CoV‐1), the virus responsible for the SARS outbreak of 2003. RESULTS: Given the severity and clinical uncertainty of patients with COVID‐19 and the increased risk of transmission to clinicians, careful consideration should be taken prior to performing tracheostomy. One concern for healthcare professionals managing the airways of COVID-19 patients is the risk of viral exposure during aerosol-generating procedures, including intubation and tracheostomy. There is a plausible risk for increased intraprocedural viral exposure via secretions and aerosolized particles when tracheostomy is performed percutaneously because this technique requires additional manipulation of the airway with multiple, repetitive dilations. Given the severity and uncertain clinical outcome of patients with COVID-19, in addition to the increased risk of transmission to clinicians during aerosol generating procedures, careful consideration should be taken prior to performing tracheostomy. doi = 10.1002/lary.28734 id = cord-281679-xmbnpawj author = Meekins, David A. title = Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date = 2020-08-16 keywords = CoV-2; SARS; pig summary = In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Cats, hamsters, and ferrets are highly susceptible to SARS-CoV-2 infection, demonstrate varying clinical and pathological disease manifestations, readily transmit the virus to naïve animals, and mount a virusspecific immune response [22] [23] [24] [25] [26] [27] [28] . Pigs are therefore unlikely to play an important role in the COVID-19 pandemic as a virus reservoir or as a pre-clinical animal model to study SARS-CoV-2 pathogenesis or develop novel countermeasures. doi = 10.1101/2020.08.15.252395 id = cord-342380-lihz7h1k author = Meguid Kassem, Abdel title = SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date = 2020-07-21 keywords = PCR; SARS summary = BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). This work has been conducted to determine the extent of infection by realtime reverse transcription polymerase chain reaction (RT-PCR) and rapid serological test (RST) for SARS-CoV-2 among frontline HCWs providing gastrointestinal services. Previous studies in developed countries reported variable infection rates in HCWs. In a study on 957 employees in a German university hospital, 52 of them (5.4%) tested positive for SARS-CoV-2 by PCR [13] . doi = 10.1016/j.ajg.2020.07.005 id = cord-030254-eevqclsy author = Mehta, Chitra title = Management of Coronavirus 2019 date = 2020-04-24 keywords = COVID-19; China; SARS; patient summary = A suspected case has been defined as a patient with acute onset respiratory infection with fever, cough, sore throat, and an epidemiological link in the form of a history of travel 14 days prior to the onset of symptoms to countries afflicted with COVID-19, or a close contact with a confirmed or probable case of COVID-19 14 days prior to symptom onset, or some acute respiratory infection requiring hospitalization with no other etiology fully explaining the clinical presentation, as per WHO guidelines. • In patients with severe COVID-19 infection requiring supplemental oxygen, lopinavir/ritonavir combination plus hydroxychloroquine plus favipiravir 1,600 mg (eight tablets) twice daily as a loading dose followed by 600 mg (three tablets) every 8 hours for 14 days is being used. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical management of severe acute respiratory infection when COVID-19 disease is suspected. doi = 10.1055/s-0040-1710401 id = cord-257805-pcp3qgn0 author = Mehta, Harsh title = Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date = 2020-05-16 keywords = SARS; respiratory summary = title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. Since its first reported case in China, more than 4 Coronaviruses are known pathogens and have previously been responsible for epidemics caused by severe acute respiratory syndrome coronavirus (SARS-CoV1) and We report a case of a high-risk pregnant woman who developed respiratory failure associated with COVID-19, and had a favorable outcome postdelivery. A repeat chest X-ray showed worsening bilateral pulmonary infiltrates, raising concern for development of acute respiratory distress syndrome (ARDS). In the data available in pregnant patients from the previous coronavirus outbreaks, no vertical transmission was reported [4] . doi = 10.1016/j.crwh.2020.e00220 id = cord-300848-0igfcixy author = Meijers, Björn title = The clinical characteristics of coronavirus-associated nephropathy date = 2020-09-02 keywords = COVID-19; SARS summary = While a minority of SARS-CoV patients did develop acute kidney injury (AKI), this was attributed to critical illness with acute tubular necrosis in post-mortem kidney tissue. In kidney tissue obtained at autopsy of 26 critically ill patients with COVID-19, diffuse proximal tubule injury also was the main finding on light microscopy [9] . This puts SARS-CoV-2 in an expanding list of other viruses with proven kidney tropism, including hantavirus [14] , the Middle East respiratory syndrome coronavirus [15] , polyomavirus (polyomavirus-associated nephropathy) [16] and the human immunodeficiency virus (HIV-associated nephropathy) [17] . To date, kidney histology of COVID-19 patients with a less severe clinical course has not been reported. In this issue of Nephrology Dialysis Transplantation, data from a large European cohort study of patients with COVID-19 are reported [3] . Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.1093/ndt/gfaa197 id = cord-314880-0cfq52hn author = Meireles, Pedro Antunes title = Acalculous Acute Pancreatitis in a COVID-19 Patient date = 2020-05-13 keywords = SARS summary = An increase in pancreatic enzymes has been increasingly recognized in patients with COVID-19, but little is known about the real prevalence of acute pancreatitis in this population. We report a case of acute pancreatitis in a patient with SARS-CoV-2 infection. Liu et al [1] showed an increase in amylase and lipase in a series of 121 patients admitted with COVID-19 pneumonia, suggesting some degree of pancreatic injury in these patients. Similarly, Anand et al [3] have reported the case of a 59-year-old female patient who was diagnosed with acute pancreatitis based on typical abdominal pain and imaging findings 10 days after positive PCR-confirmed SARS-CoV-2 infection. The authors report a case of acute pancreatitis in a COVID-19 patient, highlighting the importance of considering SARS-CoV-2 as a new aetiological agent of acute viral pancreatitis. We suggest that pancreatic enzymes should be evaluated in COVID-19 in-patients presenting with gastrointestinal symptoms, since it could reveal unrecognized pancreatic involvement in this population. doi = 10.12890/2020_001710 id = cord-354315-yfn9vaan author = Meirson, Tomer title = Structural basis of SARS-CoV-2 spike protein induced by ACE2 date = 2020-05-24 keywords = ACE2; SARS summary = This conformational changes lead to an alternating pattern in conserved disulfide bond configurations positioned at the hinge, indicating a possible disulfide exchange, an important allosteric switch implicated in viral entry of various viruses, including HIV and murine coronavirus. The critical step in SARS-CoV-2 infection which involves the transition between a metastable prefusion state to a stable post-fusion state is triggered by binding to ACE2 which induces conformational changes in the RBD and the hinge region (Gui, et al., 2017; Pallesen, et al., 2017; Song, et al., 2018; Walls, et al., 2020) . To gain insights into the effects of ACE2 interaction on the S protein of SARS-COV-2, we analyzed the intramolecular structural variations in the bound versus the unbound-closed Numerous structures of the prefusion human CoV S proteins were determined at different states, and the key regions responsible for the interaction with the receptor were previously reported (Lan, et al., 2020; Shang, et al., 2020; Walls, et al., 2020; Wan, et al., 2020; Wrapp, et al., 2020; Yan, et al., 2020) . doi = 10.1101/2020.05.24.113175 id = cord-322129-uyswj4ow author = Melin, Amanda D. title = Comparative ACE2 variation and primate COVID-19 risk date = 2020-10-27 keywords = ACE2; CoV-2; SARS; Supplementary; site summary = Infection studies of rhesus monkeys, long-tailed macaques, and vervets as biomedical models have made it clear that at least some nonhuman primate species are permissive to SARS-CoV-2 infection and develop symptoms in response to infection that resemble those of humans following the development of COVID-19, including similar age-related effects [11] [12] [13] [14] [15] [16] . We assessed the variation at amino acid residues identified as critical for ACE2 recognition by the SARS-CoV-2 RBD and undertook an analysis of positive selection and protein modeling to gauge the potential for adaptive differences and the likely effects of protein variation. In particular, the twelve sites in the ACE2 protein that are critical for binding of the SARS-CoV-2 virus are invariant across the Catarrhini, which includes great apes, gibbons, and monkeys of Africa and Asia (Fig. 1) . doi = 10.1038/s42003-020-01370-w id = cord-342344-jjnf4yje author = Mello, C. J. title = Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date = 2020-06-26 keywords = PCR; RNA; SARS summary = Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. doi = 10.1101/2020.06.24.20139584 id = cord-304626-ffao7vka author = Mellors, Jack title = Viral Evasion of the Complement System and Its Importance for Vaccines and Therapeutics date = 2020-07-09 keywords = MAC; MBL; SARS; cell; complement summary = A better understanding of this virus-host interplay and its contribution to pathogenesis has previously led to: the identification of genetic factors which influence viral infection and disease outcome, the development of novel antivirals, and the production of safer, more effective vaccines. Infected host cells which present viral antigens on the cell surface membrane can activate the classical pathway, as the antigens bind IgM/IgG to induce complement dependent cytotoxicity (CDC). Non-neutralizing antibodies can still bind the viral target with the potential to cross-link with Fc receptors, or activate complement and interact with complement receptors, to enhance viral infection of host cells (241) . Use of the non-neutralizing influenza virus M2 extracellular vaccine in mice required functional C3 to confer protection and induce effective humoral and cell-mediated immune responses (245) . doi = 10.3389/fimmu.2020.01450 id = cord-268755-13xmmin1 author = Meltzer, Martin I. title = Multiple Contact Dates and SARS Incubation Periods date = 2004-02-17 keywords = SARS summary = Many severe acute respiratory syndrome (SARS) patients have multiple possible incubation periods due to multiple contact dates. I present a simple spreadsheet-based method that uses multiple contact dates to calculate the possible incubation periods of SARS. I present a simple method that allows a simulation of the frequency distribution, including confidence intervals, of the possible incubation periods (in days) for SARS. The method can also be used to calculate when infectious persons are most likely to have transmitted SARS to susceptible persons, even when multiple days of possible transmission exist. Simulation of frequency distribution of incubation period of severe acute respiratory syndrome. Many of the patients included in the database had multiple possible incubation periods (see Table) , resulting in the confidence intervals displayed for each day. The method readily "accepts" data in which patients have multiple possible incubation periods. doi = 10.3201/eid1002.030426 id = cord-321552-lsz1onrj author = Membrilla, Javier A. title = Headache as a Cardinal Symptom of Coronavirus Disease 2019: A Cross‐Sectional Study date = 2020-09-28 keywords = COVID-19; SARS; headache; patient summary = OBJECTIVE: To describe the semiology of pain and its associated features in patients with coronavirus disease 2019 (COVID‐19) and headache presenting to the emergency department who do not require urgent services. 27 We hypothesized that COVID-19-related headache might be one of the most frequent symptoms of the infection and can have a more severe presentation in patients with migraine. We aimed to describe the semiology of pain and associated symptoms in patients with COVID-19-related headache in a clinical setting who visit the emergency department but do not require urgent services. Study Population and Eligibility.-Patients attending the emergency department of our hospital were included if they met all of the following inclusion criteria: (1) patients classified by the Manchester Triage System 29 as priority levels 5 (non-urgent) and 4 (standard); (2) fulfilled the criteria for a "probable COVID-19 case" or "confirmed COVID-19 case" according to the WHO guidance on global surveillance for COVID-19; 30 (3) and presented with headache alongside other COVID-19-related symptoms. doi = 10.1111/head.13967 id = cord-278648-hkvurb2k author = Menachery, Vineet D. title = Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis date = 2017-11-15 keywords = IFN; MERS; SARS; nsp16 summary = While the absence of 2′O-MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Generation of mutants with changes in the NSP16 KDKE active site resulted in IFN-mediated in vitro and in vivo attenuation of both mouse hepatitis virus (MHV) and SARS-CoV (9, 10) . While a more rapid CPE following both WT and dNSP16 mutant MERS-CoV infections precluded an equivalent finding at late time points, the SARS-CoV results suggest that the absence of NSP16 activity eventually initiates host response changes that contribute to attenuation at late time points. doi = 10.1128/msphere.00346-17 id = cord-277039-yo5ojr0s author = Mendenhall, Ian H. title = Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date = 2019-04-17 keywords = Kazakhstan; SARS; bat summary = In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. The zoonotic SARS-coronavirus (SARS-CoV) outbreak originated in southern China from horseshoe bats, where wet markets permitted atypical contact between species, including subsequent spillover to humans [9] . On the other hand, camels are the putative natural reservoir for MERS-coronavirus, although recent phylogenetic analysis indicated that bats harbor coronaviruses that are ancestral to the MERS-CoV lineage [11] . In this study, we collected fresh bat guano from three caves at different locations in Kazakhstan and conducted molecular screening for coronaviruses. To further understand the evolutionary relationships of these viruses, we analyzed novel bat coronavirus sequences in combination with 2811 RdRp sequences of coronavirus from different host species worldwide, representing the three genera: Alpha-, Beta-, and Gamma-coronaviruses. The Alpha-CoV genus comprises a large number of coronaviruses from diverse hosts, including bats, shrews, dogs, cats, ferrets, pigs, and humans. doi = 10.3390/v11040356 id = cord-296268-kb7fgfaq author = Mendonça, Luiza title = SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date = 2020-11-05 keywords = CoV-2; SARS; SEM summary = Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Understanding the genome 27 replication, assembly and egress of SARS-CoV-2, a multistage process that involves different 28 cellular compartments and the activity of many viral and cellular proteins, is critically Krios to identify each individual infected cell (39.2 % for MOI of 0.1 and 45.4% for MOI 124 0.5) where cryoET tilt series were collected at the cell periphery. The grids were then 125 transferred to a FIB/SEM dualbeam instrument and the same infected cells were subjected to 126 either serial cryoFIB/SEM volume imaging (Zhu et al., 2021) or cryoFIB milling of cellular 127 lamellae where additional cryoET tilt series were collected (Sutton et al., 2020) . doi = 10.1101/2020.11.05.370239 id = cord-353953-83d0g8ix author = Mendoza, Emelissa J. title = Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2 date = 2020-05-31 keywords = Protocol; SARS summary = Plaque assays are a quantitative method of measuring infectious SARS‐CoV‐2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen. Plaque assays are a quantitative method of measuring infectious SARS-CoV-2 by quantifying the plaques formed in cell culture upon infection with serial dilutions of a virus specimen (Harcourt et al., 2020) . The first plaque assay method that we describe (Basic Protocol) uses Noble agar as the matrix in a solid overlay and neutral red as the stain to enhance plaque visualization. This protocol outlines a plaque assay method that can be used for the quantification of SARS-CoV-2 plaque-forming units (PFUs) in virus specimens, including viral stocks prepared from infected cell culture supernatants, and with further optimization, bodily fluids from animals infected with SARS-CoV-2. Use Formula 8 (see Basic Protocol) to calculate the titer of SARS-CoV-2 in the specimen using the identified dilution factor and the inoculum volume of 0.1 ml. doi = 10.1002/cpmc.105 id = cord-315598-qwh72inx author = Mendoza, Jose Luis Accini title = ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date = 2020-10-06 keywords = AMCI; COVID-19; Care; China; Coronavirus; Disease; EPP; FUNDAMENTO; HCQ; PCR; PEEP; SARS; SDRA; TCZ; UCI; Wuhan; acute; clinical; como; con; del; las; los; pacientes; para; patient; por; que; recomienda; respiratory; una; uso summary = De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). doi = 10.1016/j.acci.2020.09.004 id = cord-264709-p835wf4f author = Menezes, A. M. B. title = High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey date = 2020-08-12 keywords = SARS summary = Using data from the most recent wave of the EPICOVID19 study, a nationwide household-based survey including 133 cities from all states of Brazil, we estimated the proportion of people with and without antibodies for SARS-CoV-2 who were asymptomatic, which symptoms were most frequently reported, the number of symptoms reported and the association between symptomatology and socio-demographic characteristics. Symptoms change in smell or taste, fever and myalgia were most likely to predict positive test results as suggested by recursive partitioning tree analysis. 62 63 Using data from the most recent wave of the EPICOVID19 study, a nationwide 64 household-based survey including 133 cities from all states of Brazil, 7 we estimate the 65 proportion of people with and without antibodies for SARS-CoV-2 who were 66 asymptomatic. The above results from the third wave of the study confirmed a high prevalence of 232 symptoms using a 4-month recall period; only 12.1% positive subjects were 233 asymptomatic, compared to 42.2% of those without antibodies. doi = 10.1101/2020.08.10.20171942 id = cord-257398-fmkfo5ju author = Meng, Qing-Bin title = Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date = 2020-10-06 keywords = PCR; SARS summary = In the present study, we collected clinical data from 652 suspected COVID-19 patients and 206 non-COVID-19 patients to investigate the diagnostic value of SARS-CoV-2 IgM/IgG antibody test kits with colloidal gold immunoassays and nucleic acid RT-PCR test kits. As recently reported, a rapid IgM/IgG October 6, 2020 Volume 8 Issue 19 combined antibody test was used for the diagnosis of SARS-CoV-2 infection, showing 88.66% sensitivity and 90.63% specificity [15] . Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. doi = 10.12998/wjcc.v8.i19.4360 id = cord-349912-em1abdrg author = Meng, Xiangming title = COVID-19 and anosmia: A review based on up-to-date knowledge date = 2020-06-02 keywords = COVID-19; SARS summary = Multiple cross-sectional studies have demonstrated that the incidence rate of Olfactory dysfunction in COVID-19 patients varies from 33.9–68% with female dominance. Clinical evidence has shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted by person-to-person [1] . Furthermore, SARS-CoV-2 was detected in the tears of COVID-19 patient and can cause nasal infection via the nasolacrimal duct [17, 18] . performed the olfactory function test (OFT)of 60 SARS-CoV-2 positive patients and took 60 subjects from previous studies as a control group matching the age and gender of the patient''s group [35] . Another investigation, using a self-reported questionnaire, analyzed the prevalence of smell and/or taste disorders in J o u r n a l P r e -p r o o f 8 OFT has been the mainstay for diagnosis of OD; however, the patients in most studies were untested by OFT. doi = 10.1016/j.amjoto.2020.102581 id = cord-297641-bgmib6xb author = Meng, Xiujuan title = Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China date = 2020-04-07 keywords = SARS summary = title: Alert for SARS-CoV-2 infection caused by fecal aerosols in rural areas in China 1 The virus causing COVID-19, designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is closely related to SARS-CoV. 2 In 2003, a SARS-CoV outbreak at Amoy Gardens in Hong Kong led to 329 confirmed cases of infection and 42 deaths. 3 Subsequent studies suggested that the plumbing and ventilation systems at Amoy Gardens interacted to allow transmission of the SARS virus and that high concentrations of viral aerosols in the plumbing were the primary mode of transmission in this outbreak. Based on these characteristics, SARS-CoV-2 is prone to cause outbreaks in the community, particularly in rural areas. In concentrated areas, residents mainly use flush toilets, which can generate huge quantities of aerosols; the ventilation and plumbing systems in these places are not effective for maximal hygiene. The feces may form high concentrations of viral aerosols that travel through the air to cause infection. doi = 10.1017/ice.2020.114 id = cord-278225-d0gxb6bx author = Meng, Yifan title = Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients date = 2020-04-30 keywords = SARS summary = title: Value and Challenges: Nucleic Acid Amplification Tests for SARS–CoV-2 in Hospitalized COVID-19 Patients It has been emphasized that diagnostic testing for SARS-CoV-2 was an especially important tool in the diagnosis and management of patients with COVID-19. All patients included in the present study were verified as positive for SARS-CoV-2 infection by reverse transcriptase polymerase chain reaction (RT-PCR). At present clinical practice, patients with improved respiratory symptoms, improved pulmonary imaging, and nucleic acid tests negative twice consecutively (sampling interval ≥ 24 hours) can be discharged. reported that potential false-negative nucleic acid testing results for SARS-CoV-2 could be caused by thermal inactivation of samples with low viral loads. Value of Diagnostic Testing for SARS-CoV-2/COVID-19 Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19 Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads doi = 10.1016/j.jinf.2020.04.036 id = cord-340619-3tjquzx8 author = Menghua, Wu title = Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date = 2020-07-23 keywords = HIV; SARS summary = title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. Here we reported a case of HIV and SARS-CoV-2 coinfection who had a prolonged viral shedding duration about 28 days. [11] reported a patient with kidney transplantation who had a prolonged viral shedding duration for 63 days. This is the first report of a patient co-infected with HIV and SARS-CoV-2 who showed a prolonged viral shedding duration. The lymphocyte count of our case was also less than 2.0 × 10 9 /L, which might be a co-factor for the prolonged viral shedding duration. Viral shedding prolongation in a kidney transplant patient with COVID-19 pneumonia doi = 10.1186/s12981-020-00301-3 id = cord-316117-o29773cz author = Menzella, Francesco title = Pharmacologicaltreatment of COVID-19: lights and shadows date = 2020-05-19 keywords = COVID-19; SARS; patient; treatment summary = At the end of December 2019, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China and then the entire world, forcing the World Health Organization (WHO) to make the assessment that the coronavirus disease (COVID19) can be characterized as a pandemic, the first ever caused by a coronavirus. The search strategy was based on the following keywords: coronavirus, SARS-CoV-2 pneumonia, COVID-19, severe acute respiratory syndrome, antivirals, corticosteroids, biologics, and anticoagulants. Current antiviral treatments are mainly based on previous experiences (favipiravir) or on experimental drugs (remdesivir) used for the treatment of viral infections due to different viruses, such as influenza virus (InfV), Ebolavirus (EBOV), human immunodeficiency virus (HIV), MERS, and SARS. 38 On the contrary, in a study with a small cohort of patients hospitalized for severe SARS-CoV-2 infection, no strong antiviral activity or clinical efficacy of the combination of hydroxychloroquine and azithromycin was found. doi = 10.7573/dic.2020-4-6 id = cord-269470-emzr3dzb author = Menéndez, Cintia A. title = Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease date = 2020-09-11 keywords = Fig; SARS summary = In addition, the authors considered the potential mutability of residues belonging to the M pro catalytic site and explained that the development of drug resistance associated with the natural evolution of M pro could wipe out efforts that target this protein for COVID-19 treatment. Apart from these residues, ebselen bound at both sites shows the lowest  factor values; however, at this specific point, this system exhibits as high flexibility as M pro -apo protein (Fig. 3A , green line). A total of more than 6 s of classical MD simulations of SARS-CoV-2 M pro -apo state and M pro -ebselen complex were run using the AMBER18 (29) simulation package (3 s, ebselen as a molecular probe; 2.4 s, shear strain analysis; 100 ns, water structure and flux analysis; 990 ns, free energy analysis). doi = 10.1126/sciadv.abd0345 id = cord-027582-ygforvya author = Mermel, Leonard A. title = Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) date = 2020-06-10 keywords = SARS summary = title: Disposition of patients with coronavirus disease 2019 (COVID-19) whose respiratory specimens remain positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) by polymerase chain reaction assay (PCR) Patients with coronavirus disease 2019 (COVID-19) infection may respiratory tract specimens positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) for several days while in isolation precautions or for several weeks after removal from isolation precautions. Thus, decisions regarding discontinuing isolation precautions for severely immunocompromised patients, or possibly those who are otherwise critically ill with COVID-19 infection, should be based on a high SARS-CoV-2 PCR cycle threshold. Are patients infectious if they previously had a COVID-19 infection, met criteria for removal from isolation precautions, and they have SARS-CoV-2 PCR-positive respiratory tract specimens over the next several weeks? doi = 10.1017/ice.2020.286 id = cord-350172-w3yoxhsg author = Mertens, Pascal title = Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date = 2020-05-08 keywords = COVID-19; PCR; Respi; SARS; Strip summary = Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. Regarding the COVID-19 pandemic and the urgency of sharing relevant data, in this original research article we describe the analytical performance of the COVID-19 Ag Respi-Strip according to the requirements of the current European Directive 98/79/EC (9) , the future European Regulation 2017/746 on in vitro diagnostic (IVD) medical devices (10) , the Scandinavian SKUP-protocol (11) used for the validation of qualitative tests and the clinical performance obtained with a multi-centric retrospective study. Overall, 328 nasopharyngeal samples from symptomatic patients suspected of SARS-CoV-2 infections attending from 19th to 30th March 2020 in three university laboratories located in Belgium were tested following the manufacturer''s instructions to assess the clinical sensitivity, clinical specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy in order to propose a diagnostic algorithm adapted to the current situation. doi = 10.3389/fmed.2020.00225 id = cord-334220-sqvfr31q author = Messina, Francesco title = Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date = 2020-11-03 keywords = COVID-19; CoV-2; SARS; protein summary = The functional analysis for all proteins, linked to many aspects of COVID-19 pathogenesis, allows to identify the subcellular districts, where SARS-CoV-2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients. In SFigure For KEGG database the gene enrichment analysis on interactomes of NS7b, ORF1a, ORF3a and ORF8 showed pathway clusters highly significant and consistent with possible pathogenic mechanisms, such as the activation of the complement and of the coagulative cascade, (29) and the TGF-β-dominated immune response (30) . We identified different host response induced by specific proteins of SARS-CoV-2, underlining the important role of ORF3a and ORF8 in phenotypes of severe COVID-19 patients. doi = 10.1101/2020.11.03.366666 id = cord-311012-wyglrpqh author = Meyers, Craig title = Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date = 2020-09-28 keywords = IPA; SARS; virus summary = AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. doi = 10.1016/j.jhin.2020.09.026 id = cord-291920-gtzc69lc author = Meyers, Kristin J. title = A cross‐sectional community‐based observational study of asymptomatic SARS‐CoV‐2 prevalence in the greater Indianapolis area date = 2020-06-16 keywords = SARS summary = The Asymptomatic novel CORonavirus iNfection (ACORN) study was designed to investigate the prevalence of SARS‐CoV‐2 infection in the asymptomatic adult population of the Indianapolis metropolitan area, to follow individuals testing positive for the development of symptoms, and to understand duration of positive test results. A nested longitudinal study for participants who test positive for SARS-CoV-2 is ongoing to investigate symptom development at approximately 2 weeks post-index testing. Further, participants who test positive are invited to return for repeat testing at approximately 2-week intervals until the nasopharyngeal swab result is negative for SARS-CoV-2 infection (for a maximum of 3 additional tests). Baseline characteristics, medical history, and overall infection risk factors were generally consistent between SARS-CoV-2 positive and negative participants (Table I) . The identified prevalence of asymptomatic SARS-CoV-2 infection in the community from the ACORN study, the high This article is protected by copyright. doi = 10.1002/jmv.26182 id = cord-271849-wxmr8eki author = Meysman, Pieter title = Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date = 2020-09-09 keywords = SARS summary = In this paper, we demonstrate the use of machine learning to classify SARS-CoV-2 epitope specific T-cell clonotypes in T-cell receptor (TCR) sequencing data. We apply these models to public TCR data and show how they can be used to study T-cell longitudinal profiles in COVID-19 patients to characterize how the adaptive immune system reacts to the SARS-CoV-2 virus. No other epitopes present in TCRex (including the 49 non-SARS-CoV-2 models) were predicted to have a single TCR target within this data set. Once established, these models can be applied to any TCR repertoire data and thus can be used to study putative SARS-CoV-2 reactive T cells in the currently available COVID-19 data. In addition, using such models on longitudinal data reveals a potential difference in temporal dynamics between T cells predicted to react against epitopes that are unique to SARS-CoV-2 and those that are shared among other coronaviruses. doi = 10.1101/2020.09.09.289355 id = cord-354113-j8odxs1h author = Miao, Congliang title = A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19 date = 2020-03-24 keywords = COVID-19; SARS summary = Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group. Methods We retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in We retrospectively collected demographic data, medical history, epidemiological, clinical, laboratory, and CT imaging characteristics of all suspected patients on admission from medical records. 22.20040782 doi: medRxiv preprint This report demonstrated that the incidence of dry cough in confirmed group was significantly higher than that in unconfirmed group, but the clinical symptoms of patients with COVID-19 were nonspecific. doi = 10.1101/2020.03.22.20040782 id = cord-308752-uylvtqlu author = Miao, Y. title = First case of acute pancreatitis related to SARS‐CoV‐2 infection date = 2020-06-03 keywords = SARS summary = title: First case of acute pancreatitis related to SARS‐CoV‐2 infection Indeed, we have made similar observations: abdominal pain mimicking surgical disease is frequent during the first days of COVID-19, specifically pancreatitis-like presentation. We report the first case of symptomatic acute pancreatitis associated with SARS-CoV-2 without pulmonary symptoms. Blood tests revealed leucocytes 5960/mm 3 , haemoglobin 13⋅7 g/dl, neutrophils 3650/mm 3 , lymphocytes 1580/mm 3 , eosinophils 30/mm 3 , platelets 242 000/mm 3 , lipase at 211 U/l (3⋅5 N), gamma-glutamyl transferase 65 UI/l, alcaline phosphatase level 83 U/l, lactate dehydrogenase 170 U/l and C-reactive protein at 13⋅8 mg/l. Lipase level peaked on day 4 (430 U/l = 7 N). 4 reported elevated lipase or amylase in 17 per cent of a Chinese cohort without mentioning abdominal pain. Covid-19-related pancreatic injury Pancreatic injury patterns in patients with COVID-19 pneumonia Binding of SARS coronavirus to its receptor damages islets and causes acute diabetes doi = 10.1002/bjs.11741 id = cord-305521-lkou3ycu author = Michel, W. title = A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay date = 2020-09-27 keywords = SARS summary = title: A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay Conclusions: Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. We compared mouthwash fluid with a 24 combined oro-nasopharyngeal swab regarding test performance. A meta-53 analysis of different SARS-CoV-2 studies showed the highest detection rates in Expected shortages of swabs led us to assess alternative diagnostic specimens. In 59 this study, we compared test performance when using mouthwash or a combined oro-60 nasopharyngeal swab. This may limit its use in patients 144 to minimize exposure of health-care personel.In conclusion, SARS-CoV2 detection 145 with mouthwash showed a low sensitivity compared to oro-nasopharyngeal swabs. doi = 10.1101/2020.09.25.20201541 id = cord-287101-k3zq75zc author = Micheli, V. title = Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase date = 2020-07-24 keywords = Italy; SARS summary = The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. A dataset of 41 genome assemblies of Sars-Cov-2 strains isolated in Italy between 20 February 2020 and 30 March 2020 were retrieved from GISAID database 12 , (see Supplementary Table 1 for details). All patients were resident in Lombardy Region, distributed in different provinces, as reported in table X: in particular, the category ''Milano'' contains also patients hospitalized for non-COVID-19 disease, for whom SARS-CoV-2 hospital acquisition was supposed; in addition, HSacco-20, in ''Other'' category, was a nurse living in Bergamo and working at Lodi Hospital. doi = 10.1101/2020.07.23.20159871 id = cord-306770-hjzlj8k3 author = Mick, Paul title = Aerosol-generating otolaryngology procedures and the need for enhanced PPE during the COVID-19 pandemic: a literature review date = 2020-05-11 keywords = AGMP; COVID-19; Health; PPE; SARS summary = During the coronavirus disease 2019 (COVID-19) pandemic, personal protective equipment (PPE) worn by health care workers is critical for reducing transmission of the infection in health care settings, particularly when aerosol-generating medical procedures (AGMP) are being performed. For example, Givi et al and the Canadian Society of Otolaryngology-Head and Neck Surgery [2] call for airborne precautions when performing AGMP on patients for whom the index of suspicion for COVID-19 infection is not high, whereas the World Health Organization, the U.S. Centers for Disease Control, and the Public Health Agency of Canada do not [3, 14, 15] . Measuring the level of aerosolized viral particles in rooms where AGMPs are being performed on patients with COVID-19 would provide indirect evidence of the degree to which these procedures put health care workers at risk of aerosolized transmission, and whether exposure concentration affects risk of infection and/or severity of disease. doi = 10.1186/s40463-020-00424-7 id = cord-274122-n9jnu2ah author = Mielech, Anna M. title = MERS-CoV papain-like protease has deISGylating and deubiquitinating activities date = 2014-02-01 keywords = CoV; MERS; SARS summary = Coronaviruses encode papain-like proteases (PLpro) that are often multifunctional enzymes with protease activity to process the viral replicase polyprotein and deubiquitinating (DUB)/deISGylating activity, which is hypothesized to modify the innate immune response to infection. Further, we compared the ability of MERS-CoV PLpro and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) PLpro to block innate immune signaling of proinflammatory cytokines. In this study, we demonstrate the deISGylating and deubiquitinating (DUB) activities of the papain-like protease from MERS-CoV, and provide new information on the potential role of coronavirus protease/DUBs to inhibit the innate immune response. Our results suggest that PLpro might contribute to the modulation of innate immune responses upon SARS-CoV and MERS-CoV infection, however, the exact mechanism and the role of coronavirus PLPs and their associated DUB and deISGylating activities in these processes remains to be determined. doi = 10.1016/j.virol.2013.11.040 id = cord-323967-2mo915u1 author = Miersch, Shane title = Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations date = 2020-11-01 keywords = Fig; RBD; SARS summary = Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Moreover, the use of a highly stable framework 77 enabled facile and modular design of ultra-high affinity nAbs in tetravalent formats that retained 78 favorable drug-like properties and exhibited neutralization potencies that greatly exceeded those 79 of the bivalent IgG format. Fab-phage were screened by ELISA and those that exhibited >50% loss in binding 92 to RBD in the presence of 200 nM ACE2 were sequenced, revealing 34 unique clones (Fig. 1A) , 93 deemed to be potential nAbs and converted into the full-length human IgG1 format for 94 purification and functional characterization. doi = 10.1101/2020.10.31.362848 id = cord-292561-iy06b9h9 author = Miesbach, Wolfgang title = COVID-19: Coagulopathy, Risk of Thrombosis, and the Rationale for Anticoagulation date = 2020-07-17 keywords = COVID-19; SARS; patient summary = The novel coronavirus infection (COVID-19) is caused by the new coronavirus SARS-CoV-2 and is characterized by an exaggerated inflammatory response that can lead to severe manifestations such as adult respiratory syndrome, sepsis, coagulopathy, and death in a proportion of patients. 5 While most patients show only mild symptoms, 6 a characteristic feature of COVID-19 is that a proportion of patients develop severe complications within a short time after infection, such as adult respiratory syndrome (ARDS) or disseminated intravascular coagulation (DIC), sepsis followed by organ failure, and death. 15 These laboratory changes are consistent with previous studies which showed that hypoalbuminemia, lymphopenia, and C-reactive protein 4 mg/dL were the predictive factors for the progression of pneumonia to respiratory failure in MERS-CoV-infected patients and that elevated lactate dehydrogenase (LDH) levels were associated with hospital-acquired infection with SARS-CoV. doi = 10.1177/1076029620938149 id = cord-339701-j0sr3ifq author = Mikami, Takahisa title = Risk Factors for Mortality in Patients with COVID-19 in New York City date = 2020-06-30 keywords = COVID-19; SARS summary = PARTICIPANTS: 6493 patients who had laboratory-confirmed COVID-19 with clinical outcomes between March 13 and April 17, 2020, who were seen in one of the 8 hospitals and/or over 400 ambulatory practices in the New York City metropolitan area MAIN MEASURES: Clinical characteristics and risk factors associated with in-hospital mortality. Cox proportional hazard regression modeling showed an increased risk of in-hospital mortality associated with age older than 50 years (hazard ratio [HR] 2.34, CI 1.47–3.71), systolic blood pressure less than 90 mmHg (HR 1.38, CI 1.06–1.80), a respiratory rate greater than 24 per min (HR 1.43, CI 1.13–1.83), peripheral oxygen saturation less than 92% (HR 2.12, CI 1.56–2.88), estimated glomerular filtration rate less than 60 mL/min/1.73m(2) (HR 1.80, CI 1.60–2.02), IL-6 greater than 100 pg/mL (HR 1.50, CI 1.12–2.03), D-dimer greater than 2 mcg/mL (HR 1.19, CI 1.02–1.39), and troponin greater than 0.03 ng/mL (HR 1.40, CI 1.23–1.62). In this study, we describe the clinical characteristics of COVID-19 in ambulatory and inpatient settings and identify risk factors associated with mortality in hospitalized patients. doi = 10.1007/s11606-020-05983-z id = cord-330213-reb9vo7x author = Miladi, Milad title = The landscape of SARS-CoV-2 RNA modifications date = 2020-07-18 keywords = RNA; SARS; TRS summary = From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). doi = 10.1101/2020.07.18.204362 id = cord-287847-rmhvc5n5 author = Miles, Brett A. title = Tracheostomy during SARS‐CoV‐2 pandemic: Recommendations from the New York Head and Neck Society date = 2020-04-20 keywords = CoV-2; SARS; tracheostomy summary = Patients with significant medical comorbidities, acute respiratory distress syndrome/severe respiratory failure and a low chance of recovery who are infected with SARS-CoV-2 should be carefully evaluated, and discussions with family members, consultants, institutional ethics committees and the treating team should focus on overall prognosis and goals of care prior to performing tracheostomy as a routine matter of care. Although there are limited data on the current pandemic to fully inform personal protective equipment (PPE) recommendations, performing tracheostomy in an actively infected SARS-CoV-2 patient is certainly a high-risk procedure for health care workers. Techniques to manage the acute airway with endotracheal intubation, video laryngoscope for example, should be utilized if possible to avoid emergent tracheostomy in SARS-CoV-2 patients due to the high risk of unsafe conditions and health care worker contaminations. • When clinically appropriate, delay of tracheostomy procedures is recommended to allow for reduced viral load and to decrease the risk of nosocomial infection to critical health care providers. doi = 10.1002/hed.26166 id = cord-350182-s10nong7 author = Milionis, Charalampos title = A brief analysis and hypotheses about the risk of COVID-19 for people with type 1 and type 2 diabetes mellitus date = 2020-07-20 keywords = COVID-19; SARS; diabetes summary = Coronavirus disease 2019 (COVID-19) is a respiratory infection which is caused by a novel virus belonging to the Coronaviridae family [1] and is officially named SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The existence of diabetes is strongly associated with an increased risk of developing severe COVID-19 in case of infection with SARS-CoV-2 [24, 25] . The present article supports that heightened inflammatory processes constitute the main pathophysiologic factor for the severity of COVID-19 among patients with diabetes mellitus, whilst impairments in immune response and diabetic comorbidities contribute to the aggravated pathogenesis. Yet it remains unclear whether the innate immune response is vitally impaired in both types of diabetes mellitus and whether hyperglycaemia favours the initial virulence of SARS-CoV-2. Furthermore, patients with diabetes mellitus may present dysfunctional type IV (delayed) hypersensitivity reaction and abnormal complement activation [35] which may hinder the immune response. Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? doi = 10.1007/s40200-020-00592-3 id = cord-330287-bkqjkhwu author = Miller, Danielle title = Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel date = 2020-11-02 keywords = Fig; Israel; March; SARS; U.S. summary = So-called genomic epidemiology allows for effective reconstruction of viral geographical spread as well as estimation of key epidemiological quantities such as the basic reproduction number of a virus, its growth rate and doubling time, and patterns of disease incidence and prevalence. Here, we set out to sequence SARS-CoV-2 from samples across the state of Israel, with the aim of gaining a better understanding of introductions of the virus into Israel, spread of the virus inside the country, and the epidemiology of the disease, including (a) the basic reproduction number of the virus before and after social distancing measures were implemented, and (b) the extent of viral superspreading within Israel. To estimate the basic reproduction number of SARS-CoV-2 in Israel initially and then following the implementation of social distancing measures, we performed coalescent-based phylodynamic inference using the PhyDyn program implemented in BEAST2 (Methods). Our phylodynamic analysis assumes an underlying susceptibleexposed-infected-recovered (SEIR)-type epidemiological model for SARS-CoV-2 transmission dynamics and explicitly incorporates transmission heterogeneity ( Supplementary Fig. 4 , Methods). doi = 10.1038/s41467-020-19248-0 id = cord-266156-xmf4emln author = Miller, Tyler E. title = Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date = 2020-08-28 keywords = CoV-2; PCR; SARS; day summary = Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. The goal of this study is to examine the clinical sensitivity and provide insights into the interpretation of the two most common SARS-CoV-2 diagnostic test modalities: polymerase chain reaction (PCR) and serology. Serologic analysis of IgM, IgA and IgG status was performed in a subset of the above SARS-CoV-2 PCR-positive patients for which we had excess material in the MGH core laboratories for clinical validation studies. To assess the sensitivity of our serology assay over time, we tested for IgM, IgG, and IgA antibodies against the RBD of SARS-CoV-2 spike protein in 157 SARS-CoV-2 PCR-positive patients using an in-house ELISA (Table 1) . doi = 10.1096/fj.202001700rr id = cord-281391-0qkku2jd author = Miller-Handley, Hilary title = Treatment Options for COVID-19 in Patients with Reduced or Absent Kidney Function date = 2020-09-17 keywords = COVID-19; SARS; clinical; patient summary = COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, was first identified in the Hubei Province of China in late 2019. Because of these findings, chloroquine and hydroxychloroquine were used as early therapies in the treatment of COVID-19, and its use was further propagated by a small, retrospective, biased study from France with 36 patients which showed decrease in viral burden, and improved outcomes in patients treated with hydroxychloroquine [17] . A retrospective study from the Veterans Affairs, looked at hospitalized patients who received hydroxychloroquine and showed no evidence that use of hydroxychloroquine reduced the risk of progression of disease including mechanical ventilation and death [20] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1053/j.ackd.2020.09.001 id = cord-301947-b6nwaost author = Millán-Oñate, José title = Successful recovery of COVID-19 pneumonia in a patient from Colombia after receiving chloroquine and clarithromycin date = 2020-04-24 keywords = COVID-19; SARS; day; patient summary = We report here the clinical features and therapeutic course of the first reported patient with confirmed COVID-19 pneumonia that recovered in Colombia, after the use of chloroquine and clarithromycin. It is essential to acknowledge that no good controlled data are supporting the use of any of these agents, except for a recent randomized, controlled, open-label trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection, that showed no benefit with lopinavir-ritonavir (LPV/RTV) treatment beyond standard care [13] . We present a confirmed case of COVID-19 from Buga, Valle del Cauca, Colombia, that successful recovered of SARS-CoV-2 infection after receiving chloroquine. Although that just based in one case, we cannot recommend the use of these drugs, our patient improved significantly, and his clinical manifestations ceased, including becoming negative for the SARS-CoV-2 infection, as observed in the rRT-PCR test. doi = 10.1186/s12941-020-00358-y id = cord-284302-odvv2yn3 author = Minagorre, Pedro J. Alcalá title = CAMBIOS A PARTIR DE LA COVID-19. UNA PERSPECTIVA DESDE LA PEDIATRÍA INTERNA HOSPITALARIA date = 2020-06-19 keywords = COVID-19; SARS summary = Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Se revisa también la implicación de las unidades pediátricas en la asistencia de adultos y la atención de pacientes crónicos complejos y se ofrecen recomendaciones sobre aspectos de seguridad, consideraciones éticas y docencia de los futuros pediatras durante la crisis. Pero ante el impacto anual del VRS y la gripe en las unidades de críticos (15, 16) y los posibles rebrotes de COVID-19, se ha de proveer una adecuada disponibilidad de recursos para el conjunto de pacientes afectados. El notable incremento del número de niños con patología crónica compleja en los últimos años obliga a todos los centros a disponer de planes asistenciales específicos para este grupo de pacientes, también en situaciones excepcionales como esta pandemia por COVID-19. doi = 10.1016/j.anpedi.2020.06.004 id = cord-274114-fglyfz8p author = Minervina, Anastasia A. title = Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date = 2020-10-01 keywords = CD4; CD8; SARS summary = In this study we use longitudinal TCRalpha and TCRbeta repertoire sequencing to quantitatively track T cell clones that significantly expand and contract after recovery from a mild COVID-19 infection, and determine their phenotype. We reveal the dynamics and the phenotype of the memory cells formed after infection, identify pre-existing T cell memory clones participating in the response, and describe public TCR sequence motifs of SARS-CoV-2-reactive clones, suggesting a response to immunodominant epitopes. At the time of writing, no data on TCR sequences specific to MHC-II class epitopes exist to map specificities of CD4+ T-cells in a similar way as we did with MIRA-specific TCRs. However, a recently published database of 1414 bulk TCRbeta repertoires from COVID-19 patients allowed us to confirm the SARS-CoV-2 specificity of contracting clones indirectly. Public TCRbeta sequences that can recognize SARS-CoV-2 epitopes are expected to be clonally expanded and thus sampled more frequently in the repertoires of COVID-19 patients than in control donors. doi = 10.1101/2020.05.18.100545 id = cord-322596-vfmzk2el author = Ming, Yi title = Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications date = 2020-07-11 keywords = ACE2; COVID-19; SARS summary = Current clinical reports indicate that SARS-CoV-2 is associated with significant morbidity of cardiovascular diseases and complications, such as hypertension (HTN), myocarditis, acute myocardial infarction, and increased heart failure [5, 6] . Based on these theoretical assumptions, it can be concluded that the S protein/host furin/ACE2 signal axis exists in the pathological process of SARS-Cov-S2 infection and mediates the occurrence of adverse cardiovascular prognosis events. Furthermore, a unique furin-like cleavage site exists in the S protein of SARS-Cov-S2 [16] ; thus, the theoretical advantage inferred from this cleavage site in disease infection models can be deduced to prevent and combat COVID-19 caused by SARS-CoV-2. However, in the process of infection, the S protein plays a direct damaging role by recognizing and binding to the ACE2 receptor and invading the host cell [10] . Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein doi = 10.1007/s42399-020-00400-2 id = cord-291513-vpehn6nx author = Minich, Jeremiah title = Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date = 2020-08-18 keywords = Fig; RNA; SARS; TMI; swab summary = Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. Here we characterize the suitability of detecting SARS-CoV-2 RNA in experimental conditions as well as COVID-19 patient and built-environment samples using viral-inactivating storage solutions and alternative medical-grade and consumer-grade swabs. In a subset of seven COVID-19 patient nares samples stored in 95% EtOH, we also detected signi cantly higher SARS-CoV-2 viral load in RNA extracted from the swab head versus eluent ( Fig. 1b ; one-tailed paired Student''s t-test p = 0.03). Based on the results from these initial experiments, we conducted a proof-of-concept study in the clinical setting by performing RT-qPCR for the SARS-CoV-2 N1 amplicon and human RNase P gene on RNA extracted from the swab head of nasal samples collected using TMI and/or CGp swabs alongside the recommended SYN swabs. doi = 10.21203/rs.3.rs-56028/v1 id = cord-294115-7t7kubf6 author = Miralles, Oriol title = Unmet needs, health policies, and actions during the COVID-19 pandemic: a report from six European countries date = 2020-10-15 keywords = COVID-19; March; SARS; care; health; old summary = The information collected from the six national reports was pulled together and discussed following the key priorities for action outlined in the UN Policy Brief: (1) Right to health and the participation in the decision-making process; (2) Social inclusion and solidarity under conditions of physical distancing; (3) Necessity of adequate, correctly funded care and support services for older adults; and (4) Need to expand participation by older adults, share good practice and harness knowledge and data [4] . In the Frenchspeaking region, the "Plan d''Urgence Hospitalier" was launched on 14th March and focused on ensuring distribution of hospital equipment, including personal protective equipment (PPE), and human resources (e.g., by reduction/ Impact of COVID-19 on health inequity: On 25th May, Belgium had reported 5734 people with confirmed SARS-CoV-2 infection in long-term care facilities (LTCF). doi = 10.1007/s41999-020-00415-x id = cord-349623-dw5o9i59 author = Miranda, José P. title = Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date = 2020-10-15 keywords = RNA; SARS summary = Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise''s buffer pH 7.2. For the standard protocol, routinely used in the laboratory for the detection of SARS-CoV-2, an aliquot of 180 ul of the sample from the nasopharyngeal swab, including 10 ul of extraction control, was used to extract RNA with the MagNA Pure 96 DNA and Viral NA LV Kit (Roche Diagnostics, Cat. No. For the standardization of the direct SARS-CoV-2 detection protocol without RNA extraction steps, 50 ul aliquots from the primary sample (nasopharyngeal swabs) of 5 anonymized patients were subjected to heat shock (65, 70, or 95 • C) during different incubation times (5, 10, or 30 min), and then were quickly placed at 4 • C until the moment of amplification. doi = 10.3389/fmed.2020.567572 id = cord-346894-iy35298o author = Miranda-Schaeubinger, Monica title = A primer for pediatric radiologists on infection control in an era of COVID-19 date = 2020-07-07 keywords = Health; PPE; SARS; covid-19; patient summary = In pediatric radiology departments, the risk involved ranges from low (e.g., office workers, remote workers, telemedicine) to very high (e.g., workers performing aerosol-generating procedures on known or suspected COVID-19 patients), depending on the job task assigned [28, 29] . Standard precautions to minimize the spread of infection within health care facilities from direct contact with contaminations include hand hygiene, use of PPE based on anticipated contact with contaminated material, respiratory hygiene/ cough etiquette, cleaning and disinfection of the environment, and proper handling of patient care equipment and waste [10] . Appropriate personal protective equipment usage stratified by COVID-19 status (Table 3) Because of the possibility of airborne transmission of the virus, the CDC recommends respirators for care of all patients with COVID-19 if adequate supplies are available. For all aerosol-generating procedures in children who have either unknown or confirmed positive COVID-19 status, radiologists should adhere to the highest level of respiratory protection available: a respirator, an eye shield, a disposable gown and gloves. doi = 10.1007/s00247-020-04713-1 id = cord-352341-dhc748pn author = Miranda-Zazueta, G. title = Manejo farmacológico de pacientes con enfermedades hepáticas y pancreáticas que involucran terapias inmunosupresoras. Posicionamiento en el marco de la pandemia de SARS-COV-2 (COVID-19) date = 2020-06-17 keywords = COVID-19; SARS summary = 5 Hasta este momento se han emitido las siguientes recomendaciones en pacientes infectados por COVID-19 que tienen una enfermedad hepática autoinmune de base y usan inmunosupresores: [5] [6] [7] [8]  El presentar alteraciones en las pruebas de función hepática no limita iniciar el tratamiento para COVID-19. Las recomendaciones generales para el manejo de pacientes con trasplante hepático y diagnóstico de COVID-19 se realizan de acuerdo con los diferentes escenarios posibles que nos podemos enfrentar en la práctica clínica. No existe hasta el momento de esta publicación información sobre el riesgo de infecciones en pacientes con inmunosupresión y Pancreatitis Autoinmune (PAI), muchos menos en el contexto del nuevo coronavirus SARS-CoV-2, Sin embargo, teóricamente este riesgo no debería ser mayor al observado para otro tipo de infecciones. doi = 10.1016/j.rgmx.2020.06.001 id = cord-258128-qtmjgrml author = Mirjalili, Mahtabalsadat title = Coronavirus Disease 2019 (COVID-19) and Transplantation: Pharmacotherapeutic Management of Immunosuppression Regimen date = 2020-07-03 keywords = COVID-19; SARS; drug; patient; transplant summary = 12 In one case report regarding the successful treatment of a kidney transplant recipient with pneumonia caused by SARS-CoV-2 in China, all the immunosuppressants were stopped and the patient received 5 g intravenous immunoglobulin (IVIG) on the first day and then 10 g/day for the next 11 days, with 40 mg/day methylprednisolone for 12 days and 5 million units/day interferon as atomization inhalation. 17, 18 Considering that adverse clinical outcomes and increased mortality and morbidity following the administration of corticosteroids in patients with respiratory infections caused by respiratory syncytial virus (RSV), influenza, SARS-CoV-1, or MERS-CoV may be due to an increased risk of secondary bacterial infections, their use for the prevention of disease progression or its treatment remains under discussion. So far, few studies have been conducted regarding the use of this drug in liver and kidney transplant patients, but if it is administered to this population, its adverse effects and interactions with immunosuppressants and other medications used in transplant patients, such as fluoroquinolones for the treatment of Gram-negative infections, should be considered. doi = 10.2147/tcrm.s256246 id = cord-103899-6tqm99g1 author = Mirzaei, Rasoul title = The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date = 2020-11-13 keywords = MERS; RNA; RSV; SARS; cell; covid-19 summary = Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. This review will summarize the recent discoveries associated with miRNAs in various respiratory infections caused by viruses, especially coronavirus, and address all feasible therapeutic options to mitigate the burden of VRIs. The humoral immunity is immunologically categorized as an acquired immune response in which T helper cells collaborate with B cells to differentiate these types of cells to plasma cells [17] [18] [19] . The immune responses against VRIs, such as IV, hRV, human coronavirus (HcoV), hMPV, and RSV, are correlated with the aberrant expression of several miRNAs in epithelial cells and participate in the pathogenesis of chronic and acute forms of respiratory disorders (Table 1 ) [16] . doi = 10.1016/j.intimp.2020.107204 id = cord-328659-miujzgtd author = Mishra, Akhilesh title = Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date = 2020-07-27 keywords = RNA; SARS summary = title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. doi = 10.1101/2020.05.07.082768 id = cord-321146-dd8z5c6d author = Mishra, Rakesh title = SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem date = 2020-07-30 keywords = SARS summary = title: SARS-CoV 2 and the Pathobiology of the Respiratory Control Mechanisms in the Brainstem It is prudent to identify if SARS CoV-2 affects the respiratory control mechanisms at the brainstem and lead to complications in addition to primary respiratory damage. 5 There are reports which suggest that involvement of pontine and medullary centres by SARS-CoV-2 is a mechanism implicated in potential central respiratory failure complicating primary pulmonary injury. Recently a case report published illustrated brainstem dysfunction due to rhombencephalitis in a patient with acute COVID-19. 7 Therefore, patients with SARS-CoV-2 with neurological symptoms must be followed up closely as they can have further deterioration in their respiratory function. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients Does SARS-Cov-2 invade the brain? Neurologic features in severe SARS-CoV-2 infection Neurological manifestations of patients with COVID-19: potential routes of SARS-CoV-2 neuroinvasion from the periphery to the brain doi = 10.1016/j.jfma.2020.07.035 id = cord-323832-w19ump0o author = Mishra, Vijaya Nath title = Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection date = 2020-09-19 keywords = SARS; phage summary = It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. Since currently available antiviral drugs attack influenza and coronavirus after they have already infected the lung cells, it is important to target the virus and prevent infection in the first stage of viral infection. Phages in the body compete with the other highly infective eukaryotic viruses for cellular receptors and thereby restrict their harmful actions on the host cell [23] . A study of staphylococcal phages on the expression of genes which are involved in antimicrobial immunity in the A549 cell line showed that there is an increased translation of interleukin-2 (IL-2) [25] . e in vitro studies on bacteriophage influence on the ability of human viruses to infect epithelial cells doi = 10.1155/2020/8844963 id = cord-154844-nuqx3tv6 author = Misirli, Goksel title = A comparative analysis for SARS-CoV-2 date = 2020-04-08 keywords = SARS summary = Comparative analyses particularly can play a key role to reveal structural changes in proteins due to mutations, which can lead to behavioural changes, such as the increased binding of the SARS-CoV-2 surface glycoprotein to human ACE2 receptors. Starting with a SARS-CoV-2 genome sequence, the report shows visualising DNA sequence features, deriving amino acid sequences, and aligning different genomes to analyse mutations and differences. The report provides further insights into how the SARS-CoV-2 surface glycoprotein mutated for higher binding affinity to human ACE2 receptors, compared to the SARS-CoV protein, by integrating existing 3D protein models. Here, we integrated secondary structure predictions and realigned the sequences in order to show how these five mutations may affect the binding of the SARS-CoV-2 protein ( Figure 6 ). Compared to the SARS-CoV secondary structures, both the CLC Genomics Workbench predictions and the SARS-CoV-2 ''6W41'' model reveal additional beta strands in the mutated region (shown using the dashed box in Figure 6 ) of the surface glycoprotein. doi = nan id = cord-253833-0lajhqn5 author = Misra-Hebert, Anita D title = Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system. date = 2020-08-19 keywords = SARS; covid-19; hcw summary = [7] [8] [9] 11 A recent prospective study in the United Kingdom and US suggested a ve-fold increased risk for HCW caring for patients with COVID-19 compared to HCW not caring for patients with COVID-19, even with the use of PPE 12 while another study of HCW in a large healthcare system showed a decrease in positive tests for SARS-CoV-2 associated with a universal masking recommendation. In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19 related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. [7] [8] [9] [10] 12 The fact that HCW identi ed as patient-facing had a signi cantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. doi = 10.21203/rs.3.rs-61235/v1 id = cord-261173-lnjh56ts author = Misra-Hebert, Anita D. title = Impact of the COVID-19 Pandemic on Healthcare Workers’ Risk of Infection and Outcomes in a Large, Integrated Health System date = 2020-09-01 keywords = SARS; covid-19; hcw summary = In this study, we aimed to assess whether HCW are at higher risk for COVID-19 infection, COVID-19-related hospitalization, and intensive care unit (ICU) admission compared to non-HCW using advanced statistical methodology to account for various confounders. 23 For the outcomes of hospital and intensive care unit (ICU) admission of COVID-19 testpositive patients, the propensity score covariates are those that were found associated with COVID-19 hospitalization outcome in our previous work including age, race, ethnicity, gender, smoking history, body mass index, median income, population per housing unit, presenting symptoms (including fever, fatigue, shortness of breath, diarrhea, vomiting), comorbidities (including asthma, hypertension, diabetes, immunosuppressive disease), medications (including immunosuppressive treatment, nonsteroidal anti-inflammatory drugs [NSAIDs]), and laboratory values (including pre-testing platelets, aspartate aminotransferase, blood urea nitrogen, chloride, and potassium). [7] [8] [9] [10] 12 The fact that HCW identified as patient facing had a significantly higher odds for SARS-CoV-2 test positivity suggests an increased risk of COVID-19 infection with work exposure. doi = 10.1007/s11606-020-06171-9 id = cord-340821-kelq45dw author = Misrahi, James J. title = HHS/CDC Legal Response to SARS Outbreak date = 2004-02-17 keywords = CDC; SARS summary = Before the severe acute respiratory syndrome (SARS) outbreak, the Centers for Disease Control and Prevention''s (CDC) legal authority to apprehend, detain, or conditionally release persons was limited to seven listed diseases, not including SARS, and could only be changed using a two-step process: 1) executive order of the President of the United States on recommendation by the Secretary, U.S. Department of Health and Human Services (HHS), and 2) amendment to CDC quarantine regulations (42 CFR Parts 70 and 71). Recognizing the cross border nature of some communicable diseases and in light of this nation''s constitutional structure, section 361 of the Public Health Service Act (42 United States Code section 264) authorizes the Health and Human Services (HHS) Secretary to make and enforce regulations necessary to prevent the introduction, transmission, and spread of communicable diseases from foreign countries into the United States and from one state or possession into another. doi = 10.3201/eid1002.030721 id = cord-292004-9rpoll7y author = Mitchell, Hugh D. title = The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections date = 2019-09-20 keywords = EGFR; SARS; figure; gene summary = The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. The same relationships between network topology, viral pathogenicity, and gene expression that were observed for influenza virus were also noted when we used a similar dataset of SARS-CoV infections, thus further validating our analysis and demonstrating that these relationships appear to apply to respiratory viruses in general. doi = 10.3389/fcell.2019.00200 id = cord-324707-9ld73wv1 author = Mitjà, Oriol title = Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date = 2020-07-16 keywords = HCQ; Jordi; SARS; covid-19 summary = Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . doi = 10.1093/cid/ciaa1009 id = cord-313755-y7regza1 author = Mitra, Kartik title = Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads date = 2020-07-22 keywords = SARS; figure summary = Further, docking of these candidates against SARS-CoV-2 3CLp and PLp indicated that nelfinavir, tipranavir, novobiocin and ofloxacin, possessed better binding potential when compared to lopinavir (binding energy ¼ -7.3 kcal/mol). Our study suggests that nelfinavir and tipranavir (existing anti-HIV protease inhibitors) which bears the desired pharmacophoric features could be considered as potential candidates for inhibiting SARS-CoV-2 proteases. It is heartening to note that these natural products identified in the study have also shown in vitro anti-viral activity against several viruses and hence can be considered as potential lead candidates for designing SARS-CoV-2 inhibitors. The top two candidates with best docking binding energy were selected from the final shortlisted candidates, namely nelfinavir and tipranavir from FDA-approved drugs and licochalcone-D and wedelolactone from natural product database for molecular dynamics simulations studies with both the proteases. doi = 10.1080/07391102.2020.1796802 id = cord-356166-fpno9zg5 author = Miyakawa, Kei title = Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles date = 2020-09-15 keywords = CoV-2; SARS summary = title: Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles However, a simple, convenient, rapid, and high-throughput test capable of directly detecting nAbs with high specificity, which could act as an ideal alternative to the neutralization assay, is yet to be developed (Ozcurumez et al., 2020) . In this report, we have developed a HiBiT-VLP-based neutralization test (hiVNT) that can readily detect SARS-CoV-2 nAbs ( Figure 1A ). We noticed a robust increase in NanoLuc activity when the LgBiT-expressing We next tested whether our newly developed hiVLP-SARS2 system could detect nAbs in the serum of COVID-19 patients. In this study, we established the hiVNT, a simple, high-throughput assay system for the quantitative and rapid determination of SARS-CoV-2 nAbs in the sera of individuals after recovery from symptomatic or subclinical COVID-19. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients'' B Cells doi = 10.1093/jmcb/mjaa047 id = cord-023871-9vi0m378 author = Mizutani, Tetsuya title = Signaling Pathways of SARS-CoV In Vitro and In Vivo date = 2009-07-22 keywords = MAPK; SARS; Vero; cell summary = doi = 10.1007/978-3-642-03683-5_19 id = cord-315337-vgi91uzg author = Mizutani, Tetsuya title = Characterization of Persistent SARS-CoV Infection in Vero E6 Cells date = 2006 keywords = SARS summary = A human intestinal cell line, LoVo, was shown to permit SARS-CoV infection, resulting in the establishment of persistent infection. This cell line expresses the viral receptor ACE-2 4 at high levels, and SARS-CoV infection of Vero E6 causes cytopathic effects within 24 h. In the present study, we established a persistently SARS-CoV-infected cell line after passage 6. Here, we reported a possible mechanism of the establishment of persistent SARS-CoV infection in Vero E6 cells (Fig. 2) . Although the majority of cells died due to apoptosis after SARS-CoV infection, activation of JNK and PI3K/Akt signaling pathways aided a minor population of cells with the potential to support persistent infection to establish persistence. pathways are required for establishing persistent SARS-CoV-infection in Vero E6 cells doi = 10.1007/978-0-387-33012-9_57 id = cord-312477-2y88gzji author = Mlcochova, P. title = Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date = 2020-06-18 keywords = COVID-19; PCR; SARS; test summary = title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. doi = 10.1101/2020.06.16.20133157 id = cord-315278-iv2zj67t author = Moazzam, Zorays title = Intussusception in an infant as a manifestation of COVID-19 date = 2020-06-20 keywords = COVID-19; SARS summary = This is the first documented case of survival in a SARS-CoV-2 positive patient presenting with intussusception as the primary manifestation. A case series from the UK documented 8 COVID-19 patients presenting with fever, abdominal pain and diarrhea with a working diagnosis of systemic sepsis secondary to suspected appendicitis [6] . According to our literature review, this is only the second such instance of a SARS-CoV-2 positive patient presenting to a healthcare center with intussusception as the primary manifestation, and the first documented case in which the patient survived. This would be the first such reported incidence of intussusception as a manifestation of SARS-CoV-2 infection, with no respiratory symptoms. We report, to the best of our knowledge, the first documented instance of survival in a case of intussusception in a SARS-CoV-2 positive pediatric patient. Clinical Characteristics of 5 COVID-19 Cases With Non-respiratory Symptoms as the First Manifestation in Children doi = 10.1016/j.epsc.2020.101533 id = cord-260062-qajk0ov4 author = Mocchegiani, Federico title = Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area date = 2020-09-10 keywords = SARS summary = title: Mild impact of SARS-CoV-2 infection on the entire population of liver transplant recipients: the experience of an Italian Centre based in a high-risk area reported 200 LTRs with 3 tested positive patients for SARS-CoV-2, none developed a clinical pulmonary disease [3] . reported three deaths among 111 long-term adult liver transplant survivors (transplanted more than 10 years ago) following severe COVID-19 while 3 of 40 recently transplanted (ie, within the past 2 years) patients who were found SARS-CoV-2 positive experienced an uneventful course of the disease [4] . reported an incidence of confirmed COVID-19 infection of 1.25% in the population of LTRs of one Milan transplant centre of whom none developed such a severe disease to require invasive ventilation [5] . During the outbreak of COVID-19, in Marche region the infection rate of SARS-Cov-2 has been of 0.44% [1], similar to that observed in our LTRs population. doi = 10.1007/s13304-020-00881-9 id = cord-274520-c674wkmt author = Moelling, Karin title = Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection date = 2020-05-28 keywords = SARS; air; human; pollution summary = title: Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection e authors concluded that there was likely no risk for contracting infectious diseases from pollutant-associated microbes, but they recommended fixing soil by vegetation to reduce the amount of airborne microbes originating from fecal and terrestrial sources, including potential allergens [31] . As observed in the New York City subway, bacterial communities showed significant similarities with those of outdoor air samples, with some human skin-associated bacteria also being present. ere is evidence that people exposed to severe air pollution are more susceptible to infection with the present SARS-CoV-2 pandemic virus and experience stronger symptoms, not only in large cities of China but also in other parts of the world [46] [47] [48] [49] [50] [51] . Potential human pathogens are typically below the detection limit in air samples even from closed environments such as subway systems, which means that there is not likely a significant risk for infection [31, 32, [34] [35] [36] [37] . doi = 10.1155/2020/1646943 id = cord-262420-vw7fnguu author = Moey, Melissa Y.Y. title = Electrocardiographic Changes and Arrhythmias in Hospitalized Patients With COVID-19 date = 2020-09-15 keywords = SARS summary = Subgroup analysis was performed by gender, race, intensive care unit (ICU) admission, troponin-I levels, and SARS-CoV-2 specific therapy (hydroxychloroquine, azithromycin, tocilizumab). Patients had significant lengthening of their QTc intervals during hospitalization regardless of whether they received SARS-CoV-2 specific therapy. Ours is the first report of electrocardiographic changes in patients hospitalized with SARS-CoV-2 showing significant prolongation of PR, QRS, and QTc intervals. PR interval prolonged significantly in all patients admitted with SARS-CoV-2 infection regardless of medication status or troponin elevation. Critically ill patients with SARS-CoV-2 admitted to ICU and those with elevated troponin-I levels had a significantly wider QRS at the time of admission and during the hospital course. Interestingly, we observed significant QTc lengthening during hospitalization in the small subgroup of patients (n=25) not receiving hydroxychloroquine or azithromycin, suggesting an additional unknown mechanism responsible for QTc prolongation in patients with SARS-CoV-2. Observational study of hydroxychloroquine in hospitalized patients with COVID-19 doi = 10.1161/circep.120.009023 id = cord-259660-x9sobzyw author = Mohakud, Nirmal K title = An Assumed Vertical Transmission of SARS-CoV-2 During Pregnancy: A Case Report and Review of Literature date = 2020-09-26 keywords = COVID-19; SARS summary = In the present report, we describe a premature newborn, who was born to a primigravida mother with HELLP (hemolysis, elevated liver enzymes, and low platelet count) syndrome and moderate COVID-19 pneumonia. The newborn tested positive at 12 hours of life for COVID-19 by real-time polymerase chain reaction (RT-PCR) of the tracheal aspirate sample [9] . The authors in one review reported 179 cases of newborns tested positive at birth, whose mothers were infected in the third trimester of pregnancy [5] . The authors of one study described that three newborns born to mothers with COVID-19 infection had positive antibodies (IgM and IgG) at birth [7, 8] . In the present report, the index newborn was tested positive at 12 hours of life without any features of symptomatic COVID-19 infection [9] . Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn A neonate born to mother with COVID-19 during pregnancy & HELLP syndrome: a possible vertical transmission doi = 10.7759/cureus.10659 id = cord-288066-sh6n2c3n author = Mohamed, Mohamed S. title = Sex differences in COVID-19: the role of androgens in disease severity and progression date = 2020-11-11 keywords = SARS; covid-19 summary = Variants in the androgen receptor gene correlate with androgen sensitivity and are implicated in diseases like androgenetic alopecia and prostate cancer, conditions that have been associated with worse COVID-19 outcomes and hospitalization. The proposed mechanism behind this effect is based on the idea that androgen receptor and, subsequently, TMPPRSS2 expression affects the SARS-COV2 virus ability to enter host cells and its spike proteins affinity to bind ACE2 receptors (Fig. 1 ). SARS-CoV2 spike proteins are then primed by TMPRSS2, allowing the interaction with ACE2 receptors to enter host cells Fig. 2 Theoretical mechanisms suggesting CAG repeats length and associated androgen sensitivity as a predictor for COVID-19 disease severity lack of control groups or testosterone levels prior to infection, the results warrant consideration. Increased androgen receptor expression might lead to a higher risk of acquiring a severe COVID-19 disease by promoting TMPRSS2 transcription (Fig. 2) . Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men doi = 10.1007/s12020-020-02536-6 id = cord-262786-otxpc46a author = Mohammadi, Soheil title = Understanding the Immunologic Characteristics of Neurologic Manifestations of SARS-CoV-2 and Potential Immunological Mechanisms date = 2020-09-01 keywords = CNS; COVID-19; CoV-2; IL-6; SARS summary = Here, we review the currently available evidence to discuss the plausible immunologic pathways that may contribute to the development of COVID-19 neurological complications, namely Alzheimer''s disease, Parkinson''s disease, stroke, multiple sclerosis, Guillain-Barre syndrome, seizure, and brainstem involvement. Although the virus, also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mainly manifests as an acute respiratory infection [2] , recent evidence suggests that 36% of affected patients exhibit neurological sequelae [3] . Systemic inflammatory response syndrome (SIRS) is defined as excessive host immune response against noxious stimuli (e.g., viral infection), through which the primary protective role of cytokine release turns into a detrimental response against host tissues, leading to impaired integrity of capillary walls and end-organ dysfunction [22] . We hypothesize that not only the persistent systemic inflammation caused by SARS-CoV-2 may act as a trigger for microglial activation but also large amounts of pro-inflammatory cytokines secreted in response to this viral infection may aggravate neurodegeneration leading to AD. doi = 10.1007/s12035-020-02094-y id = cord-349445-yh6ndtgm author = Mohammed El Tabaa, Manar title = Targeting Neprilysin (NEP) pathways: A potential new hope to defeat COVID-19 ghost date = 2020-05-27 keywords = ACE-2; Ang; Angiotensin; COVID-19; NEP; RAS; SARS summary = Therefore, researchers suggested that the use of angiotensin converting enzyme inhibitors (ACEIs) and/or angiotensin receptor blockers (ARBs), may show a positive trend towards the severe inflammatory reactions and endothelial dysfunction caused by stimulating the function of ACE/Ang II/AT-1 axis and thereby, towards the bad pulmonary effects associated with the COVID-19 infection [29, 30] . Since IL-6 would inactivate endothelial nitric oxide synthase (eNOS), it could disrupt NO production [90] , decreasing its level and inducing a state of oxidative stress that may lead to Ang II-induced impairment in endothelial responses [91] Postulating impaired endothelium functions as a principal factor in the pathogenesis of heart failure, hypertension and diabetes, it will be expected to classify the patients of such diseases as high risk groups for COVID-19 development [92] [93] [94] . Taken into consideration the numerous harmful effects possibly induced by Ang II during COVID-19 pathogenesis, we found that most novel studies aim to use the anti-hypertensive drugs which act either by inhibiting the ACE activity or by blocking AT1 receptor, suggesting that action may mitigate the disease severity in COVID-19 patients. doi = 10.1016/j.bcp.2020.114057 id = cord-343136-kftffes0 author = Mohon, Abu Naser title = Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2 date = 2020-09-15 keywords = LAMP; SARS summary = A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. Limit of detection of the LAMP assay was evaluated by using a nasopharyngeal (NP) swab sample infected with SARS-CoV-2 for which the viral load was quantified using digital droplet PCR (see Supplementary Methods). Twenty four replicates from a serial dilution containing 25-50 copies of SARS-CoV-2 which equates to 1X LOD (patient sample NP swab in VTM viral load confirmed by digital droplet PCR) per reaction were tested using dual-target RT-LAMP (Table 3) . The dual-target RT-LAMP test for SARS-CoV-2 developed in this study has comparable analytical sensitivity and specificity, limit of detection, precision, and achieved excellent agreement compared to the reference RT-PCR methods used internationally. doi = 10.1016/j.jviromet.2020.113972 id = cord-296007-1gsgd22t author = Mohseni, Amir Hossein title = Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date = 2020-09-12 keywords = HLA; SARS summary = Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV N proteins prefers the 2 2 1 hydrophobic amino acid residues (e.g. Ile, Leu, Met, and Phe), and the second position of these hit peptides 2 2 2 is an hydrophobic amino acid residue Pro forming five strong VDW forces with residues Y99, V67, M45, 2 2 3 Y7, and F9 and two H-bonds with residues K66 and E63 on MHC molecule ( Figure S2A , left). Visualization of interactions in the atomic level structure of a TCR-pMHC complex in the hit peptide of 2 4 9 SARS-CoV-2 N protein for HLA-E ( Figure S3C ) within 20 and 8 Å was generated on-the-fly using of the homologous peptide antigens of all queries has no detectable binding to both MHC and TCR. doi = 10.1101/2020.09.12.294413 id = cord-305330-mklkugj5 author = Moiseev, Sergey title = Cancer in intensive care unit patients with COVID-19 date = 2020-05-28 keywords = SARS summary = susceptible to severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection and complications, although data on COVID-19 and malignancies remain limited. noted that patients with cancer were more likely to experience severe sequelae of SARS-CoV-2 infection, such as intensive care admission, invasive ventilation or death. 2 However, Wang and Zhang argued that the most important morbidity factor is exposure to an infection source, whereas worse outcomes from SARS-CoV-2 infection could be associated (at least partly) with older age of patients with cancer 3 . In a nationwide study, we evaluated the prevalence of malignancies among 1307 intensive care unit (ICU) patients with SARS-CoV-2 pneumonia who required respiratory support. However, our data suggest that other factors, such as older age and comorbidities, contribute significantly to the more severe course of SARS-CoV-2 infection in cancer patients. doi = 10.1016/j.jinf.2020.05.053 id = cord-284068-sbon3aes author = Mok, Chee Keng title = Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date = 2020-06-22 keywords = CoV-2; SARS summary = Validation assays to determine changes in infectious virus titres upon treatment was carried out by testing selected hit compounds in dose-dependent assays in Vero E6 to confirm the primary screen observation and also in the human hepatocarcinoma HuH7 cell line as the latter cell line expresses high levels of the ACE2 receptor (10) and supports replication of coronaviruses (11) . While recent data has shown that vitamin D levels are negatively associated with morbidity and mortality of COVID-19 cases (13, 14) , this is the first report of a direct inhibitory effect of calcitriol on SARS-CoV-2. The authors speculated that vitamin D supplementation could protect against SARS-CoV-2 infection and improve patient disease outcomes (16) , and our finding certainly provides credence to this hypothesis. Given the high transmissibility of SARS-CoV-2 globally (23), if these findings can be replicated in clinical trials, calcitriol may certainly prove to be an effective tool in the effort to control the pandemic while waiting for an effective vaccine to be rolled out globally. doi = 10.1101/2020.06.21.162396 id = cord-296339-23yi8so0 author = Mok, Wendy title = Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens date = 2007-09-26 keywords = SARS summary = We used computational methods to examine the extent to which this practice can result in inaccurate ''retrodiction.'' Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance. Herein, we show that adopting molecular clock assumptions can yield inaccurate estimated origin times, considering as an example data from the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) infection in humans. Recognizing that this change in substitution rate would violate a molecular clock assumption and could cause pairwise genetic distances to yield inaccurate evolutionary divergence estimates (especially if genetic distance calculations were performed with respect to a reference sequence representing an hypothetical common ancestor), we quantifi ed the extent to which failing to account for dynamic SARS-CoV evolution might affect estimating an origin time. doi = nan id = cord-345717-ktajrf7d author = Monagin, Corina title = Serologic and behavioral risk survey of workers with wildlife contact in China date = 2018-04-03 keywords = China; SARS; animal; risk summary = We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. The present study focuses on the potential for zoonotic viral transfer through contact with wildlife in Guangdong prefectures in China, and seeks to augment our understanding and identification of risky populations, occupations, and behaviors, as well as the perceptions of risk at these interfaces. We performed a serological survey and concurrent behavioral questionnaire of individuals with wildlife contact in Guangdong Province, China, in order to better characterize occupations and community-level behavioral risks that contribute to zoonotic transmission of various wildlife pathogens with pandemic potential. We targeted high-risk individuals, defined as individuals with high levels of exposure to wildlife (wild animal blood or bodily fluids)-primarily hunters, persons working in wet markets and restaurants that butcher wild game, who could be followed over a period of time. doi = 10.1371/journal.pone.0194647 id = cord-272419-y3ebt4jm author = Monari, Caterina title = A Focus on the Nowadays Potential Antiviral Strategies in Early Phase of Coronavirus Disease 2019 (Covid-19): A Narrative Review date = 2020-08-09 keywords = COVID-19; HCQ; LPV; SARS; patient summary = Possible inhibition of SARS-CoV-2 3-chymotrisyn-like (3CL)-protease and papain-like protease Lopinavir is excreted in the gastrointestinal (GI) tract, and thus coronavirus-infected enterocytes might be exposed to higher concentrations of the drug LPV/r tab 200/50 mg: 2 tab BID LPV/r oral sol 80/20 mg: 5 mL BID DRV/cobi tab 800/150 mg: 1 tab QD Gastrointestinal: diarrhea, nausea, vomiting, increased amylase, lipase, total cholesterol and triglycerides (risk factor for pancreatitis) Hepatotoxicity: increasing in GGT, AST, ALT, total bilirubin, hepatitis Cardiological: QT-and PR-interval prolongation, hypertension, bradyarrhytmias; torsade de pointes have been reported in patients treated with LPV/r Metabolical: hyperglycemia and diabetes mellitus, increased uric acid Recently, a randomized, controlled, open-label trial comparing the efficacy of LPV/r versus standard of care was conducted in 199 hospitalized adult patients with severe COVID-19: no significant difference between the two groups neither in the time of clinical improvement (hazard ratio [HR] 1.31; 95% CI 0.95-1.80; p 0.09), nor in the 28-day mortality rate (19.2% versus 25.0%; 95% CI −17.3 to 5.7) was observed [40] . doi = 10.3390/life10080146 id = cord-297879-6xb25uhx author = Moncunill, G. title = SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up date = 2020-08-25 keywords = August; HCW; SARS; preprint summary = A follow-up survey one month after the baseline (April-May 2020) measured SARS-CoV-2 infection by real time reverse-transcriptase polymerase chain reaction (rRT-PCR) and IgM, IgA, IgG and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein by Luminex. We found that 9.3% (95% CI: 7.1-12.0) of the participants were seropositive and the cumulative prevalence of SARS-CoV-2 infection (considering a past or current positive result to either antibody testing or rRT-PCR) was 11.2% (95% CI: 8.8-14.1). We measured IgM, IgG, and IgA isotypes and subclasses, and assessed the factors associated with new infections as well as levels and kinetics of antibodies. Levels (median fluorescence intensity, MFI) of IgM, IgG, and IgA against receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein stratified by asymptomatic participants and participants who reported COVID-19 compatible symptoms at recruitment (month 0, M0), month 1 (M1) or at both visits (M0&M1). doi = 10.1101/2020.08.23.20180125 id = cord-266308-fjpq1ljp author = Mondal, Priya title = Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation date = 2020-11-05 keywords = ACE2; SARS; support summary = Binding energies (BEs; kcal/mol) of selected bioactives from medicinal plants with SARS-CoV-2 M pro , S-protein and human ACE2 and their chemical interactions with the binding site. Among the standard drugs, nelfinavir, an anti-retroviral and protease inhibitor, has shown a stronger affinity towards all three targets of SARS-CoV-2 with the BE of À8.3 kcal/mol for M pro , À6.6 kcal/mol for S-protein and À6.4 kcal/mol for ACE2 (Supporting Information Table S1 ). In our current study, the selected bioactives from medicinal plants as well as standard drugs have shown interaction towards the key residues of the S-protein receptor-binding motif, as shown in Supporting Information Fig. S4 and S5 . The interactions of the standard drugs and medicinal plant bioactives were also similar towards hotspot residues of the ACE2 receptor as shown in Supporting Information Fig. S7 and S8. doi = 10.1080/07391102.2020.1842246 id = cord-292350-cmrtg91a author = Mondal, Samhati title = Thromboembolic disease in COVID-19 patients: A brief narrative review date = 2020-09-14 keywords = COVID-19; SARS; patient; thrombosis summary = Table 1 & 2 summarize the various thrombotic complications noted in COVID-19 patients as published as of June 6 th , 2020 obtained by a literature search on PubMed and EMBASE using combinations of the following MeSH terms: COVID-19, SARS-COV2, novel corona virus, thrombosis, thromboembolic complications, pulmonary embolism. Clinical signs and symptoms of thrombosis such as cutaneous manifestations ("COVID toe") [84] , overt line thrombosis, arterial or venous clots, unexplained increase in oxygen requirement, or organ dysfunction should raise suspicion and prompt further investigation and/or discussion about therapeutic intervention [7] As new information becomes available, it appears increasingly important to routinely monitor platelet count, PT/aPTT, d-dimer, and fibrinogen to assist in anticipating and managing thrombotic complications. ICU patients positive for COVID-19 with elevated d-dimer levels and/or clinico-radiological suspicion for thrombosis as noted above should be considered for therapeutic anticoagulation only after careful assessment of their bleeding risk. doi = 10.1186/s40560-020-00483-y id = cord-327169-sz4ildnd author = Mondoni, Michele title = Utility and safety of bronchoscopy during SARS-CoV-2 outbreak in Italy: a retrospective, multicenter study date = 2020-08-28 keywords = COVID-19; SARS summary = The primary aim of the present study was to describe the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swab(s) and a clinical and radiological suspicion of COVID-19 pneumonia. The indications of bronchoscopy were: -diagnosis of SARS-CoV-2 pneumonia in patients with previously negative nasopharyngeal swab (clinical and radiological suspicion of pneumonia); -need for undelayable procedures in COVID-19 patients (e.g., massive hemoptysis, post-obstructive atelectasis). The diagnostic yield of bronchoscopy was calculated dividing the number of patients with a molecular diagnosis of SARS-CoV-2 infection following the collection of bronchoscopic specimens by the number of patients with a suspected diagnosis of COVID-19 pneumonia. This is to our knowledge the largest study on the diagnostic yield of bronchoscopy in patients with negative nasopharyngeal swabs and a clinical/radiological suspicion of SARS-CoV-2 infection. Urgent/life-saving bronchoscopies were performed in 31 patients with a confirmed COVID-19 diagnosis for obstructive atelectasis, suspected concomitant lower respiratory tract infections, severe hemoptysis, suspected tracheal lacerations in patients mechanically ventilated, tracheostomy complications, and suspected concomitant pulmonary tuberculosis. doi = 10.1183/13993003.02767-2020 id = cord-232446-vvb2ffhv author = Mongia, Aanchal title = A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date = 2020-07-03 keywords = SARS; covid-19; drug; matrix; virus summary = In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. doi = nan id = cord-328287-3qgzulgj author = Moni, Mohammad Ali title = Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date = 2014-10-24 keywords = HIV; HIV-1; SARS; disease; gene; infection summary = Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . doi = 10.1186/1471-2105-15-333 id = cord-021152-6znmkvy9 author = Montecino-Latorre, Diego title = Reproduction of East-African bats may guide risk mitigation for coronavirus spillover date = 2020-02-07 keywords = SARS; bat; coronavirus; detection; specie summary = doi = 10.1186/s42522-019-0008-8 id = cord-293127-c27qh5y7 author = Monteleone, Pedro AA title = A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments date = 2020 keywords = China; MERS; SARS; covid-19 summary = In this review, we summarize the latest research progress related to COVID-19 epidemiology and the reported data of pregnant women, and discuss the current evidence of COVID-19 infections during pregnancy and its potential consequences for assisted reproductive treatments. The current outbreak of the novel 2019 coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China in December 2019 and subsequently spread to many other countries. Coronaviruses are a large family of viruses known to cause symptoms ranging from a common cold to more severe diseases, such as the severe acute respiratory syn A review of initial data on pregnancy during the COVID-19 outbreak: implications for assisted reproductive treatments Pedro AA Monteleone 1,2 , Mayra Nakano 1,2 , Victor Lazar 1 , Alecsandra P Gomes 1 , (Drosten et al., 2003; Ksiazek et al., 2003) , and MERS coronavirus (MERS-CoV) was the pathogen responsible for severe respiratory disease outbreaks in the Middle East in 2012 (Zaki et al., 2012) . doi = 10.5935/1518-0557.20200030 id = cord-291028-ejidqmpm author = Montero Feijoo, A. title = Recomendaciones prácticas para el manejo perioperatorio del paciente con sospecha o infección grave por coronavirus SARS-CoV-2 date = 2020-03-17 keywords = EPI; SARS summary = Debe de estar compuesto por: mascarilla N95 o preferiblemente FFP3, protección ocular ajustada de montura integral o facial completa, bata impermeable, doble guante, gorro y calzas impermeables La higiene de manos debe ser realizada por el personal antes y después de todo contacto con el paciente, particularmente antes de ponerse y después de quitarse el EPI Se deben minimizar los procesos que generen aerosoles y en el caso de ser necesarios usar siempre las medidas de protección recomendadas En el caso de ser necesaria la intubación traqueal se recomienda debe ser realizada por el profesional más experimentado disponible, realizar una inducción de secuencia rápida, evitar la ventilación manual, usar videolaringoscopio y preferiblemente tubo endotraqueal con aspiración subglótica Iniciar de forma precoz el tratamiento de soporte a los pacientes con compromiso respiratorio (taquipnea, hipoxemia) o shock séptico El uso de gafas nasales de alto flujo o ventilación mecánica no invasiva debe ser evitado en la medida de lo posible y reservado para pacientes muy concretos, puesto que son dispositivos que generan aerosoles La administración de antimicrobianos no está recomendada inicialmente, tan solo si existe sospecha de sepsis asociada o sobreinfección bacteriana. doi = 10.1016/j.redar.2020.03.003 id = cord-341531-w788qwya author = Montero Feijoo, A. title = Practical recommendations for the perioperative management of patients with suspicion or serious infection by coronavirus SARS-CoV date = 2020-05-04 keywords = PPE; SARS; patient summary = Protective measures should be maximised when caring for patients with confirmed infection, in critically ill patients with a high viral load, and in patients that require invasive aerosol-generating procedures and manoeuvres such as aerosol therapy and nebulisation, aspiration of respiratory secretions, bag-mask ventilation, non-invasive ventilation, intubation, respiratory sampling, bronchoalveolar lavage, tracheostomy or cardiopulmonary resuscitation. If postoperative surveillance is necessary, it will be carried out in adequately monitored isolation units, preferably with negative pressure Avoid using aerosols, high-flow nasal oxygen or non-invasive ventilation as far as possible in patients requiring postoperative oxygen therapy Healthcare personnel who care for patients during postoperative surveillance must wear appropriate personal protective equipment at all times and must be taught donning and doffing techniques The same recommendations for transferring patients to the operating room apply to postoperative transfer doi = 10.1016/j.redare.2020.03.002 id = cord-305616-2obemy16 author = Montes, Maria Teresa title = Neonatal nursing in the COVID-19 pandemic: can we improve the future? date = 2020-07-10 keywords = SARS; care summary = Contingency plans due to the covid-19 pandemic have impacted on three key areas: 1) the organization and workflow of neonatal units, 2) perinatal and neonatal care, including breastfeeding, and 3) communicationcollaboration with parents. Many centres have adopted very restrictive policies to care for pregnant women who are positive for SARS-CoV-2 in the maternal area, as well as in the NUs, in order to control the spread of the virus and protect health professionals. Initial recommendations to the management regarding the SARS-CoV-2-positive puerperant supported changes to delivery plans by introducing restrictions, both in vaginal deliveries and caesarean sections on the presence of the other parent at childbirth and postpartum unit, early skin-to-skin contact, and late-cord clamping . In addition to frequent hand-washing, cleaning of the breast before breastfeeding and skin-to-skin contact, and wearing face masks, the risk to others can be reduced, for example, by testing parents and health professionals for SARS-CoV-2 and restricting their access to where their child is placed. doi = 10.1016/j.jnn.2020.07.005 id = cord-325595-y9ae6zbr author = Montopoli, M. title = Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality date = 2020-10-23 keywords = SARS summary = title: Genetic and hormonal influence on SARS-CoV-2-infection susceptibility: Re: The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality in the Annals of Oncology reported findings congruent with the prevailing notion that high SARS-CoV-2 infection rates and disease severity in men may be the result of high androgen-driven TMPRSS2 expression in the lungs. The authors posit that since TMPRSS2 is under positive transcriptional control by the androgen receptor (AR), reduction of TMPRSS2 expression following androgen deprivation therapy (ADT) in prostate cancer patients would be expected to correlate with reduced SARS-CoV-2 incidence, and in case of infection, with lesser disease severity. In particular, disease stage and the type of treatment that may affect AR or TMPRSS2 expression and/or patients'' The current thinking posits that under ADT, expression of TMPRSS2 (a co-factor for SARS-CoV-2 activation and virulence) would be reduced in the lungs, leading to less severe disease, hospitalizations, ICU admissions, and deaths. doi = 10.1016/j.annonc.2020.07.022 id = cord-268049-7xqln70d author = Montrief, Tim title = COVID-19 respiratory support in the emergency department setting date = 2020-08-08 keywords = COVID-19; NIV; SARS; patient summary = DISCUSSION: Patients presenting with SARS-CoV-2 infection are at high risk for acute respiratory failure requiring airway management. [29] [30] [31] [32] Based on currently available evidence, the WHO states that "HFNC and NIV systems with good interface fitting do not create widespread dispersion of exhaled air and therefore should be associated with [a] low risk of airborne transmission." 15 The risk of respiratory pathogen transmission when using HFNC is subject to a variety of factors, including the duration of support, maximal flow rate, patient sneezing or coughing, cannula fit, and patient cooperation. 35 Many guidelines, including those by Australian and New Zealand Intensive Care Society (ANZICS), the WHO, and the Surviving Sepsis Campaign recommend the use of HFNC in COVID-19 patients presenting with acute hypoxemic respiratory failure unresponsive to conventional oxygen therapy. 20 Notably, the SCCM guidelines on the management of critically ill patients with COVID-19 recommend "a trial of NIV with close monitoring and shortinterval assessment for worsening of respiratory failure" if HFNC is not available and there is no urgent indication for intubation. doi = 10.1016/j.ajem.2020.08.001 id = cord-339669-p61j2caf author = Monzani, Alice title = QTc evaluation in COVID‐19 patients treated with chloroquine/hydroxychloroquine date = 2020-05-18 keywords = HCQ; SARS summary = In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China and has spread rapidly initially throughout Europe and later USA (1). In late December 2019, a cluster of pneumonia cases caused by a novel coronavirus occurred in Wuhan, China, and has spread rapidly initially throughout Europe and later in the United States. Despite poor real clinical evidence of unequivocal beneficial effect of chloroquine/hydroxychloroquine (CQ/HCQ), the absence of an effective COVID-19 treatment and the social pressure raised the demand of these drugs for its compassionate use, both in hospital and outpatient settings. 10 High-dosed HCQ showed promising potential effect in reducing SARS-CoV-2 viral load in COVID-19 patients with enhanced effects in combination with azithromycin or several antiviral drugs. In so forth, we believe that is probably time to have prospective clinical trials that will evaluate the safety and efficacy of HCQ during treatment of COVID-infected patients. doi = 10.1111/eci.13258 id = cord-340516-9dfaqsv7 author = Moore, Anne C. title = Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date = 2020-09-06 keywords = CoV-2; SARS; vaccine summary = We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Here, we report the induction of neutralizing antibody (Nab), IgG and IgA antibody responses, and T cell responses in mice following immunization of rAd vectors expressing one or more SARS-CoV-2 antigens. We have previously demonstrated that an oral, tableted rAd-based vaccine can induce protection against respiratory infection and shedding following influenza virus challenge 15 as well as intestinal immunity to norovirus antigens in humans 12 . In summary, these studies in mice represent our first step in creating a vaccine candidate, demonstrating the immunogenicity of the construct at even low vaccine doses and the elucidation of the full-length spike protein as a leading candidate antigen to induce T cell responses and superior systemic and mucosal neutralizing antibody. doi = 10.1101/2020.09.04.283853 id = cord-289407-8fje16z1 author = Moore, G. title = Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date = 2020-09-25 keywords = CoV-2; RNA; SARS summary = Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. 6 Air samples taken during tracheostomy procedures, high flow nasal oxygen treatment, non-invasive ventilation and nebulisation have not contained SARS-CoV-2 RNA 7 and HCWs exposed to unrecognised COVID-19 patients undergoing similar high-risk AGPs have not become infected. . https://doi.org/10.1101/2020.09.24.20191411 doi: medRxiv preprint Several studies, utilising a range of air and surface sampling methods, have been carried out to determine the presence and prevalence of SARS-CoV-2 in the healthcare environment. [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients doi = 10.1101/2020.09.24.20191411 id = cord-282724-zzkqb0u2 author = Moore, Jason H. title = Ideas for how informaticians can get involved with COVID-19 research date = 2020-05-12 keywords = COVID-19; SARS; datum; health; patient; research summary = Some key considerations and targets of research include: (1) feature engineering, transforming raw data into features (i.e. variables) that ML can better utilize to represent the problem/target outcome, (2) feature selection, applying expert domain knowledge, statistical methods, and/or ML methods to remove ''irrelevant'' features from consideration and improve downstream modeling, (3) data harmonization, allowing for the integration of data collected at different sites/institutions, (4) handling different outcomes and related challenges, e.g. binary classification, multi-class, quantitative phenotypes, class imbalance, temporal data, multi-labeled data, censored data, and the use of appropriate evaluation metrics, (5) ML algorithm selection for a given problem can be a challenge in itself, thus strategies to integrate the predictions of multiple machine learners as an ensemble are likely to be important, (6) ML modeling pipeline assembly, including critical considerations such as hyper-parameter optimization, accounting for overfitting, and clinical interpretability of trained models, and (7) considering and accounting for covariates as well as sources of bias in data collection, study design, and application of ML tools in order to avoid drawing conclusions based on spurious correlations. doi = 10.1186/s13040-020-00213-y id = cord-331831-gw42e6ce author = Moore, Luke S P title = Near-patient SARS-CoV-2 molecular platforms: new-old tools for new-old problems date = 2020-10-08 keywords = SARS summary = In their prospective, interventional, non-randomised, controlled trial published in The Lancet Respiratory Medicine, Nathan Brendish and colleagues 1 move COVID-19 diagnostics forward, both by expanding the repertoire of in-situ evaluated molecular platforms, and also methodologically, with a diagnostic controlled trial using clinical impact as a primary outcome measure, analogous to their previous work on other respiratory viruses. 1 Nevertheless, this level of accuracy is attractive in the context of the recently published (yet perhaps already outdated) Cochrane review 3 of early-tomarket, rapid, point-of-care molecular tests for SARS-CoV-2, which looked at 13 evaluations of four platforms, finding a mean sensitivity of 95·2% (86·7-98·3) with a specificity of 98·9% (97·3-99·5). Brendish and colleagues also showed that the fast turnaround time of the QIAstat-Dx Respiratory SARS-CoV-2 Panel decreased the time taken for patients to be placed in an appropriate care area, and led to fewer bed moves and faster time to enrolment into other COVID-19 clinical trials-all significant advantages. Clinical impact of molecular point-ofcare testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study doi = 10.1016/s2213-2600(20)30451-3 id = cord-328712-7q9mg2tu author = Moore, Nicholas title = Chloroquine for COVID-19 Infection date = 2020-04-07 keywords = SARS summary = Caused by a new virus, SARS-CoV2, COVID-19 is related to the common cold and the SARS-CoV1 virus that was responsible for the 2003 Severe Acute Respiratory Syndrome (SARS) infection in Asia, causing about 8000 cases and 774 deaths (https ://www. Raoult was based on theory [5] , on the effects of the drug on coronavirus replication in vitro [1, 4, [6] [7] [8] , and on experimental data [2] showing SARS-CoV inhibition [3] , concluding to a hypothetical effect of hydroxychloroquine on COVID-19 [9] without clinical proof other than a non-randomized open study of 20 patients, purported to show extraordinary results on virus washout (notwithstanding a slew of typical biases) [10] . In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19) doi = 10.1007/s40264-020-00933-4 id = cord-345183-80rflm7u author = Moore, Nicholas M. title = Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2 date = 2020-07-23 keywords = ACOV; CDC; SARS summary = We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. In this study, we compared the performance of the ACOV and IDNOW assays and a laboratory developed test that is a modification of the CDC 2019-nCoV assay (CDC COV) for the detection of SARS-CoV-2 RNA from upper respiratory tract specimens. doi = 10.1128/jcm.00938-20 id = cord-307160-1vz0gw1w author = Morais-Almeida, Mário title = COVID-19, asthma, and biologic therapies: What we need to know date = 2020-05-16 keywords = SARS; covid-19; patient summary = Ongoing prospective cohort studies (SARP, NHLBI and others) provide a unique opportunity to examine the effects of COVID-19 on severe asthma and potential interactions with therapy, including inhaled and oral corticosteroids, as well as targeted treatment with biologics. It was believed that low eosinophil counts in peripheral blood would be related to the infection with the SARS-CoV-2 virus itself, and not necessarily an indicator that treatments which reduce eosinophil counts in patients with asthma would be associated with more severe COVID-19 disease. As in the placebo controlled trials with omalizumab, mepolizumab, benralizumab, reslizumab and dupilumab in asthmatic patients, no risk of increased infection susceptibility or immunosuppressive effect was reported to date and, in the case of omalizumab, there is a possible anti-infectious effect; hence we do not need to discontinue these treatments during the current pandemic. doi = 10.1016/j.waojou.2020.100126 id = cord-348392-e35cd9sg author = Moraleda, Cinta title = Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date = 2020-07-25 keywords = SARS summary = Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. doi = 10.1093/cid/ciaa1042 id = cord-283432-od5nnxvg author = Morawska, Lidia title = How can airborne transmission of COVID-19 indoors be minimised? date = 2020-05-27 keywords = SARS; airborne; transmission summary = We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. While evidence for airborne transmission of COVID-19 is currently incomplete, several hospital-based studies have performed air-sampling for SARS-COV-2, including one published paper (Ong et al. doi = 10.1016/j.envint.2020.105832 id = cord-253459-tcn10pho author = Moreau, Gregory Brett title = Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection date = 2020-07-28 keywords = SARS; mouse summary = 4 A transgenic mouse model to study SARS-CoV-1 infection was developed that expresses the hACE2 gene under the control of the human cytokeratin 18 promoter. To investigate the potential of this transgenic mouse strain as a model for COVID-19 infection, five K18-hACE2 mice were intranasally inoculated with 8 × 10 4 Median Tissue Culture Infectious Dose (TCID50) of SARS-CoV-2, and five mice were mock-infected with sterile Dulbecco''s Modified Eagle''s Medium (DMEM). In the mouse model expressing hACE2 under the mouse ACE2 promoter, infected mice did not exhibit any clinical symptoms other than maximal weight loss on day 3 postinfection, and those mice recovered. 10 In contrast to these models, in which mice exhibited mild symptoms and recovered, only 60% of the mice survived past day 5 in the mouse strain expressing hACE2 under the lung ciliated epithelial cell HFH4 promoter. doi = 10.4269/ajtmh.20-0762 id = cord-337636-3yc0ribg author = Morehouse, Zachary P. title = A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date = 2020-08-25 keywords = PCR; SARS; viral summary = Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. Using human coronavirus 229E (HCoV-229E) as our model organism, we developed a novel two-step methodology of optimized shaker-mill homogenization parameters that allowed for direct-to-PCR viral detection. doi = 10.1186/s12985-020-01405-y id = cord-322348-8opy5z9h author = Morelli, Mara title = Parents and Children During the COVID-19 Lockdown: The Influence of Parenting Distress and Parenting Self-Efficacy on Children’s Emotional Well-Being date = 2020-10-06 keywords = Italy; SARS; child; parent summary = Within the Social Cognitive Theory framework, a path model in which parenting self-efficacy and parental regulatory emotional self-efficacy mediated the relationship between parents'' psychological distress and both children''s emotional regulation, and children''s lability/negativity, was investigated. (2020) in Italy showed that it was the parenting stress related to the health emergency, the pandemic, and the lockdown that increased children''s psychological, emotional, and behavioral problems. For this reason, this study focused on identifying which parental psychological variables can mediate the relationship between parents'' psychological distress during the pandemic and the lockdown and their children''s emotional regulation, in order to understand which possible intervention should be implemented to ameliorate families'' well-being. A SEM was employed to test the hypothesized mediation model in which parenting self-efficacy and parents'' regulatory emotional self-efficacy (related to the COVID-19 lockdown) mediated the relationship between parents'' psychological distress and both children''s emotional regulation and children''s lability/negativity. doi = 10.3389/fpsyg.2020.584645 id = cord-102411-0mo1198e author = Moreno Borraz, LA title = PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date = 2020-11-13 keywords = PCR; SARS summary = Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. El objetivo principal del estudio fue conocer la prevalencia de infección por Coronavirus SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia de Zaragoza en el pico de la pandemia en España, entre el 20 de marzo y el 21 de abril de 2020. doi = 10.1016/j.regg.2020.10.005 id = cord-304734-r0k1rfmt author = Moreno-Casbas, María Teresa title = Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI date = 2020-05-25 keywords = SARS summary = La población diana está constituida por profesionales de la salud de todas las Comunidades Autónomas de España, con actividad en cualquier centro que atienda a pacientes con COVID-19 y que sean un caso confirmado de infección por SARS-CoV-2 por laboratorio. Laborales y epidemiológicas: lugar y unidad de trabajo, tiempo trabajado en los últimos 10 años, elementos de protección (disponibilidad, utilización y percepción del uso correcto), métodos y frecuencia de la higiene de manos y de otras medidas higiénicas en el trabajo, carga de trabajo en la última jornada, existencia de protocolos de protección, motivo de realización del test y responsable de indicarlo, fechas de inicio de síntomas, de test positivo y test negativo, contactos previos al test, aislamiento y sus características y reincorporación al trabajo. En relación a la percepción de los profesionales, en las primeras semanas de la pandemia, de la disponibilidad de medidas de protección en la categoría "siempre/frecuentemente" fue: para mascarilla FPP1 57,3%, guantes 89,5%, jabón 95% y solución hidroalcohólica 91,5%. doi = 10.1016/j.enfcli.2020.05.021 id = cord-295130-e7j7kac0 author = Moreno-Contreras, Joaquín title = Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date = 2020-09-22 keywords = RNA; SARS summary = In this study, we compared the RT-qPCR results from 253 paired samples obtained from saliva and swabs of ambulatory patients; the RNA in the swab samples was extracted using a commercial RNA purification kit, and the saliva samples were directly mixed with a lysis buffer, boiled, and used for the RT-qPCR protocol. To evaluate if saliva is a good source of viral RNA for the RT-qPCR, we determined the presence of the SARS-CoV-2 genome in paired saliva and swab samples from 253 ambulatory patients. Direct lysis of nasopharyngeal or oropharyngeal swab samples in viral transport medium using the QE buffer has been reported as a suitable method for direct RT-qPCR for SARS-CoV-2 detection, with rates similar to those of methods based on column purification (11, 15) . doi = 10.1128/jcm.01659-20 id = cord-282839-3ii79g6j author = Moreno-Fernández Ayala, Daniel J. title = Age-related mitochondrial dysfunction as a key factor in COVID-19 disease date = 2020-11-07 keywords = COVID-19; SARS; age; inflammation; mitochondrial summary = Thus, it seems clear that mitochondrial dysfunction is an important factor in the proinflammatory profile caused by the release of inflammatory cytokines produced by activation of NLRP3 inflammasome and other mechanisms over-activated in aging and in metabolic diseases. It seems clear that, mitochondrial dysfunction in diabetic patients contributes importantly to the low-grade inflammatory profile associated with this disease that is aggravated during aging and has been associated with higher severity in COVID-19 infection. Mediterranean diet, rich in plant foods, is associated with reduced risk of developing age-J o u r n a l P r e -p r o o f related chronic diseases by inducing protection against oxidative stress and improving mitochondrial activity that could be the cause of a reduced inflammation level (Tosti et al., 2018) . Mitochondrial dysfunction releases many damage signals to cytosol that end in the activation of inflammasome and the release of inflammatory cytokines that cause the chronic inflammation associated with aging and age-related diseases. doi = 10.1016/j.exger.2020.111147 id = cord-278050-wl83d6gs author = Morgenstern, Birgit title = Ribavirin and interferon-β synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines date = 2005-01-28 keywords = IFN; SARS summary = Abstract Initial in vitro investigations demonstrated type I interferons (IFNs: IFN-α, IFN-β) to inhibit replication of SARS coronavirus (SARS-CoV), but found the nucleoside analogue ribavirin ineffective in Vero cells. In this report, ribavirin was shown to inhibit SARS-CoV replication in five different cell types of animal or human origin at therapeutically achievable concentrations. The influence of the infectious dose on the anti-SARS-CoV activity of ribavirin was investigated in Caco2 cells infected at different MOIs by measurement of virus titre. For example, in Caco2 cells infected with SARS-CoV FFM1 strain (MOI 0.01), ribavirin concentrations inhibiting virus production in combination with IFN-b were at least 10-fold lower when compared with cultures receiving single treatment with ribavirin. These clinical findings together with the observation of antiviral activity in different SARS-CoV-infected cell lines encourage the testing of treatment strategies using ribavirin in combination with other antiviral agents such as IFNs to increase inhibitory effects on virus replication and subsequently minimised immunopathological damages. doi = 10.1016/j.bbrc.2004.11.128 id = cord-344614-5zcylf6k author = Moriconi, Diego title = Obesity prolongs the hospital stay in patients affected by COVID-19, and may impact on SARS-COV-2 shedding date = 2020-06-04 keywords = SARS; obesity summary = Partial least square regression analysis showed that BMI, age and CRP at admission were related to longer length of hospital stay, and time for negative swab. Our study shows that obesity is associated with a severer respiratory presentation of COVID-19 and severer elevation of inflammatory markers, likely leading to higher oxygen demands at admission, prolonged oxygen requirement during hospitalization, delayed viral clearance and extended hospital stay. For this reason, beyond the potential impact on the lung mechanics, obesity might influence the clinical presentation and evolution of SARS-COV-2 infection through J o u r n a l P r e -p r o o f exacerbation of the immune-inflammatory response related to the disease, as confirmed by the increased levels of several inflammatory markers detected in the peripheral blood of patients with obesity in our population. doi = 10.1016/j.orcp.2020.05.009 id = cord-329262-ybr1auo2 author = Moriel‐Carretero, María title = The hypothetical role of Phosphatidic Acid in subverting ER membranes during SARS‐CoV infection date = 2020-05-18 keywords = SARS summary = Subsequently, a major path for viral internalization relies on the endocytic pathway and culminates with the release of the viral RNA genome into the cytoplasm of the infected cell (reviewed in 3 After this, +RNA viruses need to establish a complex capable of amplifying and further expressing their genome, the "replication/transcription complex", as well as additional (termed "non-structural") proteins capable of coordinating accessory functions. A relevant point when analyzing the morphological particularities of DMVs induced during SARS-CoV infection is that, in contrast to those triggered by other +RNA viruses, the inner layer indeed constitutes a closed circle, but the outer one is continuous all along with that of the other DMVs, giving the impression that the whole is disconnected from the cytoplasm ( Figure 1A , right panel) 11 . doi = 10.1111/tra.12738 id = cord-292256-jp80u828 author = Moriguchi, Takeshi title = A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date = 2020-04-03 keywords = CoV-2; SARS summary = We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient''s nasopharyngeal specimen is negative. doi = 10.1016/j.ijid.2020.03.062 id = cord-326503-ljle4vq3 author = Morioka, Shinichiro title = Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study date = 2020-07-30 keywords = SARS summary = key: cord-326503-ljle4vq3 authors: Morioka, Shinichiro; Nakamura, Keiji; Iida, Shun; Kutsuna, Satoshi; Kinoshita, Noriko; Suzuki, Tetsuya; Suzuki, Tadaki; Yamamoto, Kei; Hayakawa, Kayoko; Saito, Sho; Ohmagari, Norio title: Possibility of transmission of severe acute respiratory syndrome coronavirus 2 in a tertiary care hospital setting: A case study Summary This report aimed to investigate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a hospital setting. A 63-year-old man with pneumonia and an asymptomatic 70-year-old man were admitted to a tertiary hospital with SARS-CoV-2 infection. He was admitted to a general ward of our hospital due to SARS-CoV-2 63 pneumonia on Day 7, and was intubated on Day 10 from diagnosis. of Novel Coronavirus-Infected Pneumonia Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient Evidence of airborne 226 transmission of the severe acute respiratory syndrome virus doi = 10.1016/j.infpip.2020.100079 id = cord-320845-imxby1b1 author = Morley, G. L. title = Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples date = 2020-07-02 keywords = DBS; SARS summary = title: Sensitive detection of SARS-CoV-2-specific-antibodies in dried blood spot samples Objective: To validate the use of dried blood spot sampling for the detection of SARS-CoV-2-specific antibodies. Results: Specific anti-SARS-Cov-2 spike glycoprotein antibodies were detectable in both serum and DBS eluate and there was a significant correlation between the antibody levels detected in matched samples (r = 0.96, p<0.0001). Using serum as the gold standard in the assay, matched DBS samples achieved a Cohens kappa coefficient of 0.975 (near-perfect agreement), a sensitivity of 98.1% and specificity of 100%, for detecting anti-spike glycoprotein antibodies. . https://doi.org/10.1101/2020.07.01.20144295 doi: medRxiv preprint against matched serum in a highly sensitive and specific SARS-CoV-2 Enzyme Linked Immunosorbent Assay (ELISA). To detect antibodies to SARS-CoV-2-anti-spike (S) glycoprotein, matched serum and DBS titration curves were generated. We show that DBS samples can be used for the detection of SARS-CoV-2-specific antibodies with high levels of sensitivity and specificity and compared well with matched serum samples. doi = 10.1101/2020.07.01.20144295 id = cord-327575-5pcnuqgy author = Morrisette, Taylor title = The Pharmacokinetic and Pharmacodynamic Properties of Hydroxychloroquine and Dose Selection for COVID-19: Putting the Cart Before the Horse date = 2020-08-01 keywords = COVID-19; HCQ; SARS summary = The objective of this review was to describe the current understanding of the PK/PD and dose selection of HCQ against SARS-CoV-2, discuss knowledge gaps, and identify future studies that are needed to optimize the efficacy and safety of treatments against COVID-19. Although studies completed thus far show variable results, Arshad and colleagues performed a large multicenter, retrospective, observational analysis that evaluated patients hospitalized because of a COVID-19-related admission receiving HCQ 400 mg twice daily on day 1, followed by HCQ 200 mg twice daily on days 2 to 5 [14] [15] [16] [17] . Furthermore, the World Health Organization discontinued the HCQ arm in the Solidarity trial because it showed ''''little or no reduction in the mortality of hospitalized COVID-19 patients when compared to standard of care'''' (HCQ dosed 800 mg twice daily on day 1, followed by HCQ 400 mg twice daily for a total of 10 days), and the Food and Drug Administration revoked the emergency use authorization to utilize HCQ for the treatment of COVID-19 [16] [17] [18] . doi = 10.1007/s40121-020-00325-2 id = cord-255602-3pzh5ur9 author = Moscadelli, Andrea title = Fake News and Covid-19 in Italy: Results of a Quantitative Observational Study date = 2020-08-12 keywords = SARS; covid-19; fake; news summary = We used the BuzzSumo application to gather the most shared links on the Internet related to the pandemic in Italy, using keywords chosen according to the most frequent "fake news" during that period. We used the BuzzSumo pplication [38] in order to gather the most shared links or posts on the Internet and social media related to SARS-CoV-2 and the Covid-19 pandemic. The 9 keywords were chosen in a consensus meeting of the research group, since they were the most likely to uncover health-related false information using the BuzzSumo search engine, and specifically fake news that would not meet our exclusion criteria. An article was immediately excluded when the content did not deal specifically with health or science, i.e., the focus may have been on the socioeconomic consequences of the pandemic, which was a topic we excluded from our fake news review. doi = 10.3390/ijerph17165850 id = cord-311240-o0zyt2vb author = Motayo, Babatunde Olarenwaju title = Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date = 2020-07-27 keywords = Africa; SARS; sequence summary = Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa. The pathogen was later identified to be a novel coronavirus closely related to the severe acute respiratory syndrome virus (SARS), with a possible bat origin (Zhou et al, 2020) . This study was designed to determine to the genetic diversity and evolutionary history of genome sequences of SARSCoV-2 isolated in Africa. Results of recombination analysis of the African SARSCoV-2 (AfrSARSCoV-2) sequences against references whole genome sequences of SARS, Recombination signals were observed between the African SARSCoV-2 sequences and reference sequence (Major recombinant hCoV-19 Pangolin/Guangu P4L/2017; Minor parent hCoV-19 B batYunan/RaTG13) between the RdRP and S gene regions (Figure 2 ). doi = 10.1101/2020.07.27.222901 id = cord-272501-byfxqsbu author = Motta, Juan Camilo title = Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report date = 2020-08-22 keywords = Cov2; SARS summary = title: Adenovirus and novel coronavirus (SARS-Cov2) coinfection: A case report We report a case of SARS-Cov2 and adenovirus coinfection, which further developed into acute respiratory distress syndrome. The exact time of coinfection could not be established, and additional poor prognostic factor to the development of severe disease added to patient''s comorbidities and reported tests [1, 6] . Although coinfection is not common, in cases with severe disease or CT findings that are not explained by COVID-19 infection [11, 14, 15] , additional studies such as nested PCR for respiratory germs are required to detect potentially treatable pathogens, such as mycoplasma or influenza virus [14] . Larger and better designed prospective analytical studies are required to determine further risk factors, clinical impact, prognosis, and the prevalence of SARS-Cov2 and another respiratory pathogen coinfection. Coinfection with SARS-CoV-2 and other respiratory pathogens in COVID-19 patients in Guangzhou doi = 10.1016/j.idcr.2020.e00936 id = cord-336053-cjq7szcn author = Mottola, Filiberto Fausto title = Cardiovascular System in COVID-19: Simply a Viewer or a Leading Actor? date = 2020-08-27 keywords = COVID-19; SARS; acute; high; patient summary = Several studies have observed a relationship between coronavirus disease (COVID-19) infection and the cardiovascular system with the appearance of myocardial damage, myocarditis, pericarditis, heart failure and various arrhythmic manifestations, as well as an increase in thromboembolic risk. Compared to those without an increase in TnT, these patients were more likely to require invasive or non-invasive ventilation (22% versus 4%, and 46% versus 4%, respectively) and to develop acute respiratory distress syndrome (59% versus 15%) or acute kidney injury (9% versus 0%; p < 0.001 for all); in addition, the mortality rate was higher (51.2% vs. A recent meta-analysis showed that cardiac troponin I (cTnI) values were significantly higher in patients with severe SARS-CoV-2 infection compared to those observed with mild forms [14] . However, myocardial damage alone is not enough and there are other factors involved in enhancing the arrhythmic risk in COVID-19: in fact, in these patients, only half showed acute cardiac injury despite the high frequency of arrhythmias [32] . doi = 10.3390/life10090165 id = cord-312524-ee5xw1r8 author = Moustafa, Ahmed M. title = Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date = 2020-06-08 keywords = SARS; figure summary = Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. Rapid sequencing of the SARS-CoV-2 pandemic virus has presented an 40 unprecedented opportunity to track the evolution of the virus and to understand the 41 emergence of a new pathogen in near-real time. Our panallelome approach to developing a whole genome (wgMLST) scheme for 58 SARS-CoV-2 uses a modified version of our recently developed tool, WhatsGNU [10], 59 to rapidly assign an allele number to each gene nucleotide sequence in the virus''s 60 genome creating a sequence type (ST). We developed the GNU-based Virus IDentification (GNUVID) system as a tool 71 that automatically assigns a number to each unique allele of the 10 open reading 72 frames (ORFs) of SARS-CoV-2 ( Figure 1A) information. When the global region of origin for each genome sequence was mapped to 102 each CC there was a strong association of some CCs with certain geographical 103 locations. doi = 10.1101/2020.06.08.139055 id = cord-280454-etf32afd author = Moustaqil, Mehdi title = SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date = 2020-06-05 keywords = Fig; GFP; IRF3; NLRP12; SARS; TAB1; cleavage summary = title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts Direct cleavage of IRF3 by NSP3 could explain the blunted TypeI IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. In this report, we show that the viral proteases PLpro and 3CLpro of SARS-CoV2 lead to the in-vitro proteolytic cleavage of three important proteins of the host immune response: IRF3, TAB1 and NLRP12 (Fig. 1B) . The presence of the five human-like cleavage sites for IRF3, TAB1 and NLRP12 in a single species shows that it is possible that the SARS viruses could have gained the new functionality of cleaving these Human Innate Immune Proteins in a single reservoir host, potentially in Myotis Davidii. doi = 10.1101/2020.06.05.135699 id = cord-277763-ihg3te63 author = Moynan, David title = The role of healthcare staff COVID-19 screening in infection prevention & control date = 2020-06-25 keywords = SARS summary = While HCW can acquire infections and contribute to cross-transmission during hospital outbreaks such as influenza or norovirus, asymptomatic staff are usually not routinely screened as part of the outbreak control measures. In March and April 2020, on three wards with two or more positive COVID-19 patients after three days of admission (designated as potential nosocomial infection), we implemented universal staff SARS-CoV-2 testing on that ward as part of outbreak management. As asymptomatic (or indeed, pre-symptomatic) HCW may have similar viral loads and may be capable of transmission as much as symptomatic individuals 9 , their detection and subsequent exclusion from work is an important aspect of a hospital''s COVID-19 strategy. In conclusion, as hospitals begin to reopen to routine non-COVID-19 services, HCW SARS-CoV-2 testing irrespective of symptoms should be considered, particularly as part of outbreak management to rapidly prevent onward transmission to patients and other staff. COVID-19: PCR Screening of Asymptomatic Health-Care Workers at London Hospital doi = 10.1016/j.jinf.2020.06.057 id = cord-266104-xqvwht7c author = Mu, Chenglin title = Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology date = 2020-08-14 keywords = Polygonati; Rhizoma; SARS summary = title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology Here using TCMSP and Swiss Target Prediction databases to sort out the potential targets of the main chemical components and GenCLiP3, NCBI, and GeneCard databases to search for COVID-19 related targets, the chemical compound-target-pathway network was analyzed. Moreover, modern and ancient pharmacological records showed that Rhizoma Polygonati has a wide pharmacological function in antibacterial, antiviral, immunity enhancement, anti-ageing, anti-cancer, anti-diabetes, anti-fatigue, and anti-heart Network pharmacology in TCM combines with multidisciplinary technologies, such as systems biology, and computational biology in order to build a complex network between drug-target-diseases, and elucidate the mechanism of drugs in treatment (Luo et al., 2020) . Therefore, to explore the active ingredients and mechanism of different species of Rhizoma Polygonati based on their active compounds concentration in the treatment of pulmonary symptoms caused by the new coronavirus will help to precisely apply TCM for anti-virus. doi = 10.1016/j.jff.2020.104149 id = cord-316859-h8lfmr3e author = Mu, Jingfang title = SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells date = 2020-04-10 keywords = SARS summary = Previous study has reported that severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N) protein displayed a VSR activity in mammalian cells via a cellular reversal-of-silencing assay (Cui et al., 2015) . We first examined whether SARS-CoV-2 N possessed VSR activity via a classic reversal-of-silencing assay, in which enhanced green fluorescent protein (EGFP)-specific shRNA was transfected into EGFP-expressing 293T cells, together with a plasmid encoding SARS-CoV-2 N protein with Flag tag. Our data showed that expression of SARS-CoV-2 N markedly restored the protein level of EGFP ( Figure 1A Because RNAi directly results in the cleavage and degradation of target mRNAs, we further examined the VSR activity of SARS-CoV-2 N using the reversal-of-silencing system via Northern blotting with a digoxin (DIG)-labeled RNA probe targeting EGFP ORF 1-400 nt. Our findings showed that SARS-CoV-2 N can antagonize RNAi in both initiation (i.e., siRNA biogenesis) and effector (i.e., RISC assembly and target RNA cleavage) steps. doi = 10.1007/s11427-020-1692-1 id = cord-261566-fn08b0y2 author = Mudgal, Rajat title = Prospects for mucosal vaccine: shutting the door on SARS-CoV-2 date = 2020-09-15 keywords = CoV; CoV-2; MERS; SARS; mucosal; vaccine summary = 15 The disease severity and lung damage in the case of SARS-CoV-2 infection can be directly correlated with the dysregulated immune response at 7-10 days after symptom onset and is characterized by exuberant production of cytokines including IL-2, IL-7, IL-10, MIP-1A, IP-10, and TNF-α. 53, [98] [99] [100] [101] [102] Ferrets are a suitable animal model for SARS-CoV vaccine evaluation as they support viral replication in the respiratory tract, develop similar disease symptoms, and display severe lung pathology. Potential ADE and waning of vaccine-induced immune response represent other obstacles in the development of a mucosal vaccine against SARS-CoV-2. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Effect of mucosal and systemic immunization with virus-like particles of severe acute respiratory syndrome coronavirus in mice doi = 10.1080/21645515.2020.1805992 id = cord-267690-g0kesgjm author = Mueller, Sarina K. title = Considerations for Continuing Semielective and Emergency Otolaryngological Procedures During the COVID-19 Pandemic date = 2020-09-07 keywords = SARS; covid-19 summary = The objective of this study was to analyze procedures and outcomes of continuing semielective and emergency surgeries during the COVID-19 pandemic. CONCLUSIONS: Continuing selected otorhinolaryngological surgeries is crucial for patients'' health, survival, and long-time quality of life, yet, the protection of the medical personnel has to be granted. In case of a negative SARS-CoV-2 test, the scheduled surgery was performed the following day without special protective equipment ( Figure 1A) . If the SARS-CoV-2 test result could not be awaited due to the condition of the patient, the surgery was performed with full protective equipment consisting of a FFP2 or FFP3 (filtering face piece mask), a gown, a face shield, and double gloves. If the SARS-CoV-2 test result was positive, surgery was also performed with the full protective equipment. If the SARS-CoV-2 test was negative, surgery was performed as in the semi-elective cases without the above named protective equipment ( Figure 1B ). doi = 10.1177/0145561320952506 id = cord-320567-7je1i8qd author = Muenchhoff, Maximilian title = Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020 date = 2020-06-18 keywords = Charité; SARS summary = The aim of this study was to compare the inter-laboratory and inter-method sensitivity of different RT-PCR assays by providing a blinded, frozen dilution series of a nucleic acid extract of a highly positive biosample to seven different diagnostic laboratories in Germany in March 2020. Digital droplet PCR quantification of the distributed dilution series of nucleic acid eluate of SARS-CoV-2-positive clinical material, Germany, March 2020 The undiluted sample showed between 4,325 and 5,015 SARS-CoV-2 RNA copies per reaction using 5 µL of eluate for the CDC N1, N2, N3 and Charité E protocols, but only 850 and 1,951 RNA copies for the Charité N and P primer/probe combinations ( Figure 1A) , respectively, indicating a lower sensitivity of the latter. Driven by false-negative results for samples with low PCR-positivity using the original Charité RdRp reaction (see below and others [8, 9] ), we compared the primer/ probe sequences with currently available SARS-CoV-2 genomes. doi = 10.2807/1560-7917.es.2020.25.24.2001057 id = cord-342254-vdovpfu1 author = Mugheddu, C. title = CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management date = 2020-06-04 keywords = SARS summary = title: CID‐19 pulmonary infection in erythrodermic psoriatic patient with oligodendroglioma: safety and compatibility of apremilast with critical intensive care management Novel coronavirus 2019 (SARS-CoV2) pandemic has particularly affected Italy, with a profound impact on the therapeutic strategy for complex disorder such as psoriasis, whose extensive skin damage might expose to an increased infective risk compared to the general population. Psoriasis treatment relies on immunosuppression, and although most experts agree that the benefit-to risk-ratio is in favor of maintaining selective biologic therapies, and small molecules such as apremilast, they recommend dismission if severe COVID-19 symptoms occur. The fact that patient with a severe form of psoriasis contracted the COVID-19 pneumonia, while on treatment with apremilast is worth of some considerations. 11 Recently, another Italian psoriasis patient contracting COVID-19 under IL-23 inhibitor treatment (guselkumab) has been reported, and completely recovered from the infection. 12 From our experience, apremilast confirms its safety in very critical patients with severe infections, including COVID-19. doi = 10.1111/jdv.16625 id = cord-257809-bq9ha4d0 author = Mukaino, Masahiko title = Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-04-08 keywords = SARS summary = title: Staying Active in Isolation: Telerehabilitation for Individuals With the Severe Acute Respiratory Syndrome Coronavirus 2 Infection T he recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a pandemic. Here, therefore, we introduce a preliminary attempt to use a telerehabilitation system to deliver exercise opportunities to individuals isolated because of SARS-CoV-2 infection. Four hospitalized individuals (aged 19-66 yrs, median age = 53 yrs, 2 male individuals), who were infected with SARS-CoV-2 during the outbreak on the Diamond Princess cruise ship, participated in the program. Using videoconferencing (Zoom by Zoom Video Communications Inc, San Jose, CA) and remote control software (TeamViewer; TeamViewer GmbH, Göppingen, Germany), a physical therapist guided each individual in a 20-min exercise program (Fig. 1) . With the pandemic spread of SARS-CoV-2, the number of isolated individuals is expected to increase. doi = 10.1097/phm.0000000000001441 id = cord-294592-zwvr57a0 author = Mukherjee, Moumita title = Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date = 2020-08-11 keywords = RNA; SARS; UTR; viral summary = title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. There are experimentally validated evidences of human RBPs binding to the regulated signals within the untranslated region of SARS-CoV RNA in order to control the viral RNA synthesis and turnover. doi = 10.1371/journal.pone.0237559 id = cord-327134-egp4t82x author = Mukherjee, Prasenjit title = Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits date = 2008-04-01 keywords = Fig; SARS-3CL; docking; pose summary = A series of phthalhydrazide based peptidic analogues 45 (Supplementary information, Fig. S1 ) with inhibitory activity against the SARS-3CL pro had been reported and was utilized in a validation study using Gold 2.2 to select the binding site definition and scoring function utilized for binding pose calculation. The group of top-ranking structurally diverse molecules obtained through the clustering analysis were visually inspected based on their (1) ability to occupy the key substrate specificity sites S1 0 , S1, S2, and S4, (2) geometric quality of the ligand binding pose, (3) hydrophilic/ lipophilic mismatches, and (4) complementarity of the key interacting features. The final docking parameters (binding site definition, scoring function for pose generation) selected through this study were identical to those used in the first phase of screening except for the addition of a constraint set. doi = 10.1016/j.bmc.2008.01.011 id = cord-265887-g5zhoyo9 author = Mukherjee, Shruti title = Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain date = 2020-08-11 keywords = Golgi; SARS; membrane; protein summary = (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention. doi = 10.1016/j.bpc.2020.106452 id = cord-296187-nnv2e7gr author = Mulgaonkar, Nirmitee title = Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date = 2020-08-18 keywords = ACE2; RBD; SARS; VSV summary = The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 μM levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction – suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. This study utilizes in silico methodology followed by in vitro experimental validation to screen existing FDA-approved small molecule drugs specific to the RBD of the spike protein of SARS-CoV-2 to identify repurposable drugs targeting further clinical validation. doi = 10.1101/2020.06.18.158196 id = cord-294551-s3nsiano author = Muller, M. P. title = Early diagnosis of SARS: lessons from the Toronto SARS outbreak date = 2006-04-04 keywords = SARS; Toronto summary = To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Patients were classified as confirmed SARS if they had a compatible clinical illness (fever or nonproductive cough or dyspnea), an exposure to SARS (direct contact with a known SARS case or travel to a SARS-endemic area or time spent at an institution where SARS transmission was occurring, within 12 days of symptom onset), and a positive microbiological test (positive acute or convalescent serology, or positive PCR from clinical or pathological specimens). Findings associated with a confirmed diagnosis included direct exposure to a known case (OR, 2.34; 95%CI, 1.01-5.40), symptomatic fever as an initial symptom (OR, 5.07; 95%CI, 2.24-11.50), a documented temperature of 38.0°C on admission to hospital (OR, 2.6; 95%CI, 1.14-5.92), and the presence of a pulmonary infiltrate by the time of admission (OR, 2.46; 95%CI, 1.09-5.56). doi = 10.1007/s10096-006-0127-x id = cord-327240-nohxk3y6 author = Muller, Matthew P. title = Adverse Events Associated with High‐Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome date = 2012-01-06 keywords = SARS; Toronto; ribavirin summary = Logistic regression was used to evaluate the association between ribavirin use and each adverse event (progressive anemia, hypomagnesemia, hypocalcemia, bradycardia, transaminitis, and hyperamylasemia) after adjusting for SARS‐related prognostic factors and corticosteroid use. 11, 12 In Toronto, Ontario, Canada, most patients seen during the initial phase of the outbreak were treated with high-dose intravenous ribavirin, based on a protocol recommended for the treatment of hemorrhagic fever. [13] [14] [15] [16] Studies of the clinical efficacy of ribavirin in patients with SARS were inconclusive, 11, [17] [18] [19] [20] and significant adverse events were reported, including severe hemolysis. 27, 28 We report the frequency of adverse events in 183 patients treated with high-dose ribavirin during the Toronto SARS outbreak. Our finding that 57% of patients developed progressive anemia (largely associated with hemolysis) is substantially higher than the 9-19% rate seen in ribavirin-treated patients with hepatitis C but is consistent with the 49-73% reported in previous noncontrolled studies of ribavirin-related adverse events in patients with SARS. doi = 10.1592/phco.27.4.494 id = cord-304073-f3iwclkm author = Mullick, Jhinuk Basu title = Animal Models to Study Emerging Technologies Against SARS-CoV-2 date = 2020-07-27 keywords = ACE2; CoV-2; SARS; human summary = Animal models are indispensable to understand these processes and develop and test emerging technologies; however, the mechanism of infection for SARS-CoV-2 requires certain similarities to humans that do not exist in common laboratory rodents. Here, we review important elements of viral infection, transmission, and clinical presentation reflected by various animal models readily available or being developed and studied for SARS-CoV-2 to help bioengineers evaluate appropriate preclinical models for their emerging technologies. Non-human primates, Syrian hamsters, ferrets, cats, and engineered chimeras mimic the human infection more closely and hold strong potential as animal models of SARS-CoV-2 infection and progression of resulting human disease. Overall, the studies show that the Syrian hamster is a useful animal model for SARS-CoV-2 infection especially to study viral replication, shedding, and transmission through the respiratory tract. In all studies, animals developed NAbs. Overall, the rhesus macaque model has been similar in many aspects to the human COVID-19 pathogenesis. doi = 10.1007/s12195-020-00638-9 id = cord-289064-435bp4rt author = Muniangi-Muhitu, Hermine title = Covid-19 and Diabetes: A Complex Bidirectional Relationship date = 2020-10-08 keywords = ACE2; SARS; cell; covid-19; patient summary = Identified risk factors for disease severity and death from SARS-Cov2 infection include older age, male sex, diabetes, obesity and hypertension. We consider roles for the immune system, the observed phenomenon of microangiopathy in severe Covid-19 infection and the potential for direct viral toxicity on metabolically-relevant tissues including pancreatic beta cells and targets of insulin action. (18) , patients with diabetes and hypertension who had been treated with ACE inhibitors or angiotensin receptor blockers (ARB) had a high number of ACE2 receptors in the lung, and could therefore be at higher risk of developing severe symptoms, if infected with Covid-19. With respect to the glycemic deterioration seen in patients with preexisting T2D during Covid-19, a very recent report (63) provides the intriguing observation that ACE2 expression at both the mRNA and protein is increased substantially in human beta cells in response to response to inflammatory cytokines, presumably rendering these cells more susceptible to infection. doi = 10.3389/fendo.2020.582936 id = cord-355841-m6dl8a0w author = Munz, Maike title = Acute transverse myelitis after COVID-19 pneumonia date = 2020-05-26 keywords = SARS summary = A repeated throat swab showed a negative SARS-CoV2 PCR. Magnetic resonance imaging (MRI) of the spine revealed T2 signal hyperintensity of the thoracic spinal cord at Th9 level suggestive of acute transverse myelitis rather than multiple sclerosis [3] (Fig. 1a) . SARS-CoV2-PCR in the CSF and oligoclonal bands were negative. Follow-up MRI on day 6 further showed a patchy hyperintensity of the thoracic myelon at Th9-10 and at Th3-5 level (Fig. 1d) , suggestive of transverse myelitis. Follow-up CSF on day 12 showed normalization of cell count (3/µl) and regressing protein levels (734 mg/l), no Maike Munz and Swen Weßendorf authors contributed equally. Cases of Guillain-Barré Syndrome in association with severe COVID-19 infections were reported [6] . In a series of 58 severely affected COVID-19 patients, 67% showed clinical corticospinal tract signs but received no spinal MRI [7] . Preprint) Acute myelitis after SARS-CoV-2 infection: A case report https doi = 10.1007/s00415-020-09934-w id = cord-310928-g553afo9 author = Murch, Simon H title = Common determinants of severe Covid-19 infection are explicable by SARS-CoV-2 secreted glycoprotein interaction with the CD33-related Siglecs, Siglec-3 and Siglec-5/14 date = 2020-08-07 keywords = CD33; MDSC; SARS; Siglec-5 summary = In contrast to the SARS secreted glycoprotein (SGP), SARS-CoV-2 SGP are thus potential ligands for Sialic acid-binding Siglecs on host immune cells, known to regulate immune function. CD33 + MDSC populations release Arginase-1 to cause arginine depletion, inducing decreased T cell receptor (TCR)- chain expression and impaired adaptive immune responses 20, 21 . There is so far no clear consensus on their eventual phenotype but these new marrow derived cells are initially characterised as Early stage MDSC (eMDSC), which do not initially express lineage markers but do express CD33 and would thus be susceptible to SARS-CoV-2 SGP manipulation until the virus was cleared ( Figure 3 ). In due course, this might allow persons who fail to respond to immunisation to be pre-treated to block Siglec binding sites, allowing them to be exposed to small infecting doses of SARS-Cov-2 in clinically controlled circumstances and thus generate a broad immune response, including to the pathogenic glycan determinants doi = 10.1016/j.mehy.2020.110168 id = cord-286441-nl3kuqw3 author = Murray, D. D. title = Design and implementation of the multi-arm, multi-stage Therapeutics for Inpatients with COVID-19 (TICO) platform master protocol: An Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative date = 2020-11-12 keywords = COVID-19; SARS; TICO; stage summary = Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. Methods: Therapeutics for Inpatients with COVID-19 (TICO), is a global multi-arm, multi-stage (MAMS) platform master protocol, which facilitates the rapid evaluation of the safety and efficacy of candidate anti-viral therapeutic agents for adults hospitalized with COVID-19. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. This approach to early futility assessment using an early intermediate outcome and a primary endpoint out to 90 days allows the study team to make rapid decisions on safety and potential efficacy of novel agents while ultimately focusing on patient-centered, longer-term outcomes. doi = 10.1101/2020.11.08.20227876 id = cord-333909-uco4c946 author = Murray, Meghan T. title = Mitigating a COVID-19 Outbreak Among Major League Baseball Players — United States, 2020 date = 2020-10-23 keywords = MLB; SARS summary = Certain MLB health and safety protocols, which include frequent diagnostic testing for rapid case identification, isolation of persons with positive test results, quarantine for close contacts, mask wearing, and social distancing, might have limited COVID-19 transmission between teams. The health and safety protocols established tiered, risk-based testing for MLB teams, which called for persons who received a positive SARS-CoV-2 test result to be placed in isolation and for close contacts to be quarantined separately. Before game play on day 4, the index team A player (an asymptomatic tier 1 risk group member who received every other day testing, per protocol) received a positive SARS-CoV-2 real-time reverse transcription-polymerase chain reaction (RT-PCR) test result from collection on day 2. Investigators received from MLB a deidentified line list of team members with diagnosed COVID-19, a timeline of the outbreak response, the duration of on-field play by potentially infectious persons (within 24 hours before the date of collection of the test-positive specimen), contact tracing procedures, and the MLB health and safety protocols. doi = 10.15585/mmwr.mm6942a4 id = cord-320740-npoje09j author = Musa, Arif title = Remdesivir for the Treatment of COVID-19: A Systematic Review of the Literature date = 2020-05-20 keywords = COVID-19; SARS summary = To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. To address the need for an effective treatment of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) remdesivir was performed. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Therefore, despite supportive data from in vitro and in vivo studies, the clinical effectiveness of IV remdesivir for treatment of COVID-19 and potential side effects remain incompletely defined in the human population. Given the worldwide urgency for an effective and safe treatment for COVID-19 and the therapeutic potential of remdesivir, this systematic review was performed to determine the outcomes and adverse events associated with this investigational, anti-viral medication. doi = 10.5811/westjem.2020.5.47658 id = cord-305816-06lddk87 author = Musarrat, Farhana title = The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections date = 2020-05-17 keywords = SARS summary = title: The anti‐HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV‐2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID‐19 infections A systematic screening of several drugs including cardiac glycosides and kinase inhibitors and inhibitors of human immunodeficiency virus (HIV) entry revealed that only the FDA‐approved HIV protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S‐n‐ and S‐o‐mediated cell fusion with complete inhibition at a 10‐μM concentration. 26 In addition to its potent activity against the HIV protease, nelfinavir mesylate was found to produce multiple effects on cellular processes including the induction of apoptosis and necrosis as well as induction of cell-protective mechanisms, including cell cycle retardation and the unfolded protein response. HRP, horseradish peroxidase; SARS CoV, severe acute respiratory syndrome coronavirus; Sn, S-new Recently, it was shown that a peptide that targeted the S-n HR1 domain S inhibited SARS-CoV-2 virus replication, virus entry, and virus-induced cell fusion. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides doi = 10.1002/jmv.25985 id = cord-301025-cf2jcw6x author = Musca, Serban C. title = A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine''s Prophylactic Effect Against Infection With SARS-CoV-2 date = 2020-08-13 keywords = SARS; covid-19 summary = title: A Simple Bayesian Method for Evaluating Whether Data From Patients With Rheumatic Diseases Who Have Been Under Chronic Hydroxychloroquine Medication Since Before the COVID-19 Outbreak Can Speak to Hydroxychloroquine''s Prophylactic Effect Against Infection With SARS-CoV-2 We propose to use data from patients with rheumatic diseases (RA, SLR) who have been chronically taking HCQ medication since before the COVID-19 outbreak (hereafter: HCQpa), in order to evaluate the potential of HCQ for preventing infection with SARS-CoV-2. If HCQ has no prophylactic effect against infection with SARS-CoV-2, COVID-19 prevalence in HCQpa will not be statistically different from that in the general population (all comers who do not take HCQ medication; hereafter: pop gen ). HCQ having a prophylactic effect against SARS-CoV-2 infection would manifest itself by a COVID-19 prevalence in HCQpa that is lower than the COVID-19 prevalence in the general population. doi = 10.3389/fmed.2020.00490 id = cord-293988-f5gvwjyh author = Musso, Nicolò title = New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date = 2020-09-11 keywords = China; CoV-2; RNA; SARS summary = The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat''s pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2. doi = 10.3390/pathogens9090746 id = cord-290123-scd9u8ix author = Mustafa, Mujahed I. title = Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors date = 2020-09-23 keywords = COVID-19; SARS; cytokine; qty summary = title: Cytokine Storm in COVID-19 Patients, Its Impact on Organs and Potential Treatment by QTY Code-Designed Detergent-Free Chemokine Receptors In this review, we will focus on cytokine storm in COVID-19 patients, their impact on the body organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. However, novel coronavirus still gains entry into humans by targeting ACE2 receptor that is found on lung cells, which destroy human lungs through cytokine storms, and this leads to hyperinflammation, forcing the immune cells to destroy healthy cells, which could be the reason behind COVID-19 patients'' frequent intensive care admission [28] . This review deals with cytokine storm in COVID-19 patients, their impact on the organs, and the potential treatment by QTY code-designed detergent-free chemokine receptors. COVID-19 triggers cytokine storm in many stages of its pathological course that causes lung fibrosis, acute respiratory distress syndrome, and eventually leads to multiorgan failure [34, 54, 61] . doi = 10.1155/2020/8198963 id = cord-332448-5fz8ef4f author = Mutnal, M. B. title = Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date = 2020-05-02 keywords = CoV-2; SARS summary = Testing for SARS-CoV-2 was performed by real-time RT-PCR assay and results were shared with State public health officials for immediate interventions. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint of this study is to encourage other laboratories to consider an early start to testing during pandemics, share 74 initial trends in this part of the world and possible impact of SARS-CoV-2 on other seasonal respiratory 75 This report describes the early trends of SARS-CoV-2 infections in the central and north Texas, 76 USA and impact of epidemiological interventions that may have led to the decrease in the incidence of was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. BSWH laboratory provided test results data on both ambulatory and inpatient 275 population, and shared patient demographics with local public health officials. doi = 10.1101/2020.04.30.20086116 id = cord-333670-qv1orlv5 author = Mutti, Luciano title = Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date = 2020-05-28 keywords = COVID-19; HLA; SARS summary = In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . doi = 10.3389/fimmu.2020.01208 id = cord-262470-nkql7h9x author = Muus, Christoph title = Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date = 2020-04-20 keywords = ACE2; COVID-19; CTSL; Data; Extended; Fig; SARS; Supplementary; TMPRSS2; at2; cell; expression summary = title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. To assess the association of age, sex, and smoking status with the expression of ACE2, TMPRSS2, and CTSL, we aggregated 22 scRNA-seq datasets of healthy human nasal and lung cells, as well as fetal samples. doi = 10.1101/2020.04.19.049254 id = cord-253606-o8a0jhx2 author = Mégarbane, Bruno title = Comment on: Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial date = 2020-08-07 keywords = SARS summary = 4 Thirdly, using in vitro anti-SARS-CoV-2 activity and drug exposure at the putative target site of action to determine the effective regimen in vivo is misleading. 4 Interestingly, one mechanistic PK/virological/QTc model developed to predict SARS-CoV-2 decline rate and QTc prolongation suggested that only elevated hydroxychloroquine regimens (>400 mg twice daily for 5 days) are predicted to rapidly decrease viral loads, reduce the infected patient proportion and shorten the treatment course, compared with routine regimens (400 mg daily). To conclude, prediction of the effective hydroxychloroquine regimen to treat the SARS-CoV-2-infected patient is doomed due to uncertainties related to the lack of in vitro model reliability and EC 50 pertinence and to the weakness of used PBPK models that did not mirror hydroxychloroquine PK complexity at the intracellular target level. Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial doi = 10.1093/jac/dkaa327 id = cord-293736-nyvwv31m author = Méry, Geoffroy title = COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella date = 2020-07-21 keywords = ACE2; ARDS; Ang1; COVID-19; SARS summary = Here we seek to explore what underlies the link between immune response and respiratory failure in CoV infections on the one hand, and the current observation of obesity as a risk factor for severe outcome in COVID-19 on the other. Indeed, during COVID-19 infection, most patients exhibit a specific cytokine profile, associating innate immunity chemokines (such as monocyte chemoattractant protein 3 and interferon gamma-induced protein 10 (IP-10), which are suggestive of macrophage activation and epithelial suffering), and pro-inflammatory macrophage-produced cytokines such as IL-6 (45). We suggest that the tampering with such pathways could also lead to abnormalities in the inflammatory response observed in severe CoV infections through their influence on immune regulation and cytokine production. Besides suffering from a pro-inflammatory environment, which favors macrophage activation and neutrophil production, obese patients exhibit abnormal responses to viral infection. doi = 10.3389/fimmu.2020.01714 id = cord-287758-da11ypiy author = Mônica Vitalino de Almeida, Sinara title = COVID-19 therapy: what weapons do we bring into battle? date = 2020-09-10 keywords = ACE2; COVID-19; CoV-2; Coronavirus; FDA; FIG; MERS; RNA; SARS; drug; patient; viral summary = The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. doi = 10.1016/j.bmc.2020.115757 id = cord-253615-qylm0koe author = Müller, Marcel A title = Human Coronavirus NL63 Open Reading Frame 3 encodes a virion-incorporated N-glycosylated membrane protein date = 2010-01-15 keywords = NL63; ORF; SARS summary = In-silico analysis of potential glycosylation sites and membrane topology suggest properties similar to SARS-CoV ORF 3a protein ( Figure 1B and Table 1 ). To analyze the expression of ORF 3 protein during viral replication, colon carcinoma cells (CaCo-2) and Rhesus monkey kidney cells (LLC-MK2) cells were infected with hCoV-NL63 and an immunofluorescence assay (IFA) was done after two and four days, respectively. In contrast to virus-infected cells, cells overexpressing ORF 3 protein from plasmid with an N-terminal FLAG epitope showed only a single band in Western blot whose migration was consistent with the hypothetical unglycosylated form ( Figure 5B, left panel) . Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice Severe acute respiratory syndrome coronavirus 3a protein is released in membranous structures from 3a protein-expressing cells and infected cells doi = 10.1186/1743-422x-7-6 id = cord-340063-nmx91h0a author = Müller, Olaf title = Epidemiologie und Kontrollmaßnahmen bei COVID-19 date = 2020-04-28 keywords = COVID-19; China; Maßnahmen; SARS; die; und summary = The Coronavirus Disease Pandemic 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), started in December 2019 in China. Es gibt bisher weder wirksame Medikamente noch eine Impfung, somit stehen nur Public-Health-Interventionen wie einerseits physisches Abstandhalten und Hygienemaßnahmen sowie andererseits gezieltes Testen gefolgt von Isolations-und Quarantänemaßnahmen zur Verfügung. Der Erreger des Coronavirus Disease 2019 (COVID19) , das Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), gehört zu einer RNA-Virusfamilie, die sowohl bei Tieren als auch beim Menschen Erkrankungen hervorrufen kann. Der Verlauf nationaler Epidemien sowie der Pandemie wird von Faktoren bestimmt, die bisher für COVID-19 noch nicht vollständig verstanden sind. Prinzipiell unterscheidet man hierbei Isolationsmaßnahmen (SARS-CoV-2-Infizierte und COVID-19-Patienten) und Quarantänemaßnahmen (Kontaktpersonen von Infizierten und Erkrankten, stark betroffene Gemeinden); diese Maßnahmen sind besonders wirksam zum Beginn einer Epidemie, wenn Infektionsketten noch nachvollziehbar sind [35] . Es ist momentan auch noch offen, welche Ausmaße die Pandemie in den Industrieländern erlangen wird; dies hängt primär von der Intensität und Dauer der durchgeführten Public-Health-Maßnahmen ab. doi = 10.1055/a-1162-1987 id = cord-314515-p40x3cxr author = NGAI, Jenny C. title = The long‐term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status date = 2010-03-19 keywords = SARS; month; survivor summary = Methods: A prospective cohort study of SARS patients at the Prince of Wales Hospital, Hong Kong was conducted, with serial assessments of lung function, 6MWD and 36 item Short Form General Health Survey at 3, 6, 12, 18 and 24 months after disease onset. 1 3 Previous studies of survivors of acute lung injury and ARDS unrelated to SARS have shown variable degrees of residual abnormalities in pulmonary function, exercise capacity and impairment in health-related quality of life. 20, 21 The objectives of the present study were to evaluate the 2-year outcome of lung function, exercise capacity, health and work status of SARS survivors based on updated normative lung function data collected in Hong Kong (HK) from 2001-2003. This prospective cohort study has shown that 52% of SARS survivors had persistent impairment in DLCO and that exercise capacity and health status were significantly lower than the normal controls of the same age groups at 24 months post-illness. doi = 10.1111/j.1440-1843.2010.01720.x id = cord-297681-m0cckidw author = Na, Joo-Young title = [Secondary Publication] Standard Operating Procedure for Post-mortem Inspection in a Focus on Coronavirus Disease-19: the Korean Society for Legal Medicine date = 2020-08-13 keywords = COVID-19; SARS summary = The Korean Society for Legal Medicine, a highly specialized organization responsible for post-mortem examination and death investigation, aims to protect multiple staff-related post-mortem examinations and prevent the spread of COVID-19 in medical institutions and communities to improve social stability through this guideline for COVID-19 post-mortem inspections. The risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during post-mortem inspection of a dead body is relatively lower than that in the case of medical procedures or treatments because dead bodies do not cough and spread droplets. Due to the nature of postmortem inspection, in most cases, there is no or insufficient ante-mortem information, so collaboration with investigative agencies, local governments, and relevant public health centers is essential to determine the possibility of SARS-CoV-2 infection. 1) After confirming the identity of the deceased, if it is necessary to confirm whether he or she has the possibility of infection with COVID-19, request confirmation to the public health center through the police in charge, and proceed with the post-mortem inspection. doi = 10.3346/jkms.2020.35.e302 id = cord-283512-qly8iclf author = Na, Ki Ryang title = Acute Kidney Injury and Kidney Damage in COVID-19 Patients date = 2020-07-07 keywords = AKI; SARS summary = METHODS: From February 21 to April 24, 2020, 66 patients diagnosed with COVID-19 at Chungnam National University Hospital were analyzed; all patients underwent routine urinalysis and were tested for serum creatinine, urine protein to creatinine ratio (PCR), and urine albumin to creatinine ratio (ACR). In this study, the clinical data of 66 patients diagnosed with COVID-19 were analyzed, and the effects of SARS-CoV-2 infection on renal function and its complications were explored. Data were collected, including age, gender, initial and follow-up SCr and eGFR (chronic kidney disease [CKD]-epidemiology collaboration), routine urinalysis with microscopy, urine PCR, urine ACR, underlying disease (diabetes mellitus [DM], hypertension, CKD, and cardiovascular disease), and whether mechanical ventilation, extracorporeal membrane oxygenation (ECMO), or renal replacement therapy was implemented. In our study, there was a lower percentage of patients with AKI (4.5%) and moderately to severely increased proteinuria (30.3%) than in previous human coronavirus infections. doi = 10.3346/jkms.2020.35.e257 id = cord-272445-0xauff51 author = Naaber, Paul title = Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date = 2020-10-27 keywords = SARS; covid-19 summary = title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients'' clinical data and the time-point the test was performed. Our study aimed to compare the performance characteristics of seven commercial and two in-house IgG/total Ab tests, which analyze the reactivity to several target proteins, and to correlate the results with the patients'' clinical data (with different symptoms score and age), and time from disease onset. doi = 10.1371/journal.pone.0237548 id = cord-296881-2g81sjnl author = Nabil, Ahmed title = Current coronavirus (SARS-CoV-2) epidemiological, diagnostic and therapeutic approaches: An updated review until June 2020 date = 2020-07-20 keywords = COVID-19; SARS; patient; treatment summary = On May 7, 2020, Gilead Sciences, announced that the Japanese Ministry of Health, Labour and Welfare (MHLW) has granted regulatory approval of Veklury® (Remdesivir) as a treatment for SARS-CoV-2 infection, the virus that causes COVID-19 acute respiratory syndrome, under an exceptional approval pathway. In COVID-19 infection, a massive number of T-lymphocytes and mononuclear macrophages are activated, emitting different cytokines such as interleukin-6 (IL-6), which binds to the IL-6 receptor on its target cells, causing the cytokine storm and severe inflammatory responses in most organs including lungs, liver, kidney and other tissues and organs. Moreover, in July 2020 the WHO discontinued clinical trials with hydroxychloroquine and lopinavir/ritonavir treatment arms for COVID-19 (WHO, 2020b), where both therapies produced little and no reduction in the mortality of hospitalized SARS-CoV-2 cases when compared to standard of care. COVID-19 infection and treatment with hydroxychloroquine cause severe haemolysis crisis in a patient with glucose-6-phosphate dehydrogenase deficiency doi = 10.17179/excli2020-2554 id = cord-268661-a56u5e2o author = Nadeau, S. A. title = The origin and early spread of SARS-CoV-2 in Europe date = 2020-06-12 keywords = Europe; SARS; european summary = Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic, including inferences of the geographic location of ancestral lineages and the number of migration events into and between European regions. Here, we fit a phylodynamic model with geographic structure to full-length SARS-CoV-2 genomes to (i) estimate the early patterns of SARS-CoV-2 spread into and across Europe, (ii) weigh genomic evidence for competing hypotheses about the geographic origin of the predominant A2a lineage in Europe, (iii) report on the epidemiological parameters, and (iv) compare the rate of new cases arising from within-region transmission versus migration during the early epidemic. doi = 10.1101/2020.06.10.20127738 id = cord-309147-c3ikb81g author = Nadeem, Muhammad Shahid title = Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19) date = 2020-04-22 keywords = ACE2; COVID-19; CoV-2; SARS summary = According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The recent reports have suggested that SARS-CoV-2 is a modified coronavirus of bat origin [22, 32] , which came to humans as a result of zoonotic transmission [33, 34] . The receptor-binding domain (RBD) of pangolin-CoV has only a one amino acid difference with that of SARS-CoV-2; the infected pangolins exhibit pathological symptoms similar to humans suffering from COVID-19, and their blood circulating antibodies can react with the spike protein of SARS-CoV-2 [35, 36] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): The epidemic and the challenges doi = 10.3390/pathogens9040307 id = cord-027253-wfmm7naa author = Nag, Pooja title = Optical Fiber Sensors for Rapid Screening of COVID-19 date = 2020-06-19 keywords = SARS; detection summary = The article provides an overview of evanescent wave absorbance and localized surface plasmon resonance-based optic fiber platform for potential screening of COVID-19. Two alternative approaches for viral infection diagnostics are possible and practiced: the first involves serological investigations for measurement of elevated biomarker levels, for example, measurement of immunoglobin M (IgM) and immunoglobin G (IgG), while the second involves direct determination of the virus itself, utilizing its unique cellular proteins. This report explores the possible approaches of development of a point of care, low-cost evanescent wave absorbance (EWA)-based optical fiber sensor for quick and specific diagnosis of SARS-CoV-2. The wave is very sensitive to changes in refractive index at the interface and this property is utilized to develop EWA-based fiber optic sensors. While Fig. 3b has specific surface proteins (of the virus) immobilized on the optical fiber for detection of IgG and/or IgM (produced as an immune response). doi = 10.1007/s41403-020-00128-4 id = cord-335292-x2vjzp18 author = Nagashima, S. title = The Endothelial Dysfunction and Pyroptosis Driving the SARS-CoV-2 Immune-Thrombosis date = 2020-06-19 keywords = H1N1; SARS; covid-19; endothelial summary = Approach and Results: Post-mortem lung (6 cases of COVID-19 group; 10 cases of H1N1 group and 11 cases of Control group) and myocardial samples (2 cases of COVID-19 and one control) were analyzed by conventional immunohistochemistry by using antibodies to identify molecules involving with endothelial activation (CD163, Interleukin-6 (IL-6), Tumor Necrosis Factor alpha (TNF-alpha), Intercellular Adhesion Molecule 1 (ICAM-1)) and pyroptosis (Caspase-1). In addition to COVID-19 endothelial activation, the probable higher significant involvement of pyroptosis, in this pandemic disease, but not in H1N1pdm09, may drive the massive endothelial cell death contributing to thrombogenic mechanism. The presence of the same pattern of tissue expression (COVID-19 patients with higher CD163, IL-6, ICAM-1, TNF-alpha, and Caspase-1 tissue expression than control patient) in the myocardial samples might suggest that endothelial dysfunction and pyroptosis mechanism could be more than a local lung process, but a systemic event. doi = 10.1101/2020.06.17.20133124 id = cord-263350-i02z0hgx author = Nagata, Noriyo title = Pathological and Virological Analyses of Severe Acute Respiratory Syndrome–Associated Coronavirus Infections in Experimantal Animals date = 2006 keywords = SARS summary = To determine the pathological features of SARS-CoV infection in experimental animals, its clinical, pathological, and virological features were investigated in cynomolgus monkeys, BALB/c mice, and F344 rats. In monkeys, following intranasal inoculation with 10 6 TCID 50 of SARS-CoV, the virus was isolated from throat and nasal swabs, and the viral genome was detected in rectal swabs collected between 2 and 7 days postinoculation (p.i.). Angiotensin-converting enzyme 2 (ACE2, a receptor for SARS-CoV 2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium in the lung of monkeys ( Figure 1A , B, and C). In BALB/c mice, the virus was detected in nasal and lung washes on days 3 and 5 after intranasal inoculation with 10 6 TCID 50 of SARS-CoV. In these experimental animals, ACE2 antigen-positive cells were observed in the virus-infected area and were repairing swelled type II alveolar epithelium (Table 1 ). doi = 10.1007/978-0-387-33012-9_92 id = cord-314333-hkyiy1gm author = Nagata, Noriyo title = Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice date = 2008-06-30 keywords = BALB; IFN-; SARS; mouse summary = title: Mouse-Passaged Severe Acute Respiratory Syndrome-Associated Coronavirus Leads to Lethal Pulmonary Edema and Diffuse Alveolar Damage in Adult but Not Young Mice Adult mice showed early and acute excessive proinflammatory responses (ie, cytokine storm) in the lungs after SARS-CoV infection, which led to severe pulmonary edema and diffuse alveolar damage. Because advanced age is associated with higher mortality in human SARS patients and SARS-CoV replicates better in aged mice, 6 -10,29 we experimentally infected 6-month-old (adult) female BALB/c mice with F-musX-VeroE6 or the Frankfurt 1 isolate. With regard to the cytokine responses of the mice, the lung homogenates of adult mice on day 1 after inoculation had significantly higher levels of monocyterelated chemokines [ie, MCP-1, macrophage inflammatory protein 1 (MIP-1), and IFN-␥-inducible protein 10 (IP-10)] than those from young mice ( Figure 5 ). doi = 10.2353/ajpath.2008.071060 id = cord-272902-kdkyzfjv author = Naghibzadeh, Mahmoud title = Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19 date = 2020-05-21 keywords = Coronavirus; SARS; microsatellite; repeat summary = An accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the Coronavirus-Covid-19 and SARS2003. Therefore, this research follows two objectives, development of a general microsatellite discoverer which can be used for different genomes, and analysis of the structures of both SARS-CoV-1 and that of Coronavirus-Covid-19 using this tool and revealing their differences. The properties and novelties of the presented method, which is named Fast MicroSatellite Discoverer (FMSD), for finding all microsatellites of a given gene, DNA, RNA, or other genome sequences including the Novel Coronavirus (GenBabk 2019) and SARS (Rota et al. Section 5 details the evaluation, reports the comparison results, and highlights the structural differences with respect to microsatellites between SARS and Coronavirus-Covid-19 as a case study. A software tool called mreps is develop to detect all tandem repeats, including microsatellites, in DNA as well as whole genome. doi = 10.1016/j.imu.2020.100356 id = cord-352943-ztonp62x author = Nagpal, Sunil title = What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date = 2020-08-20 keywords = LDA; SARS; mutation summary = Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a ''Bag of Words'' to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes). In fact, Latent Dirichlet Allocation (LDA), an unsupervised machine learning approach, is particularly known for identifying latent topics in large document collections and deciphering the words that define the inferred topics using a generative statistical model. Classical LDA was employed to generate topic models leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through rigorous hyper-parameter tuning for coherence optimization (Figure 2) . doi = 10.1101/2020.08.20.258772 id = cord-349762-f5no10eq author = Nagura-Ikeda, Mayu title = Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date = 2020-08-24 keywords = RNA; SARS summary = The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). Here, we describe the clinical performance of various molecular diagnostic methods, including the RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, 3 direct RT-qPCR kits, and RT-LAMP, and a commercial SARS-CoV-2 RAT used on self-collected saliva specimens in diagnosing COVID-19. The RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed different sensitivities for detecting viral RNA in saliva specimens, but each can be selectively used according to the clinical setting and facilities if close attention is paid to any false-negative results. doi = 10.1128/jcm.01438-20 id = cord-273961-ja8xggnd author = Nakagawara, Kensuke title = Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date = 2020-07-26 keywords = SARS summary = title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . doi = 10.1016/j.ijid.2020.07.034 id = cord-343691-sjz5og78 author = Nakajima, Kei title = Serious Conditions in COVID-19 Accompanied With a Feature of Metabolic Syndrome date = 2020-05-08 keywords = COVID-19; SARS summary = Retrospective research has shown that COVID-19 is frequently observed in people with obesity, diabetes, and hypertension [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] , which are pivotal components of metabolic syndrome (MetS), a cluster of cardiometabolic risks based on excess visceral fat. In recent decades, many investigators have convincingly shown that people with obesity, prediabetes, diabetes and MetS are at increased risk for impaired lung function, and especially impaired restrictive lung pattern [16] [17] [18] [19] [20] [21] [22] , which is primarily determined by reduced predicted forced vital capacity. In patients with any of the specific metabolic abnormalities of MetS, pre-existing impaired lung function can predispose them to SARS-CoV-2 infection and even accelerate it, potentially worsening the condition. doi = 10.14740/jocmr4187 id = cord-324328-olnwynfu author = Nakamichi, K. title = Outcomes associated with SARS-CoV-2 viral clades in COVID-19 date = 2020-09-25 keywords = SARS; September; clade; preprint summary = This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Even though we found several baseline clinical factors to be significantly associated with clade 2 in univariate analyses and history of malignancy in the multivariate model, rates of hospitalization were not significantly different between patients infected with the two major clades of virus in our study (p=0.063), nor were mortality rates (p=0.58). Patient demographics and clinical history were strongly predictive of hospitalization, and viral clade information did not substantially improve predictions, suggesting that it contributes minimally to determination of outcome. doi = 10.1101/2020.09.24.20201228 id = cord-331155-jkm4fuw4 author = Nakashima, Akiko title = Virus database annotations assist in tracing information on patients infected with emerging pathogens date = 2020-10-08 keywords = COVID-19; SARS; d614 summary = Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. COVID-19 presents varied symptomatic features [2] , [3] , [4] , [5] , [6] , [7] with a wide range of incubation periods and epidemic curves J o u r n a l P r e -p r o o f 4 are occurring [21] , [22] , the pathogenicity and origins of the mutated substrains of SARS-CoV-2 should be available in real time to adopt early measures by authorities at the onset of emergence. We examined the nucleotide mutations and visualized the transmission trajectories of SARS-CoV-2 by consulting the world specimens registered in the virus data bank of the National Center for Biotechnology Information (NCBI) [32] . Collectively, the annotations in the virus genome database are of fundamental use to hypothesize the pathogenicity and to trace the transmission route at the early phase of emergence of the new substrains. doi = 10.1016/j.imu.2020.100442 id = cord-339516-xfwxtjry author = Nakashima, Tsutomu title = Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses date = 2020-05-05 keywords = SARS summary = title: Olfactory and gustatory dysfunction caused by SARS-CoV-2: Comparison with cases of infection with influenza and other viruses Two nurses working in the National Cancer Center Hospital underwent the viral PCR test because they had similar symptoms, and they were both SARS-CoV-2 positive, although they had neither fever nor cough (Asahi Shimbun newspaper [digital], March 28, 2020). [2] [3] [4] The influenza and parainfluenza type 3 viruses were reported to be causative of olfactory loss most frequently. However, the adverse effect of olfactory dysfunction due to influenza vaccination was also reported. Suzuki et al 8 confirmed the presence of various viruses in the nasal discharge of patients with postviral infection olfactory dysfunction, such as rhinovirus, parainfluenza virus, Epstein-Barr virus, and coronavirus. However, only short-term follow-up investigation has been conducted regarding the effect of SARS-CoV-2 infection on the chemosensory function. We believe that epidemiological investigation is required regarding the effect of SARS-CoV-2 on the olfactory and gustatory functions in terms of the frequency, time course, and relationship with other symptoms. doi = 10.1017/ice.2020.196 id = cord-346413-2njl0fd3 author = Nakazawa, Daigo title = Immunothrombosis in severe COVID-19 date = 2020-08-15 keywords = SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread all over the world immediately after the first patient infected with this virus was discovered in Wuhan, China, in December 2019. It has been demonstrated that SARS-CoV-2 infection induces vascular endothelial injury, resulting from coagulation [3] . Because these are degradation products of fibrin or neutrophil extracellular traps (NETs), an enhanced turnover of coagulation and NET formation appears to characterize severe COVID-19. Based on the loss of CD31 + cells in the endothelium that were close to the aggregated NETs, Leppkes and coworkers suggested that the injury of vascular endothelial cells infected with SARS-CoV-2 could trigger neutrophil attraction and NET formation (Fig. 1) . Leppkes and coworkers suggested that the prevention of excessive NET formation and aggregation could provide an approach to inhibit vascular occlusion and the development of severe COVID-19. When SARS-CoV-2 injures vascular endothelial cells, coagulation is invoked, and simultaneously, DAMPs are secreted from the damaged cells. doi = 10.1016/j.ebiom.2020.102942 id = cord-314662-nem6dw34 author = Nakra, Natasha A. title = Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management date = 2020-07-01 keywords = Kawasaki; MIS; SARS summary = Initial reports surfaced in the UK [3] and Italy [4] , followed by New York and other parts of the U.S. Preliminary accounts of the features of this syndrome resemble those of known entities such as Kawasaki Disease (KD), toxic shock syndrome (TSS), and secondary hemophagocytic lymphohistiocytosis (SHLH)/macrophage activation syndrome (MAS). Early consultation of specialists to assist in management, such as intensive care, cardiology, rheumatology, infectious diseases, allergy/immunology, neurology Abbreviations: ALT, alanine transaminase; AST, aspartate transaminase; pro-BNP, pro-B-type natriuretic peptide; BUN, blood urea nitrogen; CRP, C-reactive protein; CT, computed tomography; ESR, erythrocyte sedimentation rate; GI, gastrointestinal; HLH, hemophagocytic lymphohistiocytosis; IL, interleukin; MIS-C, multisystem inflammatory syndrome in children; NK, natural killer; NP, nasopharyngeal; PT, prothrombin time; PTT, partial thromboplastin time; RT-PCR, reverse transcriptase polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. doi = 10.3390/children7070069 id = cord-292423-jupcit75 author = Narkhede, Rohan R. title = Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences date = 2020-06-17 keywords = SARS; covid-19; protease summary = With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. We proposed some natural products including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene as potential candidate for exerting the antiviral activity against SARS-CoV-2 infection using molecular docking study. The results acquired after docking analysis in terms of ligand binding affinity (kcal/mol), the interaction of natural products with the COVID-19 main protease, and the drug-like properties were shown in (Table 1 ). A promising binding to the COVID-19 main protease was observed in the case of rhein and berberine where both natural products were found to exhibit an affinity of − 8.9 and − 8.1 kcal/mol respectively. doi = 10.1007/s13659-020-00253-1 id = cord-269474-94c1mudi author = Nasef, Nehad title = Lessons from SARS: A retrospective study of outpatient care during an infectious disease outbreak date = 2010-07-20 keywords = NNFU; SARS summary = In response, a decision was made by the neonatal neuro-developmental follow up (NNFU) clinic staff to select patients with scheduled appointments to have a mail/telephone assessment using Ages and Stages Questionnaire (ASQ) or to postpone/skip their visit. The objective of this study was to compare the developmental assessment and its outcome in two groups of NNFU clinic patients, SARS versus non-SARS, over three standard clinic appointments. The objective of this retrospective study was to compare the developmental assessment and its'' outcome in two groups of NNFU clinic patients, SARS versus non-SARS over an assessment trajectory of 3 booked clinic appointments (labeled before, during and after according to the time of clinic closure during SARS). Of 30 patients diagnosed with developmental delay at the before visit in the SARS group, 8 were contacted by mail or telephone and 22 were never contacted during the period of clinic closure. doi = 10.1186/1471-2431-10-51 id = cord-291190-f6km3c7z author = Nasi, Aikaterini title = Reactive oxygen species as an initiator of toxic innate immune responses in retort to SARS-CoV-2 in an ageing population, consider N-acetylcysteine as early therapeutic intervention date = 2020-06-18 keywords = COVID-19; ROS; SARS summary =  SARS-CoV has been reported to modulate PARP function and thereby NAD+ biosynthesis  Cellular homeostasis and redox imbalances by SARS-CoV2 can cause stress responses  Antioxidants such as NAC could limit ROS mediated tissue damage during COVID-19 Hereby, based on literature review from the current pandemic and previous outbreaks with corona viruses we analyze the impact of the virus infection on cell stress responses and redox balance. PLA2G2D expression was shown to be increased in the lungs of middle aged mice, resulting in decreased survival and impaired T cell responses upon infection with SARS-CoV1 [20] . Interestingly, NAC administration to aged mice, diminished PLAG2D expression in both lung cells and CD11c+ DCs. In addition, increased levels of oxidized phospholipidsare a common feature associated with acute respiratory distress syndrome (ARDS) caused by viruses including SARS and H5N1. doi = 10.1016/j.toxrep.2020.06.003 id = cord-320909-p93gxjm2 author = Natoli, S. title = Does SARS‐Cov‐2 invade the brain? Translational lessons from animal models date = 2020-05-22 keywords = CNS; MERS; SARS; infection summary = Animal models of SARS and Middle East respiratory syndrome, caused by structurally similar CoVs during the 2002 and 2012 epidemics, have provided valuable data on nervous system involvement by CoVs and the potential for central nervous system spread of SARS‐CoV‐2. The expression of this receptor in neurons and endothelial cells hints that SARS‐CoV‐2 may have higher neuroinvasive potential compared with previous CoVs. However, it remains to be determined how such invasiveness might contribute to respiratory failure or cause direct neurological damage. Highly pathogenic coronavirus (CoV) infections are well-established sources of previous epidemics in humans, i.e. severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice doi = 10.1111/ene.14277 id = cord-344446-5d7yuoz1 author = Naughton, Sean X. title = The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection date = 2020-05-12 keywords = SARS summary = One of the more perplexing aspects of the recent SARS-CoV-2 pandemic is the high level of variability among patients in terms of disease severity. Exposure to environmental toxins as well as lifestyle choices can affect ACE2 expression, and may possibly increase the severity of infection. For example, exposure to ultrafine particulate matter from air pollution (PM 2.5) has previously been shown to increase the expression of ACE2 [4] . In line with these findings, a recent report indicates that higher levels of air pollution may be a contributing factor to the increased fatality rate among COVID-19 patients in northern Italy [5] . Dietary/lifestyle factors may also play a role in determining resilience or susceptibility to severe outcomes after SARS-CoV-2 infection. Thus, it is possible that multiple independent variables may affect ACE2 expression and thereby confer resilience or susceptibility towards severe life-threatening conditions after SARS-Cov-2 infection. doi = 10.1038/s41370-020-0232-4 id = cord-027499-mvqoarsh author = Navel, Valentin title = Coronavirus: good or bad news for ocular diseases? date = 2020-06-09 keywords = SARS; ocular summary = Even if SARS-CoV-2 involves conjunctivitis and external ocular infections, 12 there are not yet published data describing the effects of a reduction of air pollutants on the ocular surface during the quarantine period, and a putative decrease in some ocular complaints-individuals being at home and less exposed to pollens and atmospheric pollutants. 16 17 SARS-CoV-2 patients without any ocular symptoms could Open access Figure 1 The decrease of global air pollution following the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic (satellite images from NASA and European Space Agency). 22 In conclusion, even if individuals are less exposed to air pollutants and environmental allergens during quarantine weeks, SARS-CoV-2 seems to be a foe both for ophthalmologists-with a risk of infection through contact with eye secretions of patients-and for patients-with a delay in their medical management. SARS-CoV-2 in the ocular surface of COVID-19 patients doi = 10.1136/bmjophth-2020-000495 id = cord-301233-nenw0f81 author = Naydenova, Katerina title = Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date = 2020-10-21 keywords = Fig; RNA; RTP; SARS summary = Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. doi = 10.1101/2020.10.21.347690 id = cord-346176-w6uaet7l author = Nayeri, Shadi title = Conducting Translational Gastrointestinal Research in the Era of COVID-19 date = 2020-08-26 keywords = PPE; SARS; research summary = In this document we provide a suggested roadmap for resuming gastrointestinal translational research activities, emphasising physical distancing and use of personal protective equipment. We discuss modes of virus transmission in enclosed environments [including clinical workplaces and laboratories] and potential risks of exposure in the endoscopy environment for research staff. Efforts focus primarily on physical distancing, use of PHASE personal protective equipment [PPE] , and addressing capacity needs of health care systems to deal with the outbreak. Local and institutional guidance is required to resume translational research activities, including patient interactions. • Invitation of persons currently infected with SARS-CoV-2 from the community into the research environment would cause unnecessary and inappropriate risk of viral transmission. These guidelines address safety precautions in relevant workspaces [including laboratory and endoscopy environments] as well as in specific research activities such as sample collection, handling, and transportation. doi = 10.1093/ecco-jcc/jjaa171 id = cord-348283-7xorq5ce author = Naz, Anam title = Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date = 2020-07-10 keywords = HADDOCK; HLA; SARS; vaccine summary = The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. doi = 10.3389/fimmu.2020.01663 id = cord-253201-r6vsa0pw author = Nazari, S. title = Central Nervous System Manifestations in COVID-19 Patients: A Systematic Review and Meta-analysis date = 2020-07-22 keywords = CNS; COVID-19; SARS summary = Despite many studies reporting respiratory infections as the primary manifestations of this illness, an increasing number of investigations have focused on the central nervous system (CNS) manifestations in COVID-19. Based on the results shown in (Table 3 and The highest incidence rate among CNS symptoms of COVID-19 patients was for headache (8.69% with 95% CI: 6.76%-10.82%), followed by Dizziness (5.94%, 95%CI: 3.66%-8.22%), and Impaired consciousness (1.9% with 95% CI: 1%-2.79%). . https://doi.org/10.1101/2020.07.21.20158691 doi: medRxiv preprint CNS: Central nervous system; COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; PHEIC: Public health emergency of international concern; WHO: World health organization; PRISMA: Preferred reporting items for systematic reviews and meta-analyses; PNS: Peripheral nervous system; BBB: Blood brain barrier; ACE2: Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms doi = 10.1101/2020.07.21.20158691 id = cord-279629-t1xjy12y author = Nazneen Akhand, Mst Rubaiat title = Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date = 2020-04-15 keywords = COVID-19; SARS; protein; vaccine summary = The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Hence, the study was designed to develop a chimeric recombinant vaccine against COVID-19 by targeting four major structural proteins of the pathogen, while revealing the evolutionary history of different species of coronavirus based on whole genome and protein domain-based phylogeny. Apart from the human coronaviruses, we introduced other coronaviruses which choose different species of bats, whale, turkey, rat, mink, ferret, swine, camel, rabbit, cow and others as host (Supplementary TableDomain analysis of spike protein of coronaviruses reveals that they contain mainly one signature domains namely, coronavirus S2 glycoprotein (IPR002552), which is present in all the candidates. Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. doi = 10.1101/2020.04.15.036285 id = cord-277874-cr53ycrm author = Neault, N. title = SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date = 2020-09-03 keywords = MPAD; PEG; RNA; SARS; covid-19 summary = We believe MPAD based SARS-CoV-2 protein quantitation represents a promising epidemiological tool with a sensitivity sufficiently superior to viral RNA measurement that, in addition to enabling early detection and population tracking of COVID-19 load, will also open the way to effective infection surveillance of specific facilities, schools and residences. Primary sludge and PEG precipitated influent fractions, collected from the contiguous cities of Ottawa and Gatineau in April through June 2020, were analysed for the presence of four SARS-CoV-2 structural proteins, N (nucleocapsid), M (membrane), S (spike), and E (envelope), by western blot. Next, in order to assure specificity for detection of SARS-CoV-2 proteins, we used MPAD with an expanded panel to simultaneously measure three viral proteins, N, S and M, along with six fecal content control proteins in PEG precipitated "influent solids" samples drawn from the Ottawa WRRF during the study period ( Fig 5) . doi = 10.1101/2020.09.01.20185280 id = cord-328853-0iqdqcp6 author = Neidleman, Jason title = SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential date = 2020-08-19 keywords = CD4; SARS summary = title: SARS-CoV-2-specific T cells exhibit phenotypic features of robust helper function, lack of terminal differentiation, and high proliferative potential SUMMARY Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19. Furthermore, the clonality of T cell receptor (TCR) sequences 54 5 is higher in patients with mild rather than severe COVID-19, suggesting a role for antigen-55 specific T cell responses in symptom resolution. We report here that SARS-CoV-2-specific CD4+ and CD8+ T cells from convalescent 86 individuals are diverse, exhibit features different from antigen-specific T cells against CMV, 87 include cells with both lymphoid and tissue homing potential, harbor phenotypic features of 88 functional effector cells, and are long-lived and capable of homeostatic proliferation. doi = 10.1016/j.xcrm.2020.100081 id = cord-282272-wy8do2z6 author = Nelson, Atiba title = Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks date = 2020-07-06 keywords = SARS summary = title: Environmental Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Medical Equipment in Long-Term Care Facilities undergoing COVID-19 Outbreaks We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. We conducted environmental sampling at long-term care facilities to determine the extent of surface contamination with SARS-CoV-2 virus. 2, 3 We conducted environmental sampling to assess the extent of surface contamination with SARS-CoV-2 virus within long-term care facilities with declared COVID-19 outbreaks. Environmental contamination with SARS-CoV-2 virus was detected at each of three COVID-19 outbreak facilities sampled in this study, including surfaces of five frequently used medical devices transferred between patient rooms, and one high-touch surface used by care staff This study contains limitations. Our findings suggest medical equipment is a potential environmental route for transmission of SARS-CoV-2 virus in long-term care facilities. doi = 10.1016/j.ajic.2020.07.001 id = cord-325830-mrtpihc7 author = Nelson, Philipp P. title = Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date = 2020-04-29 keywords = SARS; respiratory; virus summary = In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. doi = 10.3389/fcimb.2020.00181 id = cord-291420-40xsypzt author = Nelson-Sathi, Shijulal title = Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date = 2020-10-01 keywords = RBD; SARS summary = title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. The structural analysis of the mutated spike glycoprotein of SARS-CoV-2 RBD domain was done to assess the impact of interface amino acid residue mutations on binding affinity towards the human ACE2 (hACE2) receptor. Comparative analysis of structures showed key differences in all three binding clusters of SARS-CoV-2 RBD wild type and mutant interfaces with human or mouse ACE2 (Figure 2C, 2D and Table S1 ). doi = 10.1101/2020.05.02.071811 id = cord-025251-evnfvc0l author = Nemunaitis, John title = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection: let the virus be its own demise date = 2020-05-26 keywords = CSF; SARS; dna; furin summary = Herein we describe the rationale and potential of repurposing a dual plasmid, Vigil (pbi-shRNA(furin)-GM-CSF), now in Phase III cancer trials, for the treatment of and, in certain circumstances, enhancement of the immune response to SARS-CoV-2. A recent publication from Nankai University (Tianjin, China) on SARS-CoV-2 reported that genome sequence analysis revealed a section of genes that was not present in SARS-CoV that had a cleavage site similar to HIV and Ebola which carry viral proteins necessary for fusogenic activity of viral species to the human cell membrane. Another immunotherapeutic intervention would be to increase the pulmonary expression of GM-CSF, which, in vivo, redirects macrophages from an M1 state of activation to an M2 activation state and enhances expression of anti-inflammatory mediators and perhaps allow more time for patients to mount an effective immune response against SARS-CoV-2 [25] . Similar to SARS-CoV-2, alveolar epithelial cells are the primary target of influenza virus (IV) and are the first site of entry and support for viral propagation and replication. doi = 10.2217/fvl-2020-0068 id = cord-293167-3bd3adip author = Nepal, Gaurav title = Neurological manifestations of COVID-19: a systematic review date = 2020-07-13 keywords = China; SARS; case; covid-19; patient summary = Most patients infected by SARS-CoV-2 have presented with a mild clinical course: beginning with fever and dry cough, progressing to a form of mild or moderate respiratory disease, and resolving without specific treatment [2] . A retrospective observational study from Wuhan, China, reported that six (2.8%) patients, out of the 214 reviewed COVID-19 cases, developed ischemic stroke. A retrospective observational study from a different center in Wuhan, China, found eleven (5.0%) patients, out of 221 reviewed COVID-19 cases, developed acute ischemic stroke. Those who had COVID-19 infection with new onset of ischemic stroke were more likely to have a severe SARS-CoV-2 presentation, an advanced age (71.6 ± 15.7 years versus 52.1 ± 15.3 years), and preexisting cardiovascular risk factors including hypertension, diabetes, and previous cerebrovascular disease. A retrospective observational study from Wuhan, China, reported one (0.45%) patient, out of 221 reviewed COVID-19 cases, who developed intracerebral hemorrhage. doi = 10.1186/s13054-020-03121-z id = cord-256217-fnjer0e0 author = Neri, Piergiorgio title = COVID-19 and the eye immunity: lesson learned from the past and possible new therapeutic insights date = 2020-04-20 keywords = COV-2; SARS summary = Corona virus represents nowadays the hot topic in the scientific world due to the outbreak of a novel serotype formerly named coronavirus disease (COVID)-19 and now identified as severe acute respiratory syndrome (SARS)-COV-2 [1] . Although ECOR was used to study retinal degeneration specifically, it might represent a possible experimental model for interesting speculations on how to approach severe SARS-COV-2 pulmonary complications. Looking at the ECOR model, it gives the impression that coronavirus creates two different phases: the first is represented by the primary infection which induces the triggering of the immune system, while the second phase is likely to be an autoimmune disease where the role of the severe postviral inflammation represents a severe occurrence worth of prompt intervention. Albeit it is true that anti-IL-6 receptor monoclonal antibody has given promising results for the control of severe SARS-COV-2 pneumonia, it is interesting to notice that retinal degeneration in ECOR is associated with an evident increase in TNF-alpha, as well as soluble TNFR2, inducing an anomaly of TNF-alpha signaling [12] . doi = 10.1007/s10792-020-01389-2 id = cord-336628-0evl3wnd author = Neufeldt, Christopher J. title = SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date = 2020-07-21 keywords = RNA; SARS; cell; sting summary = Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. doi = 10.1101/2020.07.21.212639 id = cord-253178-c41xejo3 author = Neuman, B.W. title = Supramolecular Architecture of the Coronavirus Particle date = 2016-09-15 keywords = SARS summary = M proteins in SARS-CoV, FCoV, and MHV virions and virus-like particles (VLPs) form homodimers (Neuman et al., 2011) , which appear to be functionally analogous to the M-GP5 heterodimers of Arteriviridae (de Vries et al., 1995; Faaberg et al., 1995; Snijder et al., 2003) . However, a recent study found that a chimeric MHV with SARS-CoV M and S transmembrane and endodomain was severely deficient in incorporating S into virions, suggesting that cellular localization signals or more complex interactions among the structural proteins may help support S incorporation (Kuo et al., 2016) . The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles doi = 10.1016/bs.aivir.2016.08.005 id = cord-301942-ppa7gb95 author = Neuman, Benjamin W. title = Ultrastructure of SARS-CoV, FIPV, and MHV Revealed by Electron Cryomicroscopy date = 2006 keywords = MHV; SARS summary = The current understanding of coronavirus ultrastructure relies heavily on transmission electron microscopy of negatively stained images. Each virus appeared approximately round in cryo-EM images, with a fringe of spikes protruding from the viral membrane and a region of lower density near the virion center ( Fig. 1A-B) . Spike-depleted SARS-CoV particles appeared similar to spike-depleted MHV particles in negative stain, but were produced in lower yield, not suitable for effective cryo-EM imaging. The arrangement of spike densities near the center of some particles approximates a rhombus, which would not be inconsistent with a paracrystalline organization of spikes as observed in the virions of pleomorphic arenavirus particles, 17 or a local hexagonal close-packing of structural proteins as observed in retroviral particles. Fine structure of influenza A virus observed by electron cryo-microscopy Cryo-electron microscopy reveals ordered domains in the immature HIV-1 particle Supramolecular organization of immature and mature murine leukemia virus revealed by electron cryo-microscopy: implications for retroviral assembly mechanisms doi = 10.1007/978-0-387-33012-9_31 id = cord-325971-volbaipv author = Neupane, Karun title = Potential Treatment Options for COVID-19: A Comprehensive Review of Global Pharmacological Development Efforts date = 2020-06-26 keywords = COVID-19; SARS; patient summary = Several drugs are being tested in the trials, and the United States Food and Drugs Administration (FDA) has given Emergency Use Authorization (EUA) for remdesivir to treat COVID-19 patients on May 1, 2020 [5] . Therapeutic remdesivir treatment in MERS-CoV inoculated rhesus macaques resulted in the reduction in clinical signs, virus replication, and the absence of lung lesions in 2/6 remdesivirtreated animals along with the reduction in lesion severity in three additional animals. In a randomized controlled clinical trial of 1063 patients conducted by the National Institute of Allergy and Infectious Disease (NIAID), remdesivir has shown the efficacy in the early results against advanced COVID-19 (NCT04280705). In a retrospective observational study involving twenty patients with severe or critical COVID-19, treatment with tocilizumab in addition to lopinavir, methylprednisolone, other symptom relievers, and oxygen therapy, resulted in body temperature of all the patients returning to normal on the first day of receiving tocilizumab and significant relief of clinical symptoms synchronously in the following days. doi = 10.7759/cureus.8845 id = cord-349500-603v8lfb author = Neurath, Markus F title = Covid-19 and immunomodulation in IBD date = 2020-04-16 keywords = ACE2; IBD; SARS; covid-19; patient summary = Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infects ACE2 expressing epithelial cells in the lung and/or the intestine. The covid-19 receptor ACE2 is particularly highly expressed in intestinal epithelial cells from the terminal ileum and to a lesser extent in the colon, where mucosal inflammation in patients with IBD (Crohn''s disease (CD); UC) is frequently detected. doi = 10.1136/gutjnl-2020-321269 id = cord-302707-cap2rgf7 author = Ng, Dianna L. title = SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood date = 2020-09-17 keywords = CoV-2; Fig; SARS; San summary = Here, we present data validating the use of the EUA authorized Abbott Architect SARS-CoV-2 IgG test for antibody detection in two populations in March 2020, a hospitalized COVID-19 patient cohort at a tertiary care hospital in San Francisco and a cohort of blood donors from the San Francisco Bay Area. These studies demonstrate that SARS-CoV-2 seroprevalence in the San Francisco Bay Area was very low, suggesting limited circulation of the virus in the community as of early March, and that IgG and IgM titers are predictive of neutralizing activity, with high positive percent agreement. To evaluate assay sensitivity, we assembled a cohort of 38 hospitalized patients and 5 outpatients at University of California, San Francisco (UCSF) Medical Center and the San Francisco Veterans Affairs (SFVA) Health Care System, all of whom received care at adult inpatient units or clinics and were real-time polymerase chain reaction (RT-PCR) positive for SARS-CoV-2 from nasopharyngeal and/or oropharyngeal swab testing ( Fig. 1a and Supplementary Table 1 ). doi = 10.1038/s41467-020-18468-8 id = cord-339762-lh8czr0a author = Ng, Dianna L. title = Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 date = 2016-03-31 keywords = CoV; East; MERS; SARS summary = title: Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014 Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. Middle East respiratory syndrome coronavirus (MERS-CoV) was initially isolated from a sputum specimen of a patient who died of respiratory and renal failure in Saudi Arabia in 2012. Although the pathogenesis of severe and fatal MERS-CoV infection is unknown, these postmortem findings provide critical insights, including evidence that pneumocytes are important targets, suggesting that direct cytopathic effects contribute to MERS-CoV respiratory symptoms. doi = 10.1016/j.ajpath.2015.10.024 id = cord-290813-6ylwj5je author = Ng, Enders K. O. title = Molecular Diagnosis of Severe Acute Respiratory Syndrome date = 2006 keywords = RNA; SARS summary = To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Subsequently, together with the improvement of viral RNA extraction in which plasma or serum requires no ultracentrifugation, two real-time quantitative RT-PCR assays, one aimed toward the polymerase region and the other toward the nucleocapsid region of the virus genome ( Fig. 1) , were developed for measuring the concentration of SARS-CoV RNA in serum/plasma samples from SARS patients (13, 14) . With the use of the real-time quantitative RT-PCR assay, SARS-CoV RNA has recently been shown to be detectable in the plasma samples of pediatric patients during different stages of SARS (Fig. 4) (14) . Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome doi = 10.1385/1-59745-074-x:163 id = cord-276874-9rjbmsvb author = Ng, M.L. title = Topographic Changes in SARS Coronavirus–infected Cells at Late Stages of Infection date = 2004-11-17 keywords = SARS; cell; figure summary = Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome–associated coronavirus at the cell surface. Scanning electron and atomic force microscopy was used for the first time to view the maturation of the severe acute respiratory syndrome-associated coronavirus at the cell surface. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. High magnification of the maturing virus particles showed a rosette appearance with short knoblike spikes under both the scanning electron and atomic force microscopes. The aim of this study was to use scanning electron and atomic force microscopes to investigate changes in the surface topography of SARS-CoV-infected cells at late infection. Scanning electron microscopy of Vero E6 cells infected with severe acute respiratory syndrome-associated coronavirus at 24 h after infection. doi = 10.3201/eid1011.040195 id = cord-260550-ld9eieik author = Ng, Man Wai title = The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese date = 2007-06-01 keywords = RANTES; SARS summary = title: The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese In this study, we investigated the single nucleotide polymorphisms (SNPs) of inflammatory chemokine genes, i.e. RANTES, IP-10 and monokine induced by gamma interferon gene (Mig) in two Chinese cohorts from Hong Kong and Beijing and found that the RANTES -28 G allele was associated with disease susceptibility and severity of SARS. Among them, 20 patients were classified as severe group, which were identified by their admissions to intensive care units or deaths from SARS (mean ± SD age = 39.45 ± 12.8, 11 male and 9 female). After correction by Bonferroni method, the significant P value should be less than 0.007 This study showed that RANTES -28 G allele was a risk factor that associated with severe clinical outcomes in both Hong Kong and Beijing Chinese SARS patients. doi = 10.1186/1471-2334-7-50 id = cord-257792-m7nij17v author = Ng, Oi-Wing title = Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection date = 2016-04-12 keywords = CD8; SARS summary = In this study, the screening for the presence of SARS-specific T cells in a cohort of three SARS-recovered individuals at 9 and 11 years post-infection was carried out, and all memory T cell responses detected target the SARS-CoV structural proteins. As shown in Fig. 1 , higher frequencies of IFN␥producing SFUs were observed for in vitro-expanded PBMCs from SARS subject 1 compared to the healthy individual, suggesting the presence of SARS-specific memory T cells at 9 years post-infection. In another study looking at SARSspecific memory T cell responses in SARS-recovered individuals at 4 years post-infection, 28.75% of them presented T cell responses to M peptides [22] , further supporting the role of M protein in eliciting dominant cellular immunity during SARS-CoV infection. In SARS subject 1 at 6 years post-infection, a HLA-B*1525-restricted memory CD8 + T cell response targeting the N53 peptide, corresponding to residues 261-275 of N protein, was detected. doi = 10.1016/j.vaccine.2016.02.063 id = cord-307036-n44yml79 author = Ng, Oi-Wing title = Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date = 2014-07-14 keywords = D1128A; N1056; SARS summary = Next, to determine if mAb 1A9 exhibits cross-neutralizing activity, S-pseudotyped virus particles, or S-pps, carrying the human SARS-CoV S or the various RBD-modified chimeric S of civet SARS-CoV SZ3 strain and bat SL-CoV Rp3 and Rf1 strains were generated and used to infect CHO-ACE2 cells in the absence or presence of different concentrations (100, 150 and 200 mg/ml) of mAb 1A9. Wild-type S, substitution S mutants, namely D1128A, N1056K, and that containing both D1128A and N1056K, were then expressed in 293 FT cells and Western Blot analysis was performed to determine the effects of these mutations on the binding of the S protein to mAb 1A9. (A) S-pp expressing S protein of humans SARS-CoV HKU39849, civet SARS-CoV SZ3, bat SL-CoV Rp3 and Rf1 and (B) S-pp containing wild-type or mutant D1128A, N1056K or D1128A/ N1056K S were generated and used to infect CHO-ACE2 cells at equal amount (as quantitated using P24 ELISA). doi = 10.1371/journal.pone.0102415 id = cord-254884-5rmnwcfd author = Ng, S. M. title = Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) date = 2006-01-21 keywords = SARS; smart summary = title: Group Debriefing for People with Chronic Diseases During the SARS Pandemic: Strength-Focused and Meaning-Oriented Approach for Resilience and Transformation (SMART) The SMART debriefing (1) aimed at boosting resilience and catalyzing transformation among persons undergoing stressful events, (2) adopted a growth-oriented and holistic approach of health promotion, and (3) employed methods drawn from various indigenous sources (e.g. Asian philosophies and Traditional Chinese Medicine). Participants (N=51) were people with chronic diseases recruited about 1 month (August 2003) after the Severe Acute Respiratory Syndrome (SARS) outbreak was eventually under control, after causing widespread panic in Hong Kong. After the one-day group debriefing, participants showed significant decrease in depression level, as measured by Brief Symptom Inventory (Derogatis & Melisaratos, 1983, Psychological Medicine, 13(3), 595–605) and changes in cognitive appraisal towards SARS. We hypothesize the SMART debriefing can promote positive growth among people with chronic diseases and reduce their distress levels at the same time. doi = 10.1007/s10597-005-9002-y id = cord-275760-hi9sj0d7 author = Ng, Siew C title = Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification date = 2020-04-22 keywords = SARS summary = title: Screening FMT donors during the COVID-19 pandemic: a protocol for stool SARS-CoV-2 viral quantification We read with interest the Correspondence by Christopher Green and colleagues 1 suggesting the need for a molecular test to screen faecal microbiota transplant (FMT ) donors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to prevent the potential risk of transmission. 5 As described by Green and colleagues, 1 the University of Birmingham Microbiota Treatment Centre (Birmingham, UK) is not actively processing new donors until a validated SARS-CoV-2 stool test is available. As per the diagnostic protocol of our local health authority, all COVID-19 cases had been confirmed by two RT-PCR tests targeting different regions of the RdRp gene in respiratory specimens. Screening faecal microbiota transplant donors for SARS-CoV-2 by molecular testing of stool is the safest way forward doi = 10.1016/s2468-1253(20)30124-2 id = cord-303018-3ka72y3p author = Ng, Siew C title = COVID-19 and the gastrointestinal tract: more than meets the eye date = 2020-04-09 keywords = SARS summary = COVID-19 and the gastrointestinal tract: more than meets the eye Siew C Ng , 1 Herbert Tilg 2 An outbreak of coronavirus disease 2019 , caused by severe acute respiratory syndrome (SARS-CoV-2), has rapidly spread from China to almost all over the world affecting over 800,000 people across 199 countries. 5 In GUT several articles report on GI symptoms, detection of the virus in faeces and potential pathophysiological aspects including viral receptor expression in the GI tract. In about 50% of COVID-19 cases, the presence of SARS-CoV-2 in faecal samples and detection of SARS-CoV-2 in intestinal mucosa of infected patients suggest that enteric symptoms could be caused by invasion of ACE2 expressing enterocytes and the GI tract may be an alternative route of infection. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms doi = 10.1136/gutjnl-2020-321195 id = cord-300627-7x4me5lx author = Ng, W. F. title = The placentas of patients with severe acute respiratory syndrome: a pathophysiological evaluation date = 2006-06-30 keywords = SARS; placenta summary = Summary Aims The pathology of the placentas delivered from pregnant women who had severe acute respiratory syndrome (SARS) in Hong Kong was studied. In three placentas delivered in the acute stage of SARS, there were increases in intervillous or subchorionic fibrin which might be related to disturbances in maternal placental blood flow due to the hypoxic respiratory disease. Extensive fetal thrombotic vasculopathy (FTV) with sharply demarcated zones of avascular fibrotic villi was noted in the placentas of two patients convalescent from SARS in the third trimester. Wong also showed that pregnant SARS patients had a higher rate of respiratory failure and drew an analogy with the more severe clinical course of epidemic influenza in pregnant women. This study was undertaken to examine the pathology of the placentas delivered from women who contracted SARS during pregnancy and to correlate the findings with the clinical and obstetric course and the neonatal outcome. doi = 10.1080/00313020600696280 id = cord-262640-4vr4cm1s author = Nguyen, N. N. title = Correlation of ELISA based with random access serologic immunoassays for identifying adaptive immune response to SARS-CoV-2 date = 2020-07-08 keywords = ELISA; SARS summary = This paper highlights the analytical characteristic of an ELISA based assay by AnshLabs and three random access immunoassay (RAIA) by DiaSorin, Roche, and Abbott that have been approved for emergency use authorization (EUA), at a tertiary academic center in a low disease-prevalence area. All discrepant samples that were positive by AnshLabs and negative by RAIA tested positive by all-in-one step SARS-CoV-2 Total (COV2T) assay performed on the automated Siemens Advia Centaur XPT analyzer. The Elecsys Anti-SARS-CoV-2 assay is performed on the Roche cobas e601 analyzer for total antibodies 126 specific for IgG, IgM and IgA which target nucleocapsid protein, in human serum or plasma. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint Table 4 shows the concordance between ELISA and RAIA results for samples that were confirmed 174 positive for SARS-CoV-2 by rtPCR. . https://doi.org/10.1101/2020.07.06.20145938 doi: medRxiv preprint non-specific binding in AnshLabs ELISA assay 320 All rights reserved. doi = 10.1101/2020.07.06.20145938 id = cord-255371-o9oxchq6 author = Nguyen, Thanh Thi title = Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date = 2020-07-10 keywords = SARS; mutation; protein; sequence summary = title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. We use 6,324 SARS-CoV-2 genome sequences collected in 45 countries and deposited to the NCBI GenBank so far and create a spreadsheet dataset of all mutations occurred across different genes. In this paper, to evaluate the possible impacts of genomic mutations on the virus functions, we propose the use of the SSpro/ACCpro 5 methods to predict protein secondary structure and relative solvent accessibility [13] . By comparing the prediction results obtained on the reference genome and mutated genomes, we are able to assess whether the detected mutations have the potential to change the protein structure and solvent accessibility, and thus lead to possible changes of the virus characteristics. doi = 10.1101/2020.07.10.171769 id = cord-291523-4dtk1kyh author = Nguyen, Thanh Thi title = Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date = 2020-07-01 keywords = CoV-2; Fig; SARS summary = Outcomes of a phylogenetic analysis suggest that the virus belongs to the genus Betacoronavirus, sub-genus Sarbecovirus, which includes many bat SARS-like CoVs and SARS CoVs. Another study in [5] confirms this finding by analysing genomes obtained from three adult patients admitted to a hospital in Wuhan on December 27, 2019. With the cut-off parameter C is set equal to 0.7, the hierarchical clustering algorithm separates the reference sequences into 6 clusters in which cluster "5" comprises all examined viruses of the Sarbecovirus sub-genus, including many SARS CoVs, bat SARS-like CoVs and pangolin CoVs (Fig. 7A) . With the results obtained in Fig. 7D (and also in the experiments with the DBSCAN method presented next), we support a hypothesis that bats or pangolins are the probable origin of SARS-CoV-2. In this Appendix, we first present results of the hierarchical clustering method applied to the dataset that combines Set 1 of reference sequences (Table 1 ) with all 334 SARS-CoV-2 sequences (see Fig. 9 ). doi = 10.1101/2020.05.12.091397 id = cord-268894-amfv3z2y author = Nguyen-Contant, Phuong title = S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date = 2020-07-21 keywords = RBD; SARS summary = Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD 31 and S2 subunit, and nucleocapsid [N] ) and non-SARS-CoV-2 proteins were related to 32 measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Approximately one-third of non-SARS-CoV-140 2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N 141 proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs ( Figure 1A ). In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E 192 and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-193 exposed subjects, consistent with the higher levels of serum IgG against these antigens ( Figure 2E -194 2H) . doi = 10.1101/2020.07.20.213298 id = cord-292883-7hvq9qaj author = Nguyen-Contant, Phuong title = S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit date = 2020-09-25 keywords = RBD; SARS summary = RBD-binding MBCs sampled in the convalescent phase of SARS-CoV-2 infection expressed Abs with relatively low numbers of V gene mutations, suggesting that this component of the response largely reflected naive B cell activation by novel epitopes (20) . Approximately one-third of non-SARS-CoV-2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs (Fig. 1A) . Since the healthy donor samples in our analysis were collected 6 to 10 years before the emergence of SARS-CoV-2, we considered the possibility that a recently circulating HCoV was responsible for the higher anti-OC43 S IgG titers in the convalescent subjects. In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-exposed subjects, consistent with the higher levels of serum IgG against these antigens (Fig. 2E to H) . doi = 10.1128/mbio.01991-20 id = cord-300324-95fty9yi author = Ni Lochlainn, M. title = Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals date = 2020-04-29 keywords = COVID-19; SARS; disease summary = Conclusions: Being older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. Visit to hospital as outcome were fit to test for association between i) self-reported obesity and ii) chronic lung disease and asthma, heart disease, diabetes and kidney disease in the following groups: 1) self-reported COVID-19 infection with classical symptoms (SR-COVID19); 2) self-reported positive COVID-19 test results (T-COVID19); 3) imputed/predicted COVID-19 infection based on symptomatology (I-COVID19) Imputation for testing positive for COVID was performed using the data at day of maximum sum of symptoms and applying a logistic regression using coefficients defined previously (2) . In this study we found that age, obesity, diabetes and pre-existing lung, renal and cardiac disease, were risk factors for a hospital visit with COVID-19 amongst a large but relatively young, community-based population of app users. doi = 10.1101/2020.04.25.20079251 id = cord-323828-ug2duzw1 author = Ni, Dongchun title = Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein date = 2020-10-12 keywords = SARS; Spike summary = Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. The clinical-grade soluble form of hACE2 has been reported to be a 74 potential novel therapeutic approach for reducing the infection of SARS-CoV-2 (Monteil et al., 2020) by preventing the viral Spike from interacting with other hACE2 present on human cells. The final 3D 115 reconstruction from 72''446 particles at 5.1Å overall resolution showed a density map corresponding to a single, 116 monomeric Spike protein in complex with hACE2 (Fig. 1a) . Figure 1 Cryo-EM maps of SARS-CoV-2 Spike-hACE2 complexes and fitted models. Cryo-EM structure of the SARS coronavirus spike glycoprotein in 352 complex with its host cell receptor ACE2 doi = 10.1101/2020.10.12.336016 id = cord-341396-0tn06al2 author = Ni, Ling title = Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals date = 2020-05-03 keywords = RBD; SARS summary = In this study, we collected blood from COVID-19 patients who have recently become 5 virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody 6 and T cell responses. NP-and S-RBD-specific 9 IgM and IgG antibodies were both detected in the sera of newly discharged patients, 10 compared with healthy donor groups. Anti-SARS-CoV-2 IgG antibodies were also more 11 obviously observed than IgM in the follow-up patients (#9-14), when compared with healthy 12 donors ( Figure 1B ). As shown in Figure 3C , compared with healthy donors, 25 the numbers of IFN-γ-secreting NP-specific T cells in patients #1, 2, 4, 5 and 8 were much 26 higher than other patients, suggesting that they had developed SARS-CoV-2-specific T cell responses. More interestingly, when combining all 14 patients in our analysis, there 9 was a significant correlation between the neutralizing antibody titers and the numbers of NPIn this study, we characterized SARS-CoV-2-specific humoral and cellular immunity in 2 recovered patients. doi = 10.1016/j.immuni.2020.04.023 id = cord-282571-ilf73g71 author = Ni, Wentao title = Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19 date = 2020-07-13 keywords = ACE2; COVID-19; SARS summary = Both SARS-CoV-2 and SARS-CoV enter host cells via the angiotensin-converting enzyme 2 (ACE2) receptor, which is expressed in various human organs. In addition to the direct viral effects and inflammatory and immune factors associated with COVID-19 pathogenesis, ACE2 downregulation and the imbalance between the RAS and ACE2/angiotensin-(1–7)/MAS after infection may also contribute to multiple organ injury in COVID-19. Autopsies of SARS patients showed that SARS-CoV infection can cause injury to multiple organs, such as the heart, kidney, liver, skeletal muscle, central nervous system, and adrenal and thyroid glands, besides the lungs [30, 31] . Several studies have shown that SARS-CoV infection can downregulate ACE2 expression on cells, thereby disrupting the physiological balance between ACE/ACE2 and Ang-II/angiotensin-(1-7) and subsequently causing severe organ injury [44] [45] [46] [47] . Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS doi = 10.1186/s13054-020-03120-0 id = cord-309120-05bg7rfa author = Niazi, Sadegh title = The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date = 2020-11-06 keywords = SARS; respiratory; virus summary = title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses'' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs doi = 10.1016/j.envpol.2020.115767 id = cord-252574-7oh0k139 author = Nicastro, Emanuele title = A Pediatric Emergency Department Protocol to Avoid Intra-Hospital Dispersal of SARS-CoV-2 during the Outbreak in Bergamo, Italy date = 2020-04-21 keywords = SARS summary = In Lombardy, the main outbreak of the infection was located in a community hospital in the Bergamo province, suggesting that the community spread of the infection probably arose from a large cohort of subjects who were in contact with SARS-CoV-2 infected patients attending health care facilities, and who were probably unrecognized at that time., so far pediatric services have not experienced the COVID-19 To address these issues, we developed a protocol addressing reception, risk-management and hospitalization of suspected SARS-CoV-2 cases at the pediatric emergency department and medical-surgical units aimed at containing intra-hospital transmission of the infection, considering that currently our hospital is the largest referral site in the primary outbreak area in Italy. Suspected COVID-19 patients requiring hospitalization are managed by health care personnel (HCP) using personal protective equipment (PPE) (FFP2/N95 respirator + eye protection goggles or face shield + 5 isolation gowns + face mask + gloves), who perform the acquisition of an NP/OP swab for SARS-CoV-2 real time-PCR testing. doi = 10.1016/j.jpeds.2020.04.026 id = cord-286006-t5gj0k54 author = Nicholas, David B. title = Pediatric epidemic crisis: Lessons for policy and practice development date = 2008-12-31 keywords = SARS; care; health; provider summary = Methods Qualitative interviews were conducted with 23 participants representing key stakeholder groups: (a) pediatric patients with probable or suspected SARS, (b) their parents, and (c) health care professionals providing direct care to SARS patients. Semi-structured, qualitative interviews were conducted with 23 participants from key stakeholder groups affected by pediatric SARS as follows: pediatric patients between the ages of 5 and 17 years (n = 5), their parents (n = 10), and frontline pediatric health care providers (n = 8). The majority of health care providers (88%) recognized the importance of their work, yet grappled with concerns related to personal vulnerability and the impact of SARS policies on patients and families. Accordingly findings speak clearly to the need for: systematic and well-orchestrated information flow; communication strategies in responding and disseminating relevant information; means to ease vulnerability among stakeholders; strategies for ensuring effective and responsive leadership; and the development of practice and policy guidelines for treatment and contingency planning for an unknown patient care path. doi = 10.1016/j.healthpol.2007.11.006 id = cord-325783-pqonn0as author = Nicholls, John M title = Lung pathology of fatal severe acute respiratory syndrome date = 2003-05-24 keywords = March; SARS; patient; respiratory summary = Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines). doi = 10.1016/s0140-6736(03)13413-7 id = cord-284841-flhfagp3 author = Nicol, Thomas title = Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech) date = 2020-06-15 keywords = ELISA; LFIA; SARS summary = METHODS: Two automated immunoassays (Abbott SARS-CoV-2 CLIA IgG and Euroimmun Anti-SARS-CoV-2 ELISA IgG/IgA assays) and one lateral flow immunoassay (LFIA NG-Test® IgG-IgM COVID-19) were tested. The aim of the study was to assess the clinical performance of CE marked assays available in Europe to detect SARS-CoV-2 antibodies: two automated immunoassays (Euroimmun and Abbott assays) targeting two different proteins and also one lateral flow immunoassay (NG Biotech). On May, 2020, the French Health Authority (Haute Autorité de Santé) and Infectious Diseases Society of America recommended that patients with symptoms consistent with COVID-19 but having a positive result for SARS-CoV-2 by RT-PCR may be diagnosed by serological tests [22, 23] . Here, we did not observe any significant difference between sensitivity of IgA ELISA and IgM LFIA In conclusion, our study showed equivalent clinical performance for IgG of three immunoassays (ELISA, CLIA and LFIA) >14 days after symptoms onset. doi = 10.1016/j.jcv.2020.104511 id = cord-343618-jjb8da4a author = Nie, Kai title = Gastrointestinal insights during the COVID-19 epidemic date = 2020-09-26 keywords = SARS; covid-19 summary = Thus, cancer and inflammatory bowel disease (IBD) management, stool viral tests, and virus exposure are major concerns in the context of COVID-19 epidemic. Patients with digestive disease bear a relatively high risk of SARS-CoV-2 infection. This finding suggests that gastrointestinal cancer patients may be more susceptible to SARS-CoV-2 infection [47] . To date, several cases of SARS-CoV-2 infection in IBD patients have been reported. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China doi = 10.12998/wjcc.v8.i18.3934 id = cord-344419-3wcfpw2z author = Niedzwiedz, C. L. title = Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study date = 2020-04-27 keywords = Biobank; SARS summary = Interpretation Some minority ethnic groups have a higher risk of confirmed SARS-CoV-2 infection in the UK Biobank study which was not accounted for by differences in socioeconomic conditions, measured baseline health or behavioural risk factors. In a large population-based cohort study in the UK, we found an increased risk of developing confirmed SARS-CoV-2 infection in Black, South Asian and White Irish ethnic groups. The ideal approach to estimating infection risk across different social groups is to analyse data from a cohort study, but most existing cohort studies which include detailed information about ethnicity and socioeconomic position are subject to long delays in data being available for analysis and are too small to provide useful estimates of infection risk. We therefore aimed to investigate the relationship between ethnicity, socioeconomic position and the risk of having confirmed SARS-CoV-2 infection in the population-based UK Biobank study. Several ethnic minority groups had a higher risk of both being diagnosed and testing positive as an inpatient with laboratory-confirmed SARS-CoV-2 infection in the UK Biobank study. doi = 10.1101/2020.04.22.20075663 id = cord-328325-yonbkrwe author = Nielsen, Sandra C. A. title = B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date = 2020-05-06 keywords = Fig; SARS summary = Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of V genes, and extensive activation of IgG and IgA subclasses without significant somatic mutation. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. We detect expansion of B cell clones as well as convergent antibodies with highly similar sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Sequences convergent to known SARS-CoV-speci c antibody IGH sequences13 were identi ed in one COVID-19 patient (7453-D2) but were not detected in the HHC samples (Fig. 4c) . doi = 10.21203/rs.3.rs-27220/v1 id = cord-312275-plqturzi author = Nielsen, Sandra C.A. title = Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2 date = 2020-09-03 keywords = IGHG1; IGHM; SARS summary = To directly test the 154 antigen specificity of these convergent clones, we expressed human IgG1 monoclonal antibodies 155 (mAbs 2A and 4A, Table S2 ) from two COVID-19 convergence groups in two patients 156 following paired immunoglobulin heavy and light chain sequencing of single B cells with the immunosorbent assay (ELISA) testing, both mAbs bound SARS-CoV-2 spike and S1 domain, 160 but not the RBD or nucleocapsid ( Figure 3C ). To evaluate whether such in silico IGH 185 sequence comparisons could predict the serological responses of patients, we tested the plasma 186 samples from COVID-19 patients in SARS-CoV RBD ELISAs and detected cross-reactivity in 187 five of the 13 patients ( Figure 3F) or RBD antigens will also stimulate B cells expressing these common antibody types in a 214 significant fraction of the human population. doi = 10.1016/j.chom.2020.09.002 id = cord-276358-so390gp4 author = Nieto-Torres, Jose L. title = Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome date = 2015-11-30 keywords = Golgi; SARS summary = title: Severe acute respiratory syndrome coronavirus E protein transports calcium ions and activates the NLRP3 inflammasome In this report, we demonstrate that SARS-CoV E protein forms protein–lipid channels in ERGIC/Golgi membranes that are permeable to calcium ions, a highly relevant feature never reported before. Previously, we reported that SARS-CoV E protein showed mild selectivity for cations (Na þ and K þ ) when reconstituted in ERGIC/ Golgi membranes, mostly conferred by the negative charges of the lipids (Verdia-Baguena et al., 2012 . Synthetic peptides representing the full-length SARS-CoV E protein, or its transmembrane domain (amino acids 7-38) containing point mutations that inhibited ion channel activity (N15A and V25F), were generated by standard phase synthesis and purified by HPLC, as previously described (Verdia-Baguena et al., 2012) . Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis doi = 10.1016/j.virol.2015.08.010 id = cord-321673-v5o49ees author = Nieto-Torres, Jose L. title = Relevance of Viroporin Ion Channel Activity on Viral Replication and Pathogenesis date = 2015-07-03 keywords = IAV; SARS summary = Modification of host-cell ionic content is a significant issue for viruses, as several viral proteins displaying ion channel activity, named viroporins, have been identified. Noticeably, these proteins oligomerize in cell membranes to form ion conductive pores, which generally display mild ion selectivity, indicating that viroporins do not show preference for particular ionic species. Influenza viruses lacking M2 ion conductivity, presented either a 15-fold reduction of viral titer in tissue culture [74] , or showed a standard production in cell culture but a restricted growth in the nasal turbinates of infected mice [75] . Several compounds inhibit viroporin ion conductivity in artificial lipid membranes, and some of them efficiently reduce viral growth when administered to infected cells. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells doi = 10.3390/v7072786 id = cord-266896-unb9yvjr author = Nihei, Yoshihito title = Continuous extracorporeal treatments in a dialysis patient with COVID-19 date = 2020-10-04 keywords = COVID-19; SARS summary = Inflammatory cytokine storm caused by SARS-CoV-2 infection has been reported to play a central role in COVID-19; therefore, treatments for suppressing cytokines, including extracorporeal treatments, are considered to be beneficial. The cytokine storm caused by SARS-CoV-2 infection, primarily characterised by elevated plasma concentrations of interleukin 6 (IL-6), plays a central role in COVID-19 [2] ; therefore, its suppression is considered a key treatment approach in patients with COVID-19. Especially, CHDF is reported to continually suppress inflammatory cytokines and has been used in critically ill patients, including those with septic shock, ARDS and infections with viruses such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus [5] . We herein present a patient on PD who became critically ill due to COVID-19 and was treated with several extracorporeal treatments including PE, PMX-DHP and CHDF to suppress the cytokine storm. doi = 10.1007/s13730-020-00538-x id = cord-335293-pac6wbgz author = Nijman, Ruud G. title = Pediatric Inflammatory Multisystem Syndrome: Statement by the Pediatric Section of the European Society for Emergency Medicine and European Academy of Pediatrics date = 2020-08-28 keywords = PIMS; SARS summary = A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome—temporally associated with SARS-CoV-2 (PIMS-TS). A rise in cases with a new hyperinflammatory disease in children has been reported in Europe and in the Unites States of America, named the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS). This statement aims to -provide information about the Pediatric Inflammatory Multisystem Syndrome temporally associated with SARS-CoV-2 (PIMS-TS); -give initial guidance on the clinical assessment and management of children suspected of this new condition for health care professionals dealing with acutely unwell children; -point out useful resources on the recognition and management of these children. The initial guidance from the Royal College of Pediatrics and Child Health in the United Kingdom provided a case definition and called this emerging disease entity the Pediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 (PIMS-TS) (28) . doi = 10.3389/fped.2020.00490 id = cord-297691-w4cdfwv0 author = Nikaeen, Ghazal title = Application of nanomaterials in treatment, anti-infection and detection of coronaviruses date = 2020-05-07 keywords = MERS; SARS; detection summary = In this special report, different strategies of using nanoparticles in dealing with coronaviruses are discussed in three parts: applications in nano-based vaccines, antiviral activity and development of diagnostic sensors. Meanwhile, as nanoparticles have been proven to have immunostimulatory effects [28] , a great deal of attention has been given to development of nano-based therapeutic agent or vaccines against different types of coronaviruses. evaluated the protective immune response stimulated by the administration of gold nanoparticles (Au NPs) conjugated with a type of coronavirus known as swine transmissible gastroenteritis virus (TGEV) in immunized mice and rabbits [29] . Recent applications of nanoparticles in developing coronaviruses sensors based on different analytical techniques and related limit of detections. The above studies on the recent applications of NPs in developing sensors based on different analytical techniques for coronaviruses and their related limit of detections are compared in Table 3 . doi = 10.2217/nnm-2020-0117 id = cord-282604-xp71rkxc author = Nikolaev, EN title = Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date = 2020-05-25 keywords = SARS; protein summary = title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. We have performed a pilot study on nasopharynx epithelial swabs already collected from patients with CODIV-19 for RT-qPCR and showed confident identification of the N protein of the SARS CoV-2 virus by mass-spectrometry with the use of a very basic sample preparation procedure. Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients doi = 10.1101/2020.05.24.113043 id = cord-340992-88t1c0zs author = Nikolai, Lea A title = Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date = 2020-09-03 keywords = COVID-19; SARS; asymptomatic summary = Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection doi = 10.1016/j.ijid.2020.08.076 id = cord-336119-8g37xsys author = Nimgampalle, Mallikarjuna title = Screening of Chloroquine, Hydroxychloroquine and its derivatives for their binding affinity to multiple SARS-CoV-2 protein drug targets date = 2020-06-24 keywords = Chloroquine; Hydroxychloroquine; SARS; protein; table summary = Our current study also shows that some of the chemically synthesized Chloroquine derivatives can also potentially inhibit various SARS-CoV-2 viral proteins by binding to them and concomitantly effectively disrupting the active site of these proteins. By using in-silico molecular docking studies, the binding potential of Chloroquine and its derivatives with different SARS-CoV-2 proteins involved in viral replication was evaluated. Based on the recent reports, some of the essential regulatory proteins and enzymes associated with the pathogenesis of SARS-CoV-2 were selected as drug targets such as the Spike glycoprotein that enables virus internalization, RNA dependent RNA polymerase that supports replication of viral genetic material, Chimeric RBD (Receptor binding domain) that interacts with the ACE 2, Main protease responsible for cleaving the viral polypeptide, Non-structural Protein3, Nonstructural Protein 10, Non-structural Protein 9 (Replicase Table 3 . doi = 10.1080/07391102.2020.1782265 id = cord-355655-l684uy4h author = Ning, Ling title = Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report date = 2020-05-08 keywords = SARS summary = title: Novel coronavirus (SARS‐CoV‐2) infection in a renal transplant recipient: Case report This case states the importance of close monitoring of the concentration of cyclosporine in patients treated with lopinavir/ritonavir; the routine treatment of corticosteroid can be continued. Further data are needed to achieve better understanding of the impact of immunosuppressive therapy on the clinical presentation, severity, and outcome of SARS‐CoV‐2 infections in solid organ transplant recipients. Laboratory results on day 6 of hospitalization showed improved creatinine level and hyponatremia; again, the sputum and oropharyngeal swab specimens tested negative on RT-PCR for SARS-CoV-2. Methylprednisolone was routinely used as baseline immunosuppression in this case, although its use for the treatment of SARS-CoV-2 infection remains controversial. 15 No clinical data exist to indicate that net benefit is derived from corticosteroids in the treatment of respiratory infection due to coronavirus included SARS-CoV and MERS-CoV. Novel coronavirus (SARS-CoV-2) infection in a renal transplant recipient: Case report doi = 10.1111/ajt.15897 id = cord-320350-zeeozmm9 author = Nisoli, Enzo title = COVID-19 and Hartnup disease: an affair of intestinal amino acid malabsorption date = 2020-07-20 keywords = ACE2; SARS; covid-19 summary = We hypothesize that SARS-CoV-2 spike protein, binding to intestinal angiotensin-converting enzyme 2, negatively regulates the absorption of neutral amino acids, and this could explain not only the GI, but also systemic disturbances in COVID-19. Altered composition of the gut microbiota (as a consequence of impaired amino acid transport and reduced secretion of antimicrobial peptides by Paneth cells in the small intestine) and changes in innate immunity contribute to the colitis phenotype observed in ACE2 knockout mice [17] . Based on clinical observations and basic research, we hypothesise that, in response to the SARS-CoV-2 binding to intestinal ACE2, the absorption of neutral amino acids is negatively regulated in COVID-19 patients. In malnourished patients or conditions of intestinal amino acid malabsorption, as in the COVID-19 or Hartnup patients, the adaptive immune response cannot be effectively initiated because the absorption of essential energy substrates is impaired by SARS-CoV-2 binding to ACE2. doi = 10.1007/s40519-020-00963-y id = cord-314386-cxq9v218 author = Nitsche, Andreas title = SARS Coronavirus Detection date = 2004-07-17 keywords = PCR; SARS summary = We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. To improve the ability to detect SARS-CoV safely and reduce the risk of eliciting false-negative results caused by genome sequence variations, we established three individual real-time RT-PCR assays. Target sequences were chosen by using the following criteria: 1) the regions are distributed over the whole genome, including the nonstructural polyprotein 1a and 1ab genes and the spike glycoprotein gene (Table 1) ; 2) the regions are highly conserved among the 89, 90, and 100 respective sequences available in public sequence databases; 3) the regions are suitable for the design of a real-time RT-PCR assay; and 4) the designed primers, 5′-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from http://www.ncbi.nlm.nih.gov/BLAST/). doi = 10.3201/eid1007.030678 id = cord-252015-9oiwcn8q author = Niu, Alex title = COVID-19 in allogeneic stem cell transplant: high false-negative probability and role of CRISPR and convalescent plasma date = 2020-06-15 keywords = COVID-19; SARS summary = Shortly thereafter, RT-PCR/CRISPR was performed on a blood sample collected on hospital day 36 for clinical purposes and demonstrated strong detection of SARS-CoV-2 RNA (Fig. 1c) . Here, we present two cases of ASCT recipients who presented with respiratory illnesses, initially testing negative for SARS-CoV-2 with conventional RT-PCR, then positive with the more sensitive RT-PCR/CRISPR technique. Our findings suggest that ASCT recipients with negative nasopharyngeal SARS-CoV-2 RT-PCR, but evidence of lower respiratory tract disease, might indeed have COVID-19 that can be detected using a CRISPR-based platform. While safety concerns with performing bronchoscopy remain high with this infection, and COVID-19specific treatments depend on securing a positive test, it may be beneficial to pursue diagnosis with other tissue sources, such as whole blood or plasma. In conclusion, early diagnosis and treatment of COVID-19 is crucial in ASCT recipients, and evaluation regarding the use of other tissue sources for detection of SARS-CoV-2 along with multimodality therapy is required in the continual evolution of this pandemic. doi = 10.1038/s41409-020-0972-8 id = cord-306508-xpwluph5 author = Nkengasong, John title = China’s response to a novel coronavirus stands in stark contrast to the 2002 SARS outbreak response date = 2020-01-27 keywords = China; SARS summary = It shows a marked departure from public health policies that, during the SARS outbreak in 2002, contributed to the deaths of 774 people, spread of the disease to 37 countries and an economic loss of over US$40 billion over a period of 6 months 6, 7 . As of 20 January 2020, the Chinese government reported 136 new cases of infection with this virus over the weekend that were spreading to other cities in the country, bringing the total cumulative cases worldwide to over 200 (ref. There is also a need for closer coordination of efforts between the Africa Centres for Disease Control and Prevention, based in Addis Ababa, Ethiopia, and China CDC for sharing information on potential people suspected of being infected who are traveling from China to Africa. China''s political openness to reporting in a timely manner and the emergence of the novel virus 2019-nCoV, coupled with the rapid sequencing and public sharing of the sequences, represents a new dawn for global health security and international health diplomacy. doi = 10.1038/s41591-020-0771-1 id = cord-356217-igm2t7md author = Noda, Sakura title = Severe COVID-19 initially presenting as mesenteric adenopathy date = 2020-10-10 keywords = COVID-19; SARS summary = We report a case of COVID-19 in a healthy teenager who initially presented with isolated mesenteric adenopathy, typically a self-limited illness, which progressed to severe illness requiring intensive care before complete recovery. A generally healthy, immunized, non-obese White 17-yearold boy presented to an outside emergency department (ED) with 3 days of initially moderate progressing to severe abdominal pain focused in the right lower quadrant, fever as high as 103°F, and vomiting without diarrhea. Although we did not obtain tissue sampling to prove that the mesenteric adenopathy was secondary to COVID-19, the boy eventually developed chest CT findings and severe hyperinflammatory response consistent with COVID-19, tested positive for SARS-CoV-2 by PCR from sputum, and recovered with primarily supportive care. This case report describes a severe case of COVID-19 in a previously healthy teenage patient who initially presented with gastrointestinal symptoms and isolated acute mesenteric adenopathy on imaging. doi = 10.1007/s00247-020-04789-9 id = cord-348209-rkkhv4mw author = Noerz, Dominik title = Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date = 2020-04-11 keywords = PCR; SARS summary = title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 30 system, a fully automated device performing extraction and real-time PCR. Due to its random-access workflow concept and rapid time-to-39 result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 40 diagnostics for urgent clinical samples in the hospital setting. For the assay presented in this study, we used a fully automated random-access platform for molecular 56 diagnostics, handling everything from extraction, amplification, signal detection to reporting of results 57 (10). Evaluation of a quantitative RT-PCR assay for 180 the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system doi = 10.1101/2020.04.07.20056234 id = cord-257994-i6hut28h author = Nogee, Daniel title = Covid-19 and the N95 respirator shortage: Closing the gap date = 2020-04-13 keywords = SARS summary = Due to extreme shortages of personal protective equipment caused by the COVID-19 pandemic, many healthcare workers will be forced to recycle protective masks intended for disposal after a single use. We propose investigating the use of ultraviolet germicidal irradiation to sterilize masks of SARS-CoV-2 for safer reuse. The Centers for Disease Control and Prevention has published guidelines for optimizing supply to extend stocks through limiting use, reuse at the patient and provider levels, and alternative personal protective equipment recommendations. Although further work will be needed to determine dosages of UVGI to effectively sterilize SARS-CoV-2 contaminated FFRs, UVGI provides a potential avenue for greatly extending the limited FFR supply in the face of the ongoing COVID-19 pandemic in a simple, cost-effective, and rapidly deployable manner. A pandemic influenza preparedness study: use of energetic methods to decontaminate filtering facepiece respirators contaminated with H1N1 aerosols and droplets Ultraviolet germicidal irradiation of influenza-contaminated N95 filtering facepiece respirators No financial support was provided relevant to this article. doi = 10.1017/ice.2020.124 id = cord-294910-gnc04ax1 author = Nogueira, Paulo Jorge title = The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases date = 2020-07-24 keywords = COVID-19; SARS; kidney; study summary = The risk factors for increased odds of death by COVID-19 were: sex (male: OR = 1.47, ref = female), age ((56–60) years, OR = 6.01; (61–65) years, OR = 10.5; (66–70) years, OR = 20.4; (71–75) years, OR = 34; (76–80) years, OR = 50.9; (81–85) years, OR = 70.7; (86–90) years, OR = 83.2; (91–95) years, OR = 91.8; (96–104) years, OR = 140.2, ref = (0–55)), Cardiac disease (OR = 2.86), Kidney disorder (OR = 2.95), and Neuromuscular disorder (OR = 1.58), while condition (None (absence of precondition); OR = 0.49) was associated with a reduced chance of dying after adjusting for other variables of interest. The data retrieved include individuals'' demographic characteristics (age, sex, region), COVID-19 disease information (death, recovery, still in treatment, hospitalization, intensive care, respiratory support), and preconditions (Asthma, Cancer, Cardiac disease, Hematological disorder, Diabetes, HIV and other immune deficiency, Kidney disorder, Liver disorder, Neuromuscular disorder, Other precondition and None (absence of precondition)). doi = 10.3390/jcm9082368 id = cord-316260-1t3ifsfi author = Nogueira-de-Almeida, Carlos Alberto title = COVID-19 and obesity in childhood and adolescence: A clinical review()() date = 2020-08-04 keywords = COVID-19; SARS; child; increase; obese; obesity summary = In severe acute respiratory syndrome coronavirus 2 infection, these organic changes from obesity may increase the need for ventilatory assistance, risk of thromboembolism, reduced glomerular filtration rate, changes in the innate and adaptive immune response, and perpetuation of the chronic inflammatory response. 3--6 The present review aims to identify the factors that contribute to the increase in the susceptibility and severity of COVID-19 in obese children and adolescents, and its health consequences, to collaborate for better clinical care of these patients. The three main risk factors that link obesity to COVID-19 demonstrated for adults 52 are also present among children and adolescents: chronic subclinical inflammation, impaired immune response, and underlying cardiorespiratory diseases. In conclusion, obesity in childhood and adolescence can be considered a risk factor for greater susceptibility and severity of COVID-19 and is associated with nutritional, cardiac, respiratory, renal, and immunological alterations, which may potentiate the complications of SARS-CoV-2 infection. doi = 10.1016/j.jped.2020.07.001 id = cord-349907-dwhyx97y author = Noh, Ji Yeong title = Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR date = 2017-02-20 keywords = MERS; SARS summary = Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] . doi = 10.1007/s00705-017-3281-9 id = cord-325134-z9n17z72 author = Nolan, Brodie title = Recommendations for emergency departments receiving patients with vital signs absent from paramedics during COVID-19 date = 2020-05-05 keywords = SARS summary = Due to their small size and potential to be suspended in the air for prolonged periods, additional precautions are required for health care workers who are exposed to AGMPs. Obtaining an accurate history and COVID-19 risk factors for patients in cardiac arrest is difficult; therefore, we suggest presuming all patients presenting vital signs absent (VSA) to be infectious with COVID-19. The purpose of this study is to provide recommendations to enhance staff and patient safety during COVID-19 by reducing unnecessary exposure to AGMPs for ED staff, paramedics, and other ED patients when receiving patients with VSA. 3 To aid in justification of our recommendations, we present a brief summary of available evidence regarding common AGMPs that occur during cardiopulmonary resuscitation (CPR) and the risks of transmission to health care workers ( Figure 1 ). doi = 10.1017/cem.2020.389 id = cord-304943-thg4fqi2 author = Noor, Aziz Ullah title = Epidemiology of CoViD-19 Pandemic: Recovery and mortality ratio around the globe date = 2020-05-17 keywords = China; MERS; SARS summary = SARS-CoV-1 disease was originated in Guangzhou city of China and the start of 2020 was again a challenging year for this country because of extremely contagion 2019-novel coronavirus (2019-nCoV) disease outbreak. Chinese health ministry took immediate action to investigate and control the disease, including quarantine measures, continuous observation of contacts, clinical and epidemiological data collection from infected people and development of diagnostic tools and efficient treatment protocols. 9 Previous study revealed that wet markets of southern China including Wuhan and Guangzhou cities have the greater risk of spreading novel corona viruses, because of wild animal trading and the absence of biosecurity measures. In-vitro studies indicated that Remdesivir has been successful in the termination of viral RNA replication, 30, 32 and showed effectiveness against the MERS-CoV, SARS-CoV and other bat originated coronaviruses. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.12669/pjms.36.covid19-s4.2660 id = cord-253869-1ouai07v author = Noorimotlagh, Zahra title = A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies date = 2020-10-02 keywords = SARS summary = title: A systematic review of emerging human coronavirus (SARS-CoV-2) outbreak: focus on disinfection methods, environmental survival, and control and prevention strategies In the current SARS-CoV-2 pandemic, identification of the chemical and/or physical disinfectant that interrupts the virus transmission routes including human-to-human, spreads via respiratory droplets, and contaminated hands or surfaces are of utmost importance. According to finding of the included studies, the SARS-CoV-2 can be easily spread via two main ways in human-tohuman transmission: (1) respiratory droplet and (2) direct and indirect contact with aerosol infected surfaces. In addition to chemical disinfectant, in the present SR, the reviewed studies reported that the efficiency of physical disinfectant including temperature (56°C, 60°C), gamma irradiation using a cobalt-60 source at 1 Mrad, and disinfection of virus in human plasma by amotosalen and ultraviolet A were in effective for inactivating coronavirus in a short contact time. doi = 10.1007/s11356-020-11060-z id = cord-293688-g6kag5ij author = Nora, Holtmann title = Assessment of SARS-CoV-2 in human semen - a cohort study date = 2020-05-29 keywords = CoV-2; SARS summary = OBJECTIVE: To investigate the presence of viral RNA in human semen of severe-acute-respiratory syndrome coronavirus 2 (SARS-CoV-2) recovered and positive patients and to evaluate its presence and relevance on semen parameters. SARS-CoV-2 RNA could not be detected in semen of recovered and acute COVID-19 positive males. SARS-CoV-2 RNA could neither be detected in semen samples from recovered nor from acute infected subjects. On another note, it is of interest, that although it was described before in the literature that viral infections have a negative impact on semen parameters like 306 volume, number of spermatozoa and motility we could not detect a negative influence of the SARS-CoV-2 infection in respect of the aforementioned sperm count parameters in recovered subjects with mild symptoms. We found no evidence of SARS-CoV-2 shedding in semen of recovered males or patients with an acute COVID-19 infection after a recovery time of 32,7 days on average. doi = 10.1016/j.fertnstert.2020.05.028 id = cord-346291-qqy9ld94 author = Noroozi, Rezvan title = Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions date = 2020-05-21 keywords = SARS summary = In the current review, we summarize the results of studies which reported alterations in cytokine levels and immune cell functions in patients affected with SARS-CoV-2 and related viruses. Alternatively named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus has been shown to induce various clinical manifestation in hosts ranging from asymptomatic conditions to severe symptoms including respiratory failure, shock, or multiorgan system dysfunction (1) Notably, this condition has been accompanied by a significant increase in the proportion of naïve helper T cells while reduction in memory helper T cells and regulatory T cells (5) . Notably, author reported significant over-production of IL-2, IL-7, IL-10, GCSF, IP-10, MCP1, MIP1A, and TNF-α in ICU patients compared with other group of SARS-CoV-2 infected persons (6) . Notably, T cell counts and cytokine concentrations in severe SARS-CoV-2 infected patients who stayed alive gradually returned to their levels in the mild cases. doi = 10.1016/j.cyto.2020.155143 id = cord-297178-moxhk2e0 author = Novaes Rocha, Vinicius title = Viral replication of SARS-CoV-2 could be self-limitative - the role of the renin-angiotensin system on COVID-19 pathophysiology date = 2020-10-01 keywords = ACE2; Ang; SARS summary = Caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus disease 2019 (COVID-19) is provoking devastating consequences on economic and social fields throughout all continents. Amongst the components of rennin-angiotensin system (RAS), the angiotensin-converting enzyme 2 (ACE2) has gained great prominence for being directly associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the coronavirus related to COVID-19 [4, 5] . ACE2 is a fundamental piece in the pathophysiology of COVID-19, since the high replication capacity of SAR-CoV-2 is directly related to the coupling to ACE2 and cell infection. The ACE2 level reduction caused by SARS-CoV-2 infection may be directly related to the pathogenesis of COVID-19 [26] . The reduction in ACE2 expression may be related to pulmonary inflammation and subsequent cytokine storm seen in patients with severe COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severeacute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensinconverting enzyme-2 (ACE2) doi = 10.1016/j.mehy.2020.110330 id = cord-270377-lfcoy8n1 author = Novazzi, Federica title = SARS-CoV-2 positivity in rectal swabs implication for possible transmission date = 2020-07-02 keywords = SARS summary = Currently, the diagnosis is based on molecular detection of SARS-CoV-2 RNA in respiratory samples such as nasal swab (NS) [1] . However, the evidence that NS in patients with pneumoniae were sometimes negative highlight the needed to collect alternative clinical specimens in whom SARS-CoV-2 RNA could be detected. From the past coronavirus epidemics (SARS-CoV and MERS-CoV) we learned that viral RNA could be also detected in several clinical specimens such as rectal swab (RS) other than respiratory samples [2] . In this perspective, we explored the potential diagnostic role of SARS-CoV-2 real-time RT-PCR performed in biological specimens different from respiratory samples. However, the very low rate of SARS-CoV-2 positivity in samples different from respiratory specimens suggest a limited J o u r n a l P r e -p r o o f Detection of SARS-CoV-2 in Different Types of Clinical Specimens doi = 10.1016/j.jgar.2020.06.011 id = cord-264421-799n9wqj author = Novelli, Antonio title = Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients date = 2020-09-11 keywords = ACE2; Rome; SARS summary = Several studies suggested that genetic variants in the ACE2 gene may influence the host susceptibility or resistance to SARS-CoV-2 infection according to the functional role of ACE2 in human pathophysiology. We therefore investigated the occurrence of ACE2 variants in a cohort of 131 Italian unrelated individuals clinically diagnosed with COVID-19 and in an Italian control population, to evaluate a possible allelic association with COVID-19, by direct DNA analysis. METHODS: As a pilot study, we analyzed, by whole-exome sequencing, genetic variants of ACE2 gene in 131 DNA samples of COVID-19 patients hospitalized at Tor Vergata University Hospital and at Bambino Gesù Children''s Hospital, Rome. Indeed, several studies inferred that genetic variants in ACE2 gene may influence the individual susceptibility or resistance to SARS-CoV-2 according to the functional role of ACE2 in human pathophysiology [12] . In this study, we, therefore, investigated the occurrence of ACE2 variants in a cohort of 131 Italian SARS-CoV-2-positive patients, extracting data on ACE2 variants by direct DNA analysis. doi = 10.1186/s40246-020-00279-z id = cord-353509-yfkiaq80 author = Nugraha, Rhea Veda title = Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date = 2020-10-10 keywords = ACE2; COVID-19; SARS; cytokine; virus summary = This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. doi = 10.1155/2020/2560645 id = cord-323603-99d0wv1h author = Nunez Garcia, B. title = Real-world data: Cancer and SARS-CoV-2 infection date = 2020-09-30 keywords = COVID-19; SARS summary = Methods: EGFR, KRAS, BRAF, BRCA1/2 mutation testing of advanced lung adenocarcinoma, metastatic colorectal, metastatic melanoma and ovarian cancer patients were performed by qPCR and NGS. Methods: During the period 11 th March to 15 th May 2020, patients diagnosed with COVID-19 infection who were attending Beaumont Hospital for systemic anti-cancer therapy were included. Those with an ECOG performance status (PS) 3 were more likely to die than those with PS 2 (p<0.001).Compared to those who recovered, patients who died from COVID-19 had higher mean number of organs affected by cancer (3.7 vs. Conclusions: Patients with cancer who contracted COVID-19 and died had more sites of metastatic disease, a poorer performance status, and a higher Palliative Prognostic Score. Results: Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. doi = 10.1016/j.annonc.2020.08.1797 id = cord-035015-slgywe0c author = Nunn, Alistair V. W. title = SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date = 2020-11-09 keywords = ACE2; COVID-19; ROS; SARS; age; cell; function; mitochondrial; virus summary = Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. doi = 10.1186/s12979-020-00204-x id = cord-319023-ucm8frol author = Nuzzo, Andrea title = Universal Shelter-in-Place vs. Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics date = 2020-06-22 keywords = AACT; SARS; contact summary = Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Conclusion Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated. Such Advanced Automated Contact Tracing (AACT) systems -which could infer exposure risk and propagate warnings to people at risk -may help curb disease spread by facilitating targeted self-isolation rather than universal mandates such as shelter-inplace. In AACT, an additional compartment Sq (Traced contacts that are exposed and under selfisolation) was used while for shelter-in-place, the compartment Q (Individuals isolated through universal enforcement measures) was used. The basic difference between the models is that isolation/quarantine is based solely on exposure history in AACT, while isolation orders apply to the entire population in universal shelter-in-place. Contact tracing can mitigate disease spread through a curated approach of identifying and isolating exposed individuals, as opposed to shelter-in-place orders. doi = 10.1016/j.mayocp.2020.06.027 id = cord-342204-9tgxijvn author = Nuzzo, Domenico title = Potential neurological effects of severe COVID-19 infection date = 2020-07-03 keywords = CNS; COVID-19; SARS summary = In this axis, virus-induced inflammation and oxidative stress could be the common mechanisms responsible for CoV neurological symptoms. People with COVID-19 generally develop respiratory symptoms but the increasing evidence shows that some patients with a severe infection also develop neurological ailments like confusion, stroke, seizure, or loss of smell and taste. Recent studies discussed the neuroinvasive potential of SARS-CoV-2; in fact, some infected subjects did show neurological effects. In fact, detection of some RNA of human-coronavirus in human brain samples clearly demonstrates that these respiratory pathogens are naturally neuroinvasive in J o u r n a l P r e -p r o o f humans and suggests that they establish a persistent infection in human CNS (Arbour et al., 2000) . Therefore, inflammation and oxidative stress systemic, induced by SARS-CoV-2 lung injury, could has effect in CNS causing neuronal dysfunction. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients doi = 10.1016/j.neures.2020.06.009 id = cord-328242-afof417h author = Nuñez, M. A. title = Invasion Science and the Global Spread of SARS-CoV-2 date = 2020-05-19 keywords = SARS; invasion summary = Invasion science inherently examines the connectedness between natural and anthropogenic systems by integrating perspectives of, inter alia, ecology, biogeography, population dynamics, evolutionary biology, risk analysis, human history, and environmental management to understand the spread and impact of introduced organisms in non-native contexts. Biomedical research on emergent infectious diseases would benefit from what invasion science can offer in terms of, for example, 1) a consolidated array of frameworks for studying the consequences of eco-evolutionary novelty, and specifically the release of organisms lacking ecological analogues in their recipient environments [4] ; 2) expanding knowledge of the eco-evolutionary factors that determine the success of transitions between stages of invasion (Figure 1 ), which are influenced by a combination of human activities, environmental conditions, and their feedbacks [4, 11, 12] ; and 3) a rich literature on the context-dependent dynamics and predictive modeling of organismal spread and their effects. doi = 10.1016/j.tree.2020.05.004 id = cord-351116-jwy6k0ih author = O''Reilly, GM title = Epidemiology and clinical features of emergency department patients with suspected and confirmed COVID‐19: A multisite report from the COVED Quality Improvement Project for July 2020 (COVED‐3) date = 2020-09-21 keywords = COVID-19; SARS summary = METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study in Australian EDs. This analysis presents data from eight sites across Victoria and Tasmania for July 2020 (during Australia''s ''second wave''). 3 The objectives of this analysis (COVED-3), undertaken during the ‗second wave'', were to explore the association between SARS-CoV-2 test result and mechanical ventilation and death in hospital and to identify clinical and epidemiological variables predictive of SARS-CoV-2 positivity. 12 These include history (age, sex, symptoms and duration of presenting complaint, epidemiological features, co-morbidities), findings on clinical examination, radiological and blood investigations, care provided in the ED and hospital (including commencement of invasive mechanical ventilation and ED disposition destination) and patient outcomes (including survival to discharge). In terms of clinical and epidemiological risk factors, SARS-CoV-2 positive patients were more likely to report close contact with a confirmed case of COVID-19 or a positive SARS-CoV-2 PCR swab result in the 14 days prior to their ED presentation. doi = 10.1111/1742-6723.13651 id = cord-301313-9595vm0k author = OKBA, NISREEN M.A. title = SARS-CoV-2 specific antibody responses in COVID-19 patients date = 2020-03-20 keywords = ELISA; MERS; SARS summary = Here, we describe development of serological assays for the detection of virus neutralizing antibodies and antibodies to the nucleocapsid (N) protein and various spike (S) domains including the S1 subunit, and receptor binding domain (RBD) of SARS-CoV-2 in ELISA format. Using a wellcharacterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house as well as a commercial platform. We evaluated SARS-CoV-2 specific antibody responses in severe and mild cases using serum samples collected at different times post-disease onset from three French PCR-confirmed CoVID-19 patients. We tested sera for SARS-CoV-2 specific antibodies using different ELISAs. Following infections, all three patients seroconverted between days 13 and 21 post onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S and S1 subunit including the N-terminal (S1 A ) domain and the receptor binding domain (RBD). doi = 10.1101/2020.03.18.20038059 id = cord-338023-gb5jgqcg author = Obara, Shinju title = Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission date = 2020-08-27 keywords = SARS; covid-19; patient summary = title: Anesthesiologist behavior and anesthesia machine use in the operating room during the COVID-19 pandemic: awareness and changes to cope with the risk of infection transmission Because SARS-CoV-2 can be transmitted via aerosols and surface contaminations of the environment, appropriate use of anesthesia machines and appropriate behavior in the operation room (OR) are required specifically in relation to this disease. For patients with confirmed or suspected COVID-19 infection, recommendations are use of (1) a high-performance hydrophobic filter (artificial nose) with a high rate of virus rejection (viral filtration efficiency > 99.99% [12] ), and (2) use of a viral filter at the expiratory gas inlet of the anesthesia machine from the expiratory circuit to protect the machine from viruses passing through the artificial nose [12, 13] . Recommendations for anesthesia in patients suspected of COVID-19 Coronavirus infection doi = 10.1007/s00540-020-02846-z id = cord-320270-lduhhdld author = Obek, Can title = Management of prostate cancer patients during COVID-19 pandemic date = 2020-07-20 keywords = ADT; EBRT; SARS; covid-19 summary = National Comprehensive Cancer Network (NCCN), European Association of Urology (EAU), and the Canadian Framework advise against routine PC screening, including prostate specific antigen (PSA) testing and digital rectal examination (DRE), for all asymptomatic individuals until the pandemic subsides [11, 14, 17] . Although authors recognize that neoadjuvant ADT prior to surgery is normally not recommended outside of clinical trials, they state that upfront ADT may be an option in patients with UIR, HR, and VHR disease during COVID-19 crisis, if prolonged surgical delays are expected [11] . Likewise, Royal College of Surgeons'' Updated Intercollegiate General Surgery Guidance on COVID-19 initial statement of "laparoscopy should generally not be used during the pandemic" was later changed to "consider laparoscopy only in selected individual cases, where clinical benefit to the patient substantially exceeds the risk of viral transmission to surgical and theater teams" [27, 28] . doi = 10.1038/s41391-020-0258-7 id = cord-303297-fiievwy7 author = Oberemok, Volodymyr V. title = SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date = 2020-04-30 keywords = COVID-19; CoV-2; SARS; virus summary = In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. doi = 10.1007/s00011-020-01352-y id = cord-336696-c3rbmysh author = Oberfeld, Blake title = SnapShot: COVID-19 date = 2020-04-30 keywords = COVID-19; SARS summary = authors: Oberfeld, Blake; Achanta, Aditya; Carpenter, Kendall; Chen, Pamela; Gilette, Nicole M.; Langat, Pinky; Said, Jordan Taylor; Schiff, Abigail E.; Zhou, Allen S.; Barczak, Amy K.; Pillai, Shiv Abstract Coronavirus disease 2019 (COVID-19) is a novel respiratory illness caused by SARS-CoV-2. The causative agent was characterized as a novel coronavirus, initially referred to as 2019-nCoV and renamed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (Zhou et al., 2020b) . This respiratory illness, coronavirus disease 2019 (COVID-19), has spread rapidly by human-to-human transmission, caused major outbreaks worldwide, and resulted in considerable morbidity and mortality. Based on our understanding of SARS and MERS, and their similarity to COVID-19, the human immune response in mild cases is likely characterized by a robust type I interferon antiviral response and CD4+ Th1 and CD8+ T cell response, resulting in viral clearance. doi = 10.1016/j.cell.2020.04.013 id = cord-259852-skhoro95 author = Oboh, Mary Aigbiremo title = Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics date = 2020-08-18 keywords = SARS; african summary = In addition to the Regional Disease Surveillance Systems Enhancement fund (US$600 million) provided by the World Bank for strengthening health systems and disease surveillance, each country should further establish an epidemic emergency fund for epidemic preparedness and response. Given the various epidemic events that have previously oc-curred in Africa, from Ebola virus disease (EVD) [4] to yellow fever, cholera, measles and Lassa fever [5] , it would almost be safe to assume that African governments have prepared proactive measures against possible future epidemics. A measure could have been applied to restrict travel even from countries with fewer than 100 confirmed SARS-CoV-2 cases given that the virus is highly transmissible, with a high reproductive number [3] . In addition to the REDISSE fund (US$600 million) created by the World Bank for strengthening health systems and disease surveillance, each country should further map out an epidemic emergency fund that will be used to address situations such as this in the future. doi = 10.3961/jpmph.20.259 id = cord-298490-p1msabl5 author = Obukhov, Alexander G. title = SARS-CoV-2 Infections and ACE2: Clinical Outcomes Linked With Increased Morbidity and Mortality in Individuals With Diabetes date = 2020-07-15 keywords = ACE2; Ang; RAS; SARS summary = As suggested by the recent reports regarding the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), upon entry into the host, this virus binds to the extracellular domain of ACE2 in nasal, lung, and gut epithelial cells through its spike glycoprotein subunit S1. In this Perspective, we bring attention to specific factors that may complicate COVID-19 in individuals with diabetes including 1) the presence of bone marrow changes (myeloidosis) that predispose those with diabetes to an excessive proinflammatory response (cytokine storm) and contribute to insulin resistance and reduced vascular repair, and worsening function of the heart, kidney, and systemic vasculature as a whole; 2) increased circulating furin levels that could cleave the spike protein and increase infectivity of SARS-CoV-2; 3) dysregulated autophagy that may promote replication and/or reduce viral clearance; and 4) gut dysbiosis that leads to widespread systemic inflammation, increased gut glucose and sodium absorption, and reduced tryptophan and other key amino acid absorption needed for incretin secretion and glucose homeostasis. doi = 10.2337/dbi20-0019 id = cord-259585-mjtxiu0t author = Occhipinti, Vincenzo title = Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date = 2020-04-21 keywords = IBD; SARS; patient summary = Every possible effort was made to quickly increase the capacity of intensive care units (ICUs) to accommodate the alarming numbers of very sick CoViD-19 patients, including constructing new units in unused areas of the hospital or converting surgical rooms into ICUs. These drastic measures were implemented in a very short period of time, and although necessary to counteract the devastation brought about by the outbreak, they also posed tremendous challenges to the care of patients with GI conditions, including those with inflammatory bowel diseases (IBD). However, for patients on biologic therapies, we have implemented a mandatory phone call-in the day before any planned hospital visit to screen for possible CoViD-19 symptoms or contact with infected individuals and to reassure patients that all possible precautions are being taken by the IBD center to reduce the risk of infection. doi = 10.1093/ibd/izaa084 id = cord-348192-ibohbjfb author = Odih, Erkison E. title = Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks? date = 2020-06-09 keywords = CoV-2; SARS; transmission summary = Endemic and epidemic transmission of multiple feco-oral pathogens via this route continues to be documented in areas without safely managed sanitation, and, therefore, the risk of SARS-CoV-2 transmission needs to be evaluated, tracked, and forestalled in such settings. Furthermore, environmental surveillance of SARS-CoV-2 in wastewater and accumulated human waste, as well as efforts to mitigate the virus'' entry into unprotected household water sources, should be a priority part of the COVID-19 response in settings without safely managed sanitation for the duration of the pandemic. 3, 5, 6 Considerable concern has been expressed in the literature that the feco-oral transmission potential for SARS-CoV-2 places endoscopists, caregivers of diapered children who shed the virus, 7 and fecal transplant recipients 8 at high risk of contracting the infection. 20, 21 Although there are as yet no reports of transmission of SARS-CoV-2 via sewage or fecal matter in settings without safely managed sanitation, or recovery from household water, these examples demonstrate that feco-oral transmission by endemic pathogenic organisms is commonplace in these settings. doi = 10.4269/ajtmh.20-0462 id = cord-254916-y1rw9q11 author = Ogando, Natacha S. title = SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date = 2020-06-22 keywords = CoV-2; Fig; RNA; SARS; Vero; cell summary = The overall level of amino acid sequence identity of viral proteins ranges from about 65 % in the least conserved parts of the S protein to about 95 % in the most conserved replicative enzyme domains, prompting the coronavirus study group of the International Committee on the Taxonomy of Viruses to classify the new agent within the species Severe acute respiratory syndrome-related coronavirus, which also includes the 2003 SARS-CoV [1] . In this report, we describe a comparative study of the basic replication features of SARS-CoV and SARS-CoV-2 in Vero E6 cells, including growth kinetics, virus titres, plaque phenotype and an analysis of intracellular viral RNA and protein synthesis. One of them is the rapid evolution -during virus passaging in Vero cells -of a specific region of the SARS-CoV-2 S protein that contains the so-called furin-like cleavage site. doi = 10.1099/jgv.0.001453 id = cord-291590-24psoaer author = Ogando, Natacha S. title = The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date = 2020-06-20 keywords = Fig; MERS; RNA; SARS summary = In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. doi = 10.1101/2020.06.19.162529 id = cord-337396-g69bb60d author = Ogawa, Yoshihiko title = Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date = 2020-11-07 keywords = PCR; SARS summary = A follow-up survey was conducted with healthcare personnel (HCP) who were exposed to a patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative PCR results. No apparent infection was found in any of the HCP who had contact exposure with and/or aerosol exposure to the patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative results of PCR tests for SARS-CoV-2. Thus, we created a policy that for patients whose sputum and/or nasopharyngeal PCR test results for SARS-CoV-2 were negative when measured twice separately over 24 h, we stopped the precautions against aerosol transmission. We did not perform PCR tests for SARS-CoV-2 until the 63rd day of illness, and the result of this test was re-negative. In conclusion, no HCP were infected by contact with and aerosol exposures to SARS-CoV-2 re-positive patients in our hospital. doi = 10.1186/s13104-020-05365-y id = cord-258614-7unadw41 author = Ogidigo, Joyce Oloaigbe title = Natural phyto, compounds as possible noncovalent inhibitors against SARS-CoV2 protease: computational approach date = 2020-10-25 keywords = Mpro; SARS; drug; figure summary = Structure-based virtual screening and molecular dynamics (MD) simulation have been employed to study their inhibitory potential against the main protease (M(pro)) SARS-CoV-2. These phytocompounds showed strong and stable interactions with the active site amino acid residues of SARS-CoV-2 Mpro similar to the reference compound. Results obtained from this study showed that momordicine and momordiciode F2 exhibited good inhibition potential (best MMGBA-binding energies; −41.1 and −43.4 kcal/mol) against the M(pro) of SARS-CoV-2 when compared with FDA reference anti-viral drugs (Ribavirin, remdesivir and hydroxychloroquine). Thus, among the 86 phytocompounds and 3 antiviral drugs screened (Supplementary material Table S1 ), 6 phyto ligands exhibited appreciable binding energies against the SARS-CoV-2 M pro and strong interactions within the binding pocket. Analysis of the per-residue additional showed that studied compounds interact with these key amino acid residues in the active site of the main protease, suggesting that these phytocompounds could emerge as ideal candidate''s inhibitors against SARS-CoV-2 M pro and another virus protease. doi = 10.1080/07391102.2020.1837681 id = cord-292836-1o2ynvy3 author = Ogimi, Chikara title = What’s New With the Old Coronaviruses? date = 2020-04-21 keywords = MERS; OC43; SARS; respiratory summary = In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] . doi = 10.1093/jpids/piaa037 id = cord-335591-r0x8yaqj author = Ohnishi, Kazuo title = Establishment and Characterization of Monoclonal Antibodies Against SARS Coronavirus date = 2007-11-28 keywords = ELISA; PBS; SARS summary = The hybridomas produce monoclonal antibodies that recognize viral component molecules, including the spike protein (S) and the nucleocapsid protein (N), enabling the immunological detection of SARS-CoV by immunofluorescence staining, immunoblot, or an antigen-capture ELISA system. Based on clinical experience, several options have been considered in the quest to develop the capacity to accurately diagnose SARS-CoV infection, including molecular biology techniques and serological tests such as antigen-capture ELISA assay and immunofluorescence assay to detect virus-infected cells in respiratory swabs (3-7) . These mAbs enable the general immunological detection of SARS-CoV by methods such as immunofluorescent staining, immunoblotting, and immunohistology, in addition to the construction of a highly sensitive antigen-capture sandwich ELISA (6). The UV-inactivated purified SARS-CoV samples (see Note 1), which are serially diluted with 1% OVA/PBS-Tween, are added to the wells and incubated for 1 h at room temperature doi = 10.1007/978-1-59745-181-9_15 id = cord-261193-960th627 author = Ohnishi, Kouji title = Evaluation of a non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold as a SARS 3CL protease inhibitor date = 2019-01-15 keywords = 3CL; SARS summary = A non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold was evaluated as a novel inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)). The synthesized decahydroisoquinolin inhibitors showed about 2.4 times potent inhibitory activities for SARS 3CL(pro) when combined with a non-prime site substituent. The residue was purified by silica gel column chromatography (hexane/EtOAc = 5:1) to give a title alcohol ( TPAP (tetra-n-propyl ammonium perrutenate, 316 mg, 0.9 mmol) was added to a solution of above alcohol (10.5 g, 47.5 mmol) and NMO (N-methylmorphline-N-oxide, 21.1 g, 180 mmol) in CH 2 Cl 2 (180 mL) at 0°C. After being stirred for 30 min, the reaction mixture was filtered through a silica gel layer and the filtrate was concentrated. The filtrate was concentrated and resulting residue was purified by silica gel column chromatography (hexane/ EtOAc = 10:1) to afford 15 (640 mg, 50%). doi = 10.1016/j.bmc.2018.12.019 id = cord-349682-kpg0vley author = Ojha, Probir Kumar title = Therapeutics for COVID-19: from computation to practices—where we are, where we are heading to date = 2020-09-02 keywords = ACE2; COVID-19; CoV-2; Fig; SARS; drug summary = For example, the broad-spectrum antiviral drug Arbidol recently entered the clinical trial for the treatment of SARS-CoV-2 which may act by inhibiting virus-host cell fusion, thus preventing the viral entry into host cells against influenza virus [37] [38] [39] . Smith and Smith [22] analyzed 8000 small drug molecules and natural products (SWEETLEAD library database) employing restrained temperature replica-exchange MD simulations combining virtual screening through the ensemble docking to identify the effective drug for COVID-19 which might stop the virus by two ways: (a) disrupting S protein and ACE2 receptor interface stability; or (b) by troubling the capability of the S protein to recognize Table 2 Pharmacological safety data of selected potential drug candidates [11, 12, 14, 34, 38, 39, 43-45, 57-59, 64, 69, 70, 89] Drug Dose Drug-drug interaction Toxicity Chloroquine phosphate (Aralen) [11, 12, 14, 43, 89] This is a genetically engineered vaccine candidate with the replicationdefective adenovirus type 5 as the vector to express SARS-CoV-2 spike protein. doi = 10.1007/s11030-020-10134-x id = cord-303056-bdse9o26 author = Okada, Masaji title = Development of vaccines and passive immunotherapy against SARS corona virus using SCID-PBL/hu mouse models date = 2007-04-20 keywords = SARS summary = The production of neutralizing antibodies against SARS CoV was observed in the serum from mice immunized with S DNA vaccine SARS (M) DNA vaccine and N DNA vaccine induced murine T cell responses against SARS [4] . Human neutralizing antibodies were induced from SCID-PBL/hu mice vaccines with SARSS [6] and M DNA vaccines (Fig. 2) . Titer of neutralizing antibody in the serum from SCID-PBL/hu mice immunized with SARS (M) DNA vaccine was 1:10. SARS S DNA vaccine which elicits effective neutralizing antibody responses that generate protective immunity in a mouse model [9] . Furthermore, SARS M DNA as well as SARSS DNA vaccine induce human neutralizing antibodies against SARS CoV by the SCID-PBL/hu model. Therefore, the effect of combination immunization with such SARS vaccines (M vaccine and S vaccine) and the specificity of human monoclonal neutralizing antibodies are now being studied. A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice doi = 10.1016/j.vaccine.2007.01.032 id = cord-308110-cco3aq4n author = Okamoto, Mika title = The chemokine receptor antagonist cenicriviroc inhibits the replication of SARS-CoV-2 in vitro date = 2020-07-30 keywords = CVC; CoV-2; SARS summary = In this study, CVC was examined for its inhibitory effect on the replication of SARS-CoV-2, the causative agent of COVID-19, in cell cultures and found to be a selective inhibitor of the virus. The 50% effective concentrations of CVC were 19.0 and 2.9 μM in the assays based on the inhibition of virus-induced cell destruction and viral RNA levels in culture supernatants of the infected cells, respectively. Considering the fact that the regulation of excessive immune activation is required to treat COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. Since not only the inhibition of viral replication but also the control of excessive immune activation is mandatory to save COVID-19 patients at the late stage of the disease, CVC should be further pursued for its potential in the treatment of SARS-CoV-2 infection. doi = 10.1016/j.antiviral.2020.104902 id = cord-347374-mryazbnq author = Okba, Nisreen M.A. title = Severe Acute Respiratory Syndrome Coronavirus 2−Specific Antibody Responses in Coronavirus Disease Patients date = 2020-07-17 keywords = ELISA; MERS; SARS summary = Using serum samples from patients with PCR-confirmed SARS-CoV-2 infections, other coronaviruses, or other respiratory pathogenic infections, we validated and tested various antigens in different in-house and commercial ELISAs. We demonstrated that most PCR-confirmed SARS-CoV-2–infected persons seroconverted by 2 weeks after disease onset. Using a well-characterized cohort of serum samples from PCR-confirmed SARS-CoV-2 and patients PCR-confirmed to be infected with seasonal coronaviruses and other respiratory pathogens, we validated and tested various antigens in different platforms developed in-house, as well as a commercial platform. We evaluated SARS-CoV-2-specific antibody responses in severe and mild cases by using serum samples collected at different times postonset of disease from 3 PCR-confirmed COVID-19 patients from France. We tested serum samples for SARS-CoV-2specific antibodies by using different ELISAs. After infection, all 3 patients seroconverted between days 13 and 21 after onset of disease (Figure 1) , and antibodies were elicited against the SARS-CoV-2 S, S1 subunit, and RBD, but only 2/3 patients had detectable antibodies to the N-terminal (S1 A ) domain. doi = 10.3201/eid2607.200841 id = cord-278238-w1l8h8g8 author = Okba, Nisreen MA title = Middle East respiratory syndrome coronavirus vaccines: current status and novel approaches date = 2017-04-13 keywords = East; MERS; Middle; SARS summary = Nisreen MA Okba, V Stalin Raj and Bart L Haagmans Middle East respiratory syndrome coronavirus (MERS-CoV) is a cause of severe respiratory infection in humans, specifically the elderly and people with comorbidities. The other candidate MVA-S, a viral-vector-based vaccine, induced systemic neutralizing antibodies and mucosal immunity which conferred protection against MERS-CoV challenge and reduced virus shedding in vaccinated camels [52 ] Therefore, this vaccine candidate may provide a means to prevent zoonotic transmission of the virus to the human population. Prophylaxis with a Middle East respiratory syndrome coronavirus (MERS-CoV)-specific human monoclonal antibody protects rabbits from MERS-CoV infection T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice The recombinant Nterminal domain of spike proteins is a potential vaccine against Middle East respiratory syndrome coronavirus (MERS-CoV) infection doi = 10.1016/j.coviro.2017.03.007 id = cord-298725-da71febn author = Okuhama, Ayako title = Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan date = 2020-11-17 keywords = COVID-19; SARS summary = title: Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Reports have been published on COVID-19 among patients receiving hemodialysis (2), but none have evaluated whether HD effluent is infectious. We report detection of SARS-CoV-2 RNA in hemodialysis effluent from a patient with COVID-19 pneumonia and prolonged inflammation. PCR results showed SARS-CoV-2 RNA of 157.9 copies/μL with cycle threshold (C t ) values of 38.3 at 1 hour after starting hemodialysis but were negative on effluent collected at 2 hours. In conclusion, we report positive qRT-PCR results for SARS-CoV-2 RNA from hemodialysis effluent in a patient receiving renal dialysis. doi = 10.3201/eid2611.201956 id = cord-334175-x10bbv7y author = Okur, Hacer Kuzu title = Preliminary report of In vitro and In vivo Effectiveness of Dornase alfa on SARS-CoV-2 infection date = 2020-09-07 keywords = Dornase; Fig; SARS; alfa summary = Dornase alfa, the recombinant form of the human DNase I enzyme, breaks down neutrophil extracellular traps (NET) that include a vast amount of DNA fragments, histones, microbicidal proteins and oxidant enzymes released from necrotic neutrophils in the highly viscous mucus of cystic fibrosis patients. We followed clinical improvement in the radiological analysis (2-of-3 cases), oxygen saturation (SpO2), respiratory rate, disappearing of dyspnea, coughing and a decrease in NET formation and SARS-CoV-2 viral load after the treatment. Also here, we share our preliminary results suggesting that Dornase alfa has an anti-viral effect against SARS-CoV-2 infection in a green monkey kidney cell line, Vero, and a bovine kidney cell line, MDBK without determined cytotoxicity on healthy peripheral blood mononuclear cells. In this study, preliminary data is presented about in-vitro and in-vivo anti-viral and nuclease activity of Dornase alfa for the clearance of SARS-CoV-2 viral load and NETs in the lungs of COVID-19 patients. doi = 10.1016/j.nmni.2020.100756 id = cord-322942-y4zd2oui author = Olagnier, David title = Identification of SARS-CoV2-mediated suppression of NRF2 signaling reveals a potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate date = 2020-07-17 keywords = Fig; NRF2; SARS summary = Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular anti-viral program, which potently inhibits replication of SARS-CoV2 across cell lines. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2. Here we demonstrate that expression of NRF2-dependent genes is suppressed in biopsies from 104 COVID-19 patients and that treatment of cells with NRF2 agonists 4-OI and DMF induces a 105 strong anti-viral program that limits SARS-CoV2 replication. Interestingly, when 176 treating Calu3 cells with DMF, another known NRF2 inducer and a clinically approved drug in 177 the first-line-of treatment of multiple sclerosis, we could also observe an anti-viral effect toward 178 SARS-CoV2 replication similar in magnitude as what we had observed with 4-OI (Fig 2p-q) as 179 well as a reduced but significant effect when using Vero cells (Fig. 2r) . doi = 10.1101/2020.07.16.206458 id = cord-351719-xqmir1ca author = Olaimat, Amin N. title = Food Safety During and After the Era of COVID-19 Pandemic date = 2020-08-04 keywords = COVID-19; SARS; food summary = The coronavirus disease 2019 (COVID-19) is a clinical syndrome caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). COVID-19 is the clinical syndrome caused by SARS-CoV-2 infection which is characterized by a respiratory disease with symptoms ranging from mild influenza (flu-like) to severe pneumonia and acute respiratory distress syndrome (Petrosillo et al., 2020) . A previous study reported that food products were a plausible transmission route for respiratory viruses including SARS-CoV-1 and influenza (Klein, 2004) . The proper use of gloves, sanitizers, and disinfectants can minimize the risk of virus spread and disease transmission (Food and Agriculture Organization of the United Nations [FAO] and World Health Organization [WHO], 2020; Food and Drug Administration [FDA], 2020a). The current guidelines issued by public health authorities are based on the disease patterns of previously encountered coronaviruses and they need to be updated according to the novel coronavirus SARS-CoV-2 as this virus is likely to persist and people will have to modify their "normal behavior" to a "new normal." doi = 10.3389/fmicb.2020.01854 id = cord-280198-bhjw6xc5 author = Olaleye, Omonike A. title = Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date = 2020-08-14 keywords = ACE2; SARS summary = title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 Spike Protein Interaction In Vitro Here in, we discovered Clioquinol (5-chloro-7-iodo-8-quinolinol (CLQ)), a FDA approved drug and two of its analogues (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ14); and 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) as potent inhibitors of SARS-CoV-2 infection induced cytopathic effect in vitro. In addition, all three compounds showed potent anti-exopeptidase activity against recombinant human angiotensin converting enzyme 2 (rhACE2) and inhibited the binding of rhACE2 with SARS-CoV-2 Spike (RBD) protein. Therefore, targeting 106 the interaction between human ACE2 receptor and the RBD in S protein of SARS-CoV-2 could 107 serve as a promising approach for the development of effective entry inhibitors for potential 108 prevention and/or treatment of COVID-19. Activity of Clioquinol (CLQ) and Analogues against ACE2 Exopeptidase Activity and 725 ACE2 and SARS-CoV-2 Spike (RBD) Protein Interaction doi = 10.1101/2020.08.14.250480 id = cord-340252-9gr2iw15 author = Olalla, J. title = Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience date = 2020-05-20 keywords = SARS summary = Conclusions: the prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This identification, together with the appropriate measures, could result in less spread of the virus from the healthcare center and, therefore, in fewer healthcare providers and patients affected by In this article, we present the results of an active search study of asymptomatic and seroprevalence carriers of SARS-CoV-2 among high-risk healthcare workers in a hospital in southern Spain. The main objective was to determine the prevalence of asymptomatic carriers of SARS-CoV-2 in healthcare professionals, defined as those individuals with PCR of a positive respiratory sample without presenting symptoms suggestive of CoVID-19 on the day of sampling. . https://doi.org/10.1101/2020.05.18.20103283 doi: medRxiv preprint workers in the total workforce presented positive PCR, although in this study it was performed testing only symptomatic workers (6) . doi = 10.1101/2020.05.18.20103283 id = cord-330433-y5dvlcda author = Olivieri, Emily R. title = Analysis of SARS-CoV Receptor Activity of ACE2 Orthologs date = 2006 keywords = ACE2; SARS summary = 2 Coronavirus spike-receptor interactions are major determinants of species specificity, and transfection of viral genomic RNA or expression of receptors in nonpermissive cell lines usually results in productive infection. The goals of this study were to determine whether ACE2 transcript is produced by permissive and nonpermissive cells derived from diverse species and to use speciesspecific differences in ACE2 to identify amino acids or other post-translational modifications critical for SARS-CoV binding and/or fusion. Cell lines derived from monkey (VeroE6, pRhMk, and pCMK), human (HRT-18, HEK293T, and Huh-7), mink (Mv1Lu), dog (MDCK), cat (CRFK), hamster (BHK-21), and chicken (CEF) were analyzed for susceptibility to SARS-CoV. This data suggests that dog ACE2 and chicken ACE2 may have amino acid or other differences, which inhibit their function as SARS-CoV receptors. 13 We used multiple sequence alignment of efficient and poor receptors, combined with difference mapping on the hACE2 structure, to identify specific residues or post-translational modifications within ACE2 that may be critical for SARS-CoV entry. doi = 10.1007/978-0-387-33012-9_46 id = cord-323468-xn7anxj6 author = Olloquequi, Jordi title = COVID‐19 Susceptibility in chronic obstructive pulmonary disease date = 2020-08-11 keywords = COPD; COVID-19; SARS summary = Chronic obstructive pulmonary disease (COPD) is a leading cause of death and disability globally, characterized by persistent respiratory symptoms and airflow limitation due to airway inflammation and/or alveolar abnormalities 10 . All rights reserved are associated to impaired lung function and risk of developing COPD 42-44 , it has also been demonstrated that people born with a diminished airway function are more likely to suffer COPD symptoms and subsequent viral infections [45] [46] [47] . In any case, there is no doubt that subjects who develop COPD are at an increased risk of suffering respiratory infections, a matter of importance in the context of COVID-19 pandemics. Increased cytokine response of rhinovirus-infected airway epithelial cells in chronic obstructive pulmonary disease DPP4, the Middle East Respiratory Syndrome Coronavirus Receptor, is Upregulated in Lungs of Smokers and Chronic Obstructive Pulmonary Disease Patients doi = 10.1111/eci.13382 id = cord-332948-h297ukuu author = Olotu, Fisayo A. title = Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. date = 2020-10-16 keywords = CoV-2; RBD; SARS; protein; site summary = authors: Olotu, Fisayo A.; Omolabi, Kehinde F.; Soliman, Mahmoud E.S. title: Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. 30 Identification of other functional (allosteric) sites on the prefusion S protein could present another dynamic and effective approach of preventing SARS-CoV-2 infectivity relative to its interaction with the host cell ACE2 and proteases. 53 Relatively, this study was implemented to (i) identify potential druggable sites across the S1 and S2 domains of the SARS-CoV-2 S protein other than the RBD-hACE2 interface (ii) perform high-throughput (virtual) screening of ~1500 FDA approved drugs against the most druggable site(s) (iii) investigate the binding dynamics and interaction mechanisms of the compounds and their consequential effects on the S-protein RBD-ACE2 complex. We believe this systematic study will be able to provide structural and molecular insights into possible allosteric sites on SARS-CoV-2 S protein suitable for selective targeting and structureComputational methodologies doi = 10.1016/j.imu.2020.100451 id = cord-338972-uq2ha8xs author = Olson, Michael T. title = Resumption of elective surgery during the COVID-19 pandemic: what lessons can we apply? date = 2020-06-05 keywords = COVID-19; SARS summary = authors: Olson, Michael T.; Triantafyllou, Tania; Singhal, Saurabh Ensure quality and quantity assessment of local PPE availability, and closely follow PPE recommendations for COVID-19+ patients, patients under investigations, and non-COVID-19 patients Re-evaluate health care facility capacity, including resources (e.g., beds, ICUs, ventilators), and expansion strategies Operating rooms should take inventory of existing surgical and cleaning supplies before re-activating elective surgeries Ensure coordination among surgery, anesthesia, nursing, engineering, housekeeping, and other hospital staff or specialties involved in multidisciplinary care; assure adequate staff volume Assign a governance committee to clarify, interpret, and iterate policies, make real-time decisions, and initiate and communicate messaging Although leading surgical societies have guided surgeons in terms of appropriate surgical practice amid the ongoing viral pandemic, certain questions remain, particularly pertaining to the safety of performing minimally invasive surgery in the setting of COVID-19. It remains to be determined how these infection-control measures, albeit contributing to the safety of the patient and staff, impact surgical care when elective surgeries are again performed. doi = 10.1007/s10353-020-00645-0 id = cord-303061-vvzkpetn author = Olyaee, Mohammad Hossein title = RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation date = 2020-08-07 keywords = SARS summary = title: RCOVID19: Recurrence-based SARS-CoV-2 features using chaos game representation Utilizing chaos game representation (CGR) as well as recurrence quantification analysis (RQA) as a powerful nonlinear analysis technique, we proposed an effective process to extract several valuable features from genomic sequences of SARS-CoV-2.  The dataset involves features that enable us to compare genomic sequences with different lengths. In this work, according to the diagram represented in Fig. 1 , several recurrencequantification-based features are extracted from the nucleotide sequences. In this paper, we introduce a new dataset which involves efficient nonlinear features related to genomic sequences of SARS-CoV-2. In the final step, by applying recurrence quantification analysis (RQA), from each extracted coordinate series, 9 features are provided and totally 18 ( ) features will be extracted. • Extract features from coordinate series by applying recurrence quantification analysis measure gives the probability that two neighbors of any state are also neighbors and is obtained as below: doi = 10.1016/j.dib.2020.106144 id = cord-273723-srfypn7j author = Omar, Sarah title = Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date = 2020-07-30 keywords = RNA; SARS summary = title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis As far as we are aware, there are currently no published data on the duration of RNA positivity in the upper respiratory of patients with mild COVID-19 that could inform a public health assessment of RT-qPCR as a tool for monitoring home isolation. At 14 days after onset, the earliest moment to discontinue home isolation currently recommended in Germany [18] , 53.5% of COVID-19 patients still had detectable SARS-CoV-2 RNA (Figure 2) . Duration of SARS-CoV-2-RNA positivity in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 (n = 537) For cases where laboratory monitoring is indispensable, knowledge of the RT-qPCR threshold cycle may improve our judgement on whether a positive result indicates infectiousness or not [20] . doi = 10.2807/1560-7917.es.2020.25.30.2001292 id = cord-330129-izr62c68 author = Omer, Sumaira title = Preventive measures and management of COVID-19 in pregnancy date = 2020-04-09 keywords = COVID-19; SARS summary = As of 17 March 2020, there are 153 countries who have reported cases of infection caused by this virus [i.e., coronavirus disease-2019 (COVID19) ], with Italy becoming the new epicentre [1] . Importantly, viral respiratory illnesses, such as influenza, can easily develop during pregnancy, which means pregnant women may be more vulnerable to COVID-19 and require prioritized medical care. Interim COVID-19 guidelines for the effective counselling and education of pregnant women are currently available from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) [5, 6] . For effective management, pregnant women with suspected COVID-19 should be isolated and then transferred to a hospital equipped with sufficient health facilities and fully trained clinicians to take proper care of critically ill obstetric patients. Interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease 2019 (COVID-19) in healthcare settings doi = 10.1007/s40267-020-00725-x id = cord-302393-hrz3bypr author = Omrani, Ali S. title = The first consecutive 5000 patients with Coronavirus Disease 2019 from Qatar; a nation-wide cohort study date = 2020-10-19 keywords = COVID-19; ICU; SARS summary = Multivariable logistic regression showed that older age [adjusted odds ratio (aOR) 1.041, 95% confidence interval (CI) 1.022–1.061 per year increase; P < 0.001], male sex (aOR 4.375, 95% CI 1.964–9.744; P < 0.001), diabetes (aOR 1.698, 95% CI 1.050–2.746; P 0.031), chronic kidney disease (aOR 3.590, 95% CI 1.596–8.079, P 0.002), and higher BMI (aOR 1.067, 95% CI 1.027–1.108 per unit increase; P 0.001), were all independently associated with increased risk of ICU admission. In this study, we describe 60-day outcomes of a nationwide COVID-19 cohort from Qatar, and explore patient characteristics associated with the need for admission to an intensive care unit (ICU). In the multivariable logistic regression, we found that older age, male sex, co-existing diabetes or chronic kidney disease, and higher BMI were all independently associated with increased risk of need for ICU admission ( Table 2) . doi = 10.1186/s12879-020-05511-8 id = cord-285018-l26px1bc author = Ong, David S.Y. title = Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date = 2020-09-07 keywords = SARS summary = title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? OBJECTIVES: The aim of this study was to assess the diagnostic performance of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2. RealAmp Kit on the sample-to-result InGenius® platform in comparison to the national reference standard in the Netherlands, and to determine the added value of nucleoprotein (N) gene detection to establish the diagnosis of COVID-19. Patients were sampled from the oral cavity and subsequently from the nasal cavity using the same nasopharyngeal swab, which was tested by a validated in-house NAT assay on the presence of COVID-19 envelope protein (E) gene and RNA dependent RNA polymerase (RdRp) gene according to a reference method that was established after international collaboration [5] . doi = 10.1016/j.jcv.2020.104632 id = cord-338001-jig46hsk author = Ong, Jacqueline S. M. title = Coronavirus Disease 2019 in Critically Ill Children: A Narrative Review of the Literature date = 2020-04-21 keywords = COVID-19; SARS; Wuhan summary = In the small cohort from Tongji Hospital (6), Wuhan, one out of the six children with COVID-19 was admitted to intensive care. Given that children appear to have mild disease and may have a clinical picture similar to that of viral bronchiolitis, the use of noninvasive ventilation (NIV), and/or high-flow nasal cannula (HFNC) for respiratory support would likely be preferred amongst PICU clinicians. Caregivers are close contacts of the infected patient, although they may be asymptomatic at the time-in the Wuhan Children''s Hospital series with active case finding of close contacts, 90% of confirmed cases had family members who were either confirmed or suspect disease (5) . Given the low rates of critical illness due to COVID-19, this process will likely exert more impact on day-to-day processes in PICUs than sick patients with confirmed infection. Paediatric Intensive Care Society UK: PICS Guidance on Management of Critically Ill Children With COVID-19 Infection doi = 10.1097/pcc.0000000000002376 id = cord-252557-f89m6xv5 author = Ong, John title = Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard date = 2020-04-02 keywords = COVID-19; SARS summary = title: Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Prevention of nosocomial SARS-CoV-2 transmission in endoscopy: international recommendations and the need for a gold standard Over 3000 healthcare workers (HCW) in China are suspected of having coronavirus disease 2019 (COVID-19) and over 1700 tested positive. PPE recommendation (general staff): ► All patients to be offered surgical face masks Contingency plan for high-risk patients detected in endoscopy: ► Not stated. PPE recommendation (general staff): ► None stated Contingency plan for high-risk patients detected in endoscopy: ► Not stated. 4 Patient screening undoubtedly is the foremost step at preventing nosocomial transmission; timely detection allows postponement of non-urgent procedures until the infection has resolved, significantly reducing transmission risk to patients and staff. Detecting ''false negatives'' that slip through processes allows for the identification of HCWs and patients with infection risk after exposure to asymptomatic or subclinical carriers in the viral incubation period at the time of endoscopy. doi = 10.1136/gutjnl-2020-321154 id = cord-255997-oer5lxxr author = Onodi, Fanny title = SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date = 2020-07-10 keywords = CoV-2; Fig; IFN; SARS summary = Here, we have studied the interaction of isolated primary SARS-CoV-2 viral strains with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. Importantly, all major aspects of SARS-CoV-2-induced pDC activation were inhibited by hydroxychloroquine, including P2and P3-pDC differentiation, the expression of maturation markers, and the production of interferon-α and inflammatory cytokines. Interestingly, pDC responded to SARS-CoV-2 by a complete activation program, including diversification into effector subsets, production of type I and type III IFN, as well as inflammatory cytokines. We also showed that hydroxychloroquine, an antimalarial drug proposed for treatment of COVID-19 patients (Das et al., 2020; Mahévas et al., 2020) , inhibits SARS-CoV-2-induced pDC activation and IFN production in a dose-dependent manner. Following 24 hours of culture, we found that HCQ inhibited pDC diversification in response to SARS-CoV-2, which is similar to the decrease observed with Flu, used as a positive control ( Fig 4A) . doi = 10.1101/2020.07.10.197343 id = cord-315283-xwan2t1u author = Ooi, Setthasorn Zhi Yang title = Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching date = 2020-09-15 keywords = SARS summary = title: Impact of SARS-CoV-2 virus pandemic on the future of cadaveric dissection anatomical teaching We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. We explore the implications of this on the future of cadaveric dissections in anatomy teaching amidst the SARS-CoV-2 virus pandemic. The Human Tissue Authority has also released a statement that medical schools in the UK (UK) are not allowed to receive body donations due to the SARS-CoV-2 virus outbreak [3] . In the upcoming academic years, incoming students of medical schools who practice cadaveric dissection teaching will miss out on the opportunity to learn anatomy through dissections. This letter aims to explore the implications of the cancellation of cadaveric dissection in anatomy teaching as a result of the SARS-CoV-2 virus pandemic. What does this mean for medical students at schools who traditionally teach anatomy through cadaveric dissections? doi = 10.1080/10872981.2020.1823089 id = cord-317971-kuwargnp author = Opatz, Till title = Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date = 2020-05-08 keywords = SARS; drug; virus summary = [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. doi = 10.1002/anie.202004721 id = cord-346153-9162w7il author = Openshaw, P J title = Crossing barriers: infections of the lung and the gut date = 2008-12-24 keywords = HIV; SARS summary = Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. However, the coronavirus copy number in some studies showed an increase between day 5 and day 10, so that maximal infectivity followed the fever, 7 leading perhaps to a false sense of security amongst those caring for SARS patients. e reason for these interactions are incompletely understood, but intriguing recent study show that in uenza and respiratory syndrome virus are both capable of causing a persistent inhibition of the innate response to bacterial superinfection, and therefore to increased bacterial replication and disease. Highly pathogenic strains of in uenza also cause intense systemic symptoms, sometimes associated with gastrointestinal disease. Microbial translocation is a cause of systemic immune activation in chronic HIV infection doi = 10.1038/mi.2008.79 id = cord-283824-c7y9zf7o author = Opitz, Sven title = Regulating epidemic space: the nomos of global circulation date = 2015-02-20 keywords = Foucault; Health; IHR; International; SARS; body; global summary = The first concerns the referent object of governmental practice: the regulatory effort to secure global public health does not focus on human life so much as it does on post-human materialities of global traffic. Most importantly, the key passages of the IHR read like a clear-cut manifestation of the liberal government of circulation: ''The purpose and scope of these Regulations are to prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which avoid unnecessary interference with international traffic and trade.'' (IHR, Article 2) The mobility of disease and the mobility of goods and people are conjoined in this problem space. These bodies of transmission belong to a governmental vision that pictures the world as a space of universal traffic and that focuses on routes and material means of global circulation. doi = 10.1057/jird.2014.30 id = cord-304232-c0cpx2q3 author = Opriessnig, Tanja title = Update on possible animal sources for COVID‐19 in humans date = 2020-06-17 keywords = SARS summary = 7 In support of these early results, an ongoing study conducted at the Friedrich Loeffler Institute in Germany further confirmed that pigs and chickens are not susceptible to intranasal infection with SARS-CoV-2 (https://prome dmail.org/prome d-post/?id=7196506). 7 Natural infection, as evidenced by the presence of antibodies, SARS-CoV-2 RNA or both, has been identified in selected dogs in close contact with COVID-19 patients (Table 3) . A recent French study, which investigated nine cats and 12 dogs in close contact with a cluster of COVID-19 patients, was unable to detect evidence of SARS-CoV-2 infection in any of the animals. Moreover, animal-to-human SARS-CoV-2 infection as well as natural animal-to-animal transmission has yet to be confirmed and none of the species considered to be susceptible to the virus at this point are presently used for xenotransplantation. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 doi = 10.1111/xen.12621 id = cord-337789-pabaoiqs author = Oprinca, George-Călin title = Postmortem examination of three SARS-CoV-2-positive autopsies including histopathologic and immunohistochemical analysis date = 2020-08-27 keywords = SARS; case; covid-19; lung summary = This paper describes three autopsy cases with postmortem diagnosis of SARS-CoV-2 infection, with detailed macroscopic examination as well as advanced microscopic studies of organ tissues collected using hematoxylin-eosin stains and immunohistochemical markers. Microscopic evaluation revealed viral cytopathic effect of type II pneumocytes with a couple of cells that presented cytoplasmic and nuclear inclusions and who tend to form clusters mimicking multinucleated giant cells. This paper describes three autopsy cases with unknown cause of death, with full macroscopic examination as well as histopathologic and immunohistochemical analysis of collected organ tissues, including the lung from which reverse transcription polymerase chain reaction (rt-PCR) tests were made to determine SARS-CoV-2 infection. Microscopic examination of the pulmonary tissue revealed large areas of alveolar damage with destruction of the alveolar wall lining and intra-alveolar septa, marked vascular congestion, accompanied by intra-alveolar hemorrhage. doi = 10.1007/s00414-020-02406-w id = cord-338351-y1t9emu1 author = Ora, Josuel title = Does bronchoscopy help the diagnosis in Covid-19 infection? date = 2020-06-11 keywords = SARS summary = The diagnosis of COVID-19 is mainly based on typical symptoms, history of exposure to an infected person and bilateral involvement on chest radiographs, and it is confirmed by a positive nucleic acid test for SARS-CoV-2 from numerous types of specimens including Oropharyngeal (OP) and nasopharyngeal (NP) swabs, anal swabs, stool, urine and bronchoalveoalr lavage fluid (BALF) 1,2 . Here we report our experience from a COVID-19 hospital in Rome, Italy, where patients with typical symptoms of the disease, suggestive CT scans and three NP/OP negative swabs performed on consecutive days and IgG and IgM serology negative for SARS-CoV-2 underwent bronchoscopy with BAL to define the diagnostic issue. In conclusion, our findings demonstrate that three negative swabs along with negative antibodies, despite a suggestive CT scan, can safely rule out the SARS-CoV-2 infection in suspected patients, hence to proceed in alternative diagnosis process. doi = 10.1183/13993003.01619-2020 id = cord-318069-logh6rnu author = Ordás, Carlos M. title = Concurrent tonic pupil and trochlear nerve palsy in COVID-19 date = 2020-09-10 keywords = SARS; pupil summary = We report a case of concurrent tonic pupil and trochlear nerve palsy in this context. A 62-year-old man reported a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. Clinical exam showed a right trochlear nerve palsy and a left mydriatic pupil. This is the first case reporting Adie''s pupil as a postinfectious manifestation of COVID-19. Here, we report a case of a fourth cranial mononeuropathy coexisting with a contralateral tonic pupil developing 2 weeks after a SARS-CoV-2 infection. A 62-year-old man with an antecedent of hypertension attended our hospital reporting a 5-day history of binocular vertical diplopia and blurred vision in his left eye, noticing that his left pupil was dilated. In conclusion, we report an exceptional case of trochlear mononeuropathy and tonic pupil occurring shortly after a SARS-CoV-2 infection, with a presumable immunemediated mechanism. doi = 10.1007/s13365-020-00909-1 id = cord-292041-a65kfw80 author = Orienti, Isabella title = Pulmonary Delivery of Fenretinide: A Possible Adjuvant Treatment in COVID-19 date = 2020-05-27 keywords = COVID-19; Fenretinide; MERS; SARS; drug summary = At present, there is no vaccine or effective standard treatment for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (or coronavirus disease-19 (COVID-19)), which frequently leads to lethal pulmonary inflammatory responses. Therefore, due to its poly-pharmacology, fenretinide administration by pulmonary formulations may be expected to be protective against acute lung injury (ALI)/ acute respiratory distress syndrome (ARDS) caused by SARS-CoV infection and could represent a useful tool in a multimodal therapy aimed at establishing a rapid anti-inflammatory and antiviral effect. Pulmonary delivery of fenretinide could be a valuable tool in COVID-19 due to the possibility of obtaining a very high drug concentration in the airway and alveolar epithelia, thus triggering a rapid onset of local anti-inflammatory response. Moreover, the pulmonary administration of fenretinide, in combination with the drugs that are currently used in SARS-CoV-2 infection, could represent a new, effective tool in COVID-19 treatment. doi = 10.3390/ijms21113812 id = cord-340627-xyvzgkxl author = Ornaghi, Sara title = Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date = 2020-09-15 keywords = PCR; SARS summary = title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening doi = 10.1371/journal.pone.0239173 id = cord-285603-f4572w5m author = Ortega, Joseph T. title = Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date = 2020-06-24 keywords = HIV; SARS; drug; protease summary = In order to gain a deeper understanding if the pharmacokinetic parameters of the SARS-CoV2 protease inhibitors could be related to positive outcomes in the therapy, we analyzed the ADME parameters of famotidine and compared with several known antiviral drugs such as ribavirin, lopinavir, and nafamostat, which were evaluated against SARS-CoV2. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Altogether, in this study, we showed that famotidine could be used as an antiviral agent against SARS-CoV2, targeting proteases involved in the virus replication, mostly the main protease, as well as the viral PLpro and human host Tmprss2. doi = 10.3390/biom10060954 id = cord-318316-9unfl966 author = Ortega, Joseph T. title = Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies date = 2020-10-23 keywords = COVID-19; CoV-2; SARS summary = SUMMARY: This review focused on the basic principles of virology and pharmacology to understand the importance of early stages of virus-cell interaction as therapeutic targets and other main processes vital for SARS-CoV-2 replication. Furthermore, we focused on describing the main targets associated with SARS-CoV-2 antiviral therapy and the rationale of drug combinations for efficiently suppressing viral replication. Another early target evaluated against SARS-CoV-2 is a cellular protease related to the priming of the spike protein (S), which exposes the fusion motive and allows the release of viral RNA into the cytosol. HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; ORF, open reading frame. Favipiravir, another antiviral agent with broad activity against other RNA viruses by inhibiting the RdRp, halting viral replication, was evaluated against SARS-CoV-2, showing effects in vitro and in vivo [43] [44] [45] . doi = 10.1159/000512141 id = cord-294692-qfz6a1kc author = Ortega, Karem L. title = SARS-CoV-2 and dentistry date = 2020-06-05 keywords = SARS summary = The identification that the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a virus transmitted through airways or by direct contact with the mucosas [2] has prompted the dental community to become alert. They concluded that human coronavirus on inanimate surfaces could be inactivated by using ethanol (62-71%), hydrogen peroxide (0.5%) or sodium hypochlorite (0.1%) for 1 min, whereas other substances such as benzalkonium chloride (0.05% and 0.2%) and chlorhexidine digluconate (0.02%) were less effective. The authors also pointed out that although no study had tested the virucidal capacity of those agents against SARS-CoV-2, they expected a similar effect against this virus [5] . However, the suggestion to use mouthwash with 1% hydrogen peroxide or 0.2% povidone in order to decrease the viral load in saliva, based on the idea that SARS-CoV-2 would be vulnerable to oxidation, does not seem to be based on scientific evidence to date. doi = 10.1007/s00784-020-03381-7 id = cord-259668-nwezszhj author = Ortiz, Alberto title = Complement and protection from tissue injury in COVID-19 date = 2020-10-04 keywords = COVID-19; SARS; complement summary = Finally, preclinical studies in endotoxaemia, another hyperinflammation syndrome characterized by lung and kidney injury, suggest that cilastatin, an inexpensive drug already in clinical use, may provide tissue protection against hyperinflammation in COVID-19. In any case, this report suggests that assessing complement peptides may eventually contribute to define clusters of COVID-19 patients, as has been done for C3 glomerulopathies/immune complex-mediated membranoproliferative glomerulonephritis [11, 12] . In non-controlled case series and case reports, relatively positive results have been reported for the anti-C5 monoclonal antibody eculizumab, for C3 inhibitor AMY-101, for the mannan-binding lectin-associated serine protease 2 blocker narsoplimab (OMS721), for aliskiren and for nafamostat mesylate, a US Food and Drug Administration-approved anticoagulant agent that has broad-spectrum serine protease inhibitory activity, including for C1 esterase [2, [19] [20] [21] [22] [23] [24] [25] [26] . [3] emphasize, the fact that the SARS-CoV-2 cellular receptor ACE2 is expressed in lipid rafts may provide two mechanisms by which cilastatin may protect from severe COVID-19: (i) stabilizing ACE2 at the cell surface lipid rafts and preventing virus/ACE2 internalization and (ii) preventing hyperinflammation-induced tissue injury as observed in rat endotoxemia. doi = 10.1093/ckj/sfaa196 id = cord-286683-mettlmhz author = Ortiz-Prado, Esteban title = Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date = 2020-05-30 keywords = COVID-19; China; CoV-2; Coronavirus; MERS; SARS; Wuhan; infection; patient; severe summary = Interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in SARS [59] and MERS diseases [60] were also reported in the early study of 41 patients with COVID-19 in Wuhan [41] . A recently published case report of a patient with mild-to-moderate COVID-19 revealed the presence of an increased activated CD4+ T cells and CD8+ T cells, antibody-secreting cells (ASCs), follicular helper T cells (TFH cells), and anti-SARS-CoV-2 IgM and IgG antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [82] . Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: Retrospective case series doi = 10.1016/j.diagmicrobio.2020.115094 id = cord-312918-iof45k1r author = Ortolani, Claudio title = Hydroxychloroquine and dexamethasone in COVID-19: who won and who lost? date = 2020-09-09 keywords = COVID-19; Health; SARS; patient summary = Recently, four large Randomized Controlled Trials (RCTs) have been performed in record time delivering reliable data: (1) the National Institutes of Health (NIH) RCT included 60 hospitals participating all over the world and showed the efficacy of remdesivir in reducing the recovery time in hospitalized adults with COVID-19 pneumonia; (2) three large RCTs already completed, for hydroxychloroquine, dexamethasone and Lopinavir and Ritonavir respectively. In 2019, at the beginning of the SARS-CoV-2 pandemic, at least 4 anti-inflammatory and antiviral drugs were available and in use, with possible efficacy for COVID-19: hydroxychloroquine, corticosteroids, remdesivir and Lopinavir / Ritonavir. Remark 1 cited a number of systematic reviews, which however had selected only observational clinical studies that addressed the efficacy and side effects of the corticosteroid treatment of viral pneumonia from SARS, H1N1 influenza virus and MERS virus, but not from SARS-CoV-2 virus [31] [32] [33] [34] . doi = 10.1186/s12948-020-00132-7 id = cord-339968-s1kmipir author = Osier, Faith title = The global response to the COVID-19 pandemic: how have immunology societies contributed? date = 2020-09-10 keywords = AAI; COVID-19; Immunology; SARS; Society; pandemic summary = Y.; Fraser, John; Lambrecht, Bart N.; Romano, Marta; Gazzinelli, Ricardo T.; Bortoluci, Karina R.; Zamboni, Dario S.; Akbar, Arne N.; Evans, Jennie; Brown, Doug E.; Patel, Kamala D.; Wu, Yuzhang; Perez, Ana B.; Pérez, Oliver; Kamradt, Thomas; Falk, Christine; Barda-Saad, Mira; Ariel, Amiram; Santoni, Angela; Annunziato, Francesco; Cassatella, Marco A.; Kiyono, Hiroshi; Chereshnev, Valeriy; Dieye, Alioune; Mbow, Moustapha; Mbengue, Babacar; Niang, Maguette D. Efforts included writing to President Donald Trump and Congressional leaders urging that they heed the advice of scientific/public health leaders, including AAI member Anthony Fauci 3 ; writing to National Institutes of Health (NIH) Director Francis Collins requesting justification for terminating an NIH-funded grant focusing on understanding the risk of bat coronavirus emergence 4 ; advocating supplemental funding for federal science agencies, including the NIH, for pandemic-related research losses and additional trainee support; and issuing a statement opposing actions taken by the Trump administration that will damage international scientific collaboration 5 . doi = 10.1038/s41577-020-00428-4 id = cord-262119-s6hc7fxs author = Ostaszewski, Marek title = COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date = 2020-10-27 keywords = ACE2; COVID-19; CoV-2; Coronavirus; Disease; Map; SARS; SBML; cell; pathway; protein summary = title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms The molecular pathophysiology that links SARS-CoV-2 infection to the clinical manifestations and course of COVID-19 is complex and spans multiple biological pathways, cell types and organs [2, 3] . With this goal in mind, we initiated a collaborative effort involving over 230 biocurators, domain experts, modelers and data analysts from 120 institutions in 30 countries to develop the COVID-19 Disease Map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [4] . The COVID-19 Disease Map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and Boolean, kinetic or multiscale simulations. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms doi = 10.1101/2020.10.26.356014 id = cord-337339-0vkigjv2 author = Osterrieder, Nikolaus title = Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date = 2020-07-20 keywords = Germany; RNA; SARS; syrian summary = We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Moreover, transgenic mice expressing human ACE2 represent a lethal SARS-CoV-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . In contrast to SARS-CoV-2 titers, histopathological changes differed markedly between young and aged Syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. Based on the data presented here, we propose that comparative preclinical assessments of SARS-CoV-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. doi = 10.3390/v12070779 id = cord-268970-uz7q6z2f author = Ott, Isabel M. title = Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date = 2020-08-04 keywords = RNA; SARS summary = Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes. Following RNA extraction 9 and RT-qPCR 10 testing for SARS-CoV-2 on the day of saliva collection 2 , the remaining sample volumes (n=20) were aliquoted and stored at -80°C, room temperature (recorded as ~19°C) and 30°C. Moreover, SARS-CoV-2 RNA remained relatively stable in saliva samples left for up to 25 days at room temperature (~19°C; Ct increase of 0.027, 95% CI: -0.019, 0.071) ( Figure 1B) . doi = 10.1101/2020.08.03.20165233 id = cord-253671-g3ypisig author = Otte, Martin Sylvester title = Riechstörungen bei COVID-19 – aktueller Wissensstand date = 2020-06-10 keywords = Patienten; Riechstörungen; SARS; Studien summary = Bislang existiert keine Studie, die mittels validierter Riechtests die tatsächliche Prävalenz von Riechstörungen bei COVID-19-Patienten zu ermitteln versucht hat. In einer retrospektiven Datenauswertung aus San Diego (USA) zeigte sich, dass Riech-und Schmeckstörungen vor allem von SARS-CoV-2-positiven Personen angegeben werden, deren Krankheit eher milde bis moderat verläuft und die ambulant mittels häuslicher Quarantäne behandelt werden können. Dies konnte auch in einer Fragebogenstudie aus Spanien bestätigt werden, in der 35,3 % von 79 Patienten mit PCR-bestätigter COVID-19-Erkrankung die Riechstörung als initiales Symptom angaben. Dies könnte jedoch auch der Tatsache geschuldet sein, dass es sich wie bei den meisten Studien zum Thema bislang um fragebogenbasierte Erhebungen handelt, die vor allem von Patienten mit geringerer Symptomatik beantwortet werden. Nachdem anfängliche Berichte über die SARS-CoV-2-Infektion Riech-und Schmeckstörungen kaum erwähnten, haben mittlerweile mehrere Studien, insbesondere aus Europa und den USA, Wahrnehmungsschwelle, Erkennungsschwelle diese Symptome als Merkmal von COVID-19 bestätigt. doi = 10.1055/a-1183-4835 id = cord-323622-229kub7c author = Ou, Xueting title = A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens date = 2020-04-16 keywords = SARS summary = title: A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens To the Editor Since December, 2019, corona virus disease 2019 (COVID-19) caused by SARS-CoV-2, has spread to the majority of countries worldwide [1, 2] . Here, we reported the clinical characteristics of a severe case with co-infection of SARS-CoV-2 and common respiratory pathogens. However, sputum samples collected on the same day were positive for SARS-CoV-2 by NGS. The patient was diagnosed as severe COVID-19, and was transferred to the First Affiliated Hospital of Guangzhou Medical University for isolation and treatment where are designed to treat severe COVID-19 cases by local health authorities. In the present study, the cause that resulted in severe condition of the patient could be the co-infection of SARS-CoV-2, Haemophilus parainfluenzae and Moraxella catarrhalis. Older patients, having diabetes, hypertension are causes of severe COVID-19 cases [3, 4] . doi = 10.1016/j.tmaid.2020.101672 id = cord-351002-msjurww1 author = Ouanes, Y. title = Does BCG protect against SARS-CoV-2 infection ?: elements of proof. date = 2020-05-06 keywords = BCG; SARS summary = Results : Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). Countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). For countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047). Based on these observations, we hypothesized that countries which have an early start of universal BCG vaccination policy would have a reduced morbidity and mortality attributed to SARS-CoV-2 infection. Or results revealed that countries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection. doi = 10.1101/2020.05.01.20087437 id = cord-301771-43fl2gwp author = Ouassou, Hayat title = The Pathogenesis of Coronavirus Disease 2019 (COVID-19): Evaluation and Prevention date = 2020-07-10 keywords = COVID-19; China; Health; SARS summary = The causative virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the World Health Organization (WHO) named the new epidemic disease Coronavirus Disease (COVID-19). Several coronaviruses can infect humans, like the globally endemic human coronaviruses HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43 that tend to cause mild respiratory disease, and the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) that have a higher case fatality rate [2] . After the diagnosis of SARS-Cov2 infection was made, the prevention and quarantine are considered as the most way to stop the fast spreading of the virus, because there is no effective vaccine, drugs, or antiviral to prevent and treat this disease despite the great efforts made by the scientists and researchers around the world to develop vaccines and treatments of coronavirus. doi = 10.1155/2020/1357983 id = cord-296259-4kdblf4z author = Oudit, Gavin Y title = Plasma angiotensin-converting enzyme 2: novel biomarker in heart failure with implications for COVID-19 date = 2020-05-14 keywords = ACE2; SARS summary = This editorial refers to ''Circulating plasma concentrations of ACE2 in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors'' † , by I.E. Sama et al., on page 1810. Angiotensin-converting enzyme 2 (ACE2) has emerged as the negative regulator of the renin-angiotensin system (RAS) and was more recently identified as the SARS-CoV-2 receptor responsible for the current COVID-19 pandemic. [3] [4] [5] Direct clinical evidence came from SARS and the current COVID-19 pandemic, where there is down-regulation of tissue ACE2 through endocytosis and proteolytic processing which leads to a corresponding increase in plasma angiotensin II (Ang II) levels as seen in COVID-19 patients (linearly correlated with SARS-CoV-2 viral load), thus providing a direct link between the tissue and systemic RAS. obtained in heart failure patients in the pre-COVID-19 period offer supporting evidence to continue ACE inhibitors or ARBs in patients at risk for SARS-CoV-2 infection. doi = 10.1093/eurheartj/ehaa414 id = cord-330315-upcf15q5 author = Oudshoorn, Diede title = Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication date = 2017-11-21 keywords = DMV; Fig; MERS; SARS; nsp3 summary = Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. To study whether the transmembrane nsp''s of MERS-CoV are able to induce DMV formation, we expressed nsp3 and nsp4 from a CAG promoter (43) either by cotransfection of cells with plasmids encoding individual proteins or by transfection with a single plasmid encoding a self-cleaving nsp3-4 polyprotein fragment ( Fig. 1A ; Table S1 ). The observation of maze-like bodies and circular double-membrane profiles, which were interpreted to represent tubular structures, led these authors to conclude that coexpression of SARS-CoV nsp3 and nsp4 was not sufficient for DMV formation. doi = 10.1128/mbio.01658-17 id = cord-302382-eifh95zm author = Owji, Hajar title = Immunotherapeutic approaches to curtail COVID-19 date = 2020-08-21 keywords = ACE2; COVID-19; CoV-2; SARS; antibody; cell; immune; patient summary = Active immunization through vaccines, interferon administration, passive immunotherapy by convalescent plasma or synthesized monoclonal and polyclonal antibodies, as well as immunomodulatory drugs, are different immunotherapeutic approaches that will be mentioned in this review. Nevertheless, the similarity of severe respiratory failure induced by SARS-CoV-2 to acute respiratory distress syndrome (ARDS) and the deterioration of patients'' conditions in around a week following the first symptoms implicate the role of immunity dysregulation in COVID-19 profile [6] . Subsequently, plasma transfusion was recommended as a safe and effective way for the prevention or treatment of the Ebola virus in 2014 and also several other severe viral infections, including MERS, SARS-CoV, and avian influenza A [35, 36] . CP extracted from the SARS-COV-2 survivors may be a promising approach for the protection of COVID-19 patients with antibody deficiency before the development of an effective vaccine [44] . doi = 10.1016/j.intimp.2020.106924 id = cord-328395-2cakgmsj author = Oxford, Alexandra E. title = Endothelial Cell Contributions to COVID-19 date = 2020-09-25 keywords = ACE2; COVID-19; CoV-2; SARS; cell; endothelial summary = Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. This review will focus on the concept of endothelial cell infection and dysfunction as an active driver of COVID-19, which begins as a respiratory illness, with vascular pathology contributing significantly to the most negative patient outcomes. Endothelial cell infection that proceeds via ACE2 shows how SARS-CoV-2 can replicate into a wide range of cells, which may explain some of the clinical symptoms found in COVID-19 patients. Thus far, we have discussed the viral mechanisms of SARS-CoV-2 and resultant COVID-19 sequelae as they relate to endotheliitis and endothelial cell infection mediated by viral spike protein-ACE2 interaction. The successful use of anti-interleukin drugs to treat the inflammatory symptoms seen in severe COVID-19 would have marked effects on endothelial pathology as these cells are highly responsive to cytokine signaling [59] . doi = 10.3390/pathogens9100785 id = cord-268340-xwj8ge5t author = Ozaki, Masayuki title = Reducing Aerosol Generation During Ventilator Weaning in a Coronavirus Disease 2019 Patient Using a Supraglottic Airway: A Case Report date = 2020-05-21 keywords = SARS summary = Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. Substituting the endotracheal tube for a supraglottic airway (SGA), which is less stimulating to the trachea, can reduce coughing with weaning from mechanical ventilation and extubation. We conducted a weaning procedure from mechanical ventilation in advance of emergence from sedation in a patient with COVID-19 by exchanging the tracheal tube to a supraglottic airway (SGA), which is associated with fewer coughs. Reducing patients'' coughing cases-anesthesia-analgesia.org a & a pRaCtICe and avoiding this aerosol-generating procedure during tracheal extubation may reduce occupational infection. To reduce the risk of occupational infection with SARS-CoV-2 at the time of weaning from mechanical ventilation, we propose replacing the tracheal tube with an SGA such as i-gel before emergence from sedation to reduce environmental distribution of the virus. doi = 10.1213/xaa.0000000000001247 id = cord-268939-ws74xprt author = Ozoner, Baris title = Neurosurgery Practice During Coronavirus Disease 2019 (COVID-19) Pandemic date = 2020-05-28 keywords = COVID-19; China; Coronavirus; SARS; patient summary = The increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. Operations of COVID-19 positive patients, and emergency cases, where screening can not be obtained, should be performed following level 3 protective measures. [5] [6] [7] In neurosurgery practice, intensive modifications were required in surgical scheduling, administration of inpatient and outpatient clinics, management of emergency cases, and even academic & educational activities. 26 A recent study from Wuhan City, China reported that some severe COVID-19 patients developed neurologic manifestations, such as acute cerebrovascular diseases (5.7%), and impaired consciousness (14.8%). 76, 80 Also, a patient with a mass lesion in the sellar region that underwent endonasal endoscopic surgery in Neurosurgery Department, Tongji Medical College, Wuhan City, China was diagnosed with COVID-19 after surgery, and disease was confirmed in 14 healthcare professionals in the same clinic afterwards. doi = 10.1016/j.wneu.2020.05.195 id = cord-294441-nehorqhi author = O’Brien, Stephen J. title = Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS date = 2006-08-31 keywords = AIDS; FIV; SARS summary = A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach. Representing carnivores, the cat family Felidae offers numerous examples of reduced genetic var-iation in natural populations common to endangered species including Asian lion (Panthera leo persica) (Gilbert et al., 1991) , cheetah (Acinonyx jubatus) (Menotti-Raymond and O''Brien, 1993) , tiger (P. Our ongoing research into host-pathogen interactions in the cat family Felidae offers additional insights on how the application of molecular genomic technologies to non-human animal species not traditionally studied in research laboratories holds real promise in conservation. doi = 10.1016/j.biocon.2006.05.001 id = cord-282965-xguotf4m author = O’Callaghan-Gordo, Cristina title = COVID-19: The Disease of the Anthropocene date = 2020-05-15 keywords = SARS; human summary = Since the emergence of AIDS, many other epidemic infectious diseases, such as Ebola, SARS and MERS to name the most recent, have been caused by the transmission of viruses from wild animal species to humans as shown in 2008 by Jones et al. The complete causal sequences and impacts of these ecological changes are still poorly understood, but frequently these emerging zoonosis appear and spread in circumstances that denote the effects of an economic and commercial practices that destroys natural habitats and animal populations, including those of humans living there, in the absence of effective protection and regulatory policies. The destruction of natural habitats and the extinction of species, the poorly regulated capture, marketing and consumption of non-human animals, the influence of lobbies to nullify or delay measures to protect natural and social systems, the limitation of current scientific knowledge and the contempt by governments and companies of the available evidence, have all worked in an orchestrated sequence to facilitate the current COVID-19 pandemic. doi = 10.1016/j.envres.2020.109683 id = cord-328262-hw8swbt5 author = O’Neill, Luke A. J. title = BCG-induced trained immunity: can it offer protection against COVID-19? date = 2020-05-11 keywords = BCG; SARS summary = Bacillus Calmette–Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. This effect was mediated by peritoneal macrophages 10 Bacillus Calmette-Guérin (BCG) vaccination has been reported to decrease susceptibility to respiratory tract infections, an effect proposed to be mediated by the general long-term boosting of innate immune mechanisms, also termed trained immunity. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. Here, we discuss the non-specific beneficial effects of BCG against viral infections and whether this vaccine may afford protection to COVID-19. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity doi = 10.1038/s41577-020-0337-y id = cord-338203-le5lbw5y author = O’Reilly, GM title = Epidemiology and clinical features of emergency department patients with suspected COVID‐19: Results from the first month of the COVED Quality Improvement Project (COVED‐2). date = 2020-06-13 keywords = COVID-19; SARS summary = METHODS: The COVID‐19 Emergency Department (COVED) Project is an ongoing prospective cohort study that includes all adult patients presenting to The Alfred Hospital ED who undergo testing for SARS‐CoV‐2. As cases accumulate, the COVED Project aims to determine and report the clinical and epidemiological predictors of a positive SARS-CoV-2 test result and the requirement for intensive respiratory support among patients presenting to the ED with suspected COVID-19. In the first full month of the COVED Project, the daily number and proportion of patients with a positive SARS-CoV-2 test remained relatively low, but the rate of patients presenting to the ED with suspected COVID-19 increased significantly. The low incidence of SARS-CoV-2 positive results over the first full month of the COVED Project has precluded valid inferential analyses regarding how COVID-19 patients differ in terms of their demographic features, clinical presentation, severity risk factors, need for intensive respiratory support and key outcomes. doi = 10.1111/1742-6723.13573 id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 keywords = Nipah; SARS; human; infection; virus summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. doi = 10.1016/b978-0-12-809633-8.90273-5 id = cord-345841-pq5f82gf author = PATBERG, Elizabeth T. title = COVID-19 Infection and Placental Histopathology in Women Delivering at Term date = 2020-10-19 keywords = SARS; covid-19; fetal summary = Conclusions – Despite the fact that all neonates born to mothers with COVID-19 were negative for SARS-CoV-2 by PCR, we found that COVID-19 in term patients admitted to Labor and Delivery is associated with increased rates of placental histopathologic abnormalities, particularly fetal vascular malperfusion and villitis of unknown etiology. In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . In a recent structured review including twenty studies with histopathology findings in 275 third trimester placentas following maternal SARS-CoV-2 infection, evidence of fetal vascular 276 malperfusion was reported in 35% of cases, which is similar to the rate observed in our cohort 277 (32.5%) 24 . doi = 10.1016/j.ajog.2020.10.020 id = cord-339772-q814d6l7 author = Pach, Szymon title = ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date = 2020-05-14 keywords = ACE2; SARS summary = To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Moreover, we compared ACE2 sequences from rodents (mouse, rat, hamster, and red squirrel) to sample additional binding pockets in the ACE2-RBD interface and predict susceptibility to SARS-CoV-2 of the red squirrel (Sciurus vulgaris). To compare three-dimensional binding interfaces of animal ACE2-RBD complexes, we developed homology models of dog, cat, ferret, hamster, mouse, rat, and red squirrel proteins. Both outlier residues are located on flexible loops of ACE2 distal to the S binding site and represent polymorphic mutations from glycine in human crystal structure to serine in homology models. Based on known susceptibility of animal species to SARS-CoV-2 and the comparison of MD trajectories, we were able to develop models for prediction of RBD binding to ACE2. doi = 10.1101/2020.05.14.092767 id = cord-268071-ow2aijmj author = Pachetti, Maria title = Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date = 2020-04-22 keywords = RNA; SARS; mutation summary = Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. Naturally occurring mutations in critical residues for drug efficacy can lead to drug resistance phenomena, with a significant loss in the binding affinity of these molecules to the RdRp. We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. Among all mutation sites analyzed, RdRp mutant is particularly interesting given that the enzyme is directly involved in viral replication and its fidelity determines the mutagenic capabilities of SARS-CoV-2. In the present work we have compared the SARS-CoV-2 reference genome to those exported from the GISAID database with the aim of gaining important insights into virus mutations, their occurrence over time and within different geographic areas. doi = 10.1186/s12967-020-02344-6 id = cord-304724-luql6159 author = Paderno, Alberto title = Smell and taste alterations in Covid‐19: a cross‐sectional analysis of different cohorts date = 2020-05-14 keywords = SARS summary = The study aims to estimate the different characteristics of OD and GD in hospitalized patients and home-quarantined subjects with a nasal/pharyngeal swab positive for SARS-CoV-2 in an epidemic area. All subjects with positive nasal/pharyngeal swab for SARS-CoV-2 were home-quarantined or Patients were not informed about the specific study aim to minimize confirmation bias. The study describes a sample of more than 500 cases with confirmed SARS-CoV-2 infection, distinguishing between hospitalized patients and home-quarantined subjects. All cases with OD and GD reported an acute onset and a significant degree of dysfunction, without solid connection with other symptoms suggestive of upper airway infection (i.e., pharyngodynia and nasal congestion). # Patients affected by olfactory and gustatory dysfunction reported these complains as delayed symptom of presentation of the infection with SARS-CoV-2 in 231 (81.6%) and 264 (82.2%) cases, respectively. doi = 10.1002/alr.22610 id = cord-324288-qgxswltx author = Padhi, Sunali title = Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study date = 2020-09-14 keywords = SARS; indian; vitamin summary = title: Lower levels of vitamin D are associated with SARS-CoV-2 infection and mortality in the Indian population: an observational study In the present study, we hypothesized that vitamin D deficiency would be associated with the SARS-CoV-2 infection rate and mortality in the Indian population. Further, a recent report highlighted a higher chance of SARS-CoV-2 infected patients being admitted to an intensive care unit compared to those with insufficient or sufficient levels of vitamin D in the UK population [9] . Low plasma 25(OH) vitamin D level is associated with increased risk of COVID-19 infection: an Israeli population-based study Current Scenario of Prevalence of Vitamin D Deficiency in Ostensibly Healthy Indian Population: A Hospital Based Retrospective Study Serum Vitamin D Levels and Alopecia Areata-A Hospital Based Case-Control Study from North-India Low levels of serum Vitamin D in chronic periodontitis patients with type 2 diabetes mellitus: A hospital-based crosssectional clinical study doi = 10.1016/j.intimp.2020.107001 id = cord-291738-nak5357h author = Padoan, Andrea title = Clinical performances of an ELISA for SARS-CoV-2 antibody assay and correlation with neutralization activity date = 2020-08-18 keywords = SARS summary = Here we describe the clinical performances of an ELISA (Novalisa NovaTec Immunodiagnostica, Dietzenbach, Germany) for the detection of SARS-CoV-2 IgA, IgM and IgG and the comparison of results with the neutralization activity. A total of 171 leftover serum samples from 41 SARS-CoV-2 negative subjects (20 healthcare workers, 13 autoimmune patients, 8 pregnant women) and 130 COVID-19 patients (9 asymptomatic/mildly symptomatic recovered at home with supportive care and isolation, and 121 hospitalized, classified with moderate or severe disease following WHO interim guidance [5] ) were included in the study. As expected, when the time frame < 12 days was considered, the diagnostic sensitivity of the three assays was very limited and the best performances were found for IgA with a sensitivity equal to 65%, thus confirming our previously reported findings, as in most patients increased antibody levels should be detected only after 6-7 days post symptom onset (PSO) [7] [8] [9] . Evaluation of an ELISA for SARS-CoV-2 antibody testing: clinical performances and correlation with plaque reduction neutralization titer doi = 10.1016/j.cca.2020.08.024 id = cord-266923-hd1tjj6b author = Padroni, Marina title = Guillain-Barré syndrome following COVID-19: new infection, old complication? date = 2020-04-24 keywords = GBS; SARS summary = Taking together all these findings, the causal association between GBS and COVID-19 remains speculative, but more probable, given that GBS and Bickerstaff''s encephalitis have been already described as postinfectious complications of other coronavirus, sharing similarities with SARS-CoV-2 (Middle East respiratory syndrome, MERS-CoV) [11] . If our hypothesis will be confirmed in larger case series, neurologists and other clinicians should be aware of the important early recognition and treatment of the potential neuromuscular and autonomic worsening leading to cardio-respiratory failure in patients with GBS and mild or controlled pulmonary COVID-19 Notwithstanding the causative relationship remains unproved, we believe that our case description provide further evidence to the heterogenous and multi-systemic complications associated with SARS-CoV-2. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study Guillain-Barré syndrome associated with SARS CoV-2 infection: causality or coincidence Toscana virus associated with Guillain-Barré syndrome: a case-control study doi = 10.1007/s00415-020-09849-6 id = cord-355935-psnqrdo2 author = Paez, Antonio title = A Spatio‐Temporal Analysis of the Environmental Correlates of COVID‐19 Incidence in Spain date = 2020-06-08 keywords = COVID-19; SARS; SUR; Spain; effect; incidence; variable summary = Use of spatial Seemingly Unrelated Regressions (SUR) allows us to model the incidence of reported cases of the disease per 100,000 population as an interregional contagion process, in addition to a function of temperature, humidity, and sunshine. We adopt a population health approach, and report results from a spatio-temporal model of the incidence of COVID-19 in the coterminous provinces in Spain, one of the countries hardest hit by the pandemic. Higher incidence is associated with higher GDP per capita and presence of mass transit systems in the province; in contrast, population density and percentage of older adults display negative associations with incidence of COVID-19. The coefficients of the spatially lagged variable are estimated for each time period ρ t and identify the intensity and the sign of the contagion effect. Fig. 3 includes three maps that display the spatial variation of our control variables, namely GDP per capita, percentage of older adults in province, population density, and presence of mass transit systems. doi = 10.1111/gean.12241 id = cord-332312-od3vjuw5 author = Pagani, G. title = Seroprevalence of SARS-CoV-2 IgG significantly varies with age: results from a mass population screening (SARS-2-SCREEN-CdA). date = 2020-06-24 keywords = SARS summary = In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. In a mass screening involving 4174 out of about 4550 total inhabits, 29 significant age-related differences in anti SARS-CoV-2 IgG seroprevalence were found, with the 30 lowest prevalence in the youngest inhabitants. Results were reported in terms of 54 estimated probabilities of being positive to IgG test as a function of age, with respective 95% 55 confidence intervals. Estimates of probabilities of 64 being positive to IgG test, from a model including only age as independent variable, are reported in 65 susceptibility to the infection. In conclusion, our findings suggest that IgG seroprevalence for SARS-CoV-2 increases with 83 increasing age and these data suggest a lower susceptibility to infection in the lower age groups. doi = 10.1101/2020.06.24.20138875 id = cord-259471-lsdodl0a author = Pagliano, Pasquale title = Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date = 2020-03-24 keywords = SARS summary = In contrast, no similar effect on early phases of coronavirus infection has been reported for other drugs proposed for SARS-CoV-2 treatment, which are able to interfere only after cell infection, affecting protease cleavage (protease inhibitors) or viral genome replication (remdesivir or ribavirin). Hydroxychloroquine, the HIV protease inhibitors (particularly lopinavir), ribavirin, and remdesivir are the most promising drugs proposed for coronavirus disease 2019 (COVID-19) treatment, but currently no drug has been proposed for postexposure or preexposure prophylaxis for those accidently exposed to SARS-CoV-2 [6] . Hydroxychloroquine''s effectiveness profile, its ability to inhibit lung viral replication for a 10-day period after only a 5-day cycle of therapy, and the large amounts of knowledge in term of safety deriving from its use for malaria prophylaxis and rheumatologic diseases lead us to recommend its preexposure or postexposure use for those performing procedures at high risk of viral diffusion in patients with COVID-19 pneumonia. doi = 10.1093/cid/ciaa320 id = cord-355854-hksq8gy4 author = Pagliaro, Pasquale title = ACE/ACE2 Ratio: A Key Also in 2019 Coronavirus Disease (Covid-19)? date = 2020-06-18 keywords = ACE2; SARS; covid-19 summary = Therefore, we wonder whether the invasion by SARS-CoV-2 and the downregulation of ACE2 are jointly responsible for a high incidence of dramatic acute respiratory distress syndrome (ARDS), cardiovascular complications, and high lethality of Covid-19. Moreover, estrogen shifts the system toward the ACE2/Ang 1-7 formation and ACE2 activity is higher in female than that in the male serum (18) ; however, the worst and most lethal Covid-19 infections occur predominantly in males [the Italian ISS (https://www.epicentro.iss.it/coronavirus/ sars-cov-2-decessi-italia, accessed on April 26th 2020) reports that among 23,188 SARS-CoV-2 patients dying in Italy, women are 8,500 (36.7%)]. It has also been suggested that the increased concentration of ACE2 receptors in in the lungs of children may have a protective effect on severe clinical manifestations due to SARS-CoV-2 invasion (36) . ACE/ACE2 ratio is increased in many pathologies (especially dis-metabolisms and cardiovascular diseases) and conditions (obesity and aging) that exacerbate Covid-19 symptomatology and worsen outcomes. doi = 10.3389/fmed.2020.00335 id = cord-273083-xrydkiu4 author = Pahmeier, Felix title = A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date = 2020-09-01 keywords = SARS summary = Here, we describe the generation and characterization of a reporter system to visualize dengue virus and SARS-CoV-2 replication in live cells. The system is based on viral protease activity causing cleavage and nuclear translocation of an engineered fluorescent protein that is expressed in the infected cells. Here we describe a reporter system that takes advantage of virus-encoded proteases that are expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. In order to generate a reporter system that can specifically indicate virus infection, we 219 designed a construct expressing a GFP fusion protein that could selectively be cleaved 220 by viral proteases. However, since no fluorescent 304 protein coding sequence is incorporated into the construct, expression of the DENV 305 polyprotein cannot be followed by live cell imaging. doi = 10.1101/2020.08.31.276683 id = cord-252279-0gozdv43 author = Pal, Amit title = Hydroxychloroquine and Covid-19: A Cellular and Molecular Biology Based Update date = 2020-06-10 keywords = SARS; covid-19; hydroxychloroquine; patient summary = Without a therapeutic vaccine or specific antiviral drugs, and with a desperate attempt to find a cure against novel Corona Virus Disease 2019 (Covid-19) [1] , the limelight was shifted to hydoxychloroquine (derivative of chloroquine that has antimalarial, antiinflammatory, immunosuppressive and antiautophagy activities [2, 3] ; upon a tweet by US president Mr. Donald J. The main aim of this review is to discuss the mode of action of hydroxychloroquine at cellular and molecular levels, that potentially support the clinical efficacy and few adverse side effects observed in Covid-19 patients treated with hydroxychloroquine, which may further help in improving the clinical outcomes by modifying or altering the drug itself or its restricted use in certain individuals by enforcing strict inclusion and exclusion criteria. Due to its cellular and molecular effects as discussed in previous sections, quite a few clinical trials are studying the effectiveness and safety of hydroxychloroquine (also chloroquine) for Covid-19 (https://clinicaltrials.gov/ct2/ results?cond=%22wuhan?coronavirus%22). doi = 10.1007/s12291-020-00900-x id = cord-333041-69n2wwn3 author = Pal, Anandita title = Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection date = 2020-08-11 keywords = DHA; SARS; SPM; infection summary = Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Obesity is an independent risk factor for increased morbidity and mortality upon infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic. The SPM precursor 17-hydroxydocosahexaenoic acid (17-HDHA) increased antibody levels and improved survival upon pH1N1 influenza vaccination and infection in lean mice by promoting B cell differentiation toward the formation of CD138 + long-lived antibody secreting cells (18) . Taken together, these data suggest that the susceptibility of obese individuals to environmental lung diseases may drive an altered pulmonary immune response and a state of SPM deficiency that increases the morbidity and mortality to respiratory infections, including COVID-19. doi = 10.3389/fimmu.2020.01997 id = cord-281346-bjhdy8mg author = Palacios Cruz, M. title = COVID-19, a worldwide public health emergency() date = 2020-04-21 keywords = China; SARS; patient summary = This new species of coronavirus has been termed 2019-nCoV and has caused a considerable number of cases of infection and deaths in China and, to a growing degree, beyond China, becoming a worldwide public health emergency. 2019-nCoV has high homology to other pathogenic coronaviruses, such as those originating from bat-related zoonosis (SARS-CoV), which caused approximately 646 deaths in China at the start of the decade. 17 Moreover, a recently published study estimated that 95% of the cases of 2019-nCoV infections in Wuhan showed symptoms before the 12th of January 2020, 18,19 a fact that, combined with the virus'' incubation period, suggests a high possibility of the disease''s travelrelated propagation. According to the WHO, a suspected case involves a patient with severe acute respiratory infection (fever, cough, requiring hospitalization) and with no other etiology that completely explains the clinical presentation, as well as a history of travel or residence in China during the 14 days before symptom onset. doi = 10.1016/j.rceng.2020.03.001 id = cord-278370-fuu20ae7 author = Palao, M. title = Multiple Sclerosis following SARS-CoV-2 infection date = 2020-07-07 keywords = CoV-2; SARS summary = However, available information about demyelinating complications of the central nervous system (CNS) is limited with only one report of acute disseminated encephalomyelitis (ADEM) in a severe COVID-19 patient being published to date 5 and a single case of meningo-encephalitis 6 , the latter with the presence of SARS-CoV-2 in the cerebrospinal fluid (CSF) confirmed by PCR. As viral infections have been linked to the development of demyelinating diseases 7 it would be interesting to know if this relationship also exists in the case of SARS-CoV-2. We present a case of first presentation of demyelinating disease in the form of optic neuritis following SARS-CoV-2 infection. In our case, the patient presented symptoms attributed to COVID-19 infection (anosmia and dysgeusia) prior to the visual manifestations. In this case, SARS-CoV-2 may have acted as a precipitating factor rather than multiple sclerosis being a direct consequence of the infection. doi = 10.1016/j.msard.2020.102377 id = cord-268501-z4oztgi0 author = Palatnik-de-Sousa, Clarisa B. title = What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date = 2020-08-26 keywords = Chadox1; SARS; Sinovac; vaccine; virus summary = In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . doi = 10.3389/fimmu.2020.02173 id = cord-311029-x0lk4110 author = Palermo, Sara title = Covid-19 Pandemic: Maximizing Future Vaccination Treatments Considering Aging and Frailty date = 2020-09-18 keywords = COVID-19; SARS; age; elderly; frailty summary = For that reason, the Clinical Trials Regulation (EC) No. 536/2014 states that "in order to improve treatments available for vulnerable groups such as frail or older people, people suffering from multiple chronic conditions, and people affected by mental health disorders, medicinal products which are likely to be of significant clinical value should be fully and appropriately studied for their effects in these specific groups, including as regards requirements related to their specific characteristics and the protection of the health and well-being of subjects belonging to these groups." Indeed, EMA develops scientific guidelines to help medicine developers address the specific requirements of older people in their medicine development programs, including in the design and conduct of clinical trials. EMA disclosed a reflection paper on "Physical frailty: instruments for baseline characterization of older populations in clinical trials" (7), actively recognizing the importance of considering the various types of aging when experimenting and developing new pharmacological treatments. doi = 10.3389/fmed.2020.558835 id = cord-350622-8tgxdbyi author = Palit, Partha title = Phytopharmaceuticals mediated Furin and TMPRSS2 receptor blocking: can it be a potential therapeutic option for Covid-19? date = 2020-10-28 keywords = ACE2; SARS; TMPRSS2; covid-19 summary = Hence, this strategy may limit life-threatening Covid-19 infection and its mortality rate through nano-suspension based intra-nasal or oral nebulizer spray, to treat mild to moderate SARS-COV-2 infection, when Furin and TMPRSS2 receptor may initiate to express and activate for processing the virus to cause cellular infection by replication within the host cell. Drug particle formulated as a harmonious combination of cocktail receptor inhibitors at optimal and pharmacologically relevant dose could block the host cell receptor Furin, and TMPRSS2 receptor located in the target organs like esophagus, lungs, as well as in colon, liver, heart, kidneys, intestine and pancreas to prevent the entry of the SARS-CoV-2. Hence, some selected lead phytopharmaceuticals can primarily be focused on anti-COVID-19 drug discovery and development as mentioned in Table 1 and Table 2 based on their anti-viral activity reported against influenza, HIV, and other RNA viruses through host cell surface receptors ACE2, Furin and TMPRSS2 blocking action. doi = 10.1016/j.phymed.2020.153396 id = cord-340103-dc3wye9s author = Pallanti, Stefano title = Importance of SARs-Cov-2 anosmia: From phenomenology to neurobiology date = 2020-05-11 keywords = COVID-19; SARS summary = All clinicians should be aware that the presentation of SARS-CoV-2''s symptoms goes far beyond respiratory and sensorial dimensions and involves psychosensorial and neurological dimensions; these clinical observations could shed light on the neurobiological substrates involved in COVID-19 disease. In the long list of clinical symptoms of COVID-19, ENT-UK (The British Association of Otorhinolaryngology) has recently identified anosmia-hyposmia and hypogeusia, respectively, the sudden loss of sense of smell and taste, as "significant symptoms" which were found even in the absence of other symptoms, so that they could identify otherwise hidden carriers of this highly contagious disease. In the present report, anticipation of anosmia and hypogeusia to respiratory symptoms seems consistent with the ENT UK hypothesis that loss of sense of smell (and taste) could be considered as a symptom of COVID-19 infection; and, if confirmed, these symptoms may represent markers or early signs of SARS-CoV-2 sufficient to trigger quarantine. doi = 10.1016/j.comppsych.2020.152184 id = cord-264045-h0vt3r9j author = Pallett, Scott J C title = Serological assays for delayed SARS-CoV-2 case identification – Author''s reply date = 2020-09-14 keywords = SARS summary = We read with interest the insightful comments put forward by Kay Weng Choy, raising important considerations for clinicians planning to use pointof-care serological assays for delayed case identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in response to those presented in our Article. Our study was designed specifically to evaluate the use of point-ofcare assays for frontline health-care workers directly involved in the clinical care of patients with SARS-CoV-2 infection; therefore, it was not possible to evaluate any difference in detection of SARS-CoV-2 IgG in young or older people. 4 An evaluation of the potential effect of immunodeficiency on assay performance was beyond the scope of our study; however, we strongly agree that this is an important issue for future studies where consideration can be given to testing in different populations. Pointof-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study doi = 10.1016/s2213-2600(20)30406-9 id = cord-327890-ocisq7e4 author = Pallett, Scott J C title = Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study date = 2020-07-24 keywords = ELISA; SARS; care; serological summary = In phase 1, two point-of-care lateral flow serological assays, the Onsite CTK Biotech COVID-19 split IgG/IgM Rapid Test (CTK Bitotech, Poway, CA, USA) and the Encode SARS-CoV-2 split IgM/IgG One Step Rapid Test Device (Zhuhai Encode Medical Engineering, Zhuhai, China), were evaluated for performance against a laboratory immunoassay (EDI Novel Coronavirus COVID-19 IgG ELISA kit [Epitope Diagnostics, San Diego, CA, USA]) in 300 samples from health-care workers and 100 pre-COVID-19 negative control samples. These include point-of-care molecular platforms for acute phase testing, and laboratory ELISA or lateral flow serological assays for antibodies specific to SARS-CoV-2 for delayed case identification. To derive a measure of sensitivity, the results of lateral flow serological assays and ELISA were compared in 300 health-care workers who had previously received PCR testing (AusDiagnostics, Sydney, Australia) at initial presentation with COVID-19 symptoms. doi = 10.1016/s2213-2600(20)30315-5 id = cord-307653-nyr6mtj1 author = Palmeira, Patricia title = Why is SARS-CoV-2 infection milder among children? date = 2020-05-11 keywords = ACE2; COVID-19; SARS; patient summary = As with SARS-CoV, COVID-19 is believed to be initiated by the binding of the SARS-CoV-2 envelope-anchored spike protein to the outer surface of the angiotensin-converting enzyme 2 (ACE2) catalytic domain (13) , promoting endocytosis where viral and host membranes fuse and consequent entry of the virus into the host cell. (16) reported that ACE2 pulmonary expression is concentrated mainly in type II alveolar cells, which express many other genes that could favor viral replication, thus offering an explanation for the severe alveolar damage associated with SARS-CoV-2 infection. In agreement with the hypothesis that ACE2 expression levels have a significant role in acute respiratory distress syndrome (ARDS), which also occurs in COVID-19, an experimental mouse model of H5N1 virus-induced lung injury and death showed ACE2 downregulation following infection (25) . doi = 10.6061/clinics/2020/e1947 id = cord-277345-bbgerem6 author = Pan, A. title = Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area date = 2020-08-22 keywords = August; SARS; hispanic summary = Disparate racial and ethnic burdens of the Coronavirus Disease 2019 (COVID-19) pandemic may be attributable to higher susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or to factors such as differences in hospitalization and care provision. In our cross-sectional analysis of lab-confirmed COVID-19 cases from a tertiary, eight-hospital healthcare system (Houston Methodist) across greater Houston, multivariable logistic regression models were fitted to evaluate the odds of hospitalization and mortality for non-Hispanic Blacks (NHBs) vs. Models adjusted for demographics, vital signs, laboratory parameters, hospital complications, and ICU admission demonstrated non-significantly lower likelihoods of in-hospital mortality among NHBs and Hispanics, aOR (CI): 0.65 (0.40-1.03) and 0.89 (0.59-1.31), respectively. Given our prior data, we hypothesized that Black race and Hispanic ethnicity will be independently associated with a higher hospitalization rate and in-hospital mortality in the population of COVID-19 patients across HM. doi = 10.1101/2020.08.19.20177956 id = cord-304355-y3fagw3t author = Pan, Boyu title = Chinese herbal compounds against SARS-CoV-2: puerarin and quercetin impair the binding of viral S-protein to ACE2 receptor date = 2020-11-11 keywords = ACE2; SARS summary = Here, we identified puerarin (PubChem CID: 5281807), quercetin (PubChem CID: 5280343) and kaempferol (PubChem CID: 5280863) as potential compounds with binding activity to ACE2 by using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). In this study, we first screened out puerarin as the candidate compound targeting human ACE2 from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and identified the potential effective herbs containing puerarin through TCMSP analysis platform. The possible interaction of these compounds with ACE2 was further investigated by molecular docking and surface plasmon resonance assays, and the results support the view that puerarin and quercetin could significantly impair the binding of viral S-protein to its human ACE2 receptor, shedding light on CHM-based new drug discovery against COVID-19 (See workflow scheme in Figure 1 ). To screen the potential CHM compounds targeting human ACE2 receptor, Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was employed. doi = 10.1016/j.csbj.2020.11.010 id = cord-312984-rzryn3on author = Pan, Daniel title = Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity date = 2020-09-19 keywords = SARS summary = title: Serial simultaneously self-swabbed samples from multiple sites show similarly decreasing SARS-CoV-2 loads in COVID-19 cases of differing clinical severity 8 From this small longitudinal cohort study on serially collected samples in acute COVID-19 cases of differing severity, we conclude that for symptomatic patients, it is difficult to obtain a ''false negative'' result on NPS, OPS, NS or CS samples, if sampled early (within 5 days) post-symptom onset, even if the swab was ''poorly'' taken. Despite a previous meta-analysis showing that sputum testing is possibly more sensitive for SARS-CoV-2 PCR testing, 9 other studies have shown that self-sampling from various URT sites performed satisfactorily for the diagnosis of acute COVID-19. Therefore, we further confirm that early (within 5 days of symptom onset), self-swabbed NPS, OPS, NS or CS samples for SARS-CoV-2 diagnostic testing in acute COVID-19 cases is a sensitive, practical approach, which reduces patient discomfort (as self-swabbing can be controlled) and minimises virus exposure to healthcare workers. doi = 10.1016/j.jinf.2020.09.016 id = cord-330022-n3d130t8 author = Pan, Daniel title = The impact of ethnicity on clinical outcomes in COVID-19: A systematic review date = 2020-06-03 keywords = BAME; COVID-19; SARS; white summary = However, emerging data from the grey literature and preprint articles suggest BAME individuals are at an increased risk of acquiring SARS-CoV-2 infection compared to White individuals and also worse clinical outcomes from COVID-19. We found 17 published studies of patients with COVID-19 which reported data on ethnicity; 1 reported an increased risk of acquiring SARS-CoV-2 in Black compared to White patients and 5 reported no association between ethnicity and clinical outcomes. 34 preprint articles on MedRxiv reported ethnicity; 13 reported an increased risk of acquiring infection with SARS-CoV-2 and 12 reported adverse clinical outcomes with COVID-19 in BAME compared to White patients. Increasing numbers of articles from the UK and USA in the grey literature and in preprint suggest that individuals from BAME communities are at increased risk of infection from SARS-CoV-2 and worse clinical outcomes including hospitalization, ITU admission and mortality, compared to White patients. doi = 10.1016/j.eclinm.2020.100404 id = cord-310947-aqau2n7q author = Pan, Ji''An title = Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date = 2008-10-01 keywords = Fig; RNA; SARS; interaction; protein summary = In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . doi = 10.1371/journal.pone.0003299 id = cord-345529-f12v6bp0 author = Pan, Q. title = Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China date = 2020-06-18 keywords = SARS summary = In order to better treat these patients and provide basis for further control measures, we analyze the epidemiological outcomes and clinical features of patients with residual Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) in Linyi city. Gender, age, exposure history to Hubei Province or contact with confirmed patients, onsets of symptoms, data of diagnosis, date of testing first negative, date of re-positive testing , severity of disease and other information were included for further analysis. The reason maybe that serious illness resulted from more virus infections, and more residual SARS-Cov-2 remained in the body of these patients, which makes the positive testing appear easier and more likely. The analysis also indicates that even discharge from hospital with negative testing at least two times, some patients still carry residual SARS-Cov-2 and show repeatedly positive testing outcome for 22.44±13.61 days. doi = 10.1101/2020.06.16.20133199 id = cord-254017-4a6fs57r author = Pan, Xiu-wu title = Identification of a potential mechanism of acute kidney injury during the COVID-19 outbreak: a study based on single-cell transcriptome analysis date = 2020-03-31 keywords = SARS summary = Colocalization analysis of ACE2 and TMPRSS genes showed relatively high coexpression in podocytes and proximal straight tubule cells, which were identified as candidate host cells (Fig. 1a, b) . Second, although there was no significant difference in the expression of TMPRSS genes, the expression of the receptor ACE2 in podocytes and proximal straight tubule cells in Occidental donors was more pronounced than that in Asian donors (Fig. S2B) , suggesting that Occidental populations might be at higher risk for developing AKI in COVID-19. In addition, comparative analysis showed that the coexpression of the receptor ACE2 and TMPRSS genes in kidney cells was no less than that in the lung, oesophagus, small intestine and colon (Fig. S2C) , suggesting that the kidney might also be an important target organ for SARS-CoV-2. Based on our findings, we conclude that the cytopathic effects of SARS-CoV-2 on podocytes and proximal straight tubule cells may cause AKI in patients with COVID-19, especially in patients with SARS-CoV-2 infection in blood samples. doi = 10.1007/s00134-020-06026-1 id = cord-339271-t7cxqkp1 author = Pan, Yanfeng title = Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers date = 2020-04-22 keywords = SARS summary = The median period from diagnosis to negative nucleic acid test was significantly different between patients with normal or atypical chest computed tomography (CT) findings (n=16, 61.5%; 7.5 days [2–20 days]) and patients with typical ground-glass or patchy opacities on CT(n=10, 38.5%; 12.5 days[8–22 days]; P<0.01). Here, we identified a total of 26 persistently asymptomatic patients with positive test results for SARS-CoV-2 nucleic acid to determine the clinical characteristics and asymptomatic carrier transmission of COVID-19 infection. A total of 26 hospitalized patients with a SARS-CoV-2 epidemiological history and positive SARS-CoV-2 nucleic acid test results were identified to analyze the epidemiological and clinical characteristics of COVID-19infected asymptomatic carriers. Discharge criteria for COVID-19 were as follows: 1) normal body temperature for more than 3 days; 2) significantly improved respiratory symptoms; 3) significantly improved chest radiography; and 4) two consecutive negative SARS-CoV-2 nucleic acid test results (sampling interval at least 1 day). doi = 10.1093/infdis/jiaa205 id = cord-297470-lx3xwg92 author = Pan, Yunbao title = Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date = 2020-10-07 keywords = SARS; Wuhan summary = title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Hence, Wuhan launched a population-scale, massive SARS-CoV-2 testing campaign for detecting viral nucleic acid and antibodies in residents to further prevent viral transmission, screen out infected patients who were in the incubation period or were asymptomatic virus carriers, and map the epidemiological sero-distribution of this infectious disease in the epicenter. The present study described the screening results of 61,437 community members in Wuchang District, Wuhan. Most of the recent studies showed detectable SARS-CoV-2 anti-IgM antibodies after one to two months (10, 11) . Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China doi = 10.1016/j.cmi.2020.09.044 id = cord-341284-jmqdnart author = Panagopoulos, Periklis title = Lopinavir/ritonavir as a third agent in the antiviral regimen for SARS-CoV-2 infection date = 2020-06-12 keywords = SARS; patient summary = Further studies are needed in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection. 9 The aim of the present study was to assess the impact of lopinavir/ritonavir as a third agent for the treatment of SARS COV 2 infection especially for patients with severe pneumonia emphasizing in the number of days needed for reduction of viral load. However, the number of days needed for the first negative result of RT-PCR for SARS-CoV-2 was significantly lower for patients of group A. The present study suggests that lopinavir/ritonavir could be a potential effective choice in treatment of patients with CoVID-19. 12 However, a retrospective study conducted in China including 134 patients with CoVID-19 showed no effect on accelerating the clearance of SARS-CoV-2. Further studies are needed with larger patient series in order to evaluate the effectiveness of lopinavir/ritonavir in the treatment of patients with SARS-CoV-2 infection and confirm the findings of the present study. doi = 10.1080/1120009x.2020.1775424 id = cord-303173-q88zdf03 author = Panchaud, Alice title = An international registry for emergent pathogens and pregnancy date = 2020-04-27 keywords = SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) pandemic is no exception. 3 To tweak resources, we have adjusted the Zika virus international web registry 9 to create COVI-Preg, a structured data collection tool available to any facility assessing pregnant patients for SARS-CoV-2 infection. For the ongoing SARS-CoV-2 pandemic, we hypothesise that the collected data will allow researchers and health-care professionals to better characterise the disease course and spectrum, quantitatively estimate associated risks, and identify specific risk factors that can be used to define screening strategies in pregnant women and adequate prevention meas ures, and to direct specific and early clinical management of women and fetuses at risk. Clinical analysis of pregnancy in second and third trimesters complicated severe acute respiratory syndrome An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes doi = 10.1016/s0140-6736(20)30981-8 id = cord-035157-97tfcgvq author = Panchin, Alexander Y. title = Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes date = 2020-07-28 keywords = SARS summary = RESULTS: We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). SARS-CoV-2 is closely related to the bat coronavirus RaTG13 with around 96% whole genome nucleotide sequence identity . We compared the relative frequencies of single nucleotide variations (which we will refer to as mutations) in SARS-CoV-2 with the relative frequencies of substitutions that it acquired since the divergence with its last common ancestor with a closely related coronavirus from bats RaTG13. On the other hand, the substitution profile of SARS-CoV-2 turned out to be quite similar to that of the other coronaviruses, lending further support to existing scenarios of its natural origin (Andersen et al., 2020) and suggesting that the changes in SARS-CoV-2 mutation frequencies have accompanied its transition to human hosts. doi = 10.7717/peerj.9648 id = cord-286895-i3g4ad4z author = Panciani, Pier Paolo title = SARS-CoV-2: “Three-steps” infection model and CSF diagnostic implication date = 2020-05-05 keywords = SARS summary = Dear Editor, An increasing number of Coronavirus Disease 2019 (COVID-19) patients shows neurological symptoms, but currently few studies have systematically analyzed the impact of SARS-CoV-2 on the Central Nervous System (CNS). (Bertran Recasens et al., 2020) In our Department we observed 3 different clinical pictures in SARS-CoV-2 infection with neurological impairment: cerebral thrombosis (CTh) with hemorrhagic infarction, demyelinating lesions and encephalopathy. SARS-CoV-2 may lead to Neuro-COVID through three phases ( Fig.1) : neuroinvasion, CNS clearance and immune response. Negative results could also be explained by the lack of apoptosis and/or necrosis as observed in pre-clinical models (Netland et al., 2008) , the lowsensitivity of the method and the CSF clearance of SARS-CoV-2 that lead to a low viral below the sensitivity of currently available instrumentation. In the last phase, the respiratory system is severely affected leading to potential hypoxia with subsequent brain damage. doi = 10.1016/j.bbi.2020.05.002 id = cord-301730-flv5lnv8 author = Pandey, Anamika title = Natural Plant Products: A Less Focused Aspect for the COVID-19 Viral Outbreak date = 2020-10-15 keywords = COVID-19; CoV; MERS; SARS summary = Despite the previous positive reports of plant-based medications, no successful clinical trials of phyto-anti-COVID drugs could be conducted to date. Medicinal plant extracts have been reported to impede the replication of several viruses including human immunodeficiency virus (HIV), hepatitis B virus (HBV), poxvirus, severe acute respiratory syndrome (SARS) virus, and herpes simplex virus type 2 (HSV-2) (Vermani and Garg, 2002; Kotwal et al., 2005; Huang et al., 2006) . Different researchers are investigating diverse plant forms based on ethnopharmacological data to find effective anti-CoV drugs with novel action mechanisms especially targeting viral replication. Moreover, creating an effective phyto-anti-COVID drug during this pandemic may provide an idea on the duration and the strategy required for the development of potent plant-based therapeutics in case of such random viral outbreaks (Figure 1) . doi = 10.3389/fpls.2020.568890 id = cord-260057-2m6jdvtc author = Pandey, Preeti title = Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis date = 2020-09-23 keywords = Fig; NSP6; RMSD; SARS; complex; protein summary = To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking–based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. The selected docking conformations of NSP6 in complex with haloperidol and dextromethorphan were sampled by 100-ns MD simulation, and the dynamic stability of the complex was elucidated by calculating the Cα-RMSD values of the protein as the function of simulation time ( Figure S3A ). In conclusion, the study elucidated the detailed interaction mechanism of dextromethorphan and haloperidol to NSP6 protein and the associated structural and dynamical changes upon drug binding. doi = 10.1007/s00109-020-01980-1 id = cord-308408-aciaj30k author = Paneesha, S. title = Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia date = 2020-04-30 keywords = CLL; SARS summary = It is likely that patients who undergo immuno-chemotherapy as part of disease management will be at increased risk of clinical complications following SARS-CoV-2 infection. As such, the clinical outcome of SARS-CoV-2 infection in patients with therapy-naive CLL is an area of considerable importance. These findings suggest that SARS-CoV-2 infection in patients with therapy-naive CLL may be associated with considerably greater clinical risk than seen in the general population and argue for strict enforcement of quarantine conditions. At clinic one month prior to final admission the blood count showed Hb 85 g/l, WBC 274 x10 9 /l and platelets 127 x10 9 /l. Clinically, it is important to recognise that this is a feature of acute SARS-CoV-2 infection in patients with CLL and that the lymphocytosis can resolve quickly. Covid-induced lymphocytosis The peripheral lymphocyte count is shown for each patient at the most recent outpatient clinic prior to onset of SAR-CoV-2 infection and also the peak value during Covid-19 infection. doi = 10.1016/j.leukres.2020.106366 id = cord-277683-9cg90zbo author = Panettieri, Reynold A. title = Asthma and COVID: What are the Important Questions? date = 2020-06-22 keywords = SARS summary = However, critical questions remain about the biologic and 40 clinical features that predispose to CSS and critical illness, including underlying comorbidities 41 such as asthma and the medications used to treat them. Older age and comorbidities, especially heart disease, hypertension, chronic obstructive 43 pulmonary disease (COPD), diabetes and obesity, are reported risk factors for the development 44 and progression of COVID-19 (3). However, controversy exists as to whether patients with 45 asthma manifest high or elevated rates of COVID-19 incidence. Inhaled steroids 62 have also been associated with decreased expression of angiotensin-converting enzyme 2 63 (ACE2), the co-receptor for SARS-CoV-2 raising the question of whether these drugs could Future studies should address whether inhaled steroids in patient with asthma and/or allergic 68 rhinitis increase or decrease risks of SARS-CoV-2 infection, and whether these effects different 69 across inhaled steroid types. Changes in medication 115 adherence among patients with asthma and COPD during the COVID-19 pandemic doi = 10.1016/j.jaip.2020.06.008 id = cord-348567-rvwxysvc author = Panfili, F. M. title = Possible role of vitamin D in Covid-19 infection in pediatric population date = 2020-06-15 keywords = SARS; covid-19; disease; vitamin summary = CONCLUSIONS: In this review, we suggest that vitamin D supplementation might play a role in the prevention and/or treatment to SARS-CoV-2 infection disease, by modulating the immune response to the virus both in the adult and pediatric population. Although the effect of normal to high levels of vitamin D on increasing CD4+ count is still unclear, a recent review proved that vitamin D plays an important role in reducing the immune activation of HIV-infected patients. In this autoimmune disease using calcitriol supplementation reduces serum levels of antibodies and slows the progression of β cell destruction down in the early stages of the disease [38] , Interestingly, it has also been demonstrated that in Systemic Sclerosis (SSc) [39] the VDR could act as a negative regulator of TGF-β/ Hydroxyproline, col1a1, col3a1 and alfa-SMA mRNAs ↓ Prevention of bleomycin-induced lung fibrosis in a murine model [48] Smad signaling, thus making vitamin D a putative antifibrotic treatment in the early stages of the disease. doi = 10.1007/s40618-020-01327-0 id = cord-274284-mi4n7xty author = Pang, Khang Wen title = Frequency and Clinical Utility of Olfactory Dysfunction in COVID-19: a Systematic Review and Meta-analysis date = 2020-10-13 keywords = COVID-19; SARS; olfactory summary = Meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if OD symptoms were explicitly asked in questionnaires or interviews or if smell tests were performed. RESULTS: The pooled frequency of OD in COVID-19 positive patients (17,401 patients, 60 studies) was 0.56 (0.47–0.64) but differs between detection via smell testing (0.76 [0.51–0.91]) and survey/questionnaire report (0.53 [0.45–0.62]), although not reaching statistical significance (p = 0.089). To investigate the estimated frequency of OD amongst COVID-19 patients, meta-analysis B included studies if they described the frequency of OD in COVID-19 positive patients and if smell tests were performed or if OD symptoms were explicitly asked in questionnaires or interviews. Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Self-reported olfactory and taste disorders in patients With severe acute respiratory coronavirus 2 infection: a cross-sectional study doi = 10.1007/s11882-020-00972-y id = cord-309554-ctc84tfy author = Pang, Ronald TK title = Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome date = 2006-03-01 keywords = SARS summary = To identify proteomic features associated only with disease, we used 2 criteria: (a) the normalized peak intensities had to be significantly higher/lower in SARS patients than in non-SARS individuals; and (b) the normalized peak intensities had to correlate with 2 or more clinical/ biochemical variables, indicating their biological meaningfulness. These potential biomarkers were found to be significantly associated with SARS-CoV viral load (2 correlated with SARS-CoV RNA), acute-phase reaction [ differentiation of sars by two-way hierarchical clustering analysis of serum proteomic fingerprints We successfully identified potential biomarkers reflecting various physiologic or pathologic responses of the body to SARS infection, including acute-phase reaction (7, 17 ) , lung damage (18 -20 ) , impairment of liver function (21) (22) (23) , neutrophil activation (24 -26 ) , and viral load (5, 10, 27, 28 ) . Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia doi = 10.1373/clinchem.2005.061689 id = cord-314714-ehxxvenb author = Pang, Xiaocong title = Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication date = 2020-06-24 keywords = ACE2; SARS summary = title: Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication However, the addition of exogenous ACE2 could be a potential treatment for SARS-CoV-2 infection, which might not only restrain the spread of SARS-CoV-2 by blocking its interaction with ACE2 on the host cell, but also modulate RAS to treat SARS-CoV-2-related underlying comorbidities and protect the lung from developing ARDS. Although Ang II receptor and ACE blockage were also effective in lung failure in animal models, this treatment could cause potential adverse effects, causing systemic hypotension in humans [22] . Currently, phase I (NCT00886353) and phase II (NCT01597635) clinical studies with a recombinant version of the catalytic ectodomain of human ACE2 (GSK2586881) have been successfully completed, providing safety and efficacy for ARDS treatment [25, 26] . Recombinant human ACE2 and the angiotensin 1-7 axis as potential new therapies for heart failure A pilot clinical trial of recombinant human angiotensin-converting enzyme 2 in acute respiratory distress syndrome doi = 10.1038/s41401-020-0430-6 id = cord-332654-nav15g8k author = Paniri, Alireza title = Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations date = 2020-08-04 keywords = HCQ; SARS; dna summary = The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy. Furthermore, growing body of evidence demonstrated that several factors including CYP450 single nucleotide polymorphisms (SNPs), and epigenetic molecules such as non-coding RNAs (ncRNAs), DNA methylation and histone acetylation influenced the expression levels of CYP450, and consequently might influence HCQ metabolism. The major purpose of this review is to discuss the pharmacokinetic and pharmacodynamic characteristics of CQ and HCQ that may be influenced by epigenetic mechanisms including ncRNAs and CYP2D6 SNPs, and thereby cause several side effects such as cardiotoxicity, prolonged QT interval, gastrointestinal problems (like dyspepsia and abdominal cramps), central nervous system or skin disorders, and especially retinopathy. doi = 10.1016/j.ejphar.2020.173454 id = cord-337026-osgi06o4 author = Panoutsopoulos, Alexios A. title = Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date = 2020-06-19 keywords = COVID-19; RNA; SARS summary = Given the uprising number of publications and case reports of COVID-19 patients showing conjunctivitis [61, 62] and the history of other coronaviruses that are found in tears, we have to consider the possibility of a separate, alternative viral mechanism through which the virus can enter the patient''s organism through epithelial cells of the eye [63] . The growing evidence on COVID-19 and its ocular implications and manifestations, in both animals and humans, is covered by many interesting reviews, all published 5 to 6 months after the novel coronavirus'' outbreak [64] [65] [66] [67] [68] , something that reveals the need to understand the virus from different perspectiveswhich at first may have seemed secondary in priority-in order to be able to reach a treatment. doi = 10.1007/s42399-020-00360-7 id = cord-318164-6rqi17oz author = Paoli, D. title = Sperm cryopreservation during the SARS-CoV-2 pandemic date = 2020-10-10 keywords = CoV-2; RNA; SARS summary = This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. This study thus aimed to evaluate the safety of sperm cryopreservation of cancer patients referred to our sperm bank after the onset of the pandemic in Italy through the assessment of the risk of SARS-CoV-2 exposure and, in selected volunteers, viral RNA testing of semen samples. This was further confirmed by testing seminal fluid samples from 10 asymptomatic cancer patients for SARS-CoV-2 RNA. doi = 10.1007/s40618-020-01438-8 id = cord-323695-jkik03lb author = Paolo, Gisondi title = Incidence rates of hospitalization and death from COVID-19 in patients with psoriasis receiving biological treatment: a Northern Italy experience date = 2020-11-05 keywords = COVID-19; SARS summary = Objective investigating the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. Materials and methods This is a retrospective multicenter cohort study including patients with chronic plaque psoriasis (n=6,501) being treated with biologic therapy and regularly followed up at the Divisions of Dermatology of several main hospitals in the Northern Italian cities of Verona, Padua, Vicenza, Modena, Bologna, Piacenza, Turin, and Milan. Incidence rates (IR) of hospitalization and death per 10,000 person-months with exact mid-p 95% confidence intervals (CI) and standardized incidence ratios (SIR) were estimated in the psoriasis patients and compared with the general population in the same geographic areas. We would not advise biologic discontinuation in patients on treatment since more than 6 months and not infected with SARS-CoV-2 to prevent hospitalization and death from COVID-19. In this study, we evaluated the incidence of hospitalization and death for COVID-19 in a large sample of patients with plaque psoriasis receiving biologic therapies compared with the general population. doi = 10.1016/j.jaci.2020.10.032 id = cord-317151-cxx5pcln author = Papa, Alfredo title = Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date = 2020-10-24 keywords = COVID-19; IBD; SARS; patient summary = 14 Since the beginning of the pandemic, the World Health Organization has provided general recommendations for the prevention of They include: to wash hands frequently and properly with soap or alcohol-based sanitizer, to maintain social distancing (at least 1 m of distance), to avoid touching eyes, nose and mouth, to cover mouth and nose when coughing or sneezing, to seek medical care early when fever, cough or difficulty in breathing are recorded, to wear personal protective equipment (PPE), in particular the facial mask when social distancing is not possible to maintain or in closed places, to stay informed and follow any advice provided by own healthcare providers. This may require further changes in the planning of healthcare activities, both by using different prioritization criteria for outpatient visits, diagnostic tests and surgical interventions and by continuing to use treatment strategies that have worked well during the pandemic such as telemedicine, psychological support to patients and the educational function of patient associations (Table 1) . doi = 10.1177/1756284820968747 id = cord-308667-6jr3z9wx author = Papachristodoulou, Eleni title = Long-term and herd immunity against SARS-CoV-2: implications from current and past knowledge date = 2020-06-08 keywords = COVID-19; SARS summary = Furthermore, data from SARS-CoV suggest that the duration of immunity may not be sufficiently significant, while the immunity response against SARS-CoV-2 may not be efficiently effective in all patients, as relapses have already been reported. In conclusion, the development of an effective vaccine is an urgent necessity, as long-term natural immunity to SARS-CoV-2 may not be sufficient for the control of the current and future outbreaks. Information from follow-up studies of patients recovered from other coronaviruses may provide a background regarding the possible long-term immune response of SARS-CoV-2 infection. (2011) reported that antibody titers were undetectable in 21/23 patients at six years post-infection, while SARS-CoV antigen-specific memory B-cell response was undetectable in all 23 patients. As a consequence, the increasing number of individuals recovered from COVID-19 may not be able to provide effective herd immunity during subsequent post-pandemic waves of infection by mutant variants (Biswas et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered 1 patient cohort and their implications doi = 10.1093/femspd/ftaa025 id = cord-284045-scd3f8vk author = Pape, Constantin title = Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date = 2020-10-07 keywords = ELISA; Fig; SARS; cell summary = Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in specific, sensitive and unbiased assay which complements the portfolio of SARS-CoV-2 serological assays. The dsRNA co-localizing pattern 213 observed for sera from the negative control cohort is by definition non-specific for SARS-CoV-2, 214 but would be classified as a positive hit based on staining intensity alone. The high information content of the IF data (differential staining patterns) 363 together with a machine learning-based approach [45] and the implementation of stable cell lines 364 expressing selected viral antigens in the IF assay will provide additional parameters for 365 classification of patient sera and further improve sensitivity and specificity of the presented IF 366 assay. doi = 10.1101/2020.06.15.152587 id = cord-352799-qmzh976f author = Paquin, Leo J. title = Was WHO SARS-related Travel Advisory for Toronto Ethical? date = 2007-05-01 keywords = SARS; Toronto summary = Guénaël R.M. Rodier thinks WHO''s decision to impose a SARS-related travel advisory was justifiable, even reasonable, though it caused a loss of over $1.1 billion in the Greater Toronto Area. However, as suggested in the Naylor report, issuing a travel advisory does not keep infected individuals from leaving Toronto and such individuals account for 5 of 6 cases where SARS was spread from Canada. "…a decision to lift the travel advisory, effective April 30, was made based on consideration of 3 criteria: a decrease to below 5 new SARS cases per day, a period of 20 days since the last case of community transmission occurred, and no new confirmed cases of exportation." 4 There are some data that suggest that Rodier is justified in his views. Why was Toronto included in the World Health Organization''s SARS-related travel advisory doi = 10.1007/bf03403714 id = cord-300640-9pvhaz8q author = Parackova, Zuzana title = Disharmonic Inflammatory Signatures in COVID-19: Augmented Neutrophils’ but Impaired Monocytes’ and Dendritic Cells’ Responsiveness date = 2020-09-29 keywords = SARS; covid-19; figure summary = We demonstrate the impaired functionality of COVID-19 dendritic cells and monocytes, particularly their low expression of maturation markers, increased PD-L1 levels, and their inability to upregulate phenotype upon stimulation. Ex vivo stimulation of peripheral whole blood with lipopolysaccharide (LPS) led to a rapid increase in surface degranulation markers CD11b and CD66b, and decrease in CD62L, a lectin involved in granulocyte trafficking, on both patient and healthy donor neutrophils ( Figure 1C and Figure S1C ). Only the COVID-19, but not the healthy neutrophils, were able to increase the production of IL-1β and TNFα upon ssRNA stimulation in comparison with untreated cells ( Figure 2B ) indicating a pro-inflammatory bias, possibly due to priming with SARS-CoV-2 or excessive cytokine/chemokine stimulation. In contrast to monocytes and DCs, COVID-19 neutrophils expressed significantly decreased levels of PD-L1 and their stimulation with ssRNA led to elevated production of proinflammatory cytokines. doi = 10.3390/cells9102206 id = cord-285203-ilxd0ih9 author = Paradiso, Angelo Virgilio title = Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date = 2020-04-06 keywords = PCR; SARS summary = Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint All the 191 subjects enrolled in the study had a SARS-CoV-2 RT-PCR test and RapidIgG/IgM test performed. The design of our study allowed us to specifically analyze two aspects of the open issue: the concordance of the rapid serological test with standard molecular testing; the trend of immunoglobulinsIgG/IgMexpression with respect to the onset of clinical symptoms. https://doi.org/10.1101/2020.04.03.20052183 doi: medRxiv preprint symptom appearance is accompanied by an improvement in serological test sensitivity compared to standard molecular testing Our study has some important limitations. Our study analyzed theclinical performance of the rapid serological test, Viva-Diag TM and confirmedthe test''s limited applicability for the diagnosis of SARS-CoV-2 infection when compared to standard molecular testing. doi = 10.1101/2020.04.03.20052183 id = cord-278440-vti6xp9v author = Paraiso, Ines L title = Potential use of polyphenols in the battle against COVID-19 date = 2020-09-09 keywords = ACE2; COVID-19; SARS summary = The present mini-review aims to report in silico and in vitro evidence of the potential of polyphenols as anti-SARS-CoV-2 agents. Screening by molecular docking of 33 molecules including natural products, antivirals, antifungals and antiprotozoal agents revealed that rutin (a citrus flavonoid) could bind to the active site of the SARS-CoV-2 3CL pro (PDB: 6Y84) with the highest affinity among the molecules screened [44] . •This study demonstrates that SARS-CoV-2 uses ACE2 as receptor for host-cell entry and the S protein needs the serine protease TMPRSS2 for priming. A: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors -an in silico docking and molecular dynamics simulation study Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA-dependent RNA polymerase (RdRp) inhibition: An in-silico analysis doi = 10.1016/j.cofs.2020.08.004 id = cord-352891-ljmkqdzx author = Parang, Keykavous title = Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date = 2020-05-17 keywords = RNA; SARS; dna summary = title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells. doi = 10.3390/molecules25102343 id = cord-353308-e4s8el0s author = Parashar, Umesh D title = Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date = 2004-05-20 keywords = Hong; Kong; SARS; respiratory summary = This dramatic chain of transmission brought to the world''s attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV) doi = 10.1093/ije/dyh198 id = cord-273898-i7icvsg1 author = Parcell, B. title = Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland date = 2020-05-11 keywords = SARS; testing summary = title: Drive-through testing for SARS-CoV-2 in symptomatic health and social care workers and household members: an observational cohort study in Tayside, Scotland Scotland recently began reporting staff absence rates in the health and social care sector showing that at the time of writing 1 in 20 staff were absent as a direct result of Current UK guidance for social distancing and self-isolation requires that HSCWs experiencing symptoms of a respiratory infection, such as cough or fever, should be absent from work for 7 days, while if a household contact is unwell, the staff member should be absent from work for 14 days to account for the incubation period of the virus. The results show a striking save of over 8000 lost working days for health and social care staff over a period of just 3 weeks which is likely to have a significant impact on the ability of health systems to respond to the SARS-CoV-2 pandemic. doi = 10.1101/2020.05.08.20078386 id = cord-339859-anatn295 author = Paret, Michal title = SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date = 2020-04-17 keywords = CoV-2; SARS summary = title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient''s NP sample. doi = 10.1093/cid/ciaa452 id = cord-307596-0bbxyyea author = Parhar, Harman S. title = Topical preparations to reduce SARS‐CoV‐2 aerosolization in head and neck mucosal surgery date = 2020-04-25 keywords = SARS; pvp summary = AIM: The COVID‐19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has put health care workers at risk when exposed to aerosolized viral particles during upper airway mucosal surgery. 12, 13 There has been very little published, however, regarding whether there exist any topical agents that could be utilized preoperatively to potentially lower the viral load in the upper aerodigestive tract thereby mitigating any risk of viral aerosolization in persons undergoing head and neck mucosal surgery. 14 While studies on virucidal activity of PVP-I have not yet been performed specifically on SARS-CoV-2, there have been numerous in vitro studies demonstrating its effectiveness against multiple viruses including related coronaviruses. Though no topical therapies have been studied to specifically reduce the viral load and potential aerosolization of SARS-CoV-2 during upper airway mucosal surgery, PVP-I solutions have demonstrated effective virucidal activity against related coronaviruses in numerous studies. doi = 10.1002/hed.26200 id = cord-283823-8n1cy0hj author = Parikh, Bijal A. title = The Brief Case: “Not Positive” or “Not Sure”—COVID-19-Negative Results in a Symptomatic Patient date = 2020-07-23 keywords = SARS summary = The diagnosis of SARS-CoV-2 has relied almost exclusively on molecular testing of upper and lower respiratory specimens. As of 7 April 2020 (when the BAL fluid sample for this patient was sent to a reference laboratory for testing), 28 of the 29 commercially available assays approved by the FDA for emergency use were for testing on nasopharyngeal swabs (Table 1 ). Case reports of SARS-CoV-2 detection in sputum, tracheal aspirate, and BAL fluid specimens suggest that these specimens may be positive when NP swabs are negative, though large-scale studies have yet to be published (5) . It has become clear that negative NP swabs alone do not rule out SARS-CoV-2 infection, and as of now, there is no single "ideal" specimen for the diagnosis of COVID-19 (5) . Updated IDSA (Infectious Diseases Society of America) guidelines for COVID-19 diagnosis describe an algorithmic approach based on patient symptomatology, suspicion for infection, hospitalization status, and availability of lower respiratory specimens (6) . SARS-CoV-2 viral load in upper respiratory specimens of infected patients doi = 10.1128/jcm.01195-20 id = cord-330814-7incf20e author = Parikh, Priyanka A title = COVID-19 Pandemic: Knowledge and Perceptions of the Public and Healthcare Professionals date = 2020-05-15 keywords = India; SARS; healthcare summary = Background and objective The recent pandemic due to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major concern for the people and governments across the world due to its impact on individuals as well as on public health. Conclusion Most healthcare professionals and the general public that we surveyed were well informed about SARS-CoV-2 and have been taking adequate measures in preventing the spread of the same. Social media platforms arguably support the conditions necessary for attitude change by exposing individuals to correct, accurate, health-promoting messages from healthcare professionals In order to investigate community responses to SARS-CoV-2, we conducted this online survey among the general public and healthcare professionals to identify awareness of SARS-CoV-2 (perceived burden and risk), trusted sources of information, awareness of preventative measures and support for governmental policies and trust in authority to handle SARS-CoV-2 outbreak and put forward policy recommendations in case of similar future conditions. doi = 10.7759/cureus.8144 id = cord-309411-2dfiwo65 author = Paris, Kristina A. title = Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date = 2020-06-23 keywords = ACE2; Fig; RBD; SARS summary = On the other hand, the loss of this pH-switch, which sequence alignments show is unique to CoV2, eliminates the transition state and allows the virus to stay bound to the ACE2 receptor for time scales compatible with the recruitment of additional ACE2 receptors diffusing in the cell membrane. Work on SARS-CoV (CoV1) has already determined that the virus enters cells via receptormediated endocytosis in a pH-dependent manner (Wang et al., 2008) that is characterized by cotranslocation of the viral spike glycoprotein and its specific functional receptor, the angiotensinconverting enzyme 2 (ACE2), from the cell surface to early endosomes. This newly discovered difference in protein sequence in the receptor binding domain of the spike glycoprotein and its impact on receptor binding reveals a mechanism that allows SARS-CoV2 internalization to take advantage of the high expression of ACE2 in the nasal epithelium¾resulting in increased retention times in the upper respiratory tract and augmented infectivity. doi = 10.1101/2020.06.16.155457 id = cord-318253-vp22xd8p author = Parisi, Ortensia Ilaria title = “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date = 2020-05-28 keywords = SARS summary = Our idea is focused on the development of "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. In this context, our idea is to develop "monoclonal-type" plastic antibodies based on Molecularly Imprinted Polymers (MIPs) for the selective recognition and binding of the RBD of the novel coronavirus SARS-CoV-2 in the aim to block the function of its spike protein (Figure 1.) . doi = 10.1101/2020.05.28.120709 id = cord-291222-n8kgsz2e author = Park, Benjamin J. title = Lack of SARS Transmission among Healthcare Workers, United States date = 2004-02-17 keywords = SARS; healthcare summary = We conducted an investigation of healthcare workers exposed to laboratory-confirmed SARS patients in the United States to evaluate infection-control practices and possible SARS-associated coronavirus (SARS-CoV) transmission. Due to the importance of healthcare facilities in transmission of SARS worldwide, state and local health departments, together with the Centers for Disease Control and Prevention (CDC), conducted a review of U.S. healthcare workers exposed to patients positive for SARS-associated coronavirus (SARS-CoV). In the United States, potential droplet-and aerosol-generating procedures were infrequent: only one patient required mechanical ventilation, and few healthcare workers reported administering aerosolized medication or performing 1 0 (0) 0 (0) a SARS, severe acute respiratory syndrome; HCWs, healthcare workers; NA, not available due to incomplete reporting. Unprotected exposures in healthcare workers exposed to laboratory-confirmed SARS patients after full infection-control procedures were initiated (n = 43) a Exposure type n (%) Any unprotected exposure 21 (49) Without eye protection 18 (42) Without N95 or higher respirator 6 (14) Direct contact without gloves 6 (14) a SARS, severe acute respiratory syndrome. doi = 10.3201/eid1002.030793 id = cord-256750-5m7psxri author = Park, Hye Yoon title = Posttraumatic stress disorder and depression of survivors 12 months after the outbreak of Middle East respiratory syndrome in South Korea date = 2020-05-15 keywords = MERS; PTSD; SARS summary = Acute infectious outbreaks of Emerging Infectious Diseases (EIDs) are known to influence the physical as well as the mental health of affected patients, as observed during similar events such as the Severe Acute Respiratory Syndrome (SARS) outbreak [3] , which was associated with such issues during the acute phase [4] and the long-term follow-up phase [5, 6] . Thus, the present study explored mental health issues and related factors in MERS survivors 12 months after the outbreak to determine the long-term psychological outcomes of this population. The univariate analysis revealed that several factors were significantly associated with PTSD, including previous psychiatry history, having a family member who died from MERS, depression and anxiety during the MERSaffected period, greater perceived stigma currently and during the illness, and negative coping strategies (Table S2) . Our study showed that nearly half the assessed MERS survivors experienced significant mental health problems, including PTSD and depression, at 12 months post-MERS. doi = 10.1186/s12889-020-08726-1 id = cord-278522-e4qa19o6 author = Park, Se Yoon title = Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs date = 2020-06-19 keywords = CoV-2; SARS summary = There are limited data on the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory specimens after resolution of coronavirus disease 2019 (COVID-19)-associated symptoms/signs. Persistent severe acute respiratory syndrome coronavirus 2 detection after resolution of coronavirus disease 2019-associated symptoms/signs Se Yoon Park 1 , Soon Gyu Yun 2 , Jeong Won Shin 2 , Bo Young Lee 3 , Hyo-Ju Son 1 , Seungjae Lee 1 , Eunjung Lee 1 , and Tae Hyong Kim 1 Since the first case of coronavirus disease 2019 (COVID-19) was reported in Wuhan, China in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than three million people in 211 countries. Few studies have investigated the duration of SARS-CoV-2 detection during the patients'' recovery phase after resolution of COVID-19-associated symptoms/signs. SARS-CoV-2 shedding continued for about 4 weeks after resolution of COVID-19-associated symptoms/signs, with the longest period being 48 days. In conclusion, we found that SARS-CoV-2 virus shedding can persist for more than three weeks after resolution of COVID-19-associated symptoms/signs. doi = 10.3904/kjim.2020.203 id = cord-329193-xuxbqbsf author = Park, Soo-kyung title = Detection of SARS-CoV-2 in Fecal Samples from Patients with Asymptomatic and Mild COVID-19 in Korea date = 2020-06-10 keywords = COVID-19; SARS summary = Methods We collected data from 46 patients (median age, 26 years; 46% men) with asymptomatic or mild COVID-19 (without fever and pneumonia) and prolonged respiratory shedding of SARS-CoV-2, quarantined from April 4, 2020 through April 24, 2020 in Korea. Conclusions In an analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea, we found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. New Findings: An analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. doi = 10.1016/j.cgh.2020.06.005 id = cord-334960-l5q5wc06 author = Park, Su Eun title = Epidemiology, virology, and clinical features of severe acute respiratory syndrome -coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19) date = 2020-04-02 keywords = COVID-19; MERS; SARS summary = 9) Two novel strains of coronavirus have jumped species from animal to human, spread by human-to-human transmission, and caused severe acute respiratory syndrome leading to high fatality rate in the past 2 decades. 10) Severe acute respiratory syndrome-associated virus (SARS-CoV), previously unknown coronavirus traced to horseshoe bats in southern China, caused 8,096 confirmed cases and 774 deaths (9.6% fatality rate) in 29 countries from November 2002 to July 2003. 19, 20) The virus was initially called 2019-novel coronavirus (2019-nCoV) upon its emergence, until the Coronaviridae Study Group of International Committee on Taxonomy of Viruses named the virus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) based on the phylogenetic analysis, on February 11, 2020. 10) Conclusion Within 3 months since the discovery of a novel coronavirus in patients with pneumonia of unknown origin in Wuhan City, China, COVID-19 has spread rapidly throughout the world and is beating SARS-CoV and MERS-CoV in the number of confirmed cases and deaths. doi = 10.3345/cep.2020.00493 id = cord-274396-l611eisi author = Park, Su-Jin title = Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets date = 2020-05-22 keywords = CoV-2; PBS; SARS; group summary = While the lopinavir-ritonavir-, hydroxychloroquine sulfate-, or emtricitabine-tenofovir-treated group exhibited lower overall clinical scores than the phosphate-buffered saline (PBS)-treated control group, the virus titers in nasal washes, stool specimens, and respiratory tissues were similar between all three antiviral-candidate-treated groups and the PBS-treated control group. Compared to the PBS-treated control group, azathioprine-immunosuppressed ferrets exhibited a longer period of clinical illness, higher virus titers in nasal turbinate, delayed virus clearance, and significantly lower serum neutralization (SN) antibody titers. In order to determine the antiviral efficacies of lopinavir-ritonavir, hydroxychloroquine (HCQ) sulfate, or emtricitabine-tenofovir for treatment of SARS-CoV-2 infection, SARS-CoV-2 antibody-free ferrets (10/group) were inoculated with 10 5.8 50% tissue culture infective doses (TCID 50 )/ml of an NMC-nCoV02 strain through the intranasal (i.n.) route ( Fig. 1 ). Therefore, although clinical symptoms were attenuated in ferret groups treated with antiviral candidates, we also evaluated virus titers in respiratory and gastrointestinal tracts using nasal washes and stool samples, respectively, from SARS-CoV-2-infected ferrets. doi = 10.1128/mbio.01114-20 id = cord-268874-ldja6aa4 author = Park, Sun Hee title = Personal Protective Equipment for Healthcare Workers during the COVID-19 Pandemic date = 2020-06-24 keywords = COVID-19; N95; PPE; SARS summary = Although no study has conclusively linked SARS-CoV-2 transmission to contaminated environmental surfaces, indirect contact with fomites is considered a possible route based on the evidence of heavy environmental contamination in healthcare settings, objects used by COVID-19 patients [26, 27] , and the finding that the virus remains viable on plastic surfaces for as long as 3 days [28] . Initially, the Korea Center for Disease Control and Prevention (KCDC) guidelines recommended coveralls with shoe covers for contact precautions, goggles/face shields for eye protection, N95 or equivalent respirators for respiratory protection, and powered airpurifying respirators (PAPRs) when AGPs are performed [46] . PPE for droplet and contact precautions, such as surgical masks with eye protection, gowns, and gloves, are recommended for HCWs in contact with suspected or confirmed COVID-19 patients, and N95 or equivalent respirators should to be worn by HCWs whenever AGPs are performed. doi = 10.3947/ic.2020.52.2.165 id = cord-297023-0qlo0mun author = Park, Sung‐Soo title = Mass screening of healthcare personnel for SARS-CoV-2 in the northern emirates date = 2020-10-17 keywords = SARS summary = While healthcare personnel (HCP) potentially has an increased risk of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the era of the pandemic [1] , the approach to testing HCP for the virus has not been uniform [2] . Given the significant percentage of asymptomatic coronavirus disease 2019 (COVID-19) infection [3] , universal testing of HCP could allow infected workers to be identified and isolated early, reduce in-hospital transmission, mitigate potential workforce depletion, and enhance healthcare workers'' safety [4] . This study aimed to evaluate the effectiveness of the universal staff screening for COVID-19 and identify any risk factor for viral infection. The staff were encouraged to notify the occupational health nurse for SARS-CoV-2 test any time if they had any suspicious symptoms of COVID-19 or close contact with COVID-19 patients. Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 COVID-19: the case for healthcare worker screening to prevent hospital transmission doi = 10.1016/j.jhin.2020.10.008 id = cord-268540-wrjzr3ws author = Park, You Jeong title = Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date = 2020-08-13 keywords = ACE2; COVID-19; Cov-2; SARS; cell; patient; spanish; virus summary = A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells'' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . doi = 10.1007/s12015-020-10026-5 id = cord-315498-gpzee1f2 author = Parkinson, N. title = Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date = 2020-09-01 keywords = MAIC; SARS; covid-19; gene summary = 2, 6, 7, 8, 9, 10 In this analysis we systematically identify and combine existing data from human betacoronavirus research to generate a comprehensive ranked list of host genes as a resource to inform further work on COVID-19. To identify existing literature which could provide informative datasets for host gene prioritisation, we conducted a systematic review of published studies and preprint manuscripts pertaining to host gene involvement in human betacoronavirus infection and associated disease. Results from identified studies, in the form of lists of implicated host factor genes, were combined using meta-analysis by information content (MAIC), 3 an approach we previously developed to identify host genes necessary for Influenza A virus (IAV) replication. Table 2 Candidate-gene human genetic studies < 5 hosts in virus group or control group in patient studies Meta-analyses, in silico anayses, re-analysis of data published elsewhere Potentially relevant pre-print manuscripts were identified by screening all papers categorised as COVID-19-related in the bioRxiv and medRxiv servers. doi = 10.1101/2020.08.27.20182238 id = cord-318205-qxkel0ww author = Parkulo, Mark A. title = Risk of SARS-CoV-2 Transmission Among Coworkers in a Surgical Environment date = 2020-10-22 keywords = SARS summary = This was an observational study of 394 health care workers in a surgical environment who were exposed to 2 known SARS-CoV-2–positive coworkers. Infections of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) among health care workers is a serious consequence of the coronavirus disease 2019 (COVID-19) pandemic. Of the COVID-19 cases reported to the US Centers for Disease Control and Prevention (CDC) between February 12 and April 9, 2020, that contained information about workers, 19% were identified as health care personnel. 2, 3 Here we report the outcome of a widespread surveillance program in a surgical area which was implemented as a result of health care workers testing positive for SARS-CoV-2 at Mayo Clinic, Jacksonville, Florida. Employee Health determined that 394 other employees worked in the surgical area at the same time as the index cases, and all were recommended to undergo SARS-CoV-2 PCR testing as surveillance. doi = 10.1016/j.mayocp.2020.10.016 id = cord-285254-8a1cia8s author = Parry, Nicola M.A. title = COVID-19 and pets: When pandemic meets panic date = 2020-12-31 keywords = COVID-19; SARS; pet summary = Concern also rapidly emerged among pet owners and the general public in late February 2020, when a dog in Hong Kong tested positive for the novel coronavirus. Although the dog had no clinical signs, he was taken to a nearby animal quarantine facility where oral, nasal, and rectal swab specimens were collected from him for SARS-CoV-2 testing. In late March 2020, health officials in Belgium reported that a cat from Liège province had also tested positive for SARS-CoV-2, about 1 week after its owner was diagnosed with COVID-19. Thus, the positive RT-PCR results in these pets do not necessarily indicate the presence of viable virus that was infectious and could potentially have put other people (or animals) at risk of SARS-CoV-2 infection. doi = 10.1016/j.fsir.2020.100090 id = cord-309829-3dlfcy31 author = Parupudi, Tejasvi title = Evidence-based point-of-care technology development during the COVID-19 pandemic date = 2020-11-09 keywords = COVID-19; POC; SARS; patient summary = As learnt from previous viral epidemicsfor example, influenza (H1N1) in 2009, Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 and the SARS outbreak during 2003 -rapid and accurate diagnostic testing with point-of-care technologies (POCTs) is beneficial in early identification [2, 3] . The need for rapid screening, triage and isolation of affected populations, the ability to monitor and stratify patients at home, in the clinic and in intensive care units (ICUs), and the associated decisions caregivers must take based on the test results underline the significance of POCTs. The WHO forum responsible for identifying immediate research needs and research gaps for COVID-19 recognized mobilizing research on rapid POC diagnostics for use at the community level and ensuring access to accurate and standardized diagnostics as one of the eight immediate research actions [4] . doi = 10.2144/btn-2020-0096 id = cord-184744-oyc2djxk author = Parvez, Md Sorwer Alam title = Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date = 2020-05-22 keywords = COVID-19; RNA; Rifampin; SARS summary = The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. The main protease proteins, RNA-dependent RNA polymerase and spike protein of SARS-CoV-2 were employed to molecular docking study with the repurposed drug candidates from plant origin for find out the better drug option towards the COVID-19 pandemic. In the present study, five plantr based therapeutics such as Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were suggested for potential inhibitors for the Main Protease protein, RNA dependent RNA polymerase and Spike protein of SARS-CoV-2 by using molecular docking based virtual screening study. doi = nan id = cord-347441-8ow952d8 author = Parvez, Md Sorwer Alam title = Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date = 2020-06-07 keywords = SARS summary = title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh. As many of the Bangladeshi people return during the COVID-19 39 outbreak mainly from China, India, Saudi Arabia, Spain, Italy, Japan, Qatar, Canada, Kuwait, USA, 40 France, Sweden, and Switzerland, the first deposited genome sequence of those countries were also 41 retrieved. In total, three models were generated using the template PDB ID: 6VSB; one model for the spike protein 118 of reference strain, and the two others were for two different mutant isolates from Bangladesh (Fig 3) . doi = 10.1101/2020.06.07.138800 id = cord-272405-jmwn8pdn author = Parvez, Mohammad K. title = Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date = 2017-08-04 keywords = SARS; ZIKV; human; virus summary = Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. doi = 10.1159/000478729 id = cord-282862-kve6fa49 author = Pastick, Katelyn A title = A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date = 2020-08-13 keywords = COVID-19; SARS; pregnant summary = Clinicaltrials.gov was searched for relevant studies, using the preprogrammed search terms "COVID-19," "SARS-CoV-2," "2019-nCoV," "2019 novel coronavirus," and "severe acute respiratory syndrome coronavirus 2." Inclusion and exclusion criteria were examined to determine whether pregnant and/or breastfeeding patients were excluded from the study. Of the actively ongoing interventional clinical trials investigating the use of a drug (including dietary supplements and biologic agents) that did not report the exclusion of pregnant or breastfeeding women, the first author contacted study personnel for each of these studies by email to discern whether or not pregnant or breastfeeding women were eligible to be enrolled. Despite available safety data in pregnancy for hydroxychloroquine and lopinavir/ritonavir, we were surprised to find 68% and 80% of the respective clinical trials had excluded pregnant or breastfeeding persons. Our review of the literature was timely and is the first study (to our knowledge) to systematically examine and compile the available data related to treatment and outcomes of COVID-19 in pregnancy and related clinical trials. doi = 10.1093/ofid/ofaa350 id = cord-345288-qyz83xx2 author = Pata, Francesco title = Enteral stoma care during COVID‐19 pandemic: practical advice date = 2020-07-21 keywords = SARS; covid-19; stoma summary = To face the COVID-19 pandemic, metamorphosis of surgical services is required to prevent in-hospital transmission, optimize allocation of scarce resources, establish new intensive care units (ICUs) and redeploy healthcare workers to emergency departments or COVID-19 dedicated wards [8] [9] [10] . Furthermore, although many recommendations suggest to consider performing stoma surgery instead of primary anastomosis in high-risk emergency surgery 14,20-23 none of those consider the potential problems related to reduced availability of stoma care services and reduced access in the hospital to caregivers for stoma training which may represent a problem for elderly and frail patients after discharge. Second, in-hospital stoma training pathways should be implemented to allow patients to confidently manage their own stomas independently prior to discharge and reduce the need for home nursing care 37 . In addition to standard precautions for infection prevention and control (i.e. correct use of PPE, keeping appropriate interpersonal distance, proper hand washing) indoor air quality should be preserved to limit the SARS-CoV-2 spread, and to protect patients and healthcare workers. doi = 10.1111/codi.15279 id = cord-317863-xf0bn3cv author = Pata, Ramakanth title = Probability of COVID-19 Being the Culprit in Neurocognitive Deception: A Case Series of Incidental Strokes in ICU Patients With COVID-19 date = 2020-08-18 keywords = April; COVID-19; SARS summary = The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, originated in Wuhan, China, and spread rapidly throughout the world, infecting millions and killing thousands. Additionally, it has a high incubation period (average 6.4 and range of 0-24 days) [2] , reproductive number (R0 ranged from 1.4 to 6.49, with a mean of 3.28) [3] , and reports have shown that the majority of patients are asymptomatic or have a mild response to the SARS-CoV-2 virus but release large amounts of viruses [2] . Furthermore, a chest X-ray showed no acute pathologies (Figure 3) , and the COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCT) was performed due to the recent outbreak of the SARS-CoV-2 virus, which came back positive. Other reports suggest a higher rate of cerebrovascular disease (mainly ischemic stroke) in severe COVID-19 patients as compared to non-severe cases [5] . doi = 10.7759/cureus.9857 id = cord-339665-nwwutduy author = Patel, Ami title = Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date = 2020-07-29 keywords = COVID-19; CoV-2; SARS summary = Prior work with the related coronaviruses, SARS-CoV and MERS-CoV, delineated that the Spike protein of these viruses was an important target for development of neutralizing antibodies, and in animal viral challenges vaccine targeted immunity (reviewed in (Du et al., 2009; Roper and Rehm, 2009; Thanh Le et al., 2020) (Liu et al., 2018; Muthumani et al., 2015; van Doremalen et al., 2020a) . These memory titers were comparable to those observed in other reported protection studies in macaques performed at the acute phase of the vaccine-induced immune response (Gao et al., 2020; van Doremalen et al., 2020b; Yu et al., 2020) and those reported in the sera of convalescent patients (Ni et al., 2020; Robbiani et al., 2020) . Our study and other published reports show that DNA vaccination with candidates targeting the full-length SARS-CoV-2 spike protein likely increase the availability of T cell immunodominant epitopes leading to a broader and more potent immune response, compared to partial domains and truncated immunogens. doi = 10.1101/2020.07.28.225649 id = cord-285459-fph03r22 author = Patel, Ami B title = SARS-CoV-2 Point Prevalence among Asymptomatic Hospitalized Children and Subsequent Healthcare Worker Evaluation date = 2020-08-28 keywords = SARS; child summary = doi = 10.1093/jpids/piaa102 id = cord-287604-w0ktwl8q author = Patel, Chirag N. title = Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation date = 2020-09-29 keywords = Fig; NPACT; SARS summary = We selected HE as a target in this study to identify potential inhibitors using a combination of various computational approaches such as molecular docking, ADMET analysis, dynamics simulations and binding free energy calculations. Virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin as potential HE inhibitors with better binding energy. In this study, we employed virtual screening approach to screen NPACT (Naturally occurring Plant-based Anti-cancer Compound activity-Target database) compounds against HE target [32, 35] and the best-scoring molecules were validated using molecular dynamics simulations analysis to better understand the interactions and conformational changes to inhibit HE target [36, 37] . Different molecular modeling techniques were employed in this study viz, molecular docking, Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) prediction, molecular dynamics simulations, and binding free energy calculations to obtain new leads from NPACT compounds [38] . doi = 10.1007/s11030-020-10135-w id = cord-276090-n8c2jpr6 author = Patel, Hiren N. title = Cerebellar Infarction Requiring Surgical Decompression in patient with COVID 19 Pathological Analysis, Brief Review date = 2020-07-29 keywords = COVID-19; SARS; patient summary = CONCLUSION: A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. angiography, CXR denotes chest X-ray, FiO2 denotes fraction of inspired oxygen, SARS-COV-2 denotes severe acute respiratory syndrome coronavirus 2, STAT denotes statum which is Latin meaning immediately, t-PA denotes tissue plasminogen activator, WHO denotes World Health Organization. A young man with COVID-19 and suspected immune dysregulation, complicated by a large cerebrovascular ischemic stroke secondary to vertebral artery thrombosis requiring emergent neurosurgical intervention for decompression with improved neurological outcomes. COVID-19 complicated with cerebral and large vessel vasculitis and its treatment will require a need for randomized clinical trials showing benefit in outcomes and mortality. This is a report of a patient with COVID-19 immune dysregulation who developed an acute cerebellar ischemic stroke secondary to vertebral artery thrombosis. doi = 10.1016/j.inat.2020.100850 id = cord-331300-u5fltc10 author = Patel, Jay title = Viability of SARS‐CoV‐2 in faecal bio‐aerosols date = 2020-06-09 keywords = SARS summary = I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) positive faecal samples in patients with coronavirus disease 2019 (COVID‐19). The authors acknowledge insufficient evidence in support of transmission via faeco‐oral route and identify the need for further research regarding the viability of SARS‐CoV‐2 in the context of human faeces. Dear Editor, I read with interest the rapid review by Gupta and colleagues [1] concerning the incidence and timing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive faecal samples in patients with coronavirus disease 2019 (COVID-19). The authors acknowledge insufficient evidence in support of transmission via faeco-oral route and identify the need for further Accepted Article research regarding the viability of SARS-CoV-2 in the context of human faeces. Put a lid on it: Are faecal bio-aerosols a route of transmission for SARS-CoV-2? doi = 10.1111/codi.15181 id = cord-338578-e0aiknb6 author = Patel, Kajal title = Applying the WHO ICF Framework to the Outcome Measures Used in the Evaluation of Long-Term Clinical Outcomes in Coronavirus Outbreaks date = 2020-09-05 keywords = ICF; SARS; measure summary = (2) Methods: EMBASE, MEDLINE, CINAHL and PsycINFO were systematically searched for original studies assessing clinical outcomes in adult survivors of severe acute respiratory distress syndrome (SARS), middle east respiratory syndrome (MERS) and coronavirus disease-19 (COVID-19) after hospital discharge. (4) Conclusions: We recommend future COVID-19 follow-up studies to use the ICF framework to select a combination of outcome measures that capture all the components for a better understanding of the impact on survivors and planning interventions to maximize functional return. The aim of this systematic review is to identify outcome measures which have been used in follow-up studies in the coronavirus outbreaks, including SARS in 2002 and MERS in 2012 [21] , and to classify them using the ICF model. In conclusion, we are proposing an ICF-based framework to assist researchers in selecting outcome measures for future follow-up studies of COVID-19 survivors. doi = 10.3390/ijerph17186476 id = cord-271781-cfv0ta10 author = Patel, Kishan P. title = Transmission of SARS-CoV-2: an update of current literature date = 2020-07-07 keywords = COVID-19; CoV-2; RNA; SARS summary = To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] . doi = 10.1007/s10096-020-03961-1 id = cord-333532-vrfduv5a author = Patel, Kishan Pravin title = COVID-19 Patients: Are Current Isolation Guidelines Effective Enough? date = 2020-05-11 keywords = SARS summary = We believe the current isolation guidelines need to be revisited and clinicians should counsel COVID-19 patients to practice contact precautions for longer durations given new evidence suggesting the possibility of a fecaloral route of transmission. Furthermore, a recent case reported an asymptomatic COVID-19 patient who retested positive for SARS-CoV-2 despite being discharged after two negative consecutive respiratory nucleic acid tests at least 24 hours apart, raising concern for inadequate discharge protocol. With consideration of its high virulence, high infectivity, and the concern for a fecal-oral route of transmission, we suggest modifying guidelines to extend isolation and/or contact precautions in the best interest of patients, healthcare workers, and the global community as a whole. Key words: COVID 19; SARS CoV-2; Gastrointestinal; Isolation; Fecal-oral; transmission; precautions doi = 10.1016/j.puhe.2020.04.048 id = cord-280001-y7pvj2l1 author = Patel, Robin title = Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date = 2020-03-26 keywords = RNA; SARS summary = If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness. doi = 10.1128/mbio.00722-20 id = cord-283152-wav0d0ws author = Patel, Sanjay K. S. title = Deploying Biomolecules as Anti-COVID-19 Agents date = 2020-06-09 keywords = COVID-19; China; SARS; human summary = Severe acute respiratory syndrome coronavirus (SARS-CoV-2) known as COVID-19 has emerged as a major threat to human existence. The emergence of a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, renamed as COVID19) in 2019 from Wuhan, China has led to a global crisis and it has been declared as a pandemic emergency by World Health Organization (WHO) due to its fast rate of transmission among human beings [1, 2] . Coronaviruses (CoVs) are a group of genetically distinct viruses, which originated from broad ranges of hosts, including animal and bird species, and primarily cause respiratory and intestinal infections to humans and animals [1, [5] [6] [7] [8] . Transmission of COVID-19 possibly involved an adaptive evolution through an intermediate host (bat) before infecting humans. Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective doi = 10.1007/s12088-020-00893-4 id = cord-029965-bt87kai8 author = Patel, Shailesh Kumar title = The kidney and COVID-19 patients – important considerations date = 2020-08-01 keywords = SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily affects the lungs, however, this virus can also affect other organs such as intestine, kidney, heart, and brain [1] [2] [3] . Studies reporting albuminuria and haematuria in the COVID-19 patients along with the detection of viral RNA from the urine samples further support the potential tropism of the SARS-CoV-2 for the renal tissues [4, 12] . Therefore, along with clinical management for pneumonia, potential intervention to protect the kidneys from the virus tropism and cytokine storm must be considered to minimize the mortalities associated with acute renal failure (Figure 1 ). Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China doi = 10.1016/j.tmaid.2020.101831 id = cord-330074-5iqqgy65 author = Patel, Smit D. title = Malignant Cerebral Ischemia in A COVID-19 Infected Patient: Case Review and Histopathological Findings date = 2020-08-05 keywords = SARS; covid-19 summary = However, this data is limited and comes from recent small case series and observational studies on stroke types, mechanisms, and outcomes.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Furthermore, evidence on the role of therapeutic anticoagulation in SARS-CoV-2 infected patients with elevated inflammatory markers, such as D-dimer, is also limited. We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection (COVID-19). We report the case of a middle-aged patient who presented with a large vessel ischemic stroke likely resulting from an underlying inflammatory response in the setting of known novel coronavirus infection . Ischemic stroke, Inflammatory conditions, COVID-19, Corona virus, SARS-CoV-2 RNA, cerebrovascular disease, hemorrhagic stroke, cerebral sinus thrombosis, vasculitis, anticoagulation, thrombotic conditions, thromboembolic conditions Introduction: doi = 10.1016/j.jstrokecerebrovasdis.2020.105231 id = cord-303506-rqerh2u3 author = Patel, V. title = A call for governments to pause Twitter censorship: a cross-sectional study using Twitter data as social-spatial sensors of COVID-19/SARS-CoV-2 research diffusion date = 2020-05-29 keywords = SARS; Twitter summary = Objectives: To determine whether Twitter data can be used as social-spatial sensors to show how research on COVID-19/SARS-CoV-2 diffuses through the population to reach the people that are especially affected by the disease. Mapping of worldwide data illustrated that high Twitter activity was related to high numbers of COVID-19/SARS-CoV-2 deaths, with tweets inversely weighted with number of publications. • Using Twitter data used as social-spatial sensors, we demonstrated that Twitter activity was significantly positively correlated to the numbers of COVID-19/SARS-CoV-2 deaths, when holding the country''s number of publications constant. Mapping of worldwide data illustrated that high Twitter activity was related to high Conclusions: This study shows that Twitter can play a crucial role in the rapid research response during the COVID-19/SARS-CoV-2 global pandemic, especially to spread research with prompt public scrutiny. doi = 10.1101/2020.05.27.20114983 id = cord-328069-a9fi9ssg author = Pathan, Refat Khan title = Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model date = 2020-06-13 keywords = SARS; mutation; rate summary = title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model This study explores the mutation rate of the whole genomic sequence gathered from the patient''s dataset of different countries. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, The United States, and the rest of the World. Using this train and testing process, the nucleotide mutation rate of 400(th) patient in future time has been predicted. The complete genomic sequence (Wuhan-HU1) of this large RNA virus (SARS-CoV-2) was first discovered in the laboratory of China on 10th January [10] and placed in the NCBI GenBank. al have performed Phylogenetic analysis of SARS-CoV-2 virus based on the spike gene of the genomic sequence [17] . An adequate amount of gene dataset is currently available in the NCBI GenBank which has the complete genome sequence of SARS-CoV-2. doi = 10.1016/j.chaos.2020.110018 id = cord-017210-5nc8f3a4 author = Pathegama, Mahinda P. title = Interactive Real-time Image Analysis System for Distant Operation date = 2005 keywords = SARS; image summary = This paper reports on the development and implementation of an integrated and interactive system for cell analysis featuring remote operation and real-time analysis for generating analytical data from microscopic images. Advancement of image processing techniques is a welcome adjunct in electronmicroscopic cell analysis and is the object of increasing interest in research for the enhancement of accuracy in disease diagnosis. The emergence and rapid spread of SARS (Severe Acute Respiratory Syndrome) has dramatically emphasised the need for both collaborative international networks [4] and linking of personnel from distant locations with laboratories monitoring and analysing test samples of the causative agent by electron microscopy. Remote users would derive considerable benefit from a system endowed with facilities enabling image acquisition, camera control, real-time monitoring, automated pattern recognition for cell feature extraction and quantitative result generation. The techniques used aid in image enhancement and provide feature highlighting needed for quantitative report generation on each cell object detected in the microscopic image. doi = 10.1007/0-387-26325-x_3 id = cord-299853-pvugij9l author = Patil, Uday P. title = Newborns of COVID-19 mothers: short-term outcomes of colocating and breastfeeding from the pandemic’s epicenter date = 2020-08-10 keywords = SARS; newborn summary = Newborns are at high risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from their infected mothers who delivered during this period; however, data remains limited [3] . Data regarding demographic and clinical characteristics, SARS-CoV-2 test results, symptoms and signs of COVID-19, colocation (rooming-in), breastfeeding, and newborn follow-up were obtained from review of electronic medical records. During the early period of the pandemic, our center tested only symptomatic pregnant women for SARS-CoV-2 and newborns of infected mothers were placed in isolation rooms based on the available literature at that time [6] . However, due to the dramatic surge in the number of SARS-CoV-2 positive mothers delivering at our center after initiation of universal screening of all pregnant women admitted for delivery, the limited isolation spaces for the newborns, early postpartum discharges, the crowded housing conditions in our community and the desire to promote breastfeeding, we utilized shared decision-making and offered rooming-in of mothers with their newborns [7] . doi = 10.1038/s41372-020-0765-3 id = cord-296020-kje1wiah author = Patoulias, Dimitrios title = Diabetes mellitus and SARS-CoV-2-related mortality: the impact of acute hyperglycemic crises and some further considerations date = 2020-08-20 keywords = SARS summary = We would like to emphasize on another aspect of SARS-CoV-2 infection among patients with DM, the triggering of acute hyperglycemic crises, either diabetic ketoacidosis (DKA) or hyperosmolar hyperglycemic state (HHS). described the presentation and clinical course of 6 patients with DM who developed DKA and HHS in the context of SARS-CoV-2 infection [2] . However, according to a recent retrospective analysis from the UK, patients with DM who develop DKA due to disease are more likely to survive compared to those patients that are not complicated by an acute hyperglycemic crisis [5] . Therefore, it would be interesting to know in future, large, observational studies the proportion of patients that developed DKA/HHS in the context of SARS-CoV-2 infection, the underlying treatment and the outcome of disease. Clinical characteristics and outcome in patients with combined diabetic ketoacidosis and hyperosmolar hyperglycemic state associated with COVID-19 :a retrospective, hospital-based observational case series doi = 10.1007/s00592-020-01593-7 id = cord-352642-u513wnu1 author = Patrocínio de Jesus, Rita title = Reactivation of SARS-CoV-2 after Asymptomatic Infection while on High-Dose Corticosteroids. Case Report date = 2020-10-02 keywords = COVID-19; SARS summary = After reviewing this case in light of current evidence and debates surrounding SARS-CoV-2 RT-PCR results, we hypothesize that patients on corticosteroids may have particular viral shedding dynamics and should prompt a more conservative approach in regard to isolation discontinuation and monitoring. Since the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the cause of the disease which was later named COVID-19, and as it progressed to the current worldwide pandemic, much investigation has been made regarding its clinical presentation, transmission route, and immunity. This could point either to a reactivation of the disease in a patient who first presented as asymptomatic or to a long incubation period (18 days from risk contact until developing symptoms, with a CT performed 3 days prior to the onset of symptoms showing an evolving disease, which is consistent with previous studies reporting typical radiological findings of COVID-19 in asymptomatic or presymptomatic patients [2] ). doi = 10.1007/s42399-020-00548-x id = cord-323241-1twnqr4k author = Patrì, Angela title = Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? date = 2020-04-09 keywords = SARS summary = title: Sexual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A new possible route of infection? 2, 3 In addition, SARS-CoV-2 RNA identification and intracellular staining of viral nucleocapsid protein in rectal epithelia demonstrated that the virus infects such epithelial cells. [2] [3] [4] Moreover, SARS-CoV-2 can also be transmitted through the saliva, and ACE2 has been detected on the mucosa of oral cavity, which is rich in epithelial cells. 4 Therefore, if saliva and feces are both capable of carrying the virus and ACE2 is expressed both in the glandular cells of rectal epithelia and oral mucosa, how can we be sure that sexual intercourse does not represent another way of contagion? 5 This means that the gastrointestinal tract may continue shedding the virus and that fecal-oral, or eventually sexual, transmission may be possible despite the apparent recovery. doi = 10.1016/j.jaad.2020.03.098 id = cord-338365-9sd62a2w author = Patrício Silva, Ana L. title = Increased plastic pollution due to Covid-19 pandemic: challenges and recommendations date = 2020-08-17 keywords = COVID-19; PPE; SARS; SUP; environmental; plastic; waste summary = This paper provides a comprehensive review on the potential impact of COVID-19 pandemic precautionary measures in the environment while considering the shift on public behaviour and policies towards single-use items and waste management. At first glance COVID-19 pandemic seems to be indirectly contributing towards the UN 2030 Sustainable Development Goals (namely 11, 12, 13, 15 SGDs) by increasing overall health and safety of cities by reducing the greenhouse gas emissions (GHG), outdoor air pollution, environmental noise level (including underwater noise due to reduced marine transportation activities), land and wildlife pressure. While the positive impacts of COVID-19 in the environment are resulting from a "postponed" anthropogenic activity that soon will entail after the pandemic scenario; the negative short-term effects (that are mostly related with plastic use, consumption and waste mismanagement as discussed below) will shortly add-up to the current environmental issues, aggravating their impact in the natural ecosystems and compromising potential mitigation/remediation measures. doi = 10.1016/j.cej.2020.126683 id = cord-269114-mdsiv6tr author = Pattabiraman, C. title = Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka date = 2020-07-11 keywords = India; SARS summary = A comprehensive study of circulating variants of the virus in Iceland, which included over 580 complete genomes in combination with epidemiological information (travel history and contact tracing) revealed that while the initial importation of the virus was from China and Southeast Asia subsequent importations were from different parts of Europe 8 . While these studies have added valuable information on circulating lineages of SARS-CoV-2 in India, they have not comprehensively linked genomic data with epidemiological information. Here we report 47 full-length SARS-CoV-2 genome sequences obtained from individuals who tested positive for the virus by RT-PCR and present an analysis of epidemiological information combined with genomic data to elucidate the introduction and spread of the virus in the state. The data from this study using a combination of genomic epidemiology and contact tracing provides evidence for multiple introductions of the virus into the state, with sustained local transmission. doi = 10.1101/2020.07.10.20150045 id = cord-274542-fpzk5k79 author = Patti, Giuseppe title = Questions and Answers on Practical Thrombotic Issues in SARS-CoV-2 Infection: A Guidance Document from the Italian Working Group on Atherosclerosis, Thrombosis and Vascular Biology date = 2020-11-03 keywords = COVID-19; SARS; VTE; patient summary = UFH should be limited to patients with CrCl < 30 mL/min An invasive "catheter"-based therapy for PE is indicated in selected cases with contraindication to anticoagulant drugs, recurrent events despite adequate anticoagulation, or when systemic fibrinolysis cannot be performed For the risk stratification of patients with VTE, monitoring of the following parameters is useful: troponin, BNP, D-dimer, blood cell count, fibrinogen, prothrombin time, activated partial thromboplastin time, and degradation products of fibrin After the initial approach, DOACs may represent an option for in-hospital treatment of a VTE episode in patients with clinical stability and decreasing inflammation After a VTE episode, DOACs should represent the therapy of choice at discharge The use of imaging techniques in diagnosing a VTE episode is complex, because of the risk of viral transmission to other patients and to healthcare workers, and must be regulated by specific in-hospital protocols aimed at limiting such risk. doi = 10.1007/s40256-020-00446-6 id = cord-352779-zdtpnip0 author = Patti, Ravi Karan title = Subacute Aspergillosis “Fungal Balls” Complicating COVID-19 date = 2020-10-15 keywords = SARS; covid-19 summary = Severe acute respiratory syndrome coronavirus-2 infection (SARS-CoV-2), commonly known as COVID-19 (coronavirus disease-2019), began in the Wuhan District of Hubei Province, China. We report the case of a 73-year-old male who presented with progressive dyspnea; diagnosed with SARS-CoV-2–related severe acute respiratory distress syndrome and complicated with lung cavitations growing Aspergillus sp. Due to persistence of the SARS-CoV-2 and severe acute respiratory distress syndrome complicated by pulmonary aspergillosis, the patient further underwent tracheostomy and was discharged to a subacute rehabilitation facility. 11 We report this case of subacute invasive pulmonary aspergillosis in a patient with SARS-CoV-2 infection, who did not have any history of pulmonary tuberculosis, sarcoidosis, or preformed cavities to predispose for aspergillus infection. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. Subacute invasive pulmonary aspergillosis as a superimposed infection in patients with SARS-CoV-2 is a rare entity. doi = 10.1177/2324709620966475 id = cord-355475-kdubhh73 author = Patton, Lauren L. title = Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date = 2020-11-05 keywords = HIV; SARS; covid-19 summary = An early survey in May and June 2020 of practicing dentists in private practice and public health settings in the United States (U.S.), a short 2 months after the first COVID-19 wave and national shortages of personal protective equipment caused offices to move to emergency only dental care, showed that 99.7% of offices had implemented enhanced infection control procedures. While hope for a COVID-19 vaccine to quell transmission is widespread, we must not lose sight of the fact that diverse vaccine development technologies and novel drug discovery efforts made today will benefit our response to the next pandemic. 14 When the diversity of oral mucosal and salivary gland disorders were observed in HIV/AIDS patients, international collaborative groups such as the European Community We learned from HIV disease management that the antiretroviral drugs can have acute and long-term toxicities including ulcers, xerostomia/parotid lipomatosis, taste disturbances, perioral paresthesia, erythema multiforme and facial fat wasting. doi = 10.1016/j.oooo.2020.10.022 id = cord-027309-8siz9rb8 author = Paul, Debjani title = Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2 date = 2020-06-19 keywords = SARS; dna summary = The recent pandemic of COVID-19 caused by the novel coronavirus (SARS-CoV-2) has drawn attention to the need for developing rapid and accurate diagnostic tests. The widespread use of these immunodiagnostic tests in clinical settings, in spite of their shortcomings, emphasizes the need for developing rapid and point-of-care (POC) tests that are based on molecular diagnostics (i.e., tests that detect the viral RNA directly in a manner similar to RT-PCR). We believe we can build on our past experience with isothermal DNA amplification techniques and paperfluidic devices to develop an isothermal amplification-based molecular diagnostic test for COVID-19 that can be deployed more easily. The ID NOW COVID-19 assay from Abbott, which recently got an emergency use authorization (EUA) from the US government for clinical use, detects SARS-CoV-2 RNA using an isothermal amplification test and can enable a clinical decision in as early as 13 min (ID NOWTM Covid-19 2020). doi = 10.1007/s41403-020-00127-5 id = cord-030870-ao5p3ra3 author = Paul, Suman title = Dynamics and risk assessment of SARS-CoV-2 in urban areas: a geographical assessment on Kolkata Municipal Corporation, India date = 2020-08-25 keywords = India; Kolkata; SARS; case summary = Nearly 85% cases are reported from major cities of India and most interestingly, Mumbai, Delhi, Ahmedabad, Chennai, Thane, Pune, Kolkata become the most contributing urban centres to SARS-CoV-2 cases (as on 19 May, 2020). Further an attempt has also been made to quantify and assess the hotspot zones along with risks of the concentrated areas of Kolkata (one of the Metro city) for proper understanding of transmission of diseases in the congested and unhealthy places as a case study [9, 15, 16] . Based on socio-economic data of slum of Kolkata Municipal Corporation and containment zone data and containment zone data from different web sources we have selected the following indicators for quantity exposure, sensitivity and resilience for assessing the risk [22] infector disease like SARS-CoV-2 (see Table 1 ). As Kolkata has experienced 1st case of SARS-CoV-2, here we have taken ward wise containment zone to find out the nature of hot spots located in the Municipal area. doi = 10.1007/s41324-020-00354-6 id = cord-270683-982eqtog author = Pavel, Shaikh Terkis Islam title = Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date = 2020-09-16 keywords = Fig; SARS; Turkey; Vero summary = We determined that the Vero E6 and MA-104 cell lines are suitable for supporting SARS-CoV-2 that supports viral replication, development of cytopathic effect (CPE) and subsequent cell death. Phylogenetic analyses of the whole genome sequences showed that the hCoV-19/Turkey/ERAGEM-001/2020 strain clustered with the strains primarily from Australia, Canada, England, Iran and Kuwait and that the cases in the nearby clusters were reported to have travel history to Iran and to share the common unique nucleotide substitutions. For whole genome sequencing of hCoV-19/Turkey/ERAGEM-001/2020, Vero E6 cells infected with the virus were used for RNA extraction. The growth kinetics study showed that SARS-CoV-2 replicated rapidly and efficiently and could be detected within 6 h post-infection in Vero E6 and MA-104 cells (Fig 6A and 6B ). Immunoblotting analysis also confirmed that only Vero E6 and MA-104 cell lines infected with SARS-CoV-2 showed the expression of the virus specific proteins expression (Fig 5) . doi = 10.1371/journal.pone.0238614 id = cord-348478-ho89o8mj author = Pawlotsky, Jean-Michel title = SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date = 2020-05-15 keywords = SARS summary = This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) doi = 10.1093/cid/ciaa587 id = cord-342383-ckswlo9o author = Pawlowski, C. title = Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date = 2020-07-28 keywords = CoV-2; PCR; SARS summary = Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). Given this study population, we assess the rates of SARS-CoV-2 infection among individuals who did and did not receive one of 18 vaccines in the past 1, 2, and 5 years relative to the date of PCR testing. In Figure 6 , we present the results from the tipping point analysis on the statistically significant associations between vaccination and reduced rates of SARS-CoV-2 infection in the overall study population. For example, for the polio vaccine at the 1 year time horizon, an unobserved confounder with a relative risk of 2.78 which is prevalent in 17.8% of the vaccinated cohort and 0% of the unvaccinated cohort could explain the differences in SARS-CoV-2 infection rates that we observe in the data. doi = 10.1101/2020.07.27.20161976 id = cord-336769-5x6xjuew author = Payne, Daniel C. title = SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020 date = 2020-06-12 keywords = COVID-19; SARS summary = In April, the U.S. Navy and CDC investigated this outbreak, and the demographic, epidemiologic, and laboratory findings among a convenience sample of 382 service members serving aboard the aircraft carrier are reported in this study. At the time of specimen collection, participants completed a questionnaire eliciting information on demographic characteristics, exposure, COVID-19 protective behaviors, health history, and symptoms; participants also reported whether they had had a previous positive COVID-19 test since deployment but before this investigation. Among a convenience sample of 382 young adult U.S. service members aboard an aircraft carrier experiencing a COVID-19 outbreak, 60% had reactive antibodies, and 59% of those also had neutralizing antibodies at the time of specimen collection. In this convenience sample of young, healthy U.S. service members experiencing close contact aboard an aircraft carrier, those with previous or current SARS-CoV-2 infection experienced mild illness overall, and nearly 20% were asymptomatic. doi = 10.15585/mmwr.mm6923e4 id = cord-319781-6thdg2up author = Payne, Kelly title = Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date = 2020-07-24 keywords = Ebola; RNA; SARS; WNV; ZIKV; Zika summary = To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). Then, we present the state of current research regarding presence in semen, sexual transmission, and fertility effects for the Zika virus (ZIKV), Ebola virus (EBOV), West Nile virus (WNV), pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-coronavirus-2 (SARS-CoV-2) ( Table 1) . In this article, we have reviewed the presence in semen, possibility of sexual transmission, and fertility implications of each of the major recent viral pandemics: Zika, Ebola, West Nile, pandemic influenza, SARS, and SARS-CoV-2. doi = 10.1016/j.sxmr.2020.06.003 id = cord-281508-zl2url8z author = Pearce, N. title = Is death from Covid-19 a multistep process? date = 2020-06-03 keywords = CFR; SARS; covid-19 summary = The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope (indicating a smaller number of steps); in contrast, seasonal and pandemic influenza showed quite different agepatterns. These findings are consistent with a multistep model of disease involving a six-step process that in the case of SARS-COV-2 is probably defined by comorbidities and age producing immune-related susceptibility. doi = 10.1101/2020.06.01.20116608 id = cord-252103-lsaa1nx0 author = Pearks Wilkerson, Alison J title = Coronavirus outbreak in cheetahs: Lessons for SARS date = 2004-03-23 keywords = SARS summary = To characterize the genomic disposition of the cheetahs'' Aju-CoV strain, PCR primers based on alignment of seven coronavirus gene segments (pol1a, pol1b, S, M, N, 7a/7b, and 3′ ′UTR), were used to amplify cDNA from archived cheetah liver and kidney tissues collected during the Winston outbreak. The phylogenetic analyses indicate a close similarity of the Aju-CoV and the FCoV strains, suggesting the cheetah virus is closely related to, if not indistinguishable from, domestic cat isolates. Fourth, while mortality among humans with SARS symptoms and house cats with FCoV is low, around 5-10%, cheetahs with Aju-CoV exhibited the opposite extreme, showing 90% morbidity and over 60% mortality. If this hypothesis is correct, the greater genetic diversity of domestic cats and humans may reduce the severity of the epidemic, and also contribute to the occurrence of rare genetically determined SARS-CoV super-spreaders who can infect with high virulence. doi = 10.1016/j.cub.2004.02.051 id = cord-354051-ro3o27pv author = Peccia, J. title = SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date = 2020-05-22 keywords = RNA; SARS summary = title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant. SARS-CoV-2 viral RNA concentrations were quantitatively compared with local hospital admission data and community COVID-19 compiled testing data. SARS-CoV-2 RNA sludge concentrations were quantitatively compared with data that are commonly used to track the community progression of COVID-19 including hospital admissions (Figure 2A This study uniquely utilized primary sewage sludge instead of raw wastewater for virus RNA measurements. doi = 10.1101/2020.05.19.20105999 id = cord-327894-b0bsseui author = Pecellín, Lidia Gestoso title = Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date = 2020-10-14 keywords = COVID-19; PCR; SARS summary = En respuesta a la COVID-19, el gobierno español inicialmente instó a limitar el contacto social como medida general, sin embargo, otros países, además, implementaron pruebas generalizadas para la infección por SARS-COV-2 desde el principio de la pandemia. Son test sencillos de hacer, pero deben ser interpretados con prudencia, en relación con el curso de la infección, sobre todo por la tasa de falsos negativos en la detección de IgM ya que la respuesta de IgM en un enfermo COVID-19 puede tardar en aparecer desde varios días a dos semanas 21 Algunos estudios han mostrado que durante los primeros 7 días desde el inicio de síntomas, menos de un 40% de pacientes presentan anticuerpos IgM detectables. doi = 10.1016/j.enfcli.2020.10.001 id = cord-262266-m0fjt483 author = Peddu, Vikas title = Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization date = 2020-05-07 keywords = CoV-2; SARS summary = METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Eight unique patient samples consisting of six positive and two negative cases of suspected SARS-CoV-2 were sequenced using RNA extracted for a qRT-PCR diagnostic assay. Despite our reference database not containing any SARS-CoV-2 genomes, the six samples that were positive for SARS-CoV-2 by qRT-PCR had reads classified to Table 2) . Phylogenetic analysis revealed that the six SARS-CoV-2 sequences found cluster within two clades representing the Washington state and European outbreaks. doi = 10.1093/clinchem/hvaa106 id = cord-320970-ru2iw0py author = Peeling, Rosanna W title = Serology testing in the COVID-19 pandemic response date = 2020-07-17 keywords = COVID-19; SARS; test summary = On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. Point-of-care molecular assays for SARS-CoV-2 detection are now available to enable community-based testing for COVID-19 in LMICs. Unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving LMICs struggling for access. On the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. doi = 10.1016/s1473-3099(20)30517-x id = cord-311207-qkkn0297 author = Pegoraro, Manuela title = Evaluation of three immunochromatographic tests in COVID-19 serologic diagnosis and their clinical usefulness date = 2020-10-20 keywords = COVID-19; SARS summary = Different assays demonstrate 41–45% of diagnostic sensitivities and 91–98% of specificities, with substantial agreement (89.3–91.2%), but a high percentage of weak positive results (13–22%) was observed with ICTs. ICTs performances were comparable to those of automated immunoassays. In COVID-19 confirmed cases (symptomatic patient with SARS-CoV-2 positive molecular detection), date of symptoms onset was used to timing infection at the moment of specimens'' collection. Three stages were identified: early (0-7 days from symptoms onset), intermediate (8China), COVID-19 IgG/IgM Rapid Test Cassette (Zhejiang Orient Gene Biotech Co., Ltd Huzhou, Zhejiang, China), and PRIMA Professional (PRIMA Lab SA, Balerbna, Switzerland) are lateral flow immunochromatographic assays. Sensitivities were assessed on confirmed COVID-19 cases, combining IgG and IgM/IgA positive results, while specificities were estimated on the group of healthy volunteer''s. Compared with the automated immunoassays, the ability of ICTs to detect anti-SARS-CoV-2 IgG was equivalent to that of CLIA-MAGLUMI and better than ELISA-Euroimmun, whose IgG positive rates ranged between 0 and 86% at 14 days after symptoms onset. doi = 10.1007/s10096-020-04040-1 id = cord-260238-2p209g2p author = Peiris, J S M title = Severe acute respiratory syndrome date = 2004-11-30 keywords = SARS; acute; respiratory; severe; syndrome summary = Severe acute respiratory syndrome (SARS) was caused by a previously unrecognized animal coronavirus that exploited opportunities provided by ''wet markets'' in southern China to adapt to become a virus readily transmissible between humans. Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Characterization of severe acute respiratory syndrome-associated coronavirus (SARS CoV) spike glycoprotein-mediated viral entry Severe acute respiratory syndrome associated coronavirus (SARS CoV) infection inhibition using spike protein heptad repeat-derived peptides Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAB to S1 protein that blocks receptor association doi = 10.1038/nm1143 id = cord-260559-n8i52e8q author = Peiris, Malik title = What can we expect from first-generation COVID-19 vaccines? date = 2020-09-21 keywords = SARS; covid-19 summary = A popular assumption is that these vaccines will provide population immunity that can reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and lead to a resumption of pre-COVID-19 "normalcy". The immunological correlates of protection from SARS-CoV-2 infection and COVID-19 have yet to be elucidated. Pre-existing neutralising antibody seemed to have afforded protection against re-infection in people on board a fishing vessel where there was an outbreak of SARS-CoV-2 with a high infection attack rate. 20 Alongside the risks of severe morbidity and mortality and of disease transmission, this framework stipulates two additional criteria for equitable vaccine allocation-namely, risks of acquiring infection and of negative societal impact. If COVID-19 vaccines have acceptable effectiveness in reducing morbidity and mortality in high-risk groups, they would have an important role, irrespective of impact on transmission and population immunity. doi = 10.1016/s0140-6736(20)31976-0 id = cord-332827-gll4nqdd author = Peixe, Paula title = Hepatology in the COVID Era: Another C Virus, again Challenging the Liver date = 2020-04-30 keywords = COVID-19; Cov2; SARS; liver summary = In published series, liver disease was not identified as a risk factor for SARS-Cov2 infection [11] [12] [13] [14] [15] . The authors state that NAFLD patients also had a higher risk of progression to severe COVID-19 and present an increased viral clearance time. Immune-mediated liver diseases, particularly autoimmune hepatitis, have not been mentioned as risk factors for COVID-19, but the immunosuppressive treatment required has triggered fears about the risk of infection in patients. Extensive records and targeted studies are needed to explore multiple open-ended questions such as the severity and mortality of COVID-19 and episodes of acute-on-chronic or decompensation associated with the presence of this disease (ascites, hepatic encephalopathy, digestive bleeding, kidney dysfunction, and the risk of infection) or the response to treatment [25, 26] . However, it is not yet possible to say whether transplantation-associated immunosuppression can alter the predisposition for the acquisition of SARS-Cov2 infection or how COVID-19 evolves in these patients. doi = 10.1159/000508116 id = cord-331423-5wpx0bd0 author = Pelea, Teodor title = SARS-CoV-2 associated Guillain–Barré syndrome date = 2020-08-08 keywords = Barré; GBS; SARS summary = Presented herein is a severe case of SARS-CoV-2 associated Guillain–Barré syndrome (GBS), showing only slight improvement despite adequate therapy. Therefore patients with SARS-CoV-2 infection are at risk of being affected by coincident immune-mediated neurological diseases such as GBS. Severe course of GBS-associated SARS-CoV-2 infections occur also in patients with mild respiratory symptoms, but must be taken into account with seriously ill cases. To date, the previously described courses of the SARS-CoV-2 infection-associated GBS do not describe a special clinical pattern. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. Taking into account that GBS can cause a considerable impairment of the respiratory system, clinicians dealing with SARS-CoV-2 positive-tested patients should have to pay attention to symptoms of the peripheral nervous system. doi = 10.1007/s00415-020-10133-w id = cord-311696-ccbc1k1m author = Pelisser, Michel title = Sports balls as potential SARS-CoV-2 transmission vectors date = 2020-07-10 keywords = SARS; ball summary = Sports objects can only harbour inactivated SARS-CoV-2 under specific, directly transferred conditions, but wiping with a dry tissue or moist ''baby wipe'' or dropping and rolling the balls removes all detectable viral traces. The transmission potential of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) includes exposure duration of the virus, the number of viral particles one is exposed to and the route of exposure such as inhalation or skin contact [1, 2] . When SARS-CoV-2 positive control materials at 1,000 and 5,000 dC/mL concentrations are applied onto the whole surface of sport balls using BD polyester swabs, there was no detectable levels of the virus when observing the variables imposed in the experiment, including very short term testing after 30 seconds. On the other hand, when positive control at 5,000 copies/mL and 10,000 copies/mL concentrations are directly applied to the surface of cricket ball there are detectable levels of the virus at 30 seconds, 5 minutes and 1 hour (experiment 3). doi = 10.1016/j.puhip.2020.100029 id = cord-271411-h3k7r2ia author = Pelletier, Jesse S. title = Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination date = 2020-08-26 keywords = SARS; pvp summary = title: Reducing transmission of SARS-CoV-2 in ophthalmology with nasal and oral decontamination We believe that, additionally, nasal and oral decontamination measures may be implemented to reduce viral aerosolization before it reaches barriers, surfaces, and fomites. Nasal and oral decontamination is currently a routine step used to reduce postoperative infectious contamination across many surgical subspecialties. Povidone-iodine (PVP-I) is nearly universally virucidal and has recently shown rapid in vitro inactivation of SARS-CoV-2. Clinical studies of PVP-I in vivo support a durable, protective effect against bacteria and possibly SARS-CoV-2. 12 Nasal and oral decontamination strategy should be effective and convenient for use in outpatient ophthalmic clinics and ambulatory surgery centers (ASCs) in both developed and developing countries alike. Rapid in-vitro inactivation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using povidone-iodine oral antiseptic rinse Is povidone iodine mouthwash effective against SARS-CoV-2? doi = 10.1177/2515841420951392 id = cord-346512-y5d8q5b9 author = Pellicciaro, Marco title = Breast cancer patients with hormone neoadjuvant bridging therapy due to asymptomatic Corona virus infection. Case report, clinical and histopathologic findings date = 2020-10-08 keywords = COVID-19; SARS; breast summary = INTRODUCTION: Breast cancer management during COVID-19 pandemic has changed and in case of COVID-19 patients with simultaneous neoplasia, it has been strongly recommended to treat Sars-CoV-2 infection firstly. According to COVID-19 breast cancer recommendations she underwent hormone neoadjuvant treatment as a bridging therapy for surgery. We report a case of woman with COVID-19 and simultaneous early breast cancer treated with neoadjuvant endocrine therapy in lieu of upfront surgery and with lymph node micrometastases at pathological examination. Immunohistochemical staining revealed strongly and diffusely ER and PR positive in tumor cells: <95% and 40% respectively ( Figure 1B Before COVID-19 pandemic, patient such as this, with clinical stage T1N0, hormone receptors positive HER2-negative breast cancer, would have been a candidate for upfront surgery [11] . Therefore, the use of bridging therapy in patients with early breast cancer, during pandemic, that could benefit from upfront surgery should be evaluated in large sample studies. doi = 10.1016/j.ijscr.2020.10.020 id = cord-295029-zki5ac2g author = Pena, Robert C.F. title = In Reply to the Letter to the Editor Regarding “Coronavirus Neurosurgical/Head and Neck Drape to Prevent Aerosolization of Coronavirus Disease 2019 (COVID-19): The Lenox Hill Hospital/Northwell Health Solution” date = 2020-11-03 keywords = SARS; covid-19 summary = 1 This simple, cost-effective method can be easily assembled and is flexible with minimal disruption of the surgery being performed, while offering the ability to shield essential personnel in the operating room during procedures involving drilling of air-cells potentially harboring SARS-CoV-2 virions. 1,10 This draping method may therefore provide additional protection to surgeons against multiple viruses aerosolized by a wide range of drill settings, although further research should be conducted regarding COVID-19 aerosol generation in relation to drill speed in neurosurgical and otolaryngology-based procedures. Finally, whereas other researchers have proposed various methods of mask modification or alternate materials to provide barrier protection against COVID-19 aerosol transmission, 9 this and prior draping techniques may offer additional simple, easy to assemble, and cost-effective intraoperative protection. Specifically, this method provides protection to neurosurgical staff during high-speed drilling in the posterior fossa, whereas previously described drapes focus more on the restricted dissemination of COVID-19-laden aerosols during intubation, extubation, positive pressure ventilation, and endonasal endoscopic procedures. doi = 10.1016/j.wneu.2020.08.116 id = cord-280970-gy0kfhy6 author = Peng, Fujun title = Management and Treatment of COVID-19: The Chinese Experience date = 2020-04-17 keywords = COVID-19; China; SARS; Wuhan summary = Since mid-December 2019, there has been a worldwide outbreak of COronaVIrus Disease 90 (COVID)-19, caused by SARS-CoV-2 (formerly 2019-nCoV or and first detected in 91 Wuhan, China. 52 However, 421 a single-center in Wuhan shared that early, low-dose and short-term (1-2mg/kg/d for 5-7 days) 422 corticosteroids was associated with a faster improvement of clinical symptoms and absorption of 423 focal lung lesions in severe cases of COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Early, low-dose and short-term application of corticosteroid treatment in patients with severe COVID-19 pneumonia: single-center experience from Wuhan, China. doi = 10.1016/j.cjca.2020.04.010 id = cord-264260-8p6pvjkn author = Peng, Hongbing title = A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report date = 2020-07-16 keywords = COVID-19; February; SARS summary = title: A synergistic role of convalescent plasma and mesenchymal stem cells in the treatment of severely ill COVID-19 patients: a clinical case report We note that the intravenous infusion of CP and MSCs for the treatment of severe COVID-19 patients may have synergistic characteristics in inhibiting cytokine storm, promoting the repair of lung injury, and recovering pulmonary function. We reviewed a case of severe COVID-19 cured successfully with convalescent plasma-umbilical cord mesenchymal stem cells and observed and analyzed the change of clinical symptoms and laboratory data before and after treatment. From admission to discharge, the researchers continue to observe and evaluate patients'' dynamic changes in clinical symptoms and laboratory results, especially after receiving plasma and stem cell therapy. Intravenous infusion of human umbilical cord Wharton''s jelly-derived mesenchymal stem cells as a potential treatment for patients with COVID-19 pneumonia doi = 10.1186/s13287-020-01802-8 id = cord-297365-11es4w0u author = Peng, Hui title = Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes date = 2020-05-07 keywords = COVID-19; SARS summary = METHODS: We retrospectively summarized the characteristics, treatment and outcomes of pediatric cases in Wuhan children''s hospital which was the only designated hospital for children with COVID-19 in Hubei Province. In December 2019, a cluster of cases caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Wuhan, Hubei The observed cases were pediatric patients who were discharged from the Wuhan Children''s Hospital from December 8, 2019 to February 29, 2020 and diagnosed with COVID-19. Chinese Center for Disease Control and Prevention has analyzed the illness severity of 44415 adult and pediatric patients, and found that severe and critical cases accounted for nearly 20% [9] . A epidemiological study in Chinese children with COVID-19 (n=2143) showed that severe and critical illness accounted for J o u r n a l P r e -p r o o f 5.8% [10, 11] . Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study doi = 10.1016/j.jcv.2020.104425 id = cord-317573-wp2wr3b5 author = Peng, Hui title = Human memory T cell responses to SARS-CoV E protein date = 2006-06-30 keywords = IFN; SARS summary = In this study, we found that peripheral blood mononuclear cells (PBMCs) from fully recovered SARS individuals rapidly produced IFN-γ and IL-2 following stimulation with a pool of 9 peptides overlapping the entire E protein sequence. To assess memory T cell response specific for E protein after SARS-CoV infection in humans, PBMCs from individuals who had fully recovered from SARS two years after infection were stimulated with a pool of 9 peptides spanning the entire amino acid sequence of the SARS-CoV E protein, or the cells were stimulated with anti-CD3 and anti-CD28 antibodies under the same culture conditions as positive controls. Similarly, the frequency of SARS-CoV E antigen-specific IFN-g-producing cells determined by IFN-g ELISPOT assay in PBMCs from 8 fully recovered SARS individuals was significantly higher than that of the cells from the normal donor controls in response to E peptides (Fig. 1B) . doi = 10.1016/j.micinf.2006.05.008 id = cord-281860-zjvrohgg author = Peng, Jing title = Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2 date = 2020-09-18 keywords = DTT; SARS summary = Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. To address this, we treated clinical sputum specimens with four commonly used reagents-saline, NALC, PK, and DTT, prior to NA extraction, and compared their performance in diagnosing COVID-19 in real practice. With the sputum samples collected from the 47 patients having non-COVID-19 diseases, no amplification curves were observed for either the ORF1ab or N gene under any treatment conditions (saline, NALC, PK, and DTT), suggesting no SARS-CoV-2 in these samples. According to the positive criteria described in the methods section, pretreatment of sputum samples with NALC, PK, and DTT increased the detection of SARS-CoV-2 + cases to 85.7% (18/21), 95.2% (20/21), and 95.2% (20/21), respectively, as compared to the 52.4% (11/21) obtained with saline pretreated sputum (see Table 1 ). doi = 10.3389/fmed.2020.549860 id = cord-318036-t05ummop author = Peng, Liang title = 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples date = 2020-02-25 keywords = SARS summary = title: 2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples We aim to detect SARS-CoV-2 nucleic acid from urine, blood, anal swab and oropharyngeal swab samples. Nine patients confirmed diagnosed with SARS-CoV-2 infection(2) were included in this prospective study. https://doi.org/10.1101/2020.02.21.20026179 doi: medRxiv preprint enrolled patients were obtained and detected SARS-CoV-2 RNA level by quantitative real-time polymerase chain reaction (qRT-PCR). Patient 7, a 31 years old female without any urinary irritation, had positive results of SARS-CoV-2 in both urine and oropharyngeal swab on the 7 th day after symptom onset. Patient 8 had three positive results in blood, anal swab and oropharyngeal swab on the 3 rd day after onset. In our study, urine, blood, anal swab and oropharyngeal swab from 9 patients were retested by qRT-PCR. Nevertheless, the relative symptoms, including diarrhea and urinary irritation did not happen to every patient with virus in anal swab and urine specimens. doi = 10.1101/2020.02.21.20026179 id = cord-286573-k4khwvt7 author = Peng, Michael title = The Role of the Ocular Tissue in SARS-CoV-2 Transmission date = 2020-10-02 keywords = ACE2; COVID-19; SARS summary = Here, we reviewed both clinical and research evidence on the ocular manifestations associated with COVID-19, the presence of SARS-CoV-2 in ocular surface tissues and tears, and the potential role of the eye in contracting SARS-CoV-2. For this review, relevant studies that emphasized ocular manifestations of COVID-19 or SARS-CoV-2, viral detection of SARS-CoV-2 in ocular surface secretions or tears, and ACE2 presence in ocular tissues were included. 29 Zhang et al also reported that one of the two COVID-19 patients with conjunctivitis was SARS-CoV-2 RNA positive in the tear sample. Similarly, in a cross sectional study of 33 COVID-19 patients, most of the ocular samples were collected more than 7 days of symptom onset, and Xie et al found only 2 cases with positive ocular SARS-CoV-2 RNA results. 44 Recent studies have attempted to determine ACE2 in ocular surface tissues, such as the conjunctiva and cornea, which are exposed to the external environment and are potential entry points for SARS-CoV-2 infection. doi = 10.2147/opth.s269868 id = cord-312065-nqy7m38f author = Peng, Philip W. H. title = Infection control and anesthesia: Lessons learned from the Toronto SARS outbreak date = 2003 keywords = SARS; Toronto; case; patient summary = PURPOSE: To describe the outbreak of severe acute respiratory syndrome (SARS) in Toronto, its impact on anesthesia practice and the infection control guidelines adopted to manage patients in the operating room (OR) and to provide emergency intubation outside the OR. S of July 10, 2003, 438 cases (250 probable, 188 suspect) of severe acute respiratory syndrome (SARS) were reported in Canada, 375 (85.3%) of which occurred in Ontario. Because of early reports of clusters of cases in community settings such as apartment buildings and the high infection rates among health care workers in Hong Kong, Taiwan, Hanoi and Toronto, the etiological agent of SARS was thought to be highly contagious. Time should be allowed for the anesthesiologist and assistant to remove contaminated gloves, gowns, face shields or masks and head cover and renew protective precautions at the end of the case. doi = 10.1007/bf03018361 id = cord-280994-w8dtfjel author = Peng, Qi title = Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date = 2020-04-23 keywords = RNA; SARS; polymerase summary = Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities doi = 10.1101/2020.04.23.057265 id = cord-351482-hzh5tyoo author = Peng, Xinxia title = Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date = 2011-11-15 keywords = Fig; RNA; SARS; small; virus summary = The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). doi = 10.1128/mbio.00198-11 id = cord-311358-nrj4aysh author = Peng, Yuzhu title = Is novel coronavirus disease (COVID‐19) transmitted through conjunctiva? date = 2020-03-16 keywords = SARS summary = In theory, the premise for transmission through conjunctiva is that SARS-CoV-2 can replicate in conjunctival epithelia. 7 Currently it is unknown whether conjunctival epithelia can express ACE2. However, oral, nasal, and nasopharyngeal epithelia do not express ACE2, 8 which can explain that most of the COVID-19 patients did not have upper respiratory symptoms. It has been proposed that ''''2019-nCoV transmission through the ocular surface must not be ignored'''' based on the nosocomial infection of some ophthalmologists and an expert who wore an N95 mask but did not wear anything to protect his eyes was infected with SARS-CoV-2. Moreover, the inEvaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical characteristics of 50466 hospitalized patients with 2019-nCoV infection doi = 10.1002/jmv.25753 id = cord-288758-onis9xmo author = Peng, Z. title = Exhaled CO2 as COVID-19 infection risk proxy for different indoor environments and activities date = 2020-09-10 keywords = CO2; SARS summary = Contrary to some earlier recommendations setting a single indoor CO2 threshold, we show that the CO2 level corresponding to a given infection risk varies by over 2 orders of magnitude for different environments and activities. Although large uncertainties, mainly from virus exhalation rates, are still associated with our infection risk estimates, our study provides more specific and practical recommendations for low-cost CO2-based indoor infection risk monitoring. In this study, we derive the analytical expressions of the probability of indoor COVID-19 infection through room-level aerosol transmission only (i.e., assuming social distance is kept so that close proximity aerosol and droplet pathways are eliminated; fomite transmission is not included), human-exhaled CO2 concentration, and subsequently a few CO2-based quantities as infection risk proxies. where N is number of occupants, Ep is the SARS-CoV-2 exhalation rate by an infector (quanta h -1 ), mex mask filtration efficiency for exhalation, V indoor environment volume (m 3 ), and λ firstorder virus loss rate coefficient (h -1 ) that includes the ventilation with outdoor air and all other virus removal and deactivation processes. doi = 10.1101/2020.09.09.20191676 id = cord-315730-fzgxuak7 author = Penman, Sophie L. title = Safety perspectives on presently considered drugs for the treatment of COVID‐19 date = 2020-07-17 keywords = COVID-19; Health; IFN; SARS; clinical; infection; patient; treatment summary = Owing to their efficacy against viruses (mostly demonstrated in vitro) including influenza, HIV, coronavirus OC43, and SARS-CoV, a large number of clinical trials (>230) have been registered worldwide using chloroquine/hydroxychloroquine alone, or in combination with other drugs (e.g. azithromycin) for the treatment of COVID-19. At the time of writing, the RECOVERY trial (clinical trial identifier NCT04381936) which is the largest randomised control trial so far conducted for the treatment of COVID, has stopped recruiting to the hydroxychloroquine arm (1542 patients compared with 3132 on standard care) because of no beneficial effect either in terms of mortality or hospital stay (P. Assessment of QT Intervals in a Case Series of Patients With Coronavirus Disease 2019 (COVID-19) Infection Treated With Hydroxychloroquine Alone or in Combination With Azithromycin in an Intensive Care Unit Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/bph.15204 id = cord-269612-pmzdovna author = Pennington, Hugh title = Politics, media and microbiologists date = 2004 keywords = Hong; Kong; SARS summary = Studies on the SARS outbreak in Hong Kong 1 -after the exclusion of two ''superspread'' events where special circumstances allowed index cases to infect many individuals (at the Prince of Wales Hospital and at the Amoy Gardens estate) -gave an estimated R 0 value of 2.7. From analyses of samples taken from Vietnam, Singapore and Hong Kong, laboratories in the network ruled out the possibility of infection by any of the known influenza virus strains or other established causes of pneumonia, and concluded that SARS was new. It meant that the Hong Kong Department of Health, Hospital Authority and laboratory surveillance facility 11 , and the WHO, were particularly well prepared to respond to the SARS outbreak. In March 1997, an outbreak of avian influenza caused by the A virus subtype H5N1 killed several thousand chickens in three rural Hong Kong chicken farms. doi = 10.1038/nrmicro846 id = cord-311847-2czqs84q author = Pennisi, Manuela title = SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms date = 2020-07-31 keywords = ACE2; CNS; COVID-19; CoV-2; Coronavirus; SARS; patient summary = Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). Although there are limitations in the epidemiological studies carried on COVID-19, as well as limited case records for determining the actual incidence of these complications, some patients reported neurological symptoms, but clinical findings and pathogenic features have not yet systematically addressed. The aims of this review are i) to summarize the available information on the relationship between CoVs and the nervous system, ii) to identify the potential targets and routes of entry of SARS-CoV-2 into the nervous system, and iii) to describe the range of the neurological features reported to date in patients with COVID-19 and the proposed pathogenic mechanisms. Indeed, no axonal transport of SARS-CoV-2 to the brain has been demonstrated in the hamster model during the first two weeks after infection [89] , and no viral accumulation or persistence has been reported in cerebral olfactory regions of autopsy material from patients with COVID-19 [90] . doi = 10.3390/ijms21155475 id = cord-351430-bpv7p7zo author = Pequeno, Pedro title = Air transportation, population density and temperature predict the spread of COVID-19 in Brazil date = 2020-06-03 keywords = Brazil; COVID-19; SARS; number summary = Further, we considered the following predictors: (1) time in days, to account for the exponential growth in case numbers during this period (Fig. 2) ; (2) number of arriving flights in the city''s metropolitan area in 2020, as airline connections can facilitate the spread of the virus (Ribeiro et al., 2020) ; (3) city population density, to account for facilitation of transmission under higher densities (Poole, 2020) ; (4) proportion of elderly people (≥60 years old) in the population, assuming that the elderly may be more likely to show severe symptoms of SARS-CoV-2 and, thus, to be diagnosed with COVID-19; (5) citizen mean income, which may affect the likelihood of people being infected by the virus, for example, due to limited access to basic sanitation or limited social isolation capabilities; (6) and the following meteorological variables: mean daily temperature ( C), mean daily solar radiation (kJ/m 2 ), mean daily relative humidity (%) and mean daily precipitation (mm). doi = 10.7717/peerj.9322 id = cord-263039-uoxaem82 author = Perchetti, Garrett A. title = Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection date = 2020-07-23 keywords = SARS summary = Nucleic acid degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can compromise the accuracy of molecular detection methods. It has been demonstrated that nasopharyngeal specimens containing SARS-CoV-2 can be stored in phosphate-buffered saline (PBS) as a substitute for viral transport medium (VTM) for up to 7 days (3). Here, we evaluate the stability of differing viral loads of SARS-CoV-2 over 28 days stored at room temperature, 4°C, -20°C, or -80°C. For the high concentration of SARS-CoV-2, regardless of storage conditions, 100% of samples were detected by qRT-PCR through day 28. For lower concentrations of virus, storage at room temperature was associated with reductions of positivity beginning at day 7, and by day 28, 0% of samples were detected for N1. At viral loads of Ͼ5,000 copies/ ml-corresponding to Ͼ75% of positive samples recovered in our clinical lab to date-different storage temperatures did not have a substantial impact on our ability to detect SARS-CoV-2 when stored in PBS. doi = 10.1128/jcm.01094-20 id = cord-340336-u59l0taa author = Perchetti, Garrett A. title = Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date = 2020-06-08 keywords = PCR; SARS summary =  -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control. doi = 10.1016/j.jcv.2020.104499 id = cord-318483-il5aq8py author = Perez Gaxiola, G. title = Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa date = 2020-07-11 keywords = SARS; covid-19 summary = Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children admitted with COVID-19 to a secondary hospital. Although the prevalence of COVID-19 in childhood represents a low percentage of the totality of reported cases, varying between 0.8% and 2.7% (9) (10) (11) , the number of children that may become affected and the different clinical presentation of the disease compared to the adult population (4, 12) may be a challenge for pediatricians and general practitioners. The objectives of this study were to describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic in the region, and of a subset of those children admitted with COVID-19 to Sinaloa Pediatric Hospital (Hospital Pediátrico de Sinaloa "Dr. Rigoberto Aguilar Pico", HPS). This case series describes the clinical and epidemiological characteristics of children infected by SARS-CoV-2 during the first three months of the pandemic in the state of Sinaloa. doi = 10.1101/2020.07.07.20146332 id = cord-301216-a0rkpez7 author = Perez, Adriana title = Presentation of SARS-CoV-2 Infection As Cholestatic Jaundice in Two Healthy Adolescents date = 2020-07-23 keywords = COVID-19; SARS summary = Liver abnormalities in severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, including hepatitis and cholestasis, have been observed in adults and is associated with worse outcomes. As of June 25, 2020, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) resulted in >9.4 million confirmed cases worldwide and > 482,000 deaths worldwide, including > 2.3 million cases and > 121,000 deaths reported in the US, among which were 84 pediatric deaths in persons < 24 years of age by June 13 2020. The incidence of liver injury in adult patients with COVID-19 has been ranges from 14.8% -53%(, being more significant in severe cases and ranging up to 78% among fatal cases.(10) Liver abnormalities described included elevation of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST), mildly elevated bilirubin levels, high gamma-glutamyl transferase (GGT) and low albumin levels (2.6-3.3 g/L) (10, 11) . We present two cases of acute hepatitis with clinically apparent jaundice and cholestasis without biliary obstruction associated with SARS-CoV-2 infection. doi = 10.1016/j.jpeds.2020.07.054 id = cord-309915-isw1arrp author = Perez-Jurado, L. A. title = Immune defects and cardiovascular risk in X chromosome monosomy mosaicism mediated by loss of chromosome Y. A risk factor for SARS-CoV-2 vulnerability in elderly men? date = 2020-04-24 keywords = LOY; SARS summary = The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has an estimated overall case fatality ratio of 1.38% in China, being 53% higher in males and increasing exponentially with age. Using comparative transcriptomic data, we have defined that XCM/LOY is associated with abnormal peripheral blood cell counts with decreased progenitor cells and multiple biomarkers of immune system dysfunction, pro-coagulation activity and increased cardiovascular risk. 8 Individuals with XCM have an increased risk for autoimmune disease, recurrent viral infections and earlier cardiovascular mortality, 9 which has been attributed to X-chromosome haploinsufficiency for multiple genes, and is associated with excessive production of proinflammatory cytokines (IL-6), decrease in anti-inflammatory cytokines (IL-10, TGF-β) and a lower CD4:CD8 ratio. 19.20071357 doi: medRxiv preprint Association analysis between LOY status and clinical data, including blood cell counts and biochemical parameters, was assessed using linear models adjusted by age. doi = 10.1101/2020.04.19.20071357 id = cord-293274-ysr1l557 author = Perisé-Barrios, Ana Judith title = Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date = 2020-09-22 keywords = CoV-2; SARS; dog summary = Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. doi = 10.1101/2020.09.22.308023 id = cord-259396-vmc2q1bi author = Periyasamy, Petrick title = Aerosolized SARS-CoV-2 transmission risk: Surgical or N95 masks? date = 2020-09-15 keywords = SARS summary = WHO underlines the use of N95 respirators or equivalent as part of personal protective equipment (PPE) for healthcare workers (HCW) managing COVID-19 positive patients when aerosolised-generating-procedures (AGP) are being conducted.This retrospective observational study describes the result of COVID-19 reverse transcriptase polymerase chain reaction (RT-PCR) in health care workers (HCW) wearing different form of personal protective equipment (PPE) who had had close contact with a confirmed COVID-19 patient during performing such procedures. Little is known about the effectiveness of different types of personal protective equipment (PPE) for preventing SARS-CoV-2 in HCWs. We describe the clinical outcome of HCWs exposed to sudden acute respiratory infection patient before the diagnosis of COVID-19 was known. This retrospective observational study describes the result of reverse-transcriptase polymerase chain reaction (RT-PCR) testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in HCWs wearing different form of PPE who had close contact with a confirmed COVID-19 patient during performing AGPs. All HCWs were quarantined for 14 days after the exposure. doi = 10.1017/ice.2020.465 id = cord-257140-ge15qrqg author = Perkmann, T. title = Increasing both specificity and sensitivity of SARS-CoV-2 antibody tests by using an adaptive orthogonal testing approach date = 2020-11-07 keywords = Abbott; Roche; SARS summary = Methods To increase sensitivity, cut-offs of three commercially available SARS-CoV-2 automated assays (Roche, Abbott, and DiaSorin) were reduced according to published values in a pre-pandemic specificity cohort (n=1117) and a SARS-CoV-2 positive cohort (n=64). In our cohort, regardless of whether the assays were used for screening or confirmation, combining Roche and Abbott delivered the best overall performance (+~10% sensitivity compared to the single tests and 100% specificity). The disadvantage of this test strategy, which was recently shown in a study for the SARS-CoV-2 antibody tests from Abbott, Roche, and DiaSorin (19) , is that the gain in specificity usually comes at the expense of sensitivity and therefore increases the number of false negatives of individual tests. The Abbott Anti-SARS-CoV-2 IgG test, in contrast, reached 100.0% specificity only when followed by the Roche assay; in the other combinations, it remained slightly below, as a few false-positives persisted (99.8-99.9%). doi = 10.1101/2020.11.05.20226449 id = cord-326730-aprb819p author = Perkmann, T. title = Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity date = 2020-06-05 keywords = Abbott; Roche; SARS summary = Methods: We included a total of 1,154 specimens from pre-COVID-19 times and 65 samples from COVID-19 patients ([≥]14 days after symptom onset) to evaluate the test performance of SARS-CoV-2 serological assays by Abbott, Roche, and DiaSorin. Conclusion: We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. The present evaluation aims to compare three of these test systems manufactured by Abbott (11), DiaSorin (12), and Roche (13) , with particular emphasis on specificity, which is crucial for an adequate positive predictive value given the current low seroprevalence worldwide. We find diagnostically relevant differences in specificities for the anti-SARS-CoV-2 antibody assays by Abbott, Roche, and DiaSorin that have a significant impact on the positive predictability of these tests. doi = 10.1101/2020.06.04.20117911 id = cord-291374-1bpcj9dw author = Pernazza, Angelina title = Early histologic findings of pulmonary SARS-CoV-2 infection detected in a surgical specimen date = 2020-04-30 keywords = Fig; SARS summary = Here we describe the pathologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who developed SARS-CoV-2 infection soon after surgery. The main histologic findings observed were pneumocyte damage, alveolar hemorrhages with clustering of macrophages, prominent and diffuse neutrophilic margination within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T lymphocytes. Here we describe the histologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who later developed SARS-CoV-2 infection. A recent autopsy report highlights the finding of diffuse alveolar damage as the major lung feature also in severe SARS-CoV-2 infection [4] . Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore doi = 10.1007/s00428-020-02829-1 id = cord-300850-59j1m2tm author = Peron, Jean Pierre Schatzmann title = Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE) date = 2020-05-11 keywords = ACE-2; ADE; SARS summary = Toward this, we raise two main points, i) increased ACE-2 expression in pulmonary and heart tissues in users of chronic angiotensin 1 receptor (AT1R) blockers; and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. Toward this, we raise two main points of discussion, i) the increased angiotensin-converting enzyme-2 (ACE-2) expression in pulmonary and heart tissues of hypertensive patients with chronic use of AT1R blockers and ii) antibody-dependent enhancement (ADE) after previous exposure to other circulating coronaviruses. SARS-CoV-2 spike proteins bind to angiotensin-converting enzyme-2 (ACE-2), which is expressed in the epithelial cells of the lungs (8, 9) . We believe that i) increased expression of ACE-2 in hypertensive patients being treated with ACE inhibitors and AT1R blockers and ii) previous exposure to circulating coronaviruses with low neutralizing capacity to SARS-CoV-2 may greatly contribute to the increased susceptibility of the elderly patients to COVID-19. doi = 10.6061/clinics/2020/e1912 id = cord-273114-eanwxkvt author = Perrone, Serafina title = Report of a series of healthy term newborns from convalescent mothers with COVID-19 date = 2020-05-11 keywords = COVID-19; SARS summary = A further case series described 7 women with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), all of whom required oxygen therapy and received Caesarean section at term; only 3 neonates were tested, of whom one was positive. Here we report a series of cases of healthy term newborns whose mother developed COVID-19 infection during the third trimester of pregnancy and were convalescent with negative test at the time of delivery. Moreover, birth date, mode of delivery, gestational age, birth weight (g), anthropometric data, Apgar score 1''-5'', amniotic fluid, mother-child contact, clinical signs or symptoms and swab results was collected by newborns. Her husband suffered from COVID-19 infection and RT-PCR assay on her nasopharyngeal swab was positive for SARS-CoV-2. We reported four cases of healthy neonates born from mothers with previous SARS-CoV-2 pneumonia in the third trimester of pregnancy. doi = 10.23750/abm.v91i2.9743 id = cord-276619-6ndkz1da author = Perrone, Serafina title = Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum date = 2020-06-02 keywords = SARS summary = title: Lack of viral transmission to preterm newborn from a COVID‐19 positive breastfeeding mother at 11 days postpartum Lack of viral transmission to preterm newborn from a COVID-19 positive breastfeeding mother at 11 days postpartum In this paper, we reported the case of a mother who presented clinical symptoms of respiratory tract infection 10 days after the spontaneous delivery of a preterm newborn. Since birth, the newborn was fed with both breastfeeding and expressed maternal milk, and received Kangaroo Mother Care sessions. Postnatal horizontal COVID-19 infection occurred in newborns but expressed breast milk analysis did not reveal traces of the virus, so breastfeeding continued and the dyad was not separate. 9, 10 Here we describe a case of preterm baby breastfeeding mother at 11 days postpartum COVID-19 affected, in a NICU setting. Clinical characteristics of novel coronavirus disease 2019 (COVID-19) in newborns, infants and children doi = 10.1002/jmv.26037 id = cord-354209-g1zynbul author = Person, Bobbie title = Fear and Stigma: The Epidemic within the SARS Outbreak date = 2004-02-17 keywords = SARS; United; asian summary = While other NCID/CDC response teams dealt with laboratory investigations, surveillance, communica-tion, and clinical infection control practices, the Community Outreach Team worked to implement rapid public health strategies to document, monitor, and assist in ameliorating specific problems associated with fear, stigmatization, and discrimination attributed to the SARS outbreak in the United States. The team carried out the following activities: 1) facilitated group discussions with key opinion leaders within the Asian community in the United States; 2) collected and monitored the CDC Public Response Service data; 3) collected and monitored Asian-language newspapers, Internet sites, and other information sources; 4) reviewed polling data and other communication information; 5) conducted community visits, panel discussions, and media interviews; 6) solicited information from state and regional minority health liaisons nationwide; 7) developed ongoing relationships with the Asian-American communities; particularly in major metropolitan areas throughout the United States; and 8) determined new datagathering strategies as needed. doi = 10.3201/eid1002.030750 id = cord-278093-0twnkv93 author = Perveen, Shagufta title = Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date = 2020-06-18 keywords = SARS; disease; virus summary = Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. doi = 10.1016/j.jsps.2020.06.006 id = cord-267917-belkwihy author = Peters, Alexandra title = Putting some context to the aerosolization debate around SARS-CoV-2 date = 2020-04-30 keywords = SARS summary = 1 The experiments reported in this letter compared the stability of SARS-CoV-2 and SARS-CoV-1 in aerosols and on a number of different surfaces. The work showed that "SARS-CoV-2 remained viable in aerosols throughout the duration of (the) experiment (3 hours), with a reduction in infectious titer from 10 3.5 to 10 2.7 TCID50 per liter of air. [2] [3] [4] These media articles'' assertions include that SARS-Co V-2 can last "three hours after being coughed out into the air", 4 and that the van Doremalen et al. 2 The media even went as far as suggesting that the aerosols generated by the three-jet Collison nebulizer "duplicated the microscopic droplets created in a cough or a sneeze". It is for these reasons that the WHO and infection prevention specialists continue to support assertion that transmission of SARS-CoV-2 is primarily through droplets and contact (including indirect contact with contaminated surfaces). doi = 10.1016/j.jhin.2020.04.040 id = cord-311026-mpr3xb2a author = Petersen, Eskild title = COVID-19–We urgently need to start developing an exit strategy date = 2020-04-29 keywords = COVID-19; Hong; Kong; PDF; SARS summary = Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state''s strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. doi = 10.1016/j.ijid.2020.04.035 id = cord-274343-y9zqbefu author = Petersen, Irene title = Three Quarters of People with SARS-CoV-2 Infection are Asymptomatic: Analysis of English Household Survey Data date = 2020-10-08 keywords = SARS; covid-19 summary = We estimated sensitivity, specificity, the proportion of asymptomatic cases (1 – sensitivity), positive predictive value (PPV) and negative predictive value (NPV) of COVID-19 symptoms as a marker of infection using results of the SARS-CoV-2 test as the "gold standard". 8 In this analysis of data from a large representative study by the English Office for National Statistics we aimed to understand the value of COVID-19 symptoms as a marker for SARS-CoV-2 infection. We estimated the sensitivity, specificity, positive and negative predictive values of COVID-19 symptoms for SARS-CoV-2 infections as well as the proportion of asymptomatic cases (1 -sensitivity). We estimated the sensitivity, specificity, and positive and negative predictive values of COVID-19 symptoms as a marker of infection by using the results of the SARS-CoV-2 test as the "gold standard". To our knowledge, the Office for National Statistics Coronavirus (COVID-19) Infection Survey pilot is the largest population survey carried out to date including information on the association between COVID-19 symptoms and SARS-CoV-2 test results. doi = 10.2147/clep.s276825 id = cord-274750-fynxciwg author = Peterson, Danielle title = Calm before the storm: understanding the role of JAK inhibitors in COVID-19 date = 2020-04-25 keywords = SARS summary = Based on these 51 considerations, we believe there is insufficient evidence to recommend continuing JAK inhibitors in 52 patients who are acutely infected with SARS-CoV-2. 53 54 Napolitano et al suggest that baricitinib and upadacitinib might be useful in treating the cytokine 55 release syndrome (CRS) that can occur in SARS-CoV-2 infection. Furthermore, there is 58 evidence in both rhesus macaques and mice infected with the original SARS virus, SARS-CoV, that a 59 suboptimal early anti-viral type I interferon response may predispose to this late manifestation. In summary, we believe there is insufficient evidence to recommend that JAK inhibitors be continued in 70 all patients taking these medications who are acutely infected with SARS-CoV-2. While JAK inhibitors 71 may prove useful in the treatment of SARS-CoV-2-associated CRS, this is a separate consideration of a 72 relatively uncommon manifestation of this viral infection that occurs late in disease course. doi = 10.1016/j.jaad.2020.04.097 id = cord-309914-1lpl26eo author = Peterson, Danielle title = The use of Janus kinase inhibitors in the time of SARS-CoV-2 date = 2020-04-09 keywords = SARS summary = During the time of the SARS-CoV-2 pandemic, questions arise regarding patients being treated with 37 immunomodulatory therapies. In particular, is there an increased risk of acquiring the infection or 38 experiencing a worse outcome from SARS-CoV-2? we can look at safety data from clinical trials to try to understand patient susceptibility to different 40 infections. In light of the 42 growing off-label use of JAKi in dermatology in addition to pharmaceutical industry sponsored clinical 43 trials of JAKi for alopecia areata, atopic dermatitis, vitiligo, etc, dermatologists need data to better 44 understand the risks of JAKi treatment in order to best manage and counsel our patients during this 45 unique time. We analyzed and collated Adverse Events data from JAKi clinical trials. We also collated pulmonary 53 toxicities of JAKi to identify potential risks of worsening severe respiratory disease from SARS-CoV-2, and 54 such toxicities are all but absent. doi = 10.1016/j.jaad.2020.03.099 id = cord-312488-uzhj4i1q author = Petrosillo, Nicola title = SARS-CoV-2, “common cold” coronaviruses’ cross-reactivity and “herd immunity”: The razor of Ockham (1285-1347)? date = 2020-05-29 keywords = SARS summary = After the rapid spread of coronavirus-19 infectious disease (COVID-19) worldwide between February and April 2020, with a total of 5,267,419 confirmed cases and 341,155 deaths as of May 25, 2020, 1 in the last weeks we are observing a decrease in new infections in European countries, and the confirmed cases are not as severe as in the past, so much so that the number of patients transferred to intensive care for the worsening of the systemic and pulmonary disease is dramatically decreasing. 8 Virologists are claiming that there is no evidence of SARS-CoV-2 mutations causing less virulence and change of pathogenicity, 9 therefore, bending the epidemic curve could be simply the effect of progressive exhaustion of people susceptible to infection either due to a COVID-19 infection or for previous/recent "common cold" coronaviruses'' infections. doi = 10.4081/idr.2020.8647 id = cord-286555-rz88g3ze author = Petrovan, Vlad title = Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date = 2020-07-11 keywords = PCR; SARS summary = The most widely used molecular method approved by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) to detect SARS-CoV-2 is the real-time reverse transcription polymerase chain reaction (qRT-PCR) [4] . The protocol for the COVID-19 PCR Diatheva Detection Kit used with Fast Gene Probe One Step Mix uses 5 µL of mix 1 mixed with 0.625 µL of mix 2, 9.375 µL of primer/probe mix, and 5 µL of RNA template, with a total volume of 20 µL. An initial interlaboratory validation was performed by the Molecular Pathology Laboratory from the University Emergency Hospital Bucharest, using the PowerCheck 2019-nCoV Real-Time PCR Kit. This study was conducted as part of a surveillance program for COVID-19 implemented by the Romanian government. To determine the analytical sensitivity of the COVID-19 commercial assays used in Romanian hospitals (PowerCheck Kogene 2019-nCoV, COVID-19 PCR Diatheva Detection Kit, and 2019-nCoV CDC EUA), we first evaluated their limit of detection (LOD) by performing 10-fold serial dilutions of the controls provided by the kits. doi = 10.3390/diagnostics10070472 id = cord-353911-hp6s6ebh author = Petráš, Marek title = Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date = 2020-11-03 keywords = SARS; vaccine summary = title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. The above laboratory procedure generated a semi-split inactivated vaccine, i.e., a vaccine with 307 the S protein separated from the viral particle exhibiting an early, both humoral and cellular, 308 immune response. Safety and immunogenicity of the ChAdOx1 nCoV-386 19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, 387 randomised controlled trial An in-depth investigation of the safety and immunogenicity of an 468 inactivated SARS-CoV-2 vaccine A double-inactivated 499 whole virus candidate SARS coronavirus vaccine stimulates neutralising and 500 protective antibody responses. Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity 526 doi = 10.1101/2020.11.03.366641 id = cord-337692-b89ow1mf author = Petti, S. title = Ecologic association between influenza and COVID-19 mortality rates in European countries date = 2020-09-11 keywords = SARS; covid-19; mortality summary = Ecologic studies investigating COVID-19 mortality determinants, used to make predictions and design public health control measures, generally focused on population-based variable counterparts of individual-based risk factors. We considered the 3-year average influenza (2014–2016) and COVID-19 (31 May 2020) crude mortality rates in 34 countries using EUROSTAT and ECDC databases and performed correlation and regression analyses. An apparently perplexing characteristic of the reported association between the two mortality rates was that while influenza virus circulation during the seasons considered in the present analysis was uncontrolled, SARS-CoV-2 circulation was probably limited by the widespread exceptional public health measures implemented in Europe [32] . This study reported an inverse association between number of hospital beds and mortality rates (Table 2) , thus showing that high influenza and COVID-19 mortality was also due to inefficiencies of the healthcare systems, and corroborated by data from several European countries [45] . doi = 10.1017/s0950268820002125 id = cord-346146-yal0ctpq author = Peyronnet, Violaine title = Infection par le SARS-CoV-2 chez les femmes enceintes. Actualisation de l’état des connaissances et de la proposition de prise en charge. CNGOF date = 2020-10-05 keywords = COVID-19; SARS; des; les; une summary = L''objectif de la rédaction de ce document est d''actualiser les connaissances des professionnels de santé sur le SARS-Covid-2, ses symptômes, la connaissance actuelle sur la transmission inter individuelle et pendant la grossesse et de proposer un protocole de prise en charge pour les femmes enceintes en France modifiant celui proposé précédemment (1) . Cependant, des symptômes plus graves ont également été décrits dans ce contexte (16 à 32%) comme la pneumonie ou le syndrome de détresse respiratoire aiguë (SDRA) qui sont présents majoritairement chez les personnes âgées, les patients présentant une immunodépression ou des comorbidités telles que le diabète, un cancer ou une maladie respiratoire chronique et les femmes enceintes (4; 8; 12-17) Les caractéristiques épidémiologiques, cliniques, biologiques et radiologiques ont été décrites dans la population générale en premier par Huang et al. Enfin une autre série française multicentrique portant sur 100 femmes enceintes avec une infection certaine rapporte 5 cas de césariennes avant 32 SA pour cause de COVID chez des patientes hospitalisées en réanimation. doi = 10.1016/j.gofs.2020.10.001 id = cord-290950-v28kilvn author = Peyrony, Olivier title = Surfaces and equipment contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Emergency Department at a university hospital date = 2020-08-07 keywords = COVID-19; SARS summary = METHODS: We performed multiple samples from different sites in ED patients care and non-patient care areas with sterile premoistened swabs and used real-time reverse transcriptase polymerase chain reaction (RT-PCR) to detect the presence of SARS-CoV-2 ribonucleic acid (RNA). CONCLUSIONS: Our findings suggest that surfaces and equipment contamination by SARS-CoV-2 RNA in an ED during the COVID-19 outbreak is low and concerns exclusively patients'' examination and monitoring rooms, preserving non-patient care areas. In this study, we aimed to assess the surface and equipment contamination by SARS-CoV-2 of an ED during the COVID-19 outbreak depending on patient care and non-patient care areas. In our study, a sample was considered positive if either both ORF1a/b and E genes were Also, we did not detect any presence of SARS-CoV-2 RNA on the different surfaces of the patients'' registration desk or COVID-19 patients'' waiting room. doi = 10.1016/j.ijheh.2020.113600 id = cord-305139-851v2qr3 author = Peys, Elise title = Haemoptysis as the first presentation of COVID-19: a case report date = 2020-10-22 keywords = COVID-19; SARS; patient summary = This case emphasises the added value of bronchoscopy with BAL in the diagnostic work-up in case of high clinical suspicion and negative serial NPS in patients presenting with severe symptoms. Here, we report an unusual case of a man who presented with life-threatening haemoptysis as the first and unique symptom of COVID-19. According to the institutional guidelines during the current COVID-19 pandemic, nasopharyngeal swab (NPS) samples on two consecutive days were obtained and tested for SARS-CoV-2 using real-time polymerase chain reaction (RT-PCR), which repeatedly returned negative. Unusually, in this case, haemoptysis was the initial and unique symptom of SARS-CoV-2 infection in a patient with underlying emphysema. [7] , haemoptysis was the only clinical symptom during the first ten days of the disease course, whereas Casey and co-workers presented a case of COVID-19 associated with acute segmental pulmonary emboli which eventually caused haemoptysis [8] . doi = 10.1186/s12890-020-01312-6 id = cord-349684-2tioh80m author = Pezzotti, Giuseppe title = Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date = 2020-06-20 keywords = Fig; Nitride; RNA; SARS; Si3N4 summary = The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. doi = 10.1101/2020.06.19.159970 id = cord-267815-4fw7xgnt author = Peña, Juan A. title = A Survey of Labor and Delivery Practices in New York City during the COVID-19 Pandemic date = 2020-06-09 keywords = COVID-19; SARS summary = We therefore developed an internet-based survey to elucidate the practices put into place to guide the care of obstetrical patients during the COVID-19 pandemic. We found that all sites made changes to their practices, and that there appeared to be agreement with screening and testing for COVID-19, as well as labor and delivery protocols, for SARS-CoV-2-positive patients. One center performed SARS-CoV-2 PCR testing for all support persons either on admission to labor and delivery (L&D), or 24 to 48 hours prior to a scheduled admission. For half of the sites, after 34 weeks, the risks of continued expectant management of a patient with COVID-19 seemed to outweigh the risks of prematurity, and these centers would forgo testing and recommend delivery. Here we report on the obstetrical practices and protocols from four academic medical centers in NYC at the height of the COVID-19 pandemic. doi = 10.1055/s-0040-1713120 id = cord-293547-29i3u83s author = Pfaar, O title = COVID‐19 pandemic: Practical considerations on the organization of an allergy clinic – an EAACI/ARIA Position Paper date = 2020-06-12 keywords = COVID-19; EAACI; SARS; allergy; article; patient summary = RESULTS: Based on diagnostic and treatment standards developed by EAACI, on international information regarding COVID‐19, on guidelines of the World Health Organization (WHO) and other international organizations as well as on previous experience, a panel of experts including clinicians, psychologists, IT experts and basic scientists along with EAACI and the "Allergic Rhinitis and its Impact on Asthma (ARIA)" inititiative have developed recommendations for the optimal management of allergy clinics during the current COVID‐19 pandemic. CONCLUSIONS: This international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients whilst ensuring necessary safety in the current COVID‐19 pandemic. In the current SARS-CoV-2 pandemic, the European Task Force on Atopic Dermatitis (ETFAD) recommends to continue all immune-modulating treatment since exacerbations of underlying diseases can have a large negative impact on the patient''s immunity [30] . doi = 10.1111/all.14453 id = cord-277025-gmy51dx4 author = Pfefferle, Susanne title = Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date = 2020-06-04 keywords = PCR; SARS summary = title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany. A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China, as the alleged cause of a cluster of severe pneumonia cases (1) . Here, we describe the full-genome sequence of a SARS-CoV-2 strain (SARS-CoV-2/ human/DEU/HH-1/2020) isolated from a female patient with COVID-19. The isolate was obtained from an upper respiratory tract specimen (oropharyngeal swab) from a 62-year-old woman who was part of a small local cluster of COVID-19 cases, originating from a household contact who likely acquired the virus while traveling in Italy. The samples after trimming contained 18,369,904 high-quality paired-end reads, with 61,312 ϫ 2 reads (e.g., 122,624 reads) mapping to the reference Wuhan-Hu-1 sequence (GenBank accession number NC_045512.2) (6). doi = 10.1128/mra.00520-20 id = cord-291965-9r9ll83m author = Pfefferle, Susanne title = Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date = 2009-09-17 keywords = MRCA; RNA; SARS; bat summary = Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc. doi = 10.3201/eid1509.090224 id = cord-304058-i8cywew0 author = Pfefferle, Susanne title = Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date = 2009-08-24 keywords = Frankfurt-1; ORF; PCR; RNA; SARS; figure summary = title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). doi = 10.1186/1743-422x-6-131 id = cord-320085-n9i54wzh author = Pfefferle, Susanne title = Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date = 2020-03-05 keywords = PCR; SARS summary = We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus. In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. doi = 10.2807/1560-7917.es.2020.25.9.2000152 id = cord-298773-vnmc6nqd author = Pfeiffer, Julie K. title = Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? date = 2015-01-20 keywords = MERS; SARS summary = title: Is the Debate and "Pause" on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? This letter is about the potential impact of the debate and pause on graduate students and postdoctoral fellows and how their future plans may be affected. To gain initial insight into how the debate and research pause have affected trainees, I created an informal survey 2 days before the National Academy of Sciences meeting. These projects involve a subset of "gain of function" experiments designed to create mouse adapted viral strains, generate drug resistant viruses to understand drug mechanisms of action, understand host immunity by analyzing viruses with resistance to certain host immune pathways, and to study factors that influence transmission by the respiratory route (which was made famous by work from the Kawaoka and Fouchier labs in 2012). Third, the debate and research pause are influencing future plans of virology trainees. doi = 10.1128/mbio.02525-14 id = cord-312646-hfv7ce3f author = Pfützner, Andreas title = Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV- 2 in a community screening setting shows low sensitivity date = 2020-06-02 keywords = SARS summary = title: Comment to Döhla et al., Rapid point-of-care testing for SARS-CoV2 in a community screening setting shows low sensitivity In this manuscript, a point-of-care rapid test for assessment of anti-SARS-CoV-2 virus antibodies (IgG/IgM) is evaluated for sensitivity and specificity to detect the viral infection. They found that the antibody rapid test only detects 36.4 % of the samples identified as positive by means of RT-PCR, and conclude that this POCT is not recommendable for community screenings. In case that recent reports are confirmed that people with past infections may become asymptomatic carriers of the SARS-CoV-2 virus [3] , the antibody tests may be the only way to differentiate PCR-positive subjects into two groups: i.) patients who are freshly infected and may soon develop clinical symptoms (negative IgG result) and ii.) patients who have developed antibodies and may now be asymptomatic virus spreaders (positive IgG result). Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity doi = 10.1016/j.puhe.2020.05.048 id = cord-255293-8necodtw author = Phakthanakanok, Krongsakda title = A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism date = 2009-01-30 keywords = SARS summary = The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. In order to perform molecular dynamics simulations, three structures of the SARS CoVMpro complexed with the octapeptides obtained from the docking, were prepared. However, one atom of the Na+ was also added in each system of the enzyme-substrate complexed of the octapeptide P3Lys and P3Arg due to it neutralized the amino acid, Lys and Arg. In the simulation, each time step was set to 2 fs and the simulation of the whole system performed for 2,000 ps (2 ns). The structure of the enzyme-substrate complex (SARS CoVMpro-octapeptide) obtained from molecular docking was then subjected to MD simulation. doi = 10.1186/1471-2105-10-s1-s48 id = cord-310160-55yltan1 author = Pham, Jimmykim title = Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection date = 2020-09-22 keywords = SARS; TMA summary = In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. The analytical sensitivity of the SARS-CoV-2 TMA assay was assessed using 2 lots of reagents to test 60 replicates each of dilution panels containing cultured SARS-CoV-2 virus strain USA-WA1/2020 (BEI Resources, Manassas, VA) and diluted in Aptima specimen transport medium (STM) matrix to a range of 0.03 to 0.0003 50% tissue culture infectious dose (TCID 50 )/ml. This analysis resulted in positive, negative, and overall agreements of 100% (95% CI, 94.3% to 100%), Clinical performance of the SARS-CoV-2 TMA assay was also assessed by testing sets of NP swab, OP swab, and nasal swab specimens co-collected from 35 symptomatic patients suspected of being infected with SARS-CoV-2. doi = 10.1128/jcm.01669-20 id = cord-325136-oyizfh2z author = Pham, Quang Thai title = The first 100 days of SARS-CoV-2 control in Vietnam date = 2020-08-01 keywords = SARS; Vietnam summary = METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). doi = 10.1093/cid/ciaa1130 id = cord-301183-k39e12cq author = Pham, Tho D. title = SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution date = 2020-07-17 keywords = SARS summary = title: SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution than 1 month after symptom resolution is concerning in light of current guidelines, which do not recommend SARS-CoV-2 screening in the general allogeneic donor population (5) . In this case, plasma viral RNA was reproducibly detected at a time point that exceeded recommendations for deferral based on time since symptom resolution (14 days). Of importance, these results are unlikely to be false-positive given that 2 different regions of the SARS-CoV-2 genome were detected in separate specimens collected on the day of donation and that quality control passed on all runs, including the absence of amplification in the negative controls. Of note, however, the infectivity of SARS-CoV-2 from blood remains unknown and, to date, we are not aware of cases of transfusion-transmitted COVID-19. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations doi = 10.7326/l20-0725 id = cord-318239-2sraqm6e author = Phan, Lan T. title = Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam date = 2020-05-28 keywords = Nguyen; SARS summary = title: Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent In this report, we describe clinical features, virus isolation, and complete genome sequences from the first two SARS-CoV-2 infections in Vietnam. A suspected case was defined as a person with an acute respiratory tract illness, who reported that he/she had fever and cough (with and without difficulty in breathing) and that within 14 days before the onset of disease, he/she had returned or came from areas where SARS-CoV-2 was spreading or had exposed to a laboratory-confirmed case of Covid-19. NP and OP swab specimens of the patients were collected in a single tube containing 3mL virus transport media and tested for SARS-CoV-2 by real-time RT-PCR assays described previously. Once the CPE was observed under the microscope, cell culture supernatants were harvested, divided into aliquots, tested for the presence of SARS-CoV-2 by real-time RT-PCR assays, and stored at -70°C until virus titration and sequencing were performed. doi = 10.1002/jmv.26075 id = cord-351169-y91fdf66 author = Phillips, Lia title = Successful management of SARS-CoV-2 acute respiratory distress syndrome and newly diagnosed acute lymphoblastic leukemia date = 2020-09-14 keywords = CoV-2; SARS summary = Corticosteroid can be given safely to patients with SARS-CoV-2 presenting with acute respiratory distress syndrome and ALL. Although recommendations are emerging for the general management of oncology patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 1,2 there is little experience in patients with newly diagnosed acute lymphoblastic leukemia (ALL). Providers may have concern about initiating multiagent chemotherapy in patients with SARS-CoV-2, particularly corticosteroids, which are an essential part of induction regimens, but raise the theoretical possibility of delayed viral clearance. We describe our experience of successfully initiating therapy for an adolescent diagnosed with ALL, while managing severe SARS-CoV-2 infection marked by respiratory failure, systemic inflammation, and autoimmune hemolytic anemia (AIHA). 1, 2 In this case, intensive remission induction chemotherapy was initially delayed due to concern for potential worsening of SARS-CoV-2 disease by exacerbating the patient''s already immunocompromised state in the setting of ALL. doi = 10.1182/bloodadvances.2020002745 id = cord-288632-2aliqy8p author = Phillips, Nicole title = The Perfect Storm: COVID-19 Health Disparities in US Blacks date = 2020-09-23 keywords = ACE2; IL-6; SARS; covid-19 summary = Specifically, Fig. 1 illustrates a conceptual model through which psychological influences (stress, anxiety, depression), pre-existing/comorbid disease (e.g., HTN, T2DM), and COVID-19 interconnect on the basis of known and unknown genetic variations that translate into human health outcomes and molecular modes of viral pathogenesis. Importantly, it is the interplay between key environmental exposures (stress; social determinants of health, SDH) and genetic predisposition for aspects of viral pathogenesis and/or comorbid disease (e.g., type 2 diabetes mellitus, T2DM; hypertension, HTN) that ultimately converges on COVID-19 manifestation and affects mortality . While there is conflicting data regarding the effects of variants in all three of the candidate genes discussed here, the remarkable relevance of associated phenotypes to COVID-19 pathophysiology together implies that genetic polymorphisms which regulate immune and stress responses may interact to affect underlying disease risk and, simultaneously, SARS-CoV-2 pathogenicity. doi = 10.1007/s40615-020-00871-y id = cord-273251-k3ltbpnb author = Phipps, Meaghan M. title = Acute Liver Injury in COVID‐19: Prevalence and Association with Clinical Outcomes in a Large US Cohort date = 2020-05-30 keywords = SARS; ULN; alt summary = In multivariable analysis, peak ALT was significantly associated with death or discharge to hospice (OR 1.14, p=0.044), controlling for age, body mass index, diabetes, hypertension, intubation, and renal replacement therapy. (18) Patients with a positive test for SARS-CoV-2 were evaluated in subsequent analyses, categorized into those with peak ALT consistent with no/mild liver injury (<2 times ULN), moderate liver injury (2) (3) (4) (5) times ULN) and severe liver injury (>5 times ULN). Although initial alkaline phosphatase levels were similar across all categories of ALT, median peak value was higher in patients with severe liver injury (p<0.001), however it was only mildly elevated. In this cohort with 2273 cases and 1108 controls, we demonstrate that initial and peak ALT are higher in those who test positive for SARS-CoV-2 compared to those who test negative with a similar clinical presentation. Higher peak ALT values were also significantly associated with overall disease severity and measured clinical outcomes. doi = 10.1002/hep.31404 id = cord-308945-i2agpvhk author = Phipps, William S title = SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date = 2020-07-15 keywords = CoV-2; PCR; SARS summary = METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. Long et al 8 have described a variable antiviral IgM and IgG immune response to SARS-CoV-2 infection in a Chinese population in which seroconversion in a group of 285 patients from 3 hospitals showed IgG positivity for all cases beyond 17 to 19 days. The goals of this study were to ascertain key performance metrics of analytical specificity and cross-reactivity for a SARS-CoV-2 IgG serologic assay, perform a detailed cross-sectional and serial assessment of IgG and IgM antibody responses in suspected COVID-19 patients, and determine their relation to disease severity. SARS-CoV-2 IgG antibody results agreed with the PCR-negative samples for 96 of 97 (99%) of cases, including 55 instances of patients with new or acute-on-chronic symptoms suspicious for COVID-19 and with known time of onset. doi = 10.1093/ajcp/aqaa123 id = cord-351107-a5bx74ao author = Phua, Ghee-Chee title = Mechanical Ventilation in an Airborne Epidemic date = 2008-06-30 keywords = H5N1; SARS; care summary = The severe acute respiratory syndrome outbreak exposed the vulnerability of health care workers and highlighted the importance of establishing stringent infection control and crisis management protocols. Approximately 20% to 30% of SARS patients required intensive care and mechanical ventilation for acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) [9] . Adjuvant strategies shown to decrease morbidity and mortality in critically ill patients on mechanical ventilation include deep venous thrombosis prophylaxis, stress ulcer prophylaxis, sedation protocols, and avoidance of neuromuscular blockage, if possible; semirecumbent position should also be employed during airborne epidemics causing hypoxemic respiratory failure [18] . With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. With the increasing threat of pandemic influenza and catastrophic bioterrorism, it is important for intensive care providers to be prepared to meet the challenge of large-scale airborne epidemics causing mass casualty respiratory failure. doi = 10.1016/j.ccm.2008.01.001 id = cord-301454-ayf42grs author = Phyu Khin, Phyu title = A potential therapeutic combination for treatment of COVID-19: synergistic effect of DPP4 and RAAS suppression date = 2020-08-14 keywords = COVID-19; SARS summary = A recent study proved that coronavirus SARS-CoV-2 also uses dipeptidyl peptidase-4 (DPP4, also known as adenosine deaminase complexing protein 2, CD26) as a co-receptor when entering cells. In particular, SARS-CoV-2 is able to infect T lymphocytes despite their very low expression level of ACE-2, implying an alternate receptor for viral entry [5, 6] . Among elderly patients (average age: 80 years) infected with SARS-CoV-2 in Italy in early 2020, the mortality rate was highest in patients with hypertension (69%), followed by those with type 2 diabetes (31%), and those with ischemic heart diseases (27%) [5] . The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based cardiovascular therapies. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients With Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China doi = 10.1016/j.mehy.2020.110186 id = cord-263308-q0iriid8 author = Piano, Carla title = An Italian Neurology Outpatient Clinic Facing SARS-CoV-2 Pandemic: Data From 2,167 Patients date = 2020-05-29 keywords = SARS; covid-19; neurological summary = Methods: Patients with chronic neurologic diseases routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for symptoms suggestive of SARS-CoV-2 infection in the pandemic period, consequences of social restrictions, and neurological disease features, concomitant medical conditions, current medical and disease-specific treatments. Specifically, the survey assessed: (1) Demographic and clinical characteristics, including age at onset, duration of illness, and disability measures (ADL/IADL) (8); (2) COVID-19 related questions, including history of recent travel in endemic areas, direct contacts with COVID-19 confirmed cases (COVID-19+), symptoms suggestive of COVID-19 infection started or worsened in the last 3 months (fever, cough/sore throat, asthenia, dyspnea, myalgia, and hyposmia/hypogeusia), and confirmatory testing for COVID-19 (nasal/pharyngeal swab test results); (3) information related to the impact of COVID-19 on disease burden, including subjective worsening of neurological symptoms, compliance with restrictions and specific effects of restriction measures on the perception of illness (need of urgent neurological care, discontinuation of pharmacological treatment or physiotherapy, difficulties in finding drugs). doi = 10.3389/fneur.2020.00564 id = cord-295523-5pv7kw6i author = Picchianti Diamanti, Andrea title = Cytokine Release Syndrome in COVID-19 Patients, A New Scenario for an Old Concern: The Fragile Balance between Infections and Autoimmunity date = 2020-05-08 keywords = COVID-19; CRS; IL-6; SARS; TNF; patient summary = However, in about 20% of patients, the infection progresses to severe interstitial pneumonia and can induce an uncontrolled host-immune response, leading to a life-threatening condition called cytokine release syndrome (CRS). We critically review the rationale for the adoption of immunosuppressive agents, commonly used in autoimmune diseases, in the treatment of SARS-CoV-2 infection and report current knowledge of ongoing studies. The exacerbated reaction to infections or to biological therapy is caused by the rapid recruitment of macrophages and neutrophils, which produce pro-inflammatory cytokines and alter the fragile balance between a controlled immune response and a host-damaging reaction. As of now, four clinical trials are recruiting patients with COVID-19, severe acute respiratory failure, and CRS, aiming at evaluating the safety and effectiveness of anakinra alone or in combination with anti-IL-6 agents (NCT04330638, NCT0432402, NCT04357366, NCT04339712). High disease activity is associated with an increased risk of infection in patients with rheumatoid arthritis doi = 10.3390/ijms21093330 id = cord-275173-ely3aen3 author = Pickering, Brad S. title = Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date = 2020-09-10 keywords = DPI; SARS summary = The work reported here aims to determine whether domestic swine are susceptible to 63 SARS-CoV-2 infection, providing critical information to aid public health risk assessments. The data presented in 66 this study provides evidence live SARS-CoV-2 virus can persist in swine for at least 13 days 67 following experimental inoculation. Two pigs (20-10, 20-11) displayed low 237 levels of viral RNA by RT-qPCR at 3 DPI (Table 2, Detection of SARS-CoV-2 was also attempted from whole blood by RT-qPCR, following 253 the sampling schedule outlined in Table 1 . To identify potential target tissues or gross lesions consistent with SARS-CoV-2 disease, 261 necropsy was performed on two animals starting at 3 DPI and every other day up to day 15; with 262 an additional two pigs necropsied at both 22 and 29 DPI (Table 1) (Table 2) . The results presented in this study define domestic swine as a susceptible species albeit at 293 low levels to SARS-CoV-2 viral infection. doi = 10.1101/2020.09.10.288548 id = cord-317057-c2bwky6e author = Pickering, S. title = Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date = 2020-06-04 keywords = ELISA; June; SARS summary = A highly specific in-house ELISA was developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs) on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative 4 ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing gold standard for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the best performing configuration of the in-house ELISA (detection of anti-S IgM and IgG antibodies), which was also most likely to represent antibodies detected by the commercial tests. doi = 10.1101/2020.06.02.20120345 id = cord-351952-lhhjax3s author = Pickering, Suzanne title = Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings date = 2020-09-24 keywords = ELISA; Fig; SARS summary = Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays—a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)—on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. Accordingly, we developed a highly specific semi-quantitative ELISA for the detection of anti-spike (S), -S receptor binding domain (RBD) and -N antibodies, and used this to cross-evaluate ten commercial antibody tests (seven lateral flow immunoassays (LFIAs), one chemiluminescent assay and two ELISAs) on a collection of 110 serum samples from confirmed RNA positive patients, and 50 pre-pandemic samples from March 2019. With no existing standardised diagnostic test for the assessment of the serological response to SARS-CoV-2, we started by comparing commercial serological assays with the configuration of the in-house ELISA most likely to represent antibodies detected by the commercial tests (detection of anti-S IgM and IgG antibodies), and that had high specificity and sensitivity (S1 Table) . doi = 10.1371/journal.ppat.1008817 id = cord-285580-gq7400tq author = Pieretti, Joana C. title = Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date = 2020-10-18 keywords = COVID-19; SARS summary = In this mini-review, we discuss recent progress concerning the antivirus activity of NO in clinical, pre-clinical and research settings, and its beneficial effects in the treatment of clinical complications in patients infected with coronaviruses and other respiratory viral diseases, including COVID-19. Although positive biological effects have been reported for the administration of NO donors, further studies are required to better evaluate the levels of inflammatory mediators and the activity of important heme-containing enzymes, such as indoleamine 2,3-dioxygenase (IDO), directly involved in the inflammatory responses in respiratory viral infections (Anderson and Russel, 2020) . In other words, NO demonstrates potential for the treatment of patients infected with COVID-19 both in severe and nonsevere conditions, improving oxygenation and antiviral mechanisms, and preventing aggravation of the disease (Ferrari et al., 2020; Parikh et al., 2020) . Protocol of a randomized controlled trial testing inhaled nitric oxide in mechanically ventilated patients with severe acute respiratory syndrome in COVID-19 (SARS-CoV-2) doi = 10.1016/j.virusres.2020.198202 id = cord-316979-uadlclsv author = Pierri, Ciro Leonardo title = SARS-CoV-2 spike protein: flexibility as a new target for fighting infection date = 2020-10-30 keywords = SARS; spike summary = The recent study of Turoňová et al., is the first to combine cryoelectron tomography, subtomogram averaging, and molecular dynamics simulations for analyzing the structure of the SARS-CoV-2 spike protein in situ, 1 i.e. while the virus interacts with tissue cultured cells. Notably, in a recent analysis of conformational changes determining the post-fusion conformation observed for a similar coronavirus spike cryo-EM structure 5 and the related SARS-CoV-2 spike 3D comparative model 2 ( Fig. 1) , it was proposed that the loss of the N-terminal domain (residues 1-703, black cartoon) causes the reorientation of the 704-715 peptide, which was involved in maintaining the tight packing of the central helix (CH) and the heptad repeat 1 (HR1) domain, together with the N-terminal domain. Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies doi = 10.1038/s41392-020-00369-3 id = cord-261718-zqoggwnk author = Pietschmann, Jan title = Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date = 2020-06-03 keywords = CoV-2; SARS summary = Available point-of-care diagnostic systems as lateral flow assays have high potential for fast and easy on-site antibody testing but are lacking specificity, sensitivity or possibility for quantitative measurements. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. For magnetic immuno-detection, immunofiltration columns were coated with a SARS-CoV-2 spike protein peptide. After addition of 176 biotinylated GaR and subsequent labelling with streptavidin-AP, the ELISA plate was read out at 177 405 nm and obtained measuring values were used to generate calibration curves for SARS-CoV-2 178 specific antibody concentrations in PBS (Fig 1, black curve) and in human serum samples (Fig 1, red 179 curve). Same calibration measurements employing dilutions of SARS-CoV-2 specific antibody were 211 done with our PoC MInD-based setup (Fig 2 and 3) . Comparable to laboratory-based ELISA, the same 212 dilutions of SARS-CoV-2 spike protein peptide specific antibody in PBS-buffer (Fig 3, black doi = 10.1101/2020.06.02.131102 id = cord-333654-8rg99di5 author = Pillai, Presaad title = COVID-19 AND MAJOR ORGAN THROMBOEMBOLISM: MANIFESTATIONS IN NEUROVASCULAR AND CARDIOVASCULAR SYSTEMS. date = 2020-10-24 keywords = COVID-19; SARS; patient summary = The disease, caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2), has to date been responsible for more than 800,000 deaths globally, economic upheaval and significant lifestyle changes. 5, 6, 7 However, more recently immune mediated thrombosis has been a consistent finding in a significant number of patients with of Covid-19 and understanding its pathophysiological mechanisms and impact on morbidity and mortality in COVID-19 may open new avenues in disease prognostication and management. Thus, D-dimer level could potentially be an early and helpful marker to improve the management of COVID-19 and point clinicians to the possibility of silent thrombosis occurring in the pre-symptomatic stage which might dictate the natural history, progression and severity of the disease in a manner that has not been seen in previous coronavirus infections. Other significant risk factors, excluding raised D-dimer and CRP, that were associated with a high mortality rate for these patients with NVD, were comorbidities, age and increased severity of COVID-19 infection. doi = 10.1016/j.jstrokecerebrovasdis.2020.105427 id = cord-346145-hnfeauow author = Pillay, Sureshnee title = Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic date = 2020-08-17 keywords = Illumina; SARS; figure summary = title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic In our SARS-CoV-2 assembly workflow, the initial assembly obtained from Genome Detective was polished by aligning mapped reads to the reference (NC_045512) and filtering out mutations with low genotype likelihoods, using bcftools 1.7-2 mpileup method. Furthermore, reagents for only 24 samples were available, as the order of Illumina TruSeq DNA Library preparation kit (x 96 sample libraries), which was placed in February and was enough to produce 480 genomes, had not arrived, due to the restrictions on international flights. The Nextera Flex library preparation kit was suggested by their technical team as a potentially better and quicker solution to produce SARS-CoV-2 genomes, which we found to be true. The Nextera Flex DNA library preparation kit was also evaluated, and we found it saved up to nine hours of hands-on time, when compared with the original ARTIC protocol that uses TruSeq. All three library preparation methods produced high-quality genomes. doi = 10.3390/genes11080949 id = cord-315556-84rgd2s9 author = Pilotto, A. title = Steroid-responsive severe encephalopathy in SARS-CoV-2 infection date = 2020-04-17 keywords = COVID-19; SARS; preprint summary = SARS-CoV-2 infection has the potential for targeting central nervous system and several neurological symptoms have been described in patients with severe respiratory distress. Here we described the case of an otherwise healthy 60-year old subject with SARS-CoV-2 infection but only mild respiratory abnormalities who developed severe progressive encephalopathy associated with mild pleocytosis and hyperproteinorrachia. The patient dramatically improved after high-doses steroid treatment suggesting an inflammatory-mediated brain involvement related to SARS-CoV-2 infection Recently, a study posted in medRxiv4 and still unpublished has reported neurological manifestations in COVID-19 in the outbreak in China in up to 36.4% of patients hospitalized, including alteration of consciousness, headache, dizziness and delirium 6 . The here described COVID-19 case is of particular interest, as the patients presented with severe encephalopathy with only mild respiratory alterations. Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. doi = 10.1101/2020.04.12.20062646 id = cord-290001-603qy8ml author = Pimentel, Lígia L. title = Cholesterol, inflammation, and phospholipids: COVID-19 share traits with cardiovascular disease date = 2020-10-17 keywords = COVID-19; SARS summary = COVID-19, the severe acute respiratory syndrome produced by the coronavirus SARS-CoV-2, has resulted to date in more than 27 million infected cases and 900000 deaths worldwide since the first reported cases in December 2019 at the Chinese city of Wuhan (for updated information readers can consult https://covid19.who.int/). Moreover, total counts of white blood cells (WBC) were significantly higher in patients in critical condition [1] and those with severe respiratory failure showed macrophage activation syndrome [4], confirmed by the presence of monocyte recruiting chemokines in bronchoalveolar fluid [2] . Furthermore, plasma lipidomic analyses have revealed a close relationship between the severity of COVID-19 and circulating lipids: a combination of larger levels of atherogenic diglycerides (DG 16:0/20:2/20:0) and triglycerides (TG 14:0/22:1/22:3), alterations of the phosphatidylinositol (PI) signalling system with decreased concentrations of phosphatidylcholine (PC) [7] and sphingosine-1-phosphate (S1P) [8] . Thus, it was observed in SARS-CoV-2 positive subjects that anticardiolipin antibodies (aCL IgG) profile (>15 U/mL) was associated to disease severity (i.e.respiratory distress) while those patients have not a previous record history of thrombosis [11] . doi = 10.1016/j.bbalip.2020.158839 id = cord-345887-ymo4mxx7 author = Pinky title = Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 date = 2020-07-13 keywords = COVID-19; MSC; SARS; cell; exosome summary = title: Mesenchymal Stem Cell Derived Exosomes: a Nano Platform for Therapeutics and Drug Delivery in Combating COVID-19 With an urgent need for the development of potential strategies, two recent studies from China using Mesenchymal Stem Cells (MSCs) to treat COVID-19 pneumonia have shed some light on a potential cure for the COVID-19 infected patients. Also, attractive features like cell targeting, low-immunogenicity, safety, and high biocompatibility distinguish these exosomes from other synthetic nano-vesicles and thus potentiate their role as a drug delivery nano-platform. However, this study is first of its kind evaluating MSCs derived exosomes therapeutic potential for COVID-19 [45] . Some of the pre-clinical studies evaluating the effect of MSC derived exosomes on lung macrophages in various lung injury models have provided insights into the exosome derived approach as a new strategy for treating nCOV associated pathogenicity. Exosomes derived from bone marrow mesenchymal stem cells as treatment for severe COVID-19 doi = 10.1007/s12015-020-10002-z id = cord-352526-t8odetzw author = Pinto, Bruna G G title = ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19 date = 2020-06-11 keywords = ACE2; SARS; covid-19 summary = Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. The molecular mechanism responsible for the increased disease severity in patients with these comorbidities is not fully understood, but previous studies suggest a role for angiotensin-converting enzyme 2 (ACE2) (5) . Here, we showed that the expression of the gene encoding the ACE2 receptor in lung tissue is upregulated by diseases representing comorbidities along with COVID-19. doi = 10.1093/infdis/jiaa332 id = cord-262958-tmp6yxlv author = Pinto, Dora title = Structural and functional analysis of a potent sarbecovirus neutralizing antibody date = 2020-04-09 keywords = CoV-2; S309; SARS summary = The SARS-CoV-2 spike (S) glycoprotein 26 promotes entry into host cells and is the main target of neutralizing antibodies. None of the mAbs studied bound to 97 prefusion OC43 S or MERS-CoV S ectodomain trimers, indicating a lack of cross-98 reactivity outside the sarbecovirus subgenus (Extended Data Fig.1) . The structural data explain the S309 cross-reactivity between SARS-CoV-2 and 148 SARS-CoV as 19 out of 24 residues of the epitope are strictly conserved ( Fig. 2f and 149 Extended Data Fig. 6a To further investigate the mechanism of S309-mediated neutralization, we 175 compared side-by-side transduction of SARS-CoV-2-MLV in the presence of either 176 S309 Fab or S309 IgG. This analysis 208 identified at least four antigenic sites within the S B domain of SARS-CoV targeted by 209 our panel of mAbs. The receptor-binding motif, which is targeted by S230, S227 and 210 S110, is termed site I. doi = 10.1101/2020.04.07.023903 id = cord-313247-55loucvc author = Pipes, Lenore title = Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date = 2020-10-07 keywords = SARS summary = We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution. There are many different methods for inferring the root of a phylogenetic tree, but they largely depend on three possible sources of information: outgroups, the molecular clock, and non-reversibility. To investigate the possible rootings of the SARS-CoV-2 phylogeny we used six different methods and quantified the uncertainty in the placement of the root for each method on the inferred maximum likelihood topology. We note that while interpretation of bootstrap proportions in phylogenetics can be problematic (see Efron et al., 1996) we performed 1,000 parametric simulations using pyvolve (Spielman and Wilke, 2015) using maximum likelihood estimates, from the original data set, of the model of molecular evolution and the phylogenetic tree, including branch lengths (see Table S2 ). doi = 10.1101/2020.06.19.160630 id = cord-193133-puqcbf8t author = Piplani, Sakshi title = In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus date = 2020-05-13 keywords = ACE2; CoV-2; SARS; protein summary = The devastating impact of the COVID19 pandemic caused by SARS coronavirus 2 (SARSCoV2) has raised important questions on the origins of this virus, the mechanisms of any zoonotic transfer from exotic animals to humans, whether companion animals or those used for commercial purposes can act as reservoirs for infection, and the reasons for the large variations in susceptibilities across animal species. Here we show how computational chemistry methods from structure-based drug design can be used to determine the relative binding affinities of the SARS-CoV-2 spike protein for its receptor, angiotensin converting enzyme (ACE)-2, a critical initiating event for SARS-CoV-2 infection, across multiple common and exotic animal species. 31, 32 Molecular docking was performed on the homology modelled SARS-CoV-2 spike protein with human and animal ACE2 proteins. The molecular dynamics simulation of complexes of SARS-CoV-2 spike protein and ACE2 receptors of various species were performed for 100ns. doi = nan id = cord-353365-ujz5nkk3 author = Pirnay, Jean-Paul title = Study of a SARS-CoV-2 Outbreak in a Belgian Military Education and Training Center in Maradi, Niger date = 2020-08-27 keywords = Maradi; Niger; SARS; belgian; covid-19 summary = The medical military command implemented testing of all Belgian soldiers for SARS-CoV-2 viral load and antibodies, two to three days before their departure on a mission abroad or on the high seas, and for specific missions immediately upon their return in Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. The SARS-CoV-2 outbreak in a Belgian military education and training center in Maradi, Niger, was characterized by mild symptoms in five soldiers and asymptomatic infection in two soldiers (one trainer), both having a viral load, as diagnosed upon their timely return to Belgium. doi = 10.3390/v12090949 id = cord-297208-f4ob3ox6 author = Pisano, Antonio title = Cardiothoracic surgery at the time of COVID-19 pandemic: lessons from the East (and from a previous epidemic) for western battlefields date = 2020-05-06 keywords = SARS; patient summary = 1 Evidently, countries which faced the severe acute respiratory syndrome (SARS) outbreak, the first coronavirus pandemic of the current century which affected more than 8000 people (mainly in China, Vietnam, Singapore and Canada) in 2003 7 , were much more prepared, both culturally and in terms of facilities and equipment, as compared with western countries (many of which had to face, in the initial stages of the emergency, the shortage of even simple and cheap devices such as surgical masks). doi = 10.1053/j.jvca.2020.04.051 id = cord-336447-hpnkou41 author = Pitlik, Silvio Daniel title = COVID-19 Compared to Other Pandemic Diseases date = 2020-07-31 keywords = COVID-19; RNA; SARS; disease; pandemic; virus summary = Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. doi = 10.5041/rmmj.10418 id = cord-253876-2dc9jq79 author = Pitocco, Dario title = Lack of type 1 diabetes involvement in SARS-COV-2 population: Only a particular coincidence? date = 2020-05-19 keywords = SARS summary = In 1591 Italian subjects affected by SARS-COV-2, there was a prevalence of 17% of type 2 diabetes. This observation needs to be confirmed and further evaluated, for example in regions with high prevalence of the disease (Scandinavian, Finland or Sardinian), but there could be a number of reasons that justify a low incidence of SARS-COV-2 in subjects with type 1 diabetes. Indeed, we cannot rule out that there are some asymptomatic subjects with SARS-COV-2 infection in type 1 diabetic population. Finally, while the infected population has a high prevalence of hypertension, type 1 diabetes is often characterized by hyperglycemia in the absence of the other cardiovascular risk factors. Prevalence and impact of diabetes among people infected with SARS-CoV-2 All the authors have made substantive contributions to the article and assume full responsibility for its content doi = 10.1016/j.diabres.2020.108220 id = cord-347221-g98q9cga author = Piyush, Ravikant title = Nucleic acid-based therapy for coronavirus disease 2019 date = 2020-09-19 keywords = RNA; SARS; dna; nucleic summary = This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen. doi = 10.1016/j.heliyon.2020.e05007 id = cord-272626-bw9lbzvt author = Pizzorno, Andrés title = Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date = 2020-04-02 keywords = Fig; HAE; SARS summary = Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Developed from biopsies of nasal or bronchial cells differentiated in the air/liquid interphase, these models reproduce with high fidelity most of the main structural, functional and innate immune features of the human respiratory epithelium that play a central role 70 in the early stages of infection and constitute robust surrogates to study airway disease mechanisms and for drug discovery (10) . Comparably, daily treatment with 20 µM remdesivir resulted in 7.3 log10 and 7.9 log10 reductions of intracellular SARS-CoV-2 viral titers at 48 hpi in nasal and bronchial HAE, respectively (Fig. 4D, upper panel) . doi = 10.1101/2020.03.31.017889 id = cord-277860-vzyrcmu4 author = Pizzorno, Andrés title = In vitro evaluation of antiviral activity of single and combined repurposable drugs against SARS-CoV-2 date = 2020-07-15 keywords = SARS summary = In vitro evaluation of antiviral activity of single and combined repurposable drugs 1 against SARS-CoV-2 2 3 Authors: Andrés Pizzorno a , Blandine Padey a,b , Julia Dubois a , Thomas Julien a,c , Aurélien 4 Traversier a , Victoria Dulière a,c , Pauline Brun a,c , Bruno Lina a,d , Manuel Rosa-Calatrava a,c* † , 5 Olivier Terrier a* † 6 7 Author affiliations: Abstract: 27 In response to the current pandemic caused by the novel SARS-CoV-2, identifying and 28 validating effective therapeutic strategies is more than ever necessary. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. We evaluated the in 29 vitro antiviral activities of a shortlist of compounds, known for their cellular broad-spectrum 30 activities, together with drugs that are currently under evaluation in clinical trials for COVID-31 19 patients. doi = 10.1016/j.antiviral.2020.104878 id = cord-253282-zwl0safn author = Plant, Ewan P. title = Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date = 2013-01-18 keywords = RNA; SARS; figure; stem summary = In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. Here, analyses using synonymous protein coding mutations demonstrate that the region of the genome that harbors the frameshift signal affects the regulation of genomic and subgenomic RNA production without altering protein sequence. Here we describe deletion and mutagenesis experiments with a dual luciferase reporter to show that the effect the sequence between stems 1 and 2 has on frameshifting efficiency is due to structural changes those mutations cause in the pseudoknot. Similar to previously described viruses containing mutations in the slippery site of the frameshift signal [7] , here we show that mutations to the SARS-CoV frameshift stimulating mRNA pseudoknot can also affect the production of viral genomic RNA. doi = 10.3390/v5010279 id = cord-329914-3b233vxl author = Plantier, L. title = Pratique des explorations fonctionnelles respiratoires pendant l’épidémie COVID-19 date = 2020-06-05 keywords = Cov2; SARS summary = Préambule et mise en garde L''objectif de ces propositions est de prévenir la transmission du virus SARS-Cov2 lors de la pratique des explorations fonctionnelles respiratoires au repos et à l''exercice, dans le contexte général de l''assouplissement progressif des mesures de distanciation sociale débuté le 11 mai 2020. On peut rappeler que la persistance dans le poumon profond de l''ARN viral au-delà du 50 e jour avait été observée chez des patients infectés par SARS-Cov1 [7] . Proposition 3 : Bien que la structure d''EFR réponde à la définition d''un secteur à faible densité virale, nous considérons que des précautions complémentaires visant à protéger les personnels et les patients sont indispensables du fait 1) de la contagiosité des sujets asymptomatiques et 2) des particularités de l''EFR et notamment de la génération de gouttelettes et/ou d''aérosols potentiellement infectants lors des manoeuvres expiratoires [12] et la toux [13, 14] , du risque de déconnexion accidentelle du filtre antimicrobien et de la possibilité d''une toux induite par l''examen. doi = 10.1016/j.rmr.2020.06.002 id = cord-323943-9916y6x0 author = Platt, Daniel E title = Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails date = 2020-04-21 keywords = COVID-19; SARS; rate summary = Therefore, we sought to understand whether the parameters of epidemic models could be determined from the trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the quality and comparability of data between jurisdictions reporting their statistics necessary for the analysis of model parameters across populations. Beside host and viral genetic impacts, other aspects driving SARS-COV-2 rates are population specific and demic, such as the impact of age on both asymptomatic and mild cases, as well as the proportion of severe and critical cases. In this paper, we seek to identify the limitations of using compartmental models to estimate or test hypotheses concerning parameters governing the growth of SARS-COV-2 epidemics. Therefore, infected population growth may be more closely reflected in the fraction of positive results normalized by total number of tests applied, in spite of very highly biased sampling selection. The rate of growth and doubling time may reflect availability and levels of testing more than the actual disease in the population. doi = 10.1101/2020.04.20.20071928 id = cord-346960-3empldlo author = Plebani, M. title = Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity date = 2020-08-04 keywords = CoV-2; SARS summary = In 184 serum samples from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT). On limiting the analysis to samples collected 12 days after onset of symptoms, the sensitivity of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. 54 SARS-CoV-2 negative subjects (33 healthcare workers, 21 autoimmune patients, 8 pregnant women) were included in the study ( Moreover, Liaison SARS-CoV-2 S1/S2 IgG (Diasorin, Sallugia-VC, Italy), ENZY-Well SARS-CoV-2 IgA and IgM were evaluated for the correlation with the neutralization results. . To provide insight on neutralization activity compared with immunoassays results, PRNT assay was performed on 52 samples from SARS-CoV-2 positive subjects. doi = 10.1101/2020.08.01.20166546 id = cord-252033-43fbfglt author = Plebani, Mario title = Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays? date = 2020-05-30 keywords = CLIA; Liaison; SARS summary = METHODS: Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Aim of this study was to evaluate different chemiluminescent (CLIA) and enzyme-linked immunosorbent (ELISA) assays for SARS-CoV-2 antibodies in COVID-19 patients and healthcare operators, to identify appropriate cut-offs and evaluate diagnostic accuracy. Donors (only for CLIA assays) and negative autoimmune patients results were included to verify possible analytical interferences and differences with respect to healthcare workers who repeatedly tested negative to nasopharyngeal swab. Rigorous comparative performance data are crucial to understanding the potential clinical usefulness of serological assays, starting from the evaluation of analytical performance characteristics to improve the definition of diagnostic accuracy not only in terms of specificity and sensitivity but also as positive and negative likelihood ratios, in order to provide reliable clinical information in different disease prevalence settings. doi = 10.1016/j.cca.2020.05.050 id = cord-284954-uuqchon4 author = Plebani, Mario title = SARS-CoV-2 antibody-based SURVEILLANCE: New light in the SHADOW date = 2020-11-05 keywords = SARS summary = The paper by Perico and coworkers, published in this issue of EBioMedicine, is a comprehensive analysis of the prevalence of SARS-CoV-2 infection in the Bergamo province, an area of Italy that experienced a massive COVID-19 outbreak, with its epicenter in the whole Lombardy region. Furthermore, in a study performed in Iceland on the measurement of SARS-CoV-2 antibodies, it is estimated that 44% of individuals infected with the virus were not diagnosed by quantitative polymerase-chain-reaction (qPCR) thus confirming the risk of under-diagnosis on using molecular testing alone [2] . The paper by Perico and colleagues is welcome for several reasons: first, it confirms the usefulness of SARS-CoV-2 antibody assay for a better knowledge of the spread of the infection in a specific population or subpopulation, and for avoiding the risk of under-diagnosis when using rRT-PCR testing alone. doi = 10.1016/j.ebiom.2020.103087 id = cord-024100-lk67yfrp author = Plewczynski, Dariusz title = In Silico Prediction of SARS Protease Inhibitors by Virtual High Throughput Screening date = 2007-04-24 keywords = PDB; SARS summary = Selected molecules having close structural relationship to a 2‐methyl‐2,4‐pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors. In this study, we exploited structural homologs of SARS-CoV protease co-crystallized with small molecules to explore opportunities for drug design of potential inhibitors for this therapeutic target enzyme. We have explored the use of structural information contained in PDB database for an in silico virtual drug discovery campaign using, as a case study, the main protease of SARS-CoV. Using this method, plausible inhibitors were generated as based only on the set of ligands from crystallized complexes of a protein Figure 1 : Two dimensional chemical structures presented in Table II: Plewczynski et al. The docking was performed on small molecules and short peptides extracted from protein-ligand complexes of the viral cysteine proteases of trypsin-fold. Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease doi = 10.1111/j.1747-0285.2007.00475.x id = cord-279932-bilr71ay author = Plotkin, Stanley A title = The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date = 2020-07-16 keywords = SARS summary = A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development doi = 10.1093/cid/ciaa1013 id = cord-294999-a5x8bmfr author = Plotkin, Stanley A title = The New Coronavirus, the Current King of China date = 2020-02-21 keywords = SARS summary = There are several candidate vaccines against MERS being developed by an international organization, the Coalition for Epidemic Preparedness (CEPI; see below) [13] . Although yet to be confirmed at this writing, it is likely that SARS-CoV-2 originated from infections transferred from small mammals in the Wuhan market to humans. Aside from the development of vaccines against SARS-CoV-2, a step the Chinese government should take is to ban the sale of small mammals in their markets to prevent the introduction of other coronaviruses or, for that matter, pathogens in general that could adapt to humans. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study A synthetic consensus anti-spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates A double-inactivated whole virus candidate SARS coronavirus vaccine stimulates neutralising and protective antibody responses doi = 10.1093/jpids/piaa018 id = cord-323216-rgj8vs9z author = Plotkin, Stanley A title = Vaccination Against Severe Acute Respiratory Syndrome Coronavirus 2 date = 2020-08-03 keywords = SARS summary = There is a universal and widely acknowledged need for a vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because of its widespread circulation and high mortality and morbidity. Although some vaccine efforts use the whole inactivated or attenuated virus, the great majority concentrate on the Spike protein, which contains 2 parts: S1 and S2. Table 1 summarizes the current approaches to development of vaccines against SARS-CoV-2. Vaccine developers have experimented with many different ways to present the S protein or, in some cases, the RBD domain to the immune system. There are many important issues that must be answered in these trials, including: Can vaccination prevent infection as well as disease? Will evolution of the SARS-CoV-2 virus require changes in vaccine antigens? Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry The challenges of vaccine development against a new virus during a pandemic doi = 10.1093/jpids/piaa093 id = cord-324949-sqy03dks author = Poe, Francis L. title = N-Acetylcysteine: a potential therapeutic agent for SARS-CoV-2 date = 2020-05-30 keywords = NAC; SARS; TNF summary = In vivo, in vitro, and human clinical trials have demonstrated N-acetylcysteine (NAC) as an effective method of improving redox status, especially when under oxidative stress. Mediation of the viral load could occur through NAC''s ability to increase cellular redox status via maximizing the rate limiting step of glutathione synthesis, and thereby potentially decreasing the effects of virally induced oxidative stress and cell death. The pathogenic factors of SARS-CoV-2 that could possibly be mediated by NAC are (1) T cell exhaustion, which manifests as lower counts and decreased functional capacity of CD4+ and CD8+ cells; (2) pro-inflammatory state via increase in TNF-ɑ, IL1β, IL18; and (3) modulation of viral activity through increased glutathione. Mediation of the viral load could occur through the ability of NAC to increase cellular redox status by maximizing the rate limiting step of glutathione synthesis, and thereby decreasing the effects of virally induced oxidative stress and cell death. doi = 10.1016/j.mehy.2020.109862 id = cord-355181-affuyn8z author = Poggio, Claudio title = Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date = 2020-07-22 keywords = COVID-19; SARS; copper; surface; virus summary = SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . doi = 10.3390/ma13153244 id = cord-257719-5s6acr7m author = Poh Ng, Lisa Fong title = The Virus That Changed My World date = 2003-12-22 keywords = SARS; Singapore summary = In the three months that Singapore was labelled as a "SARS country" by the World Health Organization (WHO), over 200 cases of SARS were reported, and 33 people died. Referring to the high standards of medical care and the societal measures put in place, Dr David Mansoor of WHO said that if not even Singapore could contain the outbreak, it was going to be very hard for other countries to prevent SARS from spreading (Chua 2003 I was to be part of the diagnostic team, and work began almost immediately. Data obtained from this work were significant for further understanding of coronavirus replication and pathogenesis, but never had I imagined that I would be able to use this knowledge in designing the SARS-CoV diagnostic kit with Roche. The months working on SARS opened my mind, as it did my heart, about the importance of research and of keeping our faith and motivation even in the toughest times. doi = 10.1371/journal.pbio.0000066 id = cord-276335-e1xlwcvc author = Poh, W.P. title = Characterization of cytotoxic T‐lymphocyte epitopes and immune responses to SARS coronavirus spike DNA vaccine expressing the RGD‐integrin‐binding motif date = 2009-05-27 keywords = RGD; RMA; SARS; dna summary = Significant cell‐mediated immune responses were characterized by cytotoxic T‐lymphocyte (51)Cr release assay and interferon‐gamma secretion ELISPOT assay against RMA‐S target cells presenting predicted MHC class I H2‐Kb epitopes, including those spanning residues 884–891 and 1116–1123 within the S2 subunit of SARS‐CoV spike protein. The production of antigen-specific antibody induced by the SARS-CoV spike DNA vaccinations was assessed For the MHC-peptide binding assay, the mean fluorescence increase (MFI) was calculated as the ratio of the fluorescence of peptide-loaded RMA-S cells to the fluorescence of unloaded RMA-S cells. Mouse IFN-g ELISPOT for splenocytes of C57BL/6 mice immunized with selected S-His and S-RGD/His DNA vaccines to confirm T-cell epitopes of spike protein. This study demonstrated that prime-boost immunization of mice with SARS-CoV spike DNA vaccine constructs S-His and S-RGD/His induced significant antigen-specific cellular immune responses, IFN-g stimulation, and CTL activation. doi = 10.1002/jmv.21571 id = cord-276209-5999g9gp author = Poland, Gregory A. title = Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine development date = 2020-06-02 keywords = SARS; vaccine summary = Very soon thereafter, the causative agent was identified as the now-named SARS-CoV-2 virus-a betacoronavirus that had crossed the species barrier to infect humans. There is no question that a vaccine against this virus, and other as-yet-to-come coronaviruses, is imperative to protect human health and to quickly respond to future viral introductions, epidemics, and pandemics. These pathways, informed by science and the past history of successes and failures, are designed to maximize the chances of efficacy and safety. Further mutations could conceivably lead to issues of original antigenic sin with resultant disease enhancement after exposure or to vaccines that simply are not effective into the future. In addition to safety issues, I raise concern over ''''S-only" vaccine approaches for the mid-to long-term control of this RNA virus. We need a vaccine-and we need it as quickly as one can be developed-that demonstrates safety and efficacy in adequately powered studies. doi = 10.1016/j.vaccine.2020.04.073 id = cord-287205-k64svq6n author = Pollet, Jeroen title = SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date = 2020-11-05 keywords = Alhydrogel; RBD; RBD219-N1C1; SARS summary = title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. The modified SARS-CoV-2 antigen, 264 RBD219-N1C1, when formulated on Alhydrogel ® , was shown to induce virus-neutralizing antibodies 265 in mice, equivalent to those levels elicited by the wild-type (RBD219-WT) recombinant protein 266 counterpart. Here we report on a yeast-expressed SARS-CoV-2 RBD219-N1C1 protein and its potential as a 397 vaccine candidate antigen for preventing COVID-19. In a mouse virus challenge model for the SARS CoV RBD recombinant protein vaccine, we 422 found that Alhydrogel ® formulations induced high levels of protective immunity but did not 423 stimulate eosinophilic immune enhancement, suggesting that Alhydrogel ® may even reduce immune The selection of the P. doi = 10.1101/2020.11.04.367359 id = cord-298669-g2up0cfi author = Pollock, David D title = Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2 date = 2020-07-13 keywords = CoV-2; SARS; Xia summary = Nevertheless, the evolutionary reasons for low GC content are still debated in even exceptionally well-studied systems with unquestioned animal origins (2020) points out, the mammalian zinc finger antiviral protein (ZAP) binds to CpG dinucleotides in viral RNA genomes and inhibits viral replication and mediates viral degradation (Ficarelli et al., 2020; Ficarelli et al., 2019; Meagher et al., 2019; Takata et al., 2017) . Despite this, Xia (2020) speculated that low viral genomic CpG levels in SARS-CoV-2 required evolutionary time in a previous host species and tissue that more actively selected for CpG depletion than do bats. In addition to being unsupported by positive evidence, Xia''s (2020) hypothesis for dogs as intermediate hosts of ancestral viruses giving rise to SARS-CoV-2 requires an unlikely history of cross-species viral transmission (see Fig. 2 for potential hypotheses) for which there is no evidence. doi = 10.1093/molbev/msaa178 id = cord-346441-b1r6i0wq author = Polverino, Francesca title = Cigarette Smoking and COVID-19: A Complex Interaction date = 2020-08-01 keywords = SARS summary = These findings have putatively important implications for patients with COVID-19 because ACE2 has been shown to be the receptor used by SARS-CoV-2 to enter the host cells (3) and yet seem in contrast with the consolidated epidemiological data worldwide indicating a low prevalence of active smokers among patients with COVID-19. Last, though it is possible that cigarette smoke increases the ACE2 expression by the bronchial epithelium, thus facilitating the entry of SARS-CoV-2, this does not necessarily translate into a higher risk for developing COVID-19 pneumonia. To conclude, what is unchallengeable is that cigarette smoke is detrimental for the lungs in several ways, and further studies are needed to clarify the reasons behind the reported low prevalence of current smokers among hospitalized patients with COVID-19. Tobacco smoking increases the lung gene expression of ACE2, the receptor of SARS-CoV-2 doi = 10.1164/rccm.202005-1646le id = cord-154170-7pnz98o6 author = Ponciano, Jos''e Miguel title = Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America date = 2020-05-22 keywords = Fig; SARS; model summary = Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. Here we show that a multi-model, multi-stages modeling approach helps elucidate i) early epidemic growth in fourteen Latin-American countries ii) the role of poverty in shaping the growth rate of the number of cases and iii) the probability that the number of cases of SARS-CoV-2 exceeds any given amount within arbitrarily defined small windows of time, starting from the present. We draw on prior work in conservation biology, population dynamics and epidemiological theory to complement the current suite of deterministic epidemiological models, characterize the role of urban poverty in shaping the region''s SARS-CoV-2 epidemics, and develop a methodology to generate short (5-15 days), sequentially updatable, process-based forecasts. doi = nan id = cord-342681-pqzcy9wu author = Pongpirul, Wannarat A. title = Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date = 2020-07-17 keywords = RNA; SARS summary = Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. During the study period, Thailand''s discharge criteria for hospitalized COV-ID-19 patients required resolution of clinical signs and symptoms and 2 respiratory specimens without detectable SARS-CoV-2 RNA collected >24 hours apart. Clinical resolution occurred a median of 12 (9-13.5 ) days after illness onset, and these patients had detectable SARS-CoV-2 RNA in upper respiratory tract specimens for a median of 14 (9-26) days after illness onset (Table 2) . However, patients became afebrile 6 days after illness onset, with a median of 9 (3-19.75 ) additional days of detectable SARS-CoV-2 RNA in respiratory specimens after resolution of fever ( Table 2 ). Other studies have described asymptomatic patients with upper respiratory specimens positive for SARS-CoV-2 (9), and evidence suggests such cases pose a risk for transmission (10) (11) (12) . doi = 10.3201/eid2607.200598 id = cord-335308-5kh7wgvx author = Ponnusamy, Rajesh title = Variable Oligomerization Modes in Coronavirus Non-structural Protein 9 date = 2008-11-28 keywords = Cys69Ala; Fig; Nsp9; SARS summary = In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Although the residue responsible for disulfide formation in HCoV-229E Nsp9, Cys69, is conserved in SARS-CoV Nsp9, and the sequence identity is as high as 45% between the two proteins (see Supplementary Data Fig. S3 ), the mode of dimerization in the latter is very different from what we observe in our structure. Wild-type SARS-CoV Nsp9 and the HCoV-229E Nsp9 Cys69Ala mutant form higher oligomers at a protein concentration of 100 μM, presumably involving interactions similar to those seen in the crystal structure. On the other hand, the HCoV-229E Cys69Ala mutant has a dimerization mode similar to that of the wild-type SARS-CoV Nsp9 but it does not show binding with the nucleic acid in the gel mobility-shift experiment (except for the small shift seen for the 55-mer, the longest oligonucleotide tested). doi = 10.1016/j.jmb.2008.07.071 id = cord-310477-vniokol0 author = Pontes, Camila title = Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date = 2020-08-21 keywords = ACE2; SARS; Sarbecovirus summary = More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). In summary, the SDPs found within these β-CoV subgenera define a specific region of the receptor binding domains: they are part of, or in direct contact with, the ACE2 interacting surface ( A second S3Det analysis was performed on the full β-CoV MSA. On the other hand, the analysis performed on individual β-CoV subgenera, i.e. Sarbecovirus, Merbecovirus and Embecovirus subgroups, allowed a fine-grained classification into subfamily clusters that clearly reflect the functional diversification of the spike protein family, that is, the specificity to different host-cell receptors (Figure 2-3) . doi = 10.1101/2020.08.21.260745 id = cord-279519-4ad8ubrt author = Poochi, Saravana Prabha title = Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein date = 2020-07-06 keywords = ACE2; SARS summary = title: Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS‐CoV‐2 main protease and ACE2 protein Angiotensin converting enzyme 2 (ACE2) and main protease (M(Pro)) are significant target proteins, mainly involved in the attachment of viral genome to host cells and aid in replication of severe acute respiratory syndrome‐coronaviruses or SARS‐CoV genome. In the present study, we identified 11 potent bioactive compounds from ethanolic leaf extract of Ipomoea obscura (L.) by using GC‐MS analysis. These potential bioactive compounds were considered for molecular docking studies against ACE2 and M(Pro) target proteins to determine the antiviral effects against SARS‐COV. In this investigation we performed in silico docking by applying Glide 5.5 (Dik-Lung, Daniel, & Chung, 2011; Glide, 2009 ), against respiratory therapeutic target ACE2 exhibited in human and M Pro in SARS-CoV-2. Employing bioactive compounds derived from Ipomoea obscura (L.) to evaluate potential inhibitor for SARS-CoV-2 main protease and ACE2 protein doi = 10.1002/fft2.29 id = cord-347289-3yi5tz04 author = Poon, L. . C. title = ISUOG Interim Guidance on coronavirus disease 2019 (COVID‐19) during pregnancy and puerperium: information for healthcare professionals – an update date = 2020-06-01 keywords = COVID-19; Coronavirus; Disease; SARS; patient; pregnant summary = American College of Obstetricians and Gynecologists (ACOG): https://www.acog.org/clinical-information/phys ician-faqs/covid-19-faqs-for-ob-gyns-obstetrics Centers for Disease Control , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health emergency. A case series of 12 pregnant women with SARS-CoV in Hong Kong, China, reported three maternal deaths, that four of seven patients who presented in the first trimester had spontaneous miscarriage, four of five patients who presented after 24 weeks had preterm birth and two mothers recovered without delivery but their ongoing pregnancies were complicated by FGR 8 . In two studies, with a combined total of 10 pregnant women with COVID-19 in the third trimester, amniotic fluid, cord blood and neonatal throat swab samples tested negative for SARS-CoV-2, suggesting there was no evidence of vertical transmission in women who developed COVID-19 pneumonia in late pregnancy 26, 76 . An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes doi = 10.1002/uog.22061 id = cord-300685-bcjnujlj author = Poon, Leo L M title = Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date = 2003-06-01 keywords = PCR; RNA; SARS summary = The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. doi = 10.1373/49.6.953 id = cord-270613-vnjuubt4 author = Poon, Terence C.W. title = Proteomic analysis reveals platelet factor 4 and beta‐thromboglobulin as prognostic markers in severe acute respiratory syndrome date = 2012-06-28 keywords = SARS; pf4 summary = The data on 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count) from 38 SARS patients before treatment were subjected to forward stepwise multiple logistic regression (SPSS, v18, IBM) for prediction of the ICU admission and/or supplemental oxygen administration in the later period. Among the 20 SARS-associated proteomic features and ten serological variables (ALT, LDH, bilirubin, total protein, albumin, globulin, C-reactive peptide, total white blood cells, lymphocyte count, neutrophil count), multiple logistic regress analyses identified four proteomic features (m/z 6634, m/z 7769, m/z 8635, m/z 8865) as statistically significant prognostic markers for supplemental oxygen administration or ICU admission in the later period. To confirm the differential patterns and the identities of the m/z 7769 and m/z 8865 proteomic features, serum samples were subjected to Western blot analysis using specific antibodies against PF4 and beta-TG. doi = 10.1002/elps.201200002 id = cord-310017-c8rd714a author = Popa, Alexandra title = Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date = 2020-07-17 keywords = CoV-2; Fig; SARS; austrian; mutation summary = Moreover, we combined our deep viral genome sequencing data with epidemiologically identified chains of transmissions and family clusters together with biomathematical analyses to study genetic bottlenecks and the dynamics of genome evolution of SARS-CoV-2. We assembled SARS-CoV-2 genome sequences, constructed phylogenies and identified low 15 frequency mutations based on high-quality sequencing results with >5 million reads per sample and >80% of mapped viral reads (Fig. S2A-B) . Our pipeline was validated by experimental controls involving sample titration and technical sample replicates ( Fig. S2CTo investigate the link between local outbreaks in Austria and the global pandemic, we 20 performed phylogenetic analysis of 305 SARS-CoV-2 genomes from the Austrian cases (>96% genome coverage, >80% aligned viral reads) and 7,695 global genomes from the GISAID database (Fig. 1B, Table S1 ). 7 Dynamics of low frequency and fixed mutations in clusters Next, we sought to gain insights into the fundamental processes of SARS-CoV-2 infection by integrative analysis of viral genomes. doi = 10.1101/2020.07.15.204339 id = cord-319831-e07vt846 author = Popescu, Saskia title = Roadblocks to Infection Prevention Efforts in Health Care: SARS-CoV-2/COVID-19 Response date = 2020-03-30 keywords = IPC; SARS summary = T he emergence of a novel coronavirus (SARS-CoV-2) causing the disease, COVID-19, in Wuhan, China, in late 2019 is currently testing international public health and preparedness efforts. 1 These IPC outbreak efforts include education, reinforcement of infection prevention standards like isolation and proper usage of personal protective equipment (PPE), and established processes to ensure that the i3 strategy (identify, isolate, and inform) is used and that the health care facilities meet the guidance of the Centers for Disease Control and Prevention and World Health Organization. Unfortunately, to truly use IPC programs for COVID-19 response, it is important to understand why health-care-associated outbreaks and infection prevention failures occur all too often. A 2018 Report by the Office Inspector General of the US Department of Health and Human Services assessed hospital readiness to emerging infectious disease threats following the 2013-2016 Ebola outbreak. doi = 10.1017/dmp.2020.55 id = cord-303407-n7j56sci author = Popofsky, Stephanie title = Impact of Maternal SARS-CoV-2 Detection on Breastfeeding Due to Infant Separation at Birth date = 2020-08-10 keywords = COVID-19; SARS; mother summary = CONCLUSION: In the setting of COVID-19, separation of mother–newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following discharge compared with unseparated mothers and infants. In the setting of COVID-19, separation of mother-newborn dyads impacts breastfeeding outcomes, with lower rates of breastfeeding both during hospitalization and at home following J o u r n a l P r e -p r o o f 3 discharge compared with unseparated mothers and infants. The Centers for Disease Control and Prevention (CDC) [4] and American Academy of Pediatrics (AAP) [5] each published interim guidelines for management of neonates born to mothers with confirmed or suspected COVID-19, including recommendations for temporary separation of these dyads. To assess the impact of our policy change surrounding mother-newborn dyad separation on breastfeeding rates, we evaluated mothers'' pre-delivery plans for feeding, and compared these with actual outcomes of breastfeeding during perinatal admission and following discharge. doi = 10.1016/j.jpeds.2020.08.004 id = cord-286631-3fmg3scx author = Pormohammad, Ali title = Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis date = 2020-06-05 keywords = East; MERS; Middle; SARS summary = title: Comparison of confirmed COVID‐19 with SARS and MERS cases ‐ Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta‐analysis The trigger for rapid screening and treatment of COVID-19 patients is based on clinical symptoms, laboratory, and radiographic findings that are similar to SARS and MERS infections. In this study, we attempted to distinguish the clinical symptoms, laboratory findings, radiographic signs, and outcomes of confirmed COVID-19, SARS, and MERS patients. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Clinical aspects and outcomes of 70 patients with Middle East respiratory syndrome coronavirus infection: a single-center experience in Saudi Arabia Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection Middle East respiratory syndrome coronavirus: a case-control study of hospitalized patients doi = 10.1002/rmv.2112 id = cord-271544-i20105lq author = Poston, Daniel title = Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection date = 2020-10-11 keywords = SARS summary = Cross-reactive immune responses elicited by seasonal coronaviruses might impact SARS-CoV-2 susceptibility and disease outcomes. We measured neutralizing activity against SARS-CoV-2 in pre-pandemic sera from patients with prior PCR-confirmed seasonal coronavirus infection. One hypothesis is that cross reactive immune responses, elicited by prior 46 infection with seasonal coronaviruses impacts the course of SARS-CoV-2 infection, perhaps 47 providing a degree of protection against severe COVID-19 disease. The numbers of rVSV/SARS-2/GFP was assessed by flow cytometric detection of 92 GFP expression as described previously To assess whether prior infection by seasonal coronaviruses could elicit antibodies with 104 neutralization activity against SARS-CoV-2, we identified 37 serum samples collected prior to 105 the COVID19 pandemic from patients who were diagnosed using PCR with a seasonal 106 coronavirus 11-291 days (median 80 = days) prior to serum sample collection. . https://doi.org/10.1101/2020.10.08.20209650 doi: medRxiv preprint neutralize rVSV/SARS-CoV-2/GFP with NT50 values ranging from 96 to 5400. doi = 10.1101/2020.10.08.20209650 id = cord-349541-7g50vg14 author = Poulikakos, Dimitrios title = SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date = 2020-07-07 keywords = SARS summary = key: cord-349541-7g50vg14 title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England cord_uid: 7g50vg14 Please cite this article as: Poulikakos D, Sinha S, Kalra PA, SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104545 Amongst the 22 (7·8%) HCW with previous SARS-Cov-2 PCR nasopharyngeal swabs, 2 were positive, 12 were negative, and 7 did not disclose the result. Positive SARS-Cov-2 IgG was detected in 17 (6%) HCW and 6 (35·3%) had been asymptomatic. All IgG positive cases were in DIPC HCW (17 out of 195; 8·7%). One IgG positive HCW did not disclose ethnicity. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients Hospital-Wide SARS-CoV-2 Antibody Screening Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics First experience of COVID-19 screening of health-care workers in England doi = 10.1016/j.jcv.2020.104545 id = cord-307287-zpq6byml author = Poulsen, Nadia Nicholine title = Cyclosporine and COVID‐19: Risk or Favorable? date = 2020-08-10 keywords = COVID-19; ICU; SARS; patient summary = A letter by Russel et al suggests that there is tantalizing in vitro evidence for cyclosporine as an anti-coronavirus agent as well as a potential disease-modifying role through inhibition of Severe Acute Respiratory Syndrome (SARS) coronavirus-mediated IL-2 induction and authors advocate that a trial of cyclosporine should be considered in the event of a future SARS epidemic 22 . The Immunonephrology Working Group of the European Renal Association-European Dialysis and Transplant Association has published recommendations for the management of patients with immune-mediated kidney disease during this current pandemic, and authors point out that patients with mild COVID-19 might continue low dose of cyclosporine due to the in vitro evidence of inhibition of coronavirus replication 84 . We are still awaiting robust data from COVID-19 patients actively treated with calcineurin inhibitors due to transplantation or autoimmune diseases but so far there is no evidence that use of cyclosporine possess an additional risk for severe COVID-19 in addition to the co-morbidities such as diabetes, smoking, hypertension and obesity that often co-exist in these patients. doi = 10.1111/ajt.16250 id = cord-284734-qioy7eso author = Pourahmad, Ramtin title = Efficacy of Plasmapheresis and Immunoglobulin Replacement Therapy (IVIG) on Patients with COVID-19 date = 2020-07-31 keywords = COVID-19; IVIG; SARS summary = According to recent observations about different modalities in treatment of patients infected with COVID-19, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection. According to the medical experiences in the treatment of patients infected with other members of coronavirus family such as SARS-CoV and MERS-CoV, plasmapheresis and intravenous immunoglobulin (IVIg) have been reported to be an effective empirical therapeutic option to control the infection [1] [2] [3] [4] [5] [6] [7] . As the world confronting a pandemic due to SARS-CoV-2, immunoglobulin replacement therapy (IVIG) could be an ideal option for prevention and treatment of COVID-19 disease. According to the reports, China has used immunoglobulin replacement therapy on several COVID-19 patients during the outbreak of this novel coronavirus which showed promising results [46] . The use of convalescent plasma therapy and remdesivir in the successful management of a critically ill obstetric patient with novel coronavirus 2019 infection: a case report. doi = 10.1007/s42399-020-00438-2 id = cord-343127-n3fs8ph8 author = Pousa, Pedro A. title = Extrapulmonary manifestations of COVID-19 in children: a comprehensive review and pathophysiological considerations date = 2020-09-22 keywords = ACE2; COVID-19; SARS summary = OBJECTIVE: The aim of this review was to summarize the most common extrapulmonary manifestations in pediatric patients with COVID-19, as well as to discuss clinical, epidemiological, and pathophysiological aspects of these clinical presentations in children. In addition, epithelial cells of the small intestine is another tissue that highly express ACE2 in cell membrane, [42] creating another potential region for SARS-CoV-2 infection and enteric manifestations of COVID-19. Hence, the present authors speculate that, although children and adults have similar rates of GI symptoms, children GI symptoms are usually associated as a primary response of SARS-CoV-2 infection, due to this minor expression of ACE2, and represent milder symptoms. Children are susceptible to liver injury, as shown by a meta-analysis of 551 laboratory-confirmed pediatric COVID-19 patients reporting that 9% (35/290) presented increased ALT and 18% (58/280), high levels of AST. Therefore, children might present less severe cases of kidney injury associated with COVID-19 due to this greater expression of AT2R than adults. doi = 10.1016/j.jped.2020.08.007 id = cord-351225-dq0xu85c author = Poutanen, Susan M. title = Transmission and control of SARS date = 2004 keywords = Hong; SARS; transmission summary = During the outbreak, it was evident that SARS was readily transmissible from person to person, especially in health Severe acute respiratory syndrome (SARS) was first recognized in China in November 2002 and was subsequently associated with a worldwide outbreak involving 8098 people, 774 of whom died. Evidence for this includes studies in Hong Kong and Toronto, Canada that show an increased risk for SARS in health care workers who entered the room of a patient with SARS, with increasing risk in those with closer proximity to the patient and those remaining in the room for a longer duration, suggesting that transmission is enhanced by close, prolonged contact [19•,20 •] In addition, an increased risk in household members of patients with SARS has been shown in those who had close, prolonged contact with the index person, and in particular, in those who shared a bed, reported being within 1 meter of the index person, and dined together [21•] . doi = 10.1007/s11908-004-0012-7 id = cord-352678-8f2ygul2 author = Prasad, Ashish title = Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading? date = 2020-08-05 keywords = ACE2; COVID-19; SARS; patient summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causal agent of Coronavirus disease 2019 (COVID19) , is a single-stranded RNA virus with a non-segmented genome. In another study with COVID-19 patients in China, an early response of IgA instead of IgG was observed in the humoral immune response against SARS-CoV-2 (11) . It has been observed that 5% of COVID-19 patients become critically ill with severe pneumonia and multiple-organ damage and cytokine storm might be a possible explanation for such an observation. A case study on 214 COVID-19 patients from three special care centers of Union Hospital, Wuhan, revealed that 36.4% of the infected people had neurologic symptoms (46) . The adverse effects of antiviral drugs like hydroxychloroquine, which is reported to cause acute toxic hepatitis (54) and cytokine burst, might be responsible for such high percentage of hepatic damage cases in severely ill patients. doi = 10.3389/fmed.2020.00370 id = cord-351845-bli3qm8w author = Prasad, Kartikay title = Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date = 2020-06-26 keywords = COVID-19; IFN; SARS; gene summary = Towards this goal, in this study, we have generated a human-SARS-CoV-2 interactome based on recently published RNA-Seq analysis of human adenocarcinomic alveolar basal epithelial (A549) cells infected with SARS-CoV-2, and identified disease-related functional genes that will provide the insights into the patho-J o u r n a l P r e -p r o o f 4 mechanisms of COVID-19. Overall, the analysis demonstrated that the upregulated genes are mainly linked to the host response to SARS-CoV-2 infection, type I interferon signaling and the cytokine-mediated signaling pathway. The PPI network analysis indicates that the pathways are enriched in host response to virus infection, type I interferons signaling, and cytokine activation. [74] reported high SARS-CoV-2 loads very early during infection, suggesting that the virus may have developed arsenals that is able to delay the IFN response by inhibiting innate immune signaling. doi = 10.1016/j.ijbiomac.2020.06.228 id = cord-335610-3v8140b6 author = Prasanth, D. S. N. B. K. title = In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2 date = 2020-06-22 keywords = COVID-19; Cinnamon; SARS summary = Our research study is intended to recognize the phyto-derived antiviral substances from Cinnamon against COVID-19 main protease enzyme and to understand the in silico molecular basis of its activity. Based on the above properties of Cinnamon, this research aimed to show a variety of active compounds across all Cinnamon varities and decide whether and how they interact with proteins i.e. main protease (Joshi et al., 2020) and spike protein, that are essential in the management of SARS-CoV-2. The crystal structure of Main protease (6LU7) and Spike receptor-binding domain complexed with its receptor ACE2 (6LZG) with selected top ligands identified from docking analysis such as Tenufolin (TEN) and Pavetannin C1 (PAV) were subjected to molecular dynamics using gromacs GPU enabled package. The main protease with tenufolin Spike protein (6LZG), associated with SARS was found to exhibit the best possible interaction with Pavetannin C1 (À11.1 kcal/mol) among the phytochemicals ( Table 2) . doi = 10.1080/07391102.2020.1779129 id = cord-294677-l1b4mw9d author = Prashantha, C.N. title = Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date = 2020-10-13 keywords = Coronavirus; SARS; protein summary = (2) Coronavirus S2 glycoprotein (662-1270) is translated as a large polypeptide that is subsequently cleaved to S1 and S2 domains from Molecular docking plays vital role in computer-aided drug discovery to predict best active molecules to the target protein. Using AutoDock 4.2 and AutoDock Vina to predict the best drug binding sites towards the affinity of active site amino acids are screened based on binding energy and number of hydrogen bonds formed to the target amino acids. • Computational Approaches to build the 3D structure of protein • Drug selection for preclinical trials to study the efficacy and disease treatment • Molecular docking approaches to screen the compounds based on binding energy doi = 10.1016/j.jmgm.2020.107769 id = cord-269025-2j37561h author = Pratelli, Annamaria title = Canine coronavirus inactivation with physical and chemical agents date = 2007-05-21 keywords = SARS; TCID summary = The methods for CCoV inactivation could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure of researchers to pathogens during routine laboratory procedures. To examine the ability of heat to inactivate CCoV, 500 lL aliquots of virus samples were incubated in duplicate in a 15 mL polypropylene conical tube (Falcon, Becton Dickinson Labware) for increasing periods of time at three different temperatures: +56°C, +65°C and +75°C. To examine formaldehyde and glutaraldehyde inactivation of CCoV, aliquots of virus and aldehyde samples, each at two different dilutions, were incubated at +4°C, +25°C and +37°C, respectively, for up to 3 days. Despite the differences in stability during heat treatment at 56°C between SARS-CoV and CCoV, the several methods of CCoV inactivation, including inhibition of viral entry, could be applied as animal models to study human coronavirus infection, reducing the risk of accidental exposure to the virus through unsafe laboratory practices. doi = 10.1016/j.tvjl.2007.03.019 id = cord-273882-tqdcb3oo author = Pratibha, title = Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date = 2020-08-21 keywords = SARS; figure summary = title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. These ubiquitous forbidden orders (UFO) are unique structures of the viruses that may provide an insight into viruses'' chemical behavior and the folding patterns of the proteins. Next, we analyzed protein sequences of 26 viruses (Figures 2, 3 , and Supplementary Figures 1 -4) to search for a ubiquitous forbidden order in each one of them. Among the 26 viruses studied, we noted that the forbidden order BPAB is unique to SARS CoV-2, Rubella, and Avian IB (Figure 3) . We found that at R-group classified sequences of N, B, A, and P in these two samples are identical up to level 4 of the amino acid ordering in the protein structures (Figures 4a, d, g) . doi = 10.1101/2020.08.21.261289 id = cord-029450-4rnrq78l author = Prattichizzo, Francesco title = Response to: Letter to the Editor on “Bonafè M, Prattichizzo F, Giuliani A, Storci G, Sabbatinelli J, Olivieri F. Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes. Cytokine Growth Factor Rev” by Eugenia Quiros-Roldan, Giorgio Biasiotto and Isabella Zanella date = 2020-07-18 keywords = HIV; SARS summary = Preliminary data on an Italian cohort suggest that only a minor portion of HIV-positive patients with probable SARS-CoV-2 infection died, which yields a low case-fatality rate if compared to other highrisk populations [3] . Of note, the mean age of all the four HIV-positive cohorts was lower compared to other reports showing data of SARS-CoV-2 infection in the general population [7] . On the basis of the literature above, we posit that testing for T-cell senescence markers (e.g. PD-1, Tim-3, CTLA-4, and TIGIT) [9] and measuring major inflammatory markers in HIV-SARS-CoV-2 co-infected patients is mandatory to disentangle the relevance of immune senescence and inflamm-aging in the COVID-19 outcome in this specific population. A randomized controlled trial evaluating the efficacy of a triple antiviral therapy with combined interferon beta-1b, ribavirin, and lopinavir-ritonavir on COVID-19 patients proved the superiority of the triple antiviral therapy compared to lopinavirritonavir alone in terms of improved clinical recovery and faster rate of viral clearance, with a striking suppression of IL-6 levels in the interferon arm of the study after 48 hours of treatment [17] . doi = 10.1016/j.cytogfr.2020.07.013 id = cord-342783-85b4lwh3 author = Prazuck, T. title = Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date = 2020-05-27 keywords = PCR; SARS summary = In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. Methods RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orleans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated. The SARS-CoV-2 IgG/IgM antibody test kits, COVID-PRESTO ® and COVID-DUO ® , are 137 RDT test, the IgM were the first antibodies to be detected and were systematically present in 209 the few positive patients with an onset of symptoms from 0 to 5 days ago (n=2 in COVID-210 PRESTO ® population; n=5 in COVID-DUO ® ). Development and Clinical Application of A 371 Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis doi = 10.1101/2020.05.27.20112888 id = cord-304787-fohgekp4 author = Prazuck, Thierry title = Investigation of a family outbreak of COVID-19 using systematic rapid diagnostic tests raises new questions about transmission date = 2020-06-29 keywords = SARS summary = 1 Herein, we describe the epidemiological, clinical and biological characteristics of 30 households in close contact with SARS-CoV-2-infected members, living in a confined environment during the French national lockdown. During the 5 days before the French national lockdown, both families moved from their usual Parisian residence to a closed property in the countryside, composed by 3 neighboring houses (A, B and C) in a park. House A was inhabited by 8 persons from a single family, including 3 couples who shared their bed for at least 4 days after the onset of symptoms. The first diagnosed case was a 67-year-old man (resident #1) living in the house A and referring to the Infectious Diseases outpatient clinic on March 17 for cough, fever and asthenia for 4 days. No transmission occurred between husbands and wives in house A although couples moved to separated rooms only 4 days after the onset of symptoms of the index case. doi = 10.1016/j.jinf.2020.06.066 id = cord-329311-p68kr4ga author = Prebensen, Christian title = SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date = 2020-09-05 keywords = RNA; SARS summary = title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . doi = 10.1093/cid/ciaa1338 id = cord-309182-t9ywnshj author = Premkumar, Lakshmanane title = The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients date = 2020-06-11 keywords = Fig; RBD; SARS summary = These results establish that most individuals, including people who have been recently exposed to acute common HCoV infections, do not have detectable levels of cross-reactive antibodies to the recombinant RBD of SARS-CoVs. To evaluate the sensitivity of the RBD of SARS-CoV-2 for identifying infected individuals, we obtained a total of 77 serum samples from 63 patients with laboratory-confirmed (i.e., PCR positive) SARS-CoV-2 infections collected at different times after the onset of symptoms. All the samples were tested for binding of total immunoglobulin (Ig) and IgM antibodies to recombinant RBD antigens from SARS-CoVs and common-cold HCoVs. The sensitivity of the assay was high (98% and 81% respectively for Ig and IgM) for specimens collected 9 days or more after onset of symptoms (Fig. 4A ). A total of 50 serum samples collected between 1 and 39 days after onset of symptoms from PCR-confirmed SARS-CoV-2 subjects were measured for Ig and IgM binding to spike RBD antigen and SARS-CoV-2 neutralization assay. doi = 10.1126/sciimmunol.abc8413 id = cord-287819-qzg4bhoy author = Priftis, Konstantinos title = COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke date = 2020-09-28 keywords = SARS summary = title: COVID-19 presenting with agraphia and conduction aphasia in a patient with left-hemisphere ischemic stroke COVID-19 following infection by SARS-CoV-2 can affect the brain causing confusion, depression, and dementia-like signs. We report on LA, a patient who was affected by a left-hemisphere ischemic stroke, probably because of SARS-CoV-2. The patient showed a highly specific neuropsychological profile characterized by severe agraphia and some signs of conduction aphasia. Therefore, in the present study, we aimed to investigate, more in depth, the specific and focal neuropsychological consequences of SARS-CoV-2, in a patient affected by lefthemisphere stroke. LA had a largely intact neuropsychological profile, except for the presence of severe agraphia and some signs of conduction aphasia. We suggest that patients affected by SARS-CoV-2 and stroke might not only show diffuse neurocognitive and neurobehavioural signs (e.g. confusion, agitation, psychosis), but they can also present with highly focal neuropsychological disorders, such as agraphia and conduction aphasia. doi = 10.1007/s10072-020-04768-w id = cord-266135-jbc9nml0 author = Princiotta Cariddi, Lucia title = Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient date = 2020-06-24 keywords = PRES; SARS summary = title: Reversible Encephalopathy Syndrome (PRES) in a COVID-19 patient Besides pneumonia, it has been demonstrated that SARS-CoV-2 infection affects multiple organs, including brain tissues, causing different neurological manifestations, especially acute cerebrovascular disease (ischemic and hemorrhagic stroke), impaired consciousness and skeletal muscle injury. To our knowledge, among neurological disorders associated with SARS-CoV2 infection, no Posterior Reversible Encephalopathy Syndrome (PRES) has been described yet. Herein, we report a case of a 64-year old woman with COVID19 infection who developed a PRES, and we suggest that it could be explained by the disruption of the blood brain barrier induced by the cerebrovascular endothelial dysfunction caused by SARS-CoV-2. Brain CT and CTA were consistent with hemorrhagic Posterior Reversible Encephalopathy Syndrome (PRES; Fig. 1a, b) . Posterior reversible encephalopathy syndrome in infection, sepsis, and shock Posterior reversible encephalopathy syndrome (PRES) and infection: a systematic review of the literature Hemorrhagic posterior reversible encephalopathy syndrome as a manifestation of COVID-19 infection doi = 10.1007/s00415-020-10001-7 id = cord-257663-i7wrqh2g author = Principi, Nicola title = Effects of Coronavirus Infections in Children date = 2010-02-17 keywords = NL63; OC43; SARS summary = The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The isolation of the coronavirus (CoV) identifi ed as the cause of severe acute respiratory syndrome and the detection of 2 new human CoVs (HCoV-NL63 and HCoV-HKU1) have led to studies of the epidemiology and clinical and socioeconomic effects of infections caused by all HCoVs, including those known since the late 1960s (HCoV-229E and HCoV-OC43). The identifi cation of SARS-CoV and the isolation of 2 novel HCoVs in humans (HCoV-NL63 and HCoV-HKU1) (5,6) have led to several studies of the epidemiology and clinical and socioeconomic effects of HCoV infections, which were greatly facilitated by the availability of modern molecular biology methods that enable direct viral identifi cation in respiratory secretions (7) (8) (9) (10) (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) . doi = 10.3201/eid1602.090469 id = cord-302735-zal2gr28 author = Priyanka title = Aerosol transmission of SARS-CoV-2: The unresolved paradox date = 2020-09-04 keywords = SARS summary = key: cord-302735-zal2gr28 title: Aerosol transmission of SARS-CoV-2: The unresolved paradox cord_uid: zal2gr28 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the aetiological agent 18 of coronavirus disease 2019 , has led to a global pandemic defying the 19 geographical borders and putting the lives of billions at risk. The commonly evident 20 symptoms include fever, altered sense of smell and/or taste, cough, sputum expectoration, 21 sore throat, dyspnoea, fatigue and myalgia; whereas the uncommon symptoms include 22 confusion, dizziness, headache, conjunctivitis, rhinorrhoea, nasal congestion, hemoptysis, 23 chest pain, bronchial breath sounds, tachypnoea, crackles/rales on auscultation, cutaneous The transmission of respiratory pathogens have been associated with three primary modes 30 known as "contact," "droplet," and "airborne" transmission. These modes are also being 31 speculated in the context of SARS-CoV-2, but the existing research-based literature and the 32 consequent guidance from the leading public health agencies are still paradoxical. Viable 117 SARS-CoV-2 in the air of a hospital room 1 with COVID-19 patients. Aerosol transmission of SARS-CoV-2? doi = 10.1016/j.tmaid.2020.101869 id = cord-311035-s3tkbh9r author = Procko, Erik title = Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community date = 2020-10-21 keywords = ACE2; RBD; SARS summary = A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. • The experimental mutational landscape of ACE2 for binding the RBD of SARS-CoV-2 provides a blueprint for engineering high affinity decoy receptors. Following FACS selection of the human culture to enrich a cell population with high binding activity for SARS-CoV-2 protein S, RNA transcripts were isolated and Illumina sequenced. The deep mutational scan of ACE2 revealed that mutations can indeed be found to enhance binding toward SARS-CoV-2 RBD (Figure 2) , suitable for engineering high affinity soluble decoy receptors [15] . A soluble ACE2 variant that combines three mutations, called sACE2 2 .v2.4, was found to be highly expressed, is a stable monodisperse dimer, binds SARS-CoV-2 S with picomolar affinity and potently neutralizes infection of a susceptible cell line by authentic virus. doi = 10.1080/14789450.2020.1833721 id = cord-258914-g6pv8zz9 author = Proud, Pamela C. title = Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date = 2020-09-25 keywords = CoV-2; SARS summary = title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19. The TLRs are key microbe-recognition receptors with a crucial role in 97 activation of host defence and protection from infections and therefore attractive drug 98 targets against infectious diseases [12] [13] [14] To determine whether TLR2/6 agonists are also active against SARS-CoV-2, we used In life samples were taken at days 1, 3, 5, 7, 10 and 12, with scheduled culls at days 137 3 (n=6) and end of study days 12-14 (n=18) (Fig 1A) . doi = 10.1101/2020.09.25.309914 id = cord-350045-85jug39x author = Pruc, Michal title = Risk of coronavirus infections among medical personnel date = 2020-05-08 keywords = SARS summary = Due to the current situation of the COVID-19 pandemic, we can predict how the morbidity of health care workers will develop based on data on other viruses from the coronavirus group. In global research on SARS-CoV-1, MERS-CoV and SARS-CoV-2, it can be seen that a very large percentage of the number of infected people are health professionals struggling with them in various medical facilities. In the Netherlands a survey was conducted from 6-8 March 2020 on 1097 health care workers, among whom the percentage of infected was 4.1%. 4 Currently, the total number of infected healthcare workers on SARS-CoV-2 is unknown due to the steadily increasing number of infections and the lack of global data on the problem. The data on SARS-CoV-1 and MERS-CoV can predict how much health care workers may be infected despite the lack of up-to-date data on SARS-CoV-2. Risks to healthcare workers with emerging diseases: lessons from MERS-CoV, Ebola, SARS, and avian flu doi = 10.1016/j.ajem.2020.05.017 id = cord-255791-ghrlj6b2 author = Pruijssers, Andrea J. title = Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date = 2020-04-27 keywords = EC50; Fig; RDV; SARS summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 μM). These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19. RDV and GS-441524 potently inhibited 110 SARS-CoV-2 replication in a dose-dependent manner in both cell types ( Fig. 2; Table 1 ). Together, these data demonstrate that RDV is potently antiviral 131 against SARS-CoV-2 in primary human lung cultures with a selectivity index of >1000. doi = 10.1101/2020.04.27.064279 id = cord-265899-skpkuzyu author = Pryzdial, Edward L. G. title = Antiviral anticoagulation date = 2020-07-06 keywords = COVID-19; HSV1; SARS; tissue summary = 129 Although known as the cold sore virus and typically not life threatening, there are numerous correlations between HSV1 and other members of the herpesvirus family to cardiovascular disease, 130, 131 suggesting links to TF: (i) HSV1 seropositivity is associated with a 2-fold increase in myocardial infarction incidence and death due to coronary heart disease 113 ; (ii) fibrin deposits in the microvasculature are linked to HSV1 infection 132, 133 ; (iii) DIC in neonates may occur during severe HSV1 infection 134 ; (iv) HSV2 is linked to ischemic and hemorrhagic stroke due to DIC 107, 135 ; (v) a history of CMV infection is linked to subclinical and clinical arterial thickening [136] [137] [138] ; (vi) CMV is strongly correlated to accelerated atherosclerosis in immunosuppressed organ transplant recipients [139] [140] [141] [142] ; and (vii) CMV infection is a strong risk factor for restenosis after angioplasty. doi = 10.1002/rth2.12406 id = cord-264497-7xz97awb author = Przedlacki, Jerzy title = Patients’ and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic date = 2020-07-27 keywords = SARS summary = title: Patients'' and healthcare personnel expectations for SARS-CoV-2 screening in dialysis unit during the Covid-19 pandemic One mandatory swab test in all patients and dialysis unit HCP taken at a "time zero", followed by swabs taken in the presence of clinical indications only (as in answer 1) 3. The members of the healthcare team had an additional option: (4) as in answer 1 plus testing "on demand", in the case of even weak clinical suspicion of SARS-CoV-2 infection. Eventually, all patients were asked to report their sense of safety related to the risk of contracting SARS-CoV-2 while attending the dialysis unit during the COVID-19 pandemic. All participants were informed that an increased frequency of screening tests is not an alternative to self-isolation or to the use of personal protective equipment during dialysis. In summary, the perception of safety in the context of the COVID-19 pandemic can be related to the availability of the SARS-CoV-2 screening test. doi = 10.1007/s40620-020-00811-3 id = cord-273604-0w5shxmf author = Psevdos, George title = Halting a SARS-CoV-2 Outbreak in a U.S. Veterans Affairs Nursing Home date = 2020-11-03 keywords = SARS; covid-19 summary = Faced with a dwindling supply of PPE, the Infection Control team distributed supplies saved for a possible Ebola outbreak; A COVID unit was created within the nursing home facilitating the geographic isolation of cases; universal testing of residents and employees allowed for the implementation of proper quarantine measures. 7 Although nationally the virus spreads like wildfire in nursing homes (among residents and working staff), the Department of Veterans Affairs (VA) reported lower COVID-19 rates in their affiliated nursing homes in a U.S. Congressional hearing. Swift detection by rapid RT-PCR testing of all asymptomatic carriers (residents and employees via universal testing) and implementation of strict infection control and isolation measures are pivotal in containing and thus eliminating a COVID-19 outbreak. Universal and Serial Laboratory Testing for SARS-CoV-2 at a Long-Term Care Skilled Nursing Facility for Veterans Hospital affiliated long term care facility COVID-19 containment strategy by using prevalence testing and infection control practices doi = 10.1016/j.ajic.2020.10.022 id = cord-351503-2f0sk24j author = Pua, Uei title = What Is Needed to Make Interventional Radiology Ready for COVID-19? Lessons from SARS-CoV Epidemic date = 2020-03-13 keywords = SARS summary = During the initial stage, Singapore recorded one of the highest number of infections outside of China (3), reminiscence of the SARS-CoV epidemic 17 years ago (4). In 2003, the authors were deployed to perform IR as well as critical care procedures in critically ill SARS-CoV patients, and today, providing IR support to the COVID-19 patients. Save for the critically ill, the vast majority of patients with viral pneumonia will not require any IR procedure (28 IR procedures in 27 patients out of the cohort of 206 during SARS-CoV epidemic) (4) . Similarly during the SARS-CoV epidemic in Singapore, among the 206 cases, there were 84 healthcare workers infection resulting in 5 deaths. To assume that the COVID-19 outbreak would be the same as the SARS-CoV epidemic, would be overly simplistic and to ignore our prior experience. doi = 10.3348/kjr.2020.0163 id = cord-288731-x2cwyvb7 author = Puenpa, Jiratchaya title = Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020 date = 2020-10-06 keywords = CoV-2; March; SARS; Thailand summary = In the current study associations between SARS-CoV-2 gene variation and exposure history during the first wave of the outbreak in Thailand between January and May 2020 were investigated. In Thailand the Ministry of Public Health reported the first laboratory-confirmed case of SARS-CoV-2 in a 61-year-old Chinese traveller who had arrived from Wuhan on 12 January 2020. Based on the genome sequences available in GIASID, nucleotide variation in four regions of the SARS-CoV-2 genome was used to conduct viral tracking and identify sites of origin of outbreaks in Thailand. One sample in the current study collected in January 2020 was closely related to the SARS-CoV-2 strain circulating in China at that time identified as type L. A new cohort of imported cases identified in May 2020 included a group of migrant workers in the southern part of Thailand 24 with type G2 SARS-CoV-2. doi = 10.1038/s41598-020-73554-7 id = cord-271338-v2k9zn87 author = Pujadas, E. title = SARS-CoV-2 Viral Load Predicts COVID-19 Mortality date = 2020-06-12 keywords = SARS summary = We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). To date, few studies have reported on SARS-CoV-2 viral loads, and no studies have assessed viral load and mortality in large patient cohorts. 2, 3, 4, 5 This letter is the first to report SARS-CoV-2 viral load at the time of diagnosis as an independent predictor of COVID-19 mortality in a large hospitalized cohort (n=1,145) within the Mount Sinai Health System in New York City. . https://doi.org/10.1101/2020.06.11.20128934 doi: medRxiv preprint Transforming front-line qualitative testing into a quantitative viral load will assist clinicians in risk-stratifying patients who should be admitted and closely monitored versus those who may safely convalesce at home. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients doi = 10.1101/2020.06.11.20128934 id = cord-259523-92hz534s author = Pullen, Lara C. title = COVID‐19: transplant works toward adaptation date = 2020-09-29 keywords = COVID-19; SARS summary = These recommendations state that during the COVID-19 pandemic, deceased donor kidney transplantations should be performed only if it is possible to transplant a SARS-CoV-2 negative organ into a SARS-CoV-2 negative patient, and that renal transplantation should be prioritized for recipients facing urgent clinical conditions "because frequent healthcare contact due to the severity of their underlying disease means that these patients will remain at high risk for acquiring SARS-CoV-2, a risk that might be greater than the risk of SARS-CoV-2 acquisition through successful transplantation," says Dr. Remuzzi. Currently, the American Society of Transplantation and the ISOT do not recommend the use of organs from living donors who are SARS-CoV-2 positive or classifi ed as high risk after screening. Recently, colleagues at Dr. Remuzzi''s institution reported the presence of SARS-CoV-2 in the kidney, and the potential for donor-derived COVID-19 infection remains unknown. Dr. Potena estimates that in a typical winter, 20 to 25% of the transplant center''s patients have COVID-like symptoms. doi = 10.1111/ajt.16298 id = cord-282009-a83mun7u author = Pundir, Hemlata title = Using Chou’s 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors date = 2020-10-20 keywords = COVID-19; Mpro; SARS; X77 summary = To identify possible inhibitors against SARS-CoV-2, we applied the Pharmacophore-based virtual screening method following Chou''s 5-step rule [16] , molecular docking, drug-like analysis, and toxicity prediction (Fig. 1) . After the pharmacophore-based screening using Chou''s 5-steps rule, we performed the molecular docking of all screened compounds with crystal structure of SARS-CoV-2 Mpro. After successful completion of MDS, the MD trajectories were used to calculate root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R g ), hydrogen bonds, solvent accessible surface area (SASA) [28] , principal component analysis (PCA) [29] , and distance to analyze the stability of Mpro and Mpro-ligand complex. Pharmacophore-based screening by Chou''s 5-steps rule X77 binds to the active site of SARS-CoV-2 Mpro with binding energy − 8.4 kcal/mol as shown in Fig. 2 . doi = 10.1007/s11030-020-10148-5 id = cord-228152-k4bw8w5g author = Pyzer-Knapp, Edward O. title = Using Bayesian Optimization to Accelerate Virtual Screening for the Discovery of Therapeutics Appropriate for Repurposing for COVID-19 date = 2020-05-11 keywords = PDTS; SARS; bayesian summary = The novel Wuhan coronavirus known as SARS-CoV-2 has brought almost unprecedented effects for a non-wartime setting, hitting social, economic and health systems hard.~ Being able to bring to bear pharmaceutical interventions to counteract its effects will represent a major turning point in the fight to turn the tides in this ongoing battle.~ Recently, the World''s most powerful supercomputer, SUMMIT, was used to identify existing small molecule pharmaceuticals which may have the desired activity against SARS-CoV-2 through a high throughput virtual screening approach. In this communication, we demonstrate how the use of Bayesian optimization can provide a valuable service for the prioritisation of these calculations, leading to the accelerated identification of high-performing candidates, and thus expanding the scope of the utility of HPC systems for time critical screening It can be seen than on every task the PDTS method of Bayesian optimization outperforms random sampling and thus shows great potential for the efficient prioritisation of HTVS testing of pharmaceuticals for activity against SARS-CoV-2. doi = nan id = cord-352871-0xgjpd80 author = Pérez Bartolomé, Francisco title = Manifestaciones oftalmológicas del SARS-Cov-2: Revisión de la literatura date = 2020-08-08 keywords = COVID-19; SARS summary = En Diciembre de 2019 se identificaron a los primeros pacientes diagnosticados con la enfermedad causada por el nuevo coronavirus (SARS-CoV2), denominada COVID-19, en Wuhan, China 1,2 . Se procedió a la combinación de diferentes palabras clave, tales como "SARS-Cov-2", "COVID 19", "2019-nCoV", "Coronavirus 2019", y (término "AND" en el proceso de búsqueda avanzada) "Ophthalmology", "Eye disease", "Conjunctivitis", "Ocular Surface", "Glaucoma", "Orbit", "Tears", "Uveitis", "Retina", "Vasculitis", "ophthalmoparesis", "palsy", "optic nerve", "anterior ischemic optic neuropathy" (AION), "retinal venous occlusion" (RVO), "retinal artery occlusion" (RAO). La primera referencia de conjuntivitis por SARS-CoV-2 figura en una carta al editor, publicada en la revista "The Lancet" 28 , en la que describe el cuadro de enrojecimiento ocular unilateral en un experto neumólogo (ataviado con su equipo de protección y una mascarilla N95, pero sin gafas protectoras), días después de haber visitado un hospital de Wuhan. doi = 10.1016/j.oftal.2020.07.020 id = cord-340070-de7sfccy author = Pérez-Martinez, Antonio title = Clinical outcome of SARS-CoV-2 infection in immunosuppressed children in Spain date = 2020-08-29 keywords = SARS; patient summary = In this series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. A retrospective study (1st to 31st of March, 2020) of children less than 15 years old with primary or secondary immunosuppression infected with SARS-CoV-2 and treated at the University Hospital La Paz, Madrid, Spain, was performed. Hydroxychloroquine was initiated upon diagnosis (positive PCR for SARS-CoV-2) when there were signs/ symptoms of moderate-severe disease (respiratory signs, pneumonia on chest X ray, blood parameters of severity such as lymphopenia or elevated CRP, D-dimer or Il-6). In this small series, 8 immunocompromised patients with COVID-19 disease are reported, accounting for 15% of the positive cases detected in children in a reference hospital. Based on our experience, monitoring of children with immunosuppression and COVID-19 disease can be performed as outpatients, if close monitoring is possible with radiological and blood test controls if necessary, and carefully selecting the patients depending on their individual risk. doi = 10.1007/s00431-020-03793-3 id = cord-302125-96w0nh9q author = Péré, Hélène title = Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date = 2020-09-03 keywords = SARS summary = title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Running title: Sequential SARS-CoV-2 serology testing in health-workers Hélène Péré 1,2,3 , Maxime Wack 4 , Benoit Védie 5 , Nathalie Demory Guinet 6 , Kassis Chikani Najiby 7 , Laurence Janot 6 , Laurent Bélec 1,2,3 , David Veyer 1, 8 surface protein, with the high-throughput UniCel DxI 800 Access Immunoassay System (Beckman Coulter), to increase hospital productivity in SARS-CoV-2 IgG serology testing. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients The authors are also grateful to Beckman Coulter, France, for providing the ACCESS SARS-CoV-2 IgG kits for the study.J o u r n a l P r e -p r o o f doi = 10.1016/j.jcv.2020.104617 id = cord-311633-i9ret7bw author = Péré, Hélène title = Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology date = 2020-08-04 keywords = SARS; covid-19 summary = We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. To analytically and clinically validate the Abbott SARS-CoV-2 IgG assay, we tested pre-epidemic sera, sera from pauci-symptomatic health-worker with SARS-CoV-2 positive RT-PCR and sera from hospitalized patients from both the COVID-positive area and the COVID-free area. doi = 10.1016/j.jcv.2020.104568 id = cord-292675-tkyngspy author = Qi, Furong title = Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses date = 2020-03-19 keywords = ACE2; SARS; cell summary = For this purpose, we collected single cell gene expression matrices from 13 relatively normal human tissues, consisting of lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] from published literatures. We analyzed the single cell co-expression profiles of 51 known ssRNA viral receptors and 400 membrane proteins, including ACE2, in the identified 119 cell types across the 13 human tissues. Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [8] , liver [9] , ileum [10] , rectum [10] , blood [11] , bone marrow [12] , skin [13] , spleen [14] , esophagus [14] , colon [15] , eye [16] , stomach [17] and kidney [18] (Table S1) . doi = 10.1016/j.bbrc.2020.03.044 id = cord-335155-x9az3twa author = Qi, Zhen title = Phylogeny of SARS-CoV as inferred from complete genome comparison date = 2003 keywords = CoV; SARS summary = SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. To date, genomes from 12 SARS-CoV isolates and 12 previously identified coronaviruses have been completely sequenced. The unrooted phylogenetic tree was constructed for genomes from 12 SARS-CoV isolates and that from 12 previously identified coronviruses (Fig. 1) . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJOI) doi = 10.1007/bf03183930 id = cord-337324-jxtch47t author = Qian, Guo-Qing title = Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series date = 2020-02-25 keywords = China; SARS; Wuhan summary = title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series 8 Three further cases were reported in Ningbo cohort as clinical-diagnosed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to National Health Commission of the People''s Republic of China guidance, though they tested negative for the SARS-CoV-2. This report, to our knowledge, is the largest case study to date of hospitalized patients with COVID-19 in Zhejiang province, which is outwith of Wuhan and Hubei. Our study provided three cases as clinical-confirmed COVID-19 pneumonia because of their epidemiological history, signs, symptoms and chest CT evidence according to guidance, though they tested negative for the SARS-CoV-2. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1101/2020.02.23.20026856 id = cord-263738-8g5ujfaf author = Qian, Jing-Yi title = Acute Kidney Injury in the 2019 Novel Coronavirus Disease date = 2020-06-18 keywords = AKI; COVID-19; China; SARS summary = COVID-19 is characterized by acute respiratory disease, with 80% of patients presenting mild like flu-like symptoms; however, 20% of patients may have a severe or critical clinical presentation, which likely causes multiple organ injuries (e.g., kidney, heart, blood, and nervous system). Novel coronavirus disease (COVID-19) is a newly discovered acute infectious disease caused by the SARS-CoV-2 virus, which is mainly manifested as acute respiratory diseases characterized by acute interstitial and alveolar pneumonia and can affect multiple organs such as the kidneys, the heart, the digestive tract, and blood [1] . In another study of 99 patients with COVID-19, seven cases developed various degrees of kidney injury with elevated serum creatinine (Scr) and/or blood urea nitrogen (BUN) levels, and 3 of them were diagnosed with AKI [4] . These results provide direct evidence that the SARS-CoV-2 virus can directly infect the renal tubular epithelium and podocytes, which may induce AKI in COVID-19 patients [17] . doi = 10.1159/000509086 id = cord-293831-28ddm9um author = Qian, Mengcen title = Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey date = 2020-02-20 keywords = SARS; Shanghai; Wuhan summary = Objective: To investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China Design: Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020 Setting: Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan) Participants: Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18 Main outcome measures: Anxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). 18.20024448 doi: medRxiv preprint We found that higher perceived risk and severity of contracting the novel coronavirus, higher perceived relative transmissibility and harm to body to SARS, and more confusion about information reliability were all significantly and positively associated with reported moderate or severe anxiety during the outbreak (Table 3 ). doi = 10.1101/2020.02.18.20024448 id = cord-343827-jo61t3m0 author = Qian, Qun title = Direct evidence of active SARS-CoV-2 replication in the intestine date = 2020-07-08 keywords = CoV-2; SARS summary = We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. doi = 10.1093/cid/ciaa925 id = cord-295559-yc8q62z8 author = Qian, Zhaohui title = Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date = 2013-10-03 keywords = MERS; SARS; Vero summary = Coronavirus S proteins are Class I viral fusion proteins like the HIV envelope (env), influenza hemagglutinin (HA) and paramyxovirus fusion (F) glycoproteins [17] , which typically require protease cleavage between the S1 and S2 domains ( Figure 1A ) to permit conformational changes in S2, activated by receptor binding and/or low pH, that mediate membrane fusion leading to virus entry and syncytia formation [3, 17, 18] . In addition to entry by endocytosis, we showed that, like SARS-CoV [21, 22] , MERS pseudovirions could enter susceptible Vero E6 cells at the plasma membrane if virions were first bound to cell surface receptors at 4°C at neutral pH in the presence of NH 4 Cl to inhibit acidification of endosomes, and also treated briefly at room temperature with trypsin to cleave the viral S protein. doi = 10.1371/journal.pone.0076469 id = cord-309999-izdl0f2i author = Qin, Ede title = Immunogenicity and protective efficacy in monkeys of purified inactivated Vero-cell SARS vaccine date = 2006-02-13 keywords = SARS; monkey; vaccine summary = Additionally, three groups of rhesus monkeys were immunized with different doses of the purified inactivated SARS vaccine (0.5, 1 and 2 μg/time/monkey) on days 0 and 7, and the monkeys were challenged with SARS-CoV GZ-01 strain. INTERPRETATION: The purified inactivated SARS vaccine could induce high levels of neutralizing antibody, and protect the monkeys from the challenge of SARS-CoV. The results showed that both the purified and the unpurified SARS vaccines can induce high levels of SARS-CoV specific neutralizing antibodies in monkeys, thus demonstrating high immunogenicity. Our observations of immunogenicity in monkeys showed that the unpurified inactivated SARS vaccine induced almost the same level of neutralizing antibody as the purified vaccine. The results indicated that the purified inactivated SARS vaccine we developed could induce high levels of neutralizing antibody, protect monkeys after a SARS-CoV challenge, and be administered safely in monkeys. doi = 10.1016/j.vaccine.2005.06.038 id = cord-334430-1udn20wo author = Qin, Li title = The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice date = 2007 keywords = SARS summary = title: The immunity induced by recombinant spike proteins of SARS coronavirus in Balb/c mice The immune effect of two recombinant protein fragments of spike protein in severe acute respiratory syndrome coronavirus (SARS CoV) was investigated in Balb/c mice. Two partial spike gene fragments S1 (322 1464 bp) and S2 (2170 2814 bp) of SARS coronavirus were amplified by RT-PCR, and cloned into pET-23a prokaryotic expression vector, then transformed into competent Escherichia E. The results showed that recombinant proteins of SARS coronavirus spike protein induced hormonal and cellular immune response in Balb/c mice. Spike protein is also the main protective antigen inducing the generation of neutralizing antibodies, and it can be detected in infected cell culture supernatants with antisera from SARS patients [7, 8] . An exposed domain in the severe acute respiratory syndrome coronavirus spike protein induces neutralizing antibodies doi = 10.1007/s11596-007-0301-0 id = cord-304271-vyayyk50 author = Qin, Yuan-Yuan title = Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial date = 2020-03-05 keywords = MERS; SARS; glucocorticoid; patient summary = title: Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial [9] During the SARS epidemic of 2003, therapeutic systemic glucocorticoids were widely administered in patients who were infected with the severe acute respiratory syndrome coronavirus (SARS-COV), and who subsequently developed severe respiratory disease. [12] In addition, a further retrospective observational study found that glucocorticoid therapy in patients with MERS was associated with delayed Middle East respiratory syndrome coronavirus (MERS-CoV) RNA clearance. [13, 20, 21] Glucocorticoid therapy was used in the treatment of severe SARS because early anecdotal experience supported it, and radiologic findings and histologic features of critically ill patients with SARS were similar to those of patients with acute respiratory distress syndrome (ARDS). Factors associated with psychosis among patients with severe acute respiratory syndrome: a case-control study Effectiveness of glucocorticoid therapy in patients with severe coronavirus disease 2019: protocol of a randomized controlled trial doi = 10.1097/cm9.0000000000000791 id = cord-259593-shrd1s7r author = Qin, Zhao-ling title = siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date = 2007-06-27 keywords = EGFP; RNA; SARS summary = title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. doi = 10.1016/j.jviromet.2007.05.017 id = cord-291467-vv2lrx2p author = Qing, Huiling title = The possibility of COVID‐19 transmission from eye to nose date = 2020-03-18 keywords = SARS summary = T he Coronavirus Disease 2019 , caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not only spreading throughout China but has reached more than 20 countries and has already posed threats to global health and economy. The reason is that although a small number of COVID-19 patients have conjunctivitis, not all of them show positive test of SARS-CoV-2 nucleic acid in conjunctival sac swabs. In addition, some patients did not have conjunctivitis despite positive test results for the SARS-CoV-2 nucleic acid in their conjunctiva sac swabs (Dr. Yanping Song from Wuhan City, China, the outbreak area in China, unpublished paper). Studies show that, like the severe acute respiratory syndrome coronavirus (SARS-CoV) that caused SARS, SARS-CoV-2 binds to human angiotensin-enzyme II (ACE2), using it as a cell entry receptor to invade respiratory and lung epithelium through the spike (S) protein (Zhou et al., 2020a (Zhou et al., ,2020b . doi = 10.1111/aos.14412 id = cord-292030-cjz4nuag author = Qiu, Guangyu title = Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection date = 2020-04-13 keywords = COVID; LSPR; PPT; SARS summary = In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. 26−29 In this work, we developed a dual-functional LSPR biosensor through combining the photothermal effect and plasmonic sensing transduction for SARS-CoV-2 viral nucleic acid detection. The plasmonic chip with the twodimensional distribution of nanoabsorbers (AuNIs) is capable to generate the local PPT heat and transduce the in situ hybridization for highly sensitive and accurate SARS-CoV-2 detection. According to the phase-sensing diagram in Figure 4b and S6a, the LSPR response of the dual-functional AuNI biosensor started to increase when the RdRp-COVID genes were injected into the microfluidic chamber at about 200 s and attained the maximum phase value after about 800 s hybridization. doi = 10.1021/acsnano.0c02439 id = cord-278256-dmrtsxik author = Qiu, Haiyan title = Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study date = 2020-03-25 keywords = COVID-19; SARS; patient summary = title: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study INTERPRETATION: Although all paediatric patients in our cohort had mild or moderate type of COVID-19, the large proportion of asymptomatic children indicates the difficulty in identifying paediatric patients who do not have clear epidemiological information, leading to a dangerous situation in community-acquired infections. All children with COVID-19 had been infected either by close contact with adults infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or by exposure to the epidemic area. By contrast with findings in adults, children with COVID-19 had milder clinical manifestations; nearly half of paediatric patients were asymptomatic (ie, no fever and no cough). When compared with children with SARS, paediatric patients with COVID-19 had much milder disease in terms of the prevalence of fever, cough, pneumonia, and severe case type. doi = 10.1016/s1473-3099(20)30198-5 id = cord-296492-knofua00 author = Qiu, L. title = Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province date = 2020-07-07 keywords = July; SARS summary = Lung transplantation recipients (LTx) were susceptible to severe acute respiratory syndrome-corona virus-2 (SARS-Cov-2) and suffered a higher mortality risk than healthy subjects. In this study, the clinical characteristics, laboratory testing and epidemiology survey results of 10 LTx recipients undergoing allograft lung transplantation surgeries in the First Affiliated Hospital of Zhengzhou University during the COVID-19 pandemic were collected. In this work, we collected characteristics of these LTx recipients and designed an epidemiology questionnaire to obtain the information of SARS-CoV-2 infection condition and after-discharge preventive measures of LTx recipients who underwent surgeries in the hospital accepting COVID-19 patients during the COVID-19 pandemic. Consistent with previous reports [12, 13] , the key reasons for the zero SARS-CoV-2 infective rate of LTx recipients in our study may be due to the good performance of hand hygiene, wearing masks and indoor disinfection, and even isolation from family members. doi = 10.1101/2020.07.06.20147264 id = cord-289349-imkgpwn0 author = Qiu, Li title = Strong immunity in the early two years of age links to frequent immunization of routine vaccines date = 2020-08-08 keywords = SARS; covid-19 summary = In this retrospective study, 25 patients under 10 years old were selected from a total of 186 laboratory-confirmed COVID-19 patients (Materials and methods, Fig. S1 , and Table S1 online). The patient age distribution revealed that children of all ages are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (Fig. 1a) . Because pediatric COVID-19 patients aged under 2 years were found to have shorter recovery times, we next further analyzed the clinical differences between children under and over 2 years old; several variables were compared between these two groups (Table S7 online). However, a previous epidemiological study revealed that the incidence of seasonal coronavirus infection in children under one year old is not significantly different from that in older children [15] . Pre-existing cross-reactive T-cell immunity to infections or vaccinations alters subsequent T-cell responses to antigens of unrelated pathogens [18] [19] [20] , thus frequently contributing to a protective or pathogenic role in infectious diseases [18, 20] . doi = 10.1016/j.scib.2020.08.012 id = cord-310909-nc82a70n author = Qiu, Maofeng title = Antibody responses to individual proteins of SARS coronavirus and their neutralization activities date = 2005-04-13 keywords = SARS; protein summary = In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. In the present study, to understand the profile of antibodies to individual proteins of the SARS-CoV, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of this virus were prepared and used to screen and monitor their specific IgG antibodies in SARS patient sera using protein microarray, and the rabbit antisera to recombi-nant proteins S3 (aa 241-591), N (full length), 3a (aa 125-274) and 9b (full length) were prepared and used to investigate their neutralizing activity to the SARS-CoV infection in Vero E6 cells. doi = 10.1016/j.micinf.2005.02.006 id = cord-334194-28ygsbo1 author = Qiu, Tianyi title = Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus date = 2020-02-20 keywords = Fig; SARS summary = title: Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Letter to the editor Identification of potential cross-protective epitope between a new type of coronavirus (2019-nCoV) and severe acute respiratory syndrome virus Recently, a new type of unknown virus causing severe acute respiratory infection was reported in Wuhan city, Hubei province, China (WHO, 2020b) . Recently, the binding sites of S protein to human ACE2 were identified as residues 455, 486, 493, 501, and 505 (numbered according to the 2019-nCoV S protein sequence), which are located near the potential CRE positions (Fig. 1E) . Possibility of an additional CRE may also exist in other regions of S protein or other antigens between 2019-nCoV and SARS-CoV. In summary, a highly similar epitope was identified computationally between the 2019-nCoV and SARS virus, in the region of the binding site of the S proteins to the human ACE2 receptor. doi = 10.1016/j.jgg.2020.01.003 id = cord-259993-hlsvu1cg author = Qiu, Wuqi title = The Impacts on Health, Society, and Economy of SARS and H7N9 Outbreaks in China: A Case Comparison Study date = 2018-06-28 keywords = China; H7N9; SARS summary = AIMS: This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country''s economy, its society, and its place in the global community. In the past 15 years China has experienced numerous public health crises caused by disease outbreaks including Severe Acute Respiratory Syndromes (SARS) in 2003 and Influenza A Virus Subtype H7N9 (H7N9) in 2013. This article discusses the impacts of SARS in 2003 and H7N9 in 2013 in China, in order to provide a better understanding to government and practitioners of why improving management of response to infectious disease outbreaks is so critical for a country''s economy, its society, and its place in the global community. doi = 10.1155/2018/2710185 id = cord-339625-ucfjo73c author = Qiu, Xiang title = Calreticulin as a hydrophilic chimeric molecular adjuvant enhances IgG responses to the spike protein of severe acute respiratory syndrome coronavirus date = 2012-07-26 keywords = CRT; S450; SARS summary = Given that rCRT/39–272 can drive the maturation of bone‐marrow‐derived dendritic cells, directly activate macrophages and B cells, and also elicit helper T cell responses in vivo, we propose that fragment 39–272 of CRT is an effective molecular adjuvant capable of enhancing target Ag‐specific humoral responses in both a T cell‐dependent and independent manner. By using DNA vaccines encoding fusion proteins between CRT and target antigens such as tumor antigen E7, N protein of SARS-CoV and Bacillus anthracis protective antigen domain IV, previous investigators have also observed that CRT can function as a molecular adjuvant (13) (14) (15) (16) . Cheng and colleagues found that intradermal immunization with a DNA vaccine encoding a fusion protein between CRT, or CRT fragments, and the E7 tumor antigen was more efficient at eliciting E7-specific CD8 + T cells and protecting against E7-expressing tumors in C57BL/6 mice (13, 14) . doi = 10.1111/j.1348-0421.2012.00467.x id = cord-305059-8z54lw2d author = Qu, Jie-Ming title = Chapter 4 Diagnosis of COVID-19 date = 2021-12-31 keywords = COVID-19; PCR; SARS; detection summary = If any one of the following pathogenic or serological tests is positive, the patient is confirmed as COVID-19: (1) positive RT-PCR results for SARS-CoV-2 nucleic acid; (2) viral gene sequencing highly homologous to the known SARS-CoV-2; or (3) serum samples positive for SARS-CoV-2-specific IgM and IgG antibodies. The fifth edition of the program was specially designed for Hubei to establish the diagnostic criteria of "clinical diagnosis cases," which include clinical compliance with the characteristics of viral pneumonia, such as corresponding clinical symptoms and imaging CT findings, especially the multiple lobes exudative ground-glass shadow and intermittent consolidation, normal or decreased total count of white blood cells in laboratory examination, and reduced lymphocyte count. The methods are: (1) real-time fluorescence RT-PCR detection of SARS-CoV-2 nucleic acid positive and (2) viral gene sequencing, highly homologous with the known novel coronavirus. doi = 10.1016/b978-0-12-824003-8.00004-8 id = cord-356084-621qzpqd author = Qu, Jiuxin title = Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-04-27 keywords = SARS; patient summary = title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus doi = 10.1093/cid/ciaa489 id = cord-337663-ow1l18li author = Qu, Liang G. title = Scoping review: hotspots for COVID-19 urological research: what is being published and from where? date = 2020-09-09 keywords = COVID-19; Italy; SARS; study summary = This comprehensive review aimed to: identify all up-to-date original publications relating to urology and COVID-19, characterise where publications were from, and outline what topics were investigated. Topics of the study included pathophysiological, administrative, and clinical fields: translational (n = 14), COVID-19-related outcomes (n = 5), urology training (n = 4), telemedicine (n = 7), equipment and safety (n = 2), urology in general (n = 4), uro-oncology (n = 3), urolithiasis (n = 1), and kidney transplantation (n = 8). A registered study in France (NCT04341714) is similarly assessing the efficiency and satisfaction of telemedicine consults, aiming to recruit 400 patients from a neuro-urology clinic. 48 studies were included, investigating pathophysiological, administrative, and clinical outcomes relating to COVID-19 and urology. Clinical fields of COVID-19-related urological research seem to focus on uro-oncology, urolithiasis, and kidney transplant recipients. Nevertheless, our review is the first to provide a comprehensive country-level analysis of current original urological research related to COVID-19. doi = 10.1007/s00345-020-03434-2 id = cord-270886-m9na7cbm author = Quadeer, Ahmed Abdul title = Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges date = 2020-08-15 keywords = SARS summary = Serological assays can also assist in detecting a large number of subclinical infections in the community arising largely due to the high proportion of asymptomatic COVID-19 cases, and in identifying donors with highly reactive antibodies for convalescent plasma therapy. In the current issue of EBioMedicine, Ng and colleagues attempt to address the above limitations of current serological assays by presenting a novel linear B cell immunodominant epitopes based assay for detecting exposure to SARS-CoV-2 [5] . Specifically, they identified a set of five immunodominant linear B cell epitopes from a peptide library of SARS-CoV-2 structural proteins by performing IgG reactivity test on pooled plasma samples of COVID-19 infected patients from Singapore. Consistent with multiple recent reports (e.g., [7, 8] ), the authors also found that the magnitude of IgG responses in COVID-19 patients against the identified epitopes correlated with disease severity. Second, the usefulness of serological assays in detecting prior exposure relies on the stimulation and persistence of SARS-CoV-2-specific antibody responses in infected patients. doi = 10.1016/j.ebiom.2020.102947 id = cord-329890-wg23sa1u author = Quah, Stella R. title = Public image and governance of epidemics: Comparing HIV/AIDS and SARS date = 2007-02-28 keywords = AIDS; HIV; SARS; Singapore; Table summary = Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people''s lifestyles and approaches to the control and prevention of epidemics. The second assumption is that in contrast to SARS, the overall negative public ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. The second assumption to be explored here is that in contrast to SARS, the overall negative social ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. doi = 10.1016/j.healthpol.2006.03.002 id = cord-260132-lqpk3ig7 author = Quartuccio, Luca title = Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome date = 2020-04-19 keywords = IL-6; SARS; lung summary = Currently, the humanized monoclonal antibody anti-interleukin-6 receptor (anti-IL-6R), namely tocilizumab, appears as a promising tool to turn off the cytokine storm, which dramatically complicates the course of the infection in some patients, causing a rapidly fatal acute respiratory distress syndrome. Importantly, SARS-CoV patients admitted to the Intensive Care Unit showed higher white blood cell and neutrophil counts, as well as higher levels of D-dimer, creatine kinase, and creatine, emphasizing the role of the systemic inflammation downstream the virus infection, and the transformation of the infectious disease into a systemic immunological and inflammatory disease. Lung pathology in 2003 SARS-CoV patients showed epithelial cell proliferation and desquamation, hyaline membranes formation along alveolar walls and cells infiltration (lymphocytes, neutrophils, and monocytes) during the early stage of the disease, while, of note, increased fibrosis and multinucleated epithelial giant cells formation at a later stage, highlighting the existence of a two-phase lung injury. doi = 10.1016/j.jbspin.2020.03.011 id = cord-349954-bozgrzvf author = Quintaliani, Giuseppe title = Exposure to novel coronavirus in patients on renal replacement therapy during the exponential phase of COVID-19 pandemic: survey of the Italian Society of Nephrology date = 2020-07-03 keywords = RRT; SARS; covid-19 summary = During the COVID-19 pandemic, among SARS-Cov-2 positive RRT patients the fatality rate was 32.8%, as compared to 13.3% observed in the Italian population as of April 23rd. CONCLUSIONS: A substantial proportion of the 60,441 surveyed RRT patients in Italy were SARS-Cov-2 positive and subsequently died during the exponential phase of COVID-19 pandemic. The urgent need for a better understanding of the epidemic in RRT patients was immediately evident, and therefore we designed a survey of the Nephrology centers in Italy, aimed to capture the main features, impact and geographical distribution of SARS-CoV-2 spread in over 60,000 prevalent RRT patients during the exponential phase of the COVID-19 pandemic in Italy. The Italian Society of Nephrology COVID-19 survey confirms and extends previous preliminary observations suggesting that RRT patients, especially those on HD, are at increased risk of developing severe SARS-Cov-2 infections. doi = 10.1007/s40620-020-00794-1 id = cord-293860-6kz0iws6 author = Qutayba Almerie, Muhammad title = The Association between Obesity and Poor Outcome after COVID-19 Indicates a Potential Therapeutic Role for Montelukast date = 2020-05-27 keywords = COVID-19; SARS; drug summary = HYPOTHESIS: Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. Through a direct anti-viral effect, or by suppression of heightened cytokine release in response to SARS-CoV2, montelukast will reduce the severity of immune-mediated multiorgan damage resulting from COVID-19, particularly in patients with central obesity and metabolic syndrome. With its prominent effect in reducing leukotriene-mediated cytokine release montelukast would have the potential to moderate the background inflammation associated with obesity and the body''s inflammatory response to SARS-CoV2. The strong association between the pro-inflammatory state found in metabolic syndrome and obesity and a more aggressive clinical course in COVID-19 suggests a potential treatment role for drugs that inhibit cytokine release and macrophage activation. doi = 10.1016/j.mehy.2020.109883 id = cord-290792-ggcz1zfw author = Qutob, N. title = Seroprevalence of SARS-CoV-2 in Palestine: a cross-sectional seroepidemiological study date = 2020-09-01 keywords = CoV-2; SARS summary = Serological tests for the 2455 serum samples were done using an Immunoassay for the qualitative detection of antibodies against SARS-CoV-2 .The random sample of Palestinians living in the West Bank yielded 0% seroprevalence with 95% CI [0,0.0036], while the lab referrals sample yielded 4 positive cases. Most authorities rely on PCR testing results to estimate number of COVID-19 cases and make up-to-date decisions 6 . The proportion of the population who have overcome the infection without being noticed can probably be approximated by testing for antibodies against SARS-CoV-2. The study included 2491 individuals (1355 from randomly selected households and 1136 from laboratory referrals; was designed to be representative by cities and used Elecsys ® Anti-SARS-CoV-2 testing. We estimated seroprevalence as the proportion of individuals who had a positive result in the total SARS-CoV-2 antibodies in the immunoassay. Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from doi = 10.1101/2020.08.28.20180083 id = cord-329190-kv9n2qj3 author = Rabaan, Ali A. title = A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective date = 2017-09-01 keywords = CoV; East; IFN; MERS; Middle; SARS summary = The current therapies have mainly been adapted from severe acute respiratory syndrome (SARS-CoV) treatments, including broad-spectrum antibiotics, corticosteroids, interferons, ribavirin, lopinavir–ritonavir or mycophenolate mofetil, and have not been subject to well-organized clinical trials. The Medline database was searched using combinations and variations of terms, including ''Middle East respiratory syndrome coronavirus'', ''MERS-CoV'', ''SARS'', ''therapy'', ''molecular'', ''vaccine'', ''prophylactic'', ''S protein'', ''DPP4'', ''heptad repeat'', ''protease'', ''inhibitor'', ''anti-viral'', ''broad-spectrum'', ''interferon'', ''convalescent plasma'', ''lopinavir ritonavir'', ''antibodies'', ''antiviral peptides'' and ''live attenuated viruses''. A position paper on the evidence base for specific MERS-CoV therapies, published by Public Health England (PHE) and the World Health Organization-International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC-WHO), suggested that benefit was likely to exceed risk for convalescent plasma, lopinavir-ritonavir, IFNs and monoclonal/polyclonal antibodies, while, by contrast, for ribavirin monotherapy and corticosteroids it was considered that the risks would outweigh the benefits [42] . doi = 10.1099/jmm.0.000565 id = cord-271998-hdkmwihu author = Rabenau, H. F. title = SARS-coronavirus (SARS-CoV) and the safety of a solvent/detergent (S/D) treated immunoglobulin preparation date = 2005-06-30 keywords = SARS; TCID summary = SARS-CoV viraemia does not seem to reach high titres, however, it has to be excluded that virus transmission may occur via blood transfusion or application of therapeutic plasma products, e.g. fresh-frozen plasma or single components derived thereof. On the basis of existing validation data for enveloped viruses, it can be anticipated that the inactivation/ removal steps incorporated into manufacturing processes for plasma-derived medicinal products will also be effective for SARS-CoV. Therefore, the inactivation of SARS-CoV by SD treatment was investigated in the laboratory scale at lowered concentration of solvent and detergent (75% of standard SD concentration) and at a shortened process time (30 min). In conclusion, the results obtained in our investigation demonstrated that the process conditions specified for the SD treatment of OCTAGAM are very sufficient to inactivate enveloped viruses such as SARS-CoV to below the limit of detection. doi = 10.1016/j.biologicals.2005.01.003 id = cord-333738-3xtb8gye author = Rabets, A. title = Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients date = 2020-08-22 keywords = MERS; SARS summary = Investigating patient serum samples after SARS-CoV-2 infection in cross-reactivity studies of immunogenic peptides from Middle East respiratory syndrome coronavirus (MERS-CoV), we were able to detect the production of antibodies also recognizing MERS virus antigens. Indeed, the peptide of the HR2 domain of the MERS spike protein, previously proven to induce antibodies against MERS-CoV is sharing 74% homology with the corresponding sequence of SARS-CoV-19 virus. If used as an antigen, the peptide of the HR2 domain of the MERS spike protein allows discrimination between post-Covid populations from non-infected ones by the presence of antibodies in blood samples. The high homology of the spike protein domain suggests in addition that the opposite effect can also be true: coronaviral infections producing cross-reactive antibodies affective against SARS-CoV-19. SARS-CoV-2 infections results in the generation of antibodies with significantly strong cross-reactive towards a MERS specific peptide with 76% homology. Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein doi = 10.1101/2020.08.20.20178566 id = cord-351567-ifoe8x28 author = Rabi, Firas A. title = SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far date = 2020-03-20 keywords = ACE-2; COVID-19; China; SARS; Wuhan summary = However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. To assess the magnitude of the risk posed by the SARS-CoV-2, we review four parameters that we believe important: the transmission rate, the incubation period, the case fatality rate (CFR), and the determination of whether asymptomatic transmission can occur. A small study of 17 patients showed that nasal viral load peaks within days of symptom onset, suggesting that transmission of disease is more likely to occur early in the course of infection [40] . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19)-China 2020 Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia doi = 10.3390/pathogens9030231 id = cord-354608-1me3nopu author = Rabinowicz, Shira title = COVID-19 in the Pediatric Population—Review and Current Evidence date = 2020-09-19 keywords = MIS; SARS; child; covid-19; disease summary = By mid-August 2020, the World Health Organization reported over 23 million confirmed cases of infection with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), resulting in more than 710,000 death worldwide [1] . We review the current evidence of epidemiology, clinical presentation, treatment, and indirect health consequences of SARS-CoV-2 on children. In reports from countries that were severely affected early in course of the pandemic, children comprise 1-2% the diagnosed COVID-19 cases, underrepresented compared with other age groups [3, [13] [14] [15] . In summary, children at any age may be infected with SARS-CoV-2, with reduced frequency and severity compared with adults, although clear epidemiologic data is still missing. Characteristics and outcomes of children with coronavirus disease 2019 (COVID-19) infection admitted to US and Canadian Pediatric Intensive Care Units American College of Rheumatology Clinical Guidance for Pediatric Patients with Multisystem Inflammatory Syndrome in Children (MIS-C) associated with SARS-CoV-2 and hyperinflammation in COVID-19. doi = 10.1007/s11908-020-00739-6 id = cord-021847-wea0qpq2 author = Race, Jeffrey D. title = Chemical, Biological, Radiological, and Nuclear Quarantine date = 2015-10-23 keywords = SARS; exposure; incident; isolation; public; quarantine summary = doi = 10.1016/b978-0-323-28665-7.00082-0 id = cord-275252-4e3cn50u author = Rad SM, Ali Hosseini title = Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date = 2020-05-16 keywords = CoV-2; RNA; SARS; mutation summary = In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. doi = 10.1101/2020.05.15.098947 id = cord-265740-wjdeps3h author = Radbel, Jared title = Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media date = 2020-05-13 keywords = PBS; SARS summary = Given that SARS-CoV-2 viral RNA has demonstrated stability, we posited that phosphate buffered saline (PBS) may be a viable transport medium, as an alternative to VTM), for clinical qPCR testing. We assessed the intraand inter-individual reliability of SARS-CoV-2 qPCR in clinical endotracheal secretion samples transported in VTM or PBS, evaluating the stability of the RT-qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that using PBS as a transport medium has high intra-and inter-individual reliability, maintains viral stability, and is comparable to VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. SARS-CoV-2 detection using standard testing of upper airway secretions requires a nasopharyngeal (NP) or oropharyngeal (OP) swab that is transported to a clinical laboratory using viral transport media (VTM) (https://www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostic-testingsars-cov-2#offeringtests, last accessed April 29 2020). doi = 10.1016/j.jmoldx.2020.04.209 id = cord-311114-ggcpsjk8 author = Radhakrishnan, Chandni title = Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date = 2020-09-09 keywords = CoV-2; India; Kerala; SARS summary = The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. In our analysis, we mapped the SARS-CoV-2 genetic variants obtained from Kerala genomes to the 132 primer or probes sequence and calculated the melting temperature (Tm) of the mutant with the wild type sequence. doi = 10.1101/2020.09.09.289892 id = cord-344270-874i31h8 author = Radke, Robert M title = Adult congenital heart disease and the COVID-19 pandemic date = 2020-06-10 keywords = ACHD; COVID-19; SARS; patient summary = Based on anatomy and additional physiological factors including symptoms, exercise capacity, heart failure, pulmonary hypertension and cyanosis, we propose a pragmatic approach to categorising patients into low-risk, intermediate-risk and high-risk groups. Patients with right heart dilatation or dysfunction are potentially at increased risk of right heart failure as mechanical ventilation and acute respiratory distress syndrome can lead to increase in pulmonary arterial pressures. While this may have ample indirect implications for the regular care of adults with congenital heart disease (ACHD) due to postponement of diagnostic and therapeutic procedures, the focus of the current review is on the direct impact of SARS-CoV-2 on congenital patients. 31 Infection with SARS-CoV-2 should be suspected in ACHD patients presenting with fever, onset or worsening of dyspnoea, lower than usual peripheral oxygen saturation but also in case of unexplained worsening of ventricular function or new arrhythmia. Patients with Down syndrome (commonly associated with congenital heart disease and immune defects) are at higher risk for pulmonary infections and ARDS. doi = 10.1136/heartjnl-2020-317258 id = cord-319333-jwbgytwd author = Radmard, Sara title = Inpatient Neurology Consultations During the Onset of the SARS-CoV-2 New York City Pandemic: A Single Center Case Series date = 2020-07-10 keywords = SARS; covid-19; neurological; patient summary = The encountered neurological problems associated with SARS-CoV-2 infection were encephalopathy (12 patients, 36.4%), seizure (9 patients, 27.2%), stroke (5 patients, 15.2%), recrudescence of prior neurological disease symptoms (4 patients, 12.1%), and neuromuscular (3 patients, 9.1%). Adult inpatients diagnosed with COVID-19 infection by nasopharyngeal swab reverse transcription polymerase chain reaction (RT-PCR) and required neurological evaluation by consultation or admission for primary neurological care were included in this single-center retrospective case-series study at Columbia University Irving Medical Center (CUIMC)-New York Presbyterian Hospital. Most of the patients in our case series developed neurological symptoms several days after COVID-19 symptom-onset and demonstrated elevated inflammatory markers. As in prior literature reviewing neurological manifestations of COVID-19 infection, our case series included instances of both ischemic stroke and intracranial hemorrhage, although our patients also had other cardiovascular risk factors for stroke. Neurological manifestations of hospitalized patients with COVID-19 in Wuhan, China: a retrospective case series study doi = 10.3389/fneur.2020.00805 id = cord-316232-7w1vrx96 author = Radon, K. title = Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19) date = 2020-05-02 keywords = SARS; international summary = For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children <14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. 28.20082743 doi: medRxiv preprint 3 a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. With the community-based household study presented in this paper, we therefore aim to study the sero-prevalence and -incidence of SARS-CoV-2 antibodies in a representative household sample of the Munich population. 28.20082743 doi: medRxiv preprint • The temporal course of SARS-CoV-2 sero-positivity in the Munich general population (point prevalence and incidence) stratified for symptomatic and asymptomatic subjects and reported cases • The daily prevalence and incidence of possible COVID-19 symptoms in the study population doi = 10.1101/2020.04.28.20082743 id = cord-283486-ji0e8yoo author = Radulesco, Thomas title = Safety and Impact of Nasal Lavages During Viral Infections Such as SARS-CoV-2 date = 2020-08-27 keywords = SARS summary = 8 Regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Carrouel et al found the use of a mouth rinses with local nasal applications that contain b-cyclodextrins combined with flavonoids agents reduce the viral load of saliva and nasopharyngeal microbiota, including potential SARS-CoV-2 carriage. Nasal mucosa have high viral loads and include cells expressing proteases responsible for virus entry (such as angiotensinconverting enzyme 2 and TMPRSS2 for SARS-CoV-2), 19, 20 The upper airway has shown to be a reservoir for descending bacterial or viral infection to the lung. 3, 23, 24 Given the potential benefits summarized above, nasal saline irrigation may enhance recovery in patients known to be infected with COVID-19. 26 The potential direct antiviral actions and reduction in viral load have led to proposals that use in patients with COVID-19 may reduce risk of nosocomial transmission. Copper enhanced nasal saline irrigations: a safe potential treatment and protective factor for COVID-19 infection? doi = 10.1177/0145561320950491 id = cord-257556-lmws8eed author = Rafiq, Danish title = Three months of COVID‐19: A systematic review and meta‐analysis date = 2020-05-18 keywords = COVID-19; China; SARS; Wuhan summary = 2 While several other human coronaviruses such as HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1 cause mild respiratory disease, others like the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV tend to have a higher fatality rate 6 (summarized in Table 1 ). Typical of respiratory viruses like influenza virus, SARS-CoV-2019 can spread through large droplets (with a transmission risk restricted tõ 6 ft from the patient). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: a data-driven Modelling analysis of the early outbreak Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: a data driven analysis in the early phase of the outbreak doi = 10.1002/rmv.2113 id = cord-285467-uxfk6k3c author = Ragni, Enrico title = Management of osteoarthritis during COVID‐19 pandemic date = 2020-05-21 keywords = COVID-19; SARS; infection; osteoarthritis; patient summary = Since an effective immune response against viral infections depends on cytotoxic T cells activation (25) , experimental evidence supports the observation that overexpression of inflammatory cytokines like IL-6 during the viral immune response might be associated with a decreased viral clearance by impairing the polarization and functionality of Th1 and CD8 cells (26), contributing to the worsening of the COVID-19 symptoms, and their management may appear an intriguing therapeutical approach. Overall, the administration of drugs for the control of inflammation, inhibiting the response of the immune system, may be detrimental in the initial phases of the viral infection, reducing the ability of the body to react to the presence of SARS-CoV-2, as observed in patients chronically treated for rheumatoid arthritis (27) . All rights reserved This shall prompt orthopaedics and clinicians in general to evaluate with extreme care the clinical conditions of OA patients not only under the perspective of OA symptoms management but also for undercurrent comorbidities, naturally occurring or OA-treatment-related, that, in the era of COVID-19 pandemic, may strongly affect patients outcomes more than the net combination of SARS-CoV-2 infection and OA. doi = 10.1002/cpt.1910 id = cord-338980-pygykil7 author = Rahaman, Jordon title = Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses date = 2016-11-09 keywords = MERS; SARS; protein; site summary = Avoiding regions symptomatic of conformational flexibility such as disordered sites and sites with nonconserved secondary structure to identify potential broad-specificity antiviral targets, only one sequence motif (five residues or longer) remains from the >10,000 starting sites across all coronaviruses in this study. For the DISOPRED2 predictions that were inferred using the nr database, the continuous disorder propensities for every site in a protein were mapped onto their corresponding position in the multiple sequence alignment as raw disorder propensities and as binary states, order or disorder, using a cutoff of 5. For regions with five or more consecutive sites that were 100% conserved in sequence across 1) all CoV or 2) across the MERS and SARS clades, the information of structural disorder prediction from IUPred and DISOPRED2 was used to identify all ungapped sites that were consistently predicted to have 100% conserved order. doi = 10.1093/gbe/evw246 id = cord-303960-86mukxg1 author = Rahimi, Farid title = Tackling the COVID-19 Pandemic date = 2020-04-24 keywords = SARS; covid-19 summary = Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. Barring the live-animal trade at the markets; revising the regulations and rules of customs, import or export across borders; supporting and expediting projects to develop vaccines and antiviral drugs; immediate quarantine of the involved regions; and also producing and supplying a large number of protective facemasks and preventing its stockpiling or smuggling are the main actions suggested to deal with the present or a forthcoming COVID-19 outbreak. doi = 10.1016/j.arcmed.2020.04.012 id = cord-316425-fnlgeubu author = Rahimi, Farid title = Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 date = 2020-04-15 keywords = SARS summary = title: Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 Case-finding: Fast, Available, and Efficient Font-line Diagnostics for SARS-CoV-2 We were delighted to read the enlightening letter titled, The Global Threat of SARS-CoV-2/COVID-19 and the Need for More and Better Diagnostic Tools submitted to the Archives of Medical Research (1). The main rationale behind the recent advances in developing diagnostics for COVID-19 is achieving fast and cheap initial detection and confirmation of SARS-CoV-2 infection in different biological samples, including fecal samples, nasopharyngeal or oropharyngeal swabs, and environmental samples. Thus, providing a rapid, accurate and cheap diagnostic kit will efficiently help the health authorities in the developing countries to expedite case-finding within the population. Global threat of SARS-CoV-2/ COVID-19 and the need for more and better diagnostic tools Mesa biotech receives emergency use authorization from FDA for a 30 minute point of care molecular COVID-19 test: Mesa Biotech doi = 10.1016/j.arcmed.2020.04.008 id = cord-283367-azzy2t1a author = Rahman, Asma title = Neurological manifestations in COVID-19: A narrative review date = 2020-09-10 keywords = COVID-19; CSF; SARS; acute summary = Some patients show neurological manifestations such as headache, dizziness, cerebrovascular disease, peripheral nerve and muscle symptoms and smell and taste impairment. Sarma and Bilello 41 1 Acute transverse myelitis A 28-year-old female patient with SARS-CoV-2 presenting lower back pain, bilateral symmetric upper, and lower extremity numbness. 50 None of the patients with post-COVID-19 GBS tested positive for SARS-CoV-2 in the CSF, 51 points to an immune mechanism such as inflammation secondary to a cytokine storm as a possible cause. During the COVID-19 pandemic, if a patient has neurological symptoms such as loss of the sense of smell and taste or delirium, testing for SARS-CoV-2 should be considered irrespective of them not having the other typical symptoms. Stroke in patients with SARS-CoV-2 infection: case series Acute myelitis after SARS-CoV-2 infection: a case report. Self-reported olfactory and taste disorders in patients with severe acute respiratory coronavirus 2 infection: a cross-sectional study doi = 10.1177/2050312120957925 id = cord-328705-024y5k72 author = Rahman, Md. Mahbubur title = Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment date = 2020-07-21 keywords = Mpro; SARS; drug summary = In this study, computational screening is performed by molecular docking of 1615 Food and Drug Administration (FDA) approved drugs against the main protease (Mpro) of SARS-CoV-2. Several promising approved drugs, including Simeprevir, Ergotamine, Bromocriptine and Tadalafil, stand out as the best candidates based on their binding energy, fitting score and noncovalent interactions at the binding sites of the receptor. The MD simulations for the main protease were conducted (6LU7) in apo-form (protein without ligand) and in holo-form (protein-drug complex) to assess any probable conformational changes to and interactions with their structures over the 100 nanoseconds (ns). The selected four drug-main protease complexes may have dissimilarities with the apo-Mpro during MD simulation regarding the energy profile. Identification of potential binders of the SARS-Cov-2 spike protein via molecular docking, dynamics simulation and binding free energy calculation doi = 10.1080/07391102.2020.1794974 id = cord-315411-11mq8wll author = Rahman, Mohammad Azizur title = Neurobiochemical Cross-talk Between COVID-19 and Alzheimer’s Disease date = 2020-10-19 keywords = Alzheimer; COVID-19; SARS summary = COVID-19 and AD share common links with respect to angiotensin-converting enzyme 2 (ACE2) receptors and pro-inflammatory markers such as interleukin-1 (IL-1), IL-6, cytoskeleton-associated protein 4 (CKAP4), galectin-9 (GAL-9 or Gal-9), and APOE4 allele. Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that attacks predominantly the human respiratory system and has also central nervous system (CNS) targeting and neuroinvasive capabilities [1, 2] . Among inflammatory markers, interleukin 6 (IL-6), interleukin 1 (IL-1), cytoskeleton-associated protein 4 (CKAP4), and galectin-9 (GAL-9 or Gal-9) had received most attention as the common links between COVID-19 and AD manifestations [18] (Fig. 1 ). Among its three alleles (ε2, ε3, and ε4), individuals carrying the ε4 allele are at a heightened risk of developing AD as the ApoE ɛ4/ɛ4 genotype increases fibrinogenesis in the brains of Alzheimer''s disease patients [41] . doi = 10.1007/s12035-020-02177-w id = cord-283439-hqdq2qrh author = Rahman, Mohammad Tariqur title = Can Zn Be a Critical Element in COVID-19 Treatment? date = 2020-05-26 keywords = COVID-19; RNA; SARS; cell summary = The suggested treatments for COVID-19 are, but not limited to, the use of (i) convalescent plasma for COVID-19 treatment [63] [64] [65] ; (ii) ribavirin, a nucleoside analogue in combination with recombinant interferon showed inhibition of MERS-CoV replication [66] ; (iii) lopinavir/ritonavir-a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus infection [67] ; (iv) remdesivir, a nucleotide analogue that inhibit RNA polymerase with a broad spectrum of anti-viral activities; in inhibition of human and zoonotic coronavirus [15, 68, 69] ; (v) favipiravir (also known as T-705, Avigan or favilavir) is a pyrazinecarboxamide derivative known to inhibit RNA polymerase [70] . In the current pandemic of SARS-CoV-2, Zn supplement could play an important role to treat COVID-19 patients such as (i) added immune boosting effects with anti-viral drugs and (ii) stopping SARS-CoV-2 replication in infected cells, if combined with chloroquine. doi = 10.1007/s12011-020-02194-9 id = cord-316536-jpbfgwhl author = Raj, V. Stalin title = Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC date = 2013-03-13 keywords = DPP4; EMC; Fig; SARS summary = Moreover, transient expression of human DPP4 in the non-susceptible COS-7 cells rendered these cells susceptible to binding the hCoV-EMC S1-Fc protein to their surface ( Supplementary Fig. 4) . e, Double-stranded viral RNA (cyan) was detected in hCoV-EMC-infected primary human bronchiolar epithelial cell cultures and appeared to be localized to nonciliated cells that express DPP4 (red). In addition, hCoV-EMC infection of human bronchiolar epithelial cell cultures appeared to be localized to the non-ciliated cells that express DPP4 (Fig. 3e) . COS-7 cells transfected with the human DPP4 expression plasmid, but not with the empty plasmid, were efficiently infected by hCoV-EMC as demonstrated by the presence of viral non-structural proteins in the cells (Fig. 4c) and of viral RNA (Fig. 4d) and infectious virus in the cell supernatants (not shown). S1 receptor-binding domains of hCoV-EMC, SARS-CoV and FIPV fused to the Fc region of human IgG, and soluble versions of DPP4 and ACE2 were expressed and purified as described in the Methods. doi = 10.1038/nature12005 id = cord-340114-ycgc6yyc author = Rajagopal, Kalirajan title = Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies date = 2020-07-28 keywords = COVID-19; SARS summary = title: Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies In this article, some oxazine substituted 9-anilinoacridines (A1–A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1–A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Using different modules (Glide, QikProp, Prime and Desmond) of Schr€ odinger suite LLC, various computational methods such as molecular docking, ADMET screening, binding free energy calculations and molecular dynamics (MD) simulations were performed to find the interactions responsible for COVID-19 inhibition. doi = 10.1080/07391102.2020.1798285 id = cord-354658-v451z3jq author = Rajagopal, Keshava title = Advanced Pulmonary and Cardiac Support of COVID-19 Patients: Emerging Recommendations From ASAIO—A “Living Working Document” date = 2020-05-11 keywords = COVID-19; China; ECMO; SARS; patient summary = The severe acute respiratory syndrome (SARS)-CoV-2 is an emerging viral pathogen responsible for the global coronavirus disease 2019 (COVID)-19 pandemic resulting in significant human morbidity and mortality. We review the rapidly changing epidemiology, pathophysiology, emerging therapy, and clinical outcomes of COVID-19; and based on these data and previous experience with artificial cardiopulmonary support strategies, particularly in the setting of infectious diseases, provide consensus recommendations from ASAIO. It is the specific goal of the present paper to provide a resource document to the clinical community regarding evolving best practice strategies for advanced pulmonary and cardiac support in patients with severe progressive COVID-19. Although central cannulation is hemodynamically advantageous (with respect to higher flow rates; hemodynamic support is not relevant in pure V-V ECMO), in light of its invasiveness, bleeding risks, and specialized training required, it is more reasonable to propose peripheral cannulation as the initial approach of choice for COVID-19-related respiratory failure. doi = 10.1097/mat.0000000000001180 id = cord-295075-cqbayzat author = Rajnarayanan, Rajendram V. title = “Teaching old drugs to kill new bugs”: structure-based discovery of anti-SARS drugs date = 2004-08-20 keywords = SARS; covalent; inhibitor summary = Several old drugs that bind to SARS 3CLpro active site were selected and in silico derivatized to generate covalent irreversible inhibitors with enhanced affinity. Structural conclusions from active site similarity within the coronavirus family and virtual screening on homology models have provided some clues regarding the class of compounds that could interact with SARS protease. The present study employs in silico derivatization as a method to ''''teach old drugs to kill new bugs.'''' We have designed irreversible covalent inhibitors by selective derivatization of top non-covalent leads, which includes several old drugs especially a class of HIV inhibitors identified from virtual screening. The side chains of His163 and Phe140 and the main-chain atoms of Met165, Glu166, and His172 form the S1 subsite, which confers specificity towards Gln. Thus, specific covalent inhibitors of SARS 3CLpro could be designed by substituting the amino acid at the P1 0 position with a thiol specific reactive organic moiety like chloromethyl ketone. doi = 10.1016/j.bbrc.2004.06.155 id = cord-291923-jvbehgb7 author = Rajoli, R. K. title = Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis date = 2020-05-06 keywords = PBPK; SARS; preprint summary = The present study used physiologically-based pharmacokinetic (PBPK) modelling to inform optimal doses of nitazoxanide capable of maintaining plasma and lung tizoxanide exposures above the reported nitazoxanide 90% effective concentration (EC90) against SARS-CoV-2. Methods: A whole-body PBPK model was constructed for oral administration of nitazoxanide and validated against available tizoxanide pharmacokinetic data for healthy individuals receiving single doses between 500 mg SARS-CoV-2 4000 mg with and without food. The model predicted optimal doses of 1200 mg QID, 1600 mg TID, 2900 mg BID in the fasted state and 700 mg QID, 900 mg TID and 1400 mg BID when given with food, to provide tizoxanide plasma and lung concentrations over the reported in vitro EC90 of nitazoxanide against SARS-CoV-2. The model and the reported dosing strategies provide a rational basis for the design (optimising plasma and lung exposures) of future clinical trials of nitazoxanide in the treatment or prevention of SARS-CoV-2 infection. doi = 10.1101/2020.05.01.20087130 id = cord-190540-zf5ksac2 author = Rakshit, Kausik title = An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation date = 2020-06-18 keywords = SARS; charge; protein summary = title: An effective approach to reduce the penetration potential of Sars-Cov-2 and other viruses by spike protein: Through surface particle electrostatic charge negotiation Reviewing the works of different authors, regarding charges, surface charge densities ({sigma}), charge mobility ({mu}) and electrostatic potentials of different aerosols under varied experimental conditions, a similar intensive study has also been carried out to investigate the electron donating and accepting (hole donating) properties of the spike proteins (S-proteins) of different RNA and DNA viruses, including SARS-COV-2. The electrostatic charges accumulated in the layers between the Gr IV Ge is sufficient enough to either fuse or repel the charges of the spike proteins of the RNA, DNA viruses including SARS-Cov-2 (RNA virus) or the aerosols. doi = nan id = cord-315632-29x6l5yh author = Rali, Aniket S title = High-flow Nasal Cannula Oxygenation Revisited in COVID-19 date = 2020-04-21 keywords = HFNCO; SARS summary = A case series of 138 COVID-19 patients from Wuhan, China showed that a total of 36 (26%) patients required ICU level care, of whom 22 (61%) developed ARDS and 17 (47.2%) required invasive mechanical ventilation. 1 Other retrospective analyses have reported similarly that 20-31% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients develop ARDS and require ICU care. [2] [3] [4] Therefore, it is critical that we explore the utility and safety of other forms of respiratory support devices, including high-flow nasal cannula oxygenation (HFNCO) in the treatment of acute respiratory failure. 4 We present a case of a SARS-CoV-2-positive patient with acute respiratory failure who was successfully treated with HFNCO. On day 3, his hypoxic respiratory failure worsened, requiring high-flow nasal cannula at 40 l/min and 90% fractional inspired oxygen, (FiO 2 ) and he was transferred to the medical ICU. Beneficial effects of humidified high flow nasal oxygen in critical care patients: a prospective pilot study doi = 10.15420/cfr.2020.06 id = cord-273553-xp4nfnq3 author = Ramatillah, D. L. title = TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA date = 2020-10-16 keywords = Oseltamivir; SARS; covid-19 summary = Conclusion: The most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine.The higher the patient''s average treatment duration, the lower the average survival rate for COVID-19 patients. Samples used in this study were patients with confirmed COVID-19 who were undergoing treatment and receiving antiviral agent therapy. Patients receiving the combination Oseltamivir + Chloroquine therapy had an average survival rate of about 17% after about 23 days of treatment. Meanwhile, patients who received combination therapy Favipiravir + Oseltamivir + Chloroquine had an average survival rate of about 10% after undergoing treatment for about 39 days. Based on the Chi-Square test, it was found that there was a significant relationship between COVID-19 antiviral agent therapy and the clinical outcome of COVID-19 patients (p = 0.025). Based on the Chi-Square test, there was no significant effect between gender (p = 0.174) and age (p = 0.065) on the clinical outcome of COVID-19 patients. doi = 10.1101/2020.10.14.20212449 id = cord-252597-ea78sjcs author = Ramazzotti, Daniele title = VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date = 2020-10-19 keywords = Material; SARS; Supplementary; VERSO; step; variant summary = Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. The outbreak of coronavirus disease 2019 (COVID19) , which started in late 2019 in Wuhan (China) [1, 2] and was declared pandemic by the World Health Organization, is fueling the publication of an increasing number of studies aimed at exploiting the information provided by the viral genome of SARS-CoV-2 virus to identify its proximal origin, characterize the mode and timing of its evolution, as well as to define descriptive and predictive models of geographical spread and evaluate the related clinical impact [3, 4, 5] . doi = 10.1101/2020.04.22.044404 id = cord-260315-uau554jj author = Ramirez, Santseharay title = Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date = 2020-10-04 keywords = Huh7.5; SARS summary = title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. Importance The cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. 137 We performed a comparative titration in various cells of the P2 VeroE6 and the P5 Huh7.5 viruses ( Figure 138 1b) and found that the infectivity titers in Huh7.5 cells after culture adaptation had increased by more 139 than 3 logs (mean of 4.7 and 8.0 Log 10 TCID 50 /mL, respectively). doi = 10.1101/2020.10.04.325316 id = cord-276548-bh3w7oas author = Ramkumar, K. title = Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer date = 2020-09-30 keywords = ACE2; SARS summary = title: Elevated AXL expression following SARS-CoV-2 infection in non-small cell lung cancer Our bulk data suggests that aerodigestive and lung cancer models express a broad range of ACE2 and TMRPSS2, particularly in epithelial cells, and would serve as good models for studying SARS-CoV-2 infection. Furthermore, SARS-CoV-2 infection reduces ACE2 expression and shifts cells to a more mesenchymal phenotype with loss of EPCAM and upregulation of ZEB1 and other EMT-associated genes. Methods: We analyzed mRNA expression of AXL and other TAM family members as well as angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor, in treatment-naïve (n¼1016) and previously treated (n¼239) NSCLC tumors and in a panel of NSCLC cell lines (n¼70). Notably, expression of ACE2 was downregulated while that of AXL and ZEB1, an EMT transcription factor, were upregulated in NSCLC cells infected with SARS-CoV-2 as compared to mock infected cells, suggesting a shift to a more mesenchymal phenotype. D. Gibbons: Advisory/Consultancy, Research grant/Funding (self Advisory/Consultancy: Synta; Research grant/Funding (self): Bayer. L.A. Byers: Advisory/Consultancy, Research grant/Funding (self doi = 10.1016/j.annonc.2020.08.1800 id = cord-343330-wuzts3mt author = Ramos da Silva, S. title = Broad SARS-CoV-2 cell tropism and immunopathology in lung tissues from fatal COVID-19 date = 2020-09-29 keywords = COVID-19; SARS summary = Background Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection in patients with Coronavirus Disease 2019 (COVID-19) prominently manifests with pulmonary symptoms histologically reflected by diffuse alveolar damage (DAD), excess inflammation, pneumocyte hyperplasia and proliferation, and formation of platelet aggregates or thromboemboli. Methods We performed multicolor staining for viral proteins, and lineage cell markers to identify SARS-CoV-2 tropism and to define the lung pathobiology in postmortem tissues from five patients with fatal SARS-CoV-2 infections. Single cell RNA sequencing (scRNA-seq) analysis of lung tissues from healthy 120 subjects have revealed that many cell types express SARS-CoV-2 entry receptor and 121 cofactors including angiotensin-converting enzyme-2 (ACE2), transmembrane serine 122 protease 2 (TMPRSS2), and furin, that are involved in viral entry, suggesting 123 susceptibility of these cells to infection. 7-10 Furthermore, scRNA-seq analysis of 124 bronchoalveolar lavage fluid (BALF), blood, oropharyngeal or lung tissues from COVID-125 19 patients has identified different types of SARS-CoV-2-infected cells, including 126 macrophages, neutrophils, type II pneumocytes (AT2), and ciliated and endothelial 127 cells. doi = 10.1101/2020.09.25.20195818 id = cord-316330-55nd3pwe author = Ramos-Lopez, Omar title = Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date = 2020-10-19 keywords = HLA; SARS; genetic summary = RESULTS: Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. CONCLUSIONS: Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments. Observational (cross-sectional, cohort, or case-control) studies exploring the role of host genetic polymorphisms in SARS-CoV disease (infection susceptibility, disease progression, and clinical outcomes) in adult subjects were included. The present systematic review revealed that 29 polymorphisms located in 21 genes were associated with SARS-CoV susceptibility/resistance, disease severity, and clinical manifestations/outcomes (Table 1) . doi = 10.1155/2020/6901217 id = cord-326911-va3x6au2 author = Ramos-Mandujano, G. title = A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date = 2020-06-29 keywords = RNA; SARS summary = We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. To date, molecular diagnosis of COVID-19 predominantly relies on detection of SARS-CoV-2 RNA using real-time reverse transcription polymerase chain reaction (rRT-PCR) assays, such as those approved by the US Centers for Disease Control and Prevention (US CDC) 1 . MAVRICS performed on par or better than commercial RNA extraction kits in rRT-PCR detection of SARS-CoV-2, influenza viruses and respiratory syncytial virus in various clinical and environmental samples. . https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint Next, we aimed to develop an efficient SiMNP-based RNA extraction protocol using the contrived SARS-CoV-2 samples and US CDC 2019-nCoV_N1 and N3 rRT-PCR assays. doi = 10.1101/2020.06.28.20141945 id = cord-253618-bosb7e63 author = Ramteke, Shobhana title = Novel coronavirus disease 2019 (COVID-19) pandemic: considerations for the biomedical waste sector in India date = 2020-08-01 keywords = COVID-19; SARS; waste summary = During this epidemic condition, expulsion of biomedical waste created from crisis facilities treating COVID-19 patients in like manner demands unprecedented thought as they can be potential bearers of the disease SARS-CoV-2. During December 2019, a novel Beta-coronavirus temporarily named 2019 novel coronavirus (2019-nCoV), and along these lines authoritatively renamed extreme intense respiratory disorder coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV), causing coronavirus ailment 2019 (or COVID19) , was related with a group of respiratory tract diseases in Wuhan, Hubei Province, China and has quickly spread across main land''s [3] . From that point forward, the whole world has been found napping by the clueless increment in the number of new cases because of the exponential increment in the pace of transmission of 2019-nCoV, presently formally alluded to as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) by the International Committee on Taxonomy of Viruses, the causative operator of COVID-19 [5] . doi = 10.1016/j.cscee.2020.100029 id = cord-265353-xwpdq8wo author = Ramzy, Danny title = Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. date = 2020-09-15 keywords = SARS summary = key: cord-265353-xwpdq8wo title: Commentary: Pneumatocele and Cysts in a Patient with SARS-CoV-2 Infection – Yet Another New Complication Associated with COVID. cord_uid: xwpdq8wo In December 2019, an outbreak of pneumonia traced to a wet market in Wuhan, China, proliferated into a global pandemic with seemingly exponential vehemence and in just eight months spread globally with over 800, 000 deaths 1,2 . Coronavirus Disease 2019 (COVID 19), is caused by the novel betacoronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which is characterized by extreme virulence and a complex spectrum of pathologies ranging in severity from mild constitutional symptoms to multi-organ failure 3 A Novel Coronavirus from Patients with Pneumonia in China The outbreak of COVID-19: An overview COVID-19 Illness in Native and Immunosuppressed States: A Clinical-Therapeutic Staging Proposal Pneumatocele and cysts in a patient with SARS-CoV-2 infection Spontaneous tension pneumothorax and acute pulmonary emboli in a patient with COVID-19 infection COVID-19 Complicated by Spontaneous Pneumothorax doi = 10.1016/j.xjtc.2020.09.012 id = cord-339558-li65qvq9 author = Rana, Rashmi title = A comprehensive overview of proteomics approach for COVID 19: new perspectives in target therapy strategies date = 2020-11-02 keywords = SARS; protein summary = Structural proteome analysis of earlier SARS epidemic in 2003 revealed a large array of proteins that could be targeted for this pandemic too. They used affinity purification followed by mass spectrometry analysis and statistical modeling of the MS1level quantitative data which allowed the identification of 1484 interactions between 1086 cellular proteins and 24 SARS-CoV bait proteins. 2013 ) A recently published study involves the development of an Opto-microfluidic sensing platform to rapidly detect antibodies against SARS-CoV2 spike protein in diluted human plasma with high sensitivity. It is the first study to detect the SARS-CoV-2 antigens in the blood plasma of COVID-19-positive patients. Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry doi = 10.1007/s42485-020-00052-9 id = cord-301226-hmc2wmst author = Randazzo, Walter title = Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date = 2020-04-27 keywords = RNA; SARS summary = Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Here, we show that SARS-CoV-2 can be reproducibly detected by RT-qPCR in longitudinal samples from sewage treatment plants that receive wastewaters from over one million inhabitants in the metropolitan area of Valencia, Spain. Following concentration of viral content by flocculation, a standard RT-qPCR procedure allowed us to detect SARS-CoV-2 RNA in 12/12 samples collected from March 9 to April 14, 2020, with Ct values ranging between 34•00 and 37•84, correspondingly revealing between 5•22 and 5•99 log 10 genomic copies (gc)/L (Table 1) . Interestingly, we consistently detected SARS-CoV-2 RNA in samples collected on March 9 and March 11, when only 50 and 76 cumulative cases were declared in the entire Region of Valencia. doi = 10.1101/2020.04.23.20076679 id = cord-300063-5jemq8nm author = Rane, Jitendra Subhash title = Targeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19 date = 2020-07-20 keywords = SARS summary = Because of the enormous therapeutic importance, we selected some well-characterized pyrimidine substituted phenols (Kumar & Rao, 2018; Table S1 , supplementary material) to investigate their efficiency in binding to the interface of the hACE2-S protein complex and modulate the pattern of infectivity of the SARS-CoV-2 virus. In this study, we aim to identify diaryl pyrimidine derivatives as a potential lead molecule which may bind at the interface of the hACE2-S protein complex with high affinity. The study presented here, using molecular docking tool, revealed significant binding interaction of diaryl pyrimidines with the interface of the hACE2-S receptor complex (hACE2-spike protein complex: PDB ID 6VW1) (Table 1) . To examine the spatial stability and mechanistic aspects of conformational dynamics underlying the molecular interaction of diaryl pyrimidine derivatives, AP-NP, AP-3-OMe-Ph and AP-4-Me-Ph with hACE2-S protein complex, we performed MD simulation in an aqueous environment for the period of 100 ns, at physiological temperature (300 K). doi = 10.1080/07391102.2020.1794969 id = cord-273906-s7l0yxc0 author = Ranga, Vipin title = Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date = 2020-07-23 keywords = HLA; MHC; SARS; Table summary = Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. In order to narrow down the specific epitopes that could elicit an effective MHC class-I-mediated T cell response, we predicted linear 9-mer immunogenic SARS-CoV-2 peptides and their prominent interacting HLA allotypes using the Immune Epitope Database and Analysis Resource (IEDB) and NetCTL1.2 web servers. In order to estimate the potential antiviral cytotoxic T-cell response linked to specific HLA allotypes, we predicted the binding affinity of all possible linear 8-to 11-mer peptides derived from the 26 proteins (Table 1 ) of the SARS-CoV-2 proteome (N 8 = 375, N 9 = 2105, N 10 = 1556 and N 11 = 2377) to HLA-A and HLA-B supertypes using the IEDB web server [25] . doi = 10.3390/vaccines8030408 id = cord-302381-oujsmf8d author = Rankin, John title = Godzilla in the corridor: The Ontario SARS crisis in historical perspective date = 2006-06-30 keywords = Ontario; RNAO; SARS; nurse summary = The following evaluation of yellow fever, cholera and the Spanish influenza will illustrate a continuity in epidemic nurses'' feelings of fear and isolation from the mid-19th to the early 20th century. The five submissions studied were: the Canadian Nursing Association Brief to the National Advisory Committee on SARS and Public Health On 5 March 2003, SARS claimed its first Ontario victim when Sui-chu Kwan, a 78-year-old woman who had returned from a trip to Hong Kong, died of the disease. Instead, the silencing of nurses proved deadly as the SARS virus continued to spread placing both the public and health care workers at heightened risk. It is evident that nurses had little knowledge of previous public health crises and no context in which to place the SARS epidemic. That is they reacted to health care crisis of unknown epidemiology with much fear and, due to the nature of nursing during these crises, are prone to feelings of isolation. doi = 10.1016/j.iccn.2005.10.001 id = cord-346978-ubkqny8j author = Ranoa, Diana Rose E. title = Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date = 2020-06-18 keywords = MS2; RNA; SARS summary = 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) . Similar results were observed with heat-inactivated SARS-CoV-2, whereby the LOD was measured to be 5000 viral copies/mL for both RNA extraction of saliva samples and direct saliva-to-RT-qPCR, with greater detection if the virus was directly analyzed in water (Supporting Limit of Detection (LOD) for assessment of SARS-CoV-2 from saliva, comparing a process utilizing RNA isolation/purification to one that bypasses RNA isolation/purification. Altogether, these findings indicate that the optimized protocol (heat treatment of saliva samples at 95°C for 30 min / addition of TBE buffer and Tween 20) yields a LOD that is comparable to reported clinical viral shedding concentrations in oral fluid, thus emphasizing the translatability of the protocol to detecting SARS-CoV-2 in patient samples. doi = 10.1101/2020.06.18.159434 id = cord-351340-7y19ystp author = Rao, Gundu H. R. title = Coronavirus Disease and Acute Vascular Events date = 2020-07-31 keywords = COVID-19; SARS; patient summary = 3 On the other hand, in a study performed in COVID-19 patients in New York, with observed ST-segment elevated myocardial infraction, 64% had normal D-dimer levels according to Dr Bangalore and associates from the New York University Grossman School of Medicine. At the time of admission, COVID-19 patients reported as having at least 1 acute comorbidity: diabetes (10%-20%), hypertension (10%-15%), or other CVD and cerebrovascular diseases (7%-40%). 12 In a seminal article by Bikdeli et al, endorsed by multiple specialty societies, the authors summarize their findings in the following way: "Coronavirus disease 2019 (COVID-19) , a viral respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), may predispose patients to thrombotic disease, both in the venous and arterial circulations, due to excessive inflammation, platelet activation, endothelial dysfunction, and stasis. Elevated plasmin(ogen) seems to be a common biomarker in people with hypertension, diabetes, CVD, and cerebrovascular diseases, who are susceptible to SARS-CoV-2 infection. doi = 10.1177/1076029620929091 id = cord-321603-lbbsnriv author = Rao, Mohan title = Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date = 2020-08-06 keywords = SARS; saliva summary = The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. doi = 10.1093/cid/ciaa1156 id = cord-334612-lxqcvqca author = Rao, Nirmala title = Sars, preschool routines and children’s behaviour: Observations from preschools in Hong Kong date = 2006 keywords = Hong; Kong; SARS summary = This paper considers the influence of the SARS epidemic on children''s routines and behaviour when preschools re-opened, after a six-week closure. Items on the survey fell into 6 categories including: Information about the preschool and children (21 questions); Routines before the SARS outbreak (4 questions); Learning during School Closure (2 questions); Preparing the kindergarten for re-opening (2 questions); Students return to kindergartens (18 questions); Lessons from SARS (4 questions); and Demographic information about the observers. The 18 items on Students'' return to kindergartens included questions on Daily routines (3 questions); Health issues (2 questions); Social Interaction among children (6 questions); Preschool Management (3 questions); and School Holidays (4 questions). During the SARS outbreak, the Education and Manpower Bureau of the Hong Kong Government issued a curriculum for children ranging in age from 3-6 years. As mentioned earlier the Education and Manpower Bureau of the Hong Kong Government developed a programme for preschool children on SARS. doi = 10.1007/bf03168205 id = cord-334564-bqh9jkds author = Raony, Ícaro title = Psycho-Neuroendocrine-Immune Interactions in COVID-19: Potential Impacts on Mental Health date = 2020-05-27 keywords = COVID-19; CoV-2; HPA; IL-6; SARS; severe summary = Since COVID-19 is associated with increased levels of pro-inflammatory cytokines (8) , an immune signature shared with several psychiatric disorders, we propose how the relationship between SARS-CoV-2/host can possibly impair interactions between the immune, nervous and endocrine systems, leading to psychiatric symptoms. Several studies have demonstrated psychiatric manifestations in patients with MERS or SARS during the acute phase, such as increased stress levels, impaired memory, symptoms of depression, anxiety, PTSD, psychoses, and suicidal behavior (28) (29) (30) (31) (32) (33) . If the increase in cytokine levels and the manifestation of psychiatric symptoms are related to the severity of the symptoms of SARS-CoV infection, the "cytokine storm" might also be related to the "mental health thunderstorms" seen in patients with COVID-19? Similar to possible mechanisms involved in the impacts of SARS-CoV-2 infection on mental health, social isolation may also be associated with dysfunctional psycho-neuroendocrine-immune interactions, which in turn can contribute to the development or the worsening of psychiatric disturbances (Figure 2) . doi = 10.3389/fimmu.2020.01170 id = cord-335599-98ovzui5 author = Raony, Ícaro title = Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus date = 2020-06-25 keywords = SARS summary = title: Retinal outcomes of COVID-19: possible role of CD147 and cytokine storm in infected patients with diabetes mellitus Notwithstanding this, it was not discussed whether the patients already presenting changes in the retina before infection with COVID-19, or even if there was any systemic disease (e.g. type 2 diabetes mellitus) that could also be associated with retinal lesions. Thus, it is possible that CD147, by mediating the breakdown of the blood-retinal barrier in a hyperglycemic context, may facilitate the invasion of retinal cells by SARS-CoV-2 in people with DM, which deserves to be investigated by future studies with animal models and humans. The reverse is also possible, with COVID-19 being able to precipitate or worsen retinal lesions present in patients with DM in the short or long term, either by direct effects of retinal SARS-CoV-2 infection, or by the indirect effects of the cytokine storm associated with COVID-19. doi = 10.1016/j.diabres.2020.108280 id = cord-298440-0pb8ssj2 author = Rascón-Ramírez, Fernando J title = Supra and infratentorial massive strokes in previously healthy young patients with SARS-CoV-2. The role of neurosurgery date = 2020-09-06 keywords = COVID-19; SARS summary = COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors, especially in patients who develop an acute respiratory distress syndrome (SARS-CoV-2). Keywords: Cerebrovascular disease; COVID-19; Coronavirus; stroke; decompressive craniectomy; Cerebellar; SARS-CoV-2. We present two massive supra and infratentorial strokes in people of young age with no known risk factors and with the severe acute respiratory syndrome (SARS-CoV-2), requiring Endotracheal Intubation (ETI). COVID-19 patients can develop large-scale ischemic strokes in previously healthy patients without risk factors. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. To the best of our knowledge, is the first reported case of partial obstruction of a vertebral artery in a patient with COVID-19. doi = 10.1016/j.neucir.2020.08.001 id = cord-270606-r46pbaf0 author = Rashed, Mohamed Z. title = Rapid detection of SARS-CoV-2 antibodies using electrochemical impedance-based detector date = 2020-10-07 keywords = SARS; impedance summary = Here, we demonstrate rapid label-free electrochemical detection of SARS-CoV-2 antibodies using a commercially available impedance sensing platform. A 16-well plate containing sensing electrodes was pre-coated with receptor binding domain (RBD) of SARS-CoV-2 spike protein, and subsequently tested with samples of anti-SARS-CoV-2 monoclonal antibody CR3022 (0.1 [Formula: see text] g/ml, 1.0 [Formula: see text] g/ml, 10 [Formula: see text] g/ml). In this study, we report a non-faradic capacitive immunosensing assay using a commercially-available impedance detection system that uses specialized well-plates that have integrated sensing electrodes from ACEA Biosciences ( Figure 1 ). Coating the wells with anti-SARS-CoV-2 antibodies instead of spike RBD antigen may enable rapid EIS detection of viral particles in patient samples, although further testing is needed to determine the limit of detection for that approach. An alternative medical Rapid Detection of SARS-CoV-2 Antibodies Figure S1 : Measurements with greater time resolution were acquired with a different impedance analyzer (Agilent 4294A, 10 kHz, 0.5 V), demonstrating improved resolution. doi = 10.1016/j.bios.2020.112709 id = cord-274007-zndtddty author = Rasmussen, Sonja A. title = Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date = 2020-02-24 keywords = COVID-19; MERS; SARS; respiratory summary = For Middle East respiratory syndrome, there were 13 case reports in pregnant women, of which 2 were asymptomatic, identified as part of a contact investigation; 3 patients (23%) died. Principles of management of coronavirus disease 2019 in pregnancy include early isolation, aggressive infection control procedures, oxygen therapy, avoidance of fluid overload, consideration of empiric antibiotics (secondary to bacterial infection risk), laboratory testing for the virus and coinfection, fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations. General principles regarding management of COVID-10 during pregnancy include early isolation, aggressive infection control procedures, testing for SARS-CoV-2 and coinfection, oxygen therapy as needed, avoidance of fluid overload, empiric antibiotics (because of secondary bacterial infection risk), fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations (Box 2). doi = 10.1016/j.ajog.2020.02.017 id = cord-009891-gqrhbhbn author = Rassool, G. Hussein title = Current issues and forthcoming events date = 2003-09-03 keywords = HIV; SARS; pain; patient summary = The Centers for Disease Control and Prevention (CDC), USA, reports that ''transmission to health care workers appears to have occurred after close contact with symptomatic individuals (e.g. persons with fever or respiratory symptoms) before recommended infection control precautions for SARS were implemented (i.e. unprotected exposures).'' There is also a possibility that the causative agent can remain viable for extended periods of time after drying on environmental surfaces. Preliminary results of a large-scale trial of a candidate AIDS vaccine announced by the US-based biotechnology company VaxGen suggest that it is possible to protect some individuals from HIV infection. The result is that poor diagnosis of pain in cancer patients remains a significant problem, with many physicians finding it difficult to differentiate between the various pain types; and, many underestimating its severity. Poor diagnosis, poor assessment, the choice of less appropriate treatments, plus patients and physicians fears about controlled drugs such as morphine all contribute to under treatment of cancer pain. doi = 10.1046/j.1365-2648.2003.02701.x-i2 id = cord-299940-nvlcwcz8 author = Rastrelli, Giulia title = Low testosterone levels predict clinical adverse outcomes in SARS‐CoV‐2 pneumonia patients date = 2020-06-03 keywords = RICU; SARS summary = OBJECTIVES: To estimate the association between T level and SARS‐CoV‐2 clinical outcomes (defined as conditions requiring transfer to higher or lower intensity of care or death) in a cohort of patients admitted in the respiratory intensive care unit (RICU). 16, 17 Thereof, we sought to estimate the association between the T levels and the SARS-CoV-2 infection clinical outcomes (defined as conditions requiring to transfer to a higher or lower intensity of care units or even death) as well as the biochemical prognostic predictors of severe and fatal SARS-CoV-2 infection in a cohort of patients admitted in the respiratory intensive care unit (RICU) of a single Hospital in Mantua, one of the epicenter of the global SARS-CoV-2 pandemic in Italy. Discussion and conclusion: Our study demonstrates for the first time that lower baseline levels of TT and cFT levels predict poor prognosis and mortality in SARS-CoV-2-infected men admitted to RICU. doi = 10.1111/andr.12821 id = cord-310124-3bc8zeww author = Ratajczak, Mariusz Z. title = SARS-CoV-2 Entry Receptor ACE2 Is Expressed on Very Small CD45(−) Precursors of Hematopoietic and Endothelial Cells and in Response to Virus Spike Protein Activates the Nlrp3 Inflammasome date = 2020-07-20 keywords = ACE2; Ang; Nlrp3; SARS summary = We demonstrate for the first time that ACE2 and the entry-facilitating transmembrane protease TMPRSS2 are expressed on very small CD133(+)CD34(+)Lin(−)CD45(−) cells in human umbilical cord blood (UCB), which can be specified into functional HSCs and EPCs. The existence of these cells known as very small embryonic-like stem cells (VSELs) has been confirmed by several laboratories, and some of them may correspond to putative postnatal hemangioblasts. Moreover, we demonstrate for the first time that, in human VSELs and HSCs, the interaction of the ACE2 receptor with the SARS-CoV-2 spike protein activates the Nlrp3 inflammasome, which if hyperactivated may lead to cell death by pyroptosis. We sorted very small CD34 + Lin − CD45 − cells (VSELs) and CD34 + Lin − CD45 + cells (HSCs) from UCB by FACS (Fig. 1) and phenotyped them by real-time PCR for expression of mRNAs for the ACE2 entry receptor for SARS-CoV-2, the spike protein-processing enzyme TIMPRSS2, the receptors for Ang II (AT 1 R and AT 2 R), and the Ang (1-7) receptor (MasR, Fig. 2) . doi = 10.1007/s12015-020-10010-z id = cord-329395-4k8js9v2 author = Ratcliff, Jeremy title = Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date = 2020-07-01 keywords = PCR; SARS summary = Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 doi = 10.1101/2020.06.24.168013 id = cord-300194-nsp53lv6 author = Rath, Soumya Lipsa title = Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date = 2020-06-19 keywords = NTD; SARS; Spike summary = Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. and S2 domains individually, with respect to the starting structure, to understand the ause for higher R S values o served at and igure The R S values of S1 domain at and were found to e around nm nearly nm more than simulations at 1 and respe tively similar trend was o served in the R S of S domain ut the differen e in values was only 1 nm lthough in this study we haven''t considered the bilayer lipid membrane of the SARS-COV-2 envelope inside which the Spike 9 glycoprotein resides, the S2 domain shows remarkable stability in its RMSD values ( Figure 2 ). doi = 10.1101/2020.06.10.145086 id = cord-323093-u3ozc9ry author = Rathnayake, Athri D. title = 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice date = 2020-08-19 keywords = CoV; Fig; MERS; SARS; compound summary = After we observed that treatment with compound 6j resulted in the survival of MERS MA -CoV-infected hDPP4-KI mice, we conducted another study by delaying treatment initiation until 3 dpi. This nucleoside analog was originally developed as an antiviral drug against Ebola virus and has been shown to be effective against both MERS-CoV and SARS-CoV in cell culture assays and in animal models of coronavirus infection (23) (24) (25) (26) . Prophylactic treatment or early therapeutic treatment of infected mice with remdesivir reduced MERS-CoV-or SARS-CoV-mediated weight loss and decreased lung virus titers and lung injury scores compared to those of vehicle-treated animals (23, 26) . The goal of this study was to evaluate the efficacy of 3CLpro inhibitors against human coronaviruses, including SARS-CoV-2, in a FRET enzyme assay and cell culture assays, as well as in a mouse model of MERS-CoV infection. doi = 10.1126/scitranslmed.abc5332 id = cord-336150-l8w7xk0b author = Rathore, Jitendra Singh title = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview date = 2020-08-25 keywords = ACE2; CoV-2; MERS; RBD; SARS summary = The essential surface glycoprotein of SARS-CoV-2 known as spike (S) protein, essential for host cell receptor binding, showed only 72% similarity with SARS-CoV at the nucleotide level. Comparative genome analysis of RaTG13, a virus from a Rhinolophusaffinis (i.e. horseshoe) bat sampled from Yunnan province in China in 2013, with SARS-CoV-2, showed that SARS-CoV-2 has 96% similarity at the nucleotide sequence level . Later, it was found that the disease was caused by a virus designated as a novel human coronavirus, MERS-CoV, phylogenetic data showed that it belonged to lineage C of the Betacoronavirusgenus and was highly similar to bat coronaviruses HKU4 (Tylonycterispachypus) and HKU5 (Pipistrelluspipistrellus; Lau et al. When cell lines over-expressed the transmembrane protein ''angiotensin-converting enzyme 2'' (ACE2) from humans, bats, pig or civet cats and were infected with SARS-CoV-2, results showed that they became hypersensitized to infection, thus indicating that ACE2 is a SARS-CoV-2 receptor . Recently, neutralizing monoclonal antibodies and nanobodies against the RBD domain of S protein showed protection against SARS-CoV and MERS-CoV (Du et al. doi = 10.1093/femspd/ftaa042 id = cord-349501-p1fttfpr author = Ratia, Kiira title = Chapter 494 Coronavirus Papain-like Peptidases date = 2013-12-31 keywords = SARS; like summary = Keywords: Coronavirus, Severe acute respiratory syndrome, SARS-CoV, polyprotein processing, ubiquitin-like domain, noncovalent protease inhibitors, de-ubiquitination, DUB, ISG-15, de-ISGylation. For coronaviruses, a family of positive-stranded RNA viruses with large genomes (28À32 kb), the gene encoding the viral non-structural proteins (nsp''s), including the RNA-dependent RNA-polymerase, is translated into a large precursor polyprotein, which must be proteolytically processed to mediate viral transcription and replication [1] . Cloning and expression of the N-terminal region of the murine coronavirus replicase polyprotein revealed that a predicted papain-family protease (papain-like protease, PLP) domain was responsible for processing the aminoterminal non-structural protein (nsp) from the replicase polyprotein [2À3] . Analysis of the N-terminal region of the replicase polyprotein of SARS-CoV revealed only one PLP domain, termed PLpro, which was shown to process the nsp1/2, nsp2/3 and nsp3/4 cleavage sites using the LXGG recognition motif [18] . Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme doi = 10.1016/b978-0-12-382219-2.00493-2 id = cord-313076-531wksez author = Rauch, J. N. title = CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic individuals uncovers a shift in viral prevalence among a university population date = 2020-08-07 keywords = CREST; Fig; SARS summary = Our results substantiate that large, population-level asymptomatic screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPRand PCR-based assays indicate expanded options for surveillance testing The objectives of our study were to: (i) establish the prevalence of asymptomatic SARS-CoV2 infection in a university population, (ii) assess for any dynamic change associated with the changing community conditions related to NPIs, and (iii) systematically compare the performance of our newly developed CRISPR-based test alongside that of the established, CDC-recommended reference testing by RT-qPCR. We used two assays to detect SARS-CoV-2 genomes in the collected OP swab samples: a CRISPR-based method we recently developed at UCSB known as CREST 23 , and the RT-qPCR test recommended by the CDC 24 (Sup. Fig. doi = 10.1101/2020.08.06.20169771 id = cord-340523-wujzihbn author = Ravelli, Angelo title = Kawasaki disease or Kawasaki syndrome? date = 2020-06-22 keywords = SARS summary = 3 4 However, between April and May 2020, a rise in the number of children and adolescents with an acute multisystem hyperinflammatory state fulfilling full or partial criteria for Kawasaki disease (KD), 5 although frequently accompanied by unusual or less common symptoms, such as abdominal pain, diarrhoea and myocardial failure, was noticed in European and North American countries or regions mostly hit by the COVID-19 pandemic. One month later, Riphagen et al 6 described the features of eight children with the aforementioned hyperinflammatory syndrome, which presented with clinical manifestations similar to atypical KD, together with prominent gastrointestinal symptoms, and progressed towards multiorgan involvement and severe shock, requiring admission to the Intensive Care Unit (ICU) and haemodynamic support. Interim guidance on Kawasaki disease and acute multisystem inflammatory syndrome in children and adolescents in the current emergency scenario of SARS-CoV-2 infection Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID-19): a multicentre cohort doi = 10.1136/annrheumdis-2020-218110 id = cord-350557-7i7122zi author = Rawlings, Stephen A title = No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date = 2020-08-07 keywords = CoV-2; SARS summary = We evaluated the presence and level of SARS-CoV-2 RNA in semen, nasal secretion, and saliva collected after confirmed infection. SARS-CoV-2 RNA was not detected in semen 6–17 days after the onset of symptoms despite concomitant shedding in oral secretions. Here, we evaluated the presence and level of SARS-CoV-2 in paired semen, nasal secretion, and saliva samples collected in the short and medium term after confirmed SARS-CoV-2 symptomatic infections. Before enrollment, 5/6 participants tested positive for SARS-CoV-2 RNA on NP swab samples collected within 1-3 days following the onset of symptoms. Upon enrollment in the study, the diagnosis of active SARS-CoV-2 infection was confirmed by positive PCR on NP swab on day 6 post-symptom onset. We found no evidence of SARS-CoV-2 in semen collected 6-17 days after the onset of symptoms despite all men having concomitant shedding of virus in oral secretions up to 792 copies/µL. doi = 10.1093/ofid/ofaa325 id = cord-307770-1igydu3y author = Rawson, Timothy M title = Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date = 2020-05-02 keywords = SARS summary = title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. doi = 10.1093/cid/ciaa530 id = cord-319469-fkuqs3ie author = Ray, A. title = Seroprevalence of anti-SARS-CoV-2 IgG antibody in hospitalized patients in a tertiary referral center in North India date = 2020-08-25 keywords = Delhi; SARS summary = While there was no significant difference in the different age groups and socio-economic classes; residence in Delhi was associated with increased risk (relative risk of 3.62, 95% CI 1.59-8.21) Key Words: SARS-CoV-2 IgG Antibody, Seroprevalence, Hospitalized patient, COVID-19 Seroprevalence studies for SARS-CoV-2 have been conducted in different settings, including community(4)(5)(6)(7), special populations like parturients (8) , liver disease patients (9) , hemodialysis patients (10) , blood donors (11) , health care workers (12) (13) as well in hospitals (14) . In this study, the seroprevalence of SARS-CoV-2 IgG antibody in patients admitted to a major tertiary hospital in Delhi was estimated as well as characteristics of the seropositive patients vis-à-vis the seronegative patients were determined. . https://doi.org/10.1101/2020.08.22.20179937 doi: medRxiv preprint statistically significant difference in seroprevalence of anti-SARS-CoV-2 IgG antibodies were observed between patients admitted with or without comorbidities. doi = 10.1101/2020.08.22.20179937 id = cord-290687-kc7t1y5o author = Ray, Soumi title = Susceptibility and Sustainability of India against CoVid19: a multivariate approach date = 2020-04-21 keywords = India; SARS; death summary = Materials and Methods: Data of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. Conclusions: Though depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation. We have considered life expectancy also to inspect its impact on the number of infected cases and deaths. In This article, the data of Bacillus Calmette-Guérin (BCG) vaccination has been compared with present death rate of different countries. These diseases have shown an impact on death rate in many countries which are badly affected by coronavirus. Negative minimum temperature, a specific range of maximum temperature, lack of BCG vaccination and tendency of other lungs diseases have shown some positive impact in increasing the number of CoVid19 cases and death. doi = 10.1101/2020.04.16.20066159 id = cord-199630-2lmwnfda author = Ray, Sumanta title = Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs date = 2020-07-05 keywords = SARS; drug; host; node; protein summary = Therefore, host-(1) We link existing high-quality, long-term curated and refined, large scale drug/protein -protein interaction data with (2) molecular interaction data on SARS-CoV-2 itself, raised only a handful of weeks ago, (3) exploit the resulting overarching network using most advanced, AI boosted techniques (4) for repurposing drugs in the fight against SARS-CoV-2 (5) in the frame of HDT based strategies. As for (3)-(5), we will highlight interactions between SARS-Cov-2-host protein and human proteins important for the virus to persist using most advanced deep learning techniques that cater to exploiting network data. As per our simulation study, a large fraction, if not the vast majority of the predictions establish true, hence actionable interactions between drugs on the one hand and SARS-CoV-2 associated human proteins (hence of use in HDT) on the other hand. doi = nan id = cord-276132-tv5y1eqc author = Ray, Upasana title = COVID-19: The Impact in Oncology Care date = 2020-10-23 keywords = SARS; cancer; care; covid-19; patient summary = The COVID-19 pandemic has imposed a critical challenge to the current oncology care and practices including late diagnoses, delayed anti-cancer treatment, and static clinical trials. Delaying anti-cancer treatment in the ongoing pandemic cannot be recommended as a sensible choice to reduce the associated infection risk in patients. The American Society of Clinical Oncology (ASCO) recommends that in cancer patients diagnosed with the infection, the immunosuppressive therapies should be withheld until the symptoms resolve like complete remission of fever without use of antipyretics along with a negative COVID-19 test. Nevertheless, contact limitation and physical distancing guidelines continue to be an important part of the cancer treatment strategies during the pandemic in order to protect the patients, health-care personnel and non-COVID-19 patients being treated in the same organization. A practical approach to the management of cancer patients during the novel coronavirus disease 2019 (COVID-19) pandemic: an international collaborative group Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan doi = 10.1007/s42399-020-00592-7 id = cord-310464-lkdkdque author = Rayko, Mikhail title = Quality control of low-frequency variants in SARS-CoV-2 genomes date = 2020-05-07 keywords = GISAID; SARS summary = During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. As a result of the collaborative efforts of the researchers worldwide, on April 14, 2020 it contained over 8,000 SARS-nCoV-2 genomes from different countries, sequenced and assembled using various technologies and approaches. GISAID database curators do a tremendous job of filtering submitted sequences, but sometimes it is difficult to distinguish real variants from errors, especially at the lack of information about coverage. Dataset 8,053 full-length (>29,000 bp) sequences of the SARS-CoV-2 were downloaded from the GISAID database ( www.epicov.org ) on April 14, 2020, including 5,556 genomes marked as "high coverage". Full table with percentage of singleton-containing genomes depending on sequencing and assembly method. doi = 10.1101/2020.04.26.062422 id = cord-264646-d7qexyav author = Raza, Syed Shadab title = Mesenchymal Stem Cells: A new front emerge in COVID19 treatment: Mesenchymal Stem Cells therapy for SARS-CoV2 viral infection date = 2020-07-15 keywords = COVID19; SARS; cell summary = Currently, treating coronavirus disease 2019 (COVID19) patients, particularly those afflicted with severe pneumonia, is challenging, as no effective pharmacotherapy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exists. Based on results from preliminary clinical investigations, one predicts that MSCs therapy for SARS-CoV-2 infected patients is safe and effective although multiple clinical trials with a protracted follow-up will be necessary to determine the long term effects of the treatment on COVID19 patients. Further, MSCs exhibit broad immune regulatory function, which makes them suitable for anti-viral therapy as safety and effectiveness of these cells have been documented in clinical trials of severe lung infections [9, 10, 11] . The first study was a case report [12] , in which a critically ill 65-year-old female with severe pneumonia, respiratory failure, moderate anemia, hypertension, and multiple organ failure received three infusions of umbilical cord MSCs (UCMSCs, 5X10 7 cells/infusion), three days apart. doi = 10.1016/j.jcyt.2020.07.002 id = cord-312677-rwznqiib author = Razmi, Mahdieh title = Immunomodulatory-Based Therapy as a Potential Promising Treatment Strategy against Severe COVID-19 Patients: A Systematic Review date = 2020-08-29 keywords = COVID-19; NCP; SARS; clinical; patient summary = Sixty-six publications and 111 clinical trials were recognized as eligible, reporting the efficacy of the immunomodulatory agents, including corticosteroids, hydroxychloroquine, passive and cytokine-targeted therapies, mesenchymal stem cells, and blood-purification therapy, in COVID-19 patients. Various studies have focused on the efficacy of the immunomodulatory agents including corticosteroids, hydroxychloroquine or chloroquine, cytokine-targeted therapies (e.g., anakinra, siltuximab, or tocilizumab), passive immunotherapy (convalescent plasma and intravenous immunoglobulin), mesenchymal stem cells, and bloodpurification therapy, mostly as adjuvant therapy for treatment of the patients with severe COVID-19 and partly have reported promising outcomes. Included clinical studies with 1-63 participants have shown that both antagonists, specially TCZ, are effective in reducing the mortality rate specially in the severely ill patients, improving the symptoms including fever resolution, oxygenation and resolved CT scans, reducing the inflammation markers (ferritin, CRP, and D-dimer), weaning from the ICU hospitalization and ventilation, and dampening the risk of disease progression to ARDS by mitigating the cytokine storm in the NCP patients [60, 62] , as applied for CRS controlling in the CAR-T therapy [90] . doi = 10.1016/j.intimp.2020.106942 id = cord-350437-dq1il88y author = Reale, Maria Lucia title = SARS-CoV-2 Infection in Cancer Patients: A Picture of an Italian Onco-Covid Unit date = 2020-08-19 keywords = COVID-19; Onco; SARS; patient summary = This retrospective study aims to collect epidemiological, clinical, laboratory, and therapeutic data from SARS-CoV-2 positive cancer patients hospitalized at the Onco-Covid unit in San Luigi Gonzaga Hospital, Italy, one of the few oncological wards for cancer patients with SARS-Cov-2 infection, in order to provide a deeper insight into the clinical evolution of infection in cancer patients, particularly in lung cancer patients. This retrospective study included all SARS-CoV-2 oncological patients accepted at the Onco-Covid Unit at San Luigi Gonzaga Hospital, Orbassano, between March 27th and April 19th 2020. The mean length of hospitalization at data cut-off was 30 days ±14 (0-53), while it resulted 16 ± 9 days (0-37) when calculated from COVID 19 positivity (characteristics and outcomes of individual patients included in the analysis are reported in Supplementary Table 2) . Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.3389/fonc.2020.01722 id = cord-293557-jcgc93it author = Recalde, Borja title = Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients date = 2020-08-23 keywords = COVID-19; SARS summary = title: Histopathological findings in fatal COVID-19 severe acute respiratory syndrome: preliminary experience from a series of 10 Spanish patients In December 2019, an outbreak of severe acute respiratory syndrome associated to SARS-CoV2 was reported in Wuhan, China. To date, little is known on histopathological findings in patients infected with the new SARS-CoV2. Postmortem multiorgan biopsies in 10 patients who died with SARS COV-2 infection were performed after oral authorisation of a first-degree relative. In this report, we describe the histopathology of lung damage in COVID-19 with DAD in all lung samples, associated with medium size arterial thrombosis in four cases, and the presence of viral RNA in all organs. It is remarkable that 9 out of the 10 patients had at least one organ with significant amount of SARS-CoV2 RNA, being most prevalent in lung tissue. Pathological findings of COVID-19 associated with acute respiratory distress syndrome doi = 10.1136/thoraxjnl-2020-215577 id = cord-299333-qu0bmov5 author = Reddy, Gireesh B. title = Clinical Characteristics and Multisystem Imaging Findings of COVID-19: An Overview for Orthopedic Surgeons date = 2020-08-17 keywords = COVID-19; China; SARS; patient summary = Since December 2019, infections with severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), a novel betacoronavirus strain responsible for coronavirus disease 2019 (COVID19) , rapidly progressed from an isolated cluster of cases in the Hubei province of east central China to a pandemic, with significant global health and economic repercussions [4, 5, 10, 24, 25, 27, 28, 44, 58, 80, 91] . Early reports from Italy and China indicated that although pulmonary diseases including ARDS and diffuse pneumonia comprise the predominant lethal complications of COVID-19, patients have also presented with or developed significant cardiac signs and symptoms [50] . COVID-19 musculoskeletal and neurologic manifestations are being reported with increased frequency, particularly in patients with more severe respiratory disease, indicating coronavirus neurotropism possibly directly related with higher viral loads, which are now detectable in cerebrospinal fluid [20] . doi = 10.1007/s11420-020-09775-3 id = cord-272318-8yfg1j0o author = Reddy, Sujan T. title = Cerebrovascular Disease in Patients with COVID-19: A Review of the Literature and Case Series date = 2020-06-11 keywords = CVD; SARS; covid-19; patient summary = To further characterize cerebrovascular disease (CVD) in COVID-19, we review the current literature of published cases and additionally report the clinical presentation, laboratory and diagnostic testing results of 12 cases with COVID-19 infection and concurrent CVD from two academic medical centers in Houston, TX, USA, between March 1 and May 10, 2020. To date, few studies have reported cerebrovascular complications in COVID-19 [3, 4] and 4 small case series have described the clinical and laboratory findings in patients with COVID-19 and concurrent stroke [5] [6] [7] [8] . We review the current literature of published cases and describe our experience of 12 cases with COVID-19 infection and concurrent cerebrovascular disease (CVD) to highlight the clinical presentation and proposed mechanisms of central nervous system (CNS) involvement by SARS-CoV-2. Additionally, we performed a retrospective chart review of all hospitalized cases with confirmed COVID-19 infection (SARS-CoV-2 RT-PCR positive) and CVD (ischemic and hemorrhagic stroke) between March 1 and May 10, 2020 seen at two comprehensive stroke centers in Houston, TX, USA. doi = 10.1159/000508958 id = cord-293559-c78wcr8m author = Rego, Gabriel N. A. title = Current Clinical Trials Protocols and the Global Effort for Immunization against SARS-CoV-2 date = 2020-08-25 keywords = COVID-19; CTP; SARS; Vaccine; figure summary = Two purified inactivated SARS-CoV-2 vaccine candidates, an mRNA-based vaccine mRNA1273, and the chimpanzee adenoviral vaccine ChAdOx1 are currently in phase III clinical trials in the respective countries Brazil, the United Arab Emirates, the USA, and the United Kingdom. Thus, during the pandemic caused by COVID-19, several vaccine candidates with attenuated virus, encoding, or presenting SARS-CoV-2 antigens have been developed globally, reaching clinical trial phases I or II for the evaluation of their safety and immunogenicity. Six protocols are developing phase II and/or III clinical trials using the chimpanzee adenoviral vector ChAdOx1 [50] [51] [52] , purified inactivated SARS-CoV-2 vaccine [53, 54] , and mRNA-1273 vaccine [55] . A Phase I Clinical Trial to Evaluate the Safety, Tolerance and Preliminary Immunogenicity of Different Doses of a SARS-CoV-2 mRNA Vaccine in Population Aged 18-59 Years and 60 Years and Above doi = 10.3390/vaccines8030474 id = cord-268390-npuvodd4 author = Rehman, Aziz ul title = The role of primary and secondary bio-molecules in optical diagnosis of pandemic COVID-19 outbreak date = 2020-08-17 keywords = COVID-19; SARS summary = • Raman and fluorescence signature of ACE-2 specific proteins is the basis for real time detection of COVID-19. This letter to the editor aims to introduce primary and secondary biomarkers whose reflectance, transmittance and fluorescence signals can be used for optical diagnosis of COVID-19 to the scientific community and persuade to build portable, cost effective, label free and real time optical devices for its detection. Keeping in view the epidemic nature of COVID-19, we need early stage, cost effective, real time diagnosis and portable devices to detect this disease so that treatment can be started to save the vulnerable population. Similarly, nucleic acid and protein bound coenzymes molecules like NADH, FAD have their own specific fluorescence biomarkers when excited with UV-A light [13] and can be used for label free detection of COVID-19 on early stages employing portable optical detection systems. doi = 10.1016/j.pdpdt.2020.101953 id = cord-324644-sz5n7a5z author = Rehman, Mahin title = Atypical Manifestation of COVID-19-Induced Myocarditis date = 2020-06-18 keywords = COVID-19; SARS summary = There was a case report that described a patient with COVID-19 with regional wall motion abnormalities who had a biopsy consistent with lymphocytic myocarditis but histopathological and viral genomic polymerase chain reaction (PCR) analysis of the biopsy did not reveal the SARS-CoV-2 viral genome to be present within the myocytes [3] . With this report, we aim to highlight an atypical presentation of COVID-19 (SARS-CoV-2)induced myocarditis as this patient was completely afebrile and had no respiratory symptoms, both of which are typical characteristics. Current consensus around COVID-19-induced myocardial injury is to maintain conservative management especially in those without suspected acute coronary syndrome (ACS) who have mild troponin elevation, as in our young patient. COVID-19-induced myocardial injury can present as a STEMI or non-STEMI (given the evidence of troponin leak) and without concurrent febrile illness or respiratory symptoms of the disease. doi = 10.7759/cureus.8685 id = cord-340666-zl9pp2h3 author = Reifer, Josh title = SARS-CoV-2 IgG antibody responses in New York City date = 2020-07-21 keywords = SARS summary = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a strain of coronavirus that causes coronavirus disease 2019 (Covid-19) and has been declared a global pandemic by the World Health Organization. Additionally, for a subset of patients, we report on the correlation between SARS-CoV-2 patient symptom severity and level of SARS-CoV-2 IgG antibody found in the patient sample. We next sought to evaluate whether semi-quantitative SARS-CoV-2 IgG antibody levels were correlated to severity of symptoms as measured by the SSI. Levels of SARS-CoV-2 IgG antibody are plotted against SSI in Figure 2A . A linear regression analysis of the data indicates that SARS-CoV-2 IgG antibody levels are positively correlated with SSI (p-value < 0.01). In addition, we tested 28,523 patient specimens for SARS-CoV-2 IgG antibody levels for whom we did not obtain a SSI. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease Antibody responses to SARS-CoV-2 in patients with COVID-19 doi = 10.1016/j.diagmicrobio.2020.115128 id = cord-346325-grt67p73 author = Reilev, M. title = Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date = 2020-05-26 keywords = COVID-19; PCR; SARS summary = Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. In this population-based study of a Danish COVID-19 cohort capturing all individuals with a positive PCR test for SARS-CoV-2 in Denmark, we provide nationwide data on clinical characteristics and predictors of hospitalization and death for all SARS-CoV-2 PCR-positive cases identified from February 27 th , 2020 to April 30 th , 2020. In this nationwide cohort of SARS-CoV-2 PCR positive cases and test-negative individuals from the general population in Denmark, we found that older age (e.g., >70 years), male sex, and number of comorbidities were risk factors for hospitalization and death. In this first nationwide population-based study, increasing age, sex, and number and type of comorbidities were closely associated with hospitalization requirement and death in SARS-CoV-2 PCR positive cases. doi = 10.1101/2020.05.24.20111823 id = cord-331673-xv1tcugl author = Reina, Giacomo title = Hard Nanomaterials in Time of Viral Pandemics date = 2020-07-15 keywords = HIV; Nanoparticles; ROS; SARS; Virus; antiviral; cell; infection; viral summary = For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). doi = 10.1021/acsnano.0c04117 id = cord-321208-zemex8bf author = Reina, Jordi title = Evaluación de diferentes genes en la detección por RT-PCR del SARS-CoV-2 en muestras respiratorias y su evolución en la infección date = 2020-05-27 keywords = SARS summary = En nuestro estudio el 96,5% de las primeras muestras positivas presentaron positividad en este gen y el 94% con el gen E, a pesar que su capacidad de detección es de unas 100 genomas-copias/reacción. Sin embargo, al analizar las segundas muestras se observa como la detección del gen E ha mostrado una disminución significativa, a pesar de que todavía el 42% de todos los pacientes seguían siendo positivos a los tres genes, frente al 84% de la primoinfección. Por ello podría afirmarse que para el primer diagnóstico de infección por SARS-CoV-2 debería utilizarse de forma preferentemente el gen E o el gen RpRd. Este mismo dato lo confirma el estudio comparativo de Nalla et al. Por ello se presenta un estudio prospectivo que evalúa la capacidad de amplificación de los tres genes del SARS-CoV-2 (E, RpRd y N) en el diagnóstico de infección por este virus. doi = 10.37201/req/045.2020 id = cord-306390-pzzev8hd author = Reisinger, Emil C. title = Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest date = 2020-06-22 keywords = ELISA; Kindern; SARS summary = title: Mütter-Screening in einem COVID-19-Niedrig-Pandemiegebiet: Bestimmung SARS-CoV-2-spezifischer Antikörper bei 401 Rostocker Müttern mittels ELISA und Immunfluoreszenz-Bestätigungstest Somit kann die Bestimmung der Antikörper gegen SARS-CoV-2 bei Müttern indirekt Auskunft über den Infektionsstatus bei deren Kindern geben. Für den in dieser Studie verwendeten ELISA-Test zum Nachweis von SARS-CoV-2-Antikörpern (Euroimmun) wird in der Literatur eine hohe Sensitivität und Spezifität angegeben [6] . In dieser Pilotstudie wurden 401 Mütter von Kindern im Alter von 1-10 Jahren als Sentinel untersucht, um die Prävalenz der Infektion mit SARS-CoV-2 auch bei Kindern abzuschätzen. Die Aussagekraft dieser Studie zur Prävalenz der Infektion mit SARS-CoV-2 bei Müttern ist durch die relativ geringe Fallzahl (5 % der Mütter mit schulpflichtigen Kindern in Rostock) limitiert. Da in dieser Studie durch die indirekte Immunfluoreszenz weder das positive Ergebnis des ELISA für IgG, noch die 11 positiven und 3 grenzwertigen Ergebnisse des ELISA für IgA bestätigt wurden, empfehlen wir, positive SARS-CoV-2-Antikörperbefunde in den hier verwendeten ELISA-Tests mittels Bestätigungstests (z. doi = 10.1055/a-1197-4293 id = cord-252857-vaq0kwln author = Rejdak, Konrad title = Adamantanes might be protective from COVID-19 in patients with neurological diseases: multiple sclerosis, parkinsonism and cognitive impairment date = 2020-04-30 keywords = SARS summary = We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson''s disease (n=5) or cognitive impairment (n=7). We hereby report on a questionnaire-based study performed to assess severity of COVID-19 in patients suffering from multiple sclerosis (n=10), Parkinson''s disease (n=5) or cognitive impairment (n=7). Hereby we report on the result of a questionaire-based study performed to assess whether adamantanes could exert protective antiviral effect against COVID-19 among different neurological disease patients including multiple sclerosis, parkinsonism and cognitive impairment. In this study, twenty-two patients (10 with multiple sclerosis, 5 with Parkinson''s disease and 7 with cognitive impairment) who were tested positive for SARS-CoV-2 and were receiving treatment with either amantadine or memantine on stable registered doses (100mg q.d. and 10mg b.i.d, respectively) for at least 3 months prior to the infection exposure, were surveyed on their laboratory results and clinical status (remote contact with verbally received information). doi = 10.1016/j.msard.2020.102163 id = cord-263965-i8yutik6 author = Relf, Michael V. title = What''s Old is New! Similarities Between SARS-CoV-2 and HIV date = 2020-04-09 keywords = HIV; SARS summary = In time, I anticipate analysts examining the domestic and global response to this pandemic will evaluate if the use of Covid-19, in an effort to reduce global anxiety and fear associated with SARS, helped or hindered governmental responses and the initial public awareness about the emerging threat. As I witness the unfolding of the Covid-19 pandemic, I continue to think back to the early years of the HIV epidemic. Today, the SARS-CoV-2 pandemic, like the HIV epidemic of the 1980s and 1990s, is a metamorphosis described as "invading the society, and efforts to reduce mortality … are called a fight, a struggle, a war" (Sontag, 1989, p. The U.S. Centers for Disease Control and Prevention (CDC) has published a great resource document, entitled COVID-19: What people with HIV should know (CDC, 18 March 2020), which is available at https://www.cdc.gov/coronavirus/2019-ncov/specific-groups/hiv.html. doi = 10.1097/jnc.0000000000000174 id = cord-299679-6z9e5gi6 author = Rello, Jordi title = Clinical phenotypes of SARS-CoV-2: implications for clinicians and researchers date = 2020-05-21 keywords = SARS; patient summary = Many intubated patients present with phenotype 4, characterised by pulmonary hypoxic vasoconstriction, being associated with severe hypoxaemia with "normal" (>40 mL·cmH(2)O(−1)) lung compliance and likely representing pulmonary microvascular thrombosis. Phenotype 5 is often associated with high plasma procalcitonin and has low pulmonary compliance, Which is a result of co-infection or acute lung injury after noninvasive ventilation. The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is broad, ranging from asymptomatic infection to flu-like illness (sometimes with digestive disturbances) to viral pneumonia. Phenotype 2 represents 80% of hospitalisations and is characterised by the presence of hypoxaemia or small opacities on chest radiographs and these patients should be referred for close respiratory monitoring ( particularly respiratory rate and oxygen saturation measure by pulse oximetry) because they are at risk of rapid deterioration progressing to death if intubation is not timely instituted. doi = 10.1183/13993003.01028-2020 id = cord-352065-960xqft4 author = Rello, Jordi title = Update in COVID-19 in the Intensive Care Unit from the 2020 HELLENIC Athens International Symposium date = 2020-10-22 keywords = ARDS; COVID-19; ICU; SARS; patient summary = Experts reviewed the latest literature relating to the COVID-19 pandemic in critically ill patients, such as epidemiology, pathophysiology, phenotypes of infection, COVID-19 as a systematic infection, molecular diagnosis, mechanical ventilation, thromboprophylaxis, COVID-19 associated co-infections, immunotherapy, plasma treatment, Catheter-Related bloodstream infections, artificial intelligence for COVID-19, and vaccination. A major problem of the coronavirus pandemic is the considerable burden imposed on National Health Systems worldwide due to the hyperacute outbreak and the proportional increase of patients requiring intensive care unit (ICU) support in an extremely limited period of time, while outcomes vary according to the burden of the disease in each country. Acute respiratory distress syndrome (ARDS) is the primary cause of death in COVID-19 [7] and a recent scope review found that for COVID-19, < 5% of patients were reported as experiencing bacterial/fungal coinfection at admission, but development of secondary infections during ICU admission is common [8, 9] . doi = 10.1016/j.accpm.2020.10.008 id = cord-306718-7wp5jmxe author = Remaeus, Katarina title = Characteristics and short‐term obstetric outcomes in a case series of 67 women tested positive for SARS‐CoV‐2 in Stockholm, Sweden date = 2020-09-27 keywords = SARS; covid-19 summary = For the care of pregnant women positive for SARS-CoV-2, National Swedish guidelines were published early in the pandemic and recommended individualized antenatal care, mode of delivery based on obstetric considerations, and no routine separation of the mother and newborn after birth. Here, we want to report a case series of 67 women with a positive test for SARS-CoV-2, who gave birth from March 19 until April 26, 2020 in the Stockholm region, Sweden. In this case series of 67 SARS-CoV-2 test-positive delivered women with varying clinical presentation ranging from asymptomatic to manifest COVID19 disease, the majority had a vaginal, term birth and delivered a healthy normal weight neonate that did not test positive for SARS-CoV-2. In this case series of 67 test-positive women few women presented with severe COVID-19 illness, a majority had a vaginal birth at term with a healthy neonate that were test-negative for SARS-CoV-2. doi = 10.1111/aogs.14006 id = cord-320864-k9zksbyt author = Remes-Troche, J. M. title = Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date = 2020-11-01 keywords = COVID-19; SARS; patient; test summary = When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. Positions have already been established on how to work and/or resume activities at those units (e.g., those issued by the American Neurogastroenterology and Motility Society [ANMS] 4 and the Grupo Español de Motilidad Digestiva [GEMD]) 5 but due to the fact that the epidemiologic behavior, protective equipment avail-ability, serologic diagnostic test performance capacity for corroborating immunity, and socioeconomic context are different throughout Latin America, a group of experts that are members of the Sociedad Latinoamericana de Neurogastroenterología (SLNG) had a virtual meeting to formulate a consensus document with recommendations for the performance of gastrointestinal motility tests. doi = 10.1016/j.rgmxen.2020.07.004 id = cord-259747-sl9q63oc author = Remmelink, Myriam title = Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date = 2020-08-12 keywords = COVID-19; PCR; SARS; patient summary = BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). In this post-mortem study, we included the first 17 adult patients (> 18 years) who died in our hospital (either in a COVID-19 unit or an intensive care unit) from March 13, 2020, with confirmed SARS-CoV-2 infection (i.e., positive RT-PCR assay on nasopharyngeal swab and/or bronchoalveolar lavage specimen). This post-mortem study showed several histopathological abnormalities in COVID-19 non-survivors; however, none of the findings was specific for direct viral injury, even though SARS-CoV-2 was detected in all examined organs using RT-PCR. doi = 10.1186/s13054-020-03218-5 id = cord-313984-7wvfnag1 author = Remy, Kenneth E title = Immunotherapies for COVID-19: lessons learned from sepsis date = 2020-04-28 keywords = COVID-19; SARS summary = Although more recent controlled studies indicate that plasma IL-6 concentrations can be in the range seen in bacterial infections, the time course of change is very different; in some cases, concentrations in patients with coronavirus disease 2019 (COVID-19) seem to increase over time with illness severity and worsening lung function. Indeed, when measured in patients infected with SARS-CoV-2, IL-10 concentrations (the most immunosuppressant cytokine in the body) are also elevated, which might lead to a different conclusion for therapeutic approaches and in understanding the disease pathophysiology. In particular, the modest inflammatory response and the progressive and profound suppression of adaptive immunity in COVID-19 relative to sepsis argues for perhaps a different therapeutic approach. However, if SARS-CoV-2 infection is similar to other chronic inflammatory and immune suppressive diseases, such as sepsis, we argue that immune stimulants, and not anti-inflammatory agents, should be considered as the first-line treatment option. doi = 10.1016/s2213-2600(20)30217-4 id = cord-327138-l2m2g0v8 author = Ren, Chao title = Comparison of clinical laboratory tests between bacterial sepsis and SARS-CoV-2-associated viral sepsis date = 2020-08-04 keywords = SARS summary = Twenty-one patients with SARS-CoV-2-induced sepsis and 46 patients with bacterial sepsis were finally recruited (Additional file 2). The median age was 64.0 years (IQR, 60.5-68.0) and 65.5 years (IQR, 49.3-77.3) for patients of SARS-CoV-2-induced sepsis and bacterial sepsis, respectively (Additional file 1). 8.0 (IQR, 6.5-9.5), P < 0.001] were consistently higher among patients with bacterial sepsis than those with SARS-CoV-2-induced sepsis. In this study, ICU patients with SARS-CoV-2-induced sepsis and those with bacterial sepsis revealed comparable demographic characteristics, like age, gender distribution, and comorbidities, after rigorous screening processes. However, patients with bacterial sepsis were found with more severe organ dysfunction and poor outcomes when compared with those caused by SARS-CoV-2-induced sepsis, including higher values in SOFA and APACHE II, as well as more ICU deaths. This is the first report that compared clinical features and host responses between bacterial and SARS-CoV-2-induced viral sepsis. Baseline characteristics of critically ill patients with SARS-CoV-2-and bacteria-induced sepsis. doi = 10.1186/s40779-020-00267-3 id = cord-353923-ou7w3zkv author = Ren, Shi-Yan title = Stability and infectivity of coronaviruses in inanimate environments date = 2020-04-26 keywords = SARS summary = Most viruses from the respiratory tract, such as coronaviruses, influenza, SARS-CoV, or rhinovirus, can persist on surfaces for a few days. The SARS-CoV-2 is presumed to be transmitted by respiratory droplets, viral aerosols, close contacts, and self-inoculation to nose, mouth, or eyes after touching a contaminated surface [16] . We therefore reviewed the persistence and infectivity of viruses on inanimate surfaces to provide clear information for containing the epidemic of SARS-CoV-2. One COVID-19 patient had upper respiratory tract infection with no pneumonia or diarrhea, and his two stool samples were positive for SARS-CoV-2 on RT-PCR. Persistence of most bacteria, fungi, and viruses (e.g., SARS-CoV) on surfaces depends on environmental conditions [37] , such as air temperature and RH [39] , inoculums, and the materials that they stayed on. Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient doi = 10.12998/wjcc.v8.i8.1391 id = cord-253656-2x4y403o author = Ren, Wenlin title = Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates date = 2020-06-24 keywords = SARS; s1-fc summary = In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. The sera were collected on Day 38 and evaluated by ELISA against SARS-CoV-2 S1-6His protein using HRP-conjugated goat anti-mouse IgG Fc-specific secondary antibodies. As shown in Table 1 and Fig. 5A , immunization of SARS-CoV-2 S1-Fc fusion protein with AD20Gold + as adjuvant also induced very high neutralizing activities with IC50 titers >3000 and IC90 titers around 440-501 in both rabbits on Day 27 after immunizations. Beside high levels of the anti-S1 antibodies elicited, higher neutralizing activities against live SARS-CoV-2 virus and/or pseudovirus from the anti-sera of macaques and rabbits. doi = 10.1016/j.vaccine.2020.06.066 id = cord-261435-wcn4bjnw author = Ren, Xianwen title = Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date = 2020-10-29 keywords = SARS; cell; covid-19; figure summary = Notably, the percentages of megakaryocytes 207 and monocytes in PBMCs were elevated, particularly in severe COVID-19 patients during 208 the disease progression stage (Figure 2A) The increased plasma B cells in peripheral blood appeared to be derived from active 231 proliferation of plasmablasts and transitions from memory B cells based on the paired BCR 232 sequencing analyses. Similarly, the clonal expansion of 398 a central memory CD4+ T cell cluster highly expressing AQP3 (T_CD4_c02-AQP3) was 399 also associated with the triad interaction by disease severity, age, and sex ( SARS-CoV-2 detected in multiple epithelial and immune cell types with 414 interferon response phenotypes 415 The enrichment of plasma B and proliferative T cells in BALF and the elevation of these 416 cells in PBMCs of COVID-19 patients highlighted the roles of these cells in combating 417 SARS-CoV-2 infection. doi = 10.1101/2020.10.29.360479 id = cord-274326-msbdrp3e author = Ren, Xiaohan title = Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 date = 2020-11-04 keywords = ACE2; COVID-19; SARS; TMPRSS2; cell summary = title: Multiple Expression Assessments of ACE2 and TMPRSS2 SARS-CoV-2 Entry Molecules in the Urinary Tract and Their Associations with Clinical Manifestations of COVID-19 We hypothesized that in critically ill patients, an inflammatory cytokine storm could directly attack specific cells in the kidney and testis due to their high expression of ACE2 and cytokine receptors, leading to injury of the urinary tract. Compared with the control group, patients with pulmonary arterial hypertension, chronic kidney disease, and diabetic Infection and Drug Resistance 2020:13 submit your manuscript | www.dovepress.com DovePress 3979 nephropathy, as well as smokers, exhibited higher expression levels of ACE2 in their affected tissues (kidneys or lungs) ( Figure 3A -D). 48 Considering the high level of IL6 in severe COVID-19 patients and the enrichment of the IL6 receptor in various testicular cells, this might be a reason for the potential orchitis caused by SARS-CoV-2 infection. doi = 10.2147/idr.s270543 id = cord-334268-n2hon61o author = Ren, Yanfang title = Risk for dental healthcare professionals during the COVID-19 global pandemic: an evidence-based assessment date = 2020-07-18 keywords = N95; SARS; asymptomatic; covid-19 summary = Considering that the primary route of transmission for COVID-19 is from respiratory droplets, and potentially from spatters or aerosols generated during dental treatments, risks of COVID-19 J o u r n a l P r e -p r o o f transmission from asymptomatic patients to DHPs are dependent on several factors: effectiveness of PPE, specifically the N95 masks in preventing virus transmission, prevalence of asymptomatic cases in the local community, rate of transmission from asymptomatic patients to healthcare providers in close contact, probability for an infection acquired from an asymptomatic patient become symptomatic, and age-adjusted infection fatality rate of symptomatic COVID-19 patients. To understand the potential impact of COVID-19 on dental care and oral health and assess the risks to DHPs from the disease while providing essential services to the community, we periodically searched and reviewed published literature in PubMed and Google Scholar using various combinations of keywords, including SARS CoV-2, COVID-19, Dental, Dentist, Dentistry, Droplets, Aerosols, Healthcare Workers, Symptomatic, Asymptomatic, Saliva, PPE, N95 Masks, Face Shields, and Infection Fatality Rate. doi = 10.1016/j.jdent.2020.103434 id = cord-254446-yxqbe1dj author = Ren, Yunzhao R. title = A Comprehensive Updated Review on SARS‐CoV‐2 and COVID‐19 date = 2020-05-29 keywords = COVID-19; China; CoV-2; Coronavirus; Disease; SARS; patient summary = The disease name -COVID-19‖ and the associated virus name -SARS-CoV-2‖ were coined by the World Health Organization (WHO) and the Coronavirus Study Group of the International Committee on Virus Taxonomy, respectively, on February 11 1, 2 . Interestingly, pharyngeal swab viral nucleic acid screening results of 2,510 patients between January 23 and February 25 from a hospital fever clinic in Hunan Province (a neighboring province of Hubei) demonstrated that the positive rate of SARS-CoV-2 (1.3%) was lower than that of Influenza A (2.3%) and Influenza B (3.3%) 42 . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1002/jcph.1673 id = cord-324270-8rgkop42 author = Renaud-Picard, Benjamin title = Delayed pulmonary abscess following COVID-19 pneumonia: a case report date = 2020-06-18 keywords = COVID-19; SARS summary = The chest radiography showed bilateral diffuse ground-glass opacities that were consistent with a COVID-19 infection ( Figure 1A) . A nasopharyngeal swab, using RT-PCR, tested positive for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between Days 8 and 25 of hospitalization, three specific serologies for SARS-CoV-2 were performed, all of which strongly demonstrated positive IgM and IgG levels (BIOSYNEX COVID-19 BSS rapid test, Strasbourg, France). We believe that patients that present with a severe form of COVID-19 pneumonia would benefit from a well-defined and specific followup after hospital discharge, including early clinical examination, chest CT, and pulmonary-function tests. Figure 1 : A: Chest radiography showing bilateral diffuse ground-glass opacities, which are consistent with a COVID-19 infection, four days after symptom onset. B: Axial chest CT, one month after symptom onset, revealing one pulmonary abscess in the right lower lobe, which is associated with sub-pleural bilateral ground-glass opacities that are consistent with partially resolved moderate-to-severe COVID-19 pneumonia. doi = 10.1016/j.resmer.2020.100776 id = cord-270475-mkpn9tz6 author = Requena, Manuel title = COVID-19 and Stroke: incidence and etiological description in a high-volume center. date = 2020-08-05 keywords = COVID-19; SARS; stroke summary = Although COVID-19 pandemic has produced an enormous collateral damage over stroke systems of care leading to a drop of mild strokes admissions and late arrival of severe strokes, only incidental cases of large vessel occlusion (LVO) in young adults infected by SARS-CoV-2 have been reported without a clear causative relationship (4) . The presence of SARS-CoV-2 infection has been associated with worse functional outcome and higher mortality among patients with acute stroke (11) ; in parallel, history of stroke has also been associated with more severe clinical symptoms and poorer outcomes in patients with COVID-19 (12) . From March 2 nd to April 30 th , 2050 patients were admitted to our center with RT-PCR confirmed SARS-CoV-2 infection; of them 21 (1.02%) presented an acute ischemic stroke 21 and 4 (0.2%) suffered an ICH. Our study shows that the frequency of acute stroke in patients with COVID-19 requiring hospital admission is low (1%) and in most cases a usual cause of stroke was identified. doi = 10.1016/j.jstrokecerebrovasdis.2020.105225 id = cord-267845-18hb5ndr author = Resende, Paola Cristina title = SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date = 2020-05-01 keywords = Illumina; SARS summary = Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. Despite those limitations, we developed a sequencing protocol that successfully obtained whole genomes from SARS-CoV-2 positive samples referred to the National Reference laboratory at FIOCRUZ in Brazil. The tiling amplicon multiplex PCR method has been previously used for virus sequencing directly from clinical samples to obtain consensus genome sequences (3). Here, we describe three protocols using a primer set designed to sequence SARS-CoV-2 directly from total RNA extracted from clinical samples, which were initially diagnosed using real-time RT-PCR (7, 8) . Here we introduce a versatile sequencing protocol to recover the complete SARS-CoV-2 genome based on reverse transcription plus an overlapping long amplicon multiplex PCR strategy, and associated with pipelines to report the data, and recover the consensus files. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples doi = 10.1101/2020.04.30.069039 id = cord-313505-2lr4xara author = Resende, Paola Cristina title = Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date = 2020-06-18 keywords = CoV-2; SARS summary = title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. Introduction 59 COVID-19, the disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 60 (SARS-CoV-2), is leading to high rates of acute respiratory syndrome, hospitalization, and death 61 genomes (> 10% of ambiguous positions), we obtained a final dataset of 7,674 sequences. The prevalence of the sub-clade 211 B.1.1 in our sample (92%) was much higher than that observed in other Brazilian sequences 212 available in GISAID (36%) (Fig. 1C) phylogenetic tree, consistent with the hypothesis of multiple independent introductions (Fig. 2) (Fig. 2) . Revealing COVID-19 Transmission by SARS-CoV-2 Genome 410 Sequencing and Agent Based Modelling. doi = 10.1101/2020.06.17.158006 id = cord-330800-s91zfzfi author = Reta, Daniel Hussien title = Molecular and Immunological Diagnostic Techniques of Medical Viruses date = 2020-09-04 keywords = HIV-1; PCR; RNA; SARS; dna summary = e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. doi = 10.1155/2020/8832728 id = cord-311635-hf6vrbyx author = Reuken, Philipp Alexander title = Between Fear and Courage: Attitudes, Beliefs, and Behavior of Liver Transplantation Recipients and Waiting List Candidates during the COVID‐19 Pandemic date = 2020-06-08 keywords = COVID-19; SARS; SOT summary = We evaluated fears, attitudes, and opinions associated with COVID‐19 in 365 SOT recipients (95% liver, 5% pancreas/kidney), 112 SOT candidates, and 394 immediate household contacts in two German transplant centers. Thus, we assessed COVID-19 prevalence/exposure, perception, compliance and behavior of transplant recipients and candidates on the waiting list in two German liver transplant centers in April 2020 using a crosssectional anonymous survey in patients and their household members. Responding to the item "I am afraid to become infected with the Coronavirus", SOT recipients reported a significantly greater fear of being infected with SARS-CoV-2 than their household controls ( Figure 1A and Supplementary Table S1). Here we demonstrate that fears associated with the SARS-CoV-2 pandemic are frequently expressed by liver transplantation recipients and candidates as well as by their household members. While fears and concerns associated with the SARS-CoV-2 pandemic are frequently expressed by SOT recipients and candidates, measures to prevent infection were frequently followed in the vast majority of patients. doi = 10.1111/ajt.16118 id = cord-256051-87alqfkd author = Revzin, Margarita V. title = Multisystem Imaging Manifestations of COVID-19, Part 1: Viral Pathogenesis and Pulmonary and Vascular System Complications date = 2020-10-01 keywords = ARDS; COVID-19; Coronavirus; Fig; SARS; patient summary = Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in coronavirus disease 2019 (COVID-19), which was declared an official pandemic by the World Health Organization on March 11, 2020. Although SARS-CoV-2 disease (or coronavirus disease 2019 ) primarily manifests as a lung infection, with symptoms ranging from those of a mild upper respiratory infection to severe pneumonia and acute respiratory distress syndrome (ARDS), other multisystemic manifestations of this disease and related complications are becoming more commonly recognized (3) . Thromboembolic complications, including pulmonary embolism (PE), peripheral venous and arterial thrombosis, and acute stroke (seen also in patients older than 50 years without risk factors) have all been reported (50-57). On the basis of the pattern and distribution of the opacities and the presence or absence of certain clinical signs (such as obesity), the authors developed a chest radiography severity scoring system that could be used as a prognostic factor of outcomes in young adult patients with COVID-19 (Fig 3) . doi = 10.1148/rg.2020200149 id = cord-284444-mgxxbm0u author = Reychler, G. title = Nebulization: A potential source of SARS-CoV-2 transmission date = 2020-08-04 keywords = SARS summary = authors: Reychler, G.; Vecellio, L.; Dubus, J.C. title: Nebulization: A potential source of SARS-CoV-2 transmission However, the Aerosoltherapy workgroup (GAT) of the Société de Pneumologie de Langue Franç aise decided at SARS-CoV2 pandemic preparedness to suggest avoiding a drug delivery via nebulization to reduce the risk of spreading the virus by this way. Indeed, some arguments suggested that the aerosol generated from the patient during the nebulization or from the nebulizer can directly exposes mucosae and eyes of the health care workers and contaminate surfaces with potentially infective droplets. One can suppose that the particles generated by the nebulizer and those exhaled by the patient will have optimal sizes to transmit the SARS-CoV2 to the healthcare workers. Based on these three elements, we think reasonable to avoid delivery of drugs via nebulization to SARS CoV2 patients for reducing the risk of exposure of the healthcare workers. doi = 10.1016/j.resmer.2020.100778 id = cord-329328-c6svx4qa author = Reydon, Thomas A. C. title = How can science be well-ordered in times of crisis? Learning from the SARS-CoV-2 pandemic date = 2020-11-03 keywords = Kitcher; SARS summary = Kitcher''s ideal should play a role in assessing the allocation of research resources in future crisis situations, as it provides a way to balance highly divergent interests and incorporate the common good into decision-making processes on research. I want to suggest that one way of doing better is to explicitly pose the question what the common good in a crisis such as the SARS-CoV-2 pandemic encompasses, and how during such a crisis and its aftermath research can be directed toward accommodating the needs of all. While this cannot and should not replace an ongoing global dialogue about how research can serve the common good in times of crisis, making Kitcher''s ideal more concrete and familiarizing researchers, policy makers and other stakeholders with it (which both are tasks for philosophers of science) will be a first step in the right direction. doi = 10.1007/s40656-020-00348-5 id = cord-287043-53oy5w34 author = Reyes‐Bueno, José Antonio title = Miller‐Fisher syndrome after SARS‐CoV‐2 infection date = 2020-06-05 keywords = Barré; SARS summary = The neurophysiological study carried out on April 14 th showed F-wave anomalies such as asymmetric latency for the lower limbs and low A-wave amplitude on the left leg, alteration of bilateral R1 responses in the Blink-Reflex and in the intermediary standard electromyography poor activity in right rectus-anterior femoral muscle and little spontaneous denervation activity in left rectus-anterior femoral (RAF) muscle; all of this was compatible with an acute Guillain-Barre type demyelinating polyneuropathy in a very early stage. In the papers reviewed, the presence of anosmia and/or ageusia was only present in one case of Guillain-Barré syndrome (11) and in the two patients described with Miller-Fisher syndrome (5) . Our case would be the 3rd patient with MFS associated with COVID-19 as far as we know. Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré Syndrome Associated with SARS-CoV-2 Guillain Barre syndrome associated with COVID-19 infection: A case report doi = 10.1111/ene.14383 id = cord-281887-b511bjdy author = Ribeiro, Reitan title = Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date = 2020-09-26 keywords = COVID-19; PCR; SARS; patient summary = DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. CONCLUSIONS: We present a protocol, focused on the patients'' outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Our objective was to present the Brazilian Society of Surgical Oncology (BSSO) protocol for rational use of resources and for reducing the risk of surgical cancer patients being operated on during the coronavirus incubation period, in the context of areas with limited resources, and focused on patient outcomes. In light of all the previous considerations, Table 3 presents our suggested protocol for the rational use of resources to reduce the risk of surgical cancer patients from being operated on during the COVID-19 incubation period, in the context of areas with limited resources. doi = 10.1245/s10434-020-09098-x id = cord-337421-4v48kkus author = Ribeiro, Servio Pontes title = Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil date = 2020-03-27 keywords = Brazil; SARS summary = After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. After the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. We developed a SIR (Susceptible-Infected-Recovered) model divided in 9 a metapopulation structure, where cities with airports were demes connected by the 10 number of flights. 142 143 Results 144 The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to 145 the airport closeness centrality within the Brazilian air transportation network. doi = 10.1101/2020.03.26.20044370 id = cord-275978-pezm1tnw author = Riccardo, Flavia title = Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic date = 2020-04-11 keywords = COVID-19; Italy; SARS; case summary = Methods We analysed data from the national case-based integrated surveillance system of all RT-PCR confirmed COVID-19 infections as of March 24th 2020, collected from all Italian regions and autonomous provinces. However, once interventions are introduced or the susceptibility in the population decreases, the transmission potential at a given time t is measured as the net reproduction number Rt. In this paper, we estimated both R0 and Rt for Italian regions in different epidemiological situations (high, intermediate and low age-adjusted attack rates), selected among those with highest data robustness. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. In this paper, we summarize key epidemiological findings from data on the first 62,843 confirmed COVID-19 cases in Italy, including 5,541 associated deaths, and initial findings on SARS-CoV-2 transmissibility across different regions. doi = 10.1101/2020.04.08.20056861 id = cord-031818-lawd185l author = Rich, Robert Soler title = Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case() date = 2020-09-12 keywords = SARS; covid-19 summary = title: Expanded mesenchymal stem cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Letter to the Editor Expanded Mesenchymal Stem Cells: a novel therapeutic approach for SARS-CoV-2 pneumonia (COVID-19). Concepts regarding a first case in Spain To the Editor: When the natural immune response does not control the replication of the SARS-CoV-2 coronavirus, it induces the production of macrophages and granulocytes with the consequent massive release of CD4 + T cells that produce IL-6 and other proinflammatory cytokines, resulting in lung tissue damage 1,2 . This challenge was faced by researchers from the University of Shanghai, intravenously infusing a suspension of mesenchymal cells (MSC), reporting rapid clinical, radiological and laboratory improvements, comparing them with those of the untreated control group 5 ; effects attributable to the massive release of anti-inflammatory and pro-regenerative cytokines from these cells that are trapped in the pulmonary capillaries. doi = 10.1016/j.medcle.2020.06.011 id = cord-282318-890mltl8 author = Richard, Mathilde title = Factors determining human-to-human transmissibility of zoonotic pathogens via contact date = 2017-02-28 keywords = Ebola; SARS; h2h summary = We used the following examples to illustrate these four modes of contact transmission: Treponema pallidum pertenue (TPE) for skin contact transmission, human immunodeficiency virus type 1 (HIV-1) for sexual contact transmission, coronaviruses (CoV) for respiratory contact transmission and Ebola virus for contact transmission via multiple routes. Other pathogen factors that have contributed to the ''success'' of HIV-1 M strain as a human pathogen, despite its relatively low infectivity (risk estimate of 1 in 1000 exposures for heterosexual transmission; [9] ), include its extraordinary propensity to evolve its genome through recombination and low-fidelity replication, allowing immune and therapeutic escape [20] , the nature of its long, ''latent'', often sub-clinical infection, during which patients can transmit the virus [21] , and high viral load. Amongst the pathogen factors that promote H2H transmission of Ebola virus is the high virus load in secreted bodily fluids combined with a very low infectious dose, as low as 10 plaque forming units as measured in experimental infection studies in nonhuman primates [56] . doi = 10.1016/j.coviro.2016.11.004 id = cord-017489-ftz9190a author = Richards, Guy A. title = Viruses in the Intensive Care Unit (ICU) date = 2005 keywords = ICU; SARS; patient; pneumonia; virus summary = Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. doi = 10.1007/0-387-23380-6_3 id = cord-352096-cc3dzycl author = Richman, Douglas D. title = Antiviral Drug Discovery To Address the COVID-19 Pandemic date = 2020-09-25 keywords = COVID-19; SARS summary = Regardless of whether or when a vaccine becomes available, antivirals for SARS-CoV-2 will still be needed for several reasons: the unlikelihood that a vaccine will be 100% effective, the incompleteness of vaccine coverage because of both vaccine hesitancy and the numerous logistical challenges to accomplishing prompt large-scale immunization of the majority of the population, the possibility of limited durability of vaccine protection, the need for additional prophylaxis for high-risk subjects and poor vaccine responders, and the future value of effective antiviral treatment for Middle East respiratory syndrome (MERS) and new coronaviruses that will likely emerge from zoonoses. suggest that the purported activity against SARS-CoV-2 of the two HIV protease inhibitors, lopinavir and nelfinavir, is probably attributable to cellular toxicity. Structurebased design of antiviral drug candidates targeting the SARS-CoV-2 main protease AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic doi = 10.1128/mbio.02134-20 id = cord-261634-vfe1lawl author = Riddell, Shane title = The effect of temperature on persistence of SARS-CoV-2 on common surfaces date = 2020-10-07 keywords = SARS summary = Currently, there are conflicting reports on the survivability of SARS-CoV-2, with data ranging from 3 to 14 days at room temperature for a single surface type, stainless steel Open Access *Correspondence: Shane.Riddell@csiro.au Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia [5, 11] . At 20 °C, infectious SARS-CoV-2 virus was still detectable after 28 days post inoculation, for all non-porous surfaces tested (glass, polymer note, stainless steel, vinyl and paper notes). The present study has demonstrated that in controlled conditions, SARS-CoV-2 at a starting viral load and in a fluid matrix equivalent to that typically excreted by infected patients, remains viable for at least 28 days when dried onto non-porous surfaces at 20 °C and 50% relative humidity. It is important to note that after 28 days, infectious SARS-CoV-2 was also recovered from stainless steel, vinyl and glass, suggesting survivability on paper or polymer banknotes was not very different from the other non-porous surfaces studied. doi = 10.1186/s12985-020-01418-7 id = cord-028711-zlj48aq7 author = Ridgway, Jessica P. title = Prolonged shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA among patients with coronavirus disease 2019 (COVID-19) date = 2020-06-24 keywords = SARS summary = Early reports from China indicate that severe acute respiratory coronavirus virus 2 (SARS-CoV-2) RNA may persist in the respiratory tracts of patients with coronavirus disease 2019 (COVID-19) for several weeks after symptom onset. To estimate the duration of SARS-CoV-2 RNA shedding, we conducted a multisite study among patients who had nasopharyngeal specimens tested for SARS-CoV-2 RNA via real-time polymerase chain reaction (PCR) assay at Providence St Joseph Health (a 51-hospital healthcare organization based in Renton, Washington), University of Chicago Medicine in Chicago, Illinois, and NorthShore University HealthSystem (a 5-hospital healthcare system based in Evanston, Illinois). 4 Our findings that SARS-CoV-2 PCR tests remain positive for >3 weeks in most patients suggest that patients following the test-based strategy may remain on precautions for prolonged periods. It was a retrospective cohort study among patients with COVID-19 who underwent SARS-CoV-2 PCR testing at the discretion of their medical providers. Duration of SARS-CoV-2 RNA Detection No. of Days After 1 st Positive SARS-CoV-2 PCR Test doi = 10.1017/ice.2020.307 id = cord-298894-t5hyfum3 author = Rifino, Nicola title = Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital, Bergamo, Italy date = 2020-10-07 keywords = CSF; SARS; covid-19; patient summary = Neurological manifestations were classified as: (a) cerebrovascular disease [53 pts (38.7%)] including 37 ischemic and 11 haemorrhagic strokes, 4 transient ischemic attacks, 1 cerebral venous thrombosis; (b) peripheral nervous system diseases [31 (22.6%)] including 17 Guillain–Barrè syndromes; (c) altered mental status [49 (35.8%)] including one necrotizing encephalitis and 2 cases with RT-PCR detection of SARS-Cov-2 RNA in CSF; (d) miscellaneous disorders, among whom 2 patients with myelopathy associated with Ab anti-SARS-CoV-2 in CSF. COVID-19 diagnosis was confirmed: (1) by real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) on nasopharyngeal specimens [13] ; or (2) by RT-PCR on bronchoalveolar lavage (BAL) obtained by bronchoscopy in case of high clinical suspicion of SARS-CoV-2 infection and negative test results on at least two nasopharyngeal swabs performed at least 24 h apart; or (3) in the presence of characteristic radiological interstitial pneumonia associated with typical symptoms (fever, dry cough, dyspnea), even with negative RT-PCR, with no other possible aetiologic explanation. doi = 10.1007/s00415-020-10251-5 id = cord-266930-a1mzxmsb author = Rigatti, S. J. title = SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population date = 2020-09-11 keywords = SARS; September summary = Using state population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. Conclusions: The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. population data from the US Census, it is estimated that this level of seropositivity would correspond to 6.98 million (99% CI: 6.56-7.38 million) SARS-CoV-2 infections in the US, which is 3.8 times the cumulative number of cases in the US reported to the CDC as of June 1, 2020. The estimated number of total SARS-CoV-2 infections based on positive serology is substantially higher than the total number of cases reported to the CDC. doi = 10.1101/2020.09.09.20191296 id = cord-346539-kxnrf5g5 author = Riggioni, Carmen title = A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date = 2020-06-14 keywords = ACE2; COVID-19; CoV-2; SARS; cell; clinical; figure; infection; patient; respiratory; severe summary = This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/all.14449 id = cord-342599-558yn6pu author = Rinchai, Darawan title = A modular framework for the development of targeted Covid-19 blood transcript profiling panels date = 2020-05-22 keywords = SARS; covid-19; figure; module; transcript summary = Here we aimed to develop an approach to support the design of focused blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: therapeutic development relevance, SARS biology relevance and immunological relevance. In this proof of principle study, we used the available transcript profiling data from two separate studies to select Covid-19 relevant sets of modules (8, 9) . One of these applications provides access to module-level transcript abundance profiles for available Covid-19 blood transcriptome profiling datasets. Despite large differences between the two studies in terms of design, range of clinical severity, technology platforms and module coverage, the combined overall changes (detected at a high-level perspective) are consistent with those observed in known acute infections, such as those caused by influenza, respiratory syncytial virus (RSV) or S. doi = 10.1101/2020.05.20.107243 id = cord-321854-cy8vyb6j author = Ripperger, Tyler J. title = Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low Prevalence Communities and Reveal Durable Humoral Immunity. date = 2020-10-14 keywords = RBD; SARS; figure summary = Relative to mild COVID-19 cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against nucleocapsid (N) and the receptor binding domain (RBD) of spike protein. However, 6.5% of the expanded negative control 149 group displayed RBD reactivity that overlapped with PCR+ individuals (Figure 1B, blue shade) , 150 some of whom may have been early into disease and had not yet generated high levels of 151 antibodies. To quantify the sensitivity of the assay relative to time of diagnosis, we measured 152 antibody levels to RBD and plotted these values against time following SARS-CoV-2 PCR+ 153 confirmation. For 308 both memory and plasma cells, there appears to be a ''sweet spot'' of antigen avidity that Taken together, we have reported a highly specific serological assay for SARS-CoV-2 323 exposure that is usable in very low seroprevalence communities, and that returns positive 324 results that are highly co-incident with virus neutralization. doi = 10.1016/j.immuni.2020.10.004 id = cord-293389-3h9vsc1a author = Risitano, Antonio M. title = Complement as a target in COVID-19? date = 2020-04-23 keywords = SARS summary = Most patients who become critically ill following infection with SARS-CoV-2, the causative agent of COVID-19, develop acute respiratory distress syndrome (ARDS) 1 . The prominent decrease in lung-infiltrating neutrophils and the reduced levels of both intrapulmonary and plasma IL-6 seen in SARS-CoV-infected C3-deficient mice suggests the potential of combining C3 inhibitors with anti-IL-6 regimens. A recent preprint study reported that lung biopsy samples from patients with severe COVID-19 showed widespread complement activation, characterized by C3a generation and C3-fragment deposition 6 . Proximal complement inhibitors (which target C3 or its upstream activators) could be more effective, but these are still in clinical development, and none has yet been approved, although limited data from phase II clinical trials are available. However, the combination of clinical indicators of ARDS progression with known biomarkers of inflammation (C-reactive protein, plasma IL-6 levels and ferritin) would allow identification of patients that could benefit from complement inhibition. doi = 10.1038/s41577-020-0320-7 id = cord-264360-eroqjkoh author = Risku, Minna title = Detection of human coronaviruses in children with acute gastroenteritis date = 2010-03-15 keywords = NL63; SARS summary = STUDY DESIGN: 878 stool specimens from children with acute gastroenteritis and 112 from control children were tested by RT-PCR to detect HCoV groups 1B, 2A and SARS. On the basis of this study, the significance of coronaviruses as gastrointestinal pathogens in children appears minor, since most of the coronavirus findings were co-infections with known gastroenteritis viruses. Our study shows that human coronaviruses OC43, HKU1, 229E and NL63 can be found in stool samples of children with acute gastroenteritis. 10 In our study one of the 36 healthy control patients had coronavirus detected in stool specimen and thus, there was no difference in the HCoV detection rate between the cases of acute gastroenteritis and control children. Future studies should investigate such mild cases for HCoVs. In conclusion, non-SARS human coronaviruses can be found in stool samples of children with acute gastroenteritis. doi = 10.1016/j.jcv.2010.02.013 id = cord-294537-wpq1492g author = Ritschl, Paul V. title = Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach date = 2020-05-10 keywords = COVID-19; SARS; transplant summary = title: Solid organ transplantation programs facing lack of empiric evidence in the COVID‐19 pandemic: A By‐proxy Society Recommendation Consensus approach 6 As no consensus guidelines or international recommendations have been published on coronavirus disease 2019 (COVID19) and organ transplant, the aim of this study was to offer a consensus-based approach to manage transplant programs until reliable data on risk and benefits of conducting organ transplants in times of a viral pandemic are available. the United Kingdom recommend a low threshold for SARS-CoV-2testing in transplant patients after contact with a positively tested person or subject to a broader spectrum of COVID-19-associated symptoms. Although SARS-CoV-2 nasopharyngeal PCR shows reasonable sensitivity, a recently published study demonstrates that of 51 COVID-19 patients only 36 were initially positive in NAT. Until now, no solid organ transplant procedure has reportedly been performed on a SARS-CoV-2-infected patient. Solid organ transplantation programs facing lack of empiric evidence in the COVID-19 pandemic: A By-proxy Society Recommendation Consensus approach doi = 10.1111/ajt.15933 id = cord-313058-nrrl4kjc author = Rivas, Magali Noval title = COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis date = 2020-10-16 keywords = MIS; SARS summary = title: COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. As of mid-September, the novel severe acute respiratory syndrome coronavirus 2 26 (SARS-CoV-2) has infected more than 30 million people, resulting in approximately one 27 million deaths worldwide, including over 200,000 deaths in the USA alone. Exacerbation of the COVID-19 immune response manifested by extensive cytokines 33 release, called cytokine storm, may lead to multisystem inflammatory syndrome that is 34 fatal in 28% of cases 1 . Interestingly, SAg-induced TSS has been associated with long-term 94 neuropsychologic deficits in adults, including cognitive decline 10 , and we identified a 95 homology between the SAg motif of SARS-CoV-2 and neurotoxin-like sequences which 96 are able to bind the TCR 5 . Clinical 131 Characteristics of 58 Children With a Pediatric Inflammatory Multisystem Syndrome 132 Temporally Associated With SARS-CoV-2 doi = 10.1016/j.jaci.2020.10.008 id = cord-305798-7b8rua4z author = Rivas-García, S title = Rhabdomyolysis as the main manifestation of coronavirus disease 2019 date = 2020-06-25 keywords = SARS summary = Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China in the late December 2019. Recent patient case series published in the setting of COVID-19 infection in China have described myalgia and elevated CK as frequent findings. High levels of CK-MB (muscle and brain isoform) were found in 4.5% of a 201 patient case series in Wuhan, [3] showing a significant association with acute respiratory syndrome distress development. Muscle weakness and elevated serum CK levels were also commonly found in coronavirus case series reported in the 2003 outbreak of SARS and the 2012 outbreak of Middle East respiratory syndrome (MERS) [4] . Even if myalgia and CK elevation are relatively frequent, rhabdomyolysis symptoms have been rarely reported in SARS-CoV-2 outbreaks. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China doi = 10.1093/rheumatology/keaa351 id = cord-266820-exl36jt3 author = Rivera, Frida title = Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date = 2020-08-19 keywords = SARS summary = title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. doi = 10.1093/cid/ciaa1225 id = cord-263509-wi0um8cm author = Rivera, Victor M title = Actitudes Terapéuticas Hacia La Esclerosis Múltiple En Centroamérica Y El Caribe Frente A La Pandemia De Sars-Cov-2 date = 2020-07-28 keywords = SARS summary = Esclerosis Múltiple (EM) en Centroamérica y el Caribe (CAC) mantiene una baja prevalencia¹ mientras que el impacto socioeconómico ejercido por esta enfermedad en los sistemas de salud de la región es severo considerando el nivel de crecimiento económico de estos países. A pesar de esta limitación, en años recientes la mayoría de los sistemas de seguridad social y algunos de atención pública en esta zona, han dedicado una gran porción de sus presupuestos a la adquisición de las variadas y onerosas terapias aprobadas por agencias internacionales para el manejo de EM². La teórica posibilidad que pacientes con EM pudieran ser especialmente vulnerables a la infección con SARS-CoV-2 considerando presencia de discapacidad neurológica y uso de tratamientos que afectan al sistema inmune, varios medicamentos de hecho causando persistente depleción linfocitaria, conllevó al Foro Centroamericano y del Caribe de Esclerosis Múltiple (FOCEM) a explorar actitudes terapéuticas en la región hispanoparlante encarando la pandemia. doi = 10.1016/j.nrl.2020.07.009 id = cord-288584-wql253d8 author = Rivera-Oyola, Ryan title = Dermatologic findings in two patients with COVID-19 date = 2020-04-28 keywords = SARS summary = Cutaneous involvement was observed both at symptom onset (8 patients) and after hospitalization (10 patients).(4) A study from Thailand described a dengue-like rash in a COVID-19 patient who was initially misdiagnosed with dengue.(5) Additionally, a recent letter reported a COVID-19 patient who simultaneously developed a non-pruritic, diffuse body rash, myalgia and cephalgia. (6) It is worth noting the variability in clinical presentation of cutaneous findings following SARS-CoV-2 infection. Similarly, we observed a diversity of morphological presentations and variability in time to onset of cutaneous manifestations in the literature (4) (5) (6) . It is unlikely that our patients'' rashes were due to a medication reaction as there had been no changes to their medication regimen, the rashes had an acute onset following COVID-19 symptom onset, and, in Case 1, the biopsy did not illustrate tissue eosinophilia. At present, there is limited data regarding the cutaneous manifestations following SARS-CoV-2 infection. COVID-19 should be considered in the initial differential diagnosis for a patient with acute skin changes following flu-like symptoms. doi = 10.1016/j.jdcr.2020.04.027 id = cord-296306-xcomjvaa author = Rivett, Lucy title = Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date = 2020-05-11 keywords = COVID-19; HCW; PPE; SARS; test summary = Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Table 3 outlines the total number of SARS-CoV-2 tests performed in each screening group (HCW asymptomatic, HCW symptomatic, and HCW symptomatic household contact) categorised according to the ward with the highest anticipated risk of exposure to high; ''amber'', medium; ''green'', low; . Three subgroups of SARS-CoV-2 positive asymptomatic HCW Each individual in the HCW asymptomatic screening group was contacted by telephone to establish a clinical history, and COVID-19 probability criteria ( Table 1) were retrospectively applied to categorise any symptoms in the month prior to testing ( Figure 2 ). 12/30 (40%) individuals from the HCW asymptomatic screening group reported symptoms > 7 days prior to testing, and the majority experiencing symptoms consistent with a high probability of COVID-19 had appropriately self-isolated during that period. doi = 10.7554/elife.58728 id = cord-322141-4a81mapc author = Rizzo, Emanuele title = A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government date = 2020-09-09 keywords = SARS summary = title: A COVID-19 exemption code to ensure post-recovery care: From the territory a proposal for the Apulia Region government For these reasons, the territorial medicine and the operators of the Apulian prevention services have decided to propose to the regional government the possibility of adopting a specific exemption code for COVID-19, taking on the economic burden deriving from treatments and diagnostic investigations once the acute phase of the disease has been overcome. Moreover, a similar procedure would also have the comfort of numbers: the sum of confirmed cases remains limited to date (as reported by the latest epidemiological bulletin -01/08/2020 h :14:00 CEST -, there are 4631 total cases of COVID-19 syndrome in Apulia, including 112 currently positive, 3967 healed subjects and 552 deaths [6] ), which makes the operation sustainable and not expensive for the regional finances. doi = 10.1016/j.eclinm.2020.100516 id = cord-291397-look6ddt author = Roberto, Palumbo title = Current treatment of COVID-19 in renal patients: hope or hype? date = 2020-09-28 keywords = COVID-19; CoV-2; HCL; SARS; patient summary = Given the lack of specific therapy about the ongoing SARS-CoV-2 infection, we conducted a brief review to summarize the mechanism of action and the potentially side effects of the treatment currently available, focusing on the effects of the drugs on renal disease at different stages in terms of therapeutic management and survival. A randomized clinical trial, handled by a Chinese group, suggested that in hospitalized adult patients with severe infection, no benefit was observed with lopinavir/ritonavir beyond standard care in terms of time to clinical improvement, reduction of mortality and safety (side effects and discontinuation of treatment) [29, 30] . Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial doi = 10.1007/s11739-020-02510-0 id = cord-314451-mqnqjn0c author = Roberts, Anjeanette title = A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice date = 2007-01-12 keywords = BALB; CoV; MA15; SARS; TCID; Urbani summary = To generate a model that satisfies these criteria, we have serially passaged SARS-CoV in the respiratory tract of young BALB/c mice, resulting in a lethal virus that causes dosedependent weight loss and mortality associated with higher viral titers in the respiratory tract than are seen with the wildtype virus and with histopathologic findings of severe pulmonary disease. Northern blot analysis of RNA from infected Vero E6 cells indicated that genomic vRNA and viral mRNA and all eight sub-genomic mRNAs were present in similar ratios for the recombinant viruses and MA15 virus as for SARS-CoV (Urbani) ( Figure 2A ). In order to evaluate whether changes in tissue tropism or levels of viral replication could contribute to the lethal phenotype of the MA15 virus, viral titers in lungs, spleen, liver, and brain of BALB/c mice were determined at various time points following intranasal inoculation with SARS-CoV (Urbani) or MA15. doi = 10.1371/journal.ppat.0030005 id = cord-321901-zpi7uis1 author = Roberts, Anjeanette title = Animal models and antibody assays for evaluating candidate SARS vaccines: Summary of a technical meeting 25–26 August 2005, London, UK date = 2006-11-30 keywords = CoV; SARS; animal; antibody; vaccine summary = Scientists at the WHO Technical Meeting on Animal Models and Antibody Assays for Evaluating Candidate SARS Vaccines held on 25-26 August 2005 in South Mimms, UK, discussed many aspects of research pertaining to the use of animal models in vaccine development including available animal models, suitability of the various models, correlates of protection, critical components of potential vaccines, and the potential for disease enhancement in vaccinated animals following exposure to SARS-CoV. It may actually be worthwhile to enhance the virulence of a SARS-CoV isolate by serial passages in an animal model to produce a challenge virus stock for vaccine studies that would elicit more reproducible disease in the animals. Although none of the studies to date have shown enhanced respiratory disease following SARS-CoV challenge in previously immunized animals, further studies in this area are warranted in view of some of the available in vitro data. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice doi = 10.1016/j.vaccine.2006.07.009 id = cord-347706-r0rs3ls1 author = Roberts, Anjeanette title = Animal Models for Sars date = 2006 keywords = BALB; CoV; SARS summary = Mice that recover from infection develop a neutralizing antibody response and are protected from subsequent challenge; antibody alone is sufficient to protect mice from replication of SARS-CoV in the lower respiratory tract and NK, NK-T, T, and B cells are not required for viral clearance. 13, 13b CoV disease, with weight loss and pneumonitis that begins with acute bronchiolitis and In summary, SARS-CoV replicates efficiently in the respiratory tract of young viremia occurs 1 to 2 days following infection and virus is detected in the liver and spleen in hamsters. As seen with the other animal models, the course of infection in experimentally infected nonhuman primates is short, with a rapid peak in viral replication and clearance of virus from the lungs by days 4 to 7 in different species. Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice doi = 10.1007/978-0-387-33012-9_83 id = cord-290690-53t7df81 author = Roberts, David J. title = Life in Times of COVID‐19 date = 2020-05-13 keywords = Kong; SARS summary = The articles by CK Lee from Hong Kong 2 and Dana Devine 3 from Canada describe how blood services in two very different epidemiological settings responded to the epidemic. However, the measures implemented for SARS in Hong Kong in 2003, namely social distancing, use of personal protective equipment and screening of donors, laid the foundation for many blood services'' response to this current epidemic. Similarly, the methods developed by Dr Lee in the SARS epidemic in 2002 described in this issue, have enable Hong Kong to maintain the blood supply in this COVID-19 pandemic and have been shared by webinar and have helped many blood services cope with the current crisis (https://education.isbtweb.org/isbt/#!*menu=8*browseby=8*sortby=2*label=19776) (Accessed 1st May 2020). Perhaps the wider lesson from the experience of Hong Kong and Canada was that very real threat posed by SARS in 2003 prompted improved pandemic planning. doi = 10.1111/tme.12688 id = cord-272566-rtnhndw3 author = Robertson, M. title = A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort date = 2020-05-04 keywords = COV2; COVID; SARS summary = Following baseline questionnaire completion, study participants will be contacted monthly (for 6 months) to complete assessments of engagement in non-pharmaceutical interventions (e.g., use of cloth masks, avoiding large gatherings); COVID-19 symptoms; SARS/COV2 testing and diagnosis; hospitalizations; healthcare access; and uptake of health messaging. 2, 3 In response to the COVID-19 pandemic the CUNY Institute for Implementation Science in Population Health (ISPH) launched the Communities, Households and SARS/COV-2 Epidemiology (CHASING) COVID Cohort "C 3 " study on March 28, 2020 . For analyses to assess subsequent disease after Month 1, incident COVID-19 disease will be defined as development of new COVID-like symptoms > 7 days after the first (positive or negative) SARS/COV2 serologic test result. The C 3 cohort is geographically and socio-demographically diverse, and includes participants from many active hotspots during the recruitment period (March 28-April 20, 2020), as well as frontline health care workers and other essential employees, and individuals who are vulnerable to severe outcomes associated with SARS/COV2 infection. doi = 10.1101/2020.04.28.20080630 id = cord-316845-k9zvsfvj author = Robertson, Mary M. title = Gilles de la Tourette Syndrome: advice in the times of COVID-19 date = 2020-04-28 keywords = COVID-19; GTS; SARS; patient summary = These include the coronaviruses, which have caused multiple major public health events that resulted in global pandemics such as severe acute respiratory syndrome (SARS; or "bat SARS"), Middle East respiratory syndrome (MERS) and the current coronavirus disease (COVID-19) (Kandeel et al., 2020). GTS, as a complex neuropsychiatric disorder, offers many angles of attack for the current COVID-19 pandemic and its consequences (social distancing, home schooling, confinement/quarantine, and living in a general climate of fear). The authors discuss similarities of COVID-19 and tics in GTS and outline specific problems that may result from the pandemic for this group of patients. I like this small paper and find it interesting to read, since it alerts us that the current pandemic may be much more challenging for patients with GTS compared to healthy people. Also in Table 1 : "Viral infection -Coronavirus 19" please change in "SARS-CoV-2".The authors describe the different symptoms associated with COVID-19 including neurological complications. doi = 10.12688/f1000research.23275.2 id = cord-288070-qwax5tg9 author = Robilotti, E. V. title = Determinants of Severity in Cancer Patients with COVID-19 Illness date = 2020-05-08 keywords = ICI; SARS; covid-19 summary = Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. On multivariate analysis, age ≥ 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. In this study, we report on the epidemiology of COVID-19 illness experienced at our cancer center over the last month, during the height of incident cases in New York City, and offer an analysis of risk factors for severe infection that is pertinent to cancer patient populations. doi = 10.1101/2020.05.04.20086322 id = cord-329844-w969lczb author = Robson, B. title = Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans date = 2020-06-08 keywords = SARS; acid; bind; glycan; protein; residue; sialic; sugar summary = The location of any sialic acid glycan binding region of SARS-CoV-2 is, a priori unclear, although intuitively (a) it would likely be associated with the cap or knob at the outer end of the spike protein, or (b) at least not involve exactly the same domain as is required for other important functions. An algorithm for predicting the domains and proteins involved in sialic acid glycan binding is developed in the course of the project described in Results Section 4, but this is primarily of a highly empirical nature. This, plus a sequence rather than three dimensional structure perspective, and a specific focus on binding sialic acid glycans rather than sugars in general, resulted in a substantial difference in scores from another major method of predicting sugar binding regions of proteins also discussed later below. doi = 10.1016/j.compbiomed.2020.103849 id = cord-333262-xvfl7ycj author = Robson, B. title = COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date = 2020-04-11 keywords = ACE2; COVID-19; KRSFIEDLLFNKV; SARS; Wuhan; bind; peptide; protein; spike; virus summary = The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). doi = 10.1016/j.compbiomed.2020.103749 id = cord-343586-28ezisog author = Rocca, María Florencia title = A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date = 2020-05-07 keywords = MALDI; SARS summary = title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied. These preliminary results suggest that MALDI-TOF MS coupled with ClinProTools software represents an interesting alternative as a screening tool for diagnosis of SARS-CoV-2, especially because of the good performance and accuracy obtained with samples in which viral presence was not detected. doi = 10.1101/2020.05.07.082925 id = cord-258221-pn8gh73b author = Rocha, José Lucas Martins title = Mesenchymal Stromal Cells in Viral Infections: Implications for COVID-19 date = 2020-09-07 keywords = COVID-19; Fig; IDO; MSC; SARS; cell; stem summary = Abbreviations: ANG, Angiogenin; ANGPT1, Angiopoietin 1; bFGF, Basic fibroblast growth factor; BV/BR, Biliverdin and Bilirubin; COX2, Cyclooxygenase-2; DAMPs, Damage-associated molecular pattern; EGF, Epidermal growth factor; ESM1, Endothelial Cell Specific Molecule 1; FAS/FASL, apoptosis antigen 1 receptor and ligand; HGF, Hepatocyte growth factor; HLA-G, Human leukocyte antigen G; HO-1, Heme oxygenase 1; IDO, Indoleamine 2,3-dioxygenase; ISGs, Interferon-stimulated genes; Kyn, Kynurenin; LIF, Leukemia inhibitory factor; LPS, Lipopolysaccharide; miRNAs, micro RNA; MMPs, Matrix metalloproteinases; MSC-EV, Extracellular vesicles from MSC; PAMPs, Pathogen-associated molecular pattern; PGE2, Prostaglandin E2; PD-1/PD-L1, Programmed death receptor and ligand; ROS, Reactive oxygen species; SOD, Superoxide dismutase; sHLA-G, Soluble human leukocyte antigen G; sPD-L1/2, Soluble Programmed death ligands 1 and 2; TGF-β, Transforming growth factor β; TLR, Toll-like receptor; TNF-α, Tumor necrosis factor α; Trp , Tryptophan; TSG-6, TNFstimulated gene 6 Similarly, long-lasting FASL interactions enable MSCs to induce T cell apoptosis [39] . doi = 10.1007/s12015-020-10032-7 id = cord-288644-ywaefpe8 author = Rodon, Jordi title = Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date = 2020-10-20 keywords = SARS; Supp; Vero; table summary = We have tested the antiviral activity of different clinically available compounds and their combinations by assessing their ability to inhibit viral induced cytopathic effect in vitro. Drug selection criteria first focused on compounds already being tested in clinical trials, along with well-known human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) protease inhibitors, as well as other compounds suggested to have potential activity against SARS-CoV-2 in molecular docking analysis or in vitro assays. Additional Food and Drug Administration (FDA)-approved compounds previously used to abrogate viral entry via clathrin-mediated endocytosis were also tested in this SARS-CoV-2-induced cytotoxicity assay (Supp . Cytopathic effect on Vero E6 cells exposed to a fixed concentration of SARS-CoV-2 in the presence of increasing concentrations of plitidepsin and its combinations with hydroxychloroquine and remdesivir. doi = 10.1101/2020.04.23.055756 id = cord-353161-mtq6yh25 author = Rodrigues, João PGLM title = Insights on cross-species transmission of SARS-CoV-2 from structural modeling date = 2020-06-05 keywords = ACE2; HADDOCK; RBD; SARS summary = We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Collectively, our results provide a structural framework that explains why certain animal species are not susceptible to SARS-CoV-2 infection, and also suggests potential mutations that can enhance binding to the viral RBD. Although it is well-known that docking scores do not quantitatively correlate with experimental binding affinities [19] , these scores suggest that SARS-CoV-2 neg species lack one or more key ACE2 residues that contribute significantly to the interaction with RBD. Models of SARS-CoV-2 neg species -chicken, duck, guinea pig, mouse, and rat -generally have higher (worse) HADDOCK scores than average (Figure 2 ), suggesting that these species'' non-susceptibility to infection could stem from deficient RBD binding to ACE2. doi = 10.1101/2020.06.05.136861 id = cord-347090-sqw7n1v2 author = Rodriguez-Gonzalez, Moises title = New onset severe right ventricular failure associated with COVID-19 in a young infant without previous heart disease date = 2020-06-16 keywords = COVID-19; SARS summary = We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. We present our recent experience with a 6-month-old infant with a personal history of short bowel syndrome that presented with fever, cyanosis, and cardiogenic shock secondary to severe pulmonary hypertension and right ventricular failure without pulmonary thromboembolism. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. If this presentation is confirmed in future research, the severe cardiovascular impairment in children with COVID-19 could be also attributable to the primary pulmonary infection, not only to a multisystem inflammatory syndrome but also in children without heart disease. doi = 10.1017/s1047951120001857 id = cord-290254-m9l8ntur author = Rodriguez-Manzano, J. title = A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date = 2020-06-30 keywords = Fig; RNA; SARS summary = In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Currently, reverse transcriptase polymerase chain reaction using real-time benchtop platform (RT-qPCR) is considered the gold standard for COVID-19 diagnosis due to its capability to detect the presence of SARS-CoV-2 RNA close to the onset of symptomatic illness which is critical for isolation. In this paper, we combined LAMP with an in-house LoC device to develop a rapid PoC diagnostic test (< 20 min) for the detection of SARS-CoV-2 RNA from extracted samples. doi = 10.1101/2020.06.29.20142349 id = cord-319833-u9uuuu38 author = Rodriguez-Martinez, Carlos E. title = Decontamination and reuse of N95 filtering facemask respirators: a systematic review of the literature date = 2020-07-08 keywords = FFR; N95; SARS; UVGI summary = METHODS: We performed a systematic review of the literature in order to identify studies reporting outcomes of at least one decontamination method for inactivating or removing any potentially infectious material from the surface of N95 FFRs, specifically addressing issues related to reduction of the microbial threat (including SARS-CoV-2 when available), maintaining the function of N95 FFRs and a lack of residual toxicity. 10 Although various decontamination methods have been used, there are concerns over certain characteristics of the N95 FFRs with respect to their utilization, such as alterations in their physical appearance/odor, structural integrity, filtration efficiency, fit and seal and filter airflow resistance, degradation of their material, and chemical residues that are potentially toxic or irritate the skin (due to the chemical disinfectants required for rinsing and drying). doi = 10.1016/j.ajic.2020.07.004 id = cord-031497-pp0p3en6 author = Rodríguez-Fuster, Alberto title = Tracheal trauma in the context of the current infection by COVID-19. About 2 cases() date = 2020-09-06 keywords = SARS; patient summary = Various authors and scientific societies have recommended limiting the number of airway procedures and manipulations and introducing stringent protection measures for health personnel in order to minimize the risk of infection. [2] [3] [4] We report 2 cases of patients diagnosed with SARS-CoV-2 infection and tracheal iatrogenic rupture following airway manipulation. She required OTI + MV for respiratory failure, and during the procedure she incurred a tracheal lesion confirmed by computed tomography and fiberoptic bronchoscopy to be a rupture of the pars membranacea measuring approximately 2 cm. To minimize the risk of aerosols, the patient was maintained in complete muscle relaxation throughout the procedure; preoxygenation and ventilatory pauses-apneas-were performed (as far as possible) in accordance with the recommendations described for tracheotomy. Emergency tracheal intubation in 202 patients with COVID-19 in Wuhan, China: lessons learnt and international expert recommendations Tracheal trauma after difficult airway management in morbidly obese patients with COVID-19 doi = 10.1016/j.arbr.2020.08.007 id = cord-280697-tovty20e author = Rodríguez‐Martínez, Carlos E. title = Efficacy, safety and cost‐effectiveness of hydroxychloroquine in children with COVID‐19: A call for evidence date = 2020-06-03 keywords = SARS summary = Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including pediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for pediatric patients) at present time (2). 1 Among these treatments, the off-label use of hydroxychloroquine (HCQ), a less toxic derivate of chloroquine, has become a common practice among clinicians, including paediatricians, despite lack of evidence of its clinical efficacy for this indication (especially for paediatric patients) at present time. We would therefore encourage nations where the undertaking of high-quality clinical trials in children during the current SARS-CoV-2 pandemic is possible, to ensure that putative treatments that would be available and affordable in low-to middle-income countries (LMICs), such as hydroxychloroquine, are included wherever possible. At a time of great uncertainty, evidence is urgently needed to inform treatment options, and therefore, randomised controlled trials are necessary to clarify further the clinical benefit of HCQ in paediatric patients with SARS-CoV-2 infections. doi = 10.1111/apa.15373 id = cord-309633-1cd74xdl author = Rogers, Julia H. title = Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study date = 2020-09-15 keywords = CoV-2; SARS; shelter summary = MEASUREMENTS: The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. CONCLUSION: Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. Surge testing was initiated on 30 March 2020 (and continued through 24 April) in collaboration with Public Health-Seattle & King County''s Communicable Disease Epidemiology Team to conduct contact tracing at 6 shelters where cases of SARS-CoV-2 were previously detected ( Figure 2 ). We calculated the test positivity rate of SARS-CoV-2 infection at shelters by dividing the number of positive cases by the total number of participant encounters in the study period. Overall, 2% of participant encounters involved positive SARS-CoV-2 results, with most cases detected through surge testing events. doi = 10.7326/m20-3799 id = cord-252473-i4pmux28 author = Rogers, Sharon title = Why can''t I visit? The ethics of visitation restrictions – lessons learned from SARS date = 2004-08-31 keywords = SARS; patient summary = It could be argued that visitation restrictions, in light of a potential outbreak of a contagious disease, are ethically sound because of the compelling need to protect public health. In a health care institution, visitation restrictions not only affect inpatients but also have an impact on ambulatory patients who must come for diagnostic tests or interventions and who, if deprived access, might develop urgent or emergent conditions. Furthermore, to be consistent with expectations of transparency, the criteria by which exceptionality to the rules of visitation restriction exists should also be published openly throughout the organization for staff, patients and visitors. For example, although current policy allows for specific times of visitation and numbers of visitors per day, a sudden outbreak might dictate a quick lockdown of the facility without patients or family members receiving prior notice. It is ethical to accept that public health protection trumps individual rights to liberal visitation. doi = 10.1186/cc2930 id = cord-263167-es806qhz author = Rogers, Thomas F. title = Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model date = 2020-06-15 keywords = ACE2; Fig; RBD; SARS summary = We showed that passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters, as revealed by maintained weight and low lung viral titers in treated animals. Donor plasma were tested for binding to recombinant SARS-CoV-2 and SARS-CoV-1 S and receptor binding domain (RBD) proteins, for binding to cell surface expressed spikes and for neutralization in both live replicating virus and pseudovirus assays (Fig. 2, B to D, and fig. The bulk-transformed ligation products for both the heavy chain and light chain were transfected and tested for binding to RBD and S protein, and for neutralization in the SARS-CoV-2 pseudovirus assay using HeLa-ACE2 target cells ( fig. To investigate the relationship between in vitro neutralization and protection in vivo against SARS-CoV-2, we selected two mAbs for passive transfer/challenge experiments in a Syrian hamster animal model based on a summary of the nAb data (table S3 and fig. doi = 10.1126/science.abc7520 id = cord-335040-1qa6pe4v author = Rogstam, Annika title = Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date = 2020-10-06 keywords = RNA; SARS; figure; nsp10 summary = The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. observed SARS nsp10 in the same space group as reported here, I213, reporting a monomer in the asymmetric unit but a dimer in solution, as was determined by size exclusion Residues shaded in red are fully conserved, while residues with text in red indicate a change to a similar residue. We determined the crystal structure and behaviour in solution of SARS-CoV-2 nsp10 in its unbound form. doi = 10.3390/ijms21197375 id = cord-287501-7it4kh0e author = Roh, Changhyun title = A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date = 2012-05-03 keywords = CoV; RNA; SARS summary = We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. 33 In this study, we report a novel approach for the inhibitor screening of SARS-CoV N protein using a quantum dots (QDs)-conjugated oligonucleotide system with wide applicability for facile and sensitive imaging analysis on a biochip. To the best of our knowledge, this is the first report on the inhibition effects of (-)-catechin gallate and (-)-gallocatechin gallate on SARS-CoV N protein using an optical nanoparticle-based RNA oligonucleotide platform. Among the polyphenolic compounds screened, (-)-catechin gallate and (-)-gallocatechin gallate showed high anti-SARS-CoV N protein activity. At a concentration of 0.05 µg mL -1 , (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a QDs-RNA oligonucleotide biochip platform. doi = 10.2147/ijn.s31379 id = cord-285979-ha5nszxi author = Rojas, Manuel title = Convalescent plasma in Covid-19: Possible mechanisms of action date = 2020-05-05 keywords = COVID-19; SARS summary = CP early administered after symptoms onset showed a reduction in mortality compared with placebo or no therapy in severe acute respiratory infections of viral etiology like influenza and SARS-CoV, however, a similar response in Ebola disease was not observed [20, 25] . This was demonstrated in B cells, where the upregulation of FCRIIB was associated with treatment efficacy for acute rejection after kidney transplantation [81] , and was J o u r n a l P r e -p r o o f a key determinant for IVIg response in patients with Kawasaki disease [82] . Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection doi = 10.1016/j.autrev.2020.102554 id = cord-322456-5at1euqm author = Rokohl, Alexander C. title = Die Rolle der Augenheilkunde in der COVID-19-Pandemie date = 2020-06-09 keywords = COVID-19; Coronavirus; SARS; und summary = Im Dezember 2019 wurde Dr. Li Wenliang, ein Augenarzt aus der Volksrepublik China, in seinem Krankenhaus auf 7 Patienten, die alle unter einem schweren akuten Atemnotsyndrom litten und vorher einen Großmarkt in Wuhan besuchten, aufmerksam. Das COVID-19 auslösende Severe-Acute-Respiratory-Syndrome-related Coronavirus-2 (SARS-CoV-2) wurde durch die Coronavirus-Studiengruppe des Internationalen Komitees zur Taxonomie von Viren (International Committee on Taxonomy of Viruses) aufgrund der sehr engen Verwandtschaft zum Sars-Virus (Sars-CoV), an dem 2002/2003 Hunderte Menschen gestorben waren, benannt. Auch Dr. Li Wenliang, der Augenarzt, der die COVID-19 als einer der Ersten entdeckte und später auch an der Krankheit verstarb, könnte von einem asymptomatischen Patienten infiziert worden sein [23] . Zudem konnte in mehreren Studien mit hospitalisierten COVID-19-Patienten SARS-CoV-2-RNA in der Tränenflüssigkeit nachgewiesen werden [2, 28, 30, 32] . Although isolated conjunctival involvement is highly unlikely, at the current point in time of the COVID-19 pandemic, practically every patient examined by an ophthalmologist could be infected with SARS-CoV-2. doi = 10.1007/s00347-020-01148-9 id = cord-350992-l6l24pco author = Roldan, Eugenia Quiros title = The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against Sars-Cov-2 infection (COVID-19): A role for iron homeostasis? date = 2020-05-13 keywords = COVID-19; Cov-2; HCQ; Sars; iron summary = Here we review what is currently known on the mechanisms of action of CQ and HCQ as anti-viral, anti-inflammatory and anti-thrombotic drugs and discuss the up-to-date experimental evidence on the potential mechanisms of action of CQ/HCQ in Sars-Cov2 infection and the current clinical knowledge on their efficacy in the treatment of COVID-19 patients. We also propose a different insight into some of CQ and HCQ effects, suggesting a potential role of iron homeostasis in Sars-Cov-2 disease (COVID-19), similarly to several other human viral infections [2] [3] [4] . The search strategy was to use different search terms alone and in any combination, such as "Sars-Cov-2 disease", "COVID-19", "Sars-Cov-2", "coronavirus", "clinical trial", "treatment", "drug", "chloroquine", "hydroxychloroquine", "iron", "virus", "viral entry", "viral spread", "anti-viral activity", "infection", "inflammation", "immunity", "innate immunity", "cytokine", "IL-6", "TNF-", "IL-1", "adaptive immunity", "thrombosis", "in vitro". doi = 10.1016/j.phrs.2020.104904 id = cord-349556-k312qkvh author = Roldán-Santiago, Ernesto title = SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date = 2020-09-18 keywords = SARS summary = title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient''s cervical LN. doi = 10.1093/cid/ciaa1422 id = cord-318920-njurbf3d author = Romana Ponziani, Francesca title = Liver involvement is not associated with mortality: results from a large cohort of SARS‐CoV‐2 positive patients date = 2020-07-06 keywords = ICU; SARS summary = CONCLUSIONS: In SARS‐CoV‐2 positive patients without pre‐existing severe chronic liver disease, baseline liver tests abnormalities are associated with the risk of ICU admission and tend to normalize over time. To investigate the prevalence of liver damage in our cohort of patients, serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT), gamma glutamyl transferase (GGT), alkaline phosphatase (ALP), total bilirubin and albumin were collected at baseline, then on the date closest to 15 days from the admission. This study demonstrates that in patients without severe chronic liver disease liver involvement during SARS-CoV-2 infection is usually mild, is not associated with increased risk of ICU admission or mortality, and tends to resolve over time. Baseline liver tests abnormalities can be found in more than 30% of cases, especially in patients with ARDS; these alterations are associated with the risk of ICU admission but not with mortality, and tend to normalize over time. doi = 10.1111/apt.15996 id = cord-278618-7tu5c7m1 author = Romano-Bertrand, Sara title = Sustainability of SARS-CoV-2 in aerosols: Should we worry about airborne transmission? date = 2020-06-12 keywords = CoV-2; SARS summary = This is based on previous knowledge [1] and the doctrine that: a patient positive for SARS-CoV-2 is contagious by respiratory secretions (>10μm in size) that disseminate only on short distance (<1m); SARS-CoV-2 carried on large droplets settles onto local surfaces and is not stable in the air; SARS-CoV-2 aerosol dispersion is possible during AGPs which extensively expose HCWs and therefore HCWs need to wear a respirator for a higher respiratory protection during AGPs. However, an experimental study of van Doremalen et al, [2] assessed the sustainability of SARS-CoV-2 in aerosols (<5μm at 65% of hygrometry (expressed in %RH for relative humidity)) performed using a high-powered machine that does not reflect normal cough conditions (https://www.who.int/publications-detail/modes-of-transmission-of-virus-causing-covid-19-implicationsfor-ipc-precaution-recommendations). They showed that SARS-CoV-2 remained viable and infective at least 3 hours in aerosols, which opened the debate on SARS-CoV-2 transmission through longdistance aerosols (>1m), and questioned the appropriateness of respiratory protection for HCWs. An individual who is well, emits 10 to 10 4 particles per liter of expired air, including 95% of <1μm-size particles [3] . doi = 10.1016/j.jhin.2020.06.018 id = cord-273408-jtpaue0z author = Romeyke, Tobias title = COVID-19 Case Report: An 84-Year-Old Man with Exacerbation of Multiple Comorbidities Due to COVID-19 Managed by a Multidisciplinary Team Using Patient-Reported Outcomes date = 2020-08-21 keywords = SARS; pain; patient summary = Patient: Male, 84-year-old Final Diagnosis: Acute bronchitis • chronic multiple pain with spondylosis with radiculopathy: lumbar region • chronic renal failure CKD 4 • derailed type 2 diabetes mellitus • diabetes mellitus type 2 • eart failure • hyperuricaemia • progressive aortic stenosis • pulmonary hypertension • SARS-CoV2 Symptoms: Appetite loss • fever • pain • sore throat Medication: — Clinical Procedure: — Specialty: General and Internal Medicine OBJECTIVE: Unusual clinical course BACKGROUND: When treating patients with comorbidities who are infected with severe acute respiratory syndrome as a result of SARS-CoV-2, it is crucial to offer multidisciplinary treatment that takes into consideration all of the health conditions with which they have been diagnosed. We collected clinical and patient-reported data on quality of life, physical functions, the sensation of pain, psychological well-being, and symptoms while taking into account the degree of chronicity of the conditions, the level of the patient''s pain, and his hospitalization in an isolation ward. doi = 10.12659/ajcr.926694 id = cord-333805-xmqs2ax7 author = Romoli, Michele title = A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date = 2020-06-05 keywords = COVID-19; CSF; PCR; SARS summary = BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. This study therefore aimed to identify clinical cases of confirmed nervous system invasion or postinfectious neurological disease in the available COVID-19 literature on the basis of a systematic review. A systematic review was carried out to study all cases reporting nervous system involvement in patients with proven SARS-CoV2 infection. There were just 2 cases with positive SARS-CoV-2 PCR in CSF among 27 patients with potential neurologic symptoms and proven COVID-19. In this regard, we see a clear need for the use of precise case definitions and focused diagnostic work-up to distinguish nonspecific complications of severe disease and focused reporting of neurological involvement in association with SARS-CoV-2 infection. doi = 10.1111/ene.14382 id = cord-014897-rnrlslfh author = Rong-bing, Wang title = Therapeutic effects of integrated traditional Chinese medicine and western medicine in treating severe acute respiratory syndrome date = 2003 keywords = SARS; chinese summary = The comprehensive effect on relieving fever, cell-mediated immunity, pulmonary inflammation and secondary infection was compared between the two groups.Results: The therapeutic effect in the ICWM group was better than that in the control group in such aspects as steadily lowering body temperature, alleviating general symptoms, accelerating the absorption of pulmonary infiltration and easing cellular immunity suppression.Conclusion: The therapeutic effect of ICWM is better in treating SARS than that of western medicine alone. In order to elevate the therapeutic effects, lighten patients" symptoms, improve the pulmonary inflammation and cellular immune inhibition that occurred in the course of the illness, a clinical study of the treatment of 68 SARS patients with integrated traditional Chinese and western medicine (ICWM), which was controlled with 67 patients treated with western medicine alone, was carried out. doi = 10.1007/bf02838610 id = cord-306733-df36w6l7 author = Rosales-Mendoza, Sergio title = What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date = 2020-04-14 keywords = COVID-19; SARS; plant; protein; vaccine; virus summary = Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. doi = 10.3390/vaccines8020183 id = cord-323094-zugrtvyo author = Rose, R. title = Intra-host site-specific polymorphisms of SARS-CoV-2 is consistent across multiple samples and methodologies date = 2020-04-29 keywords = April; SARS summary = Here, we quantify and characterize intra-host variation in SARS-CoV-2 raw sequence data uploaded to SRA as of 14 April 2020, and compare results between two sequencing methods (amplicon and RNA-Seq). While mutations resulting from amplification and/or sequencing errors cannot be excluded, the observation of shared polymorphic sites with high MAF across multiple samples and sequencing methods is consistent with true underlying variation. Our goal in this study was to quantify and characterize intra-host variation in all SARS-CoV-2 raw sequence data available in SRA as of 14 April 2020, and compare results between two All rights reserved. . https://doi.org/10.1101/2020.04.24.20078691 doi: medRxiv preprint 5 percent of the genome covered at 10x and 25x remained high with the amplicon data (10x IQR: 0.987 -0.997; 25x IQR: 0.980 -0.997), the range was much broader for the RNA-Seq data (10x IQR: 0.240 -0.997; 25x IQR: 0.024 -0.993). doi = 10.1101/2020.04.24.20078691 id = cord-347472-n6811ens author = Rosebrock, Adam P. title = Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date = 2020-05-15 keywords = CDC; RNA; SARS; dna summary = The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. doi = 10.1101/2020.05.13.094839 id = cord-351189-56am76lb author = Rosen, Melissa H title = Management of Acute Severe Ulcerative Colitis in a Pregnant Woman With COVID-19 Infection: A Case Report and Review of the Literature date = 2020-05-12 keywords = COVID-19; SARS summary = As the patient was improving on steroids and given the rapidly increasing rate of COVID-19 infected patients at our institution, the decision was made to discharge the patient home on an oral prednisone taper on hospital day 5 with plans to start infliximab as an outpatient. Although intravenous steroids are the mainstay of treatment for acute severe UC in the hospitalized patient, the use of steroids in the first trimester of pregnancy may be associated with a risk of cleft lip or cleft palate. The necessity for guidance was addressed by the International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) in their publication, "Management of Patients with Crohn''s Disease and Ulcerative Colitis During the COVID-19 Pandemic: Results of an International Meeting." 9 The recommendation is to continue biologic therapy in the absence of SARS-CoV-2 infection. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes doi = 10.1093/ibd/izaa109 id = cord-274761-c2hgkbg6 author = Rosenberg, Eli S. title = Cumulative incidence and diagnosis of SARS-CoV-2 infection in New York date = 2020-06-17 keywords = COVID-19; NYS; SARS summary = SARS-CoV-2 cumulative incidence was estimated from antibody reactivity by first post-stratification weighting then adjusting by antibody test characteristics. CONCLUSIONS: From the largest US serosurvey to date, we estimated > 2 million adult New York residents were infected through late March, with substantial disparities, although cumulative incidence remained below herd immunity thresholds. Cumulative incidence among non-institutionalized adults, by geographic and demographic features, was estimated from weighted reactivity rates that were adjusted for validated test characteristics. We estimated SARS-Cov-2 cumulative incidence from observed antibody reactivity using two sequential steps: 1) post-stratification weighting to standardize to the New York State population and 2) adjustment by estimated antibody test characteristics. Test-characteristic adjusted cumulative incidence values were multiplied by the one-and two-way non-institutionalized adult populations (e.g. excluding settings such as prisons and nursing homes) from the American Community Survey 2014-2018 Public Use Microdata Sample file [23] . doi = 10.1016/j.annepidem.2020.06.004 id = cord-336522-y9nzsv95 author = Rosenke, Kyle title = Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date = 2020-09-30 keywords = PPMO; SARS summary = title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers Cell viability was 33 evaluated with an ATP-based method and viral growth was measured with quantitative RT-PCR 34 and TCID50 infectivity assays. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. Results: PPMO designed to base-pair with sequence in the 5''-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. In this study, five PPMO were designed to target the 5'' UTR 107 and first translation start site-region of SARS-CoV-2 positive sense genomic RNA ( Table 1) . doi = 10.1101/2020.09.29.319731 id = cord-296148-za3j19k5 author = Rosenzweig, Ivana title = Does damage to hypothalamic paraventricular nucleus underlie symptoms of ultradian rhythm disorder and an increased anxiety in coronavirus disease 2019? date = 2020-08-17 keywords = PVN; SARS summary = Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may directly target parts of the brain, more specifically the hypothalamus and its paraventricular nucleus, and possibly lead to increased prevalence of anxiety disorders. Any changes in the PVN circuitries, due to their major control over most of neuro-endocrine axes and neuronal autonomic centers, may cause robust alteration in homeostatic regulation, and through influence on regulatory brain centers impact on sleep and wakefulness, increased propensity to affective disorders and anxiety, and alteration of ultradian rhythms. We correspondingly argue a direct SARS-CoV-2 effect on the specific part of the brain''s hypothalamic paraventricular nucleus (PVN) circuitry ( Figure 1 ) as a neurologic mechanism that may, at least in part, underlie previously reported ultradian disruption, and that may lead to an increased anxiety symptomatology (7) . We propose that SARS-CoV-2 may target the distinct ACE2-tagged part of the PVN-subcircuitry (8), via a direct monosynaptic subfornical route (Figure 1 ), leading to the pleomorphic dysautonomic ultradian presentation, which is further compounded with nocturnal sleep fragmentation. doi = 10.3325/cmj.2020.61.377 id = cord-356009-emn2w8if author = Roshandel, M. R. title = What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date = 2020-10-13 keywords = COVID-19; CoV-2; RNA; SARS summary = Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. The searches included medical subject headings (MeSH) and keywords for SARS-CoV-2, COVID, Corona, together with shedding, persistence, urine, urinary, specimen, viral load, or RNA body fluids. We completed the data abstraction process using created forms to record study characteristics, clinical data, and laboratory data including study year and design, country of study origin, total initial population size, test type for disease diagnosis, test type for samples (urine/stool/rectal swab/blood), patients age (including mean and range), number of positive and total patients and/or (wherever applicable) number of positive and total specimens collected for each test category, disease severity, ICU admission, and fatality rate. doi = 10.1101/2020.10.08.20209544 id = cord-290148-6cxndab8 author = Rossi, Gian Paolo title = Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients date = 2020-04-06 keywords = ACE-2; SARS summary = The discovery of angiotensin converting enzyme-2 (ACE-2) as the receptor for SARSCoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) has implicated the renin-angiotensin-aldosterone system in acute respiratory distress syndrome (ARDS) and respiratory failure in patients with coronavirus disease-19 (COVID-19). However, they differ markedly: ACE-1 cleaves the dipeptide His-Leu from angiotensin I, thus generating angiotensin (Ang) II, which causes vaso-and broncho-constriction, increases vascular permeability, inflammation, and fibrosis and thereby promotes the development of ARDS and lung failure in patients infected with the SARS-CoV and SARS-CoV-2 (Yang et al., 2015) (Figure 1, panel B) . In one commentary ACE-2 was suggested to be secreted at higher amounts in patients with cardiovascular disease than in healthy individuals, and in another, it was also stated that ''ACE-2 levels can be increased by the use of ACEIs'' , albeit no evidence of this occurring in the lungs Mechanisms of COVID-19 by which the SARS-COV-2 virus infects the lower airway cells and modalities to increase circulating soluble ACE-2 for therapeutic use. doi = 10.7554/elife.57278 id = cord-331571-v01kstbr author = Rossoff, Jenna title = Benign course of SARS‐CoV‐2 infection in a series of pediatric oncology patients date = 2020-06-23 keywords = SARS summary = Repeat SARS-CoV-2 testing the next day was again negative, and blood cultures grew both Acinetobacter junii and Pseudomonas aeruginosa. He had an uncomplicated hospital course, but still tested positive for SARS-CoV-2 on the day of discharge and again 5 days later. Repeat testing after another 10 days, 6 weeks after symptom onset, was negative. Our series of pediatric oncology patients with relatively benign courses of SARS-CoV-2 infection is consistent with reports from both Italy and New York city, where five and 20 pediatric cancer patients, respectively, were identified as having mild or asymptomatic SARS-CoV-2 infection, 8, 9 and mirror the experience in some patients on biologics for immune-mediated inflammatory disease. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China Patients with cancer appear more vulnerable to SARS-COV-2: a multi-center study during the COVID-19 outbreak doi = 10.1002/pbc.28504 id = cord-294571-qd0qjo3y author = Rothan, Hussin A. title = Molecular Aspects of COVID-19 Differential Pathogenesis date = 2020-07-06 keywords = ACE2; COVID-19; SARS summary = Angiotensin-converting enzyme-2 (ACE2) represents the primary SARS-CoV-2 entry receptor, and its physiological role is crucial in the progress of COVID-19 illness. Previous studies on SARS-CoV-1 reported that the binding of viral spike (S) protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . The levels of ACE2 expression, which could be sex-and age-dependent, have a protective role against lung and kidney injuries that could impact the severity of COVID-19 illness in male vs. The susceptibility of cardio-metabolic patients to develop severe COVID-19 illness and the high mortality rate could be linked to the ACE2 function during SARS-CoV-2 infection and the cardio-metabolic treatments that may interfere with ACE2-virus interaction. Previous studies on SARS-COV-1 reported that the binding of viral S protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . doi = 10.3390/pathogens9070538 id = cord-309289-vm0k7hfx author = Rothan, Hussin A. title = The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date = 2020-04-14 keywords = COV-2; SARS summary = title: The FDAapproved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, antiinflammatory and anti-ROS properties. We investigated the anti-viral activity of auranofin against SARS-CoV-2 and its effect on virus-induced inflammation in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury. doi = 10.1101/2020.04.14.041228 id = cord-315637-7td617dm author = Rothe, M. title = A systematic review of mask disinfection and reuse for SARS-CoV-2 date = 2020-11-12 keywords = N95; SARS; UVGI summary = However, results show it is possible to achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) disinfection on N95 masks. However, results did show that it is possible to 160 achieve >3 log reduction of SARS-CoV-2 using appropriate concentrations and contact times of chemical 161 (ethanol, hydrogen peroxide, peracetic acid), radiation (PX-UV, UVGI), and thermal (autoclaving, heat) 162 disinfection. Given the wide differences in test conditions, results are 185 summarized by disinfection agent for N95s only, for agents with >5 samples or those agents identified in 186 the disinfection efficacy section as achieving >3 log reduction of SARS-CoV-2, including ethanol, 187 hydrogen peroxide, peracetic acid, PX-UV, UVGI, autoclaving, and heat. doi = 10.1101/2020.11.11.20229880 id = cord-333868-qrnsmhws author = Rothman, Richard E. title = Respiratory Hygiene in the Emergency Department date = 2006-08-23 keywords = CDC; SARS; health; respiratory summary = These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection. doi = 10.1016/j.annemergmed.2006.05.018 id = cord-336677-h62angfw author = Rousseau, Antoine title = Sars-Cov-2, Covid-19 Et Œil: Le Point Sur Les Données Publiées date = 2020-05-30 keywords = COVID-19; SARS; des summary = Par ailleurs, la protéine Spike de SARS-CoV-2 comprend aussi un site de clivage compatible avec l''action de la furine, une autre protéase membranaire déjà connue pour être impliquée dans la pénétration d''autres coronavirus [14, 20] , et là encore, des inhibiteurs spécifiques de la furine sont à l''étude pour connaître leur propriété antivirale sur SARS-CoVUn second récepteur cellulaire semble jouer un rôle important dans la sensibilité au virus, il s''agit du récepteur CD147, aussi nommé basigine ou encore EMMPRIN (extracellular matrix metalloproteinase inducer). Les propriétés antivirales de l''hydroxychloroquine ont d''ailleurs été suspectées pour un grand nombre d''autres virus que SARS-CoV-2, mais jusqu''à présent, aucun des essais thérapeutiques chez l''homme n''a montré son efficacité dans ces autres infections [25] . Les essais thérapeutiques visant à réguler cette réaction immunitaire exacerbée représentent une part importante de l''effort de recherche clinique sur les formes sévères de COVID-19, et c''est d''ailleurs dans ce domaine que l''un des premiers essais randomisés contrôlé a montré des résultats préliminaires encourageants, (mais qui restent encore à confirmer) à propos d''un inhibiteur de l''interleukine 6 (le tocilizumab) [38] . doi = 10.1016/j.jfo.2020.05.003 id = cord-262276-5nue46dm author = Roussel, Yanis title = SARS-CoV-2: fear versus data date = 2020-03-19 keywords = CoV-2; SARS summary = The first, severe acute respiratory syndrome (SARS) coronavirus, had very little impact on global morbidity and mortality, with more than 80 0 0 recognized cases and 774 deaths [15 , 16] . Among the Organisation for Economic Co-operation and Development (OECD) countries, 7476 patients have tested positive for SARS-CoV-2, with 96 deaths (mortality rate 1.3%) ( Table 3 ). In France, 191 people have tested positive for SARS-CoV-2, with three deaths (mortality rate 1.6%). If the extrapolation of deaths in AP-HM hospitals is correct, in metropolitan France, this would represent 543/0.8 * 100 = 67 875 cases of patients hospitalized with a respiratory infection with common coronaviruses in 2 months, which is almost as many cases as for SARS-CoV-2 worldwide. Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China doi = 10.1016/j.ijantimicag.2020.105947 id = cord-305262-23qylbmg author = Rowan, Neil J. title = Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic – Implications for efficacy, re-use and sustainable waste management date = 2020-09-10 keywords = COVID-19; N95; PPE; Rowan; SARS summary = Important countermeasures for preventing COVID-19 transmission include mitigating potential high risk aerosol transmission in healthcare setting using medical PPE (such as filtering facepiece respirators (FFRs)) and the appropriate use of face coverings by the general public that carries a lower transmission risk. Given that disposable, plastic-based, PPE (gowns, eye protection, gloves, face masks, filtering facepiece respirators (FFRs)) are heat sensitive, existing healthcare technologies were considered to be either not available, unsuitable or not configured for reprocessing of PPE in healthcare for emergency use (Rowan and Laffey, 2020) . However, potential solutions for effective reprocessing of PPE that considered virus inactivation, material compatibility and device functionality (filtration efficacy, penetration, fit test and so forth) post processing included use of low temperature hydrogen peroxide vapour (VH2O2), ultraviolet germicidal light (UVGI), moist heat, and use of weak bleach for liquid decontamination (Rowan and Laffey, 2020; CDC, 2020) . doi = 10.1016/j.scitotenv.2020.142259 id = cord-263090-29n9tsk9 author = Roy, Susmita title = Dynamical asymmetry exposes 2019-nCoV prefusion spike date = 2020-04-21 keywords = Fig; RBD; SARS summary = In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. B. Side and top views of the homo-trimeric structure of SARS-CoV-2 spike protein with one RBD of the S1 subunit head rotated in the up conformation. A number of Cryo-EM structures captured the ''up'' and ''down'' conformations of the RBD domain of spike proteins of other coronaviruses including SARS-CoV-2 where the S1 subunit undergoes a hinge-like conformational movement prerequisite for receptor binding (Fig. 2C) (7, 8, 10, 17) . Analysis of all the simulations yields the 2-D free energy landscape of the trimeric spike protein of SARS-CoV-2 ( Fig 3B) with its all possible conformations. This generates a homo-trimeric SARS-CoV-2 spike where this initial structure has important components in terms of intra and inter-chain contacts (interaction) leading to an ''S1-head-up'' and an ''S1-head-down'' conformation for each protomer. doi = 10.1101/2020.04.20.052290 id = cord-306901-uuwgpuhw author = Roy, Sylvie title = Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date = 2020-09-16 keywords = SARS summary = title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. High amounts of SARS-CoV-2 DS protein are incorporated into MLV VLPs released 142 from stable producer cells. A VLP-derived SARS CoV-2 vaccine will be a viable option if 143 sufficient amounts of S protein are incorporated at the surface of the released particles. In conclusion, we have developed and characterized a new MLV VLP platform that can 243 efficiently incorporate the S protein from SARS-CoV-2, and that has the potential to produce a pan-244 coronavirus vaccine. doi = 10.1101/2020.09.16.298992 id = cord-018057-p1l6xtsq author = Ruan, Li title = SARS Epidemic: SARS Outbreaks in Inner-land of China date = 2008 keywords = Beijing; China; Guangdong; Prevention; SARS summary = Since 2002, SARS has broken out three times: the first epidemic spread worldwide from November 2002 to July 2003 (WHO, 2004) ; the second spread locally in Guangdong province between December 2003 and February 2004 (Liang et al., 2004) ; and the third developed on a small scale from laboratory infection in the inner-land of China from March to April 2004 (Ministry of Health, People''s Republic of China, 2004) . A study in Guangdong found SARS cases among people, such as restaurant cooks and meat animal''s vendors or purchasers, who had no history of contact with SARS patients but had been in contact with wild animals Peng et al., 2003; Yang et al., 2003 ; Leadership Group of SARS Prevention and Control in Beijing, Epidemiological features of severe acute respiratory syndrome in Beijing, 2003; Chinese Center for Disease Control and Prevention, 2003) . doi = 10.1007/978-0-387-75722-3_5 id = cord-347458-za7cot2n author = Ruan, Qiurong title = Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China date = 2020-03-03 keywords = SARS summary = title: Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China Using the database of Jin Yin-tan Hospital and Tongji Hospital, we conducted a retrospective multicenter study of 68 death cases (68/150, 45%) and 82 discharged cases (82/150, 55%) with laboratory-confirmed infection of SARS-CoV-2. Patients met the discharge criteria if they had no fever for at least 3 days, significantly improved respiratory function, and had negative SARS-CoV-2 laboratory test results twice in succession. It should be noted that patients with cardiovascular diseases have a significantly increased risk of death when they are infected with SARS-CoV-2 (p < 0.001). Based on the analysis of the clinical data, we confirmed that some patients died of fulminant myocarditis. KY, WXW, LYJ and JXS contributed to the analysis and interpretation of the data. doi = 10.1007/s00134-020-05991-x id = cord-267013-nbwrl4g3 author = Ruan, R title = Subacute Thyroiditis might be a complication triggered by SARS-CoV-2 date = 2020-10-13 keywords = SARS summary = The actual coronavirus disease 2019 (COVID-19) pandemia, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached more than 16 million confirmed cases worldwide, being the United Kingdom, Spain and Italy the most affected countries in Europe. We describe a clinical case of SAT following SARS-CoV-2 infection. Thyroid scintigraphy with 5.73 mCi of 99m Tc-pertechnetate was performed on May 26th, which showed absence of uptake in the gland (figure 1). To date, four cases of subacute thyroiditis during or shortly after SARS-CoV2 infection have been reported 2-5 . SAT is a clinical entity that must be suspected in patients that experience a sudden onset of neck pain and tenderness, during or after COVID-19 disease. Subacute thyroiditis in a patient infected with SARS-COV-2: an endocrine complication linked to the COVID-19 pandemic Hormones (Athens) A case of subacute thyroiditis associated with Covid-19 infection SARS-CoV-2: a potential trigger for subacute thyroiditis? Subacute Thyroiditis After Sars-COV-2 Infection doi = 10.1016/j.endinu.2020.09.002 id = cord-300149-djclli8n author = Ruan, Yijun title = Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection date = 2003-05-24 keywords = SARS; sequence summary = title: Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection METHODS: We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations. All genetic variations of Singapore isolates identified when compared with available SARS-CoV genome sequences were further confirmed by primer extension genotyping technology (Sequenom, San Diego, CA, USA). These sequences showed that the genomes of SARS-CoV isolated in Singapore are comprised of 29 711 bases, with the exception of a five-nucleotide deletion in strain SIN2748 and a six-nucleotide deletion in SIN2677. doi = 10.1016/s0140-6736(03)13414-9 id = cord-282920-s4yixzuy author = Rubin, Elizabeth S. title = Detection of COVID-19 in a Vulvar Lesion date = 2020-07-02 keywords = SARS summary = While current research suggests COVID-19 viral antigen is not found in vaginal secretions, its detectability in the female lower genital tract may have clinical implications for obstetric and gynecologic care for women. While vertical transmission has largely not been reported, the presence of detectable virus in the female lower genital tract makes this a continued possibility and area of study. Given her other reported symptoms, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nasopharyngeal test was also ordered, and the patient was instructed to have the test performed at an offsite outpatient testing site specifically designated for this purpose. This patient represents the first reported case of SARS-CoV-2 viral shedding detected in a vulvar lesion. [4] [5] [6] Finally, while vertical transmission of COVID-19 to fetuses and newborns has not been definitively shown, 7-9 the presence of detectable virus in the lower genital tract should prompt continued studies into this possibility. SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection doi = 10.1055/s-0040-1713665 id = cord-311044-kjx0z1hc author = Rubio-Pérez, Inés title = COVID-19: key concepts for the surgeon date = 2020-05-28 keywords = COVID-19; China; SARS; case; patient summary = Abstract In view of the current pandemic by SARS-CoV-2 it deems essential to understand the key concepts about the infection: its epidemiological origin, presentation, clinical course, diagnosis and treatment (still experimental in many cases). The authors have provided a narrative review of the literature available for certain key aspects of COVID-19 epidemiology, clinical presentation, diagnosis and treatment, which are of special interest to the readers of the journal. Decisions on whether or not to proceed with elective surgery in cancer patients currently depend on the local epidemiological situation, availability of operating rooms J o u r n a l P r e -p r o o f and ICU at the corresponding hospital, disease status and the risk of progression or complications (individualized), assessment of surgical risk and potential complications of the procedure. doi = 10.1016/j.cireng.2020.05.009 id = cord-345864-87b5qdjx author = Rudolph, James L. title = Temperature in Nursing Home Residents Systematically Tested for SARS-CoV-2 date = 2020-06-09 keywords = SARS summary = Abstract Objectives Many nursing home residents infected with SARS-CoV-2 fail to be identified with standard screening for the associated COVID-19 syndrome. The objective of this study is to describe the temperature changes before and after universal testing for SARS-CoV-2 in nursing home residents. We report the temperature in window of the 14 days before and after universal SARS-CoV-2 testing among CLC residents. Administration Community Life Centers (CLCs) infected with SARS-CoV-2 do have 57 temperature elevations well ahead of a confirmatory test, but also that peak temperatures will not 58 typically meet the current screening criterion threshold of 38°C that follows the Centers for 59 Disease Control''s (CDC) guidance. The purpose of this analysis is to compare temperature 73 trends and identify maximum temperatures in nursing home residents fourteen days prior to and 74 following systematic testing for SARS-CoV-2 throughout VHA CLCs. 75 doi = 10.1016/j.jamda.2020.06.009 id = cord-302160-4yfvspaq author = Ruetalo, Natalia title = Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date = 2020-10-07 keywords = SARS summary = Strikingly, short exposure of high titer surface dried virus (3*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total reduction of SARS-CoV-2 infectivity. We hence conducted a "real-life" application approach simulating the 66 inactivation of dried surface residing infectious SARS-CoV-2 by a mobile handheld UV-C 67 emitting device and an UV-C box designed to decontaminate medium-size objects. Simulating the situation that exhaled droplets or aerosols from infected 115 individuals contaminate surfaces, we produced a high-titer SARS-CoV-2 infectious stock and 116 dried 35µL of this stock corresponding to ~4*10^6 IU/ml in each well of a 6-well plate. Of note, even short UV-C treatment of the dried virus in the context of the moving "fast" 135 regimen completely inactivated SARS-CoV-2, as no infected cells were detected based on 136 fluorescence protein expression (Fig. 1b) . Altogether, our data 143 demonstrate that UV-C regimens that expose high-titer SARS-CoV-2 to doses down to 16 144 mJ/cm² are sufficient to achieve complete inactivation of the virus. doi = 10.1101/2020.09.22.308098 id = cord-319933-yp9ofhi8 author = Ruiz, Sara I. title = Chapter 38 Animal Models of Human Viral Diseases date = 2013-12-31 keywords = Nipah; SARS; animal; clinical; day; disease; experimental; human; infection; model; mouse; virus summary = An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. doi = 10.1016/b978-0-12-415894-8.00038-5 id = cord-353548-kf4om6iu author = Ruiz-Manriquez, J. title = Knowledge of Latin American gastroenterologists and endoscopists regarding SARS-CoV-2 infection date = 2020-05-31 keywords = COVID-19; SARS summary = An electronic questionnaire was applied that was designed to evaluate the knowledge of symptoms, risk groups for severe disease, prevention measures, and the reprocessing of endoscopes utilized in patients with COVID-19. [10] [11] The aim of the present study was to evaluate the knowledge of Latin American gastroenterology and endoscopy professionals in relation to the characteristics of SARS-CoV-2 infection and the prevention measures recommended during patient care and the performance of endoscopic procedures, including the reprocessing of equipment utilized on patients with the disease. We conducted a cross-sectional study on gastroenterologists and endoscopists (residents and specialists) working in public hospitals from nine Latin American countries (Mexico, Costa Rica, Ecuador, Paraguay, Peru, Guatemala, Uruguay, Honduras, and the Dominican Republic). The present study described the current knowledge of 133 Latin American residents and specialists in gastroenterology and endoscopy about symptoms, risk groups, transmission, and endoscopic equipment reprocessing in relation to COVID-19. doi = 10.1016/j.rgmxen.2020.04.002 id = cord-310411-l0slp1wa author = Rusanen, J. title = Rapid homogeneous assay for detecting antibodies against SARS-CoV-2 date = 2020-11-04 keywords = November; SARS summary = 73 We have previously set up rapid homogeneous (wash-free) immunoassays utilizing time(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In this study we introduce rapid wash-free LFRET assays for detection of antibodies 114 against SARS-CoV-2 N and S antigens and compare them with ELISAs and 115 microneutralization. ; https://doi.org/10.1101/2020.11.01.20224113 doi: medRxiv preprint 119 LFRET assays for SARS-CoV-2 S and N were set up using Eu-labeled in-house antigens 120 and AF-labeled protein L. 140 In order to compare the performance of LFRET with classical serology, we tested the set (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. After overnight incubation at Protein expression and purification 299 We initially attempted producing SARS-CoV-2 S protein in Expi293F cells utilizing the (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.11.01.20224113 id = cord-320587-936cavob author = Ruscio, M. title = Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay date = 2020-11-07 keywords = Beckman; Coulter; SARS summary = This analytical assessment encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, and comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using DiaSorin Liaison SARS-CoV-2 S1/S2 IgG and Roche Elecsys Anti-SARS-CoV-2 total antibodies. The assessment of this novel Beckman Coulter Access SARS-CoV-2 IgG immunoassay on UniCel DxI800 has originally encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, as well as comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using two other commercial anti-SARS-CoV-2 immunoassays, as comprehensively described below. As for the diagnostic performance calculated using manufacturers'' cut-off, the AUCs of Beckman Coulter Access SARS-CoV-2 IgG (p<0.001) and Roche Elecsys Anti-SARS-CoV-2 (p=0.01) antibodies titers were found to be both significantly higher than that of DiaSorin Liaison SARS-CoV-2 S1/S2 IgG, whilst they were not significantly different between them (p=0.785). doi = 10.1101/2020.11.05.20226555 id = cord-291505-vt5vpp60 author = Rusconi, Chiara title = SARS-CoV-2 Interstitial Pneumonia Treated With Tocilizumab in a Patient Affected by Classical Hodgkin Lymphoma date = 2020-09-01 keywords = SARS; covid-19 summary = [5] [6] [7] We therefore report a case of SARS-CoV-2 interstitial pneumonia in a patient with classical Hodgkin Lymphoma (cHL) successfully treated with tocilizumab. 6, 7 More recently, a series of hematological cancer patients SARS-CoV-2 infected has been described: 3 out of 25 patients received tocilizumab, in 2 cases together with steroids, and a successful outcome has been reported for two of them. The first cHL patient affected by COVID-19 has been described by O''Kelly and colleagues: at symptoms onset, a PD-1 inhibitors induced pneumonitis was suspected, and treatment against SARS-CoV-2 was started after NPS test resulted positive. 14 To the best of our knowledge, this is the first extended report on successful tocilizumab treatment for a lymphoma patient affected by COVID-19; immunocompromised subjects may mount an antibody response and overcome SARS-CoV-2 infection, even in case of severe interstitial pneumonia. doi = 10.1097/hs9.0000000000000472 id = cord-029813-o2uzcuai author = Rusconi, Stefano title = COVID-19: studying the global pandemic – foreword date = 2020-07-27 keywords = CoV-2; SARS; covid-19 summary = This special issue of Future Virology contains nine articles on diverse aspects of the COVID-19 pandemic and its causative agent, SARS-CoV-2. The topics range from basic virology on coronavirus evolution and replication to identification of repurposed therapeutics for clinical testing to public health issues including the conundrums of asymptomatic viral transmission and risks to homeless populations. The Commentary by Parvez [1] briefly reviews the detection of SARS-CoV-2 RNA in fecal samples, including its persistence, and the finding of gastrointestinal complaints in a minority of hospitalized patients. While it is clear that this phytochemical has multiple pharmacological activities, as reviewed previously [10] , this in silico report does not provide biologic data on rutin''s possible effects in SARS-CoV-2 infection. Detection of relatively high SARS-CoV-2 RNA loads in upper respiratory tract samples has been reported in both presymptomatic (late incubation period) and truly asymptomatic infected persons. Transmission and clinical characteristics of asymptomatic patients with SARS-CoV-2 infection doi = 10.2217/fvl-2020-0211 id = cord-289890-sf2uxubd author = Rushworth, S. A. title = Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay date = 2020-06-12 keywords = Mount; SARS; covid-19 summary = We evaluated the FDA approved SARS-CoV-2 immunoassay (developed at Mount Sinai, by Krammer and colleagues) for the identification of COVID-19 seroconversion and potential cross-reactivity of the assay in a United Kingdom (UK) National Health Service (NHS) hospital setting. In summary, we report that the Mount Sinai IgG ELISA assay is highly sensitive test for SARS-Cov-2 infection, however modification of thresholding was required to minimise false positive results. Figure 2A shows that 42/47 samples from this group were established as negative for SARS-CoV-2 IgG antibody in the first RBD screening test step, and 5/47 required confirmatory assessment with the second dilution assay. On testing of the control group, 70/72 patient samples were identified as being negative for SARS-CoV-2 IgG antibody following the RBD step of the assay using the 5 SD threshold. To conclude, here we report that the Mount Sinai IgG ELISA assay is highly sensitive and apparent cost-effective test for SARS-Cov-2 infection in a UK NHS acute hospital laboratory setting. doi = 10.1101/2020.06.11.20128306 id = cord-158628-71n1tgrw author = Russo, Giulia title = In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform date = 2020-05-05 keywords = CoV-2; SARS; UISS; cell summary = Recently, specific findings about the genome sequencing of SARS-CoV-2 in different countries where cases of infection were registered, revealed its relative intrinsic genomic variability, its virus dynamics and the related host response mechanisms, unveiling interesting knowledge useful for the formulation of innovative strategies for preventive vaccination. Specifically, SARS-CoV-2 sequencing along with its relative intrinsic genomic variability [10] , the presence of minority variants generated during SARS-CoV-2 replication [11] , the involved cellular factors that favors SARS-CoV-2 cell entry [12] , the timing in which viral load peaks (during the first week of illness), its gradual decline (over the second week) and the increasing of both IgG and IgM antibodies (around day 10 after symptom onset) represent some of the relevant insights so far delineated and considered by research community about SARS-CoV-2 virus [13] . UISS is an immune system simulation platform that was designed to be applied to several and different scenarios, especially to carry on in silico trials to predict the efficacy of a specific prophylactic or therapeutic vaccine against a particular disease. doi = nan id = cord-344714-0cam9ipf author = Russo, Maria title = Roles of flavonoids against coronavirus infection date = 2020-07-28 keywords = 3CL; ACE2; COVID-19; CoV; RNA; SARS summary = Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Inhibition of TMPRSS2 and Furin protease activities can be considered an interesting therapeutic option against coronavirus infection, especially COVID-19, allowing the block and/or prevention of SARS-CoV-2 infection, as recently reported [28] . Based on these observations, it is not surprising that molecular docking approach, summarized in Fig. 3 , supports the role of flavonoids in the inhibition of SARS-CoV 3CL pro by binding His41 and Cys145 of the catalytic site and other active site residues (e.g., Met49, Gly143, His163, His164, Glu166, Pro168, and Gln89), stimulating their validation by in vitro and in vivo studies. doi = 10.1016/j.cbi.2020.109211 id = cord-298350-pq1dcz3a author = Ryan, Jeffrey R. title = Category C Diseases and Agents date = 2016-03-25 keywords = MERS; Nile; Nipah; SARS; WNV; West summary = Specific examples explored in this chapter include Nipah virus, hantavirus, West Nile fever virus, and the coronaviruses that cause severe acute respiratory syndrome and Middle East respiratory syndrome. Remarkably, researchers noted that human case patients had an association with infected animals from a concurrent and severe outbreak of respiratory disease in pigs and that there was a notable absence of illness in children. Research shows that many HPS case patients acquired the virus after having been in frequent contact with rodents or their droppings for long periods (Centers for Disease Control and Prevention, Special Pathogens Branch, 2007) . Initially, Saint Louis encephalitis virus was believed to be the cause of the human infections until WNV was isolated from the human and animal specimens. Patients infected with the SARS-coronavirus disease are likely to present to health-care facilities. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia doi = 10.1016/b978-0-12-802029-6.00005-0 id = cord-337511-20yaol5r author = Ryan, Paul MacDaragh title = COVID-19 and relative angiotensin-converting enzyme 2 deficiency: role in disease severity and therapeutic response date = 2020-06-11 keywords = ACE2; RAS; SARS summary = Interestingly, comparative analysis of two successive SARS epidemics in early 2000s showed that increased affinity of the SARS virus for human ACE2 receptor strongly predicted severity of clinical disease suggesting that spike protein conformation is potentially a key determinant of virulence. 15 Interestingly, in several Wuhan cohorts cardiac injury and arrythmia were prominent in high-risk Figure 3 Homeostasis of RAS-ACE2 under normal healthy conditions 10 19 ; perturbation of RAS-ACE2 homeostasis in cardiovascular disease, hypertension and diabetes mellitus 22 27 ; COVID-19 may potentially further upregulate RAS in CVD patients and deplete ACE2 33 ; proposition that rhACE2 replacement therapy improves RAS-ACE2 balance by augmenting ACE2 and decreasing RAS activation. 35 If the same holds true for SARS-CoV-2, then soluble rhACE2 may reduce ongoing SARS-CoV-2 access to membrane-bound ACE2 receptor, alter favourably local AngII/Ang1-7 levels and inhibit deleterious RAS effects on remaining at risk tissues in COVID-19 patients. doi = 10.1136/openhrt-2020-001302 id = cord-325055-todb1d4x author = Rychter, Anna Maria title = Should patients with obesity be more afraid of COVID‐19? date = 2020-06-24 keywords = SARS; covid-19; obesity summary = Furthermore, obesity is increasingly considered as a yet another risk factor, particularly, because it has been observed that people suffering from excessive body weight may experience a more severe course of COVID‐19 infection. Although the data regarding the impact of SARS-CoV-2 in individuals with obesity are limited and their association has not been fully defined yet, it has been observed that people suffering from excessive body weight may experience a more serious COVID-19 infection. 68 Whether the obesity paradox will be present among COVID-19 patients remains to be seen, nevertheless, the phenomenon was reported among other respiratory diseases, such as COPD or ARDS. 53, 69 Its pathophysiological basis remains unknown; however, an increased BMI seems to be associated with a better survival and a slower decline in the lung function in patients with a mild course of chronic obstructive pulmonary disease. Obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Association of obesity with disease severity among patients with COVID-19. doi = 10.1111/obr.13083 id = cord-315181-emf4i6ir author = Ryoo, Nayoung title = Coping with Dementia in the Middle of the COVID-19 Pandemic date = 2020-10-27 keywords = SARS; covid-19; dementia; patient summary = • Home based exercise and planned outdoor activities, avoiding densely populated areas, with caregivers are encouraged • Have more organized daily plans that include enjoyable therapeutic activities • Create a new routine which fits within the context of the current circumstances • Prevent overuse or addiction to TV/video by scheduling and restricting daily use • Counselling for behavioural management of FTD via telephone hotlines is helpful • Providing self-help guidance for reducing stress through electronic media can result in beneficial effects for FTD patients ADL = activities of daily living, PPE = personal protective equipment, COVID-19 = coronavirus disease 2019, BPSD = behavioral and psychological symptoms of dementia, VD = vascular dementia, AD = Alzheimer''s disease, FTD = frontotemporal dementia, ICU = intensive care unit, DLB = diffuse Lewy body. doi = 10.3346/jkms.2020.35.e383 id = cord-267482-afqfymbq author = Ryu, Seungjin title = Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date = 2020-09-12 keywords = A59; COVID-19; SARS; cell; figure; mouse summary = Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of γδ T cells in lungs. Also, initial studies that employ lung ciliated epithelial cell-specific HFH4/FOXJ1 promoter driven hACE2 transgenic mice show SARS-CoV-2 infection induces weight loss, lung inflammation and approximately 50% mortality rate, suggesting the usefulness of this model to understand the mechanism of immune dysregulation (Jiang et al., 2020) . Moreover, given our recent findings that ketogenesis inhibits inflammation and expands tissue resident ϒδ T cells (Goldberg et al., 2019) while SARS-CoV-2 infection in patients is associated with depletion of ϒδ T cells (Lei et al., 2020; Rijkers et al., 2020) , we next tested whether elevating BHB by feeding a ketogenic diet (KD) protects against mCoV-A59-driven inflammatory damage in aged mice. doi = 10.1101/2020.09.11.294363 id = cord-316788-4x5l2h4d author = Ryu, Young Bae title = Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition date = 2010-11-15 keywords = 3CL; SARS; pro summary = Following bioactivity-guided fractionation, eight diterpenoids (1–8) and four biflavonoids (9–12) were isolated and evaluated for SARS-CoV 3CL(pro) inhibition using fluorescence resonance energy transfer analysis. As part of an ongoing investigation of potential SARS-CoV 3CL pro inhibitors from medicinal plants, we performed an initial screen of ethanol extracts of the leaves of Torreya nucifera using a fluorescence resonance energy transfer (FRET) assay. We isolated 12 phytochemicals-eight diterpenoids and four biflavonoids-with SARS-CoV 3CL pro inhibitory activity from the ethanol extracts of the leaves of T. Of the isolated compounds, biflavonoid amentoflavone (9) was identified as a potent inhibitor of SARS-CoV 3CL pro , exhibiting an IC 50 value of 8.3 lM. nucifera, is an effective inhibitor of SARS-CoV 3CL pro and is more effective than the corresponding flavones (apigenin and luteolin) and biflavonoid derivatives containing various numbers of methoxy groups. doi = 10.1016/j.bmc.2010.09.035 id = cord-321714-yhruzu7f author = Ryu, Young Bae title = SARS-CoV 3CL(pro) inhibitory effects of quinone-methide triterpenes from Tripterygium regelii date = 2010-03-15 keywords = 3CL; SARS summary = Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). Isolated quinone-methide triterpenes (1-4) and 5 were evaluated for SARS-CoV 3CL pro inhibitory activities and showed potent inhibitory activities with IC 50 values of 10.3, 5.5, 9.9 , and 2.6 lM, respectively, whereas the corresponding 5 having phenol moiety was observed in low activity (IC 50 = 21.7 lM). We then further characterized the inhibitory mechanism of the isolated quinone-methide triterpenes against SARS-CoV 3CL pro activity. Although all isolated quinone-methide triterpenes has previously been known compounds, this is the first time it has been shown to possess SARS-CoV 3CL pro inhibitory activity. doi = 10.1016/j.bmcl.2010.01.152 id = cord-307463-bheq9p5w author = Rödel, Franz title = Low-dose radiation therapy for COVID-19 pneumopathy: what is the evidence? date = 2020-05-09 keywords = SARS; dose summary = Due to the current lack of effective pharmacological concepts, this situation has caused interest in (re)considering historical reports on the treatment of patients with low-dose radiation therapy for pneumonia. Although these historical reports are of low-level evidence per se, hampering recommendations for decision-making in the clinical setting, they indicate effectiveness in the dose range between 0.3 and 1 Gy, similar to more recent dose concepts in the treatment of acute and chronic inflammatory/degenerative benign diseases with, e.g., a single dose per fraction of 0.5 Gy. This concise review aims to critically review the evidence for low-dose radiation treatment of COVID-19 pneumopathy and discuss whether it is worth investigating in the present clinical situation. This situation has caused interest in (re)considering the historical treatment of patients with low-dose radiation therapy for pneumonia. This review on 15 reports covers 863 patients with severe pneumonia of K different pathogeneses, including two studies of viral origin treated with low doses of kilovoltage X-rays. doi = 10.1007/s00066-020-01635-7 id = cord-281294-dnaith3a author = Röhr, Susanne title = Psychosoziale Folgen von Quarantänemaßnahmen bei schwerwiegenden Coronavirus-Ausbrüchen: ein Rapid Review date = 2020-04-27 keywords = Personen; Quarantänemaßnahmen; SARS; Studien; Zusammenhang; die summary = Im April 2020 unterstand weltweit mehr als ein Drittel der Menschheit Quarantänemaßnahmen, um die Ausbreitung des neuartigen Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) einzudämmen. Die durch die Infektion mit SARS-CoV-2 ausgelöste Atemwegserkrankung Corona Virus Disease 2019 (COVID19) wurde erstmals im Dezember 2019 in der chinesischen Millionenstadt Wuhan beschrieben und entwickelte sich bereits im Januar 2020 zur Epidemie in China [1] . Evidenz über psychosoziale Folgen von Quarantänemaßnahmen im Zusammenhang mit den genannten Ausbrüchen können Grundlage für entsprechende Untersuchungsansätze und Handlungsempfehlungen im Rahmen der COVID-19-Pandemie sein. Insgesamt konnten 13 Studien identifiziert werden, die konsistent psychosoziale Folgen von Quarantäne-und Isolationsmaßnahmen bei der SARS-Pandemie 2002/2003 und lokalen MERS-CoV-Ausbrüchen in den Zehnerjahren beschrieben, darunter Depressivität, Ängstlichkeit, Wut, Stress, Schlafstörungen, Sorgen, soziale Isolation, Einsamkeit und Stigmatisierung. Erste Fallstudien aus Deutschland bestätigen erhöhte psychische Belastungen infolge von COVID-19 und unterstreichen den Bedarf für eine Public-Health-Agenda, die Maßnahmen zum Schutz der psychosozialen Gesundheit während der Massenquarantäne hierzulande forciert [46] . doi = 10.1055/a-1159-5562 id = cord-292985-w62xaa4f author = Römer, Rudolf A. title = Flexibility and mobility of SARS-CoV-2-related protein structures date = 2020-07-12 keywords = SARS; protein; structure summary = We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. doi = 10.1101/2020.07.12.199364 id = cord-260503-yq4dtf8n author = SAMARANAYAKE, LAKSHMAN P. title = Severe acute respiratory syndrome and dentistry A retrospective view date = 2004-09-30 keywords = Hong; Kong; SARS; disease; patient summary = Objectives The authors trace the emergence of the SARS outbreak from southern China and its spread worldwide, discuss the viral etiology of the infection and its clinical features, and review the infection control guidelines issued during the outbreak by the health authorities in Hong Kong, the Centers for Disease Control and Prevention, the World Health Organization and the American Dental Association. Conclusions and Clinical Implications Researchers believe that a combination of factors, including the universal infection control measures that the dental community has implemented and/or the low degree of viral shedding in the prodromal phase of SARS, may have obviated the spread of the disease in dental settings. Interim domestic infection control precautions for aerosol-generating procedures on C L I N I C A L P R A C T I C E patients with severe acute respiratory syndrome (SARS) doi = 10.14219/jada.archive.2004.0405 id = cord-355477-7xd93aqv author = SATIJA, NAMITA title = The Molecular Biology of SARS Coronavirus date = 2007-04-23 keywords = RNA; SARS; protein summary = abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells doi = 10.1196/annals.1408.002 id = cord-257022-6vw88jib author = SHANG, Lei title = Polymorphism of SARS-CoV Genomes date = 2006-04-30 keywords = SARS; bj202 summary = Abstract In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. In this work, the genome of one SARS-CoV isolated directly from the stool sample of a SARS patient was completely sequenced. We aligned 116 complete genome sequences of SARS-CoV (including BJ202 ) to analyze their single nucleotide polymorphism (SNPs). The 21.9-23.9 kb region, which falls into OrfS, had the third highest mutation frequency, in which 39 polymorphic sites were found in the nearly 2 kb stretch of genomic sequence (1 9.5 SNPs in 1 kb). Although it was reported that the in vitro mutation rate of the SARS-CoV in Vero cell passage was negligible[''81, there might be difference between the genomic sequences obtained directly from clinical samples and from isolates of the cell culture. In this work, we completed the sequencing of SARS-CoV genome directly from the stool sample and analyzed the polymorphism of the SARS-CoV genome. doi = 10.1016/s0379-4172(06)60061-9 id = cord-288651-bgo8istm author = SHI, Yi title = Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date = 2005-03-17 keywords = RNA; SARS summary = RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. The results show that all siRNA duplexes specifically reduced SARS-CoV genes expression to different extents compared with the control (Fig. 1) . Kinetic study results (Fig. 2B ) revealed a continuous increase in the specific inhibition of SARS-CoV genes expression by No. 5, No. 6, and No. 16 siRNA from 24 to 72 h after transfection. doi = 10.1038/sj.cr.7290286 id = cord-286072-kgpvdb42 author = Sa Ribero, Margarida title = Interplay between SARS-CoV-2 and the type I interferon response date = 2020-07-29 keywords = IFN; MERS; SARS; cell; response summary = While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection. IFN, interferon; IFNAR, interferon alpha and beta receptor; IκB, inhibitor of nuclear factor κB; IKKε, IκB kinase-ε; IRF, IFN regulatory factor; ISG, IFN-stimulated gene; JAK, Janus kinase; M, membrane; MAVS, mitochondrial antiviral signaling protein; MDA5, melanoma differentiation-associated gene 5; N, nucleocapsid; Nsp, nonstructural protein; ORF, open reading frame; P, phosphate; PLP, papain-like protease; RIG-I, retinoic acid-inducible gene 1; SARS-CoV, severe acute respiratory syndrome coronavirus; STAT, signal transducer and activator of transcription; TANK, TRAF family member associated NF-κB activator; TBK1, TANK-binding kinase 1; TRAF3, tumor necrosis factor receptor-associated factor 3; TYK2, tyrosine kinase 2. doi = 10.1371/journal.ppat.1008737 id = cord-296494-6kn4mr04 author = Saban-Ruiz, J. title = COVID-19: A Personalized Cardiometabolic Approach for Reducing Complications and Costs. The Role of Aging Beyond Topics date = 2020-05-12 keywords = ACE2; CMM; COVID-19; SARS; age; patient summary = Bearing this in mind, it is quite likely, that if we have fewer complications, particularly severe ones (cardiac arrest, ventricular tachyarrhythmia, acute heart failure, acute coronary syndrome, haemorrhagic or massive ischaemic stroke), this integrated approach could cut down the elevated mortality in the highest risk group (cancer, COPD and oldest subjects with comorbidities), usually preceded by a multi-organ failure. In aged COVID-19 patients or with history of coronary artery disease (CAD) an acute coronary syndrome (ACS) can also be seen for plaque vulnerability in the presence of a pro-inflammatory state with cytokine release (71) but from the experience in animals, could it be plausible that any of them could be due to arteritis? The third aspect would be the combination of T2DM and Heart failure (HF) (the most frequent cardiac complication in any of the phases of the disease), which is present in a high percentage of patients, especially those at higher risk. doi = 10.1007/s12603-020-1385-5 id = cord-296214-xeezt6f7 author = Sabatino, Jolanda title = Women''s perspective on the COVID-19 pandemic: Walking into a post-peak phase date = 2020-08-13 keywords = ACHD; COVID-19; SARS summary = Therefore, we discussed the impact of COVID-19 pandemic on women, children and young patients, particularly those with underlying cardiovascular comorbidities or congenital heart disease. Although the so far evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is likely to have a lower fatality rate in women, the course of the disease during pregnancy is not fully understood. Indeed, in rat lungs a higher expression of ACE2 has been observed in younger females animals than in adult males [26] Despite adult patients with cardiovascular co-morbidities have a worse course of the disease, and higher mortality rate, when we look at children infected by SARS-CoV-2 with concomitant congenital heart disease (CHD), they seem to have the same clinical trend and mortality of peers without CHD. An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes doi = 10.1016/j.ijcard.2020.08.025 id = cord-294440-zd0arwmr author = Sacco, Guillaume title = COVID-19 in seniors: Findings and lessons from mass screening in a nursing home date = 2020-06-26 keywords = COVID-19; SARS; resident summary = CONCLUSIONS: The pauci-symptomatic expression of COVID-19 in older residents, together with the high prevalence of asymptomatic forms in caregivers, justifies mass screening in nursing homes, possibly prioritizing residents with suggestive combinations of clinical signs including dyspnea, falls, anorexia and/or altered consciousness. The objective of the present study was to clarify symptoms and chronological aspects of the propagation of the SARS-CoV-2 in a nursing home, both in residents and staff members. The study consisted in a five-week retrospective observational cohort study in a middle-sized nursing home in Maine-et-Loire, West of France, having performed COVID-19 mass screening of residents (n=87) and staff members (n=92). The present report of COVID-19 mass screening in a nursing home showed a high prevalence of asymptomatic infected staff members, and confirmed that older residents exhibit few and mainly nonspecific symptoms. doi = 10.1016/j.maturitas.2020.06.023 id = cord-179749-qdbmpi7j author = Sacks, Daniel W. title = What can we learn about SARS-CoV-2 prevalence from testing and hospital data? date = 2020-08-01 keywords = SARS; covid; test summary = We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on who gets tested, using Indiana data on hospital inpatient records linked to SARS-CoV-2 virological tests. In this paper, we propose a new approach to measuring the point-in-time prevalence of active SARS-CoV-2 infections in the overall population using data on patients who are hospitalized for non-COVID reasons. The combination of these assumptions with linked testinghospital data leads to relatively tight upper and lower bounds on the prevalence of active SARS-CoV-2 infections in the overall population in Indiana in each week from mid-March to mid-June. We maintain the test monotonicity assumption throughout, and we derive upper and lower bounds on prevalence in the population under two alternative assumptions about the representativeness of non-COVID hospitalizations for the broader population. Equivalently, the independence assumption implies that SARS-CoV-2 prevalence is the same among people who are hospitalized for non-COVID conditions and the general population. doi = nan id = cord-286301-7sjw5ci7 author = Sadasivan, Jibin title = Cytoplasmic tail of coronavirus spike protein has intracellular targeting signals date = 2017-04-18 keywords = OC43; SARS; protein summary = SARS-S-Y was absent from surface in most of the cells and localized at the intracellular compartments (figure 5a), and OC43-S protein was mainly localized in distinct puncta that could represent endocytic structures following internalization from the plasma membrane (figure 5b). Our studies clearly demonstrated that the KXHXX motif is the major intracellular localization signal of the full-length SARS-S protein and the C-terminal proximity is not essential. Our alanine mutation studies on the KXHXX motif confirm the importance of the lysine and histidine in the full-length wild-type HCoV-SARS S protein; the mutant protein showed localization in plasma membrane instead of the usual ER and ERGIC. In contrast, Lysosomal acid phosphatase, also a type I membrane protein with a cytosolic tail GYXXØ motif located 7 residues from both transmembrane domain and the carboxy termini (Tm-RMQAQPPGYRHVADGEDHA) delivered mainly via the cell surface (Braun et al. doi = 10.1007/s12038-017-9676-7 id = cord-300783-pvn2qq0f author = Sadykov, Mukhtar title = Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date = 2020-08-07 keywords = SARS summary = title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5''-UCG-3'' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins. One such 34 mechanism is the CpG dinucleotide reduction observed in many single-stranded RNA 35 fraction of the observed C>U changes represent multiple, independent events ( Figure S3 ). CpG Dinucleotides in SARS-CoV-2 Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host 396 antiviral defense Multi-site co-398 mutations and 5''UTR CpG immunity escape drive the evolution of SARS-CoV-2 doi = 10.1101/2020.06.19.161687 id = cord-345304-n74m5ucs author = Safadi, Marco Aurelio Palazzi title = THE CHALLENGING AND UNPREDICTABLE SPECTRUM OF COVID-19 IN CHILDREN AND ADOLESCENTS date = 2020-09-07 keywords = COVID-19; SARS summary = 6 Based on current evidence, older adults and people of all ages with underlying medical conditions, including severe obesity, chronic lung disease, cardiovascular disease, diabetes mellitus, chronic kidney disease, liver disease, active cancer, transplantation and immunocompromised have been associated with poor clinical outcomes and higher fatality rates from COVID-19. One of the largest pediatric cancer programs in the USA, in New York city, reported that 20/178 (11%) children and adolescents with cancer had positive test for SARS-CoV-2. 11 The overwhelmed public health systems by the COVID-19 pandemic represents a serious risk for pediatric general health, limiting access of children and adolescents to basic health care, compromising immunization coverages and postponing consultations for patients with underlying conditions. Clinical characteristics of 58 children with a pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 Clinical characteristics and outcomes of hospitalized and critically Ill children and adolescents with coronavirus disease 2019 (COVID-19) at a tertiary care medical center in New York City doi = 10.1590/1984-0462/2020/38/2020192 id = cord-104507-xx7t26rl author = Safari, Saeid title = Extracorporeal Hemoperfusion as a Potential Therapeutic Option for Severe COVID-19 patients; a Narrative Review date = 2020-08-22 keywords = SARS; covid-19; inflammatory; patient summary = Based on previous experience of blood purification to treat cytokine storm syndrome (CSS) in severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), here we aimed to review the current literature on extracorporeal hemoperfusion as a potential therapeutic option for CSS-associated conditions, with a focus on severe COVID-19. To date, various centers in different countries including Italy, China, USA, Germany, and Iran have reported or are investigating the beneficial effects of different hemoperfusion systems, including HA380/HA330 cartridges, CytoSorb, and polymyxin B immobilized fiber column in treatment of critically-ill COVID-19 patients. To date, a large number of experimental and clinical data, mostly from case reports and case series, have introduced CytoSorb as an effective rescue therapy for removal of inflammatory cytokines and achievement of hemodynamic stabilization in critically ill patients with septic shock and kidney failure (47) (48) (49) . doi = nan id = cord-286269-vrjyj2y1 author = Sagheb, Setareh title = Two seriously ill neonates born to mothers with COVID-19 pneumonia- a case report date = 2020-09-21 keywords = COV-2; COVID-19; SARS summary = They evaluated cord blood, amniotic fluid and even breast milk samples of mothers diagnosed with COVID-19 pneumonia, but SARS-COV-2 tests were negative in all cases. Consequently, because of performing all the aforementioned droplet and contact precautions during hospitalization, having high LDH, lymphopenia and SIADH soon after birth may be due to early-onset infection of SARS-COV-2. Furthermore, another study conducted on a limited number of patients showed a high level of SARS-COV-2 IgM in neonates born from COVID-19 infected mothers within 2 first hours of their birth [7] , which may indicate infection transmission from mother to fetus. It is worth noting that, although our neonates'' RT-PCR tests'' results for SARS-COV-2 were negative 1 hour after their birth, they tested positive on day 7 and 12. Neonatal Early-Onset Infection With SARS-CoV-2 in 33 Neonates Born to Mothers With COVID-19 in Wuhan, China doi = 10.1186/s13052-020-00897-2 id = cord-335467-0b0m8v5r author = Saha, Asit title = Novel coronavirus SARS‐CoV‐2 (Covid‐19) dynamics inside the human body date = 2020-07-19 keywords = SARS summary = A time‐dependent nonlinear system of ordinary differential equations model was constructed involving type‐I cells, type‐II cells, SARS‐CoV‐2 virus, inflammatory mediators, interleukins along with host pulmonary gas exchange rate, thermostat control, and mean pressure difference. The cybernetic model can simulate a dynamic response to the reduced pulmonary alveolar gas exchange rate, thermostat control, and mean pressure difference under a very critical condition based on equilibrium (steady state) values of the inflammatory mediators and system parameters. 13, 14 In the present study, we aim to understand the chain of events after the SARS-CoV-2 virus invaded the human body, creating chaos in the respiratory system, thermostat control, and multiple organ failure systematic networks using the knowledge-based cybernetic model. doi = 10.1002/rmv.2140 id = cord-269187-lt0uo7q3 author = Saha, Indrajit title = Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date = 2020-07-11 keywords = SARS; indian summary = Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. Based on this information, they developed an SNP-based PCR assay to show differentiation between To address the above facts, we have analyzed publicly available 566 Indian complete or near complete SARS-CoV-2 genomes in order to find the mutation points as substitution, deletion J o u r n a l P r e -p r o o f and insertion. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs. The genomic sequences of Indian SARS-CoV-2 virus was collected from Global Initiative on Sharing All Influenza Data (GISAID) 1 in fasta format on 11th June 2020. doi = 10.1016/j.meegid.2020.104457 id = cord-196608-k4f79dr4 author = Saha, Sovan title = Computational modeling of Human-nCoV protein-protein interaction network date = 2020-05-05 keywords = PPIN; SARS; human summary = Our developed computational model of nCoV-Human PPIN contains high quality interactions (HQI) and proteins identified by Fuzzy affinity thresholding and spreadability index validated by SIS model respectively. With the gradual progress of the work, it has been observed that the selected human spreader nodes, identified by our proposed model, emerge as the potential protein targets of the FDA approved drugs for COVID-19. Target proteins of the potential FDA drugs for COVID-19 are found to overlap with the spreader nodes of the proposed computational nCoV-Human protein interaction model. Target proteins of seven potential FDA drugs: Lopinavir 30 , Ritonavir 31 , Hydroxychloroquine 32, 33 , Azithromycin 33 , Remdesivir 34-36 , Favipiravir 37, 38 and Darunavir 39 for COVID-19 as mentioned in the DrugBank white paper 26 overlap with the spreader nodes of the proposed in silico nCoV-Human protein interaction model (see Figure 5 ). doi = nan id = cord-255755-5jccb3nh author = Saha, Sovan title = Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date = 2020-04-23 keywords = PPIN; SARS summary = title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network The new network attribute spreadability index along with generated SIS values of selected top spreader nodes when compared with the other network centrality based methodologies like Degree centrality (DC), Closeness centrality (CC), Local average centrality (LAC) and Betweeness centrality (BC) is found to perform relatively better than the existing-state-of-art. In the proposed methodology, Protein-protein interaction network (PPIN) has been used as the central component in identification of spreader nodes in SARS-CoV. Once it is formed, spreader nodes are identified in each of SARS-CoV proteins, its level 1 and level 2 of human network by the application of a new network attribute i.e. spreadability index which is a combination of three terminologies: 1) edge ratio [28] 2) neighborhood density [28] and 3) node weight [29] . doi = 10.1101/2020.04.12.038216 id = cord-275360-uphdzj5l author = Sahajpal, Nikhil Shri title = Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date = 2020-07-30 keywords = SARS; sample summary = Herein, we propose a mass population screening approach, based on sample pooling strategy for rapid and wide-scale population screening that may be adopted by laboratories currently using RT-PCR based methods to test for SARS-CoV-2. The strategy we propose leverages on existing high throughput systems that employ high analytically sensitive [limit of detection (LOD) 5-20 copies/ml] real-time PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. 6 The advantages of this approach include the potential to catch up with huge testing deficits, reducing turnaround times and most importantly ensuring enormous savings through the most efficient use of RNA extraction and/or testing kits, which even today are in significant short supply. The strategy we propose leverages existing high throughput systems which employ analytically high sensitive RT-PCR chemistries, coupled with pooling of samples based on current COVID-19 incidence rates. doi = 10.1016/j.jmoldx.2020.07.001 id = cord-356370-jjl1hbeb author = Sahajpal, Nikhil Shri title = Role of clinical laboratories in response to the COVID-19 pandemic date = 2020-06-19 keywords = PCR; SARS summary = In response to the outbreak, several state authorities and commercial companies have developed diagnostic assays to test individuals for the SARS-CoV-2 infection. In the US, clinical laboratories are required to perform ''bridging studies'' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. Although, the reverse transcription-polymerase chain reaction (RT-PCR) based assays for the detection of SARS-CoV-2 nucleic acid regions might be the most practical approach at present, qualitative assays are far from providing insights into the evolution of the virus and the varied immune response in different populations. In addition, the RT-PCR based assays provide a unique opportunity to implement pooling sample strategy for wide-scale population screening for SARS-CoV-2. Several studies, including from our laboratory (under review) have demonstrated that pooling sample strategy is a practical and feasible method for screening populations for SARS-CoV-2 [2] . Laboratories should therefore prime for serologic testing by validating assays using RT-PCR confirmed COVID-19 samples. doi = 10.4155/fmc-2020-0129 id = cord-153725-jjefjlx2 author = Sahoo, Suban K title = Computational evidence on repurposing the anti-influenza drugs baloxavir acid and baloxavir marboxil against COVID-19 date = 2020-09-02 keywords = BXA; SARS summary = In this communication, molecular docking analyses of two influenza antiviral drugs baloxavir acid (BXA) and baloxavir marboxil (BXM) were performed with the three therapeutic target proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp). Considering the need of new potential drugs to repurpose against COVID-19 pandemic, this research was carried out to investigate the effective binding of the drugs BMX and BXA with the three functional proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The molecular docking of the drugs were performed with the therapeutic target proteins and their affinity of binding at the active site was compared. Therefore, to provide computational evidence on the comparative potency of the two influenza antiviral drugs BXA and BXM (Fig. 1) , the molecular docking experiments were performed in Autodock Vina with the therapeutic target proteins of SARS-CoV-2, i.e., Mpro, PLpro and RdRp. The blind molecular docking was performed where the grid box was selected to cover the whole protein structure. doi = nan id = cord-339727-q8pjwl3s author = Sahu, Kamal Kant title = Mesenchymal Stem Cells in COVID-19: A Journey from Bench to Bedside date = 2020-07-30 keywords = COVID-19; SARS; cell summary = Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. Recently, research exploring the therapeutic application of mesenchymal stem cells (MSCs) in critically ill patients suffering from COVID-19 has gained momentum. [6] [7] [8] [9] [10] Recently, a few studies have examined the role of mesenchymal stem cells (MSCs) in critically ill patients with COVID-19. Because H7N9 and SARS-CoV-2 share similar complications-ARDS, hypoxic respiratory failure, severe inflammation, overt immune response, and multiorgan dysfunction syndrome-MSCs therapy may be beneficial for patients with COVID-19 pneumonia as well. Rationale for the clinical use of adipose-derived mesenchymal stem cells for COVID-19 patients Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: the case for compassionate use doi = 10.1093/labmed/lmaa049 id = cord-307671-f9l2l8fi author = Said, Mohammed title = The Forgotten Element in the Resumption of Elective Bariatric Surgery During the COVID-19 Pandemic: the Patient Consent! date = 2020-09-19 keywords = SARS; covid-19 summary = The aim was to assess their knowledge and expectations regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A total of 233 (87.6%) candidates believed that they were prone to a higher risk of severe SARS-CoV-2 infection, and 24.4% of them believed that bariatric surgery, during the pandemic, would improve their immunity. The present study aims to help in answering these questions through an assessment of patients'' concepts regarding bariatric surgery resumption after the peak of the COVID-19 pandemic. The following four questions assessed the patient opinion regarding bariatric surgery and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Bariatric teams need to ensure that candidates for surgery share the required knowledge regarding the methods of transmission of SARS-CoV-2 infection and are willing to follow the protective measures. doi = 10.1007/s11695-020-04976-5 id = cord-277830-6fsz9iy7 author = Saikatendu, Kumar Singh title = Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date = 2005-11-08 keywords = ADP; ADRP; RNA; SARS; Ymx7; figure summary = The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. A view of the proposed active site of SARS ADRP along with the superimposed structures of AF1521 and yeast Ymx7 are shown in Figure 4B , highlighting the interactions that are likely between residues of the protein with the ligand. doi = 10.1016/j.str.2005.07.022 id = cord-262441-slh52nxm author = Sakai, Yusuke title = Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication date = 2017-07-21 keywords = F121L; Fig; H120N; SARS summary = To determine the crucial amino acid residue(s) in SARS-CoV nsp4 required to induce membrane rearrangements through the interaction with nsp3C, we constructed additional expression plasmids encoding deletion mutants of SARS-CoV nsp4, pCAG nsp4 Δ112-126-HA and pCAG nsp4 Δ126-164-HA, as shown in Fig. 1B . To determine the effect of the two amino acid residues, H120 and F121, in SARS-CoV nsp4 on the membrane rearrangements thorough interaction with nsp3C, 293T cells transfected with pCAG nsp4-HA or pCAG nsp4 H120N/F121L-HA together with pCAG nsp3C-3xFLAG at 30 h posttransfection were subjected to transmission electron microscopy (TEM) analysis. As we expected, expression of renilla luciferase was detected in cells transfected with pBAC-SARS-Rep-wt, but not in those with pBAC-SARS-Rep-H120N/F121L or pBAC-SARSRep-SAD (Fig. 7C) , suggesting that both H120 and F121 in SARS-CoV nsp4 play critical roles in the viral replication by remodeling the membrane through binding with nsp3. doi = 10.1016/j.virol.2017.07.019 id = cord-301080-xr7kl573 author = Sakanashi, Daisuke title = Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 date = 2020-09-30 keywords = SARS summary = title: Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19 Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Therefore, the present study aimed to compare nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19. Among them, five patients had been diagnosed with COVID-19 by reverse transcription real-time polymerase chain reaction (rRT-PCR) of nasopharyngeal swabs and were hospitalized before the first collection of paired specimens, whereas seven were outpatients suspected to have COVID-19 based on their clinical symptoms. doi = 10.1016/j.jiac.2020.09.027 id = cord-291954-wormplcu author = Sakulkonkij, Parichart title = A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date = 2020-08-08 keywords = COVID-19; PCR; SARS summary = A novel betacoronavirus, the seventh member of coronaviruses, which is shown to infect humans and lately named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an ongoing outbreak of respiratory illness that began in December 2019 in China called coronavirus disease 2019 . On admission, a nasopharyngeal and throat swabs for SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) revealed a positive result, other laboratory findings included white blood cell count (WBC) 2480 cells/mm 3 , lymphocyte (L) 18%, neutrophil (N) 78%, and C-reactive protein (CRP) 62.7 mg/L. Although acute hypoxemic respiratory failure from COVID-19 in elderly and KT recipients in our cohort seemed to be prominent, early investigation in high-risk populations, prompt initiation of potential therapy, and intensive supportive care are important to prevent adverse consequences and mortality. Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? doi = 10.1002/iid3.337 id = cord-312401-y1tat1bf author = Sakurai, Aki title = Natural History of Asymptomatic SARS-CoV-2 Infection date = 2020-06-12 keywords = SARS summary = On February 1, a passenger from Hong Kong, who traveled for 5 days from Yokohama and left the ship at Hong Kong on January 25, tested positive for SARS-CoV-2. Ten of 31 symptomatic passengers, crew and their cabinmates tested positive for SARS-CoV-2 on February 5, when the quarantine was implemented off the coast. Given the circumstances, a decision was made to accommodate some of the asymptomatic SARS-CoV-2 confirmed cases, both passengers and crew as well as their cabinmates who tested negative on the ship, at this hospital to continue their isolation and observation off the ship. Asymptomatic confirmed cases were cohorted on two floors, while their cabinmates who tested positive on the ship were isolated in private rooms on a separate floor to prevent further transmission. If the test was positive, they were cohorted with asymptomatic SARS-CoV-2 confirmed cases. doi = 10.1056/nejmc2013020 id = cord-337089-ksh62ni0 author = Salajegheh Tazerji, Sina title = Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review date = 2020-09-21 keywords = COVID-19; CoV-2; MERS; SARS summary = In addition to the considerable COVID-19 cases, hospitalizations, and deaths in humans, several cases of SARS-CoV-2 infections in animal hosts (dog, cat, tiger, lion, and mink) have been reported. Therefore, this study aimed to gather information about the reported cases of COVID-19 transmission in animals through a literary review of works published in scientific journals and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. However, based on recently published findings, other authors hypothesized that an immunological cross-protection between SARS-CoV-2 and canine respiratory coronavirus (CRCoV) exists due to the high homology between the spike protein epitopes of the two taxonomicallyrelated coronaviruses [21] . The objective of the present study was to gather, present, and discuss information on the reported cases of COVID-19 in animals focusing on the virus transmission cases in pets and perform genomic and phylogenetic analyses of SARS-CoV-2 isolated from animal hosts. doi = 10.1186/s12967-020-02534-2 id = cord-335652-v98gv5uf author = Salazar, Cecilia title = Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date = 2020-05-10 keywords = CoV-2; SARS; Uruguay summary = Methods We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16th to 19th) of COVID-19 outbreak in Uruguay. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region. This global health emergency has deployed international efforts to apply genomic epidemiology to track the spread of SARS-CoV-2 in real time. The recent development of targeted sequencing protocols by the ARTIC Network [3] , open sharing of genomic data through the GISAID (www.gisaid.org) database and straightforward bioinformatic tools for viral phylogenomics [4] , provides the opportunity to reconstruct global spatio-temporal dynamics of the COVID-19 pandemic with unprecedented comprehensiveness and resolution. We therefore aimed to characterize the spatio-temporal dynamics of SARS-CoV-2 by sequencing around 10% of cases occurred during the first week of outbreak in Montevideo, allowing us to identify transmission patterns, geographic origins and genetic variation among local strains. doi = 10.1101/2020.05.09.086223 id = cord-321784-nubu5fuz author = Salazar, E. title = Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas date = 2020-05-13 keywords = SARS; covid-19; patient summary = Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. 22 We performed the present study to provide additional data on these initial clinical observations of patients'' clinical course and subsequent improvement after receiving convalescent plasma therapy for COVID-19. Although our study has limitations, the data indicate that transfusion of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Our study was performed to evaluate the safety and potential benefit of transfusing convalescent plasma to patients with severe COVID-19 disease. Outcomes from this case series of 25 patients indicates that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. doi = 10.1101/2020.05.08.20095471 id = cord-343333-4krrmjio author = Salazar, Martín title = COVID-19, Hipertensión y Enfermedad cardiovascular date = 2020-06-18 keywords = COVID-19; SARS summary = Las comunicaciones provenientes de China en el inicio de la pandemia de COVID-19 mostraron una marcada asociación de los casos severos y la mortalidad con la edad avanzada, la hipertensión arterial, las enfermedades cardiovasculares y la diabetes. Las estimaciones de China coinciden con estos datos: que mientras la mortalidad sin comorbilidades fue de 0,9%, se incrementó a 10,5% con enfermedad Page 4 of 13 J o u r n a l P r e -p r o o f 4 cardiovascular, 6,3% con enfermedad pulmonar obstructiva crónica, 6% con hipertensión arterial y 5,6% con cáncer. En el reporte Morbidity and Mortality Weekly Report (MMWR), con datos al 28 de marzo, 78% de los pacientes internados en terapia intensiva por COVID-19 tenían comorbilidades, las más frecuentes eran la enfermedad cardiovascular (29%) y la enfermedad pulmonar crónica (21%). peor evolución del COVID-19, encontrando que la prevalencia de esta patología entre quienes fallecen o requieren cuidados críticos debido a la infección por SARS-CoV-2 es elevada, rondando entre un 7,5 y 39,5%, según los distintos reportes. doi = 10.1016/j.hipert.2020.06.003 id = cord-297832-picpuzvo author = Salazar, Rafael title = Decreased Mortality in Patients With Severe Bronchospasm Associated With SARS-CoV-2: An Alternative to Invasive Mechanical Ventilation date = 2020-10-06 keywords = SARS; patient summary = The number of patients with acute episodes of severe bronchospasm needing intubation and ventilatory support has increased rapidly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus disease 2019 (COVID-19) pandemic. Anteroposterior chest X-ray at the time of acute bronchospasm with Radiographic Assessment of Lung Edema (RALE) score 2 The initial management comprised placing the patient in the prone position and administering oxygen at high flow through a non-rebreather mask with flow between 10 and 15 liters per minute until reaching 100% FiO 2 . To improve ventilatory mechanics and ultimately postpone the need for IMV due to acute bronchospasm in patients diagnosed with COVID-19, we put in place a therapeutic approach consisting of early respiratory therapy and pharmacological bronchospasm rescue approach. The therapeutic bundle of early respiratory therapy, consisting of deep inspiration with inspiratory hold, and pharmacological bronchospasm rescue decreased the need for invasive mechanical ventilation in patients with bronchospasm associated with SARS-CoV-2 and reduced the mortality rate. doi = 10.7759/cureus.10822 id = cord-259925-g28sx9qu author = Saleemi, Mansab Ali title = Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date = 2020-10-06 keywords = CD4; HIV; SARS summary = The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. Up to date, it is unclear how SARS-CoV-2 interacts with the host antiviral immunity, hence lessons can be learned from previous studies of other members of the coronavirus family and also human pathogenic viruses, such as human immunodeficiency viruses and severe acute respiratory syndrome (SARS) CoV known as human CoVs (HCoVs) due to their ability to cause human infections (Andersen et al., 2020) . doi = 10.1016/j.meegid.2020.104583 id = cord-332595-874tpi09 author = Salehi, Najmeh title = Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients date = 2020-09-08 keywords = CoV-2; SARS summary = To this purpose, SARS-CoV-2 full genome sequence profiling of 20 patients in Iran and different countries that already had a travel history to Iran or contacts with Iranian cases were provided from the GISAID database. The bioinformatics analysis showed 44 different nucleotide mutations that caused 26 nonsynonymous mutations in protein sequences with regard to the reference full genome of the SARS-CoV-2 sequence (NC_045512.2). On the other hand, nineteen sequences of the full genome sequence of SARS-CoV-2 on the GISAID database from patients in different countries that had a travel history to Iran or contacts with Iranian cases were retrieved from the database. In this study, the full genome sequences of SARS-CoV-2 from the 20 Iranian related COVID-19 patients were profiled in detail. B. The nucleotide and protein mutations, the number of mutation events in data from the 20 Iranian related patients, the entropy values of these mutations in all 3927 SARS-CoV-2 sequences, and the corresponded proteins are depicted. doi = 10.22074/cellj.2020.7524 id = cord-338543-q6cl5kjp author = Salguero, Francisco J. title = Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date = 2020-09-17 keywords = SARS summary = Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Throat swabs from cynomolgus macaques contained 147 higher levels of viral RNA early in infection (one to three dpc) and remained ≥4.5 x 148 10 4 copies/ml for all animals between four and nine dpc. However viral RNA 159 levels above the LLOQ were detected at both three dpc and five dpc in cynomolgus 160 macaques in comparison to two dpc and three dpc in rhesus macaques ( Figure 2D ). doi = 10.1101/2020.09.17.301093 id = cord-346299-2s9j01q7 author = Salim Khan, S Muhammad title = Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date = 2020-09-04 keywords = District; SARS summary = title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar. 65 Besides, assuming that antibodies provide partial or total immunity, seroprevalence surveys give Here, we present the results of a cross-sectional seroprevalence study in District Srinagar, 70 conducted between 1 st and 15 th July 2020, to estimate the prevalence of IgG antibodies against 71 SARS-CoV-2 among adults using a sensitive and specific chemiluminescent microparticle 72 immunoassay (CMIA)-based test. 156 We estimated the number of infections till two weeks before the study period, i.e., 15 th June 2020 157 to 30 th June 2020, by applying the age-and gender-specific seroprevalence rates found in the Table) . doi = 10.1101/2020.09.04.282640 id = cord-294427-6eiligyy author = Salimi, Ali title = The North American Layman''s Understanding of COVID-19: Are We Doing Enough? date = 2020-07-03 keywords = Americans; COVID-19; SARS summary = Methods: In this cross-sectional observational study, an online survey targeted to North Americans focused on the public''s knowledge of COVID-19, risk perception, and precautionary behaviors taken in response to this pandemic. The results of this study highlight that this relatively young and educated sample of North Americans had a high level of knowledge about COVID-19 and a large proportion of them were taking the precautionary measures against this pandemic. To that end, this study aimed to compare and contrast the level of knowledge, risk perception, and precautionary measures taken in response to COVID-19, between populations of the United States of America (US) and Canada. To date, the US has reported the highest rate of COVID-19 positive cases in the world and therefore, by understanding the public''s attitude and risk perception toward the current pandemic, we hope to provide valuable information to help develop adequate populationtailored communication protocols that are effective in disease prevention and containment. doi = 10.3389/fpubh.2020.00358 id = cord-273451-xnce010o author = Salisbury-Afshar, Elizabeth M. title = Vulnerable Populations: Weathering the Pandemic Storm date = 2020-04-22 keywords = CoV-2; SARS summary = Yet, even with awareness that all individuals deserve access to services, and that supporting marginalized populations will slow the spread of SARS-CoV-2, resource limitations will demand difficult allocation determinations. 3 Many individuals experiencing homelessness with SARS-CoV-2 will not meet hospitalization criteria and will be discharged into the general population. 11 In response to SARS-CoV-2, the Substance Abuse and Mental Health Services Administration has developed emergency regulations to support medication for opioid use disorder via telehealth, 12 and temporarily waived the requirement for in-person physical exam to be able to initiate buprenorphine. These often forgotten populations-people incarcerated, homeless, or using drugs-are likely to experience higher risk of exposure to SARS-CoV-2 because of their social circumstances. Planning should incorporate dedicated efforts, funding, and policies/guidelines specific to individuals who experience homelessness, are incarcerated, or are coping with substance use disorders both because these populations deserve care and services, and because not doing so poses great risk to the broader community. doi = 10.1016/j.amepre.2020.04.002 id = cord-255872-e2b7ox6b author = Sallam, M. title = Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study date = 2020-08-25 keywords = August; MENA; SARS; d614 summary = This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Similar to other RNA viruses, SARS-CoV-2 can be the subject of phylogenetic analysis due to its high evolutionary rate, and the application of molecular clock analysis might be of value to determine the timing of introductions of large clusters that imply networks of transmission (Duffy et al., 2008; Forster et al., 2020; Pybus and Rambaut, 2009 ). The total number of MENA SARS-CoV-2 S gene sequences that were included in final analysis was 553, distributed as follows: Oman (n=159), KSA (n=140), Egypt (Table 1) . Phylogenetic analysis of the MENA S gene SARS-CoV-2 sequences showed a relatively low level of phylogenetic clustering (15%), which hints to a large number of virus introductions into the region. doi = 10.1101/2020.08.24.20176792 id = cord-267134-5gz2dotn author = Sallenave, Jean-Michel title = Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date = 2020-05-28 keywords = ACE2; CoV; SARS; cell; virus summary = The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus doi = 10.3389/fimmu.2020.01229 id = cord-025119-201ac32t author = Salman, Saad title = Virtual screening of immunomodulatory medicinal compounds as promising anti-SARS-COV-2 inhibitors date = 2020-05-21 keywords = COV-2; SARS; compound summary = Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Here, we analyzed different medicinal compounds using a virtual screening method to obtain promising inhibitors for these viral proteins that could be further utilized for SARS-COV-2 treatment. More than 300 medicinal compounds with immunomodulatory and antiviral activity were added to the Raccoon2 plugin of Autodock vina to perform virtual screening to obtain promising inhibitors for SARS-COV-2 proteins. This study aimed to obtain novel drug candidates that have the capability to interact with the active site of all of these viral proteins and should possess efficient pharmacokinetic profile with low toxicity to ensure safety during administration. • Docking interaction of immunomodulatory medicinal compounds library filtered six promising medicinal compounds against severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) viral proteins. doi = 10.2217/fvl-2020-0079 id = cord-033333-880jx1bt author = Salman, Saad title = In silico analysis of protein/peptide-based inhalers against SARS-CoV-2 date = 2020-10-08 keywords = SARS; protein summary = The molecular docking was performed for these inhalers including human neutralizing S230 light chain-antibody (monoclonal antibodies [mAbs]), alpha-1-antitrypsin (AAT), short-palate-lung and nasal-epithelial clone-1-derived peptides (SPLUNC1) and dornase-alfa (DA) against spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to assess their inhibitory activity. Protein-protein interaction (PPI) of COVID-19 spike glycoprotein with alpha-1-antitrypsin (1atu), dornase-alfa (4AWN), angiotensin-converting enzyme-2 (ACE-2) (PDB ID:1R4L), human palate, lung and nasal epithelium clone protein (SPLUNC1) (4n4x) and human neutralizing the S230 light chain antibody was evaluated through HawkDock. We attempted to address this issue by analyzing a variety of protein/peptide-based inhalers/antimucolytic agents and previously utilized mAb (used in asthma) to observe their possible interaction with the SARS-CoV-2 spike protein. • Molecular docking analysis of protein/peptide-based inhalers revealed that the S230 light chain antibody and dornase-alfa demonstrated a strong affinity for SARS-CoV-2 spike protein. doi = 10.2217/fvl-2020-0119 id = cord-319408-841c0g1c author = Salvatore, Christine M title = Neonatal management and outcomes during the COVID-19 pandemic: an observation cohort study date = 2020-07-23 keywords = COVID-19; SARS; neonate summary = [8] [9] [10] [11] [12] [13] [14] We aimed to follow up neonates born to mothers positive for SARS-CoV-2 at time of delivery, to elucidate best practices regarding infection control and identify potential risk factors associated with transmission. For this observational cohort study, we identified all neonates born between March 22 and May 17, 2020, at New York Presbyterian-Komansky Children''s Hospital, Weill Cornell Medicine, New York Presbyterian-Lower Manhattan Hospital, and New York Presbyterian-Queens in New York City to mothers who tested positive for SARS-CoV-2 from a nasopharyngeal swab sample at the time of delivery. Data collected included demographics, neonatal and maternal clinical presentation at time of delivery, during hospit alisation, and once discharged, microbiology results (SARS-CoV-2 rtPCR testing), and infection control practices in the hospital and at home. doi = 10.1016/s2352-4642(20)30235-2 id = cord-277410-lt19mijb author = Salvatore, Phillip P title = Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date = 2020-09-28 keywords = SARS summary = METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). Given the paucity of data examining associations of these factors with Ct value at the time of diagnosis, we sought to identify relationships between Ct values and time since onset, demographic factors, and symptoms among laboratory-confirmed COVID-19 cases identified in a multistate investigation of SARS-CoV-2 household transmission. Cycle threshold (Ct) values for SARS-CoV-2 rRT-PCR target probes N1 and N2 are plotted against the time elapsed between symptom onset and NP specimen collection in panel 1A. doi = 10.1093/cid/ciaa1469 id = cord-340049-6rqmc89u author = Salvatori, Giovanni title = SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines date = 2020-06-03 keywords = CoV-2; SARS summary = Evidence of the key role played by the S protein in counteracting coronavirus infection came from studies on human-neutralizing antibodies from rare memory B cells of individuals infected with SARS-CoV [2] or MERS-CoV [3] . Journal of Translational Medicine antibody responses, and vigorously neutralized SARS-CoV-2 S-mediated entry into cells, thus further encouraging the use of this molecular target for vaccination and immunotherapies [4] . Given the above and that the coronavirus S glycoprotein is surface-exposed and mediates entry into host cells by interacting with angiotensin-converting enzyme 2 (ACE2), it rapidly became the main target of neutralizing antibodies and the focus of therapeutic and vaccine design. Several companies and research institutes have started developing a vaccine that has the SARS-CoV-2 protein S as its target (see Table 1 ), although the various vaccination strategies show a differing ability to induce in the host both an antibody-mediated humoral response and a cell response mediated by CD4 or CD8 T lymphocytes in preclinical models. doi = 10.1186/s12967-020-02392-y id = cord-343919-n8884bli author = Salvio, Gianmaria title = Bone Metabolism in SARS-CoV-2 Disease: Possible Osteoimmunology and Gender Implications date = 2020-09-01 keywords = COVID-19; RANKL; SARS summary = We present a brief review of the molecular mechanisms linking inflammatory diseases to increased fracture risk/osteoporosis and of the therapeutic strategies that can prevent bone resorption in patients with inflammatory disease, focusing on the RANK-RANKL system. A subsequent in vitro study showed that a specific SARS-CoV protein, 3a/X1, directly promotes osteoclastogenesis, accelerating osteoclast differentiation from monocyte/macrophage precursors, enhancing the expression of receptor activator of NF-kB ligand (RANKL) and inflammatory cytokines such as TNF-α, which indirectly promote osteoclastogenesis [20] . As will be explained later in the text, IL-6 represents an important cofactor for bone resorption in inflammatory diseases; therefore, during SARS-CoV-2 infection, men, though less affected by osteoporosis, may experience more bone metabolism alterations than women for higher levels of IL-6 resulting from the lack of suppression by estrogen. doi = 10.1007/s12018-020-09274-3 id = cord-311429-adcmgd1i author = Salzberger, B. title = Epidemiologie von SARS-CoV-2/COVID 19: Aktueller Stand date = 2020-10-29 keywords = Infektionen; SARS; der summary = Die Basisreproduktionszahl R0 (Mittelwert der Zahl von Personen, die von Tab. 1 Kennzahlen der Epidemiologie von SARS("severe acute respiratory syndrome")-CoV("coronavirus")-2 Die Altersverteilung kann sich über die Zeit ändern, in Deutschland ist ein deutlicher Trend zu sehen: Infektionen nach Mai treten überwiegend bei jüngeren auf, die Infektionsraten bei diesen Gruppen sind in der Periode nach der ersten Welle höher als in der ersten Periode (. Der Anteil der Infektionen bei Personen des medizinischen Personals lag in China bei 2,7 %, in Italien bei 11,1 % und in Deutschland bei 5,8 % [9, 18, 27] . Die Ausbreitung lag bei den genannten Influenzapandemien zwischen 9 und 40 % der Gesamtbevölkerung -eine starke Motivation zur effektiven Kontrolle der SARS-CoV-2-Infektion. SARS-CoV-2 hat sich nach dem ersten Ausbruch in Wuhan rasch international verbreitet, und eine Verbreitung und eine Übertragung sind auf allen Kontinenten zu verzeichnen. doi = 10.1007/s11377-020-00479-y id = cord-324963-zg3ghl2m author = Salzberger, B. title = COVID-19 – eine neue und vielseitige Herausforderung date = 2020-08-03 keywords = SARS; die summary = Affinität zum ACE2-Rezeptor kann die Infektion in den oberen Atemwegen stattfinden Das Virus ist ein neues β-Coronavirus, das vermutlich von Fledermäusen auf eine noch unbekannte Säugerspezies übergesprungen ist. Es bindet wie SARS-CoV an den Angiotensinconverting-enzyme-2(ACE2)-Rezeptor, aber mit einer sehr viel höheren Affinität, sodass die Infektion in den oberen Atemwegen stattfinden kann. In einer ersten großen genomweiten Studie konnten einige genetische Faktoren als Risiken identifiziert werden, für eine individuelle Risikoabschätzung sind alle diese Daten jedoch noch nicht geeignet [5] . Die schweren Krankheitsverläufe einer Infektionskrankheit mit der realen Gefahr nosokomialer Infektionen konnten spezialisierte Infektions-oder Intensivmediziner nicht allein behandeln, es waren breit interdisziplinäre Teams im Einsatz, die von der Diagnostik über die Therapie bis zu Isolations-und Quarantänestrategien ein breites Portfolio von klinischen und organisatorischen Aufgaben lösten. Immunmodulatorische Therapien sind bisher kaum systematisch evaluiert worden, in einer randomisierten Studie aus Großbritannien konnte gerade erstmals gezeigt werden, dass Dexamethason bei schwer verlaufender COVID-19-Erkrankung die Prognose verbessert [9] . Epidemiologie von SARS-CoV-2-Infektion und COVID-19 doi = 10.1007/s00108-020-00851-8 id = cord-353092-4hz2yyl5 author = Sama, Iziah E title = Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin–angiotensin–aldosterone inhibitors date = 2020-05-14 keywords = ACE2; SARS summary = CONCLUSION: In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. We therefore investigated plasma concentrations of ACE2 in two large and independent cohorts of men and women with heart failure according to the use of RAAS inhibitors. In two large independent cohorts of patients with heart failure, we found that plasma ACE2 concentrations were higher in men than in women. In two large cohorts of patients with heart failure, plasma ACE2 concentrations were higher in men than in women, possibly reflecting higher tissue expression of this receptor for SARS coronavirus infections. doi = 10.1093/eurheartj/ehaa373 id = cord-328557-f6o1aynz author = Samad, Abdus title = Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach date = 2020-07-17 keywords = CTL; SARS; figure; vaccine summary = So, targeting S-protein can provide an immunogenic response in the human host, and has been chosen for designing a multi-epitopes vaccine candidate against the SARS-CoV-2. For the prediction of CTLs epitope, the sequence of the selected protein was submitted into the NetCTL v1.2 server available at http://www.cbs.dtu. For this purpose, we submitted the refined vaccine model as ligand and TLR4 protein as immunological receptor into the ClusPro v2.0 server, available at https://cluspro.bu.edu/, for molecular docking (Kozakov et al., 2017) . Due to the high number of potential epitopes, we selected the top four CTL epitopes for the final vaccine construction based on the antigenicity score (Table 1) . Likewise, we considered the top four HTL epitopes for incorporating into the final vaccine construct based on the antigenic score (Table 2) . In this study, we designed an epitope-based vaccine that could provide a strong immune response against SARS-CoV-2, thereby, preventing the COVID-19 pandemic. doi = 10.1080/07391102.2020.1792347 id = cord-313684-61hkogdh author = Samaddar, Arghadip title = Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date = 2020-09-17 keywords = COVID-19; IFN; MERS; RNA; SARS; cell; patient; treatment summary = Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. doi = 10.3389/fphar.2020.585888 id = cord-334550-xb0alubj author = Samaddar, Arghadip title = The Enigma of Low COVID-19 Fatality Rate in India date = 2020-07-28 keywords = BCG; CoV-2; SARS; covid-19; indian summary = These include some ongoing mutations that can alter the virulence of the circulating SARS-CoV-2 strains, host factors like innate immunity, genetic diversity in immune responses, epigenetic factors, genetic polymorphisms of ACE2 receptors, micro RNAs and universal BCG vaccination, and environmental factors like high temperature and humidity which may alter the viability and transmissibility of the strain. Researchers from Translational Bioinformatics Group at International Center for Genetic Engineering and Biotechnology (ICGEB) in collaboration with the Department of Biochemistry, Jamia Hamdard, New Delhi, India, performed an integrated mutational analysis of SARS-CoV-2 genomes from different geographical locations, including India, Italy, United States, Nepal and Wuhan, and observed a novel mutation in S protein (A930V, 24351C>T) of the Indian strain, which was absent in other strains (Sardar et al., 2020) . While this apparent protection among Indians is largely attributed to non-heritable influences as discussed earlier, a safe and effective vaccine against SARS-CoV-2 can reduce disease severity, control transmission, and prevent future infections across all populations. doi = 10.3389/fgene.2020.00854 id = cord-026792-jsqa4pmu author = Samanta, Jayanta title = 2019 Novel Coronavirus Infection: Gastrointestinal Manifestations date = 2020-05-16 keywords = IBD; SARS; covid-19 summary = The modern world is facing a major public health crisis due to novel corona virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) which has caused a pandemic involving at least 210 countries. The extrapulmonary effects and modes of transmission gained attention when the first confirmed case of SARS-CoV-2 reported from the United States had gastrointestinal (GI) complaints of nausea and vomiting followed later by diarrhea and patient''s fecal specimen tested positive on day 7 of illness. This review aims to comprehensively outline the GI manifestations of this virus, its potential to spread via the feco-oral route and its implications and an overview of management strategies for other GI diseases, such as inflammatory bowel disease (IBD) coexisting with coronavirus-19 disease (COVID-19) infection. doi = 10.1055/s-0040-1712077 id = cord-297693-lqyc49t6 author = Samec, Matthew J title = 80-year-old man with dyspnoea and bilateral groundglass infiltrates: an elusive case of COVID-19 date = 2020-05-27 keywords = COVID-19; SARS summary = COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. COVID-19 is a novel viral infection caused by severe acute respiratory syndrome-coronavirus-2 virus, first identified in Wuhan, China in December 2019. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a ''crazy paving'' pattern on chest CT imaging and a negative initial infectious workup. We present a case of a patient with minimal respiratory symptoms but prominent bilateral groundglass opacities in a ''crazy paving'' pattern on chest CT imaging and a negative initial infectious workup. The case was reviewed with the institutional infection prevention and control team who recommended repeating SARS-CoV-2 PCR 48 hours from the initial test. 14 There have been three published case reports of initially negative COVID-19 PCR tests in patients subsequently new disease determined to have COVID-19 infection. doi = 10.1136/bcr-2020-236069 id = cord-259229-e8m8m4ut author = Samidurai, Arun title = Cardiovascular Complications Associated with COVID-19 and Potential Therapeutic Strategies date = 2020-09-16 keywords = ACE2; COVID-19; China; CoV-2; Coronavirus; SARS; Wuhan; patient summary = Emerging evidence reveals a direct interplay between COVID-19 and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. Respiratory illness and acute cardiac injury are major clinical manifestations observed in patients infected with SARS-CoV-2 during the late stage complications of the disease [38] . Based on the available clinical data, potential myocardial injury is a relevant challenge among hospitalized patients with COVID-19 with increased risk of mortality; therefore, it is essential for multidisciplinary assessment, including blood pressure control in hypertensive patients as well as cardiovascular evaluation and therapy to reduce the morality for COVID-19 infection. Association of Renin-Angiotensin System Inhibitors With Severity or Risk of Death in Patients with Hypertension Hospitalized for Coronavirus Disease 2019 (COVID-19) Infection in Wuhan, China doi = 10.3390/ijms21186790 id = cord-326929-ytix4l1o author = Samillan, V. J. title = Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru date = 2020-09-18 keywords = Peru; SARS; case summary = In this study, we explored the relationship between the cumulative number of infections and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection and mortality of SARS-CoV-2 in Peru. Although more studies are necessary, the rate of infection and the severity of the diseases seems different for people living in cities at high altitudes, where not only hipoxia is a major factor, but other factors such as air quality, solar radiation, and population density, could play a role in SARS-CoV-2 person-to-person transmission. The main objectives of this study was to explore the relationship between SARS-CoV-2 infection and mortality cases, case-fatality rates with a set of climate (temperature, precipitation, solar radiation, water vapor pressure, and wind), environmental data (elevation, NDVI, PM 2.5 and NO 2 concentration), and population density in Peru. doi = 10.1101/2020.09.16.20196170 id = cord-333320-ndmmbckb author = Samore, M. title = SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample date = 2020-10-27 keywords = Government; October; SARS; USC summary = Probability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah. Although seroprevalence has been touted as a more standardized way to estimate the incidence of SaRS-COV-2 infection across different populations, it also presents challenges because of inconsistencies in test performance and sampling methods. Using a statistical sampling frame and adjusting for test performance and non-response, we estimated the prevalence of IgG antibody to SARS-CoV-2 in four urban counties in Utah between May and June to be only 0.8%. We used a serological test that is reported by the manufacturer to have a specificity at 99.6%; however, even at this level of accuracy, statistically accounting for false positives is necessary given the low population prevalence of IgG antibody to SARS-CoV-2. doi = 10.1101/2020.10.26.20219907 id = cord-261025-y49su5uc author = Sampathkumar, Priya title = SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date = 2003-07-31 keywords = Kong; SARS; patient; respiratory summary = Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.4065/78.7.882 id = cord-320964-1gg33gdn author = Sampieri, Clara Luz title = Revisión de nuevas evidencias acerca de la posible transmisión vertical de la COVID-19 date = 2020-06-20 keywords = COVID-19; SARS summary = En el contexto de la pandemia por COVID-19 se ha generado nueva evidencia tras la publicación de la guía de la Organización Mundial de la Salud, el 13 de marzo de 2020 14 , por lo que efectuamos una revisión sistemática de la literatura en PubMed de estudios revisados por pares publicados entre el 27 de marzo y el 21 de mayo de 2020, enfocándonos en aquellos trabajos que incluyeran análisis de muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical y Se identificaron 107 registros, de los cuales dos condujeron a la misma referencia y uno indicó una ruta de acceso no válida. En los estudios incluidos se identificó la etapa en que la madre tuvo la confirmación de la infección por SARS-CoV-2 o el diagnóstico clínico de COVID-19, el pronóstico del binomio madre-hijo/a, los resultados del análisis de SARS-CoV-2 del bebé, y las muestras clínicas de líquido amniótico, placenta o membranas, sangre del cordón umbilical o leche humana. doi = 10.1016/j.gaceta.2020.06.005 id = cord-319920-vn5si7xm author = Sampogna, Gianluca title = Spinal cord dysfunction after COVID-19 infection date = 2020-09-30 keywords = COVID-19; SARS; SCD summary = INTRODUCTION: We observed individuals affected by spinal cord dysfunction (SCD) after coronavirus disease 2019 (COVID-19). Case 1, aged 69 years, experienced T10 AIS B paraplegia upon awakening due to spinal cord ischemia from T8 to conus medullaris, besides diffuse thromboses, 27 days after the onset of COVID-19 symptoms. Prior to SCD, all three individuals suffered from respiratory failure due to COVID-19, required mechanical ventilation, had cardiovascular risk factors, experienced lymphopenia, and received tocilizumab (TCZ). The aim of our report is to provide our initial experience with people experiencing SCD after COVID-19 in a referral USU in the Northern Italian region most affected by the SARS-CoV-2 infection. As a consequence of the neurotropic and neuro-invasive potential of this virus, it has been reported that 36.4% of patients with COVID-19 suffer from neurological complications, and up to 45.5% patients in case of severe SARS-CoV-2 infection [14] . doi = 10.1038/s41394-020-00341-x id = cord-313084-l7odplqg author = Sampson, Victoria title = Could there be a link between oral hygiene and the severity of SARS-CoV-2 infections? date = 2020-06-26 keywords = COVID-19; SARS; oral summary = The risk factors already identified for developing complications from a COVID-19 infection are age, gender and comorbidities such as diabetes, hypertension, obesity and cardiovascular disease. This paper investigates the potential link between SARS-CoV-2 and bacterial load, questioning whether bacteria may play a role in bacterial superinfections and complications such as pneumonia, acute respiratory distress syndrome and sepsis. 1 While COVID-19 has a viral origin, it is suspected that in severe cases, bacterial superinfections may contribute to causing complications such as pneumonia and acute respiratory distress syndrome (ARDS). 18 It is common for respiratory viral infections to predispose patients to bacterial superinfections, leading to increased disease severity and mortality; for example, during the influenza pandemic in 1918, where the primary cause of death was not from the virus itself but from bacterial superinfections. Bacteria present in patients with severe COVID-19 are associated with the oral cavity and improved oral hygiene may play a part in reducing the risk of complications. doi = 10.1038/s41415-020-1747-8 id = cord-289588-n61gz7pi author = Samudrala, Pavan Kumar title = Virology, pathogenesis, diagnosis and in-line treatment of COVID-19 date = 2020-07-17 keywords = COVID-19; CoV-2; Coronavirus; SARS summary = Literature reported a significant mutation in receptor binding sites and membrane proteins of the previous SARS-CoV to turned as SARS-CoV-2 virus, responsible for most dreadful pandemic COVID-19. As far as safety is a major concern, 424 Gilead Sciences announced phase III clinical trial of remdesivir to prove its safety and 425 efficacy in COVID-19 infection (Keown, 16 .03.2020). Epidemiology, causes, clinical manifestation and 687 diagnosis, prevention and control of coronavirus disease (COVID-19) during the early 688 outbreak period: a scoping review First known person-to-784 person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 785 the USA Clinical 803 features of patients infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 (COVID-19) Vaccine Development and Production: An 817 Severe acute respiratory 845 syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The 846 epidemic and the challenges Unique epidemiological and clinical features 949 of the emerging 2019 novel coronavirus pneumonia (COVID-19) implicate special control 950 measures doi = 10.1016/j.ejphar.2020.173375 id = cord-334425-6zrmavps author = SanJuan-Reyes, Sindy title = COVID-19 in the environment date = 2020-08-14 keywords = COVID-19; Goh; SARS summary = The WHO has named it COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV2). New studies provide information of the role of the environment in COVID-19 transmission process, mortality related to this infectious disease and the impact on human health. The following review aims to analyze information on the implications of COVID-19 infection on human health and the impact of its presence on the environment, from its transmission capacity and the role of air pollutants and climatological factors to reducing the air pollution during confinement. Until now, there are no specific pharmacological treatment or vaccines against COVID-19 infection 104 for potential therapy in humans, so extensive isolation measures and the use of disinfection products 105 have been implemented to reduce their transmission from person to person. First known person-to-person transmission of severe acute 593 respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA doi = 10.1016/j.chemosphere.2020.127973 id = cord-280172-6o1gqe8v author = Sanami, Samira title = Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date = 2020-07-15 keywords = HLA; SARS; vaccine summary = In this research, first, the CTL, HTL, and B-cell epitopes of the S protein were predicted using ProPred-1, ProPred, and ABCPred servers, respectively, and then were selected base on antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Next, the physicochemical properties of the construct were investigated, the 3D structure of the protein was predicted, and finally, its affinity to the MHC I and II molecules was investigated through docking, following that, was performed the molecular dynamics (MD) simulation of docking complexes. The antigenicity of the epitopes were calculated by VaxiJen v2.0 server (http://www.ddgpharmfac.net/vaxijen/VaxiJen/VaxiJen.html), which is based on the transformation of the protein sequences auto cross-covariance (ACC) into uniform vectors of main amino acid properties. selected N, M, and S proteins as the target antigen for the prediction of T and B-cell epitopes and designed a multi-epitope vaccine against SARS-CoV-2 [48] . doi = 10.1016/j.ijbiomac.2020.07.117 id = cord-146091-kpvxdhcu author = Sanchez-Lorenzo, Arturo title = Anomalous atmospheric circulation favored the spread of COVID-19 in Europe date = 2020-04-26 keywords = Europe; SARS; Spain summary = In this study we show that an unusual persistent anticyclonic situation prevailing in southwestern Europe during February 2020 (i.e. anomalously strong positive phase of the North Atlantic and Arctic Oscillations) could have resulted in favorable conditions, in terms of air temperature and humidity, in Italy and Spain for a quicker spread of the virus compared with the rest of the European countries. These results evidence that it seems plausible that the positive phase of the NAO, and the atmospheric conditions associated with it, provided optimal conditions for the spread of the COVID-19 in southern countries like Spain and Italy, where both the start and the most severe impacts of the outbreak in Europe were located. Taking into account these results, we claim that the major initial outbreaks of COVID-19 in Europe (i.e., Italy and Spain) may be favored by an anomalous atmospheric circulation pattern in February, characterized by a positive phase of the NAO and AO. doi = nan id = cord-283372-c20i99qa author = Sanchis-Gomar, Fabian title = Amiodarone in the COVID-19 Era: Treatment for Symptomatic Patients Only, or Drug to Prevent Infection? date = 2020-08-01 keywords = COVID-19; SARS; amiodarone summary = Amiodarone, one of the most widely prescribed antiarrhythmic drugs to treat both ventricular and supraventricular arrhythmias, has been identified as a candidate drug for use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We present the rationale of using amiodarone in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe coronavirus disease 2019 (COVID-19), based on current evidence. However, amiodarone is not free of secondary adverse effects, contraindications and interactions with other drugs, including the potential to cause pulmonary toxicity and fibrosis, thyroid disease, hepatic toxicity, increased creatine levels, QT interval prolongation, and bradyarrhythmia [9] . We present here the rationale for amiodarone use in the COVID-19 scenario, as well as whether or not amiodarone administration represents a potential strategy to prevent SARS-CoV-2 infection, rather than simply used to treat patients already symptomatic and/or with severe COVID-19, based on current evidence. doi = 10.1007/s40256-020-00429-7 id = cord-102920-z5q3wo7v author = Sang, Eric R. title = Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date = 2020-06-28 keywords = ACE2; Fig; RBD; SARS summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. Along with showing a broad susceptibility potential across mammalian species based on structural analysis [26] [27] [28] , our results further reveal that domestic animals including dogs, pigs, cattle and goats may evolve previously unexamined immunogenetic diversity to restrict SARS-CoV2 infections. In addition to structural analysis of simulated S-RBD-ACE2 interaction, we propose that several immunogenetic factors, including the evolution of S-binding-void ACE2 isoforms in some domestic animals, the species-specific IFN system, and epigenetic regulation of IFN-stimulated property of host ACE2 genes, contribute to the viral susceptibility and the development of COVID-19-like symptoms in certain animal species [15, 38, 39, 49] . doi = 10.1101/2020.06.27.174961 id = cord-265697-bbvlowyo author = Sang, Eric R. title = Integrate structural analysis, isoform diversity, and interferon-inductive propensity of ACE2 to predict SARS-CoV2 susceptibility in vertebrates date = 2020-08-31 keywords = ACE2; IFN; RBD; SARS summary = Previous reports using structural analysis of the viral spike protein (S) binding its cell receptor of angiotensin-converting enzyme 2 (ACE2), indicate a broad potential of SARS-CoV2 susceptibility in wild and particularly domestic animals. In addition to showing a broad susceptibility potential across mammalian species based on structural analysis, our results also reveal that domestic animals including dogs, pigs, cattle and goats may evolve ACE2-related immunogenetic diversity to restrict SARS-CoV2 infections. (C) We also detected several short ACE2 isoforms (underlined) in the domestic animals including dog, pig, goat and cattle, which have an N-terminal truncation spanning 10-13 key residues in the contacting network to S-RBD but keeping the enzyme active sites (indicated by Yellow triangles), thus resulting in little engagement by the viral S protein and predicting an unexpected evolutionary advantage for relieving potential COVID-19 risk caused by the viral engagement and functional distortion on the classical long ACE2 isoforms in these animal species. doi = 10.1016/j.heliyon.2020.e04818 id = cord-314679-lmfalzni author = Sangith, Nikhil title = Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions date = 2020-06-24 keywords = SARS summary = title: Unique Fibrinogen-binding motifs in the Nucleocapsid Phosphoprotein of SARS CoV-2: Potential Implications in Host-Pathogen Interactions This report describes the presence of two unique motifs in the SARS CoV-2 nucleocapsid phosphoprotein (N-protein) that can potentially interact with fibrinogen and possibly prothrombin. aureus)coagulase, Efb (Extracellular fibrinogen binding) and vWBP (von Willebrand factor Binding Protein), which are known to regulate the blood clotting cascade and the functions of host immune response. aureus proteins, the N-protein of this virus can mimic their functions, which may in turn play a crucial role in formation of blood clots in the host and help the virus evade host immune response. The role of the fibrinogen-binding motif of N-protein in formation of blood clots and 142 mimicking functions of Efb for pathogen survival in host will be investigated. Staphylococcus aureus secretes coagulase 187 and von Willebrand factor binding protein to modify the coagulation cascade and establish 188 host infections doi = 10.1016/j.mehy.2020.110030 id = cord-263292-qjfe2t9v author = Sansone, A. title = Addressing male sexual and reproductive health in the wake of COVID-19 outbreak date = 2020-07-13 keywords = COVID-19; SARS; patient summary = Despite being a trivial matter for patients in intensive care units (ICUs), erectile dysfunction (ED) is a likely consequence of COVID-19 for survivors, and considering the high transmissibility of the infection and the higher contagion rates among elderly men, a worrying phenomenon for a large part of affected patients. Testicular function in COVID-19 patients requires careful investigation for the unclear association with testosterone deficiency and the possible consequences for reproductive health. However, independently of whether testosterone is a friend or foe for COVID-19, it should be acknowledged that the testis is a target for SARS-CoV-2 and the possibility for long-lasting consequences on the endocrine function exists, even for recovered patients. Drugs such as β-blockers and antihypertensive agents, routinely used in COVID-19 patients, have the potential to impair sexual function [41] ; therefore, both the cardiovascular consequences and their treatment might ease progression from subclinical to a clinically overt ED [42, 43] . doi = 10.1007/s40618-020-01350-1 id = cord-350235-yoy3hj3j author = Sansonetti, Philippe J title = COVID‐19, chronicle of an expected pandemic date = 2020-05-04 keywords = SARS; disease; virus summary = Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. doi = 10.15252/emmm.202012463 id = cord-323424-86wh4u6l author = Santos, M. M. title = Survival and predictors of deaths of patients hospitalised due to COVID-19 from a retrospective and multicentre cohort study in Brazil date = 2020-09-07 keywords = COVID-19; SARS summary = The co-variables used to compare survival curves were socioeconomic factors (age, sex, race, education and area of residence), clinical signs and symptoms (fever, cough, sore throat, diarrhoea and vomiting), hospital variables (influenza-like outbreak, hospital-acquired infection, dyspnoea, respiratory distress, O 2 saturation <95%, intensive care unit (ICU) admission, ICU length of stay and X-ray result), chronic disease (heart disease, haematology, Down''s syndrome, liver disease, asthma, diabetes mellitus, neurological disease, pneumopathy, immunodepression, kidney disease and body mass index (BMI)), if the patient has had a flu vaccine, use of antiviral against influenza and what is the type of such antiviral. This multicentre retrospective cohort study of patients hospitalised with COVID-19 found important differences in survival times, as well as risk factors or protection for the death of patients in Brazilian hospitals. doi = 10.1017/s0950268820002034 id = cord-291363-re45w37d author = Sanville, Bradley title = A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date = 2020-03-30 keywords = SARS; case summary = title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . doi = 10.1093/cid/ciaa347 id = cord-269202-re2djjrc author = Sapino, Anna title = The autopsy debate during the COVID-19 emergency: the Italian experience date = 2020-04-29 keywords = COVID-19; SARS summary = "in patients dying with SARS-CoV-2 infection, the autopsies can confirm laboratory and radiological findings and can contribute to an accurate diagnosis and to a better understanding of mechanisms of the disease." In the meantime, the SIAPC Board accepted to collaborate with the Scientific Society of Hospital Forensic Medicine of the National Health System (COMLAS) to produce a joint document, which was available on the SIAPEC web site on March 22 [2] . In addition, in cases of autopsies without apparent SARS-CoV-2 infection, we recommend (i) to discuss with the clinicians the reason why the post-mortem examination is requested; (ii) and if available, to perform nasal-oropharyngeal swabs on corpses This article is part of the Topical Collection on Quality in Pathology * Mattia Barbareschi mattia.barbareschi@apss.tn.it within 2 h of death to assess the presence of SARS-CoV-2 infection to implement the safety measures [3] . doi = 10.1007/s00428-020-02828-2 id = cord-317707-r0q7ipa6 author = Saracco, Margherita title = Carrying on with Liver Transplantation during the COVID-19 emergency: Report from Piedmont Region date = 2020-08-07 keywords = COVID-19; SARS summary = We aimed to analyze the number of LT performed between February 24 th , 2020 and April 17 th , 2020 with the same period of time in 2019, in our high-volume transplant Center (median 150 LT/year). Furthermore, among the 5 intensive care units of our hospital, the one dedicated to transplants was maintained COVID-free, by testing each transplant recipient in advance with SARS-CoV-2 RNA in NPS or BAL, starting from the 22 nd of March. Between February 24 th , 2020 and April 17 th , 2020, among 22 admissions in our 7-bed sub-intensive liver unit, a 40-year-old woman, who was listed during hospitalization, developed fever during hospitalization and tested positive for SARS-CoV-2 RNA in NPSs. Immediately transferred to a COVID unit, she came back to our unit after 7 days and 2 negative SARS-CoV-2 RNA in NPS and underwent LT the day after readmission to our unit. Despite all our efforts to maintain a transplant COVID-free pathway, two transplant patients, one before and one after LT were tested SARS-CoV-2 virus positive during hospitalization and both were safely discharged home. doi = 10.1016/j.clinre.2020.07.017 id = cord-029167-bq6ogxyq author = Sarada, B. V. title = Fight Against COVID-19: ARCI’s Technologies for Disinfection date = 2020-07-14 keywords = ARCI; SARS; UVC summary = In this context, ARCI has quickly made efforts to develop disinfection systems including a UVC-based disinfection trolley, honeycomb air heater and a fogging chamber using UVC germicidal lamps, dry heat sterilization and HOCl-based chemical disinfectant to provide rapid and effective inactivation of microorganisms causing the pandemic. Though the virus survives as aerosols and on environmental surfaces for various durations of time, it can easily be inactivated by several types of physical and chemical disinfection methods (Mackenzie 2020) including UVC disinfection (Malayeri et al. Physical, dry heat and chemical disinfection methods have been developed by using UVC lamps, honeycomb air heater and HOCl fogging system, respectively. (MIL), has co-developed a UVC disinfection trolley to fight against COVID-19 by a simple physical process where rapid cleaning is possible within few minutes especially in hospital settings avoiding the use of harsh chemicals. doi = 10.1007/s41403-020-00153-3 id = cord-268795-tjmx6msm author = Sardar, Rahila title = Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date = 2020-03-21 keywords = SARS; genome summary = title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Our analysis shows unique host-miRNAs targeting SARS-CoV2 virus genes. CELLO2GO (7)server was used to infer biological function for each protein of SARS-CoV2 genome with their localization prediction. Assembled SARS-CoV2 genomes sequences in FASTA format from India, USA, China, Italy and Nepal used for coronavirus typing tool analysis. For the phylogenetic analysis, we compared the sequences of 6 SARS-CoV2 isolates from different countries namely, Wuhan, India, Italy, USA and Nepal along with other corona virus species ( Figure 1 ). doi = 10.1101/2020.03.21.001586 id = cord-354349-hbk2p6ej author = Sardar, Sundus title = COVID-19 and Plasmodium vivax malaria co-infection date = 2020-06-20 keywords = COVID-19; SARS summary = With its variety of clinical manifestations including, but not limited to, fever, cough, diarrhea, vomiting, headache, myalgia and fatigue, it may be challenging to distinguish COVID-19 from a spectrum of diseases with similar presentations, such as malaria, especially in endemic areas. The coronavirus infection 2019 (COVID-19), which is caused by SARS-CoV-2, emerged in Wuhan, China in December 2019 and has since reached pandemic proportions affecting more than 8 million cases worldwide with total deaths exceeding 400,000 [1] . SARS-CoV-2, COVID-19, malaria, Plasmodium vivax, co-infection, artesunate In this case, artesunate and artemether were initiated as the treatment regimen; whether these agents offered protective effects from respiratory deterioration or multi-organ involvement despite SARS-CoV-2 infection is unclear and should be further explored. Our case highlights the importance of identifying possible underlying secondary infections in concurrence with SARS-CoV-2, which may be otherwise overlooked amidst the challenges of the current unprecedented COVID-19 pandemic. doi = 10.1016/j.idcr.2020.e00879 id = cord-292416-3hhi4wps author = Sarid, Ronit title = Investigating an Emerging Virus During a Sudden Pandemic Outbreak date = 2020-07-31 keywords = RNA; SARS; viral; virus summary = Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. doi = 10.5041/rmmj.10414 id = cord-267666-i7uuf3ck author = Sarkar, Bishajit title = Engineering a Novel Subunit Vaccine against SARS-CoV-2 by Exploring Immunoformatics Approach date = 2020-11-11 keywords = SARS; epitope; vaccine summary = Therefore, in this study, immunoinformatics methods were exploited to design a novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. Thereafter, several in silico validations i.e., the molecular docking, molecular dynamics simulation (including the RMSF and RMSD studies), and immune simulation studies were also performed which predicted that the designed vaccine should be quite safe, effective, and stable within the biological environment. The MHC class-I and class-II epitopes were predicted from the target protein sequences for 503 constructing the vaccine. Exploring Leishmania secretory proteins 1232 to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach Immunoinformatics approaches 1236 to explore Helicobacter Pylori proteome (Virulence Factors) to design B and T cell multi-epitope 1237 subunit vaccine. Immunoinformatics-guided designing of 1405 epitope-based subunit vaccine against the SARS Coronavirus-2 (SARS-CoV-2) doi = 10.1016/j.imu.2020.100478 id = cord-102833-hh4641o0 author = Sarkis-Onofre, Rafael title = Decontamination of N95 respirators against SARS-CoV-2: a scoping review date = 2020-11-13 keywords = N95; SARS; decontamination summary = These masks are intended for single use and, based on the manufacturer''s instructions, they are heat sensitive and not designed to be sterilized; however, due to their high costs and limited availability [6, 13] , different methods to decontaminate N95 [5, 13, [15] [16] [17] [18] [19] respirators have been discussed to allow multiple usages. (2020) performed an in vitro study and compared the use of a high-level decontamination cabinet that generates aerosolized peracetic acid and hydrogen peroxide with ultraviolet C light and dry heat at 70 °C for 30 minutes. Decontamination and Reuse of N95 Respirators with Hydrogen Peroxide Vapor to Address Worldwide Personal Protective Equipment Shortages During the SARS-CoV-2 (COVID-19) Pandemic Decontamination and reuse of surgical masks and N95 filtering facepiece respirators during COVID-19 pandemic: a systematic review Decontamination of face masks and filtering facepiece respirators via ultraviolet germicidal irradiation, hydrogen peroxide vaporisation, and use of dry heat inactivates an infectious SARS-CoV-2 surrogate virus doi = 10.1016/j.jdent.2020.103534 id = cord-262149-qrjprsv5 author = Sarode, Gargi S. title = Clinical status determines the efficacy of salivary and nasopharyngeal samples for detection of SARS-CoV-2 date = 2020-10-12 keywords = SARS summary = To draw a meaningful conclusion in this regard, the most important study design would be a comparative cross-sectional analysis of salivary and nasopharyngeal samples (NPSs) in the detection of SARS-CoV-2 RNA with a cycle threshold value. (Table 1 ) All the studies projected saliva as potential sampling material for the detection and diagnosis of SARS-CoV-2 RNA using RT-PCR. In asymptomatic cases, the sensitivity and detection rate was more in salivary samples as compared to NPS [2, 7] . On the contrary, in asymptomatic cases, NPS could not be a representative sample (probably due to absent or limited viral localization) for the detection of SARS-CoV-2. Looking at this discriminative trend, prescription of saliva samples for asymptomatic cases and NPS for symptomatic cases would be a valuable recommendation subject to validation in future randomized prospective studies. A direct comparison of enhanced saliva to nasopharyngeal swab for the detection of SARS-CoV-2 in symptomatic patients doi = 10.1007/s00784-020-03630-9 id = cord-296392-2u9mz6d3 author = Sarıgül, Figen title = Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date = 2020-08-26 keywords = Diagnovital; PCR; SARS summary = title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic This value being higher than 0.73 coefficient obtained through comparison of RdRps of the two kits only, showed that inclusion of a secondary biomarker by Diagnovital improved the correlation of different kits. In this study, we investigated the compatibility between the two different SARS-CoV-2 PCR kits produced in Turkey during the COVID-19 pandemic. Nevertheless, the strong correlation of the two kit results suggested that two different RNA targeting gene assays were appropriate as suggested by WHO in the diagnosis of COVID-19 disease [20] . showed that similar results were found; the PCR kit with two different genes of the SARS-CoV-2 had a higher yield than the other two kits performing one gene analysis [21] . doi = 10.2217/fvl-2020-0169 id = cord-323839-a4oejky0 author = Sasaki, Michihito title = SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells date = 2020-08-28 keywords = SARS; Vero summary = These results indicated that S gene mutants are resistant to the 1 5 9 treatment with TMPRRSS2 inhibitors, but are sensitive to antivirals that target post entry In an effort to understand the selection mechanisms underlying the generation of these 1 6 4 mutant variants, we estimated the frequency of S gene mutants in virus population of 1 6 5 SARS-CoV-2 that had undergone serial passage in cultured cells. In contrast, nucleotide sequence 1 7 2 deletions around the S1/S2 cleavage site corresponding to del1 and del2 mutants were 1 7 3 observed in all three biological replicates of SARS-CoV-2 populations passaged in Vero 1 7 4 cells (Fig. 5a) . Moreover, we must be very objective when interpreting the results 2 3 0 from studies using Vero-passaged virus, especially those focused on S protein cleavage, Cells were infected with either WT or S mutants of SARS-CoV-2 at an MOI of 1. doi = 10.1101/2020.08.28.271163 id = cord-332207-dmxbk7ad author = Sastry, Sangeeta R. title = Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence date = 2020-07-23 keywords = SARS summary = title: Universal screening for the SARS-CoV-2 virus on hospital admission in an area with low COVID-19 prevalence In 2 New York City (NYC) hospitals, 13.7% of asymptomatic pregnant women admitted for delivery tested positive for SARS-CoV-2 virus. 3 Universal screening of healthcare populations may prevent in-hospital transmission of SARS-CoV-2 virus. Upon developing real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) tests in-house with >98% sensitivity, as well as increasing the availability of PPE at our institution, we initiated universal screening of patients on hospital admission using nasopharyngeal swabs to identify and isolate asymptomatic positive patients to prevent in-hospital transmission of SARS-CoV-2. On April 27, 2020, our 1,000-bed academic center instituted universal SARS-CoV-2 testing of patients on hospital admission. Universal screening for the detection of SARS-CoV-2 at our institution revealed that during the study period, the number of asymptomatic persons admitted to the hospital was relatively small. doi = 10.1017/ice.2020.358 id = cord-342786-dl8vjwfn author = Sattar, Yasar title = COVID-19 Cardiovascular Epidemiology, Cellular Pathogenesis, Clinical Manifestations and Management date = 2020-07-14 keywords = ACE-2; COVID-19; Disease; SARS; patient summary = Abstract Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. Coronavirus Disease 2019 (COVID-19) is a rapidly progressing global pandemic that may present with a variety of cardiac manifestations including, but not limited to, myocardial injury, myocardial infarction, arrhythmias, heart failure, cardiomyopathy, shock, thromboembolism, and cardiac arrest. The infected patients may also present with cardiovascular disease (CVD) like acute coronary syndrome(ACS) and congestive cardiac failure(CHF) [6] . The systemic inflammation in COVID-19 may also dysregulate the post-translational modification of cardiac ion channels resulting in arrhythmia [25, 26] It is also noteworthy that viral proteins of SARS-CoV-2, ORF3 and ORF8, activate NLRP3 inflammasomes which inturn promotes atrial fibrillation [27, 28] . doi = 10.1016/j.ijcha.2020.100589 id = cord-335958-dtvlo0kz author = Satyam, Rohit title = Deciphering the SSR incidences across viral members of Coronaviridae family date = 2020-09-21 keywords = Coronaviridae; SARS; SSR summary = Thus, the aims of the current study were 1) to analyze various facets of the distribution and dynamics of SSRs in the genomes of Coronaviridae members, 2) to identify patterns of SSR incidences across genomes, if any i.e the underrepresentation/overrepresentation of specific repeat motif classes, 3) the preferential genomic localization of SSRs & 4) to investigate if SSRs serves as mutation hotspots in SARS-CoV-2, a novel SARS strain causing COVID-19 outbreak. Additionally, the attributes of SSRs across genomes under study were quite similar in terms of length (preferentially found to be 12-13 nucleotides long with polyA repeats of varying lengths), GC composition, abundance (SSR frequency didn''t exceed 2 irrespective of genome size) and localization. The BED files (eg.sequence_perf_default.tsv) so produced by PERF comprise of SSRs genomic coordinates (Column 1-3) followed by repeat class, repeat Length, repeat Strand, motif Number & actual repeat (more details: https://github.com/RKMlab/perf) and were used for the downstream analysis. doi = 10.1016/j.cbi.2020.109226 id = cord-275438-drywzvx8 author = Satış, Hasan title = Prognostic value of interleukin-18 and its association with other inflammatory markers and disease severity in COVID-19 date = 2020-09-29 keywords = COVID-19; IL-18; IL-6; SARS summary = Serum IL-18 levels were remarkably higher in COVID-19 patients compared to healthy subjects with being highest in severe pneumonia group (p < 0.001). According to the disease course, COVID-19 patients may be roughly divided into two groups; asymptomatic or mild cases that usually recover and severe cases that develop multi organ failure, primarily respiratory failure, requiring intensive care unit (ICU) admission [5, 6] . In this study, we found that both IL-6 and serum IL-18 concentrations are remarkably increased in patients with COVID-19 and correlated with other inflammatory markers and disease severity. There are differences in cytokine production among COVID-19 patients, such as men are more susceptible to SARS-CoV-2 infection than women and children, in whom it could present as Kawasaki disease [29, 30] , as well as serum cytokine levels tend to be higher in men explaining their worse prognosis [29] . doi = 10.1016/j.cyto.2020.155302 id = cord-253472-3s142p6u author = Saurabh, Suman title = Author’s reply to correspondence regarding the article ‘Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals’ date = 2020-09-18 keywords = SARS summary = title: Author''s reply to correspondence regarding the article ''Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals'' 1 This is since 95% SARS-CoV-2 infected individuals (including both symptomatics and asymptomatics) were found to have virus persistence of up to 20.92 days. 1 Further, they go on to state that ''as per test-based strategy for asymptomatic patients, two respiratory specimens (≥ 24 hours apart) are required to be negative, irrespective of initial date of COVID-19 detection''. Test-based discharge is not practicable with an overwhelming number of SARS-CoV-2 infected individuals and a large proportion of them undergoing home isolation. Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards doi = 10.1093/qjmed/hcaa269 id = cord-015376-z739ifu5 author = Savarino, Andrea title = Potential therapies for coronaviruses date = 2006-08-31 keywords = ACE2; HIV-1; RNA; SARS; inhibitor summary = These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. doi = 10.1517/13543776.16.9.1269 id = cord-282384-qbcqbhk4 author = Savastano, Alfonso title = Peripapillary Retinal Vascular Involvement in Early Post-COVID-19 Patients date = 2020-09-08 keywords = RPCP; SARS; covid-19 summary = Furthermore, we performed an additional analysis within the post-COVID-19 group correlating the primary outcome measures with the other examined variables to detect potential risk factors for RPCP impairment in post SARS-CoV-2 patients. Spearman''s Test revealed a statistically significant linear correlation between RNFL average thickness and both RPCP perfusion density (p < 0.001) ( Figure 3 ) and RPCP flow index (p < 0.001) (Figure 4) within the post-COVID-19 group. Our study examined this aspect outlining the correlation of the RPCP perfusion density and RPCP flow index with the RNFL average thickness also in early post-COVID-19 patients. In this regard, it is interesting to notice that patients in the post-COVID-19 group showed a lower mean age, a lower prevalence of diabetes and systemic arterial hypertension, and a higher prevalence of females (typically affected by milder manifestations of the disease) compared to the reported SARS-CoV-2 epidemiologic data [38] . doi = 10.3390/jcm9092895 id = cord-279750-if9vphb2 author = Savić, Dragan title = Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report date = 2020-07-27 keywords = SARS; covid-19 summary = title: Ruptured cerebral pseudoaneurysm in an adolescent as an early onset of COVID-19 infection: case report We are presenting a case of a 13-year-old girl with a ruptured cerebral pseudoaneurysm of the left middle cerebral artery (M2 segment) with severe intracerebral hemorrhage as the earliest manifestation of COVID-19 infection. There are rare case reports of adult patients (the youngest was a 31-year-old male, other patients over 60 years old) with COVID-19 infection and ruptured cerebral aneurysm with subarachnoid hemorrhage [1, 16, 19] . In this paper, we present an adolescent girl with COVID-19 infection, who developed an intracerebral hematoma due to cerebral pseudoaneurysm rupture. As far as we know, this is the first reported case of an adolescent with ruptured cerebral pseudoaneurysm as the initial presentation of COVID-19 infection. As a consequence of the infection, a multisystem inflammatory syndrome or the direct damage by the virus has resulted in severe brain hemorrhage attributable to the ruptured pseudoaneurysm. doi = 10.1007/s00701-020-04510-7 id = cord-260077-xf4sofyc author = Sawalha, Amr H. title = Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients date = 2020-04-08 keywords = ACE2; SARS summary = title: Epigenetic dysregulation of ACE2 and interferon-regulated genes might suggest increased COVID-19 susceptibility and severity in lupus patients Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Oxidative stress induced by viral infections exacerbates the DNA methylation defect in lupus, possibly resulting in further ACE2 hypomethylation and enhanced viremia. Examining whole-genome DNA methylation data generated using an array-based approach, we observe significant hypomethylation in the ACE2 gene in this T cell subset compared to KIR − CD11a low T cells isolated from the same lupus patients (Fig. 1A) . Therefore, it is reasonable to suggest the possibility that the DNA methylation defect in lupus patients, exacerbated by oxidative stress generated from SARS-CoV-2 infection, will further enhance viral entry in lupus patients through epigenetic de-repression of ACE2 and increased ACE2 expression. doi = 10.1016/j.clim.2020.108410 id = cord-024133-zv0ysi8m author = Saxena, Shailendra K. title = Current Insight into the Novel Coronavirus Disease 2019 (COVID-19) date = 2020-04-30 keywords = COVID-19; CoV-2; SARS summary = doi = 10.1007/978-981-15-4814-7_1 id = cord-316003-xt59voyt author = Say, Daphne S. title = Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol date = 2020-03-31 keywords = SARS; patient summary = title: Risk Stratification and Personal Protective Equipment Use in Pediatric Endoscopy During the Coronavirus Disease 2019 Outbreak: A Single-center Protocol Endoscopists face risk for infection with viruses like SARS-CoV-2, as the aerosol generating nature of endoscopy diffuses respiratory disease that can be spread via an airborne and droplet route. It is unclear how much of the risk was related to community transmission or to breaches in use of personal protective equipment (PPE) during the care of patients with COVID-19. Given initial limitations in the availability of testing for SARS-CoV-2 infection, however, our institution''s current screening algorithm specifies testing only individuals with influenza-like illness and exposure to a patient with known COVID-19. If viral testing for SARS-CoV-2 infection is not available, patient risk stratification before endoscopy may be accomplished based on symptoms and sick contacts. At minimum, those in the pediatric endoscopy suite will require use of gloves, water-resistant gowns, surgical face masks, eye protection, and hair coverings for all endoscopic procedures. doi = 10.1097/mpg.0000000000002731 id = cord-332179-du1zjupf author = Sayed, Shomoita title = COVID-19 and Diabetes; possible role of polymorphism and rise of telemedicine date = 2020-08-31 keywords = ACE2; SARS; covid-19; t1d summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is facilitated by interaction with Angiotensin Converting Enzyme-2 (ACE2) and possible polymorphisms in ACE2 can be a determining factor in host-viral protein interaction. Another population study in England showed a 31.4% mortality rate for type 2 diabetes (T2D) patients suffering from COVID-19 infection [17] . So, increased viral entry via increased ACE2 expression and circulating proteases, lymphocytopenia and concurrent increase of inflammatory cytokines can exacerbate SARS-CoV-2 infection in patients with diabetes [23] . Diabetic patients on medication with abovementioned drugs with their elevated ACE2 expression can be susceptible to facilitated SARS-CoV-2 entry, leading to increased chances of disease severity. Whether the polymorphisms have more pronounced effects among diabetic patients with COVID-19 infection should be taken into consideration while exploring the possible role of viral entry in hosts. doi = 10.1016/j.pcd.2020.08.018 id = cord-339431-kyr5lv15 author = Saçar Demirci, Müşerref Duygu title = Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date = 2020-03-17 keywords = RNA; SARS summary = In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. doi = 10.1101/2020.03.15.992438 id = cord-266512-xh6zed03 author = Scala, Enrico title = Atopic statusprotects from severe complications of COVID‐19 date = 2020-08-16 keywords = SARS; patient summary = In infection, the Th2 response counteractsthe microbicidal Th1 response, which could limit the tissue damage induced by Th1-mediated inflammation (4) on one hand, but also cause a less efficient anti-virus response, as shown in a study on experimental Coronavirus 229E infection in healthy volunteers, where atopy appeared to be associated with a more severe rhinitis score (5) .Further, atopic subjects show a reduced expression of ACE2, the SARS-CoV-2 receptor, which could be associated with reduced susceptibility to the virus (6) . The multiple logistic regression analysis(details in supplementary material) confirmed a significant association between atopic status andmilder COVID-19;non-atopic patients had a significantly higher risk of having severe Covid-19 (OR adj 3.0, 95% CI 1.6-5.7, p =0.001) ( Table 1) In severe SARS-CoV-2 infection hyper-expressed cytokines include IFN-gamma, TNF-alpha, and IL-6, which cause fever, fatigue, flu-like symptoms, vascular leakage due to endothelial dysfunction, cardiomyopathy, hypotension, lung injury, activation of the coagulation cascade, and diffuse intravascular coagulation (7) . doi = 10.1111/all.14551 id = cord-313227-6zwkfzab author = Scala, Stefania title = Fighting the Host Reaction to SARS-COv-2 in Critically Ill Patients: The Possible Contribution of Off-Label Drugs date = 2020-05-27 keywords = IL-6; SARS; TNF; patient summary = Interestingly, in patients infected by SARS-COv-2, there is an increase in IL1β, IFNγ, IP10, and MCP1, probably leading to activated T-helper-1 (TH1) cell responses, and increased production of T-helper-2 (TH2) immunosuppressive cytokines, such as IL4 and IL10 (18) . Peripheral blood examinations on admission in the majority of patients with COVID-19 displayed lymphopenia, elevated infection-related biomarkers (i.e., procalcitonin, erythrocyte sedimentation rate, serum ferritin, and C-reactive protein) (20) and several elevated inflammatory cytokines (i.e., tumor necrosis factor (TNF)-α, interleukin (IL)-2R and IL-6). Despite markedly reducing virus titers, anti-S-IgG caused lung injury during the early stages of infection, impairing the wound-healing macrophage response and TGF-β production, while promoting pro inflammatory cytokine IL-8, MCP1 production, and inflammatory macrophage accumulation (22) . Another proteasome inhibitor, VR23, possess powerful antiinflammatory activity reducing IL-6 in synovial cells from RA patients, and improving LPS-induced acute lung injury by decreasing neutrophil migration, TNF-α secretion, and tissue inflammation in a mice model (52) . doi = 10.3389/fimmu.2020.01201 id = cord-252506-8u9oiqoc author = Scarfò, Lydia title = COVID-19 severity and mortality in patients with chronic lymphocytic leukemia: a joint study by ERIC, the European Research Initiative on CLL, and CLL Campus date = 2020-07-09 keywords = CLL; COVID-19; SARS; patient summary = authors: Scarfò, Lydia; Chatzikonstantinou, Thomas; Rigolin, Gian Matteo; Quaresmini, Giulia; Motta, Marina; Vitale, Candida; Garcia-Marco, Jose Antonio; Hernández-Rivas, José Ángel; Mirás, Fatima; Baile, Mónica; Marquet, Juan; Niemann, Carsten U.; Reda, Gianluigi; Munir, Talha; Gimeno, Eva; Marchetti, Monia; Quaglia, Francesca Maria; Varettoni, Marzia; Delgado, Julio; Iyengar, Sunil; Janssens, Ann; Marasca, Roberto; Ferrari, Angela; Cuéllar-García, Carolina; Itchaki, Gilad; Špaček, Martin; De Paoli, Lorenzo; Laurenti, Luca; Levin, Mark-David; Lista, Enrico; Mauro, Francesca R.; Šimkovič, Martin; Van Der Spek, Ellen; Vandenberghe, Elisabeth; Trentin, Livio; Wasik-Szczepanek, Ewa; Ruchlemer, Rosa; Bron, Dominique; De Paolis, Maria Rosaria; Del Poeta, Giovanni; Farina, Lucia; Foglietta, Myriam; Gentile, Massimo; Herishanu, Yair; Herold, Tobias; Jaksic, Ozren; Kater, Arnon P.; Kersting, Sabina; Malerba, Lara; Orsucci, Lorella; Popov, Viola Maria; Sportoletti, Paolo; Yassin, Mohamed; Pocali, Barbara; Barna, Gabor; Chiarenza, Annalisa; dos Santos, Gimena; Nikitin, Eugene; Andres, Martin; Dimou, Maria; Doubek, Michael; Enrico, Alicia; Hakobyan, Yervand; Kalashnikova, Olga; Ortiz Pareja, Macarena; Papaioannou, Maria; Rossi, Davide; Shah, Nimish; Shrestha, Amit; Stanca, Oana; Stavroyianni, Niki; Strugov, Vladimir; Tam, Constantine; Zdrenghea, Mihnea; Coscia, Marta; Stamatopoulos, Kostas; Rossi, Giuseppe; Rambaldi, Alessandro; Montserrat, Emili''; Foà, Robin; Cuneo, Antonio; Ghia, Paolo Of the 190 patients studied, four Spanish cases were previously published in extenso [12] , 47 patients were included in a report describing the impact of SARS-CoV-2 pandemic infection on the practical management of CLL in Italy with only limited clinical data [18] . doi = 10.1038/s41375-020-0959-x id = cord-351367-ral9sbfy author = Scarlattei, Maura title = Unknown SARS-CoV-2 pneumonia detected by PET/CT in patients with cancer date = 2020-06-22 keywords = PET; SARS summary = METHODS: We report 5 patients with unknown SARS-CoV-2 infection undergoing positron emission tomography (PET)/computed tomography (CT) with radiopharmaceuticals targeting different tumor processes: (18)F-FDG, (18)F-choline (FCH), and (68)Ga-PSMA. Correct management of a PET session presents many difficulties because of the coexistence of asymptomatic SARS-CoV-2 infection and patients with mild symptoms before the PET scan (https://www.sirm.org/2020/03/30/ covid-19-caso-69/), mostly not tested on RT-PCR, but variably presenting with chest CT findings compatible with pulmonary interstitial infiltrates, potentially associated with infection or drug-related reactions. In this study, we report 5 patients (Table 1) with unknown SARS-CoV-2 infection undergoing PET/CT scan for restaging breast and prostate cancer (patients 1, 3, 4), characterization of lung nodule (patient 2), and focal splenic lesions (patient 5). Recent case series about PET in patients with SARS-CoV-2 pneumonia showed high 18 F-FDG uptake in lung lesions accompanied by nodal involvement detectable on PET/CT images. doi = 10.1177/0300891620935983 id = cord-327661-osx42wdh author = Schaefer, E. J. title = Coronavirus Disease-2019 Case, Death, and Testing Rates in the United States and Worldwide: Primary Data and Review date = 2020-10-14 keywords = SARS; international summary = ABSTRACT Coronavirus disease-2019 (COVID-19), due to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has been associated with a world-wide pandemic, with the United States (US) having the largest total number of cases and deaths (>7 million and >200,000, respectively) at this time. We assessed data as of September 1, 2020 from our combined laboratories and as reported for selected states and countries for case, death, and testing rates per 1 million in the population. Our positive rates per state agreed reasonably well with reported Centers for Disease Control and Prevention (CDC) data (r=0.609, P<0.0001) based on 19,898 cases, 593 deaths, and 271,637 tests, all per 1 million in the US population. 7 Our goals were to assess our own data as well as available US and worldwide data in terms of cases, deaths, and testing per 1 million in the population, in order to examine potential causes for the large rate differences observed between states and countries. doi = 10.1101/2020.10.13.20172957 id = cord-340010-t1m7dxzc author = Schaefer, Esperance A. K. title = Interrelationship Between Coronavirus Infection and Liver Disease date = 2020-05-21 keywords = COVID-19; SARS summary = Several published studies have characterized the frequency and severity of liver biochemistry abnormalities on presentation, and a few have determined whether these abnormalities are associated with increased disease-related morbidity or death, as summarized in Table 1 . 9, 10, [12] [13] [14] [16] [17] [18] [19] [20] [21] [22] [23] [24] The largest published study to date encompassed 5700 hospitalized patients in New York and examined admission serologies: aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were both frequently elevated (58.4% and 39.0% of subjects, respectively), and a separate large cohort found elevations to be more common in severe disease. 28 Thus, the liver injury observed in COVID-19 may reflect a direct viral effect, but other potential contributors must be considered, both at the time of initial presentation and during disease progression and management. Hepatic injury from SARS-CoV2 infection is observed from the time of initial contact with the medical system, suggesting that the primary insult is unrelated to medical management but rather due to either direct effect of the virus or a consequence of the systemic disease. doi = 10.1002/cld.967 id = cord-313282-z5cues67 author = Schaefer, Inga-Marie title = In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID-19 date = 2020-06-19 keywords = COVID-19; DAD; Fig; SARS summary = Among five patients with acute-phase DAD (≤7 days from onset of respiratory failure), SARS-CoV-2 was detected in pulmonary pneumocytes and ciliated airway cells (N = 5), and in upper airway epithelium (N = 2). The findings suggest that SARS-CoV-2 infection of epithelial cells in lungs and airways of patients with COVID-19 who developed respiratory failure can be detected during the acute phase of lung injury and is absent in the organizing phase. The aim of this study was to examine the gross and histologic patterns of tissue injury in correlation with viral protein expression in the conducting airways and lungs at autopsy in a series of patients with confirmed SARS-CoV-2 infection. Overall, the different stages of DAD observed histologically correspond to the estimated time interval from onset of respiratory failure to death; however, the exact timing of severe lung injury may be difficult to determine in certain cases given reports of silent hypoxemia in COVID-19 infected patients [27, 28] . doi = 10.1038/s41379-020-0595-z id = cord-034371-j3xxmkjd author = Schellack, Natalie title = COVID-19: Guidelines for pharmacists in South Africa date = 2020-06-10 keywords = COVID-19; SARS; patient summary = This evidence-based review is aimed at providing guidance for pharmacists in community, hospital and other settings in South Africa, on the management of patients with suspected or confirmed coronavirus disease 2019, or COVID-19. • Epidemiology • The virus, its modes of transmission and incubation period • Symptom identification, including the differentiation between influenza, allergic rhinitis, sinusitis and COVID-19 • Social media myths and misinformation • Treatment guidelines and medicines that may need to be kept in stock • Treatment and prevention options, including an update on vaccine development • The case for and against the use of NSAIDs, ACE-inhibitors and angiotensin receptor blockers (ARBs) in patients with COVID-19 • Interventions and patient counselling by the pharmacist. The current NDoH/NICD guidelines do not recommend the use of chloroquine (CQ)/ hydroxychloroquine (HCQ), due to insufficient evidence, in the treatment of patients with suspected or confirmed COVID-19. doi = 10.4102/sajid.v35i1.206 id = cord-296649-h6oyjz56 author = Scherf-Clavel, Oliver title = Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date = 2020-11-06 keywords = HCQ; SARS; gs-441 summary = In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. The value obtained from our experiments falls in that range and is comparable to the V z obtained in mice from blood concentrations and to plasma V z measured in humans (see Table 4 ). doi = 10.1101/2020.09.16.299537 id = cord-348243-e5tdb08v author = Schermer, Bernhard title = Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date = 2020-11-02 keywords = LAMP; RNA; SARS summary = METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. doi = 10.1371/journal.pone.0238612 id = cord-191741-2vuiafv0 author = Schifanella, L. title = Massive viral replication and cytopathic effects in early COVID-19 pneumonia date = 2020-04-30 keywords = Fig; SARS summary = Here we show that SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes causes focal lung injury in an individual with no history of pulmonary symptoms. Ground glass opacities or patchy infiltrates in the lungs in CT images of asymptomatic SARS-CoV-2 infected individuals [5] [6] [7] suggest that lung infection and associated tissue injury may be detectable in individuals who did not have severe pneumonia or respiratory failure 7 . We have already shown images that suggested that vRNA+ macrophages could acquire vRNA by phagocytosis of infected type II pneumocytes or vRNA released from lysed cells (Fig. 1, 2) , and now show further evidence in support of that conclusion. We show in a SARS-CoV-2 infected individual with ostensibly early infection, who had no known history of pulmonary symptoms, that there was a region of the lung with focal pneumonia in which massive SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes directly contributes to lung pathology. doi = nan id = cord-016921-64mfqks9 author = Schillmeier, Michael title = Risiko-Akteur-Netzwerke date = 2009-08-07 keywords = Akteur; Risiko; SARS; der; die; und summary = Should SARS continue to spread, the global economic consequences -already estimated at around US $ 30 billion -could be great in a closely interconnected and interdependent world." (WHO 2003: 5) Die Welt bekam es mit einem Akteur zu tun, der in der Lage war, gesellschaftliches und individuelles Leben zu tangieren, zu bedrohen oder gar zu vernichten. Gerade die Möglichkeit, dass wir Menschen mit Hilfe von Flugzeugen weltweit schnell von einem Ort zum anderen reisen können, machte die Gefährlichkeit des SARS-Virus aus, da dieser das Risiko darstellte, als eine Art blinder Passagier mitzureisen und sich so ebenso global entlang dieser Flugrouten und darüber hinaus auszubreiten. SARS markiert ein "kosmo-politisches Ereignis" (Schillmeier & Pohler 2006) : Es stellt einen grenzüberschreitenden, öffentlichen Akteur dar, der nicht nur gesellschaftliche Ordnungsmuster, sondern auch die etablierten Routinen seiner Beschreibung kontingent erscheinen lässt und reformuliert. Bereits an dieser Stelle lässt sich erkennen, dass mit dem Risiko-Akteur SARS eine prozessuale, man könnte auch sagen, eine propagationale Perspektive von Handlung erforderlich ist, die sich der klassischen Konzeptionen und Begrifflichkeiten sozialwissenschaftlicher Methode entziehen. doi = 10.1007/978-3-531-91674-3_16 id = cord-281551-0aj2zwx8 author = Schlagenhauf, Patricia title = Repurposing antimalarials and other drugs for COVID-19 date = 2020-04-02 keywords = COVID-19; SARS summary = A French paper reporting on the use of drug combinations in infected patients highlighted the possibility that hydroxychloroquine is effective in the treatment of COVID-19 patients [4] particularly in combination with azithromycin. For instance, teicoplanin was proposed as a potential treatment in COVID-19 patients and has already shown inhibitory effects on cell entry of Ebola virus, SARS-CoV and MERS-CoV in the past. However, it has to be acknowledged that in this and other cases, it is a long, expensive and time-consuming way, even if there is an accelerated avenue to expedite promising developments, from in vitro assays indicative of antiviral effects to the initiation steps of safety and efficacy assessments in humans, Finding compounds that can block the entry of the virus into the cell could be an important approach to find potential therapies for COVID-19. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) doi = 10.1016/j.tmaid.2020.101658 id = cord-103112-m6cg67lz author = Schloer, Sebastian title = Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date = 2020-08-16 keywords = SARS; cell summary = As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of 27 acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-28 2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity 29 against two currently circulating influenza A virus subtypes, an effect which was also observed 30 upon treatment with the FIASMAs amiodarone and imipramine. doi = 10.1101/2020.07.27.222836 id = cord-270329-t60t639i author = Schloer, Sebastian title = Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date = 2020-10-16 keywords = SARS summary = title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. While drugs 87 directly acting on virus structures are much more likely to completely eliminate the 88 pathogens in shorter treatment time, emerging viral resistance to these antivirals is a major 89 concern, as observed with the influenza neuraminidase inhibitor oseltamivir (Kim et al., itraconazole antiviral activity in SARS-CoV-2 infected Vero cells (Fig. 1b) . doi = 10.1101/2020.10.16.342410 id = cord-287289-zgehbwve author = Schmidt, M. title = FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity date = 2020-05-01 keywords = SARS summary = title: FACTFrankfurt adjusted COVID-19 testinga novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity We applied a novel protocol to NAT testing of respiratory swabs for SARS-CoV-2: First, to evaluate for suitability of different mini-pool sizes, swabs were contaminated with a defined SARS-CoV-2 virus concentration of 1x10 4 copies/ml, and then placed in a series of 10 tubes with lysis buffer for 5 minutes each. P-value for individuals sample and mini pool NAT was 0.299 and 0.354 for the ORF region and E-gene, respectively, which we consider not statistically significant. Ct-values did not differ significantly between mini-pool and the single sample testing (p-value for the ORF region and E gene were 0.44 and 0.46, respectively) (table 4). Here, we present an alternate protocol (FACT) that is based on incubation of a respiratory swab first in a single sample tube, and then again in a mini-pool tube. doi = 10.1101/2020.04.28.20074187 id = cord-318738-7dgbc4um author = Schmidt, Marco Florian title = Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening date = 2008-03-17 keywords = SARS summary = A potential anti‐SARS drug has been developed by dynamic ligation screening (DLS), by which nucleophilic fragments are directed to the protein''s active site by reversible reaction with an aldehyde inhibitor. To establish DLS for site-directed identification of inhibitory fragments, at first a fluorescence-based assay [4] for SARS-CoV M pro activity was developed by employing the substrate Ac-TSAVLQ-AMCA (1). To obtain an entirely non-peptidic inhibitor of SARS-CoV M pro targeting both the S1'' and S1 pockets, the dynamic ligation screening was conducted iteratively in a "reverted" mode ( Table 2 ). Dynamic ligation screening for the S1'' site was performed for a library of 234 nucleophilic fragments using 1 mm of SARS-CoV M pro , 200 mm 1, 400 mm of one nucleophilic fragment per well, and 50 mm of the peptide aldehyde inhibitor Ac-DSFDQ-H (2) on a 384-well microtiter plate. doi = 10.1002/anie.200704594 id = cord-291264-akuvt5ig author = Schnichels, Sven title = Kann SARS-CoV-2 das Auge infizieren? – Ein Überblick über den Rezeptorstatus in okularem Gewebe date = 2020-06-24 keywords = ACE2; Expression; SARS; TMPRSS2 summary = At the time of the research, angiotensin-converting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV‑2. Auch in dieser Studie war die exprimierte Menge von ACE2 in der epithelialen Kornea zwischen 5-und 20-mal geringer als in den anderen untersuchten Geweben (Hoden, Dünndarm, Herz) [22] . Des Weiteren wurde TMPRSS2 auch in Proben der Konjunktiva und Hornhaut nachgewiesen, mit einem im Vergleich zu ACE2 ubiquitäreren Färbungsmuster. At the time of the research, angiotensinconverting enzyme 2 (ACE2) was clearly identified as the receptor and transmembrane serine protease 2 (TMPRSS2) as the necessary protease to enable the infection of human cells with SARS-CoV-2. Aufgrund der geringeren ACE2-und TMPRSS2-Expression ist das Auge nicht als Hochrisikogewebe anzusehen. Expression of SARS coronavirus S protein functional receptor-Angiotensin-converting enzyme 2 in human cornea and conjunctiva doi = 10.1007/s00347-020-01160-z id = cord-294789-07hto8qn author = Schoch-Spana, Monica title = The public’s role in COVID-19 vaccination: human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States date = 2020-10-29 keywords = COVID-19; Health; SARS; public; vaccination; vaccine summary = Members of the working group-listed as authors on this paper-included national figures in public health and social science with research, policy, and practice expertise in vaccinology, vaccine hesitancy/confidence, health disparities, infectious disease, bioethics, epidemiology, bioinformatics, public health law, pandemic mitigation, public health preparedness, mass vaccination campaigns, community engagement, and crisis and emergency risk communication. A combination of literature reviews on vaccination, pandemic planning, and health crisis communication; an assessment of current news and social media trends regarding COVID-19 vaccines; and key informant interviews with each working group member focusing on their respective expertise formed the basis of the research presented in this article. To ensure a successful COVID-19 vaccination campaign, it is necessary for sponsors to invest in time-critical investigations on human factors related to vaccine acceptance, and for public health authorities and other stakeholders to act on the social and behavioral findings of this research. doi = 10.1016/j.vaccine.2020.10.059 id = cord-018460-wbtaoo0o author = Schomburg, Dietmar title = SARS coronavirus main proteinase 3.4.22.69 date = 2013 keywords = SARS; reversibility summary = doi = 10.1007/978-3-642-36260-6_3 id = cord-355728-wivk0bm0 author = Schoof, Michael title = An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date = 2020-08-17 keywords = Fig; RBD; SARS; Spike summary = Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Class I nanobodies emerged with highly 144 variable activity in this assay with Nb6 and Nb11 as two of the most potent clones with IC50 145 values of 370 and 540 nM, respectively (Table 1) To define the binding sites of Nb6 and Nb11, we determined their cryogenic electron 156 microscopy (cryo-EM) structures bound to Spike* ( Fig. 2A state RBDs only contacts a single RBD (Fig. 2D) . 277 278 mNb6-tri displays further gains in potency in both pseudovirus and live SARS-CoV-2 infection 279 assays with IC50 values of 120 pM (5.0 ng/mL) and 54 pM (2.3 ng/mL), respectively (Fig. 4H-I, 280 Table 1). doi = 10.1101/2020.08.08.238469 id = cord-294590-1niaplc2 author = Schrag, Stephanie J. title = SARS Surveillance during Emergency Public Health Response, United States, March–July 2003 date = 2004-02-17 keywords = CDC; SARS; States; United summary = In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003 , a total of 398 (27%) met clinical and epidemiologic SARS case criteria. On March 14, 2003 , the U.S. Centers for Disease Control and Prevention (CDC) launched an emergency public health response and established national surveillance for SARS to identify case-patients in the United States and determine if domestic transmission was occurring. doi = 10.3201/eid1002.030752 id = cord-351305-6vtv2xuh author = Schramm, Markus A. title = COVID-19 in a Severely Immunosuppressed Patient With Life-Threatening Eosinophilic Granulomatosis With Polyangiitis date = 2020-08-28 keywords = COVID-19; SARS summary = The current pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compels clinicians to develop recommendations for successful clinical management and surveillance of immunocompromised patients at high risk for severe disease progression. With only few case studies published on SARS-CoV-2 infection in patients with rheumatic diseases, we report a 25-year-old male who developed moderate coronavirus disease 2019 (COVID-19) with fever, mild dyspnea, and no major complications despite having received high-dose prednisolone, cyclophosphamide, and rituximab for the treatment of highly active, life-threatening eosinophilic granulomatosis with polyangiitis (EGPA). Thus, due to severity and refractory disease the previously healthy patient was continuously hospitalized from January to March 2020, receiving intravenous cyclophosphamide (CYCLOPS-protocol, cumulative dose 4.76 g), rituximab (4 × 375 mg/m 2 ), and a long-term, slowly tapered high-dose prednisolone treatment (up to 1 g/day). Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients doi = 10.3389/fimmu.2020.02086 id = cord-312955-gs65c3fy author = Schreiber, Gideon title = The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19 date = 2020-09-30 keywords = COVID-19; IFN; SARS; cell; interferon; type summary = Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I–receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Thereby, it inhibits the nuclear transport of phosphorylated STAT1, rendering cells refractory to IFN-Is. Another example of viral mechanisms that evolved to eliminate IFN-I functions in inducing innate immunity is given by the SARS corona virus, where both the production of IFNb and the IFN-I induced signaling are attenuated. This gene was found to preferentially cleave the ubiquitin-like modifier interferon-stimulated gene 15 (ISG15), FIGURE 4 | SARS-CoV-2 has multiple effects on the immune system, including inhibition of IFNb production, which results in ISGs not to be produced, CD4+ and CD8+ exhaustion and increased levels of pro-inflammatory proteins (TNFa, IL6, NF-kB). doi = 10.3389/fimmu.2020.595739 id = cord-284478-c1uj3jra author = Schub, David title = High levels of SARS-CoV-2–specific T cells with restricted functionality in severe courses of COVID-19 date = 2020-10-15 keywords = CD4; CD8; SARS summary = RESULTS: Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2–specific T cells as compared with convalescent individuals. So far, mainly nonspecific general changes in the number and functionality of blood cells have been described, whereas specific T cell immunity directed against SARS-CoV-2 has as yet not been studied as extensively (7) (8) (9) (10) (11) , especially in patients with different disease severity. As shown in Figure 3A , the percentage of multifunctional, SARS-CoV-2-specific CD4 + T cells with the ability to simultaneously produce all 3 cytokines was significantly lower in patients with severe courses as compared with convalescent individuals. Nevertheless, the SEB-reactive and SARS-CoV-2-specific cytokine profiles exhibited similar differences between patients with severe disease and convalescent individuals ( Figure 3A ). We also analyzed expression of cytotoxic T lymphocyte antigen 4 (CTLA-4) on SARS-CoV-2-specific and SEB-reactive T cells as phenotypical correlates of altered functionality commonly observed during active infections. doi = 10.1172/jci.insight.142167 id = cord-305589-ofpna4k1 author = Schubert, Katharina title = SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date = 2020-07-07 keywords = Fig; Nsp1; SARS; translation summary = By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. Based on these results we assembled in vitro a 40S-Nsp1 complex and determined its structure at 2.8 Å resolution using cryo-EM (Extended Data Fig. 2 ). As observed in the high-resolution structure of the 40S-Nsp1 complex, the C-terminal part of Nsp1 in the mRNA entrance channel (Fig. 1e ) folds into two helices that interact with h18 of the 18S rRNA as well as proteins uS3 in the head and uS5 and eS30 in the body, respectively ( Fig. 1f; Fig. 2a ). Our structural data suggest that SARS-CoV-2 Nsp1 inhibits translation by sterically occluding the entrance region of the mRNA channel and interfering with binding of cellular mRNAs (Fig. 4a,b) . doi = 10.1101/2020.07.07.191676 id = cord-332303-0bbw64p5 author = Schuit, Michael title = Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight date = 2020-06-11 keywords = SARS summary = This study examined the effect of simulated sunlight, relative humidity, and suspension matrix on the stability of SARS-CoV-2 in aerosols. Therefore, the present study examined the influence of both simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in different liquid matrices. Two different environmentally controlled rotating drum aerosol chambers, with volumes of 16-L and 208-L, were used in the present study to expose aerosols containing SARS-CoV-2 to controlled levels of temperature, relative humidity, and simulated sunlight. The present study examined the influence of simulated sunlight and relative humidity on the stability of SARS-CoV-2 in aerosols generated from virus suspended in either simulated saliva or culture medium at 20°C. The half-lives estimated from the mean decay constants across all relative humidity levels without simulated sunlight present were 55 and 86 minutes for aerosols generated from virus suspended in culture medium and simulated saliva, respectively. doi = 10.1093/infdis/jiaa334 id = cord-347428-2isuaiyx author = Schulz-Stübner, Sebastian title = Hygiene in der Anästhesie in Zeiten der SARS-CoV-2-Pandemie date = 2020-07-31 keywords = SARS; der; und summary = Im Verlauf kann es bei etwa 20 % der Patienten zu einer klinischen Verschlechterung kommen, mit Entwicklung von Dyspnoe und/oder Hypoxämien, typischerweise ca. In einer systematischen Übersicht aus dem Jahr 2016 wurde gezeigt, dass N95-Atemschutzmasken (entspricht FFP2) zwar im Laborversuch einen größeren Schutz gegen die Erreger akuter Atemwegsinfektionen einschließlich pandemischer Influenza zu bieten scheinen als chirurgische Masken, dass sich mittels Metaanalyse aber kein höherer Schutzeffekt für medizinisches Personal bei klinischer Anwendung nachweisen lässt [8] . Sie berichtet retrospektiv, in einer Gondelbahn neben einer Person mit Symptomen einer viralen Atemwegsinfektion gesessen zu haben, sie entwickelt 4 Tage nach Arbeitsbeginn selbst Symptome und wird positiv auf SARS-CoV-2 getestet. Effectiveness of N95 respirators versus surgical masks in protecting health care workers from acute respiratory infection: a systematic review and meta-analysis Medical masks vs N95 respirators for preventing COVID-19 in healthcare workers: A systematic review and meta-analysis of randomized trials. doi = 10.1055/a-1174-7359 id = cord-281677-pspmmrq7 author = Schulze-Koops, Hendrik title = Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie e. V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 date = 2020-08-05 keywords = Patienten; SARS summary = V. für die Betreuung von Patienten mit entzündlich rheumatischen Erkrankungen im Rahmen der SARS-CoV-2/COVID-19-Pandemie – Update Juli 2020 A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Daten aus COVID-19-Registern, Fallserien und Fallberichten legen aber nach derzeitigem Wissensstand nahe, dass Patienten mit ERE im Vergleich zur nicht rheumatisch erkrankten Bevölkerung kein grundsätzlich erhöhtes Risiko einer Infektion mit SARS-CoV-2 aufweisen [7] [8] [9] [10] [11] . unten) -die medikamentöse antirheumatische Therapie ein Risiko für einen schweren Verlauf von COVID-19 bei Patienten mit ERE darstellt [11] . Abstract A few days after the SARS-CoV-2 infection was declared a pandemic, the German Society for Rheumatology (DGRh) compiled first recommendations for the care of patients with inflammatory rheumatic diseases (IRD). Aktuelle Handlungsempfehlungen der Deutschen Gesellschaft für Rheumatologie für die Betreuung von Patienten mit rheumatischen Erkrankungen während der SARS-CoV-2/Covid 19-Pandemie doi = 10.1007/s00393-020-00851-x id = cord-347262-q88g1561 author = Schutzer‐Weissmann, J. title = Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date = 2020-07-11 keywords = COVID-19; SARS; respiratory; transmission summary = Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review doi = 10.1111/anae.15221 id = cord-124012-5zxkd2jy author = Schwab, Patrick title = predCOVID-19: A Systematic Study of Clinical Predictive Models for Coronavirus Disease 2019 date = 2020-05-17 keywords = CoV-2; ICU; SARS summary = Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. In addition, [48] performed a cohort study for clinical and laboratory predictors of COVID-19 related inhospital mortality that identified baseline neutrophil count, age Fig. 2 : The presented multistage machine-learning pipeline consists of preprocessing (light purple) the input data x, developing multiple candidate models using the given dataset (orange), selecting the best candidate model for evaluation (blue), and evaluating the selected best model''s outputsŷ. Owing to the recent emergence of SARS-CoV-2, there currently exists, to the best of our knowledge, no prior systematic study on clinical predictive models that predict likelihood of a positive SARS-CoV-2 test, hospital and intensive care unit admission from clinical, demographic and blood analysis data that accounts for the missingness that is characteristic for the clinical setting. doi = nan id = cord-327501-8s6dvanf author = Schwaiger, Julia title = No SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced From Plasma Collected Before the 2020 Pandemic date = 2020-09-17 keywords = IVIG; SARS summary = Testing 54 intravenous immunoglobulin preparations, produced from plasma collected in Europe and the United States, confirmed highly potent neutralization of a seasonal coronavirus; however, no cross-neutralization of the new SARS-CoV-2 was seen. The question is of significant clinical relevance, as SARS-CoV-2 cross-neutralizing antibodies in IVIGs, if they were present, might afford some protection to people with immune deficiencies and may even represent a treatment option for coronavirus disease 2019 (COVID-19) patients. The current study tested a representative number of IVIG lots for nAbs against SARS-CoV-2 and the longer-circulating HCoV-229E, to establish clarity about cross-neutralization of the pandemic virus by antibodies induced by earlier circulating seasonal coronaviruses. SARS-CoV-2 nAb titers were below the limit of detection for all 54 IVIG lots tested, irrespective of geographic origin of the plasma (Europe vs United States) and plasma collection modality (recovered vs source) ( Figure 1A) . doi = 10.1093/infdis/jiaa593 id = cord-342739-iy9vjpuh author = Schwartz, David A. title = Potential Maternal and Infant Outcomes from Coronavirus 2019-nCoV (SARS-CoV-2) Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections date = 2020-02-10 keywords = China; MERS; SARS; pregnant; woman summary = In order to assess the potential of the Wuhan 2019-nCoV to cause maternal, fetal and neonatal morbidity and other poor obstetrical outcomes, this communication reviews the published data addressing the epidemiological and clinical effects of SARS, MERS, and other coronavirus infections on pregnant women and their infants. The most common adverse obstetrical outcomes associated with maternal pneumonias from all causes include This newly recognized coronavirus, producing a disease that has been termed COVID-19, is rapidly spreading throughout China, has crossed international borders to infect persons in neighboring countries, and humans infected by the virus are travelling via commercial airlines to other continents. Pregnant women may develop severe disease and fatal maternal and/or fetal outcomes as a result of MERS-CoV infection; however, little is known of the pathophysiology of this infection during pregnancy. doi = 10.3390/v12020194 id = cord-308356-ojx3tasi author = Schwarz, Silke title = Corona bei Kindern: Die Co-Ki Studie: Relevanz von SARS-CoV-2 in der ambulanten pädiatrischen Versorgung in Deutschland date = 2020-11-03 keywords = KJÄ; Kindern; SARS summary = Hintergrund Die aktuelle Studienlage deutet darauf hin, dass Kinder und Jugendliche eine geringere Rate symptomatischer SARS-CoV-2-Infektionen (COVID-19) aufweisen als Erwachsene und mehrheitlich keine oder nur milde Symptome entwickeln [1] [2] [3] . Darüber hinaus ist leider nicht bekannt, wie viele der vom RKI erfassten Kinder symptomatisch waren, und ob ihre etwaigen Symptome auf SARS-CoV-2 zurückzuführen sind. Diese KJÄ meldeten insgesamt 9803 Kinder und Jugendliche, die aufgrund eines Verdachts der Eltern oder eines Kontaktes mit einem SARS-CoV-2-Infizierten in der Sprechstunde vorgestellt wurden. Die KJÄ ihrerseits hatten den klinischen Verdacht auf eine SARS-CoV-2-Infektion bei 3654 Kindern, wobei einzelne KJÄ mehr eigene Verdachtsfälle als Vorstellungen mit Verdacht meldeten, und das Wort "ebenfalls" in Frage 4 wohl ignorierten, weshalb die 3654 nicht eine reine Teilmenge von den 9803 sind. Die höhere Rate an Antikörperpositivität hängt mit der Tatsache zusammen, dass mehr Kinder getestet wurden, die zuvor Symptome und/oder einen positiven PCR-Test hatten. doi = 10.1007/s00112-020-01050-3 id = cord-331666-iwkuwnun author = Schweitzer, Wolf title = Implications for forensic death investigations from first Swiss post-mortem CT in a case of non-hospital treatment with COVID-19 date = 2020-06-30 keywords = COVID-19; PMCT; SARS; case summary = Comment: With the pandemic impact of SARS-COV-2, a range of issues unfolds, also for medicolegal investigations into deaths, as we report the first Swiss case with post-mortem CT where death had occurred due to a SARS-COV-2 infection, with features of a severe acute respiratory distress syndrome, as an outpatient. Control: Case of a 24 year old woman who had no acute respiratory distress syndrome related findings at all; there was post-mortem hypostasis dorsally at the right lung. While this man''s subjective report apparently did not include dyspnea, even less than a day prior to his death, the pulmonary pathology of this outpatient, as evidenced by PMCT, appears to extend beyond the severity shown in descriptions of currently published SARS-CoV-2-related fatalities, all of which apparently had obtained prior hospital and intensive-care treatment [39] [40] [41] . As post-mortem RT-PCR testing for SARS-CoV-2 in a forensic setting may not be available or too slow, PMCT may identify lung changes possibly related to COVID-19. doi = 10.1016/j.fri.2020.200378 id = cord-319799-h9kot3og author = Schäfer, Alexandra title = Epigenetic Landscape during Coronavirus Infection date = 2017-02-15 keywords = ISG; SARS; dna; epigenetic; figure summary = By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host''s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. By utilizing Calu3 cells, we have developed a robust human model platform to study innate immune regulatory control and epigenetics following emerging coronavirus and influenza virus infections as well as other highly pathogenic viruses ( Figure 6 ). Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. doi = 10.3390/pathogens6010008 id = cord-284867-p4jgyusp author = Schöler, Lara title = A Novel In-Cell ELISA Assay Allows Rapid and Automated Quantification of SARS-CoV-2 to Analyze Neutralizing Antibodies and Antiviral Compounds date = 2020-10-09 keywords = CoV-2; SARS; figure summary = Altogether, the SARS-CoV-2 icELISA test allows rapid (<48 h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs and antiviral drugs using reagents and equipment present in most routine diagnostics departments. The fact that the infection and the resulting icELISA signal were neutralized by NAbs present in immune sera indicated that the fast and automated icELISA format is applicable for icNTs. Although most SARS-CoV-2 NTs have not been formally validated and certified, classic plaque reduction neutralization tests (PRNT) are currently considered to represent the gold standard for the detection of SARS-CoV-2-specific NAbs. Various commercially available IgM, IgA, and IgG ELISAs have been compared to PRNTs [e.g., (30) ]. Given the excellent signal-to-noise ratio between infected and uninfected cells, the test was applicable to quantify the efficacy of antiviral compounds, here shown for IFNb, and SARS-CoV-2-specific NAbs present in immune sera. doi = 10.3389/fimmu.2020.573526 id = cord-324919-ciamusjs author = Scialo, Filippo title = ACE2: The Major Cell Entry Receptor for SARS-CoV-2 date = 2020-11-10 keywords = ACE2; COVID-19; CoV-2; SARS summary = Since the beginning of the COVID-19 pandemic, hypertension and diabetes have been correlated with higher risk of mortality, and initial reports speculated that angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs), which are commonly used therapeutic agents for these conditions, would up-regulate ACE2 expression, thus increasing the risk of severe illness [37] . Binding of S1 subunit of the Spike protein of SARS-CoV-2 to the ACE2 receptor triggers the cleavage of ACE2 by ADAM17/tumor necrosis factorconverting enzyme (TACE) at the ectodomain sites [41] and a soluble form that retains its catalytic activity (sACE2) is produced [42] . ACE2 shedding can be stimulated by proinflammatory cytokines such as IL-1β and tumor necrosis factor (TNF)-α, and endotoxin [47] that could result in a positive effect reducing SARS-CoV-2 entry, but at the same time, may cause an increase in AngII and further activation of the AngII/AT1R axis worsening inflammation (discussed below) (Fig. 1) . Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.1007/s00408-020-00408-4 id = cord-275979-cx2h5bsw author = Scutelnic, Adrian title = Vascular Events, Vascular Disease and Vascular Risk Factors—Strongly Intertwined with COVID-19 date = 2020-10-08 keywords = SARS; covid-19; patient; risk summary = According to the INTERSTROKE study, the 10 most frequent modifiable vascular risk factors are arterial hypertension, physical inactivity, overweight, dyslipidaemia, smoking, unhealthy diet, cardiac pathologies, diabetes mellitus, stress/depression and overconsumption of alcohol. Also, a higher rate of infection with COVID-19, severe COVID-19 and bad outcome has been demonstrated in patients with pre-existing vascular disease and vascular risk factors. A higher rate of infection with COVID-19, severe COVID-19, and worse outcome has been demonstrated in patients with pre-existing vascular disease and risk factors, compared with young and healthy persons [1, 6, 8-11, 28, 29] . Several potential mechanisms increasing this risk of COVID-19 in patients with diabetes mellitus have been proposed: (1) higher affinity of cellular binding of SARS-CoV-2 and higher levels of circulating furin facilitating virus entry, (2) increased ACE2 expression in the lungs, (3) decreased viral clearance, (4) diminished T cell function, (5) increased susceptibility to inflammation and cytokine storm syndrome and (6) co-existence of vascular disease and risk factors [5] . doi = 10.1007/s11940-020-00648-y id = cord-306424-gf0bglm0 author = Scutigliani, Enzo Maxim title = Interaction of the innate immune system with positive-strand RNA virus replication organelles date = 2017-06-27 keywords = IFN; RNA; SARS; viral; virus summary = Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus doi = 10.1016/j.cytogfr.2017.05.007 id = cord-284234-9cd2v6bt author = Sebastian, S title = Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date = 2020-06-10 keywords = COVID-19; IBD; MERS; SARS summary = Understandable concerns have been raised on the safety of steroids, immunosuppressive drugs, and biologics used in patients for a variety of indications including immune mediated inflammatory disease such as inflammatory bowel diseases (IBD), which do increase the risk of opportunistic bacterial, viral and fungal infections (5) . Therefore, continuing concerns remain both from IBD patients and the A c c e p t e d M a n u s c r i p t clinicians managing them, regarding the potential of IBD related drugs causing more frequent infections by SARS-CoV2, and increased risk of severe complications from COVID-19 (13) . Corticosteroids are thought to have a divergent effect on viral infections including SARS COV viruses; on one hand they inhibit host immune response acting on migration and chemokines production leading to impaired viral clearance and the resultant prolonged Moreover, a prospective, randomized double-blinded, placebo-controlled trial compared early hydrocortisone treatment (before day seven of the illness) with a placebo and found that early hydrocortisone therapy was associated with a higher subsequent plasma viral load (61) . doi = 10.1093/ecco-jcc/jjaa120 id = cord-284589-j1609xlu author = Sedova, Mayya title = Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence date = 2020-05-29 keywords = CoV-2; SARS summary = RESULTS: Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context. At the same time, with the exception of the spike protein mutations, there are no publicly available resources that provide analysis for all the other structurally characterized regions of the SARS-CoV-2 proteins. For commercial re-use, please contact journals.permissions@oup.com MN908947.3), with information on boundaries of the predicted proteins, currently available SARS-CoV-2 structures and a histogram of the aminoacid mutation frequency. The first of the lower level panels (Figure 1b) provides interactive visualization of the selected structure or model, with an option for coloring the chain according to the mutation frequency. The Coronavirus3D server was designed to provide users with information and tools to carry out their own analysis of how mutations in the SARS-CoV-2 proteins may affect their 3D-structures and their functions. doi = 10.1093/bioinformatics/btaa550 id = cord-284163-3jmqzemf author = Seffer, Malin-Theres title = Heparin 2.0: A New Approach to the Infection Crisis date = 2020-07-02 keywords = SARS; Seraph; patient summary = This narrative review will give a brief overview regarding some of the extracorporeal devices that could be used to treat COVID-19 patients, including the Seraph® 100 Microbind® Affinity Blood Filter, produced by ExThera Medical (Martinez, CA, USA), first licensed in the European Economic Area in 2019. Bacteria, viruses, fungi, and toxins have been shown to bind to the immobilized heparin in a similar way to the interaction with heparan sulfate on the cell surface. Of note, it has recently been demonstrated that SARS-CoV-2 attaches to heparin through its surface protein Spike 1 receptor-binding domain [21] . The Seraph ® 100 Microbind ® Affinity Blood Filter is an extracorporeal hemoperfusion device whose functional core, that is, polyethylene beads (diameter of 0.3 mm) with immobilized heparin bound to it, mimics a naturally mammalian cell surface (Fig. 1) . Cytokines in blood from septic patients interact with surface-immobilized heparin doi = 10.1159/000508647 id = cord-309418-dx6e0lri author = Segalés, Joaquim title = Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain date = 2020-10-06 keywords = COVID-19; CoV-2; SARS summary = Several models for SARS-CoV-2 infection have been so far developed in animals, including Egyptian fruit bat, ferret, golden Syrian hamster, cat, humanized angiotensin-converting enzyme 2 (ACE2) transgenic mice (hACE2 mice), and some nonhuman primate species (3) (4) (5) (6) (7) (8) . The clinical condition was finally attributed to a feline hypertrophic cardiomyopathy, but the animal was also infected by SARS-CoV-2. The detection of SARS-CoV-2 RNA in several samples of C1, all of them with Ct values over 30 (low viral load), and presence of antibodies (neutralizing and nonneutralizing) in both C1 and C2, indicated both animals suffered from a productive viral infection, probably linked to the exposure of the cats to COVID-19−affected owners. These experimental results, together with the few reports on SARS-CoV-2 detection in domestic cats and wild felids, indicate that felines are susceptible to infection by the novel coronavirus. doi = 10.1073/pnas.2010817117 id = cord-312178-tojgojjf author = Segars, James title = Prior and Novel Coronaviruses, COVID-19, and Human Reproduction: What Is Known? date = 2020-04-16 keywords = ACE2; COVID-19; Coronavirus; MERS; SARS summary = Evidence suggests that COVID-19 infection has a lower maternal case fatality rate than SARS or MERS, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a pandemic of Coronavirus Disease 2019 (COVID-19) across the globe. The novel SARS-CoV-2 virus spreads rapidly, with 2-3 people infected from every index case, a reproduction number (R 0 ) or transmission rate of 2.24 -3.58 (2) . The aim of this review is to summarize what is currently known about the impact of prior coronaviruses and the novel SARS-CoV-2 infection on reproduction and pregnancy. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: Report of two cases & review of the literature An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes doi = 10.1016/j.fertnstert.2020.04.025 id = cord-295794-glcg36si author = Seghers, Victor J. title = After the initial COVID-19 surge: a phased radiology departmental re-opening plan date = 2020-08-22 keywords = COVID-19; SARS; patient; radiology summary = Social distancing, stay home/work safe orders, protective measures for vulnerable individuals (e.g., immunocompromised patients), masking protocols, visitation policies, testing and many more measures resulted in an accelerated but necessary ramping down of elective hospital services [4] [5] [6] [7] [8] [9] . While the radiologist-in-chief also participates in daily meetings with other clinical service chiefs and executive leadership for the hospital, the radiologist-in-chief is an integral member of the systemwide "Phased Recovery and Redesign Team" as well, which includes team captains for infection control, surgery, anesthesia, emergency and urgent care centers, radiology, pathology, ambulatory medicine, specialty care centers, e-health, revenue cycle and billing, and marketing and public relations. This can include patient-directed online scheduling and expanded access to imaging, offering same-day service with hours and locations adapted to the patient and family lifestyle; improved use of virtual dashboards to more easily track various metrics including MR efficiency, sedation utilization, and length of patient stay in the imaging department; and investment in Table 2 Radiology: the opportunity to re-design operations post COVID-19 doi = 10.1007/s00247-020-04792-0 id = cord-274948-ze6scnae author = Segondy, Michel title = Les Coronavirus humains date = 2020-10-31 keywords = SARS summary = Toutefois, à côté de ces infections à coronavirus endémiques, ont récemment émergé chez l''homme, à partir de réservoirs animaux, des coronavirus responsables de syndromes respiratoires sévères avec un taux de mortalité élevé [2] . Ce sont des virus enveloppés dont le génome est un ARN de polarité positive d''une taille de l''ordre de 30 kilobases, ce qui en fait le génome le plus grand chez les virus à ARN [3] . Des coronavirus génétiquement très proches du Mers-CoV ont été identifiés chez des chauves-souris qui représentent le réservoir de virus [29] . Bien que le plus souvent inapparente ou bénigne chez le jeune enfant, l''infection par le Sars-CoV-2 peut être à l''origine d''un syndrome hyper inflammatoire similaire à la maladie de Kawasaki [38] . ◗t Les coronavirus émergents sont responsables d''infections respiratoires sévères avec une mortalité élevée. En moins de vingt ans, ce sont trois coronavirus responsables d''infections respiratoires sévères avec une mortalité élevée qui ont émergé dans la population humaine. doi = 10.1016/s1773-035x(20)30311-7 id = cord-322417-9e95m4kz author = Segovia-Juarez, Jose title = High altitude reduces infection rate of COVID-19 but not case-fatality rate date = 2020-07-15 keywords = COVID-19; SARS summary = authors: Segovia-Juarez, Jose; Castagnetto, Jesús M.; Gonzales, Gustavo F. title: High altitude reduces infection rate of COVID-19 but not case-fatality rate It is suggested that life at high altitude may reduce COVID infections and case-fatality rates (cases/deaths). A recent paper with data as of April 7th from the Tibet, Bolivia and Ecuador suggests that high-altitude (HA) may provide protection from pathogenesis of SAR-CoV-2 infection (Arias-Reyes et al, 2020). The current study has been designed to determine COVID-19 cases, deaths by COVID-19 and case-fatality rates in Peru in an altitude range from 3 to 4,342 meters above sea level. The sex ratio (male/female) for positive cases of COVID-19 is maintained at any altitude of residence ( Figure 1D ). Another important finding from our study is that the cumulative case-fatality rate (cumulative deaths/cumulative positive cases) by COVID-19 does not appear to change with altitude of residence ( Figure 3 ). doi = 10.1016/j.resp.2020.103494 id = cord-308075-1ftswsm8 author = Segura, Patricia Sanz title = Involvement of the digestive system in COVID-19. A review date = 2020-10-09 keywords = COVID-19; SARS; gastrointestinal; patient summary = 4 Recent studies have indicated detection of SARS-CoV-2 by PCR in the faeces of infected patients, with a higher prevalence in those with gastrointestinal symptoms, in particular diarrhoea. Moreover, the cohort studies that have analysed the course of COVID-19 in patients with viral hepatitis (hepatitis B) 41 and those that have assessed the impact of non-alcoholic fatty liver disease on the disease due to the novel coronavirus, especially in the absence of obesity, have concluded that there is a higher risk of developing a serious form of pneumonia and having more prolonged hospital stays, 42 although the available data in this regard remain insufficient. doi = 10.1016/j.gastre.2020.06.004 id = cord-319571-fspmgg4s author = Sehailia, Moussa title = Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 date = 2020-07-22 keywords = HCQ; RBD; SARS summary = Although, functional importance of different targets has been linked to the viral replication and maturation of coronaviruses'' family such as Chymotrypsin-like protease(3CLpro) or known as Mpro (Khan et al., 2020; Muralidharan et al., 2020) or Envelope protein (E) (Gupta et al., 2020; Boopathi et al., 2020) but it has been confirmed that the binding of the viral trimeric surface spike glycoprotein (SProtein) of SARS-CoV-2 to the human receptor angiotensin-converting enzyme 2 (hACE2) is the first step in host infection . Therefore, it is very likely that selective interaction of HCQ with the surface of SARS-CoV-2 SProtein through the formation of an inclined tape over the hydrophobic pocket responsible for hosting the Lys353 hotspot (the OH group in this case is acting like a hook by forming a hydrogen bond with Asn501), can be responsible for the prevention of tighter binding with hACE2 protein via restricting penetration of Lys353 into its finally assigned destination on the SProtein RBD (Figure 2 ). doi = 10.1080/07391102.2020.1796809 id = cord-336722-41eqt97y author = Sehmi, P. title = Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review date = 2020-06-29 keywords = SARS summary = title: Presence of Live SARS-CoV-2 Virus in Feces of Coronavirus Disease 2019 (COVID-19) Patients: A Rapid Review Recent studies have confirmed the presence of SARS-CoV-2 nucleic acids in feces of Coronavirus disease 2019 (COVID-19) patients using RT-PCR tests. Larger studies are needed to corroborate these findings, as well as to determine its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. . https://doi.org/10.1101/2020.06.27.20105429 doi: medRxiv preprint A total of 4 studies describing isolation of live SARS-CoV-2 virus in fecal samples of COVID-19 patients were included. The findings from these four studies, though limited by the small sample sizes, confirm that live SARS-CoV-2 virus is present in fecal samples of COVID-19 patients, and therefore supports the hypothesis that COVID-19 could potentially be transmitted via the feco-oral route. Larger high-quality studies are urgently needed to better characterize the magnitude of live SARS-CoV-2 viral shedding in feces, as well as its potential for disease transmission and infection, and possible implications for COVID-19 discharge and isolation policies. doi = 10.1101/2020.06.27.20105429 id = cord-353373-zhkqnu0w author = Seidu, Samuel title = The impact of obesity on severe disease and mortality in people with SARS‐CoV‐2: A systematic review and meta‐analysis date = 2020-08-14 keywords = BMI; COVID-19; SARS summary = BACKGROUND: Obesity accompanied by excess ectopic fat storage has been postulated as a risk factor for severe disease in people with SARS‐CoV‐2 through the stimulation of inflammation, functional immunologic deficit and a pro‐thrombotic disseminated intravascular coagulation with associated high rates of venous thromboembolism. METHODS: Observational studies in COVID‐19 patients reporting data on raised body mass index at admission and associated clinical outcomes were identified from MEDLINE, Embase, Web of Science and the Cochrane Library up to 16 May 2020. 2 Recent studies have increasingly described obesity as an associating factor for people at an increased risk of severe disease. 15 In order to attempt to quantify the relationship between raised body weight and severe outcomes from COVID-19, we conducted a systematic review and meta-analysis to determine whether people with overweight or obesity and with SARS-CoV-2 have different outcomes compared to those within normal weight thresholds. doi = 10.1002/edm2.176 id = cord-326375-8m4110k3 author = Seitzman, Gerami D. title = No Time for Tears date = 2020-03-26 keywords = SARS summary = In this issue, Jun et al, 1 (https:// www.aaojournal.org/article/S0161-6420(20)30311-0/fulltext) from the National Health Care Group Eye Institute in Singapore, report that they were unable to detect SARS-CoV-2 in the tears of 17 patients diagnosed with COVID-19. 2, 3 In a separate study that evaluated conjunctival swabs of 30 patients with COVID-19 pneumonia in China, only 1 patient demonstrated conjunctivitis, and those swabs showed positive results for SARS-CoV-2 by reverse-transcriptase polymerase chain reaction analysis. Patients who seek treatment from an ophthalmologist and screen positive for signs, symptoms, or both of COVID-19 should forgo an eye examination for prompt SARS-CoV-2 screening. Patients with conjunctivitis seeking treatment from ophthalmology departments should be considered contagious, and SARS-CoV-2 precautions should be taken. Assessing viral shedding and infectivity of tears in coronavirus disease 2019 (COVID-19) patients SARS-CoV-2 viral load in upper respiratory specimens of infected patients Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection doi = 10.1016/j.ophtha.2020.03.030 id = cord-312115-foy3dsq4 author = Sekine, Takuya title = Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 date = 2020-08-14 keywords = CD8; SARS; figure summary = In line with these data, we found that CD8 + T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) more commonly expressed CD38, but not HLA-DR, Ki-67, or PD-1, in patients with acute moderate or severe COVID-19 compared with convalescent individuals and healthy blood donors, indicating limited bystander activation and proliferation during the early phase of infection with SARS-CoV-2 ( Figure 2A , B and Figure S3C ). On the basis of these observations, we quantified functional SARS-CoV-2-specific memory T cell responses across five distinct cohorts, including healthy individuals who donated blood either before or during the pandemic, family members who shared a household with convalescent individuals and were exposed at the time of symptomatic disease, and individuals in the convalescent phase after mild or severe COVID-19. These donors exhibited robust memory T cell responses months after infection, even in the absence of detectable circulating antibodies specific for SARS-CoV-2, indicating a previously unanticipated degree of population-level immunity against COVID-19. doi = 10.1016/j.cell.2020.08.017 id = cord-309541-2vqk7fx1 author = Sekizuka, Tsuyoshi title = Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak date = 2020-08-18 keywords = February; SARS summary = Here, we have generated a haplotype network of the SARS-CoV-2 outbreak using genome-wide single nucleotide variations (SNVs), identifying the genotypes of isolates that disseminated in the DP cruise ship after quarantine on February 5, 2020. The frequencies of SNVs suggested that all 73 isolates shared a SNV: The G nucleotide at the 11,083 position on the Wuhan-Hu-1 genome sequence was mutated to T (G 11083 T transversion), leading to a nonsynonymous amino Significance On February 5, 2020, the Diamond Princess cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed to have coronavirus disease 2019. Maximum-likelihood (ML) phylogenetic analysis including other SARS-CoV-2 genome sequences that are publicly available on GISAID and haplotype networks from genomic SNVs (HN-GSNVs) were used to map the genotypes of the SARS-CoV-2 isolates that disseminated in the DP cruise ship after isolation of the passengers on February 5, 2020 (Fig. 2) . doi = 10.1073/pnas.2006824117 id = cord-310392-fmobf1f1 author = Sekizuka, Tsuyoshi title = SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date = 2020-06-05 keywords = Egypt; SARS summary = A field FIGURE 1 | Summary of travel history, clinical course, and PCR testing for 10 SARS-CoV-2-positive travelers who returned to Japan from Egypt, as well as the associated patients who were their close contacts. In this study, we have evaluated viral genome sequences from SARS-CoV-2-positive travelers who returned from Egypt, and characterized the haplotype networks to demonstrate possible routes of the spread. SARS-CoV-2 genome sequences with nearly fulllength information (≥ 29 kb) were retrieved from the GISAID EpiCoV database on March 30, 2020, and we generated haplotype networks by median-joining network analysis using PopART software 3 to highlight and trace a potential infectious route among COVID-19 patient populations. P2-1 and P2-2 had visited Egypt together and traveled aboard the same Nile River cruise ship, and SARS-CoV-2 genome sequences isolated from them are identical with that of P1 (Figure 3) . doi = 10.3389/fmicb.2020.01316 id = cord-315085-rucfowvv author = Sekulic, Miroslav title = Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date = 2020-05-26 keywords = CoV-2; FFPE; RNA; SARS; lung summary = In this study we report postmortem findings and detection and sequencing of SARS-CoV-2 viral RNA from formalin-fixed paraffinembedded (FFPE) samples of multiple organs collected in 2 patients with antemortem detection of SARS-CoV-2. The patient''s medical history was otherwise notable for dementia, radiologic evidence of a left lung mass (managed with hospice care), coronary artery disease (status post coronary artery bypass grafting), atrial fibrillation (biventricular pacemaker implanted), congestive heart failure, peripheral artery disease (status post iliac stenting), diabetes mellitus, hypertension, dyslipidemia, chronic kidney disease, gout, smoking, cerebrovascular accidents, and urinary tract infections. On day 1 after admission, ❚Image 2❚ (Case 1) Postmortem microscopic examination of the lungs showed diffuse alveolar damage characterized by hyaline membrane formation (A, ×100) and scattered squamous metaplasia of distal airways (B, ×100) on a background of emphysematous changes. doi = 10.1093/ajcp/aqaa091 id = cord-289255-qwzg7prx author = Seligman, Stephen J. title = Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants date = 2007-02-15 keywords = SARS summary = title: Evidence for Quasi Species in Severe Acute Respiratory Syndrome-associated Coronavirus Deletion Mutants have reported data on a 386-nt deletion in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) [1] . Because 1 patient had both the L386del variant and the wild-type variant in the same specimen, they raised the possibility that SARS-CoV exists as a quasi species, at least in some patients. Previous authors studying single-nucleotide variants from Beijing-area isolates in 2003 [2] and from the Singapore 2004 outbreak [3] have also found multiple viral sequences in the same sample that they attributed to quasi species. Although these 3 studies clearly establish the presence of a diversity of SARS-CoV genomes in individual patients, the issue of whether SARS-CoV quasi species exists remains open, particularly with respect to the 386-nt deletion. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? SARS-associated coronavirus quasispecies in individual patients doi = 10.1086/510917 id = cord-310063-8nbmrjrw author = Selva, K. J. title = Distinct systems serology features in children, elderly and COVID patients date = 2020-05-18 keywords = SARS summary = . https://doi.org/10.1101 /2020 6 147 To interrogate Ab functionality and cross-reactivity between antigens of selected CoV signatures, we 148 conducted a correlation network analysis, focusing upon significant correlations of Ab features 149 selected by Elastic-Net. The children''s network (Figure 1f ) demonstrates how SARS-CoV-2 Abs that 150 engaged FcγRIIa-H131 are associated with SARS-CoV-2 IgG, specifically of IgG1 subclass. In particular, we found that in the majority of COVID-19 190 patients, the SARS-CoV-2 antigen-specific Abs bound to FcγRIIIaV158 and FcγRIIaH131 soluble 191 dimers at high levels, even at 1:800 plasma titrations, suggesting potent ADCC and ADCP CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.05.11.20098459 doi: medRxiv preprint 8 notably being the healthy exposed SARS-CoV-2 PCR-negative individual (Figure 3d) The majority of COVID-19 moderate/severe samples were collected upon hospital presentation, 235 whereas mild samples were collected upon convalescence (Extended Data Table 3 ). doi = 10.1101/2020.05.11.20098459 id = cord-336177-p7b7yw28 author = Selvi, Valeria title = Convalescent Plasma: A Challenging Tool to Treat COVID-19 Patients—A Lesson from the Past and New Perspectives date = 2020-09-22 keywords = COVID-19; SARS; convalescent; plasma summary = Regarding the pandemic 2009 influenza A H1N1, the results from the prospective cohort study by Hung and colleagues showed that plasma treatment reduced mortality (the patients involved in the study were seriously ill and required intensive care); no adverse events were observed [4, 8, 20] . A meta-analysis by Mair-Jenkins and colleagues, including 32 studies of SARS coronavirus and severe influenza, reported that convalescent plasma reduced mortality and it was safe (no relevant adverse events or complications after treatment were reported). Based on the evidence from past experience in passive immunization, the BRN explained that there was a considerable possibility that the application of whole blood (as well as plasma, serum, or immunoglobulin concentrates) from convalescent persons could be effective in the treatment/prevention of infectious disease. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection doi = 10.1155/2020/2606058 id = cord-269496-tnw7sxlh author = Sen Gupta, Parth Sarthi title = Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date = 2020-10-28 keywords = Importin; Ivermectin; RNA; SARS summary = Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). Together, being conserved and a necessary component for the replication of coronavirus, a multi-functional protein, Nsp13-helicase, is another vital SARS-COV-2 target (Jia et al., 2019) , which can be considered further for antiviral drug discovery provided a very small number of Nsp13 inhibitors reported to date . Molecular docking of Ivermectin with twelve SARS-COV-2''s targets along with Importin-a was carried out, followed by binding mechanism exploration and structural stability analysis using molecular dynamics (MD) simulation through the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g ), and binding free energy of the complexes of Ivermectin with the best targets. doi = 10.1080/07391102.2020.1839564 id = cord-280922-w6a5ec06 author = Sen, Sanjana title = Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date = 2020-10-29 keywords = SARS; abs; covid-19; ep9 summary = Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Furthermore, a recent review on antibody-dependent enhancement of SARS-CoV-2 stated, "At present, there are no known clinical findings, immunological assays or biomarkers that can differentiate any severe infection from immune-enhanced disease, whether by measuring antibodies, T cells or intrinsic host responses (7) ." This conclusion inspired our study. The results demonstrate that Abs to a specific epitope from N protein plus disease risk factors strongly correlate with COVID-19 disease severity. The DRFS of patients with αEp9 Abs strongly correlates with COVID-19 disease severity (Pearson''s r = 0.72, p-value <0.0001, and R 2 = 0.52) (Fig. 4A) . doi = 10.1101/2020.10.15.341743 id = cord-340138-u8hxyfml author = Seneviratne, Chaminda Jayampath title = The Role of Dentists in COVID-19 Is Beyond Dentistry: Voluntary Medical Engagements and Future Preparedness date = 2020-10-06 keywords = COVID-19; SARS; Singapore; dental summary = Keywords: COVID-19, dentistry, voluntary work, preparedness, infection control BACKGROUND The emergence of the highly infectious novel coronavirus has led to a global pandemic in a span of just 3 months. Thus, the robust training of clinical medicine in dentistry strengthens the candidature of dentists to volunteer services for COVID-19 control and spread. Many dentists have therefore discontinued the provision of elective dental treatment, in accordance with guidelines released by national-level government healthcare authorities such as the Centers for Disease Control and Prevention (CDC) in the US and National Health Service (NHS) in the UK. In this context, dental clinics that are well equipped with facilities to control aerosol spread of infections, such as negative pressure rooms and high-volume excavators, can offer help to augment the capacity for COVID-19 screening. Precautions when providing dental care during Coronavirus Disease 2019 (COVID-19) pandemic doi = 10.3389/fmed.2020.00566 id = cord-301547-d4wt9dqp author = Seng, J. J. B. title = Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics date = 2020-05-11 keywords = COVID-19; MERS; SARS; health summary = Study selection Studies which evaluated health literacy related to novel coronavirus disease 2019 (COVID-19), Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS) Data extraction Data on the characteristics of study designs, instruments, participants and level of health literacy were collected. Keywords employed in the search strategy included terms related to health literacy as well as the viruses and syndromes implicated in the three coronavirus pandemics which were namely COVID-19, MERS and SARS. Studies which evaluated health literacy related to COVID-19, SARS or MERS among adult participants aged ≥ 18 years old from the general population, healthcare sectors and infected patients were included. Questions from instruments used across included studies were classified into three main themes, which were 1) knowledge, 2) attitudes and 3) practices, to help guide future development of standardised COVID-19 and pandemic health literacy tools. doi = 10.1101/2020.05.07.20094227 id = cord-342756-rgm9ffpk author = Senger, Mario Roberto title = COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date = 2020-10-02 keywords = ACE2; COVID-19; CoV-2; Fig; MERS; RNA; SARS; clinical; drug; protein summary = Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. doi = 10.1590/0074-02760200254 id = cord-333632-i2bjap7m author = Senthil Kumar, K. J. title = Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells date = 2020-06-19 keywords = ACE2; HT-29; SARS; oil summary = title: Geranium and Lemon Essential Oils and Their Active Compounds Downregulate Angiotensin-Converting Enzyme 2 (ACE2), a SARS-CoV-2 Spike Receptor-Binding Domain, in Epithelial Cells The results suggest that geranium and lemon essential oils and their derivative compounds are valuable natural anti-viral agents that may contribute to the prevention of the invasion of SARS-CoV-2/COVID-19 into the human body. To the best of our knowledge, this is the first report indicating that geranium and lemon essential oils and their major components citronellol, geraniol, limonene, linalool, and neryl acetate downregulate ACE2 receptor activity in virus-host epithelial cells. In this study, we presented the first piece of evidence that geranium and lemon essential oils and their major compounds, citronellol, geraniol, limonene, linalool, and neryl acetate, could downregulate ACE2 expression in epithelial cells, thereby blocking virus entry into host cells, and eventually preventing viral infection. doi = 10.3390/plants9060770 id = cord-320848-bz9pf2p6 author = Sepehrinezhad, Ali title = COVID-19 virus may have neuroinvasive potential and cause neurological complications: a perspective review date = 2020-05-16 keywords = OC43; SARS summary = Here, we reviewed the evidence of the neuroinvasive potential of coronaviruses and discussed the possible pathogenic processes in CNS infection by COVID-19 to provide a precise insight for future studies. Therefore, the aim of the present study was to review neuroinvasive potential and neurotropism effects of human coronaviruses (HCoVs) and discuss the probable neurological complication followed by COVID-19 to give an insight for future studies. We used the terms "coronavirus," "SARS," "SARS-CoV-2," "MERS," "229E-CoV," and "COVID-19," w i t h c o m bi n a t i o n th e t e r m s " n er vo us sy s t e m , " "neuroinvasion," and "neurological manifestation." In vitro studies on neurotropism potentials of CoVs on neural or glial cells cultures were considered. Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 doi = 10.1007/s13365-020-00851-2 id = cord-330626-0aidit63 author = Sepulveda, Jorge title = Bacteremia and Blood Culture Utilization during COVID-19 Surge in New York City date = 2020-07-23 keywords = SARS; covid-19 summary = A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase in blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity. Frequent ordering of blood cultures for patients with COVID-19 may overwhelm a laboratory''s capacity to perform and process these tests, which may negatively impact the overall benefit of testing for the entire medical center. doi = 10.1128/jcm.00875-20 id = cord-346370-jdfsacds author = Sergi, Consolato M. title = The Facemask in Public and Healthcare Workers– A Need not a Belief date = 2020-05-13 keywords = COVID-19; SARS summary = Strict isolation and social distancing measures can flatten the coronavirus infectious curve, and the use of facemask needs to be encouraged and facilitated in crowded places, particularly in hospitals where the 6-feet social distancing cannot be adopted because of physical barriers. I If most people wear a mask in public at any time the transmission rate can easily decrease beneath 1.0, thus stopping the spread of the disease and limit the long-standing Lockdown measures 13 . It is important to emphasize that while a protective mask may reduce the likelihood of infection, it will not eliminate the risk, particularly when a disease has more than one route of transmission, as identified in SARS-Cov-2. While strict isolation and social distancing measures can flatten the infectious curve, the use of facemask needs to be encouraged and facilitated where the 6-feet social distancing cannot be implemented because of physical barriers. doi = 10.1016/j.puhe.2020.05.009 id = cord-301921-i1o18nmw author = Sernicola, Alvise title = How to Deal With Post-viral Cutaneous Eruptions in the Era of Coronavirus Infection date = 2020-05-12 keywords = COVID-19; SARS summary = In our routine clinical practice during the COVID-19 outbreak, we are observing a growing number of post viral cutaneous eruptions in apparently healthy individuals in the second or third decade of life that we feel is remarkable compared to the usual local epidemiology of this season. A dermatopathologist from our country has shared the report of skin biopsies performed on two patients with COVID-19 disease, matching the histology of Giannotti-Crosti syndrome, that is a non-specific manifestation of a viral infection (11) . These observations hint at the possible role of specific genetic factors that, while a predisposition to the development of skin eruptions, may protect from severely symptomatic presentations of coronavirus infection. In our current cases of atypical skin eruptions, in which a relationship with conventional viral agents has been ruled out by laboratory testing and clinical history, molecular testing with PCR could be performed on pharynx swabs to support the hypothesis of a possible association with the novel coronavirus. doi = 10.3389/fmed.2020.00224 id = cord-262282-9xh51cd1 author = Serwer, Philip title = Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date = 2020-05-15 keywords = RNA; SARS; phage; vaccine summary = Without going into details concerning live vaccine production via eukaryotic viruses, I think it reasonable to assume that eukaryotic virus production is more difficult, more expensive and less rapid than the production of phages. However, current efforts to human-engineer improved antigens for anti-RNA virus vaccines have shown that neutralizing antibodies typically react with viral proteins that are in states that are context dependent and unstable [12, 13, 15, 20] . I take the liberty of responding here to the obvious objection that no membrane-covered, single-stranded RNA phage has ever been isolated [21] and that the pandemic viruses include influenza, Zika-type and coronaviruses, all in this category. A non-specialist observer reasonably concludes that DNA and RNA vaccines, when viewed in the context of our overall objective, are examples of type 2 strategy options. Given that eukaryotic viruses have doubling times much greater than those of phages (2-5 min for typical coliphages), meeting this objective implies that a live virus vaccine has to be already present in the environment. doi = 10.3390/antibiotics9050255 id = cord-338741-gy3ovkrt author = Sethi, Atin title = Evaluation of Current Therapies for COVID-19 Treatment date = 2020-07-22 keywords = COVID-19; SARS; patient; study summary = No survival benefit for those not requiring respiratory support [22] Convalescent plasma n = 10 severely ill patients Treatment: 200 mL IV In all 10 patients, fever, cough, shortness of breath, and chest pain disappeared or largely improved within 1-3 days of therapy initiation [23] In vitro study determining the activity of convalescent plasma from a recovered SARS-1 patient against SARS-CoV-2 Although the focus of this study was not to explore the efficacy of hydroxychloroquine/azithromycin, it outlines the importance of appropriate risk-benefit analysis while treating patients with COVID-19. This randomized control trial [10] of 199 patients explored the efficacy of lopinavir-ritonavir in hospitalized COVID-19 patients with relatively mild respiratory illness. Efficacy of hydroxychloroquine in patients with COVID-19: Results of a randomized clinical trial Clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-19 patients with at least a six-day follow up: A pilot observational study doi = 10.3390/microorganisms8081097 id = cord-257613-o0q7hvn3 author = Shafiee, Abbas title = Coronavirus disease 2019: A tissue engineering and regenerative medicine perspective date = 2020-08-21 keywords = ARDS; COVID-19; SARS; cell summary = To date, numerous studies have been conducted to evaluate the safety and efficacy of tissue engineering and regenerative medicine (TERM) products, including mesenchymal stem cells (MSCs), and their derivatives (eg, exosomes) for coronavirus infections, which could be applied for the COVID‐19. Over the COVID-19 outbreak, the funding for many TERM projects is being cut, which has a significant impact on the present and future of Current clinical trials highlight the potential benefits of stem cell therapies for COVID-19 patients. Effective multi-institutional collaboration and adequate funding from government and nongovernment sources are also needed to collect and analyze the data from ongoing and new human trials, to better understand the potential benefits of stem cell therapies for COVID-19 patients. Clinical study of mesenchymal stem cell treating acute respiratory distress syndrome induced by epidemic Influenza A (H7N9) infection, a hint for COVID-19 treatment. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial doi = 10.1002/sctm.20-0197 id = cord-341045-75of9ys6 author = Shah, Abdullah title = Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries date = 2020-09-14 keywords = SARS summary = By multiple sequence alignment of amino acids, we observed substitutions and deletion in S protein at 13 different sites in the isolates of five countries (China, USA, Finland, India and Australia) as compared to the reference sequence. Interestingly, in ORF8 substitution of Leucine, a nonpolar to Serine a polar amino acid at same position (aa84 L to S) in 23 isolates of five countries i.e. China, USA, Spain, Taiwan and India were observed, which may affect the conformation of peptides. Thus, we observed several mutations in the isolates thereafter the first sequencing of SARS-CoV-2 isolate, NC_045512.2, which suggested that this virus might be a threat to the whole world and therefore further studies are needed to characterize how these mutations in different proteins affect the functionality and pathogenesis of SARS-CoV-2. Thus, further studies are required to characterize how these amino acids substitutions in different proteins affect the functionality and pathogenesis of SARS-CoV-2. doi = 10.1016/j.genrep.2020.100886 id = cord-285569-ei9w19i7 author = Shah, Aditya title = Guide to Understanding the 2019 Novel Coronavirus date = 2020-02-28 keywords = China; SARS summary = A cluster of cases of pneumonia caused by a novel coronavirus, COVID-19, was first reported in Wuhan in the Hubei province in China in late December 2019. 1 Beta coronaviruses include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the coronavirus variant COVID-19 virus first described in Wuhan. SARS-CoV disproportionately impacted health care workers (HCWs) in countries with the most reported cases. Similar to SARS-CoV, presentation is typically fever with symptoms of lower respiratory tract infection and radiographic evidence of pneumonia or ARDS. 16 The Centers for Disease Control and Prevention (CDC) has issued interim guidance for HCWs. 17 Novel coronavirus should be suspected if patients meet the criteria described in Table 1 . Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1016/j.mayocp.2020.02.003 id = cord-317240-d7ioosi6 author = Shah, Niyati title = Review: An insight into coronaviruses: Challenges, security and scope date = 2020-08-04 keywords = ACE2; SARS summary = In principle, a molecule can act as an anti-viral drug if it inhibits some stage of the virus replication cycle, without being too toxic to the body cells. Out of these, the data of 8 patients could not be analyzed F I G U R E 2 A general mechanism of viral replication in host cells and functions of inhibitors at various stages during the process. A drug which is designed to be a fusion inhibitor will function at this stage by preventing the virus from binding with the receptor. This trial reported reduced mortality rates and also clinical improvements in 68% of the patients by the use of remdesivir. In cell culture, chloroquine shows activity against the SARS-CoV-2 virus, but the dosage requirements are usually high which may lead to serious toxicities if administered to humans. Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (H1N1) 2009 virus infection doi = 10.1002/rmv.2138 id = cord-302238-l8j1vy0y author = Shah, Prakesh S. title = Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates date = 2020-04-21 keywords = SARS summary = title: Classification system and case definition for SARS‐CoV‐2 infection in pregnant women, fetuses, and neonates The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. The possibility of mother-to-fetus transmission of SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is currently a highly debated concept in perinatal medicine. Vertical transmission of coronavirus Disease 19 (COVID-19) from infected pregnant mothers to neonates: a review Neonatal early-onset infection with SARS-CoV-2 in 33 neonates born to mothers with COVID-19 in Wuhan, China. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn doi = 10.1111/aogs.13870 id = cord-282867-kbyxdegu author = Shah, Sayed Zulfiqar Ali title = Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date = 2020-08-26 keywords = COVID-19; SARS; USWT; patient; respiratory summary = The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living. doi = 10.1155/2020/3642143 id = cord-268483-joiajgs4 author = Shah, Vibhuti Kumar title = Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past date = 2020-08-07 keywords = COVID-19; CoV-2; MERS; SARS; cell; coronavirus summary = As there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like SARS, MERS, HIV, ebola, malaria, and tuberculosis are being given to COVID-19 patients, and clinical trials for many such drugs have already begun. An ELISA-based time kinetics study to detect the COVID-19 specific humoral immune response showed that the patients produced IgM and IgG antibodies that did not cross-react with other human coronaviruses except SARS-CoV. A case study on pediatric patients reports that 5 out of 6 children showed a protective humoral response, with neutralizing IgG and IgM antibodies targeting the N and S-RBD proteins of SARS-CoV-2 (65) . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice doi = 10.3389/fimmu.2020.01949 id = cord-331472-kd4uxcve author = Shahid, Zainab title = COVID‐19 and Older Adults: What We Know date = 2020-04-20 keywords = COVID-19; CoV-2; SARS summary = Studies have shown that this virus causes worse outcomes and a higher mortality rate in older adults and those with comorbidities such as hypertension, cardiovascular disease, diabetes, chronic respiratory disease, and chronic kidney disease (CKD). 5 The Centers for Disease Control and Prevention (CDC) reported that although individuals older than age 65 comprise 17% of the total population in the United States, they make up 31% of COVID-19 infections, 45% of hospitalizations, 53% of intensive care unit admissions, and 80% of deaths caused by this infection. 15, 16 These symptoms are also common in older adults; one study on 21 critically ill patients with SARS-CoV-2 infection, with a mean age of 70 years, found that the most common presenting symptoms were shortness of breath (76%), fever (52%), and cough (48%). 19 One study on 46 fatal cases of SARS-CoV-2, in which 84% of patients were older than age 60, found that diabetes is likely associated with increased mortality. doi = 10.1111/jgs.16472 id = cord-271469-lozvq3y6 author = Shaikh, Faiq title = Current landscape of Imaging and the potential role for Artificial intelligence in the management of COVID-19 date = 2020-06-27 keywords = COVID-19; SARS summary = The clinical presentation of COVID-19 COVID-19 is primarily a respiratory tract infection caused by the SARS-CoV2 virus. Currently, the imaging features related to the neurologic complications of the virus are consistent with stroke related to large vessel occlusion and encephalopathy (Fig. 5) with reported leptomeningeal enhancement and cranial nerve palsies [25, 26] , which in the vast majority are seen in subjects with severe alternate manifestations of Covid-19 infection [27, 28] . Given that it has been shown to be useful for imaging lung infections, such as tuberculosis and atypical pneumonia [33] , its potential role in COVID19 management, albeit small may be extrapolated (Fig. 6) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response Severity assessment of coronavirus disease 2019 (COVID-19) using quantitative features from chest CT images doi = 10.1067/j.cpradiol.2020.06.009 id = cord-324246-liyk6mna author = Shakoor, Hira title = Be well: A potential role for vitamin B in COVID-19 date = 2020-08-15 keywords = SARS; covid-19; vitamin summary = Vitamin B assists in proper activation of both the innate and adaptive immune responses, reduces pro-inflammatory cytokine levels, improves respiratory function, maintains endothelial integrity, prevents hypercoagulability and can reduce the length of stay in hospital [7, 8] . In a recent preprint it is suggested that PLP supplementation mitigates COVID-19 symptoms by regulating immune responses, decreasing pro-inflammatory cytokines, maintaining endothelial integrity and preventing hypercoagulability [22] . J o u r n a l P r e -p r o o f Vitamin B not only helps to build and maintain a healthy immune system but it could potentially prevent or reduce COVID-19 symptoms or treat SARS-CoV-2 infection. In particular, vitamin B modulates immune response by downregulating pro-inflammatory cytokines and inflammation, reducing breathing difficulty and gastrointestinal problems, preventing hypercoagulability, potentially improving outcomes and reducing the length of stay in the hospital for COVID-19 patients. doi = 10.1016/j.maturitas.2020.08.007 id = cord-293543-87ulnpdm author = Shalhoub, Sarah title = Interferon beta-1b for COVID-19 date = 2020-05-10 keywords = SARS summary = 8 In The Lancet, Ivan Fan-Ngai Hung and colleagues 9 present the results of an open-label, randomised, phase 2 trial that examined the effect of a triple combination regimen of interferon beta-1b 8 million international units (0·25 mg) on alternate days, lopinavir 400 mg plus ritonavir 100 mg every 12 h, and ribavirin 400 mg every 12 h, compared with lopinavir 400 mg plus ritonavir 100 mg every 12 h alone. However, as the authors acknowledge, future studies to examine the efficacy of interferon beta-1b alone or in combination with other drugs to treat severe or critically ill patients with confirmed COVID-19 compared with placebo are warranted. Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study Triple combination of interferon beta-1b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial doi = 10.1016/s0140-6736(20)31101-6 id = cord-314669-lvibjx97 author = Shang, Guifang title = Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 date = 2007-11-26 keywords = CoV; SARS; Shenzhen summary = title: Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 STUDY DESIGN AND METHODS: Case onset dates from the 2003 Shenzhen SARS epidemic and investigational results from Taiwan on viremia in humans are used to estimate the number of cases that were viremic throughout the epidemic. RESULTS: Based on data from Shenzhen, Hongkong and Taiwan, the maximum and mean risk (per million) of SARS-CoV transmission from donors in Shenzhen were estimated as 23.57 (95% CI: 6.83–47.69) and 14.11 (95% CI: 11.00–17.22), respectively. Theoretically estimated risk of severe acute respiratory syndrome transmission through blood transfusion during an epidemic in Shenzhen, Guangdong, China in 2003 Then, using this information and information on the asymptomatic or subclinical SARS-CoV infection-to-clinically confirmed SARS ratio (R), the proportion of infected individuals who remain asymptomatic (A), and the population size, we estimated the risk of SARS-CoV transmission by transfusion from a unit of blood donated at time t during the epidemic. doi = 10.1016/j.transci.2007.09.004 id = cord-316647-jj8anf5g author = Shang, You title = Management of critically ill patients with COVID-19 in ICU: statement from front-line intensive care experts in Wuhan, China date = 2020-06-06 keywords = AKI; ARDS; China; ICU; SARS; clinical; covid-19; patient summary = RESULTS: A comprehensive document with 46 statements are presented, including protection of medical personnel, etiological treatment, diagnosis and treatment of tissue and organ functional impairment, psychological interventions, immunity therapy, nutritional support, and transportation of critically ill COVID-19 patients. Statement 8 Convalescent plasma therapy should probably be used for severe and critically ill patients with COVID-19 (Grade 2+, weak recommendation). However, critically ill patients with COVID-19 have a longer mechanical ventilation time, and daily sedatives interruption is not suggested for patients receiving deep sedation in order to reduce lung damage during early stage of severe ARDS. Light sedation is suggested for severe COVID-19 patients receiving HFNC oxygen therapy and non-invasive mechanical ventilation, and also for critically ill patients in the recovering stage (expert opinion). Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial doi = 10.1186/s13613-020-00689-1 id = cord-305856-xt3zxajf author = Shanmugam, Chandrakumar title = COVID-2019 – A comprehensive pathology insight date = 2020-09-18 keywords = COVID-19; China; CoV-2; SARS; acute summary = Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. The current pandemic of corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2) led to complete lockdown in many countries contributing to major socio-economic crisis and irreparable recession, globally. [22, 31, 32, 33] Similar to SARS CoV, a recent study reported non-O blood group specifically group A had higher infection and death rates due to COVID-19 owing to absence of protective anti-A IgM antibodies. Pulmonary pathology of early phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer The clinical pathology of severe acute respiratory syndrome (SARS): a report from China doi = 10.1016/j.prp.2020.153222 id = cord-330827-gu2mt6zp author = Shanmugaraj, Balamurugan title = Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date = 2020-02-22 keywords = China; SARS; plant; virus summary = The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. doi = 10.3390/pathogens9020148 id = cord-351837-vasuu70k author = Shannon, Ashleigh title = Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date = 2020-09-17 keywords = Fig; RNA; SARS; Supplementary; t-705 summary = title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 . doi = 10.1038/s41467-020-18463-z id = cord-296390-jv86w4j9 author = Shao, Chen title = Evolution of SARS-Co-2 RNA test results in a fatal Covid-19 patient: a case report date = 2020-05-11 keywords = February; SARS summary = On day 9 after admission, chest CT scan showed diffuse ground-glass shadows in patient''s bilateral lungs. How SARS-CoV-2-infected patients progress to critical disease is a key issue in clinical practice. He was confirmed as Covid-19 positive in February 2 nd by qPCR analysis for SARS-CoV-2RNA of samples collected by nasopharyngeal swabs. He progressed to septic shock, severe metabolic acidosis and respiratory acidosis occurred successively and then, the patient died on February 14 th . It is worthy to note that the patient received SARS-CoV-2 RNA tests by nasopharyngeal swabs six times ( Table 1 ). Since February 6 th , four times SARS-CoV-2 RNA testing by nasopharyngeal swabs were negative (Table 1) . Given the missed diagnosis of the potential bacterial infection, antibiotics treatment was started too later in this patient, which might have resulted in multi-organ failure due to a septic shock. Clinical manifestation and lung histological alteration showed that this patient suffered from SARS-CoV-2 viral pneumonia. doi = 10.1016/j.humpath.2020.04.015 id = cord-286429-voem879q author = Shao, Yi‐Ming title = Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors date = 2007-08-23 keywords = SARS; protease summary = Optimization of TL-3 as an inhibitor against the 3CL protease by replacement of the peripheral Val-Ala residues or the two central phenyl groups was based on the rationale that the binding mode of TL-3 in the protein-ligand complex mainly involves at least a dipeptide scaffold. We thus synthesized two compounds to test the binding mode hypothesis: one with two Trp groups adjacent to the central diol (4, Scheme 1) and the other with two additional Val-Ala residues as in 9. The consensus complex structure was compared with the differential density map, which shows the superimposition of the differential electron density map and the modeled binding mode of compound 4. The ligand-protein complex shown in Figure 1 B was different from the top-ranked Trp-Trp binding mode predicted from the preliminary modeling task (for differences see Figure S2 ). The subsequent refinement of the complex structure significantly improved the accuracy of the binding model, and provided a working model for further optimization of the lead compounds. doi = 10.1002/cbic.200700254 id = cord-305025-pqye1ebh author = Sharifi, Majid title = Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date = 2020-09-28 keywords = COVID-19; PCR; SARS; detection summary = The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 637 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 638 RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Rapid COVID-19 detection causative virus (SARS-CoV-2) in human 933 nasopharyngeal swab specimens using field-effect transistor-based biosensor doi = 10.1016/j.talanta.2020.121704 id = cord-309794-scqkyr5g author = Sharif‐Askari, Fatemeh Saheb title = Are patients with chronic rhinosinusitis with nasal polyps at a decreased risk of COVID‐19 infection? date = 2020-08-05 keywords = ACE2; SARS summary = In fact, higher SARS-CoV-2 viral load was detected in nasal compared to throat swabs obtained from COVID-19 infected patients [4] , and that was attributed to the difference in ACE2 expression between both tissues. Interestingly, a significant reduction in the expression of ACE2 and TMPRSS2 was observed in the nasal polyps of CRSwNPs patients compared to healthy controls ( Figure 1A ). This data suggest that eosinophilic inflammation and the associated type 2 cytokines downregulate the expression of ACE2 in nasal tissue of CRS patients and thus may have a protective role against COVID-19 infection. In conclusion, as presented in Figure 2 , our data suggest that the type of inflammation underlying CRS, as well as corticosteroid treatment, may modulate ACE2 and TEMPRSS2 gene expression levels in the nasal polyps of CRSwNPs patients. doi = 10.1002/alr.22672 id = cord-324480-7u5lh4jx author = Sharma, A. title = Structural stability of SARS-CoV-2 degrades with temperature date = 2020-10-14 keywords = CoV-2; SARS summary = Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter. However an understanding of how SARS-CoV-2 survives different environmental conditions is still incomplete and mechanisms of virus particle degradation are poorly mapped out. A key challenge in studying SARS-CoV-2 is the extreme level of threat associated with the live virus and the resultant need for high safety standards for such work. Here we used this technology to study the stability of the viral envelope and associated proteins (M, E, and S) under different environmental conditions. Environmental stability of SARS-CoV-2 on different types of surfaces under indoor and seasonal climate conditions doi = 10.1101/2020.10.12.336818 id = cord-026130-ki7bn67o author = Sharma, Anand Kumar title = Novel Coronavirus Disease (COVID-19) date = 2020-06-05 keywords = COVID-19; SARS; people; virus summary = In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. doi = 10.1007/s12045-020-0981-3 id = cord-283120-hyzk59qv author = Sharma, Ashish title = Liver disease and outcomes among COVID-19 hospitalized patients- a systematic review and meta-analysis date = 2020-10-16 keywords = COVID-19; SARS; liver summary = In this meta-analysis, we aim to study the occurrence and association of liver injury, comorbid liver disease and elevated liver enzymes in COVID-19 confirmed hospitalizations with outcomes. MATERIALS AND METHODS: Data from observational studies describing comorbid chronic liver disease, acute liver injury, elevated aspartate aminotransferase (AST), alanine aminotransferase (ALT) levels and outcomes of COVID-19 hospitalized patients from December 1, 2019, to June 30, 2020 was extracted following PRISMA guidelines. The aim of the study is to evaluate the role of the comorbid chronic liver disease (CM-CLD), elevated liver enzymes and COVID-19 associated acute liver injury (COVID-19 ALI) in predicting the outcomes in confirmed COVID-19 hospitalized patients. The Maentel-Haenszel formula was used to calculate dichotomous variables to obtain odds ratios (ORs) along with its 95% confidence intervals to describe the association of comorbid liver disease, elevated liver enzymes, acute liver injury and outcomes of COVID-19 patients in each study. doi = 10.1016/j.aohep.2020.10.001 id = cord-312708-9ywu6r2t author = Sharma, Dhruv title = Cadaveric Simulation of Otologic Procedures: An Analysis of Droplet Splatter Patterns During the COVID-19 Pandemic date = 2020-05-19 keywords = SARS; droplet summary = OBJECTIVE: The otolaryngology community has significant concerns regarding the spread of SARS-CoV-2 through droplet contamination and viral aerosolization during head and neck examinations and procedures. RESULTS: There were no fluorescein droplets or splatter contamination observed in the measured surgical field in any direction after myringotomy and insertion of ventilation tube. 7 As a result, the American Academy of Otolaryngology-Head and Neck Surgery has issued a position statement to limit elective procedures requiring interaction with upper airway mucosal surfaces or those with increased risk of aerosolization, which may include otologic procedures such as myringotomy and mastoidectomy. Since the upper respiratory tract harbors a high viral load, 3 otolaryngologists are vulnerable to SARS-CoV-2 transmission while performing head and neck procedures that utilize suction and powered instrumentation, such as the surgical drill, especially if they are doing so without appropriate protective personal equipment. doi = 10.1177/0194599820930245 id = cord-322446-ddv86eoy author = Sharma, Kulbhushan title = SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date = 2011-05-27 keywords = Fig; LMB; NES; SARS; cell summary = We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. Analysis of 9b-YFP localization showed that in addition to the extranuclear region, some amount of 9b was also present within the nucleus similar to the SARS-CoV infected cells (Fig. S1 , panel (i), (ii) and (iii)). Panel (ii) shows that even in in-vitro transport assay, SARS-CoV 9b protein localizes in both cytoplasm as well as nucleus. As shown in panel (v), the SARS-CoV 9b protein was able to enter the nucleus even in the presence of WGA showing that its entry is independent of active transport pathway. The SARS-CoV 9b protein triggers caspase 3 mediated apoptosis when retained in the nucleus of mammalian cells While performing pulse-chase assays, we found that a significant number of Vero E6 cells, in which nuclear export of 9b has been inhibited (either by treating with LMB or using NES deficient 9b), were showing caspase 3 dependent apoptosis. doi = 10.1371/journal.pone.0019436 id = cord-336103-ufvq0ngl author = Sharma, R. title = Optimal sample pooling: an efficient tool against SARS-CoV-2 date = 2020-07-04 keywords = SARS; sample summary = 2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2 doi = 10.1101/2020.07.03.20145953 id = cord-320704-rrq6x25k author = Sharma, Shruti title = COVID-19: A Concern for Cardiovascular Disease Patients date = 2020-07-29 keywords = ACE2; SARS summary = The organism responsible for the cause of disease is Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Coronavirus Disease (COVID-19) is a recently emerged disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2), a novel coronavirus that leads to adverse pulmonary pathological features [1] . Therefore, in the present review, the role of ACE2 receptors in the viral entry into the host cell, the effect of COVID-19 on the symptoms and prognosis of CVDs, impact of ACE inhibitors (ACEI), and angiotensin receptor blockers (ARBs) on patients of CVDs suffering from COVID-19 have been discussed. Various cardiac complications like cardiovascular disease, arrhythmia (ventricular tachyarrhythmia, atrial fibrillation and ventricular fibrillation), hypertension, cardiac injury, heart failure, and fulminant myocarditis have been found to influence the mortality of the COVID -19 patients [27] . There is a possibility that polymorphism in ACE2 gene, linked to hypertension, particularly, in Asian populations, affects the susceptibility of SARS-CoV-2 infection and COVID-19 disease outcome. ACE2 receptor polymorphism: Susceptibility to SARS-CoV-2, hypertension, multi-organ failure, and COVID-19 disease outcome doi = 10.1007/s12012-020-09596-0 id = cord-257008-7q5s1vu1 author = Sharma, Virender K. title = Environmental chemistry is most relevant to study coronavirus pandemics date = 2020-05-20 keywords = SARS; virus summary = In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) doi = 10.1007/s10311-020-01017-6 id = cord-290472-w77cmljm author = Sharon, Donald title = Systems Biology Approaches to Disease Marker Discovery date = 2010-06-09 keywords = RNA; SARS; cancer; disease; marker; protein summary = These markers, such as protein (including autoantibodies, which are antibodies specific to self-antigens [43] ), hormonal markers (such as lack of insulin in Type I diabetic patients [89] ), and genetic/genomic markers (such as BRCA1 mutation in breast cancer patients [52] ), enable clinicians to diagnose the disease while it is still at early stages, to ensure appropriate surgical intervention, efficient drug treat-ment and monitoring, and to predict an individual''s risk of developing specific diseases before they experience symptoms. Scientists, such as the group led by Gil Mor at Yale University, recruited proteomics-based approaches using antibody-based protein microarrays to identify new serum biomarkers, which, in combination with CA-125, may enhance the early detection of ovarian cancer [48, 66, 110] . To date, no studies that attempt to identify novel breast cancer markers have been performed using high-density protein microarrays. doi = 10.3233/dma-2010-0707 id = cord-281937-yztlb0fn author = Sheahan, Timothy P title = The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health date = 2020-06-04 keywords = China; SARS summary = A new paradigm for human coronavirology was born with the emergence of severe acute respiratory syndrome CoV (SARS-CoV) in November 2002 in Guangdong Province, China. The epidemic strain of SARS-CoV, is believed to have emerged from a bat reservoir through a civet intermediate host in live animal markets and then spilled over into humans 2 . This notion of CoV emergence was further solidified with discovery of the novel highly pathogenic Middle East respiratory syndrome CoV (MERS-CoV) in 2012, which also likely emerged from an ancestral bat-CoV but through a camel intermediate host which continues to seed human MERS-CoV infections to this day 2,3 . Given the diversity and prevalence of CoV circulating among wild birds and mammals, it is not surprising that the potential for emerging CoV to cause severe disease outbreaks and epidemics is not limited to humans. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence doi = 10.1016/j.coviro.2020.05.010 id = cord-300608-eju7wnb9 author = Sheervalilou, Roghayeh title = COVID‐19 under spotlight: A close look at the origin, transmission, diagnosis, and treatment of the 2019‐nCoV disease date = 2020-05-26 keywords = COVID-19; China; SARS; patient summary = 2.1 | Respiratory system SARS-CoV-2 tends to infect the respiratory tract, thus, pneumonia is a primary clinical finding in patients with COVID-19 Li, Guan, et al., 2020; Zhu et al., 2020) . A number of investigations recently conducted on COVID-19 have reported that IL-6 levels was actually higher in the patients with severe disease (Cai, 2020; Chen, Liu, et al., 2020; Xiang et al., 2020) . Impaired liver function tests have been reported for a number of patients with SARS-CoV-2 infection, suggesting hepatic damage as an extrapulmonary complication of COVID-19 in almost one half of the patients (Chen, Zhou, et al., 2020; Wang, Hu, et al., 2020) . Since H7N9 and SARS-CoV-2 can result in similar complications, for example, ARDS and respiratory failure, MSC-based therapy might lead to a new path in treatment of COVID-19-associated pneumonia . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.1002/jcp.29735 id = cord-263450-v6vdg8os author = Shegogue, Daniel title = Object-oriented biological system integration: a SARS coronavirus example date = 2005-05-15 keywords = SARS; object; system summary = Results: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. In addition, applying a well-defined software engineering process and object-oriented methodology provide an effective means to capture specifications from experimental data and integrate the biological system information. Finally, this process provides a guideline for the development of an integrated biological system, represented as an object-oriented software architecture, in a widely accepted objectoriented modeling language (such as UML), which can facilitate communication about complex systems among software engineers, biologists and other users. To demonstrate the efficacy of a well-defined software engineering process in the translation of a biological system to a model grounded in object-oriented principles, we used UML in the development of a severe acquired respiratory syndrome-coronavirus (SARS-CoV) model. doi = 10.1093/bioinformatics/bti344 id = cord-033551-eojpkxz9 author = Shekh, Shamasoddin title = In silico allicin induced S-thioallylation of SARS-CoV-2 main protease date = 2020-09-16 keywords = CoV-2; SARS summary = In the current report, using virtual screening methods, reactive sulfur species allicin is subjecting for covalent docking at the active site of SARS-CoV-2 M(pro) using PX-12 as a benchmark reference compound. Figure 1a shows the structure of SARS-CoV-2 M pro with free cysteine thiols and active site dyad residues. Figure 2b shows the formation of cysteine allyl disulfide at the Cys-145 residue of SARS-CoV-2 M pro after covalent docking with allicin. Figure 4b and c show the formation of cysteine allyl disulfide at Cys-85 and Cys-156 residue of SARS-CoV-2 M pro after covalent docking with allyl sulfenic acid. Table-S2 provides a summary of covalent docking of allicin/PX-12/allyl sulfenic acid at cysteine thiols of four different co-crystal structures of SARS-CoV-2 M pro . Figure 5b shows the sulfur mediated hydrogen bonding by the sulfur of allyl disulfide formed after covalent docking of allicin at the active site of SARS-CoV-2 M pro . doi = 10.1080/17415993.2020.1817457 id = cord-299156-1dwsm3ie author = Shemer, Asaf title = Ocular involvement in coronavirus disease 2019 (COVID-19): a clinical and molecular analysis date = 2020-09-14 keywords = COVID-19; SARS; patient summary = The aim of this study was to assess the clinical and molecular ocular involvement among patients with confirmed COVID-19 admitted to a tertiary care facility. CONCLUSIONS: Among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was noted in one out of five cases, and was associated with loss of smell and taste. Among patients with COVID-19, active conjunctival injection was associated with loss of smell and loss of taste as part of the clinical presentation (66.7% vs 7.7%, p = 0.018). In this study, we evaluated the ocular signs and symptoms, as well as the presence of SARS-CoV-2 in conjunctival swab samples among patients with COVID-19 in one tertiary referral center during March and April of 2020. To conclude, among patients admitted to a tertiary referral center with confirmed COVID-19, active conjunctival injection was present in 19% of cases and was associated with loss of smell and taste as part of the clinical presentation. doi = 10.1007/s10792-020-01592-1 id = cord-312533-4u3bmb0e author = Shen, Li Wen title = TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections date = 2017-08-01 keywords = H1N1; MERS; SARS; TMPRSS2 summary = Recently, a great deal of evidence has suggested that a transmembrane protease, serine 2 (TMPRSS2), a type II transmembrane serine protease (TTSP), plays a critical role in SARS and Abbreviations: ARE, androgen receptor element; AEBSF, 4-(2-Aminomethyl) benzenesulfonyl fluoride hydrochloride; BHH, Bromhexine hydrochloride; CoV, coronavirus; DESC1, serine protease DESC1; EST, (2S,3S)-trans-Epoxysuccinyl-Lleucylamido-3-methylbutane ethyl ester; FDA, Food and Drug Administration; HAT, human airway trypsin-like protease; HAI-2, hepatocyte growth factor activator inhibitor 2; HGF, hepatocyte growth factor; IFITM, Interferon-induced transmembrane protein; MMP-2, matrix metalloproteinase-2; MSPL, transmembrane protease, serine 13; PAI-1, plasminogen activator inhibitor 1; PAR-2, protease activated receptor 2; PPMO, peptide-conjugated phosphorodiamidate morpholino oligomer; RBS, receptor binding subdomain; THE, human tracheal epithelial; TMPRSS2, transmembrane protease, serine 2; TMPRSS4, transmembrane protease serine 4; TTSP, type II transmembrane serine protease; vRNPs, viral ribonucleoproteins. Although FDA-approved inhibitors that specifically inhibit TMPRSS2 are not yet available, some drugs such as camostat and nafamostat that have inhibitory activity against a variety of serine proteases have been approved for the treatment of other diseases and also suppress influenza virus and coronavirus infections. doi = 10.1016/j.biochi.2017.07.016 id = cord-327318-qhrsli0b author = Shen, Qian title = Consensus recommendations for the care of children receiving chronic dialysis in association with the COVID-19 epidemic date = 2020-04-24 keywords = SARS summary = In turn, a set of recommendations for the prevention and control of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 in pediatric hemodialysis (HD) centers and in home peritoneal dialysis (PD) settings have been proposed. The recommendations are based on the epidemiological features of the SARS-CoV-2 virus and COVID-19 disease, susceptibility factors, and preventive and control strategies. In turn, the factors associated with an increased risk for contracting SARS-CoV-2 infection among pediatric chronic dialysis patients, especially those who receive in-center HD, include the following: (a) compromised immune system (the result of long-term malnutrition, uremia, and/or immunosuppressants); (b) close proximity to other Preventive and control strategies for in-center HD Staff management (Table 2 ) In order to effectively prevent and control the transmission of SARS-CoV-2 among children who receive maintenance dialysis, we formulated this set of recommendations based on infectious disease guidelines and our experience with the COVID-19 epidemic, which healthcare staff in pediatric dialysis centers can refer to. doi = 10.1007/s00467-020-04555-x id = cord-350957-10wcqgaq author = Shen, Zu T. title = SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice date = 2016-06-28 keywords = MG11; SARS; TCR summary = Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). Previously, we reported that incorporation of another immunomodulatory peptide, GF9, that employs the SCHOOL mechanisms of action and targets triggering receptor expressed on myeloid cells 1 (TREM-1), into synthetic HDL-like nanoparticles of spherical shape (sHDL) significantly reduces the effective therapeutic dosage of GF9 in animal models of sepsis, lung cancer, and RA 33, 34 . As expected from the anti-arthritic activities demonstrated in animal models of autoimmune arthritis for TCR CP 20,21,23 and HIV gp41 FP 18 , the SARS-CoV FP-derived peptide sequence MG11 significantly suppresses CIA in mice: the peptide at 25 mg/kg/day inhibits inflammation in CIA as assessed by clinical evaluation and scoring of the disease (Fig. 2) . doi = 10.1038/srep28672 id = cord-276327-wyevh4xv author = Sheng, Calvin C title = Canakinumab to reduce deterioration of cardiac and respiratory function in SARS‐CoV‐2 associated myocardial injury with heightened inflammation (canakinumab in Covid‐19 cardiac injury: The three C study) date = 2020-08-24 keywords = COVID-19; SARS; patient; study summary = We designed a proof‐of‐concept randomized controlled trial to evaluate whether treatment with canakinumab prevents progressive respiratory failure and worsening cardiac dysfunction in patients with SARS‐CoV2 infection, myocardial injury, and high levels of inflammation. The three C Study is a prospective, IRB approved, blinded randomized-controlled Phase II study designed to evaluate whether treatment with canakinumab prevents progressive heart and respiratory failure in patients with Covid-19 associated myocardial injury and increased inflammation. This blinded randomized controlled trial is designed as a proof of concept study to demonstrate whether IL-1β antagonism can dampen the deleterious autoinflammatory response to SARS-CoV2 infection in patients with myocardial injury and heightened inflammation. In evaluating this hypothesis, the Three C study will help inform whether targeting inappropriate activation of the innate immune system should be investigated in larger clinical trials to improve survival in patients with Covid-19 and myocardial injury. doi = 10.1002/clc.23451 id = cord-333897-isodrtly author = Shenoy, Niraj title = Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting? date = 2020-08-19 keywords = ACE2; SARS; covid-19 summary = Finally, it discusses potential implications of specific clinical observations and considerations in COVID-19 patients on target oxygen saturation, such as diffuse systemic endothelitis and microthrombi playing an important pathogenic role in the wide range of systemic manifestations, exacerbation of hypoxic pulmonary vasoconstriction in the setting of pulmonary vascular endothelitis/microthrombi, the phenomenon of "silent hypoxemia" with some patients presenting to the hospital with severe hypoxemia disproportional to symptoms, and overburdened health systems and public health resources in many parts of the world with adverse implications on outpatient monitoring and early institution of oxygen supplementation. -The LOCO-2 trial [2] where ARDS (acute respiratory distress syndrome) patients were randomized to conservative (target partial pressure of arterial oxyHere, we examine the above two studies guiding current target oxygen saturation recommendations for COVID-19; discuss, with supporting transcriptomic analyses, the influence of hypoxia on ACE2 (angiotensin converting enzyme-2, target receptor for SARS-CoV-2 entry) expression; reflect on relevant clinical observations and considerations in COVID-19 patients; and propose a reevaluation of target oxygen saturation in these patients-both in the inpatient and outpatient settings. doi = 10.1186/s12916-020-01735-2 id = cord-338648-5evr2v3r author = Shental, Noam title = Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers date = 2020-09-11 keywords = SARS; best summary = We developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, which identifies all positive subjects within a set of samples using a single round of testing. Here, we developed P-BEST, a method for Pooling-Based Efficient SARS-CoV-2 Testing, using a single-stage nonadaptive group-testing approach, which significantly reduces the number of tests required to identify all positive subjects within a large set of samples. PCR results for each of the pools are provided to the detection algorithm (see Methods), which identifies all positive carriers without the need for an additional testing stage (Fig. 1 , A to C). RNA was extracted from each single sample and pools and was then tested for SARS-CoV-2 using the Seegene COVID-19 diagnostic kit. Using a pooling scheme designed for a carrier rate of ~1%, we showed that our method correctly identified all positive carriers in sets of 384 samples pooled into 48 pools, thereby providing an eightfold reduction in the number of required tests. doi = 10.1126/sciadv.abc5961 id = cord-346711-2k736hvr author = Shetty, Rohit title = Stem cell therapy in COVID-19 – current evidence and future potential date = 2020-11-09 keywords = COVID-19; Mesenchymal; SARS; cell summary = Acute respiratory distress syndrome (ARDS) caused by an unregulated host inflammatory response towards the viral infection, followed by multi-organ dysfunction or failure, is one of the primary causes of deaths in severe cases of COVID-19 infection. Expanded Umbilical Cord Mesenchymal Stem Cells (UC-MSCs) as a Therapeutic Strategy in Managing Critically Ill COVID-19 Patients: The Case for Compassionate Use Clinical remission of a critically ill COVID-19 patient treated by human umbilical cord mesenchymal stem cells FDA approved mesenchymal stem cell (MSC) treatments as compassionate use in the very sickest COVID-19 patients Adipose-derived mesenchymal stromal cells for the treatment of patients with severe SARS-CoV-2 pneumonia requiring mechanical ventilation. Treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (START study): a randomised phase 2a safety trial, The Lancet Therapeutic Effects of Human Umbilical Cord-Derived Mesenchymal Stem Cells in Acute Lung Injury Mice doi = 10.1016/j.jcyt.2020.11.001 id = cord-290978-e7imc11r author = Shevachman, M. title = A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic date = 2020-08-07 keywords = SARS; cg-101; test summary = A long-lasting sanitizing skin protectant that can effectively inactivate SARS-CoV-2 and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. Hence, development of an effective hand sanitizer that can generate long-lasting protective effects can offer significant benefits in minimizing rampant viral transmissions and maximize virus inactivation in a pandemic situation like SARS-CoV-2 outbreak [15, [17] [18] [19] . In order to determine the prolonged protective effects of IonLAST TM in contrast to the currently marketed products containing 70% ethyl alcohol, an in-vitro efficacy study was conducted using E. We evaluated the virucidal effects of IonLAST TM gel and the active CG-101 (5% w/w in purified water) against human Coronavirus strain 229E (hCoV229E) using a virucidal suspension test (in-vitro time-kill method) based on industry/regulatory-relevant global standardized methodologies (ASTM E1052-20). doi = 10.1101/2020.08.04.20161067 id = cord-270591-0szbkhiz author = Shi, Chen title = Comprehensive Landscape of Heparin Therapy for COVID-19 date = 2020-10-22 keywords = COVID-19; IL-6; SARS; heparin summary = Clinical observations found that systemic symptoms caused by SARS-CoV-2 infection are attenuated when using the anticoagulant agent heparin, indicating that heparin may play other roles in managing COVID-19, in addition to prevention of pulmonary thrombosis. This review discusses the pharmacological mechanisms of heparin regarding its anticoagulant, anti-inflammatory and direct antiviral activities, providing current evidence concerning the effectiveness and safety of heparin therapy for this major public health emergency. In addition to its anticoagulant and anti-inflammatory activity, heparin may possess a direct antiviral effect to SARS-CoV-2, based on the preclinical studies for other viral infections. There are both preclinical evidence and clinical data to demonstrate the benefits of heparin therapy for SARS-CoV-2 infection.With anticoagulant and anti-inflammatory effects, heparin can offer supportive treatment and alleviate the systematic symptoms of COVID-19. doi = 10.1016/j.carbpol.2020.117232 id = cord-333429-bq7kfpby author = Shi, Ding title = Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date = 2020-07-02 keywords = RNA; SARS; patient summary = title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. doi = 10.1093/infdis/jiaa388 id = cord-320175-w00rcvd8 author = Shi, Jiahai title = The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain date = 2006-02-08 keywords = HSQC; SARS; dimerization; protease summary = Based on this, a super‐active triple‐mutant STI/A with a 3.7‐fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild‐type (WT) and STI/A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Based on this, a super-active triple-mutant STI ⁄ A with a 3.7-fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild-type (WT) and STI ⁄ A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. Dynamic light scattering (DLS) was used to measure the apparent molecular mass resulting from monomer-dimer equilibrium of the wild-type and mutated proteases at three different NaCl concentrations. doi = 10.1111/j.1742-4658.2006.05130.x id = cord-263847-kyak5cy4 author = Shi, Tzu-Hau title = Andrographolide and its fluorescent derivative inhibit the main proteases of 2019-nCoV and SARS-CoV through covalent linkage date = 2020-08-25 keywords = SARS; pro summary = We herein demonstrate that both andrographolide and its fluorescent derivative, the nitrobenzoxadiazole-conjugated andrographolide (AndroNBD), suppressed the main protease (M(pro)) activities of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV). Further mass spectrometry (MS) analysis suggests that andrographolide formed a covalent bond with the active site Cys(145) of either 2019-nCoV M(pro) or SARS-CoV M(pro). Moreover, lopinavir/ritonavir, previously identified as HIV protease inhibitors and found to exhibit anti-SARS-CoV activity in vitro and in clinical, have been proposed to bind 2019-nCoV M pro and are being investigated for COVID-19 treatments [6, 7] . Lopinavir/ritonavir, the HIV protease inhibitors previously identified with anti-SARS-CoV activity in vitro and in clinical, was proposed to bind 2019-nCoV M pro and thus has been investigated for COVID-19 treatments [6, 7] . In this study, we revealed that andrographolide and its derivative inhibits the activity of main protease and thus likely to impair the replication of SARS-CoV and 2019-nCoV. doi = 10.1016/j.bbrc.2020.08.086 id = cord-349365-2ot1kf2k author = Shi, Yi title = Antisense downregulation of SARS‐CoV gene expression in Vero E6 cells date = 2004-11-15 keywords = SARS summary = Cells were then treated with the antisense oligonucleotides used by adding them to the culture medium, which then reached the nuclei and resulted in sequence-specific antisense downregulation of SARS-CoV gene expression. We conclude that the antisense PS-ODNs could effectively and sequence-specifically downregulate SARS-CoV gene expression in a dose-dependent manner. In this work, we have evaluated the down-regulation effects of 26 antisense PS-ODNs targeting different sites along the open reading frames (ORFs) of E, M, and N proteins and obtained 12 antisense oligos which could reduce target gene expression by over 50% in Vero E6 cells at the concentration of 50 µM in the culture medium. Our present results indicate a sequencespecific down-regulation effect of antisense PS-ODN (20mer) in Vero E6 cells, and we found an effective range of concentrations, where the antisense oligo inhibited expression of the E, M, and N genes of SARS-CoV in a concentration-dependent manner. doi = 10.1002/jgm.640 id = cord-103940-a2cqw8kg author = Shi, Yuejun title = Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date = 2020-06-09 keywords = RBD; SARS summary = Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in lying and standing state, respectively. In this study, 130 we selected SARS-CoV, SARS-CoV-2, and HCoV-229E as models, which adopt the 131 two RBD states, and evaluated and compared immune responses to the S trimers and 132 7 RBDs of these coronaviruses through immunological and bioinformatics approaches. 133 We also investigated the mechanism through which the HCoV-229E S trimer 134 produced effective nAbs. Finally, we provide possible vaccine strategies for alphaTo address this issue, we performed B-cell epitope predictions for the S trimers 152 and RBDs of alpha-CoV (HCoV-229E) and beta-CoVs (SARS-CoV and 153 SARS-CoV-2). Taken together, these results showed that the intact and stable S1 subunit of 240 HCoV-229E is a prerequisite for the production of effective nAbs. Furthermore, our experimental results show that RBD has a higher ability to bind 242 12 to the receptor hAPN (Fig. 4B) , which indicates that the characteristics of RBD itself 243 may lead to the generation of less neutralizing antibodies. doi = 10.1101/2020.06.09.141580 id = cord-335955-2bw2sly8 author = Shi, Yuejun title = A Dimerization-Dependent Mechanism Drives the Endoribonuclease Function of Porcine Reproductive and Respiratory Syndrome Virus nsp11 date = 2016-04-14 keywords = Fig; K173A; PRRSV; S74A; SARS; nsp11 summary = The crystal structures of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp15 and murine hepatitis virus (MHV) nsp15 show that the biological unit of nsp15 is a hexamer (19, 21) and that the N-terminal domain (NTD) is important for oligomerization (23) . We report the crystal structure of PRRSV endoribonuclease nsp11 and demonstrate that the folding of NendoU active site residues is widely conserved among members of the order Nidovirales (families Arteriviridae and Coronaviridae). Additionally, the structural comparison demonstrated that residues His129, His144, Lys173, Thr177, Asp180, Asp204, and Tyr219 from nsp11 superimpose well onto the corresponding residues of coronavirus nsp15 (Fig. 5 and 6 ), indicating the relative conservation of key active site residues and similar endoribonuclease cleavage mechanisms shared among nidoviruses (families Arteriviridae and Coronaviridae). In this study, endoribonuclease activity of the wild-type and mutant nsp11 protein was measured, and the results are shown in Fig. 7C . doi = 10.1128/jvi.03065-15 id = cord-354893-tku1dr32 author = Shi, Zhengli title = Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology date = 2010-12-24 keywords = SARS summary = Comparative genome sequence analysis indicated that SARS-CoVs civets experience rapid ongoing mutation, suggesting that the viruses were still adapting to the host rather than persisting in equilibrium expected for viruses in their natural reservoir species Song et al., 2005) . Analysis of all the viral sequences available from human patients and animals revealed two major hallmarks of rapid virus evolution during the initial stages of the 2002À2003 outbreaks: (1) All isolates from early patients and market animals contained a 29-nt sequence in ORF8 that is absent in most of the publicly available human SARS-CoV sequences derived from later phases of the outbreaks; (2) a characteristic motif of single-nucleotide variations (SNVs) were identified in SARS-CoV of different phases, and all these SNVs were located in the S gene that codes for the spike protein responsible for attachment to host cellular receptor . Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections doi = 10.1016/b978-0-12-384890-1.00027-3 id = cord-355514-2qjbc3bd author = Shibata, Shun title = High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection date = 2020-07-25 keywords = RIAT; SARS summary = title: High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 1 High incidence of false-positive results of IgG antibody against SARS-CoV-2 with rapid immunochromatographic antibody test due to human common cold coronavirus infection 2 Because of high incidence of false positive RIAT results, cross antigenicity between human common cold coronaviruses and SARS-CoV-2 can be considered. We experienced a patient suffering human coronavirus HKU1 pneumonia who showed false-positive results for IgG against SARS-CoV-2 using an RIAT. We performed RIAT using a commercially available kit for IgM and IgG against SARS-CoV-2 in serum samples of 24 patients with laboratory-confirmed COVID-19 (admitted from February to April 2020), 7 patients with human common cold coronavirus pneumonia (Table 1) and IgM with median 12 days from illness onset was compatible with previous reports [3, 4] . doi = 10.1016/j.rmcr.2020.101180 id = cord-346816-xys0g8b8 author = Shichijo, S. title = Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity date = 2004-10-20 keywords = SARS; peptide summary = title: Assessment of synthetic peptides of severe acute respiratory syndrome coronavirus recognized by long‐lasting immunity Abstract: In order to determine highly immunogenic severe acute respiratory syndrome coronavirus (SARS‐CoV) epitope peptides capable of inducing long‐lasting immunity, we first screened immunoglobulin‐G (IgG) antibodies reactive to 197 different overlapping 15‐mers from the SARS‐CoV proteins in the sera of three infected patients. The significantly higher levels of IgG antibodies specific to three (S791, M207 and N161) of 42 peptides were detectable in the post‐infection sera from 23 (51%), 27 (60%) and 19 (42%) of 45 patients, respectively. In contrast to these four peptides, significant levels of IgG reactive to the remaining 36 peptides were either scarcely or not detected in the patients (Table 1) Fig. 5 . Dynamic observation IgG and IgM antibodies in patients with severe acute respiratory syndrome doi = 10.1111/j.1399-0039.2004.00314.x id = cord-352080-3rcqbgl7 author = Shidham, Vinod B. title = Severe acute respiratory syndrome coronavirus 2 (the cause of COVID 19) in different types of clinical specimens and implications for cytopathology specimen: An editorial review with recommendations date = 2020-04-10 keywords = SARS; specimen; table summary = It is therefore mandatory to practice all the universal/standard precautions with basic protective measures while handling any biological specimen irrespective of SARS-CoV-2 status [Tables 1 -3] . [16] Although, appropriate disinfectants and precautions related to cytopathological/histological fixation and processing of samples during the current COVID 19 pandemic are not known, information can likely be extrapolated from other recent coronaviruses (e.g., SARS and MERS). 5. If the diagnostic testing specimens are processed outside of a BSL-2 laboratory, [33] such as preparation of cytology direct smears, rinsing of FNAB aspirates for cell block, the Standard Precautions (similar to those mentioned under Table 1 ) should be practiced as a barrier between the specimen and personnel. [14, 15] In cases suspected or positive for SARS-CoV-2 virus-perform the processing in certified Class II [35] Biological Safety Cabinet FNAB procedure [22] Based on the aforementioned, SARS-CoV-2 in any specimen processed with routine fixatives in cytopathology should be inactivated [ Table 5 ]. doi = 10.25259/cytojournal_24_2020 id = cord-355760-2a12nsnl author = Shields, A. M. title = SARS-CoV-2 seroconversion in health care workers date = 2020-05-19 keywords = SARS summary = Conclusions In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. In a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. Evidence before the study To date, no study has examined the cross-sectional seroprevalence of anti-SARS-CoV-2 antibodies in health care workers during the COVID-19 pandemic. We conducted a cross-sectional study of 554 staff at UHBFT to determine the incidence of infection and seroconversion in health care workers and their relationship to prior symptoms of COVID-19. In light of further evidence of asymptomatic infection and seroconversion, the impact of mandatory screening of health care workers should be thoroughly investigated [12] The seroprevalence of SARS-CoV-2 antibodies amongst the UK general population remains unknown and few studies have considered seroprevalence in other populations. In conclusion, we provide evidence of SARS-CoV-2 seroconversion in health care workers with and without prior symptomatic illness. doi = 10.1101/2020.05.18.20105197 id = cord-325966-0g7a9s5z author = Shih, Hsin-I. title = Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date = 2020-05-30 keywords = BCG; COVID-19; CoV-2; RNA; SARS; vaccine summary = Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. However, these clinical, laboratory, and imaging findings are nonspecific and cannot differentiate COVID-19 from other viral respiratory infections; viral diagnostic methods specific for SARS-CoV-2 should be applied for disease confirmation. An open-label study published in 2004 suggested, by comparison with a control group that received only ribavirin, that the addition of lopinavir-ritonavir (400 mg and 100 mg, respectively) to ribavirin reduced the risk of adverse clinical outcomes (acute respiratory distress syndrome or death) and viral load among patients with SARS [29] . Some available candidate drugs targeting different levels of human responses to COVID-19, such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, IL-6 blocker and convalescent plasma, may improve the clinical outcomes of critical COVID-19 patients. doi = 10.1016/j.bj.2020.05.021 id = cord-337867-hqmf6r7t author = Shim, Byoung-Shik title = Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses date = 2010-12-31 keywords = PEI; SARS; dna summary = title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses RESULTS: In the present study, the immune responses of BALB/c mice immunized via intranasal (i.n.) route with SARS DNA vaccine (pci-S) in a PEI/pci-S complex form have been examined. The result showed that SARS S-specific IgA antibody response was significantly (P < 0.01) increased in lung wash from mice immunized with PEI/pci-S complexes ( Figure 2B ). B220 + cells from mice immunized with PEI/pci-S complexes were highly proliferated after in vitro re-stimulation with SARS-CoV S protein ( Figure 2C ). The surface expression of CD80 and CD86 co-stimulatory molecules were significantly (P < 0.05) higher on DCs from mice treated with PEI/pci-S complexes than those from SARS-CoV DNA S vaccine alone ( Figure 3 ). DNA vaccine encoding full-length S protein has shown to induce humoral, cellular and protective immune responses against SARS-CoV [6] . doi = 10.1186/1471-2172-11-65 id = cord-275746-3sgbpn13 author = Shimamoto, Yasuhiro title = Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors date = 2015-02-15 keywords = 3CL; SARS summary = After the reaction mixture was cooled to room temperature, water was added and the whole was extracted with AcOEt. The organic layer was washed with 1 M HCl and brine, dried over MgSO 4 , filtered, and concentrated. After the mixture was stirred for 12 h, the reaction was quenched with saturated aqueous NH 4 Cl and the whole was extracted with AcOEt. The organic layer was washed with brine, dried over Na 2 SO 4 , filtered, and concentrated. The residue was purified by silica gel column chromatography (hexane/AcOEt = 3:1) to give a title alcohol ( 21 .0 mmol) in CH 2 Cl 2 (50 mL), and the mixture was stirred for 8 h at room temperature. The residue was purified by silica gel column chromatography (hexane/AcOEt = 6:1) to give 32 ( Tris-HCl buffer pH 7.5 containing 7 mM DTT) was incubated with the R188I SARS 3CL pro28 (56 nM) at 37°C for 60 min in the presence of various inhibitor concentrations at 37°C for 60 min. doi = 10.1016/j.bmc.2014.12.028 id = cord-281101-gv1sgbk1 author = Shin, Gu-Choul title = Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date = 2006-08-30 keywords = ELISA; SARS; protein summary = Severe acute respiratory syndrome-coronavirus nucleocapsid (SARS-CoV N) protein has been found to be important to the processes related to viral pathogenesis, such as virus replication, interference of the cell process and modulation of host immune response; detection of the antigen has been used for the early diagnosis of infection. Reactivity of SARS-N mAbs with SARS-CoV infected cells was determined by immunofluorescence assay, performed according to the instructions of the manufacturer (Euroimmun, Germany). To further assess the specificity of the mAbs, antigen-capture ELISA was performed with human coronavirus-infected cell lysates and BrSARS-N protein as positive control (Fig. 6B) . (B) Cross-reactivity of SARS-N mAbs was examined by antigen-capture ELISA using human coronavirus OC43 lysates (256 HA unit), BrSARS-N protein (500 ng/well) and PBST buffer with 1% BSA as control. These mAbs were available for use in detecting SARS-CoV N protein by various diagnostic methods, such as immunoblot assay, immunofluorescence assay and antigen-capture ELISA (Table 3) . doi = 10.1016/j.virusres.2006.07.004 id = cord-303661-etb19d6y author = Shin, Hyoung-Shik title = Empirical Treatment and Prevention of COVID-19 date = 2020-06-22 keywords = COVID-19; SARS; patient; treatment summary = Though the COVID-19 showed pandemic spread and unexpected clinical manifestations characterized by various symptoms throughout the whole body, SARS-CoV-2 seems to be less virulent especially in children and adolescents, in whom the disease mimics common cold caused by seasonal coronaviruses [7] . At the early stage of the epidemic, it had been recommended to apply the treatment regimen of middle east respiratory syndrome coronavirus (MERS-CoV) in the case of the patients with severe symptoms [23] . Considering that the infection can be asymptomatic and as it can rapidly spread across national borders, studies-to elucidate the life cycle of SARS-CoV-2, innate and adaptive immune responses to the virus, and side effects of medicationsshould be conducted on a global scale; this would help in developing appropriate treatment strategies. doi = 10.3947/ic.2020.52.2.142 id = cord-350679-69lv4wbz author = Shinde, Rajesh S. title = To Do or Not to Do?—A Review of Cancer Surgery Triage Guidelines in COVID-19 Pandemic date = 2020-05-11 keywords = COVID-19; SARS; cancer; patient summary = In the absence of actual data on cancer surgery care during this pandemic, clinical decisions should be based on careful consideration of disease-related and patient-related factors. As cancer surgeries involve significant healthcare resources in terms of infrastructure, intensive care unit beds, blood products and manpower, surgical oncologists face a dilemma regarding the triage of surgical patients during this period of uncertainty. A particular concern for a cancer surgeon is to weigh the risk of deferring cancer surgery versus the risk of COVID-19 exposure and infection to patients as well as health care providers. Smoking, one of the commonest risk factors in lung cancer, has not been independently shown to affect the mortality in SARS-CoV-2 patient; however, pre-existing chronic obstructive lung disease is associated with increased mortality [4] . Clinical management of lung cancer patients during the outbreak of 2019 novel coronavirus disease (COVID-19) doi = 10.1007/s13193-020-01086-7 id = cord-254464-6l7fwylu author = Shingare, Ashay title = COVID‐19 in recent kidney transplant recipients date = 2020-06-08 keywords = SARS; covid-19 summary = Younger age, absence of other comorbidities and lower dose of anti‐thymocyte globulin (ATG) used as induction possibly contributed to good outcome in our recent LDKT recipients compared with earlier published cases of recent deceased donor kidney transplant recipients with COVID‐19. Sooner or later we would need to restart transplant programs, both LDKT & deceased donor kidney transplant (DDKT), as dust settles on the acute era to a post-COVID-19 new normal, where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will be a possibility. During the further follow-up over next 2 months, 2 of these 7 patients tested positive for SARS-CoV-2 by nasopharyngeal swab real-time reverse transcription polymerase chain reaction (rRT-PCR), 3 tested negative and 2 were not tested as they were asymptomatic. Due to intensive immunosuppression, recent transplant recipients (< 3 months post-transplant) are at increased risk of developing severe disease due to COVID-19. doi = 10.1111/ajt.16120 id = cord-355788-6hteott0 author = Shirvani, Edris title = Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2 date = 2020-07-29 keywords = NDV; Newcastle; SARS summary = In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Currently, a number of DNA and RNA virus vector platforms are under evaluation for a SARS-CoV-2 vaccine, including attenuated vaccinia virus, replication-defective adenovirus, vesicular stomatitis virus, human parainfluenza viruses, and alphavirus replicons. Keeping these limitations in mind, we think Newcastle disease virus (NDV), as avian virus, has a number of characteristics that make it suitable for use as a vaccine vector for SARS-CoV-2. The effectiveness of NDV-vectored vaccines has already been evaluated against SARS-CoV in monkeys [8] , against MERS-CoV in camels [9] , and against avian infectious bronchitis virus (IBV) in chickens, a natural host challenge model [10] . Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus doi = 10.3390/pathogens9080619 id = cord-254636-3lr008th author = Shishir, Tushar Ahmed title = In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date = 2020-08-16 keywords = Bangladesh; CoV-2; SARS summary = We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. We conducted comparative analysis of publicly available genome sequences of SARS-CoV-2 from 27 countries to predict the origin of viruses in Bangladesh by studying a time-4 resolved phylogenetic relationship. Later, we analyzed the variants present in different isolates of Bangladesh to understand the pattern of mutations in relation to the ancestral Wuhan strain, find unique mutations, and possible effect of these mutations on the stability of encoded proteins, and selection pressure on genes. doi = 10.1101/2020.07.20.212563 id = cord-350095-hsl1hfds author = Shiu, Stephen Y. W. title = Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? date = 2003-06-16 keywords = SARS; melatonin summary = title: Urgent search for safe and effective treatments of severe acute respiratory syndrome: is melatonin a promising candidate drug? Since the end of February of this year, global health is being threatened by the emergence of a new infectious disease, severe acute respiratory syndrome (SARS), caused by a novel coronavirus [1] [2] [3] . However, the most immediate concerns to the health authorities of Hong Kong and mainland China are to contain the spread of the disease and to reduce the mortality of those SARS patients who succumb to acute respiratory failure. While health officials are working hard to contain the spread of the disease in the hard-hit places such as China, Hong Kong [4] , Singapore and Canada [5] , clinicians are racing against time to find effective drugs to rescue SARS patients from serious illness and death. doi = 10.1034/j.1600-079x.2003.00068.x id = cord-295302-vwrxentv author = Shivarov, Velizar title = Potential SARS-CoV-2 Preimmune IgM Epitopes date = 2020-04-30 keywords = SARS; epitope summary = While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. For the present study, the degrees of the vertices representing the natural SARS-CoV-2 epitopes, all of which belonged to the giant component, were used as the number of adjacent mimotopes parameter. A simple comparison for exact matches to peptides from the SARS-CoV-2 proteome yielded 3 heptapeptides-two in the open reading frame 1ab ( 3518 AQTGIAV 3524 and 5198 TKGPHEF 5204 ) and one in the spike protein ( 108 TTLDSKT 114 ). This loop is adjacent to the loop representing the epitope of the neutralizing antibody LCA60 on the SARS-CoV spike (8, 9) . Thus, it is quite possible that the SARS-CoV-2 spike epitope TTLDSKT is bound by B cells that will contribute to the induced immune response. doi = 10.3389/fimmu.2020.00932 id = cord-276058-1mpp7sbt author = Shlomai, A. title = Global versus focused isolation during the SARS-CoV-2 pandemic-A cost-effectiveness analysis date = 2020-04-01 keywords = SARS; isolation summary = Objective: To compare the cost-effectiveness of global isolation of the whole population to focused isolation of individuals at high risk of being exposed, augmented by thorough PCR testing. We used R0=2.4 (range 1.4-3.9) (13), we assumed that the recovery time is 26 days, thus the transmission rate from infected (carrier) patients to susceptible population (β) was 0.09 (range 0.031 to 0.186)(13). In strategy 1, r1_HR_c represents the proportion of the population under relaxed isolation due to a high risk of contact with SARS-CoV-2 patients (0.7%). We next tested our model with a strategy of strict isolation of all infected individuals, relaxed isolation for two weeks of the high-risk group and a global quarantine of the susceptible population (strategy 1). https://doi.org/10.1101/2020.03.30.20047860 doi: medRxiv preprint each high-risk individual during the 14 days of isolation, and therefore ~10,000-15,000 tests will be needed daily for a country the size of Israel. doi = 10.1101/2020.03.30.20047860 id = cord-355912-ioihqf0r author = Shomuradova, A. S. title = SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors date = 2020-05-25 keywords = CD4; CD8; SARS; TCR summary = Here we assayed both antibody and T-cell reactivity to SARS-CoV-2 antigens in COVID-19 convalescent patients and healthy donors sampled before and during the pandemic. 20.20107813 doi: medRxiv preprint Analysis of the humoral immune response to SARS-CoV-2 demonstrated that the IgG antibodies of the majority of COVID-19 -CPs were specific to one or more viral antigens. To describe the structure and clonality of SARS-CoV-2 directed T-cell immune response we performed analysis of T-cell receptor (TCR) repertoires of FACS-sorted IFNγ-secreting CD8+/CD4+ cells and MHC-tetramer-positive populations as well as the total fraction of PBMC by high throughput sequencing using the Illumina platform. Two patients (p1472 and p1473) had no detectable antibody levels in the serum to any of the tested SARS-CoV-2 antigens and no T-cellular response to any of the peptide pools, albeit they had T-cells reactive to the recombinant S-protein. doi = 10.1101/2020.05.20.20107813 id = cord-255909-m94j1rh4 author = Shree, Priya title = Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study date = 2020-08-27 keywords = COVID-19; Giloy; SARS summary = title: Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants – Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) – a molecular docking study Molecular docking study showed six probable inhibitors against SARS-CoV-2 M(pro) (Main protease), two from Withania somnifera (Ashwagandha) (Withanoside V [10.32 kcal/mol] and Somniferine [9.62 kcal/mol]), one from Tinospora cordifolia (Giloy) (Tinocordiside [8.10 kcal/mol]) and three from Ocimum sanctum (Tulsi) (Vicenin [8.97 kcal/mol], Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte [8.55 kcal/mol] and Ursolic acid [8.52 kcal/mol]). Active phytoconstituents of Ayurvedic medicinal plants Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi) predicted to significantly hinder main protease (M(pro) or 3Cl(pro)) of SARS-CoV-2. Through molecular docking and molecular dynamic simulation study, Withanoside V, Somniferine, Tinocordiside, Vicenin, Ursolic acid and Isorientin 4′-O-glucoside 2″-O-p-hydroxybenzoagte were anticipated to impede the activity of SARS-CoV-2 M(pro). doi = 10.1080/07391102.2020.1810778 id = cord-331611-pwj226j0 author = Shrimp, Jonathan H. title = An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date = 2020-06-23 keywords = AMC; SARS; TMPRSS2 summary = We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan for pancreatitis due to their inhibition of trypsin-like proteases. The structurally related trypsin-like serine protease inhibitor nafamostat was shown to similarly inhibit spike protein-mediated cell fusion of MERS-CoV 7 . Herein we report the development of a TMPRSS2 fluorogenic biochemical assay and testing of clinical repurposing candidates for COVID19. To identify inhibitors of TMPRSS2 that may be used to validate its role in SARS-CoV-2 entry and potentially expedite to clinical trials, we developed a biochemical assay using active TMPRSS2 protease and a fluorogenic peptide substrate ( Figure 1B) . We developed a fluorogenic biochemical assay for measuring recombinant human TMPRSS2 activity for high-throughput screening that can be readily replicated and used to demonstrate that nafamostat is a more potent inhibitor than camostat and gabexate. doi = 10.1101/2020.06.23.167544 id = cord-317761-tkqmu1va author = Shukla, Ashutosh M title = Chloroquine and hydroxychloroquine in the context of COVID-19 date = 2020-04-28 keywords = COVID-19; HCQ; SARS; chloroquine summary = This review aims to present the available in vitro and clinical data for the role of chloroquine/hydroxychloroquine in COVID-19 and attempts to put them into perspective, especially in relation to the different risks/benefits particular to each patient who may require treatment. 1 These agents have also shown a promising role in viral infections, and with the recent declaration on March 12th, 2020, by the World Health Organization that coronavirus disease (COVID) of 2019 (COVID-19) is a pandemic, these compounds have rapidly gained worldwide attention for their ability to control the causative virus, severe acute respiratory syndromecoronavirus-2 (SARS-CoV-2). 1 These include inhibition of ligand-based toll-like receptor stimulation, inhibition of nuclear factor kappalight-chain-enhancer of activated B cells (NFkB) pathways in macrophages with resultant reduction in the generation of pro-inflammatory cytokines, reduced processing of the endogenous and exogenous ligands through lysosomes and endosomes with resultant reduction in the availability of processed antigens for presentation to the major ISSN: 1740-4398 REVIEW -Chloroquine, hydroxychloroquine, and COVID-19 drugsincontext.com histocompatibility complex-T cell receptor interactions, and downstream activation of cellular immunity. doi = 10.7573/dic.2020-4-5 id = cord-308342-ycdok8fc author = Shutler, J. title = Risk of SARS-CoV-2 infection from contaminated water systems date = 2020-06-20 keywords = CoV-2; SARS; water summary = Collectively this evidence suggests that SARS-CoV-2 virus can survive 45 within water and the viral loads within untreated sewage effluent are likely high in countries 46 of high infection rates, a portion of which is viable virus, and therefore water contaminated 47 We note that adenoviruses are 122 known to be particularly resilient, and therefore likely to represent an upper estimate, but 123 also that our selected range is consistent with the 10 -3 value used elsewhere for assessing 124 viral risk in water systems (eg 14 ), including one assessment for SARS CoV-2 transmission 125 risk to wastewater workers 18 . Collectively this means that if a drinking water source 156 was to become infected with SARS-CoV-2 the standard virus removal and disinfection 157 approaches of ultraviolet exposure and chlorination may not reduce the virus below 158 detectable limits. doi = 10.1101/2020.06.17.20133504 id = cord-017516-qbksb83c author = Si, Yain-Whar title = Hidden Cluster Detection for Infectious Disease Control and Quarantine Management date = 2009-09-30 keywords = Figure; SARS; patient summary = Our prototype Infectious Disease Detection and Quarantine Management System (IDDQMS), which can identify and trace clusters of infection by mining patients'' history, is introduced in this paper. The SARS (Severe Acute Respiratory Syndrome) outbreak in 2003 and recent world-wide avian flu infections have contributed to the urgent need to search for efficient methods for prevention and control of highly infectious diseases. Given this background, this research aims to develop a decision support system which can be used to locate the source of an outbreak by mining clusters and communities from the patients'' past activities (testimonies) using techniques from infectious disease control, information visualization, and database management systems. IDDQMS (see Figure 1 ) consists of four modules; information extraction, data analysis, hidden cluster detection, and quarantine management. In this paper, we have described our novel prototype system on Infectious Disease Detection and Quarantine Management, which can be used to identify and trace clusters of infection by mining patients'' history. doi = 10.1007/978-1-4419-0312-9_10 id = cord-278055-v2ed3tei author = Sia, Sin Fun title = Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date = 2020-05-14 keywords = Fig; N=3; RNA; SARS summary = Previous study of SARS-CoV (Urbani strain) in 5-weeks-old golden Syrian hamsters showed robust viral replication with peak viral titers detected in the lungs on 2 dpi, followed by rapid viral clearance by 7 dpi, but without weight loss or evidence of disease in the inoculated animals 20 . Our results indicate that the golden Syrian hamster is a suitable experimental animal model for SARS-CoV-2, as there is apparent weight loss in the inoculated and naturally-infected hamsters and evidence of efficient viral replication in the nasal mucosa and lower respiratory epithelial cells. c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. e, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one donor on 6 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. doi = 10.1038/s41586-020-2342-5 id = cord-287477-aios0h8s author = Sicari, Daria title = Role of the early secretory pathway in SARS-CoV-2 infection date = 2020-07-28 keywords = Golgi; SARS; protein summary = CoV-2 infection starts when its spike (S) protein binds to angiotensin I-converting enzyme 2 (ACE2) receptors on the host cell membrane (Lake, 2020; Letko et al., 2020) . Thus, virion spread critically depends on recruiting the most efficient secretory machineries of host cells (Su et al., 2016; Proteins of the early secretory pathway bound by SARS-CoV-2 As the entire world asks for ways to stop CoV-2, many laboratories are investigating the virus''s Achilles heel(s). The role of glycosylation and protein quality control in SARS-CoV-2 infections Most CoVs bud at the ERGIC level ( Fig. 1) and are then transported along the exocytic pathway (Klumperman et al., 1994; Stertz et al., 2007) . We observed enrichment for five host-derived virus-interacting proteins (GOLGB1, PDE4DIP, TOR1A, HMOX1, and HYOU1) involved in different processes and related to quality control and ER-Golgi homeostasis maintenance. doi = 10.1083/jcb.202006005 id = cord-355674-mhi85px5 author = Siddiqi, Hasan K. title = Increased prevalence of myocardial injury in patients with SARS-CoV-2 viremia. date = 2020-11-10 keywords = SARS; covid-19 summary = The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. The objective of this study is to understand the relationship between SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized COVID-19 patients. Conclusions: Hospitalized COVID-19 patients with SARS-CoV-2 viremia have a significantly higher prevalence of detectable troponin and myocardial injury during their hospitalization, compared to non-viremic patients. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. This first report of the relationship between SARS-CoV-2 viremia, detectable troponin and myocardial injury in COVID-19 patients points to additional mechanistic pathways that require deeper study to understand the complex interplay between these unique findings, cardiovascular outcomes and mortality in COVID-19. doi = 10.1016/j.amjmed.2020.09.046 id = cord-333144-gyuh2fvl author = Siddiqui, Arif Jamal title = Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 date = 2020-08-05 keywords = COVID-19; HCQ; MERS; SARS summary = Therefore, this review focuses on the current use of various drugs as single agents (hydroxychloroquine, ivermectin, azithromycin, favipiravir, remdesivir, umifenovir, teicoplanin, nitazoxanide, doxycycline, and dexamethasone) or in combinations with immunomodulators additionally. While some drugs have shown therapeutic effect against COVID-19 infection such as hydroxychloroquine (Al-Kofahi et al., 2020; Choudhary & Sharma 2020; Liu et al., 2020; Sinha & Balayla 2020) , azithromycin, (Andreani et al., 2020a; Choudhary & Sharma 2020) ivermectin (Caly et al., 2020; Chaccour et al., 2020; Choudhary & Sharma 2020) and some other antivirals (Asai et al., 2020; Boopathi et al., 2020; Lian et al., 2020) . Consequently, this review will provide an insight and comprehensive view on different therapeutic approaches including combining of different known anti-parasitic drugs, as well as proposing novel suggestions of chemoprophylaxis drug therapy, which can be used in the current treatment and vaccine development strategies against COVID-19 disease. doi = 10.1080/07391102.2020.1802345 id = cord-315198-v4ay9kwg author = Siddiqui, Ruqaiyyah title = SARS-CoV-2: The Increasing Importance of Water Filtration against Highly Pathogenic Microbes date = 2020-08-13 keywords = SARS; water summary = Additionally, the frequent use of contaminated water for bathing, nasal irrigation, swimming, and ablution can be a risk factor in contracting infectious agents such as the brain-eating amoebae and possibly SARS-CoV-2. For example, the observation of primary amoebic meningoencephalitis due to brain-eating amoebae (i.e., Naegleria fowleri) is mostly unnoticed, especially in rural areas and disadvantaged communities, and is known to be associated with nasal irrigation for cleansing, ritual ablution, bathing, and swimming. Thus, the contamination of human waste as well as human wastewater into drinking water supplies highlights a major risk factor in contracting infectious agents such as brain-eating amoeba and possibly COVID-19, especially for developing countries. The use of simple tap water filters in households prior to ablution or nasal irrigation ( Figure 1E ,F) can be effective in eradicating microbial contaminants. doi = 10.1021/acschemneuro.0c00468 id = cord-331087-kpze9xux author = Siddiqui, S. title = SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting date = 2020-09-03 keywords = SARS; covid-19 summary = To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW. We conducted a prospective longitudinal observational study to estimate the prevalence of anti SARS-CoV-2 antibodies among workers of a private hospital in Delhi with different levels of exposure to COVID-19 cases. The present study was conducted to estimate the seroprevalence of SARS-CoV-2 infection in Delhi and to observe how long the antibodies persist in the body. In a recently published brief report from Mumbai, India, conducted among the HCWs of three hospitals, highlighted that SARS-CoV-2 antibodies are not detected after 50 days, in RT-PCR positive individuals contrasting our observations 24 . doi = 10.1101/2020.09.02.20186486 id = cord-312473-7i7efdp2 author = Sidhom, John-William title = Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date = 2020-06-20 keywords = SARS summary = We first examined the distribution of TCRs within the McPas database over the types of pathogens present in the database and cross-referenced the SARS-CoV-2 specific TCRs into the McPas database ( Figure 1A) , and we noted that there was a statistically significant enrichment (from 17.3% to 32.9%) of SARS-CoV-2 specific TCRs that had known specificity to the immunodominant M1 GILGFVFTL epitope We then examined the distribution of TCRs within the ImmuneCode database across the various open readings frames (orfs) and mapped the M1 specific TCRs within this database ( Figure 1B) . In conclusion, while these results are preliminary in a small cohort of individuals, we have identified a set of TCRs that is known to both recognize an immunodominant epitope derived from Influenza and SARS-CoV-2, suggesting that immune control of one infection may play a role in the control of the other. doi = 10.1101/2020.06.20.160499 id = cord-276234-2nkeq4ud author = Siedlecki, Jakob title = COVID-19: Ophthalmological Aspects of the SARS-CoV 2 Global Pandemic date = 2020-05-06 keywords = AAO; COVID-19; SARS; patient summary = Indeed, ophthalmologists seem to rank among the medical specialties with the highest risk for COVID-19 infection, probably due to close patient contact during examination, e.g., at the slit lamp [4] , and possible conjunctival involvement during the course of the disease [5, 6] . In this paper, a systematic review of current COVID-19 literature relevant for ophthalmological practice is performed, with a special focus on modes of transmission, the prevention thereof, structural adjustments of clinical care required during the pandemic, and possible ocular manifestations of this novel disease. The novel coronavirus SARS-CoV 2, currently causing the COVID-19 pandemic, has severe implications for ophthalmologybe it because the eyes represent an important route of infection, most probably through lacrimal drainage into the nasal mucosa, or because of ocular manifestations, which, even if rather rare, can represent the first symptoms of this novel disease [29] . doi = 10.1055/a-1164-9381 id = cord-276758-k2imddzr author = Siegel, Jane D. title = 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date = 2007-12-07 keywords = CDC; Control; MRSA; PPE; Precautions; SARS; Standard; Staphylococcus; States; United; base; care; health; infection; outbreak; patient; transmission summary = Activities currently assigned to ICPs in response to emerging challenges include (1) surveillance and infection prevention at facilities other than acute care hospitals (eg, ambulatory clinics, day surgery centers, LTCFs, rehabilitation centers, home care); (2) oversight of employee health services related to infection prevention (eg, assessment of risk and administration of recommended treatment after exposure to infectious agents, tuberculosis screening, influenza vaccination, respiratory protection fit testing, and administration of other vaccines as indicated, such as smallpox vaccine in 2003); (3) preparedness planning for annual influenza outbreaks, pandemic influenza, SARS, and bioweapons attacks; (4) adherence monitoring for selected infection control practices; (5) oversight of risk assessment and implementation of prevention measures associated with construction and renovation; (6) prevention of transmission of MDROs; (7) evaluation of new medical products that could be associated with increased infection risk (eg, intravenous infusion materials); (8) communication with the public, facility staff, and state and local health departments concerning infection control-related issues; and (9) participation in local and multicenter research projects. doi = 10.1016/j.ajic.2007.10.007 id = cord-260257-phmd0u6d author = Siegler, Aaron J title = Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date = 2020-06-30 keywords = SARS; covid-19; home summary = METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. 8, 9 Calls for home-based specimen collection or drive-through specimen collection models to address SARS-CoV-2 virus test scale-up have cogently argued that these approaches have the benefit of (1) avoiding burdening hospitals at a critical time, (2) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), (3) likely lowering costs, and (4) potentially achieving rapid scale-up due to laboratory centralization. We conducted an online survey to assess patient willingness to use the following SARS-CoV-2 testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. Across a diverse sample of 1,435 participants, one-third more persons reported that they would be willing to collect specimens at home for SARS-CoV-2 testing if they experienced illness, compared to clinic-based testing. doi = 10.1093/ofid/ofaa269 id = cord-277812-4cz2hziz author = Sieni, Elena title = Favourable outcome of coronavirus disease 2019 in a 1‐year‐old girl with acute myeloid leukaemia and severe treatment‐induced immunosuppression date = 2020-05-19 keywords = COVID-19; SARS summary = Since the beginning of coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults.1 Few cases of infection in children with cancer are described; also in these patients, except for one reported case,2 the disease was largely asymptomatic.3 Nevertheless, the management of COVID-19 in young patients with comorbidities, particularly cancer, remains a challenge for the clinician; further data are required to optimize the clinical approach to these cases. Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic outbreak, it has emerged that the clinical course and outcome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is definitely more favourable in children than in adults. On day 18, routine laboratory testing further improved (WBC 2080 cells/µl with 48% neutrophils, Hb 112 g/l, PLTs correspondence 297 000/µl, negative CRP), and she was finally discharged, despite persistent positivity for SARS-CoV-2 at nasal swab, with oral prophylactic anti-microbial therapy. doi = 10.1111/bjh.16781 id = cord-308077-hbxpn5a1 author = Siepmann, Timo title = Variability of symptoms in neuralgic amyotrophy following infection with SARS‐CoV‐2 date = 2020-10-01 keywords = SARS summary = The report of Cacciavillani and colleagues contributes to the discussion of the possibility of peripheral nerve involvement in coronavirus disease 2019 (COVID-1 9) and adds to our observation of neuralgic amyotrophy following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Interestingly, research prior to the COVID-19 pandemic showed that earlier coronaviruses such as hemagglutinating encephalomyelitis virus may first enter peripheral nerve terminals before traveling to the central nervous system (CNS) via synapse-connected routes. In fact, peripheral nerve damage might occur in almost 10% of patients hospitalized for SARS-CoV-2 infection. Whether peripheral nervous system complications following COVID-19 such as neuralgic amyotrophy result from direct neuroinvasion or from an auto-immune post-infectious mechanism needs to be elucidated. The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients doi = 10.1002/mus.27084 id = cord-289144-d6fgs8qg author = Sieńko, Jerzy title = COVID-19: The Influence of ACE Genotype and ACE-I and ARBs on the Course of SARS-CoV-2 Infection in Elderly Patients date = 2020-07-21 keywords = ACE2; COVID-19; SARS; ace summary = Moreover, there is evidence that ACE genotype affects the outcomes of acute respiratory distress syndrome (ARDS) treatment, the most severe consequence of SARS-CoV-2 infection. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 8, 13 The aim of this narrative review was to analyze and identify the mechanisms of ACE-I and ARBs with particular emphasis on angiotensin receptors and their polymorphism in the light of COVID-19 pandemic as these medications are commonly prescribed to elderly patients. 63 This upregulation of the ACE2 receptor causes an increase in SARS-CoV-2 binding sites, which can lead to COVID-19 infection. Association of inpatient use of angiotensin converting enzyme inhibitors and angiotensin II receptor blockers with mortality among patients with hypertension hospitalized with COVID-19 doi = 10.2147/cia.s261516 id = cord-296997-ba7f2mf3 author = Sikora, Mateusz title = Map of SARS-CoV-2 spike epitopes not shielded by glycans date = 2020-07-03 keywords = Appendix; Fig; SARS summary = To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. Our simulation system contained four membrane-embedded SARS-CoV-2 S proteins assembled from resolved structures where available and models for the missing parts (SI Appendix, Fig. S5 ). In the ray analysis, we illuminated the protein model by diffuse light; in the Fab docking analysis, we performed rigid body Monte Carlo simulations of S and the SARS-CoV-2 antibody CR3022 Fab to determine the steric accessibility to an antibody Fab. To account for protein and glycan mobility, we performed both analyses individually for 4 × 193 snapshots taken at 10 ns time intervals from the 1.93 µs MD simulation with four glycosylated S proteins. doi = 10.1101/2020.07.03.186825 id = cord-354101-8a7tohcx author = Silva de Oliveira, Daniela title = Immune response in COVID-19: What do we currently know? date = 2020-09-09 keywords = SARS summary = In 2002/2003 there was a pandemic denominate SARS (severe acute respiratory syndrome), caused by the SARS-CoV virus that belongs to the genera Betacoranavirus and the family Coronaviridae, generally responsible for influenza infections. In mid of 2019, a new disease by the coronavirus named by COVID-19 (SARS-CoV-2) emerged, both infections have flu symptoms, however they are infections that variable intensity, being medium to severe. The acute respiratory syndrome is a disease caused by the SARS-CoV-2 virus (COVID-37 19), where symptoms include difficulty breathing, high fever, and cough (WHO, 2020). Clinicopathologic, immunohistochemical, and ultrastructural findings of 673 a fatal case of Middle East respiratory syndrome coronavirus infection in the United 674 Immune responses in COVID-19 700 and potential vaccines: Lessons learned from SARS and MERS epidemic Middle East respiratory syndrome coronavirus Middle East respiratory syndrome coronavirus 766 (MERS-CoV) sheets/detail/middle-east-respiratory-syndrome-coronavirus-(mers-cov)> Access Pathological findings of COVID-19 associated with acute respiratory 786 distress syndrome. doi = 10.1016/j.micpath.2020.104484 id = cord-260871-dtn5t8ka author = Silva, Marcus Tulius T. title = SARS-CoV-2: Should We Be Concerned about the Nervous System? date = 2020-07-17 keywords = COVID-19; SARS; patient; respiratory summary = Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system doi = 10.4269/ajtmh.20-0447 id = cord-252991-gvlyn6j7 author = Silva, V. O. title = PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL date = 2020-10-21 keywords = October; SARS; covid-19 summary = To evaluate previous exposure to the virus we estimated the prevalence of antibodies against-SARS-CoV-2 among HPs in Adolfo Lutz Institute, State of Sao Paulo, Brazil. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay and SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants. . https://doi.org/10.1101 Professionals from laboratory areas were 25% while workers who had no direct contact with patients (administrative areas, security and cleaning staff) had a higher infection rate, especially in the areas of logistics (Faíco-Filho, et al., 2020) In our study, we chose to use a rapid test for preliminary results, despite the its reported performance (Sensitivity: 86, 43% [95% CI: 82, 51%~89, 58%] and Specificity: 99, 57% [95% CI: 97, 63%~99,92%]).. doi = 10.1101/2020.10.19.20213421 id = cord-295765-c7o2ukm6 author = Silvas, Jesus A. title = Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date = 2020-07-20 keywords = SARS summary = VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. As SARS-CoV-2 replication 174 damages the cell monolayer, impedance measurements decrease over time, providing a detailed 175 assessment of infection kinetics. Based on the toxicity window of 1-20 221 h.p.t. determined with the VPS34 inhibitors, neither Triacsin C nor Orlistat induced early 222 cytotoxic effects, even at the highest concentrations of 50uM and 500uM, respectively ( Figure 223 3A and 3C). Here, we demonstrate that two VPS34 inhibitors, Orlistat, and Triacsin C each have clear effects 308 on SARS-CoV-2 replication and the morphology of viral replication centers. In contrast, the compounds did not exhibit any activity against 384 SARS-CoV-2 in Vero E6 cells whereas Triacsin C did. doi = 10.1101/2020.07.18.210211 id = cord-344070-17oac3bg author = Silverman, Justin D title = Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date = 2020-04-03 keywords = COVID; ILI; SARS summary = ILI correlates with known patterns of SARS-CoV-2 spread across states within the US, suggesting the surge is unlikely to be due to other endemic respiratory pathogens, yet is orders of magnitude larger than the number of confirmed COVID cases reported. We find that as the seasonal surge of endemic non-influenza respiratory pathogens declines, this excess ILI correlates more strongly with state-level patterns of newly confirmed COVID cases suggesting that 75 this surge is a reflection of ILI due to SARS-CoV-2 (Pearson ρ = 0.8 and p < 10 −10 for the last two weeks; Figure S1 ). However, if we assume the excess non-influenza ILI is almost entirely due to SARS-CoV-2, an assumption that becomes more valid as the virus becomes more prevalent, we can use the excess non-influenza ILI to understand the constraints and mutual dependence of exponential growth rates, the rate of subclinical infections, and the time 95 between the onset of infectiousness and a patient reporting as ILI Figure 3 . doi = 10.1101/2020.04.01.20050542 id = cord-347079-1zbsbcdd author = Silverman, Justin D. title = Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date = 2020-06-22 keywords = ILI; March; SARS summary = To estimate the proportion and magnitude of the March 2020 US ILI surge attributable to SARS-CoV-2 infections, we made the following three assumptions: (1) that the patient population reported by sentinel providers is representative of their state each week; (2) that changes in care-seeking behavior of ILI patients is occurring at a similar rate as that of other non-ILI patients; and (3) that the total number of patients in the US who require medical care over the course of a year has not substantially changed since 2018. The goal of our study was to use publicly available data to estimate the number of patients seeking care for non-influenza ILI in excess of seasonal trends during the three weeks spanning March 8 to March 28, 2020 and then use this ILI surge to estimate COVID-19 incidence in March and parameterize epidemiological model growth rates and clinical rates. doi = 10.1126/scitranslmed.abc1126 id = cord-260365-neili1bd author = Silverstein, Jenna S. title = Acute Respiratory Decompensation Requiring Intubation in Pregnant Women with SARS-CoV-2 (COVID-19) date = 2020-06-04 keywords = COVID-19; SARS summary = Data from China suggest that pregnant women with COVID-19 have favorable maternal and neonatal outcomes, with rare cases of critical illness or respiratory compromise. However, we report two cases of pregnant women diagnosed with COVID-19 in the late preterm period admitted to tertiary care hospitals in New York City for respiratory indications. 8 We report here two pregnant women with no medical comorbidities, one under 18 years of age, diagnosed with COVID-19 at 34 and 36 weeks of gestation, respectively, who rapidly decompensated and underwent caesarean delivery under general anesthesia followed by prolonged mechanical ventilation. The risks and benefits of delivery in pregnant patients with critical respiratory illness from COVID-19 infections are not yet known, but prior experience with maternal acute respiratory distress syndrome (ARDS) and viral 2009/H1N1 influenza requiring mechanical ventilation in pregnancy reveals increased risk of fetal HR abnormalities, as well as fetal and neonatal mortality. doi = 10.1055/s-0040-1712925 id = cord-326257-rcv8sh22 author = Simmonds, P. title = Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date = 2020-05-01 keywords = RNA; SARS; c->u summary = C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5''U/A and 3''U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). doi = 10.1101/2020.05.01.072330 id = cord-325481-uzch2hwd author = Simmons, Graham title = Different host cell proteases activate the SARS-coronavirus spike-protein for cell-cell and virus-cell fusion date = 2011-05-01 keywords = ACE2; Fig; SARS; cell summary = For instance, the majority of strains of the murine coronavirus mouse hepatitis virus (MHV) contain Sproteins that are cleaved by furin in infected cells, and these viruses are believed to enter target cells by receptor-dependent, pH-independent fusion with the plasma membrane (de Haan et al., 2004; Nash and Buchmeier, 1997; Qiu et al., 2006) , although some of these findings are controversial (Eifart et al., 2007) . Treatment of cell-bound virus with trypsin was shown to allow infectious SARS-S-driven entry into ammonium chloride-treated cells (Simmons et al., 2005) , indicating that trypsin can functionally replace cathepsin L as a SARS-S-activating protease under these conditions ("trypsin bypass"). The fusion efficiency is then quantified by the addition of virions to leupeptin-treated (to exclude an impact of host cell proteases on SARS-S activation) HeLa cells, which express the EnvA receptor TvA, and which are not susceptible to SARS-S-driven infection (Simmons et al., 2005) . doi = 10.1016/j.virol.2011.02.020 id = cord-339344-qd73h1ie author = Simon, David title = Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion date = 2020-07-24 keywords = COVID-19; CoV-2; IMID; SARS summary = To test whether differences in social exposure between the groups account for the low prevalence of SARS-CoV-2 IgG responses in IMID patients treated with cytokine inhibitors, we assessed exposure risk variables (contact with persons with a respiratory infection, presence at workplace outside home, travel to risk areas) of IMID patient groups and control groups. The low seroprevalence of SARS-CoV-2 in anti-cytokine treated IMIDs could have two principle explanations: While (i) the four groups were recruited in the same region, (ii) the HC control group having the highest prevalence for SARS-CoV-2 IgG was in direct contact with the IMID patients and (iii) all participants were exposed to similar detailed information regarding social behavior during the outbreak of the COVID-19 pandemic in Germany, IMID patients may have followed an even more stringent exposure prophylaxis than healthy individuals. doi = 10.1038/s41467-020-17703-6 id = cord-281285-5g1rw202 author = Simonis, Alexander title = A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date = 2020-11-03 keywords = COVID-19; HCQ; RDV; RNA; SARS summary = Based on its MOA, repurposed drugs with anti-SARS-CoV-2 activity can be divided into substances that prevent viral entry into host cells (1-2) and inhibit viral proteases (3) and inhibitors of viral replicase (4). The disappointing clinical results might be related to sub-therapeutic levels for inhibition of SARS-COV-2 because application of 400/100 mg of lopinavir/ritonavir twice daily was shown to yield median serum concentrations of 7.2 mg/l (11.5 µM) in patients with HIV (van der Lugt et al, 2009), which is significantly lower than the observed EC 50 in the in vitro studies. In this comparative review, we focus on repurposed drugs with antiviral effects against SARS-CoV-2 in cell-based assays as those substances offer great opportunities for a treatment early in the course of COVID-19 by inhibition of viral replication and might be even suitable for preventive strategies as shown for neuraminidase inhibitors in case of influenza (Jefferson et al, 2014) . doi = 10.15252/emmm.202013105 id = cord-355589-3zdv9zim author = Simons, David title = The association of smoking status with SARS‐CoV‐2 infection, hospitalisation and mortality from COVID‐19: A living rapid evidence review with Bayesian meta‐analyses (version 7) date = 2020-10-02 keywords = COVID-19; SARS; patient; smoker summary = However, early data from the COVID-19 pandemic have not provided clear evidence for a negative impact of current or former smoking on SARS-CoV-2 infection or COVID-19 disease outcomes, such as hospitalisation or mortality 11 . We aimed to produce a rapid synthesis of available evidence pertaining to the rates of infection, hospitalisation, disease severity and mortality from SARS-CoV-2/COVID-19 stratified by smoking status. Sixty studies reported disease severity in hospitalised patients stratified by smoking status (see Table 4 ). Current smokers were at reduced risk of testing positive for SARS-CoV-2 and former smokers were at increased risk of hospitalisation, disease severity and mortality compared with never smokers. Clinical Course and Outcomes of Patients with Severe Acute Respiratory Syndrome Coronavirus 2 Infection: a Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19 Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.1111/add.15276 id = cord-297217-pe6mehjv author = Simpson, A. Hamish R. W. title = COVID-19: potential transmission through aerosols in surgical procedures and blood products date = 2020-07-23 keywords = SARS; covid-19 summary = A six-fold increased risk of transmission of viral diseases, such as severe acute respiratory syndrome (SARS) has been reported during anaesthetic procedures such as endotracheal intubation. 2 no definite transmission has been reported due to surgical procedures, however unlike other viral diseases such as SARS and middle east respiratory syndrome (meRS), CoVid-19 appears to be both severe and highly transmissible and therefore could pose a far higher risk to surgeons and operating room staff. 9, 11 in comparison to SARS, in which only very low plasma levels of virus have been reported, 12 the blood of CoVid-19 patients is likely to have a higher potential for aerosols produced during surgical procedures to carry the virus. there is increasing evidence that a significant number of potentially up to 50% or more of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) are asymptomatic. doi = 10.1302/2046-3758.94.bjr-2020-0130 id = cord-308080-1heu9vuv author = Simulundu, Edgar title = First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date = 2020-10-06 keywords = COVID-19; SARS; Zambia summary = title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient''s household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient''s SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. doi = 10.1016/j.ijid.2020.09.1480 id = cord-293259-o51fnvuw author = Sinaei, Reza title = Why COVID-19 is less frequent and severe in children: a narrative review date = 2020-09-25 keywords = ARDS; COVID-19; MIS; SARS; child summary = Thus far, only a small number of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection have involved children, so that they have accounted for only 1-5% of total patients [2, [6] [7] [8] [9] [10] . Severe SARS-CoV-2 infection is characterized by a hyperproinflammatory response or cytokine storm state that results to acute respiratory distress syndrome (ARDS) and multisystem inflammatory syndrome (MIS). The search strategy was constructed based on searching terms 2019 novel coronavirus, COVID-19, SARS-CoV-2 with using and/or, also the terms of child, pediatric, newborn, infant, adolescence, adult, age, age groups, severity, epidemiology, prevalence, difference, immune system, etiology, reasons in title, abstract, and key words. The first results stem from some considerations that children have a less vigorous immune response to the virus than adults because the cytokine storm is thought to be important in the pathogenesis of severe SARS-CoV-2 infections [28] . doi = 10.1007/s12519-020-00392-y id = cord-331022-tek4u751 author = Sinderewicz, Emilia title = Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience? date = 2020-09-09 keywords = CD4; Coronavirus; MERS; SARS summary = The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. The current study reviewed the role of interleukins (ILs) with tumor necrosis factors (TNFs), chemokines and interferons (IFNs) in the immune response to HCoVs. A comparison of the content of proinflammatory Th1 and Th2 cytokines in the serum of SARS patients with healthy controls documented a significantly greater concentration of TNF-α, IL-6, IL-8, IL-10, and IL-12 in the early stage of the SARS-CoV infection [32, 40] . doi = 10.3390/pathogens9090739 id = cord-290290-wyx9ib7s author = Sinegubova, Maria V. title = High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date = 2020-11-05 keywords = CHO; CoV-2; RBD; SARS; cell; protein summary = title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector Based on the previously developed p1.1 vector, containing the regulatory sequences of the Eukaryotic translation elongation factor 1 alpha gene (EEF1A1) from Chinese hamster, we created two expression constructs encoding SARS-CoV-2 RBD with C-terminal c-myc and polyhistidine tags. Previously we have developed the plasmid vector p1.1, containing large fragments of non-coding DNA from the EEF1A1 gene of the Chinese hamster and fragment of the Epstein-Barr virus long terminal repeat concatemer [21] and employed it for unusually high-level expression of various proteins in CHO cells, including blood clotting factors VIII [22] , IX [23] , and heterodimeric follicle-stimulating hormone [24] . We have proposed that SARS-CoV-2 RBD, suitable for in vitro diagnostics use, may be expressed in large quantities by stably transfected CHO cells, bearing the EEF1A1-based plasmid. doi = 10.1101/2020.11.04.368092 id = cord-350972-0n4dumgg author = Sing, Chor-Wing title = Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date = 2020-07-16 keywords = SARS; VHD summary = title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. doi = 10.1093/cid/ciaa992 id = cord-254207-uru7bkr4 author = Singanayagam, Anika title = Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020 date = 2020-08-13 keywords = SARS summary = Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Understanding the duration of infectiousness in persons who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to developing evidence-based public health policies on isolation, contact tracing and return to work. In the first 3 months of the COVID-19 pandemic in the United Kingdom (UK) (late January to early April 2020), we received 754 URT samples from 425 symptomatic cases that tested positive for SARS-CoV-2 by RT-PCR targeting the RNA-dependent RNA polymerase (RdRp) gene [1] and that had a clear record of the dates of symptom onset and sample collection. doi = 10.2807/1560-7917.es.2020.25.32.2001483 id = cord-271871-8grkln6o author = Singer, J. S. title = Low Prevalence (0.13%) of COVID-19 Infection in Asymptomatic Pre-operative/Pre-procedure Patients at a Large Academic Medical Center Informs Approaches to Perioperative Care date = 2020-08-14 keywords = COVID-19; SARS; patient summary = Abstract Background The COVID-19 pandemic has resulted in reduced performance of elective surgeries and procedures at medical centers across the U.S. Awareness of the prevalence of asymptomatic disease is critical for guiding safe approaches to operative/procedural services. Conclusions These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to inform perioperative protocols during the COVID-19 pandemic. These data demonstrating low levels (0.13% prevalence) of COVID-19 infection in an asymptomatic 117 population of patients undergoing scheduled surgeries/procedures in a large urban area have helped to 118 inform perioperative protocols during the COVID-19 pandemic. As a large urban referral center, we adopted the CDC and ACS recommendations early in the pandemic, 327 suspending elective surgical and interventional procedures, and later relaxing those suspensions while 328 balancing local/regional COVID-19 epidemiology, data regarding our pre-operative/pre-procedure 329 testing results, and health system resources and priorities. doi = 10.1016/j.surg.2020.07.048 id = cord-289114-ifnk41oq author = Singh, Angaraj title = Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date = 2020-10-28 keywords = PCR; SARS; covid-19; patient summary = The SARS-CoV-2 infected patients with the cardiovascular problem have a higher fatality rate as compared to general COVID-19 patients. The ACE-2 has been suggested as a medicine for the treatment of diabetes because it reduces inflammation .Therefore, the diabetes and COVID-19 patients treated with ACE-2 have higher risk of infection (Zachary, 2020) . Although, the specific drug for SARS-CoV-2 is not discovered till date, the medical observers are attempting with different antiviral drugs for the treatment of COVID-19 infection . All rights reserved patients demonstrated that the combination of a new antiviral drug remdesivir and chloroquine slowed down the growth of SARS-CoV-2 (Abdul et al., 2017) . Convalescent plasma therapy has been observed as a better alternative for the treatment of severely infected COVID-19 patients. A research report suggested that plasma treatment is more effective at the initial stage (within 14 days of symptoms) of COVID-19 infection. doi = 10.1002/mds3.10140 id = cord-254452-gqqdx2r5 author = Singh, Awadhesh Kumar title = Remdesivir in COVID-19: A critical review of pharmacology, pre-clinical and clinical studies date = 2020-05-12 keywords = COVID-19; Remdesivir; SARS summary = METHODS: We systematically searched the PubMed, ClinicalTrial.Org and MedRxiv database up till May 5, 2020 using specific key words such as "Remdesivir" or ''GS-5734″ AND "COVID-19" or "SARS-CoV-2" and retrieved all the article published in English language, that have reported the pharmacology and the clinical outcomes of remdesivir in patients with COVID-19. A preliminary report (April 29, 2020) from an interim analysis of an ongoing double-blind randomized controlled trial (RCT) recently suggested that remdesivir had a 31% faster time to recovery, compared to the placebo (p<0.001), in patients with COVID-19 [15] . In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) No evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for COVID-19 infection with oxygen requirement: results of a study using routinely collected data to emulate a target trial doi = 10.1016/j.dsx.2020.05.018 id = cord-286638-bqxyb61p author = Singh, Awadhesh Kumar title = Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations date = 2020-04-09 keywords = ACE-2; COVID-19; SARS; patient summary = The disease burden of coronavirus infectious disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) has been increasing continuously with more than a million confirmed patients and more than 45 thousand deaths globally [1] . Emerging data suggests that COVID-19 is common in patients with diabetes, hypertension, and cardiovascular disease (CVD), although the prevalence rate varied in different studies as well in country-wise data. Evolving data also suggest that patients of COVID-19 with diabetes are more often associated with severe or critical disease varying from 14 to 32% in different studies [15e18, 20, 22, 24] . Though there is limited data about the association of blood glucose levels with disease course in COVID-19 at present, data from other infections like SARS and influenza H1N1 has shown that patients with poor glycemic control have increased risk of complications and death [60, 61] . doi = 10.1016/j.dsx.2020.04.004 id = cord-295973-41jqgsv0 author = Singh, Awadhesh Kumar title = Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries date = 2020-03-26 keywords = COVID-19; HCQ; SARS summary = In this review article, we have systematically searched the medical data base until and collated all the available evidences that have emerged so far on the efficacy of chloroquine and hydroxychloroquine, in the treatment of patients with COVID19 , with or without diabetes and present a perspective on both these compounds. A Chinese study involving more than 100 patients of COVID-19 found chloroquine superior to the control group in reducing symptom duration, exacerbation of pneumonia including radiological improvement and promoting virus-negative seroconversion without any severe side effects [18] . The expert consensus from the Department of Science and Technology and Health Commission of Guangdong province published on 20th February (based on in vitro evidence and still unpublished clinical experience) chloroquine phosphate tablet at a dose of 500 mg twice per day for 10 days for patients diagnosed as mild, moderate and severe cases of SARS-CoV-2 pneumonia in the absence of contraindication to the drug [21] . doi = 10.1016/j.dsx.2020.03.011 id = cord-338417-7kw9lws0 author = Singh, Awadhesh Kumar title = Comorbidities in COVID-19: Outcomes in hypertensive cohort and controversies with renin angiotensin system blockers date = 2020-04-09 keywords = ACE-2; COVID-19; SARS summary = RESULTS: From the pooled data of all ten available Chinese studies (n = 2209) that have reported the characteristics of comorbidities in patients with COVID-19, hypertension was present in nearly 21%, followed by diabetes in nearly 11%, and established cardiovascular disease (CVD) in approximately 7% of patients. Emerging data suggests that older COVID-19 patients with other comorbid conditions such as diabetes, hypertension, cardiac and pulmonary disease are in particular more susceptible, compared to general populations and have higher mortality. We have systematically searched the PubMed medical database up till March 27, 2020 using MeSH key words that include Covid-19, coronavirus, hypertension, diabetes, cardiovascular disease, angiotensin receptor blockers, angiotensin converting enzyme inhibitors. Interestingly, in the pooled data from the ten Chinese studies (n ¼ 2209) that have reported the characteristics of comorbidities in patients with COVID-19; associations of hypertension, diabetes and presence of established cardiovascular disease (CVD) are larger, varying from 15 to 30% (average 21%), 5e20% (average 11%) and 2e40% (average 7%) respectively (Table 1) . doi = 10.1016/j.dsx.2020.03.016 id = cord-319241-div9rzax author = Singh, Bhuchitra title = Severe Acute Respiratory Syndrome‐Corona Virus‐2 (SARS‐CoV‐2) and its Effect on Gametogenesis and Early Pregnancy date = 2020-09-23 keywords = ACE2; COVID-19; CoV-2; SARS summary = There is also evidence of significant placental pathology in SARS‐CoV‐2 infection, but it is unclear what effects there may be for early pregnancy, though available data suggest less severe effects compared to other respiratory virus outbreaks. We searched for articles that contained information related to SARS-CoV-2 and reproductive tissues (ovaries, testes), gametes, placentation, and early pregnancy in humans. Our search phrases included: "severe acute respiratory syndrome coronavirus 2", "2019 ncov", "sarscov 2", "SARS-Cov-2", "pregnancy", "gravidity", "abortion", "germ cells", "oocytes", "gametes", "embryonic structures", "embryo", "fertility", "testes", "miscarriage"(See Appendix 1 for completed list of databases search strategy and Figure 1 for PRISMA table). Specifically, 10 women with severe COVID-19 were tested or SARS-CoV-2 in vaginal fluid, with all samples negative for virus [48] . Another study performed during the 2002-2003 SARS pandemic showed that 4 of 7 (57%) pregnant women infected with SARS-CoV had a spontaneous miscarriage in the first trimester of pregnancy [55] , though notably no viral inclusion bodies or particles were detected in the products of conception. doi = 10.1111/aji.13351 id = cord-263245-2qub96mz author = Singh, D. title = Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date = 2020-09-29 keywords = SARS; alcohol; hand; virus summary = This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . doi = 10.1017/s0950268820002319 id = cord-256872-jekx1czw author = Singh, Manvendra title = A single-cell RNA expression map of human coronavirus entry factors date = 2020-09-03 keywords = ACE2; SARS; TMPRSS2; figure summary = To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell transcriptomics across various healthy human tissues. Evidence of impaired gonadal function in male COVID-19 patients was also recently presented The high level of TMPRSS2, ACE2 and other coronavirus receptors such as ANPEP in the trophectoderm, which gives rise to the placenta, combined with low levels of IFITMs in this lineage (Figure 2A and Figure S1A ) raises the possibility that the developing placenta may be vulnerable to SARS-CoV-2 infection. Our study, along with several others (Table S1 ) have tapped into vast amount of publicly available scRNA-seq data to profile the expression of host factors thought to be important for entry of SARS-CoV-2 in healthy tissues. doi = 10.1016/j.celrep.2020.108175 id = cord-285636-cs26uuwx author = Singh, N. K. title = Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer date = 2020-09-25 keywords = SARS; international summary = In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads as benchmarked by RT-qPCR within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). The major hurdle in repurposing a glucometer for direct detection of SARS-CoV-2 is that the target biomarkers (e.g., protein N and S) are present at low concentrations in biological samples The average CoVID-19 viral load in nasal/throat, sputum, and saliva samples is 3×10 6 , 7.50×10 5 , and 3.5×10 7 copies/ml 24, 25 , respectively, necessitating signal amplification to generate product (i.e. glucose) in quantities similar to physiological levels in human blood (i.e. 10-600 mg/dL or 0.6-33 mM) 21, 26 . To transduce antigen binding SARS-CoV-2 N or S protein specific biotinylated aptamer is conjugated to streptavidin coated magnetic bead (MB) and pre-hybridized with a complementary antisense oligonucleotide strand that is covalently attached to an invertase enzyme. doi = 10.1101/2020.09.24.20200394 id = cord-334540-ggnkdnky author = Singh, Pankaj title = Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie date = 2020-07-01 keywords = Patienten; SARS; der summary = title: Entwicklung und Implementierung eines Betriebskonzeptes in einer Universitätsaugenklinik im Rahmen der SARS-CoV-2-Pandemie Bei infizierten Patienten lässt sich regelhaft (auch schon in der Anfangsphase der Erkrankung) eine hohe Viruslast in den oberen und unteren Atemwegen nachweisen. Im Eingangsbereich zum Haupthaus des Klinikums werden alle Patienten nach dem MTS "triagiert" [4, 5] und bezüglich einer möglichen COVID-Erkrankung befragt. Ergibt sich der Verdacht auf eine CO-VID-19-Erkrankung, wird der Patient abgestrichen und bei möglicher ambulanter Behandlung mit Medikation nach Hause geschickt. B. einer pp-Vitrektomie bei Amotio retinae, die in Intubationsnarkose stattfinden sollen, erfolgt unmittelbar vor stationärer Aufnahme des Patienten ein Rachen-/Nasenabstrich zum Nachweis/Ausschluss von SARS-CoV-2. Auch im Op.-Bereich sind die Patienten so terminiert worden, dass zwischen den Op.s ein ausreichender Zeitabstand eingehalten werden kann, entsteht und der genügend Zeit für die Einhaltung und Umsetzung aller Hygienestandards lässt. Implementierung eines Betriebskonzeptes in einer HNO-Klinik im Rahmen der SARS-CoV-2-Pandemie. doi = 10.1007/s00347-020-01156-9 id = cord-281005-6gi18vka author = Singh, Praveen Kumar title = Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development date = 2020-09-01 keywords = RBD; SARS; protein summary = title: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. In this study, we aimed to predict the mutations in the spike protein (S) of SARS-CoV-2 genomes available in the database (whole genome sequences as well as partial coding sequences of spike protein) and analyze the effect of each mutation on the antigenicity of the predicted epitopes. doi = 10.1055/s-0040-1715790 id = cord-353494-72fvkx7f author = Singh, Rajveer title = Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study date = 2020-10-10 keywords = Mpro; SARS; TMPRSS2 summary = The RMSD plots of all the three ligand-protein complexes showed very stable conformation throughout the simulation study, which demonstrates that it has a huge impact on the Mpro target ( Figure S2A ) as the reference compound N3. RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). RMSF study of the three natural compounds with SARS-COV-2 Mpro showed very less fluctuations, and the value was found to be less than 0.2 nm, which indicates that the ligands bind properly with the active sites of the protein such as the reference compounds ( Figure S3A ). The molecular dynamic simulation showed that the selected natural compounds bind and stabilized the active site of both the proteins such as Mpro and TMPRSS2. doi = 10.3390/molecules25204604 id = cord-026340-2nf97zvc author = Singh, Ranjana title = Chloroquine: A Potential Drug in the COVID-19 Scenario date = 2020-06-07 keywords = COVID-19; HCQ; SARS; virus summary = In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19'' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell''s receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. doi = 10.1007/s41403-020-00114-w id = cord-336554-n8n5ii5k author = Singh, Thakur Uttam title = Drug repurposing approach to fight COVID-19 date = 2020-09-05 keywords = ACE2; COVID-19; RNA; SARS; clinical; drug; patient; treatment; virus summary = Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . doi = 10.1007/s43440-020-00155-6 id = cord-317092-5qba9jiq author = Singh, Tulika title = Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date = 2020-05-08 keywords = SARS; child; covid-19 summary = The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children''s immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. doi = 10.1093/cid/ciaa547 id = cord-280427-smqc23vr author = Singla, Rubal title = Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date = 2020-09-14 keywords = COVID-19; RNA; SARS; animal; virus summary = The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. doi = 10.1007/s11259-020-09781-0 id = cord-026788-4d3r9rj8 author = Singla, Vikas title = Hepatobiliary and Pancreatic Manifestations of Coronavirus Disease 2019 date = 2020-05-16 keywords = COVID-19; SARS summary = The disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the Coronaviridae family. Drugs used to treat severe COVID-19 may cause liver injury and may have an effect on the underlying disease activity. Coronavirus disease 2019 (COVID19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has spread throughout the globe in a very short span of time, which is beyond the imagination of most of us. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in November 2002 and resulted in more than 800 deaths. Patients with decompensated liver disease may be more prone to infection by SARS-CoV-2 because of underlying immunocompromised state, and the disease may be severe in these patients. In conclusion, SARS-CoV2 can cause hepatic and pancreatic injury, which is more common in patients with severe disease. doi = 10.1055/s-0040-1712079 id = cord-266350-yybunc6z author = Sinha, Saurabh K. title = An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets date = 2020-05-13 keywords = SARS; Saikosaponin summary = From the binding energy and interaction studies, the Saikosaponins U and V showed the best affinity towards both the proteins suggesting them to be future research molecule as they mark the desire interaction with NSP15, which is responsible for replication of RNA and also with 2019-nCoV spike glycoprotein which manage the connection with ACE2. The docking simulation study of total 23 Saikosaponins (Supplementary file) was performed on the 1.9 A crystal structure of NSP15 Endoribonuclease from SARS CoV-2 in the complex with a citrate (PDB ID: 6W01) and prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up (PDB ID: 6VSB) which was retrieved from protein data bank (https://www.rcsb.org). Our observations revealed that, the Saikosaponin V having two oxane rings substituted with 3 hydroxyl group and the side chain contains 4 hydroxyl and an ester linkage showed very high binding with active site having a furrow between the two b-sheets, carries amino acids Lys290, Thr341, Tyr343 and Ser29. doi = 10.1080/07391102.2020.1762741 id = cord-351446-j4ambec5 author = Sinonquel, P. title = COVID‐19 and gastrointestinal endoscopy: what should be taken into account? date = 2020-04-26 keywords = COVID-19; SARS; patient summary = With this report we aim to provide recommendations and practical relevant information for gastroenterologists based on the limited amount of available data and local experience, to guarantee a high‐quality patient care and adequate infection prevention in the gastroenterology clinic. [6] SARS-CoV-2 virus spreads via droplets and aerosols, and indirectly by contact with contaminated surfaces which implies the absolute need of personal protective equipment (PPE) for both patients and health care workers/professionals, especially those operating in the aero-digestive tract. The aim of this report is to provide a practical guide for the protective management when performing endoscopic/endoluminal procedures of the GI tract in emergency, ambulatory or hospitalized patients, based upon the current available information worldwide and local experience in our tertiary university hospital. Before any procedure can be performed, the patient should wear a surgical mask and should be questioned about contact with COVID-19 positive individuals and recent or present symptoms like fever, cough and dyspnea, rhinitis, sudden loss of smell and/or taste. doi = 10.1111/den.13706 id = cord-300320-07tdrd4w author = Siordia, Juan A. title = Systematic and Statistical Review of Coronavirus Disease 19 Treatment Trials date = 2020-07-15 keywords = SARS; covid-19; study summary = Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, tocilizumab, favipiravir, heparin, and dexamethasone. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Medical therapies investigated included lopinavir/ritonavir, arbidol, hydroxychloroquine, remdesivir, favipiravir, heparin, glucocorticoids, interferon, ivermectin, and convalescent plasma. Key words included COVID-19, SARS-CoV2, randomized, This article is part of the Topical Collection on Covid-19 controlled, human, retrospective, prospective, trial, chloroquine, hydroxychloroquine, lopinavir, ritonavir, arbidol, umifenovir, tocilizumab, favipiravir, steroids, dexamethasone, glucocorticoids, interferon, ivermectin, remdesivir, azithromycin, heparin, and low-molecular weight heparin. Lopinavir/ritonavir, arbidol, hydroxychloroquine, favipiravir, remdesivir, and heparin are medications that have been tested in human controlled trials for COVID-19 treatment. In human trials, arbidol shows no significant positive-negative conversion rate or recovery time compared to standard therapy or lopinavir/ritonavir [4, 9] . Combining T, treatment group (remdesivir); C, control group all the hydroxychloroquine human trials showed no benefit with reducing COVID-19 viral shedding time. doi = 10.1007/s42399-020-00399-6 id = cord-334715-902pfxyz author = Sirico, Domenico title = Cardiac imaging in congenital heart disease during the coronavirus disease-2019 pandemic: recommendations from the Working Group on Congenital Heart Disease of the Italian Society of Cardiology date = 2020-06-01 keywords = COVID-19; SARS; patient summary = The aim of this position paper is to provide clinical recommendation regarding the execution of imaging investigations for the cardiac diagnostic work-up of paediatric patients with suspected or confirmed infection. In particular, the Echo-Lab leading team along with referring physicians should identify all those investigations that have an urgent/emergent indication and reschedule all the elective ones, especially for patients at higher risk of infection and low priority for echocardiogram. Echocardiogram execution Echocardiographic studies performed on paediatric patients with suspected or confirmed COVID-19 should be as focused as necessary to be of any diagnostic value. In the case of an echocardiogram in a suspected or confirmed COVID-19 hospital inpatient, a bedside investigation with a portable machine in the isolated room should be preferred, avoiding moving patients within the clinic or hospital. In this setting (suspected/confirmed COVID-19 and signs of myocarditis), CMR can be performed, considering the risk/benefit ratio according to the patient''s hemodynamic status and exam''s therapeutic impact. doi = 10.2459/jcm.0000000000000990 id = cord-260225-bc1hr0fr author = Sirpilla, Olivia title = SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date = 2020-07-20 keywords = Coronavirus; NMD; Protein; RNA; Respiratory; SARS; Syndrome; acute summary = Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). doi = 10.1021/acs.jproteome.0c00421 id = cord-311835-dmqfij6j author = Siu, Kam-Leung title = Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 date = 2014-01-13 keywords = HKU1; SARS; UPR summary = title: Comparative analysis of the activation of unfolded protein response by spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus HKU1 We and others have previously shown that severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis virus (MHV) spike (S) proteins induce ER stress and activate cellular unfolded protein response (UPR) in the ER [3] [4] [5] . We compared the UPR-activating activity of SARS-CoV and HCoV-HKU1 S proteins in terms of their influence on the expression of UPR effectors Grp78, Grp94, CHOP and PERK. To analyze further whether PERK activity is required for transcriptional activation of Grp78 and Grp94 promoters by SARS-CoV and HCoV-HKU1 S proteins, we made use of a dominant negative (DN) mutant of PERK which constitutively inhibits PERK kinase activity [48] . To determine whether the UPR-activating property of SARS-CoV S protein is mediated by S1 (amino acids 1-770) or S2 (amino acids 771-1255) subunit, we expressed them in 293FT cells ( Figure 6A, lanes 2 and 3) . doi = 10.1186/2045-3701-4-3 id = cord-338320-jc00ulx5 author = Siu, Kam-Leung title = Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain date = 2014-02-10 keywords = IFN; SARS summary = title: Suppression of innate antiviral response by severe acute respiratory syndrome coronavirus M protein is mediated through the first transmembrane domain We have previously shown that severe acute respiratory syndrome (SARS) coronavirus M protein suppresses type I interferon (IFN) production by impeding the formation of functional TRAF3-containing complex. 12 , 13 We have previously reported that SARS coronavirus M protein suppresses type I IFN production potently by preventing the formation of functional TRAF3-TANK-TBK1/IKKe complex. IFN antagonism of SARS coronavirus M protein was mediated by N-terminal TM1 (amino acids 1-38), which targets M protein to the Golgi complex and associates with TRAF3 to prevent it from interacting with TANK, TBK1 and IKKe. Our findings provide additional molecular details for suppression of type I IFN production by SARS coronavirus M protein. Notably, human coronavirus HKU1 M protein also targets the Golgi complex, interacts with TRAF3, but does not suppress IFN production. doi = 10.1038/cmi.2013.61 id = cord-337681-579cz2tc author = Sk, Md Fulbabu title = Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations date = 2020-06-01 keywords = 3CL; COVID-19; SARS; figure; pro summary = title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations In the present work, we have elucidated the mechanism of binding of two inhibitors, namely α-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. The initial coordinates for our molecular dynamics simulations were obtained from the X-ray crystallographic structure of the SARS-CoV-2 3CL pro complexed with the inhibitors a-ketoamide (PDB: 6Y2G) and Z31792168 (PDB: 5R84) (Berman et al., 2002; Zhang et al., 2020) . Next, in our study, the binding affinity of a-ketoamide was further evaluated and compared with the FDA approved anti-HIV protease inhibitors, such as lopinavir and darunavir, which has been reported as potent drugs against 3CL pro of SARS-CoV-2. doi = 10.1080/07391102.2020.1768149 id = cord-329643-hhk900c1 author = Skalina, K. A. title = Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date = 2020-05-20 keywords = PCR; SARS summary = Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. determined that short delays (up to 4 days) in processing influenza nasal and throat swabs did not significantly affect the ability to detect viral particles by real-time RT-PCR.(5) More recently the stability of SARS-CoV-2 detection in different types of storage media over a 14-day period was evaluated. This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. doi = 10.1101/2020.05.16.20104158 id = cord-268476-3lxsh1zz author = Skoog, Hunter title = Tracheotomy in the SARS‐CoV‐2 pandemic date = 2020-04-29 keywords = CoV-2; SARS summary = The severe acute respiratory syndrome (SARS)‐CoV‐2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. The severe acute respiratory syndrome (SARS)-CoV-2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. Our priorities in establishing these guidelines included: optimal patient care, protection of medical personnel, minimizing further spread of the virus and preservation of important resources (ICU beds, ventilators, and PPE). Due to the paucity of data regarding the current SARS-CoV-2 epidemic, the literature from the SARS epidemic of In Canada, 43% of cases occurred in health care workers as a result of AGPs. 1,2 One instance involved a difficult intubation of a patient who was under investigation for SARS. There are multiple reports 3,4 of safely performing tracheotomy on patients with SARS without infecting health care workers. doi = 10.1002/hed.26214 id = cord-273253-rgqvdzna author = Skowronski, D. M. title = Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 date = 2020-07-15 keywords = March; SARS summary = title: Low SARS-CoV-2 sero-prevalence based on anonymized residual sero-survey before and after first wave measures in British Columbia, Canada, March-May 2020 The goal of these serial snapshots was to establish baseline and early pandemic sero-prevalence for future attack rate comparison; to estimate cumulative incidence, residual susceptibility and the extent to which community transmission was suppressed; and to assess surveillance underascertainment across the winter-spring 2020 period in BC. Two of 869 sera were dual-assay positive at the March snapshot giving a crude seroprevalence of 0.23% (95%CI=0.03-0.83) and age-standardized sero-prevalence of 0.28% (95%CI=0.03-0.95). We estimated sero-prevalence based on dual-assay positivity and report cumulative incidence of 0.28% by the start of first wave population-level measures in March. Results of SARS-CoV-2 sero-survey screening by chemiluminescent assay for antibodies to spike (S1) and nucleocapsid proteins, by age group, March and May 2020 snapshots, Lower Mainland, BC, Canada Table 2 . doi = 10.1101/2020.07.13.20153148 id = cord-269213-tsm6zoe3 author = Slaughter, Laura title = A framework for capturing the interactions between laypersons’ understanding of disease, information gathering behaviors, and actions taken during an epidemic date = 2005-01-30 keywords = Hong; Kong; SARS; action; information summary = This paper provides a description of a methodological framework designed to capture the inter-relationships between the lay publics'' understanding of health-related processes, information gathering behaviors, and actions taken during an outbreak. This methodological framework, based on narrative analysis, is a tool for learning about how laypersons use information to build representations of an epidemic situation and how the results of this process influence their decisions to act. For example, the interview texts also result in a list of information needs expressed by the lay public concerning an outbreak as well as a general list of actions taken for SARS prevention. The arrangement of the interview into time periods (before, during, and upcoming events related to the epidemic) facilitates the data analysis when looking at the interactions and influences between informa-tion received, lay understanding, and actions taken. doi = 10.1016/j.jbi.2004.12.006 id = cord-272759-dqkjofw2 author = Small, Michael title = Super-spreaders and the rate of transmission of the SARS virus date = 2006-03-15 keywords = Hong; SARS summary = The main conclusions of this study are: (i) "super-spreaders" may occur even if the infectiousness of all infected individuals is constant; (ii) consistent with previous reports, extended exposure time beyond 3–5 days (i.e. significant nosocomial transmission) was the key factor in the severity of the SARS outbreak in Hong Kong; and, (iii) the spread of SARS can be effectively controlled by either limiting long range links (imposing a partial quarantine) or enforcing rapid hospitalisation and isolation of symptomatic individuals. 1 Two characteristic features were observed during the SARS outbreak in Hong Kong in 2003 (see Fig. 1 ) [3, 4] : so-called super-spread events (SSE), in which a single individual initiates a large number of cases; and persistent transmission within the community. In this paper, we apply these methods to the modelling of the spread of SARS in Hong Kong; transmission is only allowed to occur along a limited number of direct links between individuals. doi = 10.1016/j.physd.2006.01.021 id = cord-355318-qm79gz8w author = Smit, Albertus J. title = Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date = 2020-08-05 keywords = HIV; SARS; covid-19; environmental; section; study; temperature summary = Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Thus, if climate factors do play a role in COVID-19 infection rates, the concurrence of transition of southern hemisphere countries to their winter season with the mid-stages of the disease transmission trajectory is of concern, especially with respect to containment policy and health system resource allocation. Environmental variables considered in preprint and peer-reviewed publications as modulators of SARS-CoV-2 transmission rates include mean, minimum and/or maximum daily temperature, and diurnal temperature range; an undefined ''humidity'' variable, relative humidity, specific humidity and absolute humidity; dew point temperature; rainfall; wind speed or wind power; air pressure; some metric of solar or UV radiation; and ''air quality'' (Supplementary Tables S1 and S2 ). The general prevalence of climatologically-coupled seasonal signals and environmental variable modulation seen in the majority of other viral respiratory diseases creates the expectation for a similar effect on SARS-CoV-2 and in COVID-19 epidemiology. doi = 10.3390/ijerph17165634 id = cord-346345-jc9bq0zu author = Smith, Colin M title = COVID-19-associated brief psychotic disorder date = 2020-08-11 keywords = COVID-19; SARS; patient summary = This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. This is the first case of COVID-19associated psychosis in a patient with no personal or family history of a severe mood or psychotic disorder presenting with symptomatic COVID-19, highlighting the need for vigilant monitoring of neuropsychiatric symptoms in these individuals. Here, we report a case of symptomatic COVID-19-related psychosis in a patient with no personal or family history of mental illness and briefly discuss the relevant literature on coronavirus-associated psychosis. 8 However, all patients were incidentally found to have positive SARS-CoV-2 test and did not present with other symptoms to suggest infection, calling into question whether the diagnosis of COVID-19 was related to the psychosis. doi = 10.1136/bcr-2020-236940 id = cord-351974-1najtyui author = Smith, E. title = Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation date = 2020-08-05 keywords = Norfolk; SARS summary = 1 2 Transmission of SARS-CoV-2 may be possible up to two-days prior to the appearance of typical symptoms yet older patients frequently have atypical presentation, 3-5 making recognition and control of infection in care homes difficult. SARS-CoV-2 has highlighted serious gaps in data intelligence surrounding care homes, 13 with regional test results typically not available to local authorities until 2 July 2020. In addition, for SARS-CoV-2-positive residents who were asymptomatic at the point of test, data on any symptoms recorded in the 14-day post-test period were extracted. Data for residents and staff tests comprised unique ID, care home ID, date of SARS-CoV-2 test(s) and test outcome(s). Early screening of residents and staff after ingress into care homes identified prevalence of truly asymptomatic infections and symptom presentation in residents relatively early in the UK COVID-19 outbreak. Early testing and screening of staff and residents in care homes can accurately identify outbreaks, prevalence of infection and death, and cause of death. doi = 10.1101/2020.08.04.20165928 id = cord-267397-b7ogeokm author = Smith, E. R. title = Protocol for a Sequential, Prospective Meta-Analysis to Describe COVID-19 in Pregnancy and Newborn Periods date = 2020-11-12 keywords = COVID-19; November; SARS; international summary = Given the scarcity of COVID data in pregnancy, differences in data collection protocols globally, and potential risks for severe illnesses in this population, there is an urgent need to rapidly generate high quality information to make evidence-based decisions and create guidelines on the prevention and treatment of COVID-19 illness in pregnant women and infants. We updated the data modules in September 2020 to reflect evolving understanding of SARS-CoV-2 infection in newborns and to reflect and an updated generic protocol developed by WHO for COVID-related pregnancy cohort studies (Supplementary File 3) . Studies will be eligible to contribute data to the PMA when they have accrued at least 25 confirmed cases with completed follow up including obtaining maternal and neonatal outcomes. Given the current state of limited, high-quality evidence to inform public health guidance and healthcare strategies for pregnant women and newborn, the proposed study will contribute timely and necessary evidence-based data for decision-making in the context of COVID-19 and maternal and neonatal health. doi = 10.1101/2020.11.08.20228056 id = cord-296378-ki93iltt author = Smith, Joan C. title = Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract date = 2020-05-16 keywords = ACE2; SARS; cell; expression; figure summary = Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination. In total, our results demonstrate that exposure to cigarette smoke increases the expression of the coronavirus receptor ACE2 in rodent and human respiratory tissue, and this upregulation is potentially reversible. To investigate a potential link between inflammation and the expression of the host factors required for coronavirus infections, we first examined the levels of ACE2 in published datasets of respiratory epithelial cells challenged with different viruses. To further verify these results, we re-analyzed a published gene expression dataset of airway epithelial cells exposed to IFN-β, and we found a similar increase in ACE2 levels following interferon treatment ( Figure 5H ) (Rusinova et al., 2013; Shapira et al., 2009) . doi = 10.1016/j.devcel.2020.05.012 id = cord-277731-thazunob author = Smith, Matthew L. title = Biosurfactants: A Covid-19 Perspective date = 2020-06-09 keywords = SARS; biosurfactant summary = In this case, the use of biosurfactants in dealing with this pandemic justifies extensive study with their potential applications being in the prevention of viral spread; dealing with the symptoms that develop after the incubation period; directly targeting viral infected cells and preventing the spread of the virus throughout the host, all in addition to also acting as potential drug delivery systems and cleaning agents. The use of biosurfactants will therefore be considered in handwashes and cleaning agents to prevent the spread of the virus; targeting and relieving the symptoms after infection; acting as drug delivery systems and additionally their use in other important areas with a key example being the production reliable antiviral facemasks. This structure will be significant in directly targeting the virus, impacting its overall emulsification activity, while also being crucial in our application of biosurfactants in drug delivery. doi = 10.3389/fmicb.2020.01341 id = cord-033780-184e64tr author = Smith, Rasheid title = Implications of current and future approaches to coronavirus disease 2019 testing date = 2020-10-13 keywords = COVID-19; CoV-2; SARS summary = The current reality is that SARS-CoV-2 is a highly transmissible airborne disease with a broad presentation of symptoms and leaves lasting damage in severe cases, and for which there is a scarcity of effective medications to treat it. Using the cycle threshold value in this manner only informs as to the presence of the virus and may not reveal disease progression, severity and viral load in the sample; and as such the results are largely qualitative despite the inherent quantitative nature of real-time RT-PCR [27] . Nevertheless, initial studies have demonstrated that chest CT imaging is more accurate than RT-PCR at detecting SARS-CoV-2 patients [32] with 97.2% versus 83% in the early stages of infection [33] . Immunoassays (antibody serum tests), such as enzyme-linked immunosorbent assays (ELISAs), are used to detect the presence of serum antibodies (either IgA, IgG or IgM) to viral proteins and can indicate when a person has developed an immune response to SARS-CoV-2. Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor doi = 10.2217/fvl-2020-0318 id = cord-341287-i1hyk962 author = Smith, Trevor R. F. title = Immunogenicity of a DNA vaccine candidate for COVID-19 date = 2020-05-20 keywords = ACE2; CoV-2; Fig; INO-4800; SARS; dna summary = Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. In subjects immunized with INO-4700 (MERS-CoV S protein DNA vaccine) durable neutralizing antibodies (nAbs) and T cell immune responses were measured, and a seroconversion rate of 96% was observed and immunity was followed for 60 weeks in most study volunteers 9 . We followed the induction of immunity by the selected immunogen in mice and guinea pigs, measuring SARS-CoV-2 S protein-specific antibody levels in serum and in the lung fluid, and antibody functionality through competitive inhibition of ACE2 binding, pseudovirus and live virus neutralization. In summary, humoral immunogenicity testing in both mice and guinea pigs revealed the COVID-19 vaccine candidate, INO-4800, was capable of eliciting functional blocking antibody responses to SARS-CoV-2 spike protein. doi = 10.1038/s41467-020-16505-0 id = cord-299133-09mbiqrr author = Smither, Sophie J. title = Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity date = 2020-06-22 keywords = SARS summary = title: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity In this study, the ability of SARS-CoV-2 to survive in the dark, at two different relative humidity values and within artificial saliva, a clinically relevant matrix, was investigated. SARS-CoV-2 was found to be stable, in the dark, in a dynamic small particle aerosol under the four experimental conditions we tested and viable virus could still be detected after 90 minutes. A recent study has shown the Washington variant of SARS-CoV-2 remains viable in a small particle aerosol for long periods [2] . Here we extend that research to look at a UK variant of SARS-CoV-2 in aerosols, at different relative humidity values, and in artificial saliva. SARS-CoV-2 England-2 variant was aerosolised in tissue culture media or in artificial saliva and maintained in a dynamic aerosol at medium RH (40-60%) or high RH (68-88%) (Supplementary Material: Table 1 ). doi = 10.1080/22221751.2020.1777906 id = cord-283430-k1ex9fes author = Smithgall, Marie C. title = Third Trimester Placentas of SARS‐CoV‐2‐Positive Women: Histomorphology, including Viral Immunohistochemistry and in Situ Hybridization date = 2020-07-21 keywords = IHC; SARS summary = CONCLUSIONS: In this study, third trimester placentas from SARS‐CoV‐2‐positive women were more likely to show evidence of maternal/fetal vascular malperfusion; however, no evidence of direct viral involvement or vertical transmission was noted by ISH and IHC. Studies to date regarding SARS-CoV-2 and placental pathology have been limited by the number of SARS-CoV-2 positive cases, 4, 5 and only one with a sample size of 5 cases has utilized in-situ hybridization (ISH) and immunohistochemistry (IHC) analyses. 6 In our study, we compared placental histopathology from 51 SARS-CoV-2-positive and 25 SARS-CoV-2negative women in their third-trimesters presenting to L&D, and tested placentas from SARS-CoV-2-positive mothers using ISH and/or IHC. Placentas from SARS-CoV-2-positive women showed non-specific evidence of maternal/fetal vascular malperfusion, including subchorionic thrombi (Fig.1A) , intervillous thrombi (Fig.1B) , infarction (Fig.1C) , chorangiosis, segmental avascular-villi (Fig.1D) , fetal thrombotic vasculopathy (Fig.1E) , and villous agglutination (Fig.1F ). doi = 10.1111/his.14215 id = cord-289740-nsiycudn author = Smithgall, Marie C. title = Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2 date = 2020-05-13 keywords = SARS summary = OBJECTIVE: This study aimed to compare two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2, to the Roche cobas SARS-CoV-2 assay for samples with low, medium, and high viral concentrations. STUDY DESIGN: A total of 113 nasopharyngeal swabs from remnant patient samples were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. CONCLUSIONS: While Xpert showed high agreement with cobas across a wide range of viral concentrations, this study highlights an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Utilizing the high volume of patient testing performed at our medical center in New York City, we sought to evaluate and compare the performance of these two rapid assays across a wide range of clinical samples. Deidentified remnant patient samples that underwent routine clinical testing with the cobas SARS-CoV-2 assay on the 6800 platform (Roche Diagnostics, Indianapolis, IN) were used to evaluate the Xpert and ID Now assays. doi = 10.1016/j.jcv.2020.104428 id = cord-341416-6bh08901 author = Smithgall, Marie C. title = Laboratory Testing of SARS CoV-2: A New York Institutional Experience date = 2020-07-19 keywords = New; SARS; York summary = The World Health Organization developed the first quantitative RT-PCR test for detecting SARS-CoV-2 and subsequently the U.S. Centers for Disease Control and Prevention (CDC) began shipping its own RT-PCR test kits after receiving Emergency Use Authorization (EUA) by the U.S. Food and Drug Administration (FDA) on February 4, 2020. To date there are more than 80 commercial laboratories and/or test kit manufacturers that have received approval for emergency use by the Federal Drug Administration (FDA) for SARS-CoV-2 testing with molecular assays accounting for the vast majority [6] . In addition, the FDA recently granted EUA for an RT-PCR lab developed test for qualitative detection of SARS-CoV-2 in saliva specimens and a test that uses a home collection kit with nasal swabs [6] for details see https://www.fda.gov/emergency-preparednessand-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization]. During this time, termed the "window period," a patient who is infected with SARS-CoV-2, but has not yet produced antibodies, would test negative on such an assay. doi = 10.1016/j.yamp.2020.07.002 id = cord-333176-6v7ficfk author = Snell, Jonathan title = SARS-CoV-2 infection and its association with thrombosis and ischemic stroke: A review COVID-19, thrombosis, and ischemic stroke date = 2020-09-30 keywords = ACE2; SARS summary = SARS-CoV-2 infection is well-documented to cause severe pneumonia, however, thrombosis and thrombotic complications, such as ischemic stroke, have also been documented in a variety of patient demographics. 5,6 This is likely due to the presence of asymptomatic or mildly symptomatic transmission of SARS-CoV-2, and its current prevalence in the human population supports the infective potential of this novel coronavirus. 37 Imbalance of the interactions between ACE2 and the RAS axis may also contribute to the thromboembolic events seen in SARS-CoV-2 infection. 44, 45 Ischemic stroke due to occlusion of large arteries has been a documented complication of SARS-CoV infection in patients with minimal to no risk factors. 46 SARS-CoV-2 infection seems to also increase risk of developing ischemic stroke, among other neurological consequences. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: A report of five cases Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Ischemic Stroke doi = 10.1016/j.ajem.2020.09.072 id = cord-259603-bh198xgl author = Snijder, E.J. title = The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date = 2016-09-14 keywords = CoV; Fig; MHV; RNA; SARS; ZBD; protein summary = Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein''s importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V''Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme''s activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. doi = 10.1016/bs.aivir.2016.08.008 id = cord-263438-9ra94uda author = Snowden, Frank M. title = Emerging and reemerging diseases: a historical perspective date = 2008-09-19 keywords = AIDS; HIV; Health; IOM; Infectious; SARS; States; United; disease summary = Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. In 1996, in addition, President Bill Clinton (28) issued a fact sheet entitled ''Addressing the Threat of Emerging Infectious Diseases'' in which he declared them ''one of the most significant health and security challenges facing the global community.'' There were also highly visible hearings on emerging infections in the US Congress (29) . The Rand Corporation intelligence report The Global Threat of New and Reemerging Infectious Diseases: Reconciling U.S. National Security and Public Health Policy (53) had two leading themes. doi = 10.1111/j.1600-065x.2008.00677.x id = cord-295800-w0dup04b author = So, Loletta K-Y title = Development of a standard treatment protocol for severe acute respiratory syndrome date = 2003-05-10 keywords = SARS; patient summary = Add combination treatment with ribavirin and methylprednisolone when: q Extensive or bilateral chest radiographic involvement q Or persistent chest radiographic involvement and persistent high fever for 2 days q Or clinical, chest radiographic, or laboratory findings suggestive of worsening q Or oxygen saturation <95% in room air Standard corticosteroid regimen for 21 days q Methylprednisolone 1 mg/kg every 8 h (3 mg/kg daily) intravenously for 5 days q Then methylprednisolone 1 mg/kg every 12 h (2 mg/kg daily) intravenously for 5 days q Then prednisolone 0·5 mg/kg twice daily (1 mg/kg daily) orally for 5 days q Then prednisolone 0·5 mg/kg daily orally for 3 days q Then prednisolone 0·25 mg/kg daily orally for 3 days q Then off Ribavirin regimen for 10-14 days q Ribavirin 400 mg every 8 h (1200 mg daily) intravenously for at least 3 days (or until condition becomes stable) q Then ribavirin 1200 mg twice daily (2400 mg daily) orally Pulsed methylprednisolone q Give pulsed methylprednisolone if clinical condition, chest radiograph, or oxygen saturation worsens (at least two of these), and lymphopenia persists q Give as methylprednisolone 500 mg twice daily intravenously for 2 days, then back to standard corticosteroid regimen Ventilation q Consider non-invasive ventilation or mechanical ventilation if oxygen saturation <96% while on >6 L per min oxygen or if patient complains of increasing shortness of breath conditioning) was increased to 10-12 changes per h. doi = 10.1016/s0140-6736(03)13265-5 id = cord-276820-l7bd5y8y author = So, Winnie K.W. title = The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong date = 2004-11-30 keywords = Hong; Kong; SARS summary = authors: So, Winnie K.W.; Chan, Sophia S.C.; Lee, Angel C.K.; Tiwari, Agnes F.Y. title: The knowledge level and precautionary measures taken by older adults during the SARS outbreak in Hong Kong Abstract The study aims to examine the knowledge and the practice of the precautionary measures taken by older adults in Hong Kong against the outbreak of severe acute respiratory syndrome (SARS). The aim of the study is to describe the knowledge about SARS and precautionary measures taken by older adults in Hong Kong. Understanding older adults'' knowledge level and adherence to the government''s recommended precautionary measures to prevent transmission of SARS is an essential step in being able to design similar promotion programmes for this population in the future. (1) What demographic variables influenced older adults'' knowledge level, beliefs, and precautionary measures taken to prevent transmission of SARS? doi = 10.1016/j.ijnurstu.2004.04.004 id = cord-345225-2s5xd1oc author = Soares, F. title = A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence date = 2020-04-14 keywords = SARS; covid-19 summary = We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). We developed a machine learning classifier that takes widely available simple blood exams as input and predicts if that suspect case is likely to be positive (having SARS-CoV-2) or negative(not having SARS-CoV-2). Based on this data, we built an artificial intelligence classification framework, ER-CoV, aiming at determining which patients were more likely to be negative for SARS-CoV-2 when visiting an ER and that were categorized as a suspect case by medical professionals. Considering the aforementioned successes in integrating AI and medicine, we propose ER-CoV, an artificial intelligence-based screening method that uses blood exams to triage patients suspect of COVID-19 arriving at emergency rooms. doi = 10.1101/2020.04.10.20061036 id = cord-296977-yzhsdz9c author = Soares, R. R. G. title = Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date = 2020-11-06 keywords = LAMP; November; RNA; SARS summary = ; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 . doi = 10.1101/2020.11.04.20225888 id = cord-032928-m0awip9y author = Sobh, Eman title = Novel coronavirus disease 2019 (COVID-19) non-respiratory involvement date = 2020-10-01 keywords = COVID-19; China; SARS; patient summary = Coronavirus disease 2019 (COVID-19) is caused by a novel single-strand ribonucleic acid (RNA) coronavirus known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 primary attacks the lower respiratory system causing viral pneumonia, but it may also affect the heart, gastrointestinal system, liver, kidney, and central nervous system leading to multiple organ failure [3] . Other researchers found elevated serum troponin levels in many patients infected with COVID-19, and it was associated with more severe disease and poor prognosis [21] . The mechanism behind acute myocardial injury caused by SARS-CoV-2 infection might be related to human angiotensin-converting enzyme 2 receptor (ACE2) [20] which are highly expressed in the heart [11] . The results of previous reports indicate that cardiac injury, arrhythmia, and venous thromboembolism should be considered in any suspected or confirmed COVID-19 case and the patient should undergo a prompt clinical evaluation. doi = 10.1186/s43168-020-00030-1 id = cord-263801-01goni72 author = Sobral, Marcos Felipe Falcão title = Association between climate variables and global transmission oF SARS-CoV-2 date = 2020-08-10 keywords = SARS; covid-19 summary = In this study, we aimed at analyzing the associations between transmission of and deaths caused by SARS-CoV-2 and meteorological variables, such as average temperature, minimum temperature, maximum temperature, and precipitation. On the basis of the assumption that different climatic conditions play a significant role in the course of COVID-19, it is essential to identify associations between environmental factors, such as average, maximum, and minimum temperatures; precipitation; and demographic density, and SARS-CoV-2 transmission and COVID-19 mortality in humans. Even with the complete specification that includes two binary variables capturing specific effects for the months of the year and controlling for population density, the results suggest that an increase in temperature is associated with a decrease in the number of infections. This study aimed to identify the associations between environmental variables and SARS-CoV-2 transmission/COVID-19 mortality. We examined the associations between climatic variables and SARS-CoV-2 transmission and COVID-19 mortality. doi = 10.1016/j.scitotenv.2020.138997 id = cord-308100-tvk47fd7 author = Soetikno, Roy title = Considerations in performing endoscopy during the COVID-19 pandemic date = 2020-03-27 keywords = PPE; SARS; covid-19 summary = Based on experiences and the literature, our objective is to provide practical suggestions for performing endoscopy in the setting of COVID-19 pandemic. 6 It is unknown how much of the risk was related to the direct care of infected patients or to the inadequate use of personal protective equipment (PPE). 9 With numbers of COVID-19 cases continuing to rise in North America and Europe, we aim to provide practical suggestions to potentially avoid the transmissions of COVID-19 in the endoscopy unit. Possible routes of SARS-CoV-2 transmission include (1) person-to-person, (2) respiratory droplets, (3) aerosols generated during endoscopy, and (4) contact with contaminated surroundings and body fluids. 13 Recently, the World Health Organization (WHO) has published an extensive guideline on the rational use of personal protective equipment (PPE) for COVID-19 and provided specific instructions for healthcare workers performing AGP on patients with COVID-19. 17 Note that as an AGP, endoscopy of PUI/COVID patients requires the use of respiratory protection. doi = 10.1016/j.gie.2020.03.3758 id = cord-350903-nwagvvc5 author = Softic, Laurent title = Inhibition of SARS-CoV-2 Infection by the Cyclophilin Inhibitor Alisporivir (Debio 025) date = 2020-06-23 keywords = CoV-2; SARS summary = Alisporivir reduced SARS-CoV-2 RNA production in a dose-dependent manner in Vero E6 cells, with a 50% effective concentration (EC(50)) of 0.46 ± 0.04 μM. For instance, chloroquine has been shown to bear potent antiviral properties against SARS-CoV-2 in vitro, and several clinical trials are under way to assess its efficacy in patients with COVID-19. Cyclosporine A (CsA), a potent cyclophilin inhibitor, blocks the replication of various coronaviruses in vitro, including HCoV-229E, HCoV-NL63, FPIV, mouse hepatitis virus (MHV), avian infectious bronchitis virus, and SARS-CoV (5, (8) (9) (10) . The antiviral effectiveness of increasing concentrations of alisporivir was measured in Vero E6 cells infected with a clinical isolate of SARS-CoV-2 at a multiplicity of infection (MOI) of 0.02 (Fig. 1A) . These results justify rapidly conducting a proof-of-concept phase 2 trial to assess the antiviral properties and the effect of alisporivir on COVID-19 clinical outcomes in infected patients. doi = 10.1128/aac.00876-20 id = cord-323930-pl3qlcpo author = Sohail, Ayesha title = Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date = 2020-04-29 keywords = SARS; virus summary = The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. doi = 10.1016/j.pbiomolbio.2020.04.002 id = cord-322184-kgv9f58a author = Sohn, Yujin title = Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date = 2020-09-10 keywords = PCR; SARS summary = Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In this study, we attempted to confirm the presence of viable virus by performing RT-PCR assay and culture using salivary and nasopharyngeal swabs of asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease and admitted to a CTC at least two weeks previously. Therefore, based on the evidence that the virus is rarely detected in respiratory specimens after 10 days following the onset of symptoms, especially in mild or asymptomatic cases of SARS-CoV-2 infection, even if viral shedding is sustained in the later phase of COVID-19, it can be expected that the transmission risk of the virus is low. doi = 10.3390/jcm9092924 id = cord-266866-z98x80zj author = Sohpal, Vipan Kumar title = Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA date = 2020-09-24 keywords = GTR; SARS summary = Hence the purpose of the present work is to assess the genomic relationship on the basis of statistical techniques between MERS-CoV, SARS-CoV, and SARS-CoV-2 with an objective to (1) maximized value of likelihood function of nucleotide substitution models, (2) transition/transversion bias and frequencies computation using maximum likelihood (ML) technique, (3) analyze the probability rate of substitution using ML. ML of different nucleotide substitution models BIC and AICc are the most important parameters for statistical analysis of ML to analyze the biological data. It indicates ML method accurately fits of 24 different nucleotide substitution models for biological data of SARS-CoV-2, MERS-CoV, and SARS-CoV under neutral evolution. In broad, the transitional/transversional varies from 0.57 (GTR model) to 0.89 (T92 + G + I), higher values indicate proportion of invariable sites (+I) and/or rate of variation across sites (+G) are more dominating in T92 model for SARS-CoV-2, SARS-CoV, and MERSCoV biological sequence. Six different nucleotide substitution models were simulated for biological sequence data of SARS-CoV, MERS-CoV and SARS-CoV-2. doi = 10.5808/gi.2020.18.3.e30 id = cord-279989-swsxez0a author = Sokolov, Elisaveta title = Non-convulsive status epilepticus: COVID-19 or clozapine induced? date = 2020-10-04 keywords = Clozapine; EEG; SARS summary = We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We present a case of non-convulsive status epilepticus in a 57-year-old woman with a schizoaffective disorder, without an antecedent seizure history, with two possible aetiologies including SARS-CoV-2 infection and clozapine uptitration. We highlight seizure disorders as a possible manifestation of SARS-CoV2 infection and describe the complexity of these presentations in the intensive care setting, especially in the context of atypical antipsychotics such as Clozapine. These two scans were done when the Findings that shed new light on the possible pathogenesis of a disease or an adverse effect patient was noted not to be waking following extubation, first as she was quadriplegic at this time and second to consider if there were any MRI features known to be associated with COVID-19. doi = 10.1136/bcr-2020-239015 id = cord-323095-q8tj826i author = Sokolowska, Milena title = Outsmarting SARS-CoV-2 by empowering a decoy ACE2 date = 2020-11-03 keywords = ACE2; SARS summary = Along with the current efforts to develop high-affinity neutralizing antibodies, Chan and colleagues engineered the soluble variant of human ACE2 with enhanced binding to the spike protein, outranking the soluble wild-type protein in blocking SARS-CoV-2 infection in vitro. There are currently a few therapeutic approaches focused on blocking SARS-CoV-2 binding to its key receptor, an angiotensin-converting enzyme 2 (ACE2), or on inhibition of virus spike cleavage (Fig. 1a) . 2 Therefore, other approaches are also intensively studied including soluble recombinant human ACE2 (rhACE2) or peptide-based binders, developed to block SARS-CoV-2-RBD-ACE2 binding interface or small molecule inhibitors blocking the host cell proteases, such as TMPRSS2 or furin, block virus fusion with the host cell. Therefore, in designing the soluble ACE2 (sACE2) variant the authors introduced the combinations of 3-7 mutations, which gave the large increases in S binding. Engineered soluble construct of ACE2 with enhanced affinity to SARS-CoV-2 spike RBD opens up several possibilities of its usage in the current pandemics. doi = 10.1038/s41392-020-00370-w id = cord-301603-gdxvbspx author = Sokouti, Massoud title = Comparative Global Epidemiological Investigation of SARS-CoV-2 and SARS-CoV Diseases Using Meta-MUMS Tool Through Incidence, Mortality, and Recovery Rates date = 2020-04-15 keywords = SARS summary = In this meta-analysis, a random effect model of relations of incidence, mortality, and recovery rates of COVID-19 and SARS world infections were determined. The meta-analysis and forest plots of two viral world infections showed that the incidence rate of COVID-19 infection is more than SARS infections, while recovery and mortality event rates of SARS-CoV are more than COVID-19 infection. In the current study, the comparisons between incidence and mortality, as well as recovery and death rates among the countries for COVID-19 and SARS-CoV with the higher incidence rates, were performed using the meta-analysis approach developed in the Meta-MUMS tool. The incidence event rates of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 1A , showing the relationships between two infectious diseases. Recovery event rate of COVID-19 and SARS-CoV infections are as below, and the forest plots are illustrated in Figure 2A , showing the relations between both diseases. doi = 10.1016/j.arcmed.2020.04.005 id = cord-334188-bggt1i2e author = Solari, Domenico title = The nose lid for the endoscopic endonasal procedures during COVID-19 era: technical note date = 2020-08-11 keywords = COVID-19; SARS; patient summary = We describe peculiar surgical technique modifications and the use of an endonasal face mask, i.e., the nose lid, to be applied to the patient during transnasal procedures for skull base pathologies as a further possible COVID-19 mitigation strategy. CONCLUSIONS: Transnasal surgery, transgressing respiratory mucosa, can definitely increase the risk of virus transmission: we find that adopting further precautions, above all limiting high-speed drill can help preventing or at least reducing aerosol/droplets. After usual nasal pyramid sterile draping, an endonasal surgery facial mask, namely a nose lid, is assembled: a sterile non-latex glove layer is used to cover nostril and fixed with adhesive protection film over the nasal bridge; initially, two and then three narrow slit cut are placed over the nares to let instruments enter the nostrils (Figs. doi = 10.1007/s00701-020-04518-z id = cord-338889-7hd3iibk author = Solbakk, Jan Helge title = Back to WHAT? The role of research ethics in pandemic times date = 2020-11-03 keywords = Declaration; Human; SARS; Selgelid; covid-19; research; risk; study summary = 10 Of the 10 standards laid down in this Code, and with which physician-researchers must comply when carrying out experiments on human subjects, standard 5, in particular, has become highly relevant these days due to pressure from influential medical stakeholders, agencies and bioethicists to permit the conduct of controlled human infection studies (CHIs), also labeled human challenge trials (HCTs), or challenge studies (CSs) to possibly shorten the development time of vaccines to protect against Covid-19 caused by the SARS-CoV-2 virus. doi = 10.1007/s11019-020-09984-x id = cord-301677-b6mnn27h author = Soleimanian, Saeede title = Harnessing Memory NK Cell to Protect Against COVID-19 date = 2020-08-20 keywords = COVID-19; HCMV; SARS; cell; infection summary = In this regard, Natural Killer (NK) cells as essential front-line responders to many viral infections in humans have been proposed for a suitable therapeutic approach in severe COVID-19 patients, and several clinical trials have begun (Market et al., 2020) . In this line, Type I IFNs have a critical role in concert with pattern PRR signaling to prime innate and adaptive antiviral responses such as stimulating natural killer (NK) cells, macrophages, and production of proinflammatory cytokines (Samuel, 2001; Murira and Lamarre, 2016) . The detection of both SARS-CoV-2 nucleic acid and specific antibodies to viral proteins have thus far become significant for primary diagnosis infection and immunity in COVID-19 patients, respectively. in a pneumonia model of SARS in mice, mimicking features of the human disease, illustrated that mice depleted of both CD4 and CD8T cells, had the ability to control SARS-CoV replication in the lungs, suggesting an immune mechanism independent of T cells, and a role for innate antiviral response and NK cells, in viral clearance. doi = 10.3389/fphar.2020.01309 id = cord-306826-vbfdxoc2 author = Solerte, Sebastiano Bruno title = Dipeptidyl peptidase-4 (DPP4) inhibition in COVID-19 date = 2020-06-06 keywords = CD26; DPP4; SARS summary = CONCLUSIONS: The use of DPP4 inhibitors, such as gliptins, in patients with COVID-19 with, or even without, type 2 diabetes, may offer a simple way to reduce the virus entry and replication into the airways and to hamper the sustained cytokine storm and inflammation within the lung in patients diagnosed with COVID-19 infection. The novel beta-coronavirus 2019 (SARS-CoV-2) has recently emerged as a threat for human kind, causing severe respiratory syndrome , associated with other systemic complications (i.e., intestinal infections, renal and heart failure) and with a relative high mortality [1] . The co-expression of ACE2 and DPP4/CD26 as receptors of spike glycoproteins could hypothesize that different human coronaviruses (CoVs) target similar cell types across different human tissues and explain the presence of similar clinical features in patients infected with different CoVs. In another case, it was shown that DPP4 acted for CoV co-receptor, thus suggesting a potential similar mechanism of entry for SARS-CoV-2 [5] . doi = 10.1007/s00592-020-01539-z id = cord-305745-9lngdjow author = Solnier, Julia title = Flavonoids: A complementary approach to conventional therapy of COVID-19? date = 2020-09-18 keywords = MERS; SARS; table summary = Chalcones isolated from Angelica keiskei were shown to inhibit both SARS-CoV proteases PLpro and 3CLpro in enzymatic, FRET-based (Table 2) and molecular docking studies (Park et al. As Table 2 demonstrates, the compounds showed generally higher inhibitory potential against SARS-CoV PLpro than when tested against the other viral proteases using fluorogenic methods, which is likely related to genomic variations in the single amino acid sequences. In particular, herbacetin, quercetin and isobavachalcone (Fig. 3) were identified as promising antiviral leads against SARS-and MERS-CoV based on their broad-spectrum activity against the viral proteases 3CL and PL of both CoVs, the number of relevant literature data, and the availability of the compounds from different plant sources. However, despite some promising inhibitory activities of flavonoids against SARS-and MERS-CoV in vitro, none of these compounds have been tested in vivo using animal and/or human cell models. doi = 10.1007/s11101-020-09720-6 id = cord-279290-wtnnlp4i author = Solorio-Pineda, Saúl title = Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? date = 2020-09-25 keywords = SARS; covid-19 summary = title: Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? BACKGROUND: In December 2019, in Wuhan, a new virus emerged, causing severe acute respiratory syndrome (SARS) secondary to infection by a type of coronavirus, causing coronavirus disease (COVID-19). A new virus emerged, causing severe acute respiratory syndrome (SARS) originated in the city of Wuhan, China, in December 2019. [6, 9] We decided to present the following remarkable case from a patient with pituitary tumor apoplexy infected with SARS-CoV-2. Unfortunately, given the patient''s condition and his timely isolation in the coronavirus disease (COVID-19) floor, it was not possible to perform a brain MRI scan. e CNS involvement in COVID-19 infection includes cerebrovascular events due to endothelial dysfunction, with pituitary apoplexy being an unusual presentation, a situation that should be confirmed in the future. Pituitary macroadenoma apoplexy in a severe acute respiratory syndrome-coronavirus-2-positive testing: Causal or casual? doi = 10.25259/sni_305_2020 id = cord-285490-tpsf05ca author = Solís, José Gabriel title = Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm date = 2020-07-29 keywords = COVID-19; SARS; rhabdomyolysis summary = title: Case Report: Rhabdomyolysis in a Patient with COVID-19: A Proposed Diagnostic-Therapeutic Algorithm He developed acute kidney injury requiring renal replacement therapy without reversibility, despite optimal treatment. 2 We report the case of a patient with confirmed SARS-CoV-2 infection who presented with rhabdomyolysis as a cardinal manifestation, discuss the possible mechanisms, and propose a diagnostic-therapeutic algorithm. Laboratory tests revealed grade 3 acute kidney injury (AKI) with a creatinine level of 11 mg/dL (basal value 0.7 mg/dL); increased blood levels of creatine kinase (CK) (> 400,000 U/L), lactate dehydrogenase (LDH), aspartate aminotransferase, alanine aminotransferase; and electrolyte disturbances with hyperkalemia, hyperphosphatemia, hypocalcemia, and severe metabolic acidosis. The underlying cause of muscle injury must be identified and treated, which is difficult in patients with COVID-19 because there is no specific therapy. Kidney disease is associated with in-hospital death of patients with COVID-19 Acute kidney injury due to rhabdomyolysis and renal replacement therapy: a critical review doi = 10.4269/ajtmh.20-0692 id = cord-321664-3qlfsei6 author = Somsen, G Aernout title = Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission date = 2020-05-27 keywords = SARS summary = title: Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission Globally, health-care authorities are searching for effective measures to prevent community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, aerosols containing a small concentration of virus in poorly ventilated spaces, combined with low humidity and high temperature, 6 might result in an infectious dose over time. To better understand the spreading of respiratory droplets and possible preventive measures, we analysed droplet production due to coughs and speech by measuring the droplet size distribution, travel distance and velocity, and the airborne time in relation to the level of air ventilation. Although we only studied healthy volunteers and did not study patients with COVID-19 or virus-laden aerosol droplets directly, our data on droplet size distribution and persistence does have implications on requirements to use face masks to prevent virus transmission. The persistence of small respiratory droplets in such poorly ventilated spaces could contribute to the spread of SARS-CoV-2. doi = 10.1016/s2213-2600(20)30245-9 id = cord-319935-ni6a8vje author = Somsen, G. A. title = Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters date = 2020-10-14 keywords = SARS summary = To demonstrate the usefulness of our novel method, we perform measurements in typical public spaces that can play a role in aerosol transmission of SARS-CoV-2, each differing in volume, number of people and ventilation rate. Using this easily applicable method, aerosol concentrations can be measured in any public space which is important to determine the risk is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Using the half-times as measured by us, we calculate that the decrease in the number of aerosol particles after these 6 minutes will vary between 50 and 100%, depending on the ventilation method and the size of the public space. Small droplet aerosols in poorly ventilated spaces; the need for specific measures to prevent SARS-CoV-2 transmission doi = 10.1101/2020.10.13.20211839 id = cord-277197-njy99jh4 author = Song, Fang title = COVID‐19: Recommended sampling sites at different stage of the disease date = 2020-04-16 keywords = SARS summary = At present, it mainly relies on Real‐time RT‐PCR to detect SARS‐CoV‐2 virus nucleic acid collected from the clinical specimens of patients as the standard for diagnosis, discontinuation of quarantine and discharge.(1,2) This article is protected by copyright. 13 Different from the suspected cases with typical clinical characteristics, the diagnosis rate can be improved by detecting the nucleic acid in fecal samples, the latest discharge standards in China still requires only the collection of respiratory specimens 1 . But it has been emphasized in the discharge standard to collect "nasal swab, sputum" and other upper and lower respiratory tract specimens at the same Based on the improvement of clinical symptoms and CT imaging, the guidelines require only two consecutive negative nucleic acid tests (≥24 hours) before discharge can be considered. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan doi = 10.1002/jmv.25892 id = cord-268075-kbislbx0 author = Song, Limin title = Cardiovascular Changes in Patients With COVID-19 From Wuhan, China date = 2020-09-02 keywords = AAO; COVID-19; SARS summary = Alternatively, ascending aortic dilation and LA enlargement might be present before infection but characterized the patient at risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Epidemiological studies have demonstrated that acute pneumonia is associated with an increased risk for cardiac complications at all levels of infection severity (4) . In this study, we retrospectively collected and analyzed detailed clinical data from patients with laboratory-confirmed COVID-19 who were admitted to the Union Hospital (Wuhan, China). Myocardial injury associated with the SARS-CoV-2 occurred in five of the first 41 patients diagnosed with COVID-19 in Wuhan, which mainly manifested as an increase in high-sensitivity cardiac troponin I levels (2) . In summary, we have shown that hypertension is a common comorbidity among hospitalized patients with COVID-19 in Wuhan, China, and cardiac injury was the most common complication. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China doi = 10.3389/fcvm.2020.00150 id = cord-256702-lwxt4587 author = Song, Lingjie title = A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date = 2020-04-06 keywords = PCR; SARS summary = title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. Although the nucleic acid test was negative or single-target positive, the low number of white blood cells and lymphocytes in laboratory tests, and GGO in the lungs by CT examination indicated SARS-CoV-2 infection. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. We report the epidemiological history and clinical information of a patient with negative (or single-target positive) SARS-CoV-2 infection with multiple RT-PCR tests. doi = 10.1101/2020.03.31.20045401 id = cord-284879-sjkni2uc author = Song, Suk-Kyoon title = IgG Seroprevalence of COVID-19 among Individuals without a History of the Coronavirus Disease Infection in Daegu, Korea date = 2020-07-16 keywords = COVID-19; SARS summary = METHODS: Serologic testing for immunoglobulin G antibody based on immunochromatographic assay was conducted in 103 patients and 95 guardians aged 18 to 82 years without any history of COVID-19 diagnosis, who visited outpatient clinics of a single university-affiliated hospital from May 25 to June 5, 2020. 4-15 However, a significant fraction of the population has developed antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suggesting that the infection is much more pervasive than implied by the number of confirmed cases. Next, we compared seroprevalence among subgroups stratified by characteristics of study subjects, including age (< 40, 40-59, ≥ 60 years), gender, body mass index (BMI) (< 25, ≥ 25 kg/m 2 ), smoking history (current, previous, never), history of doctor-diagnosed diabetes or hypertension (yes, no), reason for the current hospital visit (patient, guardian), and the presence of COVID-19 confirmed cases among close contacts (yes, no). doi = 10.3346/jkms.2020.35.e269 id = cord-305858-gp1u4kh7 author = Song, Xiang title = High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date = 2020-07-19 keywords = ACE2; COVID-19; SARS; USA; figure summary = To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. To determine whether platelets were directly targeted by SARS-CoV-2 or trigged by viral inflammatory reactions, we examined the ACE2 expression on the highly-purified CD41b + CD42a + platelets from human peripheral blood ( Figure 3A Our previous work established that platelets could release mitochondria contributing to the immune modulation and islet b-cell regeneration [13] . Thus, the virus-infected alveolar macrophages play a critical role in the pathogenesis of COVID-19 and SARS [28] [29] [30] and may recruit the lung infiltration of additional immune cells through predominantly releasing cytokines and chemokines [31, 32] , resulting in pulmonary edema and hypoxemia: the hallmark of acute respiratory distress syndrome (ARDS) ( Figure 6 ). doi = 10.1101/2020.07.18.210120 id = cord-320632-369kax2m author = Song, Yang title = COVID-19 Treatment: Close to a Cure? – A Rapid Review of Pharmacotherapies for the Novel Coronavirus date = 2020-07-04 keywords = COVID-19; China; LPV; SARS; patient summary = The selection of medications in this review is based the 7 th edition of COVID-19 diagnosis and treatment guideline issued by the National Health Commission (NHC) of the People''s Republic of China ( Table 2) and relevant clinical studies. In a phase 2 open-label COVID-19 trial, which enrolled 127 patients from 6 Hong Kong hospitals, Hung and his colleagues compared triple therapy (lopinavir/ritonavir 400/100 mg PO every 12 hours, ribavirin 400 mg PO every 12 hours, and interferon β-1b 8 million IU SQ on alternative days) with a control group of LPV/r [33] . During the 2013 SARS epidemic, observational studies and case reports described IVIG for the treatment of critically ill patients in combination with antiviral therapies. In a COVID-19 case series study, the combination of umifenovir, lopinavir/ritonavir and traditional Chinese medicine alleviated pneumonia symptoms in all four patients and decreased viral load to undetectable in two [68] . doi = 10.1016/j.ijantimicag.2020.106080 id = cord-325045-ak7rouhb author = Sotgiu, Giovanni title = Advanced forecasting of SARS‐CoV‐2‐related deaths in Italy, Germany, Spain, and New York State date = 2020-05-11 keywords = SARS summary = Based on this model, we aimed at predicting SARS-Cov-2-related mortality in Italy, 7 Germany, 8 Spain, 9 and New York State. 10 To validate the model, we calculated R 2 correlations for Italy (0.995), Germany (0.996), Spain (0.988), and New York State (0.998) after 30, 18, 11, and 10 days of prediction, respectively, thus confirming the reliability of our modeling approach during the first month of this outbreak in each of these countries ( Figure 1A) . Instead, the expected SARS-Cov-2related mortality is more closely related to early events within the first days of the outbreak and to timing to regional/national interventions (eg, social distancing, confinement), which suggests that superspreading events (eg Lombardia region, Italy) deeply impact on the magnitude of the curve and, in turn, on the number of deaths. Figure 1B illustrates the curves of the expected deaths based on daily peak after 28 and 21 days in Italy, Germany, Spain, and New York State. doi = 10.1111/all.14327 id = cord-261921-c97ygxq2 author = Souders, Colby P. title = Considerations for Bedside Urologic Procedures in Patients with Severe Acute Respiratory Syndrome Coronavirus-2 date = 2020-04-24 keywords = SARS; patient summary = METHODS: Urologic trainees and attending physicians at our institution, who are familiar with existing safety recommendations and guidelines regarding the care of infected patients, were queried regarding their experiences to determine an expert consensus on best practices for bedside procedures for SARS-CoV-2 positive patients. RESULTS: Our team developed the following general recommendations for urologic interventions on SARS-CoV-2 positive patients: maximize use of telehealth (even for inpatient consults), minimize in-room time, use personal protective equipment appropriately, enlist a colleague to assist, and acquire all supplies that may be needed and maintain them outside the room. Our aim is to share our experiences performing bedside urologic procedures on SARS-CoV-2positive patients and offer considerations to maximize the safety of the patients and providers involved and conserve supplies while maintaining a high standard of care. Outlined above are our experiences with inpatient consultations and bedside procedures in SARS-CoV-2 patients and how we have attempted to address urologic challenges that have emerged with this pandemic. doi = 10.1016/j.urology.2020.04.066 id = cord-339817-qqitdrz6 author = Sousa Gonçalves, Catarina title = Erythematous Papular Rash: A Dermatological Feature of COVID-19 date = 2020-06-10 keywords = SARS summary = COVID-19 is the clinical expression of the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection. The cutaneous clinical spectrum is wide and includes maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, and pityriasis rosea-like, violaceous and pustular lesions. Clinicians should be aware of patients presenting only with cutaneous symptoms, which in some cases are the initial clinical feature of COVID-19. The clinical presentation of SARS-CoV-2 infection is called COVID-19 and has a wide spectrum of clinical manifestations. As with other viral infections, SARS-CoV-2 may also have cutaneous manifestations. In the absence of other possible syndromes and diseases, the skin rash was very likely due to SARS-CoV-2 infection. The cutaneous manifestations include maculopapular, urticarial, varicelliform and petechial rashes, pseudo perniosis, livedo reticularis, pityriasis rosea-like and violaceous lesions, and vesicular and maculopapular pustular lesions (as in other viral infections). doi = 10.12890/2020_001768 id = cord-267402-kca05rvz author = South, Kieron title = Preceding infection and risk of stroke: An old concept revived by the COVID-19 pandemic date = 2020-07-24 keywords = SARS; covid-19; infection; patient; stroke summary = What follows herein is a detailed summary of the current literature surrounding COVID-19, encompassing the immune and inflammatory responses to infection, thrombotic manifestations and vascular consequences of infection with a focus on possible mechanisms by which these elements may contribute to acute stroke events. 89 This is not the case in COVID-19 (and the previous SARS outbreak) and a recent retrospective cohort study has suggested an incidence of stroke 7-8 times higher in patients hospitalized with COVID-19 infection compared with those hospitalized by influenza, 90 supporting the possibility of a SARS-CoV-2-driven hyper-coagulant state. [91] [92] [93] Obesity, in particular, is emerging as a prominent risk factor in the development of severe COVID-19 disease and is generally associated with increased incidence and increased severity of respiratory viral infection. Notably, the cytokine IL-33 is persistently elevated in obese individuals and is capable of stimulating endothelial cells to release pro-coagulant tissue factor 97 which may expose them to more severe COVID-19 disease and/or stroke. doi = 10.1177/1747493020943815 id = cord-314229-9k2dd95b author = Spaccaferri, G. title = Cas groupés d’infections au nouveau coronavirus (SARS-CoV-2) aux Contamines-Montjoie, Haute-Savoie, janvier–février 2020 date = 2020-09-30 keywords = COVID-19; SARS summary = Matériels et méthodes Un cas possible était défini comme tout patient présentant des signes cliniques d''infection respiratoire aiguë et ayant un lien avec le cas index ou avec un cas confirmé lié à ce cas index ; un cas confirmé était un cas possible avec un prélèvement positif par RT-PCR à SARS-CoV-2. Cinq autres touristes anglais ayant séjourné dans le chalet après le départ du cas index ont été en contact avec les cas confirmés symptomatiques : l''un d''eux a été confirmé positif à SARS-CoV-2 le 15/02, traduisant une seconde chaîne de transmission au sein du chalet ; aucun des 6 cas confirmés en France ne présentaient alors de signe de gravité. Introduction Peu de cas de COVID-19 chez des patients infectés par le VIH ont été rapportés dans la littérature. doi = 10.1016/j.medmal.2020.06.142 id = cord-274510-fo7p98np author = Spadera, Lucrezia title = Potential Role of GcMAF in suppressing the severity of COVID-19-induced immune responses: lesson learned from HIV date = 2020-09-24 keywords = COVID-19; SARS summary = Based on the aforementioned findings and on documented analogies between SARS-CoV-2 and HIV [13] , we hypothesized that the reduced conversion activity of the Gc protein (human groupspecific component (Gc)) into the macrophage activating factor (MAF) could have a key role in the dysregulate immune response induced by SARS-CoV-2, just like for HIV infected patients [14] [15] . In particular, based on their antiviral activity [68] , chloroquine and hydroxychloroquine, initially conceived as antimalarial therapeutics, were proposed to treat patients hospitalized with COVID-19, better if associated to azithromycin, showing promising efficacy in "inhibiting the exacerbation of pneumonia, improving lung imaging findings, promoting a virus negative conversion and shortening the disease course" [69] [70] . So, in sight of this, given its multifunctional properties, we believe that GcMAF could have a very important role in the pathophysiology of organ damage induced by SARS-CoV-2, providing explanations which are consistent with the clinical, radiological and histopathological findings observed in patients with COVID-19. Effects of vitamin D(3)-binding protein-derived macrophage activating factor (GcMAF) on angiogenesis doi = 10.1016/j.mehy.2020.110293 id = cord-281500-5mm1nnwv author = Spadera, Lucrezia title = Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey date = 2020-08-04 keywords = COVID-19; SARS; SOL summary = The questionnaire was composed of five sections: (a) respondents'' workplace, age, and sex of the patient; (b) general information about the risk of exposure to COVID-19, asking to specify if the patient is a healthcare professional; (c) clinical information: onset of symptoms, grade of olfactory loss (OL) with three subjective levels (mild, moderate, and severe/complete), presence or absence of: ageusia, hypogeusia and/or dysgeusia gathered together under the name of "taste symptoms"; nasal discharge and/or congestion, other accompanying symptoms (e.g., fever, fatigue, dry cough, dyspnoea, and myalgia), comorbidities and complications; d) execution and results of nasopharyngeal (NP)/oropharyngeal (OP) swab; e) short description about the clinical case. The mean time of SOL onset before or after the first typical COVID-19 symptom (fever, dry cough, and dyspnoea) was 2.4 days (SD ± 2.7); anosmia/hyposmia occurred as the first symptom in 46.7% of cases, as sole symptom in 16.7% of cases or in association with other clinical manifestations in 31.2% of patients. doi = 10.1007/s00405-020-06252-9 id = cord-294498-fv545rfa author = Spiegel, Martin title = The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein date = 2004-07-31 keywords = SARS summary = title: The antiviral effect of interferon-beta against SARS-Coronavirus is not mediated by MxA protein In this study, we demonstrated that multiplication of SARS-CoV in cell culture can be strongly inhibited by pretreatment with interferon-beta. In this study, we investigated the potential of different IFNs to inhibit replication of SARS-CoV in cell culture and determined whether the human MxA protein contributes to the antiviral effect of type I IFNs. African green monkey kidney (Vero) cells were grown in Dulbecco''s modified Eagle''s medium containing 10% fetal calf serum. We investigated the inhibitory effect of type I and II IFNs on SARS-CoV multiplication in cell culture. Therefore, we tested growth of SARS-CoV in Vero cell lines which stably express MxA (Frese et al., 1995) . Thus, the search for antiviral effects against SARS-CoV should focus on other IFN-induced proteins such as PKR or RNase L. doi = 10.1016/j.jcv.2003.11.013 id = cord-320729-imyfo83x author = Spiga, Ottavia title = Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein date = 2003-10-10 keywords = SARS summary = The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. After sequence alignment of SARS S protein (SwissProt Accession Number P59594) with the corresponding ones from human and canine coronaviruses, model building of S1 and S2 subunits was obtained by using the latter two pdb files and shuffled PsiPred runs [13] , with subsequent manual optimisation to enhance the overlapping between the predicted and observed secondary structure elements. As a final remark, it should be underlined that the consistent series of structural features, exhibited by the proposed models for the S1 and S2 subunits of the SARS_CoV spike protein, supports their reliability as a possible rational starting point for anti-viral drug design. doi = 10.1016/j.bbrc.2003.08.122 id = cord-278453-ogbmaw3o author = Spiller, Tobias R. title = Development of health care workers'' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies date = 2020-08-13 keywords = SARS summary = title: Development of health care workers'' mental health during the SARS-CoV-2 pandemic in Switzerland: two cross-sectional studies BACKGROUND: Virus outbreaks such as the current SARS-CoV-2 pandemic are challenging for health care workers (HCWs), affecting their workload and their mental health. Since both, workload and HCW''s well-being are related to the quality of care, continuous monitoring of working hours and indicators of mental health in HCWs is of relevance during the current pandemic. METHODS: We conducted two cross-sectional online studies among Swiss HCWs assessing working hours, depression, anxiety, and burnout. With this study, we aimed to assess changes in working hours and mental health (assessed as symptoms of anxiety, depression, and burnout) in Swiss HCWs at the height of the SARS-CoV-2 pandemic (T1) and again after its flattening (T2). In the conducted network analyses burnout and anxiety were both independently related to lower perceived support by the employer in both studies, a well-described association also in non-pandemic contexts (Shanafelt & Noseworthy, 2017) . doi = 10.1017/s0033291720003128 id = cord-275784-n6jv72l7 author = Spina, Alfio title = The Management Of Neurosurgical Patients During The Covid-19 Pandemic date = 2020-04-30 keywords = COVID-19; SARS summary = An adequate management protocol can reduce hospital viral spread, improving safety both for patients and healthcare professionals. 1 The management of an ever-increasing number of patients, particularly those suffering from coronavirus disease 2019 (COVID-19) pneumonia has deeply affected the organization of healthcare facilities. 11 In a single-center Chinese case series of 138 hospitalized patients, presumed hospitalrelated infection of COVID-19 was suspected in 41% of patients, with a reported mortality of 4.3% and an intensive care unit admission rate of 26%. 12 Furthermore, COVID-19 transmission rate to healthcare worker was reported up to 20% 13 These data suggest that, inadequate hospital setting may represent a relevant route of SARS-CoV-2 spread both for patients and healthcare professionals. Whenever possible, elective surgery for confirmed cases (i.e. Group 1) should be rescheduled, because of this class of patients show higher risks of intensive care need and death. doi = 10.1016/j.wneu.2020.04.161 id = cord-269902-sbp18486 author = Springer, Steffen title = Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin date = 2020-05-06 keywords = SARS summary = title: Google Trends reveals: Focus of interest in the population is on treatment options rather than theories about COVID-19 animal origin tigris) in the Bronx Zoo were reported [Gollakner & Capua, 2020] , corresponding peaks were revealed in search queries by Google Trends, in particular for the unusual transmission to lions and tigers (figure 1). For the Pearson correlation coefficient, a high correlation between the search terms "CoViD-19" and "tiger" (r = 0.669, p < 0.05) was found for the period from 1 st January 2020 to 24 th April 2020. For the search term "palm civet" a low Pearson correlation coefficient was found (r=0.148; p < 0.05). Our data support that the main interest of the population is currently rather in the medical therapeutic direction and, apart from anecdotal individual reports (e.g. Bronx Zoo cats), there is less interest in possible virus carriers or the animal origin and reservoir. doi = 10.1016/j.bbi.2020.05.005 id = cord-338544-eph89g47 author = Spuntarelli, Valerio title = COVID-19: is it just a lung disease? A case-based review date = 2020-07-28 keywords = COV-2; COVID-19; SARS summary = COVID-19 pandemic reached 3.78 million confirmed reported cases worldwide, and it is generally associated to the acronym that precedes its name: severe acute respiratory syndrome (SARS). A prospective study investigating left ventricular performance in 46 patients with severe acute respiratory syndrome showed subclinical diastolic impairment without systolic involvement [3] . Pathological findings of COVID-19 associated with acute respiratory distress syndrome showed few interstitial mononuclear inflammatory infiltrates, but no other substantial damage in the heart tissue [7] . A case report highlights myocarditis as a complication associated with COVID-19, even without symptoms and signs of interstitial pneumonia in an otherwise healthy 53-year-old white woman [8] . The authors concluded that the presence of the characteristic features of symmetric, multifocal lesions with thalamic involvement suggests that this is a case of acute necrotizing hemorrhagic encephalopathy associated with COVID-19. Guillain Barre syndrome associated with COVID-19 infection: a case report doi = 10.1007/s42399-020-00418-6 id = cord-299635-bxdf27sv author = Squire, M. M. title = Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions date = 2020-08-24 keywords = August; SARS summary = The objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. Hence, hospital operations require the assessment of energy efficiency when evaluating Coronavirus Disease 2019 (COVID19) intervention measures, due to COVID-19 being caused by the Severe Acute Respiratory Disease Coronavirus-2 (SARS-CoV-2). As potential infection control interventions for COVID-19 are considered, information that pertains to energy consumption at hospitals provides additional context on costs related to implementation of mitigation strategies for person-to-person transmission, as well as environmental contamination. This paper evaluates the energy implications and impact of NP and XP-UV infection control measures on decreasing secondary transmission of SARS-CoV-2 in acute care hospitals. 21.20178855 doi: medRxiv preprint This study seamlessly combines projections of COVID-19 hospitalizations, evaluation of energy use, and the impact of infection control measures among three different hospital sizes. doi = 10.1101/2020.08.21.20178855 id = cord-301823-fbeb1nw1 author = Sridhar, Sushmita title = A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date = 2020-10-21 keywords = Cov2; PCR; SARS; sample summary = Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. doi = 10.12688/wellcomeopenres.15937.2 id = cord-331429-mh2hd5fe author = Srikantiah, Padmini title = SARS Clinical Features, United States, 2003 date = 2005-01-17 keywords = CoV; SARS summary = We compared the clinical features of 8 U.S. case-patients with laboratory-confirmed severe acute respiratory syndrome (SARS) to 65 controls who tested negative for SARS coronavirus (SARS-CoV) infection. Shortness of breath, vomiting, diarrhea, progressive bilateral infiltrates on chest radiograph, and need for supplemental oxygen were significantly associated with confirmed SARS-CoV infection. Case-patients with laboratory-confirmed SARS were compared to a convenience sample of persons who met the clinical and epidemiologic criteria for suspected or probable SARS but subsequently tested negative for SARS-CoV infection. Controls had negative findings on all testing performed for SARS-CoV, including the absence of antibody against the virus in convalescent-phase serum samples obtained >21 days after onset of symptoms. Over the course of their illness, findings suggestive of a lower respiratory tract infection developed in all 8 patients with laboratory-confirmed SARS; these findings included dyspnea (n = 8), rales (n = 5), and hypoxia (n = 5) (Table 1) . doi = 10.3201/eid1101.040585 id = cord-300625-fvirvpyl author = Srinivasan, Suhas title = Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins date = 2020-03-25 keywords = SARS; interaction; protein; structural summary = In addition to the global structural genomics, an initiative that focuses on determining the 3D structures of individual proteins on a genome scale [34] , as well as to the specific efforts aimed at rapid structural characterization of proteins in emerging viruses [35] [36] [37] [38] , multiple works have used comparative modeling to predict the structures of protein-protein interaction complexes [39] [40] [41] , facilitate structure-based drug discovery [33, 42, 43] , infer protein functions [44] , determine the macromolecular interaction network [45] [46] [47] [48] , and provide molecular insights into the viral evolution [49] [50] [51] . To do so, we structurally characterized individual proteins as well as intra-viral and human-virus protein complexes, extracted the information on their interaction interfaces and ligand binding, and superposed the evolutionary difference and conservation information with the binding information. doi = 10.3390/v12040360 id = cord-327392-9psblokc author = Srivastava, A.K. title = Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date = 2020-10-21 keywords = SARS; SPR; graphene; virus summary = Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. doi = 10.1016/j.mtchem.2020.100385 id = cord-274053-406dfdih author = Srivastava, Kamna title = Association between COVID-19 and cardiovascular disease date = 2020-07-14 keywords = ACE2; COVID-19; SARS summary = SARS-CoV-2 infects host cells through ACE2 receptors, leading to COVID-19-related pneumonia. Search methods and strategies for identification of studies Literature search was performed in WHO reports, PubMed, Scopus, Science Direct and also in American Heart Association journals, Nature, JAMA, BMJ and THE LANCET journals using following terms:ACE2, coronavirus, COVID-19 and 2019-nCoV, COVID-19 and CVD, Cardiovascular Risk and Diseases to find articles published from January 05 to May 20, 2020. SARS-CoV-2 shares both high sequence similarity and the use of the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV). In another study [43] , we have reported the role of Angiotensin type I receptor in patients with essential hypertension and normal healthy controls as pathological and physiological differential expression at mRNA and protein levels. In a report by Huang et al [3] myocardial injury associated with the SARS-CoV-2 was found in 5 of the first 41 patients diagnosed with COVID-19 in Wuhan. doi = 10.1016/j.ijcha.2020.100583 id = cord-340432-vm6m0kb4 author = Srivastava, Sukrit title = Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date = 2020-09-06 keywords = Patches; SARS summary = title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide Methodology A novel reverse epitomics approach, "overlapping-epitope-clusters-to-patches" method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. Multi-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, "Overlapping-epitope-clusters-to-patches" method. In the present study, we have reported a novel method to design a 1170 vaccine against SARS-CoV-2 by utilizing multiple antigenic patches from the viral 1171 proteins. The designed MPVs from the antigenic patches of SARS-CoV-2 proteins 1182 have several advantages over to the subunit and multi-epitope based vaccines. Design of multi epitope-based peptide vaccine against E 1409 protein of human 2019-nCoV: An immunoinformatics approach Multi-epitope based peptide 1549 vaccine design against SARS-CoV-2 using its spike protein In silico approach for designing of a multi-epitope based 1587 vaccine against novel Coronavirus (SARS-COV-2) doi = 10.1101/2020.09.06.284992 id = cord-282317-k9mtf6yl author = Srivastava, Vivek title = Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2 date = 2020-10-14 keywords = SARS; active summary = The main objective of the present study is to carry out molecular docking analysis of Glycyrrhiza glabra active compounds, Glycyrrhizic acid, Liquiritigenin and Glabridin against the main protease (M pro ) one by one followed by molecular interaction study (hydrogen bond prediction between target and drugs), drug-likeness behaviour and ADMET prediction to confirm the efficiency and efficacy of these active compound against SARS-CoV2. The molecular docked pose of the minimum binding affinity conformer of the Gg active compounds that is glycyrrhizic acid, Glabridin and Liquiritigenin demonstrated that they also firmly goes and bind to the active site of the M pro protein of the SARS-CoV-2 ( figure 4 and table 2 ). Molecular docking indicated that the three active compounds of Glycyrrhiza glabra namely glycyrrhizic acid, Liquiritigenin, and Glabridin successfully docked with the amino acid molecule at the catalytic site of the M pro with a high negative binding affinity and formed several molecular interaction with the main protease of SARS-CoV2. doi = 10.1016/j.matpr.2020.10.055 id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 keywords = SARS; protein; virus summary = To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. doi = 10.1101/2020.08.28.269175 id = cord-272690-r8lv1zzx author = St. John, Ronald K. title = Border Screening for SARS date = 2005-01-17 keywords = Canada; SARS summary = With the rapid international spread of severe acute respiratory syndrome (SARS) from March through May 2003, Canada introduced various measures to screen airplane passengers at selected airports for symptoms and signs of SARS. Because of the continuing outbreak in Toronto, domestic spread in other affected countries in Southeast Asia, and international spread to other countries, Health Canada intensified its initial response by instituting both inbound and outbound passenger screening to identify persons with symptoms or signs compatible with SARS. In parallel to these measures, Health Canada initiated a pilot study on May 8, 2003 , on the use of infrared thermal scanning machines to detect temperatures >38°C in selected international arriving and departing passengers at Vancouver''s International and Toronto''s Pearson International airports. Careful analysis of the travel histories of suspected and probable SARS patients who traveled to Canada showed that persons became ill after arrival and would not have been detected by airport screening measures. doi = 10.3201/eid1101.040835 id = cord-261941-xf1k5uj1 author = Stackhouse, Robin A. title = Severe acute respiratory syndrome and tuberculosis date = 2005-03-01 keywords = SARS; patient; respiratory summary = Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients doi = 10.1016/j.atc.2004.06.002 id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 keywords = CoV; RNA; SARS; protein; virus summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1038/nrmicro775 id = cord-279642-0j5828ah author = Stafford, Emma G. title = Pharmacovigilance in Patients with Diabetes: A Data-Driven Analysis Identifying Specific RAS Antagonists with Adverse Pulmonary Safety Profiles That Have Implications for COVID-19 Morbidity and Mortality date = 2020-06-01 keywords = SARS summary = Angiotensin converting enzyme inhibitors (ACEIs) and angiotensin-II receptor blockers (ARBs) are considered first-line agents in diabetics due to their nephroprotective effects but administration of these drugs leads to upregulation of angiotensin-converting-enzyme-2 (ACE2), responsible for viral entry of severe-acute-respiratory-distress-syndrome, coronavirus-2 (SARS-CoV-2). In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. In this study, the aim 24 was to assess the prevalence of pulmonary adverse drug effects (ADEs) in diabetic patients taking ACEI 25 or ARBs to help provide guidance as to how these medications could affect outcomes in acute respiratory 26 illness, such as SARS-CoV-2 infection. doi = 10.1016/j.japh.2020.05.018 id = cord-303741-1ou0cy5k author = Stafstrom, Carl E. title = COVID-19: Neurological Considerations in Neonates and Children date = 2020-09-10 keywords = CNS; COVID-19; CoV-2; SARS; child; infection summary = An especially apropos case demonstrated maternal viremia, placental infection shown by immunohistochemistry, and high placental viral load with subsequent neonatal viremia, implying transplacental transfer of SARS-CoV-2 from pregnant mother to fetus [24] ; this newborn presented with neurological symptoms as discussed in Section 3. The lack of unequivocal reports of SARS-CoV-2 being recovered from the CSF of individuals affected with presumed neurological involvement nor in brain tissue from the limited number of autopsied cases strengthens the possibility that the virus does not often directly cause the symptoms but rather, that the neurological sequelae are secondary to hypoxia, cytokine involvement, or some other non-direct mechanism (see Section 6). Finally, 4 of 27 children with COVID-19 associated MIS-C developed new neurologic symptoms including encephalopathy, headache, weakness, ataxia, and dysarthria [81] ; two patients had lumbar punctures and CSF was negative for SARS-CoV-2 in both. doi = 10.3390/children7090133 id = cord-314798-n6oofe3i author = Stall, N. M. title = Sex-specific differences in COVID-19 testing, cases and outcomes: a population-wide study in Ontario, Canada date = 2020-05-06 keywords = SARS summary = In this population-wide study in Ontario, Canada we report on all 194,372 unique residents who received testing for SARS-CoV-2 between January 23, 2020 and April 28, 2020. This population-wide cohort study included all residents of Ontario, Canada who received a nasopharyngeal swab for SARS-CoV-2 between January 23, 2020 (date swab was performed for first reported case of COVID-19 in Canada) and April 28, 2020. We obtained data for this study from the Ontario Ministry of Health as part of the province''s emergency "modeling table", including deidentified line level data on all SARS-CoV-2 testing via the Ontario Laboratories Information System (OLIS) and from the integrated Public Health Information System (iPHIS) for all reported COVID-19 cases and related clinical outcomes. We reported sex-and age-disaggregated data on SARS-CoV-2 testing, COVID-19 cases and related rates of hospitalization, intensive care unit (ICU) admission and death. doi = 10.1101/2020.04.30.20086975 id = cord-342942-1s32o9m8 author = Stamatakis, George title = Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date = 2020-06-22 keywords = HLA; SARS; erap1 summary = Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. doi = 10.1101/2020.06.22.164681 id = cord-253331-z443e8lk author = Stanhope, Michael J. title = Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV date = 2004-03-31 keywords = PLATO; SARS summary = Based on evolutionary analyses of coronavirus DNA sequences, encompassing an approximately 13kb stretch of the SARS-TOR2 genome, we provide evidence that SARS-CoV has a recombinant history with lineages of types I and III coronavirus. Our results act to both corroborate and extend their findings, adding further support to the idea that SARS has had a recombinant history involving different coronavirus lineages and suggest the possibility that the genome could have arisen through a combination of host jumping and recombination events in a manner analogous to previous outbreaks of influenzae (Gregory et al., 2003; Zhou et al., 1999) . Our results indicate that SARS-CoV recombined with a member of the group III lineage, suggesting that an avian coronavirus was involved, a further point of general agreement between our results and that of Rest and Mindell (2003) . doi = 10.1016/j.meegid.2003.10.001 id = cord-275690-83nrzfon author = Stanifer, Megan L. title = Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date = 2020-04-24 keywords = CoV-2; Fig; IFN; SARS summary = title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, and in agreement with the results observed in cells depleted of the type III IFN receptor, this increase in infectivity was also associated with an increase in infectious denovo virus particle production ( Fig. 3G ). All together, these results strongly support a model where the type III IFN mediated signaling controls SARS-CoV-2 infection in human intestinal epithelial cells. All together these results show that human colon organoids can support SARS-CoV-2 infection, replication and spread and that the type III IFN response plays a critical role in controlling virus replication. doi = 10.1101/2020.04.24.059667 id = cord-277549-sg7tzhdm author = Stanley, Kate E. title = Coronavirus disease (COVID-19) and fertility: viral host entry protein expression in male and female reproductive tissues date = 2020-05-08 keywords = ACE2; SARS; TMPRSS2; figure summary = Single cell RNA sequencing (scRNAseq) in human and non-human primate respiratory tissues have shown co-expression of ACE2 and TMPRSS2 in pneumocytes in the lungs and goblet secretory cells in the nose (6) , indicating that these cell types may serve as foci for infection and potentially explaining the range of respiratory symptoms associated with COVID-19. Cell-type specific expression patterns of genes that produce viral host entry proteins, and identification of potential loci of infection within the reproductive system, are therefore necessary in order to predict whether SARS-CoV-2 is likely to have any impact on fertility. Categorizations for protein expression correspond to the categorizations given by the Human Protein Atlas and the Human Proteome Map. Published scRNAseq datasets in human testicular (18) and non-human primate ovarian (19) tissue were used to assess the cell-type specific expression pattern of SARS-CoV-2 entry receptor ACE2 and entry-associated protease TMPRSS2 and their coexpression. doi = 10.1016/j.fertnstert.2020.05.001 id = cord-283850-kt8n6pg2 author = Steardo, Luca title = Psychiatric face of COVID-19 date = 2020-07-30 keywords = CNS; COVID-19; IL-6; SARS; brain; inflammatory summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), similarly to other coronaviruses demonstrate neurotropism; the viral infection of the brain stem may complicate the course of the disease through damaging central cardio-respiratory control. Post-mortem analysis of nervous tissue from tissue of a 54 years-old man who died from severe respiratory failure associated with COVID-19 identified SARS-COV-2 viral particles in the olfactory nerve, in the gyrus rectus and in the brainstem with signs of profound damage to all elements of the tissue including glial cells, neurones, their axons and myelin 37 . Infection with SARS-CoV-2 (even in moderate clinical cases) thus promotes cognitive disorders with emergence of delirium, acute psychosis, exacerbation of mild cognitive impairment or with accelerating of dementia associated with various neurodegenerative conditions, including Alzheimer''s disease (AD) 85, 86 . Patients with COVID-19 could present with a wide range of neuropsychiatric symptoms, which result from systemic inflammation, CNS effects of cytokines, infection of neural cells by SARS-COV-2, neuroinflammation, glial dysfunction or aberrant epigenetic modifications of stress-related genes. doi = 10.1038/s41398-020-00949-5 id = cord-290195-8uaai9nv author = Stebbing, Justin title = Mechanism of baricitinib supports artificial intelligence‐predicted testing in COVID‐19 patients date = 2020-05-30 keywords = Fig; IL-6; SARS; baricitinib; covid-19; patient summary = Furthermore, baricitinib treatment resulted in a significant reduction (p<0.05) from baseline in plasma IL-6 at week 12 in patients with active RA who had an inadequate response to methotrexate from a phase 2b (Tanaka, Emoto et al., 2016) , randomized, placebo-controlled, dose-ranging study (Fig. 1B) . As shown in Figure 3A , all four patients showed improvement with baricitinib treatment in signs and symptoms such as cough, fever, and reduction in plasma IL-6 levels, along with a reduction in the SARS-CoV-2 RNA viral load, as detected by the real-time reverse-transcriptase-polymerase chain reaction (RT-PCR) signal from the nasopharyngeal carriage. Therefore, the impact of baricitinib on the subsequent development of protective humoral and cell-mediated anti-viral immunity in COVID-19 patients must be evaluated in randomized clinical trials (Ottoviani & Stebbing, 2020) . The finding that baricitinib is a potent AAK1/BIKE/GAK inhibitor that may reduce host cell infectivity, along with reaffirmation of its anti-cytokine profile, provide reasons to study this intervention in randomized clinical trials. doi = 10.15252/emmm.202012697 id = cord-302616-1uwrcvjx author = Steenblock, Charlotte title = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis date = 2020-05-07 keywords = ACE2; HPA; SARS; stress summary = title: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis Furthermore, it has to be considered that certain therapies impacting expression of ACE2 might also influence the RAAS and the neuroendocrine stress axis, which may lead to long-term consequences, as prolonged exposure to stressors increases the risk to develop major depressive, anxiety and post-traumatic stress disorders [42] . In addition to contributing to the progression of the immune response against viral infection, cytokines activate the HPA axis, resulting in the release of adrenal glucocorticoids [43] . In relation to coronavirus infections, it was shown that pulmonary stem/progenitor cells that express ACE2 are targeted by SARS-CoV in primary cultures [73] . Increasing brain angiotensin converting enzyme 2 activity Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the neuroendocrine stress axis decreases anxiety-like behavior in male mice by activating central Mas receptors doi = 10.1038/s41380-020-0758-9 id = cord-290796-x9xqqcj6 author = Stefanelli, P. title = Longevity of seropositivity and neutralizing titers among SARS-CoV-2 infected individuals after 4 months from baseline: a population-based study in the province of Trento date = 2020-11-13 keywords = CoV-2; SARS summary = All individuals above ten years of age resident in 5 municipalities of the Autonomous Province of Trento, northern Italy, who resulted IgG positive for anti-SARS-CoV-2 nucleocapsid (NC) antibodies in a serosurvey conducted on May 2020 were retested after 4 months. The duration of protection against infection with common human coronaviruses appears to be rather short 2, 3 , and there are studies showing declines in IgG antibodies against SARS-CoV-2 among both symptomatic and asymptomatic individuals 4, 5 . In order to evaluate the persistence of SARS-CoV-2 antibodies, we repeated a serosurvey in five municipalities of the Autonomous Province (AP) of Trento, Italy, recruiting those individuals who had resulted positive in a large population-based seroprevalence study conducted 4 months before 14 . The analyser automatically calculates SARS-CoV-2 NC IgG antibody concentration expressed as an is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint doi = 10.1101/2020.11.11.20229062 id = cord-303868-aes92l6s author = Steffen, Tara L. title = The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date = 2020-08-22 keywords = RBD; SARS summary = In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. In this study, we identify the spike protein subunits that contain antigenic determinants and examine the neutralization capacity of polyclonal sera from a cohort of patients that tested qRT-PCR-positive for SARS-CoV-2. This suggests that polyclonal antibody binding to the RBD domain of the spike protein represents the key target of neutralizing antibody to SARS-CoV-2 after natural infection. Most importantly, our antigen-specific antibody depletion approach demonstrated that the RBD domain of the spike protein is responsible for 70% +/-18.9% of the human polyclonal neutralizing antibody activity to spike after natural SARS-CoV-2 infection. Although our study shows that the dominant target of IgG neutralizing antibody response after natural SARS-CoV-2 infection is the RBD domain of the spike protein, we have evaluated a limited number (n=10) of patients by antigen-specific antibody depletion. doi = 10.1101/2020.08.21.261727 id = cord-345014-qp13h0un author = Stein, Richard Albert title = The 2019 coronavirus: Learning curves, lessons, and the weakest link date = 2020-03-13 keywords = SARS; coronavirus summary = 14 In the most recent of the three coronavirus outbreaks, several clusters of patients with pneumonia started to be reported on December 8, 2019 from Wuhan, China, and most of them were epidemiologically linked to the Huanan Seafood Wholesale Market. 24, 25 The virus shares >70% genetic similarity with the 2002-2003 SARS-CoV strain, 5 is most closely related to coronaviruses of bat origin, 17 its spike glycoprotein gene appears to have emerged by recombination between a bat coronavirus and a coronavirus of unknown origins, and relative synonymous codon usage bias analyses indicate that snakes may be a potential reservoir. 26 The SARS-CoV spike protein receptor binds the angiotensin-converting enzyme 2 (ACE2) on host cells, an interaction that shapes cross-species and human-to-human transmission. 10,58-60 Every outbreak brings something new, provides opportunities to reap the benefits gained from past epidemics and pandemics, and provides novel lessons that will shape the framework to manage emerging infectious diseases. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in Wuhan, China doi = 10.1111/ijcp.13488 id = cord-328778-mjzsz7rz author = Steinchen, N. title = Biologikatherapie nach COVID-19-Infektion: Keine Reaktivierung einer COVID-19-Infektion bei positivem Antikörperstatus SARS-CoV-2 unter Biologikatherapie date = 2020-06-08 keywords = SARS; der; und summary = In der kurzen Beobachtungszeit zeigten sich bis heute erfreulicherweise keine klinischen Hinweise auf eine Reaktivierung der COVID-19-Infektion, die bDMARD-Therapie wurde nebenwirkungsfrei vertragen. Die Fragen, ob bei Vorliegen einer entzündlich rheumatischen Erkrankung eine besondere Gefahr besteht, sich mit SARS-CoV-2 zu infizieren, und im Fall einer Infektion diese auch schwerer verläuft, sind bis heute aufgrund begrenzter Daten nicht sicher zu beantworten. Die Patienten*innen standen alle unter einer Zytokinhemmertherapie und wiesen im Vergleich zu den 2 Kontrollen (ohne Anti-Zytokin-Therapie) keine Antikörper gegen SARS-CoV-2 auf, während bei 2 % des nichtmedizinisch tätigen und 4 % des medizinisch tätigen Kontrollpersonals Antikörper gegen Corona-Virus detektierbar waren. Ursache des geringen Antikörpernachweises gegen SARS-CoV-2 in der Gruppe der Patienten*innen mit entzündlich rheumatischen Erkrankungen unter Anti-Zytokin-Therapie könnte sein, dass im Vergleich zu den anderen beiden Gruppen die RKI-Abstands-und Hygieneempfehlungen konsequenter aus Furcht vor einer Ansteckung unter immunsuppressiver Therapie umgesetzt wurden. Andererseits kann die Schlussfolgerung, dass eine Biologikatherapie vor einer SARS-CoV-2-Infektion mit einem schweren Verlauf möglicherweise schützt, aus den Daten nicht abgeleitet werden. doi = 10.1007/s00393-020-00824-0 id = cord-353209-qkhfp66l author = Steiner, Daniel J. title = Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date = 2020-06-16 keywords = CoV-2; SARS; air summary = We report a multiplex label-free antigen microarray on the Arrayed Imaging Reflectometry (AIR) platform for detection of antibodies to SARS-CoV-2, SARS-CoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43) and three strains of influenza. Aminereactive substrates for fabrication of AIR arrays were provided by Adarza BioSystems, Inc. For ELISA assays, SARS-CoV-2 full-length spike and RBD were produced in-house using a mammalian expression system, 20,21 as was influenza A/H1N1/California 2009 hemagglutinin. To that end, we have presented preliminary data on a 15-plex array on the AIR platform, developed in response to the need to study SARS-CoV-2 but incorporating antigens for other coronaviruses and influenza. Responses to SARS-CoV-2 antigens on the array effectively discriminated between serum samples from uninfected and COVID-19 convalescent subjects, with generally good correlation to ELISA data. doi = 10.1101/2020.06.15.153064 id = cord-335386-eflyypev author = Steinman, Jonathan Baruch title = Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics date = 2020-10-06 keywords = ACE2; COVID-19; SARS; TMPRSS2 summary = Exploring why the pediatric population is generally far less likely to develop COVID-19, even though their rate of infection is similar to adults (10), may offer productive clues, enabling strategies for (1) Coronavirus associated with common colds in children may offer some protection due to cross-reactive T cell immunity and crossreactive antibody immunity between common coronaviruses and SARS-CoV-2, and due to reduced ACE2 in nasal mucosa of children. A reasonable conjecture might be that, if ACE2 and/or TMPRSS2 expression is diminished in children, then viral infection of respiratory cells by SARS-CoV-2 might be less likely at any given viral load, and, additionally, there might be reduced expression of associated inflammatory modules. T[h]2 inflammation may predispose individuals to experience better COVID-19 outcomes through a decrease in airway levels of ACE2 that override any countervailing effect from increased expression of TMPRSS2." It is indeed surprising that the Th2 immune type associated with allergic diseases including asthma, and with eosinophilia, provides some protection to COVID-19 in children. doi = 10.1073/pnas.2012358117 id = cord-277529-z2r14w2k author = Stella, Alessandro title = Familial Mediterranean Fever and COVID-19: Friends or Foes? date = 2020-09-18 keywords = COVID-19; MEFV; Pyrin; SARS summary = We were intrigued by the remarkable overlap between these clinical manifestations and some of the typical manifestations of Familial Mediterranean Fever (FMF), a largely recessively inherited monogenic inflammasomopathy (autoinflammatory disorder involving the inflammasome) caused by mutations in the MEFV gene that is particularly prevalent in the Mediterranean basin (14) . It is tempting to speculate that FMF patients carrying V726A and R761H variants-which represents the wild type residues in all bats and pangolin sequences-might modulate better their cytokine response to SARS-CoV-2 infection. Thus, the severity of COVID-19 disease in FMF patients, once infected, might be influenced, at least partially, depending on specific MEFV genotypes which shows country-specific differences. FMF, in which Pyrin activity and consequent ASC oligomerization are increased because of MEFV pathogenic variants, may therefore represent a unique opportunity as a disease model to investigate the regulation of the inflammatory response to novel emerging viruses. doi = 10.3389/fimmu.2020.574593 id = cord-316894-zhmuzv7z author = Stetzenbach, L.D. title = Airborne Infectious Microorganisms date = 2009-02-17 keywords = SARS; disease; infection; virus summary = Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. doi = 10.1016/b978-012373944-5.00177-2 id = cord-326710-vc9wkcro author = Stevens, Bryan title = Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA date = 2020-08-06 keywords = SARS; Xpert summary = BACKGROUND: Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). METHODS: A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. CONCLUSIONS: The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity. In this study, we demonstrated comparable test performance between the Cepheid Xpert Xpress SARS-CoV-2 assay and the Panther Fusion SARS-CoV-2 assay, with an overall agreement of 99%. doi = 10.1093/jalm/jfaa135 id = cord-318339-j35w1vsw author = Stockman, Lauren J title = SARS: Systematic Review of Treatment Effects date = 2006-09-12 keywords = IFN; SARS; Table summary = METHODS AND FINDINGS: In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. In response to the WHO request we conducted a systematic review of the published literature on ribavirin, corticosteroids, lopinavir and ritonavir (LPV/r), type I interferon (IFN), intravenous immunoglobulin (IVIG), and SARS convalescent plasma from both in vitro studies and in SARS patients. This paper reports on this systematic review designed to summarise available evidence on the effects of ribavirin, lopinavir and ritonavir (LPV/r), corticosteroids, type I IFN, intravenous immunoglobulin (IVIG), or convalescent plasma in relation to (1) SARS-CoV replication inhibition in vitro; (2) mortality or morbidity in SARS patients; and (3) effects on ARDS in adult patients. doi = 10.1371/journal.pmed.0030343 id = cord-299443-nggl87u6 author = Stockman, Lauren J. title = Coronavirus Antibodies in Bat Biologists date = 2008-06-17 keywords = SARS summary = To address the possibility that the antibodies from this serum sample were not specifi c to SARS-CoV, we tested it against recombinant N proteins of human CoVs, HCoV-229E, HCoV-OC43, NL63, and HKU-1. If the antibodies were induced by a SARS-like CoV infection, we would expect to have also detected antibodies against recombinant S protein (9) or recombinant fragments representing antigenically distinct regions of the N protein of SARS-CoV. We did not detect either; instead, we detected antibodies against the antigenically distinct N fragments from group 1 and 2 human CoVs. Thus, this survey of a sample of bat biologists, who were exposed primarily to North American bats but also to bats from Asia and Africa, showed no evidence of SARSlike CoV infection. Recombinant protein-based assays for detection of antibodies to severe acute respiratory syndrome coronavirus spike and nucleocapsid proteins. Antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (SARS) coronavirus and polyclonal antisera of antigenic group I animal coronaviruses: implication for SARS diagnosis doi = 10.3201/eid1406.070964 id = cord-338589-1ent68fx author = Stoddard, Shana V. title = Optimization Rules for SARS-CoV-2 M(pro) Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site date = 2020-08-26 keywords = SARS; figure summary = The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 M(pro) active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 −log(10)(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M(pro) [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The use of multiple conformations when using docking will assist in the prediction of new antivirals agents targeting SARS-CoV-2 M pro as the diversity of accessible variations can produce distinct binding poses for an inhibitor compound. doi = 10.3390/v12090942 id = cord-304372-6eqnr52t author = Stolle, Claudia title = Bedarfe der Langzeitpflege in der COVID-19-Pandemie date = 2020-10-28 keywords = Befragten; Einrichtungen; SARS; der; die summary = Hier wiesen die Befragten auf eine Lücke bei notwendigen Informationen und Verfah-renshinweisen im Umgang mit kognitiv beeinträchtigten und verhaltensveränderten Pflegebedürftigen während der COVID-19-Pandemie hin. 70 % der Befragten, zusammengefasst in der Unterkategorie SARS-CoV-2-Testungen, forderten die Durchführung von "systematischen" und "regelmäßigen" Reihentestungen (n = 72) zum einen beim Personal der Einrichtungen und zum anderen bei den Pflegebedürftigen. 22 % der Befragten gaben an, dass entsprechende Kontaktpersonen nicht immer ausreichend qualifiziert erschienen, um mit praxisnahen Problemlösungen in den Einrichtungen weiterhelfen zu können, sodass ein Bedarf an einer fachlich "kompetenten Beratung" bestehe (n = 16). Dazu äußerten die Befragten einen konkreten Bedarf an "Beratung zur Umsetzung" (n = 12) der Vorgaben und Empfehlungen in den Einrichtungen. Mit der Dynamik und den steigenden Erkenntnissen in der Pandemie wurden auch die Empfehlungen zum Umgang SARS-CoV-2 in den Pflegeeinrichtungen seitens des RKI angepasst. Um die vulnerable Gruppe der Pflegebedürftigen und die Mitarbeitenden von Pflegeeinrichtungen in der aktuellen Situation vor SARS-CoV-2-Infektionen zu schützen, ergeben sich aus den Ergebnissen v. doi = 10.1007/s00391-020-01801-7 id = cord-305496-t8ykkekl author = Stone, E. Taylor title = Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date = 2020-08-21 keywords = HPI; SARS; Vero summary = One such tool for evaluating neutralizing antibody response is a 88 plaque/focus neutralization reduction test (PRNT/FRNT), which evaluates the ability of polyclonal 89 sera samples to prevent or reduce infection of a cell monolayer in vitro. We examined the impact of cell density on foci formation for both Vero WHO and Vero E6 cells 144 by plating identical dilutions of SARS-CoV-2 virus stocks on 96-well plates seeded with differing 145 numbers of WHO or E6 cells (3 × 104, 1.5 × 104 or 3 × 104 cells/well) one day prior to infection 146 of the cell monolayer. To determine the optimal time frame for infection of SARS-CoV-2 on a Vero WHO cell 172 monolayer to form individual foci, we tested a variety of incubation times. The FFA relies on an immunostaining protocol of an infected cell monolayer in order to 197 quantify infectious virus titer and is therefore dependent upon SARS-CoV-2-specific antibody 198 doi = 10.1101/2020.08.20.259838 id = cord-342796-f7n8sxbu author = Stowe, J. title = Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design date = 2020-09-18 keywords = CoV-2; SARS; influenza summary = Findings: The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible pathogenic competition between the two viruses. The odds of ventilator use or death and ICU admission or death was greatest among coinfection patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Severity and risk of death among individuals with a coinfection: The mortality rate among individuals with a SARS-CoV-2 and influenza coinfection and those with SARS-CoV-2 infection who tested negative for influenza was calculated by dividing the number of deaths by the total number of individuals tested by age group. We also found strong evidence that coinfection with influenza and SARS-CoV-2 was associated with an increased risk of death or severe disease and that this appears to be beyond the additive effect of the two viruses acting independently. doi = 10.1101/2020.09.18.20189647 id = cord-317359-7yuygcew author = Straccia, Patrizia title = Description of a new biosafe procedure for cytological specimens from patients with COVID‐19 processed by liquid‐based preparations date = 2020-08-07 keywords = LBC; SARS summary = CONCLUSIONS: Despite some minor changes in the morphology of the cells, the results of this study highlight that the adoption of the new protocol for the biosafety of LBC‐processed samples in pathology laboratories is important for minimizing the risk for personnel, trainees, and cytopathologists without impairing the diagnostic efficacy of the technique. 8 The new coronavirus, Cancer Cytopathology Month 2020 originally called 2019 novel coronavirus (2019-nCoV) and officially renamed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses, and the disease it causes, namely coronavirus disease 2019 (COVID-19), have quickly become of tremendous concern worldwide. Because the laboratory personnel might be exposed to contamination during the preparation and handling of fresh specimens from such patients, a new procedure for the sterilization of material to be processed by liquid-based cytology (LBC) has been applied. doi = 10.1002/cncy.22341 id = cord-295144-tyyc81uc author = Stradner, Martin H. title = Rheumatic Musculoskeletal Diseases and COVID-19 A Review of the First 6 Months of the Pandemic date = 2020-10-09 keywords = COVID-19; HCQ; RMD; SARS; SLE; patient summary = In this review, we summarize the published cases of COVID-19 infections in RMD patients, including patients with inflammatory arthritis and connective tissue diseases as well as anti-phospholipid syndrome and Kawasaki syndrome. It also reviews the general risk of viral infections in patients with RMD, the impact of disease modifying anti-rheumatic drugs (DMARDs) on the outcome of infections, and gives a comparison between present and previous coronavirus pandemics. This argues against a protective role of HCQ (in the usually administered dose for RMD patients) in SARS-CoV-2 infection, which is also supported by pharmacological in vitro data describing a much higher level needed for effective viral inhibition (61) . In conclusion, data published in the first 6 months do not consistently describe a higher risk for infection with SARS-CoV-2 or a more severe course of COVID-19 in patients with either inflammatory arthritis or connective tissue diseases. doi = 10.3389/fmed.2020.562142 id = cord-258431-8zgwj2fa author = Strafella, Claudia title = Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications date = 2020-07-03 keywords = ACE2; SARS; italian summary = The eQTLs analysis located in and targeting ACE2 revealed a high distribution of eQTL variants in different brain tissues, suggesting a possible link between ACE2 genetic variability and the neurological complications in patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. The final goal of the study has been the research of variants potentially affecting ACE2 expression and function, which may contribute to SARS-Cov-2 spreading among worldwide populations, and may have a clinical significance regarding the clinical variability and outcome displayed by patients with COVID-19. Moreover, they found a higher allelic frequency of eQTL variants, which is associated with higher ACE2 expression in tissues, suggesting a different susceptibility or response to SARS-Cov-2 infection with respect to other populations under similar conditions [28] . doi = 10.3390/genes11070741 id = cord-343864-0258nh92 author = Straughn, Alex R. title = Withaferin A: a potential therapeutic agent against COVID-19 infection date = 2020-07-19 keywords = ACE2; COVID-19; SARS summary = Therefore, WFA demonstrates real potential as a therapeutic agent to treat or prevent the spread of COVID-19 due to the reported interference in viral S-protein to host receptor binding and its lack of effect on ACE2 expression in the lungs. Data from four SARS-CoV-2 hot spots (the United States, Italy, Spain and China) has shown that cancer patients infected with the novel coronavirus have a significantly increased risk of admission to an intensive care unit (ICU) and/or requiring mechanical ventilation, as well as an increase in patient mortality [15, [17] [18] [19] . Withaferin A alone or in combination with drugs, such as: hydroxychloroquine, dexamethasone or other treatments (under clinical trials), could be developed into an attractive therapeutic agent for both the general population and cancer patients due to its anti-tumorigenic properties and the preliminary studies showing that it is capable of binding to the Sprotein of SARS-CoV-2, thereby potentially inhibiting infection and/or spread of the disease. doi = 10.1186/s13048-020-00684-x id = cord-327273-7ntp7x8d author = Street, Renée title = COVID-19 wastewater surveillance: An African perspective date = 2020-07-03 keywords = SARS summary = Abstract The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water, and sanitation in public health. In the current COVID-19 pandemic, tracking of wastewater has been proposed as a platform for SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease [11, 12] . Thus SARS-CoV-2 surveillance through water-based epidemiology (WBE) is a potential complimentary and cost-effective approach to enable wide scale screening which would reduce labor intensive and costly personal COVID-19 testing and tracings [11, 17, 18] . Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges doi = 10.1016/j.scitotenv.2020.140719 id = cord-353749-2vlc11rx author = Stricker, Raphael B title = Flattening the Risk: Pre-Exposure Prophylaxis for COVID-19 date = 2020-10-19 keywords = COVID-19; HCQ; SARS summary = 24 In one uncontrolled study, HCQ prophylaxis in a hospital setting with a known SARS-CoV-2 exposure prevented dissemination of viral infection. 40 The second case-control study of HCWs found that four or more weekly doses of HCQ resulted in significantly less infection with SARS-CoV-2 (adjusted odds ratio 0.44, p<0.001). 45 In a retrospective cohort study of 32,109 rheumatic disease patients from the US Veterans Health Administration, the incidence of SARS-CoV-2 infection was equivalent regardless of chronic HCQ use (0.3% in users versus 0.4% in non-users), but mortality was significantly decreased in patients taking HCQ (odds ratio 0.70, p=0.0031). SARS-CoV-2 infection in a patient on chronic hydroxychloroquine therapy: implications for prophylaxis Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study Hydroxychloroquine in the COVID-19 pandemic era: in pursuit of a rational use for prophylaxis of SARS-CoV-2 infection doi = 10.2147/idr.s264831 id = cord-266348-tbr2ynx0 author = Stroemer, A. title = Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera date = 2020-06-17 keywords = CoV-2; SARS summary = Here, we compare the diagnostic accuracy of six commercially available SARS-CoV-2 IgG (Abbott SARS-CoV-2 IgG; Diasorin Liaison SARS-CoV-2 S1/2 IgG; Epitope EDI Novel Coronavirus COVID-19 IgG ELISA Kit; Euroimmun Anti-SARS-CoV-2 ELISA (IgG); Mikrogen recomWell SARS-CoV-2 IgG) or total SARS-CoV-2 antibody assays (Roche Elecsys Anti-SARS-CoV-2). The majority of assay results were confirmed in a laboratory-developed plaque reduction neutralization test and by a SARS-CoV-2 IgG-specific line assay including measurement of generally low IgG avidities (Mikrogen recomLine Coronavirus IgG [Aviditaet], prototype). Out 132 of the remaining 34 samples, only one serum (#20; Figure 1 ) which was obtained ten days after a positive 133 RT-PCR was tested negative for SARS-CoV-2 IgG/total antibodies in the six assays. Six of them -including three family members of a 153 confirmed COVID-19 case (#22; Figure 1 ) -were classified SARS-CoV-2 IgG/total antibody positive by the 154 majority of the tests. doi = 10.1101/2020.06.15.20131672 id = cord-297072-f5lmstyn author = Struck, Anna-Winona title = A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 date = 2012-01-16 keywords = ACE2; RBD; SARS summary = title: A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2 Peptide (438)YKYRYL(443) is part of the receptor-binding domain (RBD) of the spike protein of SARS-CoV. The interaction of SARS-CoV with its receptor ACE2 is an attractive drug target as epitopes of the RBD on the spike protein may serve as leads for the design of effective entry inhibitors (Du et al., 2009) . This method allows the determination of the binding specificity, as Table 2 Synthetic peptide library of fourteen 6mer peptides comprising RBD-residues N435-E452 and A471-S500 of SARS-CoV spike protein. We found a hexapeptide in the receptor-binding domain (RBD) of the S protein of SARS-CoV that carries a significant portion of the binding affinity of the virus to the human cell. Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein doi = 10.1016/j.antiviral.2011.12.012 id = cord-279725-d82sj80v author = Ströher, Ute title = Severe Acute Respiratory Syndrome-Related Coronavirus Is Inhibited by Interferon-α date = 2004-04-01 keywords = IFN; SARS summary = We evaluated the susceptibility of the SARS-related coronavirus (SARS CoV) to ribavirin and interferon (IFN)-α in vitro by use of cytopathic effect, plaque assay, and immunoblot analysis. To support the search for effective antiviral treatments, we evaluated the susceptibility of SARS CoV isolates (detailed studies were performed with the Tor2 isolate [Toronto, Canada]) to ribavirin and interferon (IFN)-a-2b in vitro. Our data indicate that ribavirin does not inhibit the virus at concentrations attainable in human serum but that IFN-a-2b may be useful and deserves further evaluation as a therapeutic agent. To quantify the effect of IFN-a-2b on the replication of the SARS CoV, Vero E6 cells were infected at an MOI of 0.001 and were incubated in the presence IFN-a-2b (0-5000 IU/mL), as described above. Whether combined therapy with IFN-a-2b and ribavirin would inhibit the replication of the SARS CoV in vitro has not yet been evaluated; the combination is more effective than either agent used alone for the treatment of HCV infection in humans. doi = 10.1086/382597 id = cord-346532-4xpnd93d author = Strömich, Léonie title = Allosteric Hotspots in the Main Protease of SARS-CoV-2 date = 2020-11-06 keywords = SARS; site summary = Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Bond-to-bond propensities have been shown to successfully detect allosteric sites on proteins [43] and we here present 141 the results in the SARS-CoV-2 M pro to that effect. After a full Bond-to-bond propensity analysis and quantile regression to rank all residues, we are able to score the active 156 site to obtain a measure for the connectivity towards the catalytic center (Tab. S8). A complementary, node-based method, Markov Transient analysis (MTA) 276 identifies areas of the protein that are significantly connected to a site of interest, the source, such as the active site, and 277 obtains the signal propagation that connects the two sites at the atomistic level. doi = 10.1101/2020.11.06.369439 id = cord-252965-30pl5tx3 author = Stutt, Richard O. J. H. title = A modelling framework to assess the likely effectiveness of facemasks in combination with ‘lock-down’ in managing the COVID-19 pandemic date = 2020-06-10 keywords = COVID-19; SARS; facemask summary = The current COVID-19 pandemic, caused by the virus species severe acute respiratory syndromerelated coronavirus, named SARS-CoV-2 [1] , has stimulated considerable controversy over the potential benefits of facemask use by the public and the timing of the initiation and termination of ''lock-down'' periods. The currently available control measures to combat SARS-Cov-2, therefore, include: physical distancing, population lock-down periods, good sanitation/hand washing/surface disinfecting, good ventilation, facemask and visor protection, as well as diagnostics followed by contact tracing and quarantine of infected and exposed individuals. We use two complementary modelling approaches to test the effectiveness of facemask wearing by sections of the population in reducing the transmission rate of SARS-Cov-2 and hence in reducing the effective reproduction number, R e (the expected number of new cases caused by a single infectious individual at a given point in the epidemic). doi = 10.1098/rspa.2020.0376 id = cord-326883-j7pbe50g author = Stöbe, Stephan title = Echocardiographic characteristics of patients with SARS-CoV-2 infection date = 2020-08-14 keywords = SARS; basal; patient summary = RESULTS AND METHODS: An extended echocardiographic image acquisition protocol was performed in 18 patients with SARS-CoV-2 infection assessing LV longitudinal, radial, and circumferential deformation including rotation, twist, and untwisting. The present paper describes the experience at the Leipzig University Hospital in detecting myocardial involvement in SARS-CoV-2-infected patients by echocardiography using a specialized extended imaging and analysis protocol to analyze different components of myocardial deformation [19] . In contrast to conventional echocardiography, deformation imaging (n = 14) revealed several interesting findings potentially documenting myocardial involvement in SARS-CoV-2-infected patients with mild/moderate and severe symptoms ( Table 2 ; Figs. The finding of a "reverse basal tako-tsubo-like syndrome" of basal LV segments might also be explained by the edema, which leads to abnormal basal rRS curves without any alterations Fig. 2 Rotational deformation pattern of the same SARS-CoV-2-infected patient with COVID-19 pulmonary disease as in Fig. 1 : normal radial strain patterns are documented in apical (a) and basal (b) left-ventricular (LV) segments. doi = 10.1007/s00392-020-01727-5 id = cord-291710-ixun0c8g author = Su, Haixia title = Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date = 2020-04-14 keywords = CoV-2; SARS; baicalein summary = A crystal structure of SARS-CoV-2 3CLpro in complex with baicalein, the first non-covalent, non-peptidomimetic small-molecule inhibitor, was also determined, revealing a unique binding mode of this natural product with the protease. To validate the binding of baicalin and baicalein with SARS-CoV-2 3CLpro and exclude the suspicion of being the pan-assay interference compounds (PAINS) (15) , their binding affinities with the protease were measured by isothermal titration calorimetry (ITC), widely known as an invaluable tool used to determine thermodynamic parameters of protein-ligand interactions such as Kd (Fig. 1, A and B ; Table 1 ). Moreover, the ITC profiles in combination with their chemical structures suggest that baicalin and baicalein act as noncovalent inhibitors of SARS-CoV-2 3CLpro with a high ligand binding efficiency. The mode of action of baicalein and the structural determinants associated with its binding with SARS-CoV-2 3CLpro were further explored using X-ray protein crystallography. doi = 10.1101/2020.04.13.038687 id = cord-267261-8z4aqfff author = Su, John R. title = Emerging viral infections date = 2005-03-01 keywords = Ebola; Nile; SARS; WNV; West; virus summary = In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients doi = 10.1016/j.cll.2004.05.002 id = cord-285965-mar8zt2t author = Su, Liang title = The different clinical characteristics of corona virus disease cases between children and their families in China – the character of children with COVID-19 date = 2020-03-25 keywords = Hubei; SARS; child summary = This study aims to analyze the different clinical characteristics between children and their families infected with severe acute respiratory syndrome coronavirus 2. Here, we report the clinical manifestations, laboratory test results, imaging characteristics, and treatment regimen of nine SARS-CoV-2 infected children and their families in Jinan, Shandong province to increase awareness of this disease, especially in children. A retrospective review was conducted of the clinical, lab tests, and radiologic findings for nine children and their families admitted to the Jinan Infectious Diseases Hospital identified to be nucleic acid-positive for SARS-CoV-2 from 24 January 2020 to 24 February 2020. All the patients were recorded with basic information and epidemiological histories [4] including (1) History of travel or residence in Wuhan and surrounding areas or other reported cases within 14 days of onset; (2) History of contact with new coronavirus infection (nucleic acid-positive) 14 days before onset; (3) history of contact with patients with fever or respiratory symptoms from Wuhan and surrounding areas, or from communities with case reports within 14 days before onset; (4) Cluster onset, along with disease condition changes. doi = 10.1080/22221751.2020.1744483 id = cord-293701-u4ntxo0y author = Su, Shan title = Learning from the past: development of safe and effective COVID-19 vaccines date = 2020-10-16 keywords = COVID-19; RSV; SARS summary = In this Perspective, we summarize examples of vaccine-associated disease enhancement in the history of developing vaccines against respiratory syncytial virus, dengue virus, SARS-CoV and Middle East respiratory syndrome coronavirus, which highlight the importance of a robust safety and efficacy profile, and present recommendations for preclinical and clinical evaluation of COVID-19 vaccine candidates as well as for vaccine design and optimization. One month later, five more candidates had also entered phase I clinical trials, and more than 100 COVID-19 vaccine candidates were in results, all of these vaccines induced antibodies against the spike protein (S protein) and the receptor-binding domain (RBD), including antibodies that neutralized pseudotyped and live SARS-CoV-2. We summarize examples of VADE in the history of the development of vaccines against respiratory syncytial virus (RSV), dengue virus (DENV), SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), each of which provides clues for safe COVID-19 vaccine development and highlights the need for rigorous preclinical and clinical safety testing. doi = 10.1038/s41579-020-00462-y id = cord-344330-zsx7wfyj author = Su, Shuo title = Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses date = 2016-03-21 keywords = HKU1; MERS; NL63; SARS summary = Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans. In humans, CoV infections primarily involve the upper respiratory tract and the gastrointestinal tract, and vary from mild, self-limiting disease, such as the common cold, to more severe manifestations, such as bronchitis and pneumonia with renal involvement [15] . A recent investigation discovered that multiple HCoV species, including MERS-CoV, beta-CoV group A, and a 229E-like virus, circulate amongst dromedary camels in Saudi Arabia [62] . Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection doi = 10.1016/j.tim.2016.03.003 id = cord-316616-j82q99in author = Su, Yen-Bo title = Cardiovascular manifestation and treatment in COVID-19 date = 2020-05-19 keywords = ACE2; COVID-19; China; SARS; patient summary = The novel coronavirus disease 2019 (COVID-19), with first presentation of atypical pneumonia, has spread rapidly from Wuhan, China, on December 12, 2019 to over 200 countries, caused 2 310 572 infected individuals and 158 691 mortalities, updated on April 19, 2020. 33, 41 In a small singlearm study of patients with confirmed COVID-19, treatment with hydroxychloroquine was associated with a significant difference in clearing of viral nasopharyngeal carriage of SARS-CoV2 within 3 to 6 days when compared with untreated controls. ACE2 levels are increased following treatment with ACE inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), which yield the concerns that using these medications might increase the severity of COVID-19, especially in patients with existing cardiovascular diseases. Patients with comorbidities including hypertension, cardiovascular diseases, and diabetes tend to have higher risk for having severe COVID-19 which leads to acute respiratory distress syndrome (ARDS) and mortality. Risk factors associated with acute respiratory distress syndrome and death in patients With coronavirus disease 2019 pneumonia in Wuhan, China doi = 10.1097/jcma.0000000000000352 id = cord-339686-oybnk1j8 author = Suassuna, José Hermógenes Rocco title = Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine date = 2020-08-26 keywords = AKI; RRT; SARS; acute; covid-19; patient summary = title: Technical note and clinical instructions for Acute Kidney Injury (AKI) in patients with Covid-19: Brazilian Society of Nephrology and Brazilian Association of Intensive Care Medicine We produced this document to bring pertinent information to the practice of nephrology, as regards to the renal involvement with COVID-19, the management of acute kidney injury cases, and practical guidance on the provision of dialysis support.As information on COVID-19 evolves at a pace never before seen in medical science, these recommendations, although based on recent scientific evidence, refer to the present moment. Every professional involved in nephrological care must provide the best possible assistance to the patients under their responsibility, adopt practices that minimize their personal risk of contamination, that of their patients and the whole range of other professionals who participate in hospital kidney support, including nurses and technicians, dialysis staff, healthcare professionals from all areas (for example, doctors and nurses in intensive care medicine), laboratory and radiology technicians, cleaning and transport staff, etc. doi = 10.1590/2175-8239-jbn-2020-s107 id = cord-311446-afhw0450 author = Suhandynata, Raymond T title = Multi-platform Comparison of SARS-CoV-2 Serology Assays for the Detection of COVID-19 date = 2020-08-07 keywords = Abbott; Roche; SARS summary = Diazyme, Roche, and Abbott SARS-CoV-2 serology assays were compared by correlating the raw quantitative values from each platform for all samples from PCR positive patients ( Supplementary Figure 2A-C) . The impact of disease prevalence on the PPV and negative predictive value (NPV) for the Diazyme, Roche, and Abbott SARS-CoV-2 serology platforms were calculated using the PPA and NPA of the ≥ 15 day patient group ( Table 4 and Supplementary Table 4 ). The prevalence for COVID-19 in the ≥ 15 day patient group was 12.3%, and the observed PPV for the Diazyme IgM/IgG panel, the Roche total Ig, and the Abbott IgG assays were 89.3%, 96.0%, and 92.6%, respectively. We evaluated longitudinal samples from 16 SARS-CoV-2 PCR positive patients with the Diazyme, Roche, and Abbott serology platforms (Figure 2A -2D) . We evaluated the PPA and NPA of the Diazyme, Roche, and Abbott SARS-CoV-2 serology assays using the same samples across all three platforms. doi = 10.1093/jalm/jfaa139 id = cord-261029-befymalm author = Sultan, Keith title = Review of inflammatory bowel disease and COVID-19 date = 2020-10-07 keywords = COVID-19; IBD; SARS summary = Early reports of the virus, now known as severe acute respiratory syndrome coronavirus 2, and its clinical disease coronavirus disease 2019 (COVID-19), has shown higher rates of morbidity and mortality in the elderly and those with pre-existing medical conditions. The authors also reported that there had been no cases of IBD/SARS-CoV-2 infected patients in the three largest tertiary IBD centers in Wuhan (Tongji Hospital, Union Hospital, and Zhongnan Hospital) at the time their manuscript was prepared, March 8, 2020. Rodriguez-Lago et al [29] reported on 40 cases of IBD (21 hospitalized) with confirmed positive tests for SARS-CoV-2 from 5 sites in the Basque Country (Spain), median age 59 years, 60% male, 32% Crohn''s disease (CD), with 28% on immune therapy, 18% biologic, and 10% systemic corticosteroids. To date, the largest national case reporting has come from a combined 24 IBD referral centers in Italy, affiliated with the Italian Group for the Study of Inflammatory Bowel Disease (IG-IBD) [32] . doi = 10.3748/wjg.v26.i37.5534 id = cord-331558-6rqd3fmj author = Sun, Chuan-bin title = Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date = 2020-04-24 keywords = MERS; PCR; SARS summary = Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. doi = 10.3389/fpubh.2020.00155 id = cord-352304-tt2q5mgs author = Sun, Dan title = Clinical features of severe pediatric patients with coronavirus disease 2019 in Wuhan: a single center’s observational study date = 2020-03-19 keywords = COVID-19; SARS; patient summary = METHODS: We included eight severe or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children''s Hospital from January 24 to February 24. The outbreak of coronavirus disease 2019 (COVID-19, previously known as 2019-nCoV) caused by SARS-CoV-2 infection in Wuhan City, China, has spread around the world [1] . We included eight severely or critically ill patients with COVID-19 who were treated at the Intensive Care Unit (ICU), Wuhan Children''s Hospital from January 24 to February 24. Critically ill COVID-19 was defined when the pediatric patients met any of the following criteria: (1) respiratory failure which requires mechanical ventilation; (2) septic shock, and (3) accompanied by other organ failure that needs ICU monitoring and treatment. Demographic information and clinical characteristics including exposure history, anamnesis, signs and symptoms, chest computed tomographic (CT) scan or X-ray results, complications, treatments, clinical outcomes, and laboratory findings of each patient were obtained from the Electronic Medical Record System of Wuhan Children''s Hospital. doi = 10.1007/s12519-020-00354-4 id = cord-298406-7wfdwou8 author = Sun, Haifang title = Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus date = 2003-12-31 keywords = SARS; pro; sars_3cl summary = title: Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus To facilitate the studies regarding the functions and structures of SARS_3CLpro, in this report the synthetic genes encoding 3CLpro of SARS_CoV were assembled, and the plasmid was constructed using pQE30 as vector and expressed in Escherichia coli M15 cells. In our previous work [24, 25] , we reported a 3D model of SARS_3CL pro and its inhibitor design by virtual screening, as well as the cloning, expression, and purification of the E protein of SARS_CoV. In this article, we would like to present the results describing the molecular cloning, expression and purification of 3CL pro of SARS_CoV, and the preliminary study on its mass spectrometric characterization is also reported. Expression and purification of SARS_3CL pro Escherichia coli M15 cells transformed with the plasmid pQE30-SARS_3CL pro were grown in 100 ml LB medium containing ampicillin (100 mg/L) and kanamycin (25 mg/L) at 37°C overnight and then inoculated into 1 L LB supplemented with both the antibiotics. doi = 10.1016/j.pep.2003.08.016 id = cord-281727-elartlro author = Sun, Jing title = Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient date = 2020-05-18 keywords = SARS summary = title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. A novel coronavirus SARS-CoV-2 emerged to cause a major outbreak of severe pneumonia in humans in China and has spread to over 100 other countries [1] . Although viral RNA can be detected in multiple organs in COVID-19 patients, infectious SARS-CoV-2 has only been isolated from respiratory specimens [3, 4] . The urine sample tested positive for SARS-CoV-2 RNA on day 12 post infection (p.i.) (February 5th) for the first time and had periodically showed positive results in RT-PCR test until March 6th. Although it is hard to determine whether the kidney, the testis or the bladder were infected and produced infectious virus from current study, isolation of infectious SARS-CoV-2 in urine raises the possibility of fecal/urine-respiratory transmission. doi = 10.1080/22221751.2020.1760144 id = cord-275340-q8d7rvnj author = Sun, JingKang title = Advances in the use of chloroquine and hydroxychloroquine for the treatment of COVID-19 date = 2020-06-21 keywords = COVID-19; HCQ; SARS; patient; study summary = CQ/HCQ may synergistically exert antiviral and immunomodulatory effects on COVID-19 through multiple mechanisms including hindering the receptor recognition process by influencing the affinity of ACE2 and S protein, and the affinity for sialic acid and ganglioside; inhibiting the membrane fusion process by suppressing endolysosome acidification; suppressing the p38 activation and affecting host defense machinery, and preventing MHC class II expression (block expression of CD154 on the surface of CD4 + T cell) and TLR signaling and reducing the production of cytokines through inhibiting the activation of T cells and B cells. ACE2, angiotensin-converting enzyme 2; COVID-19, coronavirus disease 2019; CQ, chloroquine; HCQ, hydroxychloroquine; CoVs, coronaviruses; MAPK, mitogen-activated protein kinase; MHC-II, major histocompatibility complex class II; TLR, toll-like receptor; cGAS, cyclic GMP-AMP synthase; IFN, interferon; IL, interleukin; TNF-α, tumor necrosis factor-α. The authors deemed that the anti-inflammatory effect of low-dose HCQ and the activity of inhibiting viral replication may have important significance in critically ill patients with COVID-19. doi = 10.1080/00325481.2020.1778982 id = cord-330045-4gj9d181 author = Sun, Jiufeng title = Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date = 2020-08-17 keywords = RNA; SARS summary = We recruited hospitalized patients with COVID-19 from 2 designated provincial emergency hospitals for e merging infectious diseases in Guangdong, China, and tested specimens by real-time reverse transcription PCR (rRT-PCR) to estimate the duration of the detection of SARS-CoV-2 RNA in various body fluids, using an accelerated failure time (AFT)-based modeling study. We used parametric Weibull regression models (AFT) to estimate the time until the loss of SARS-CoV-2 RNA detection in each body fluid and reported findings in medians and 95th percentiles using R software version 3.6.1 with flexsurv, survival, and survminer packages (9) . We used Weibull models to estimate the median and the 95th percentile for the time until the loss of SARS-CoV-2 RNA detection in swab, sputum, and fecal samples (Table; Figures 1, 2) . In this study, we estimated the time for COVID-19 case-patients to clear SARS-CoV-2 RNA in the acute phase of infection through an AFT-based modeling study. doi = 10.3201/eid2608.201097 id = cord-319447-xanewi59 author = Sun, Jiya title = Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date = 2020-05-01 keywords = MERS; SARS; figure summary = To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. In this study, we used the SARS-CoV-2 strain isolated from patients [11] to infect in vitro Calu-3 cells, and performed RNA sequencing to determine the time-series transcriptome profiling data of the host. Next, to gain possible explanations for the distinct patterns in host antiviral capacity and cytokine production during SARS-CoV-2 infection, dynamic expression of four types of key genes were evaluated, including virus receptors for cell entry, pathogen recognition receptors (PRRs) for an innate immune startup, regulator genes for induction of antiviral-related genes and interferon production (Figure 4) . doi = 10.1101/2020.04.30.071274 id = cord-268740-ldz5366v author = Sun, Mei title = Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients date = 2020-08-14 keywords = COVID-19; SARS summary = title: Anal swab as the potentially optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients We propose anal swabs as the potentially optimal specimen for SARS-CoV-2 detection for evaluation of hospital discharge of COVID-19 patients. In this study, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of a few cured patients, which challenges the current standards for discharge and termination of compulsory isolation for COVID-19 patients. In summary, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of several cured patients. • SARS-CoV-2 detection is positive in anal swabs but negative in throat swabs and sputum swabs of a few discharged patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. • Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients. doi = 10.2217/fmb-2020-0090 id = cord-345275-h0hvaxgx author = Sun, Mengyao title = Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date = 2020-07-04 keywords = Ebola; SARS summary = title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection doi = 10.1016/j.ijid.2020.06.107 id = cord-307263-znuqdzdp author = Sun, Niuniu title = A Qualitative Study on the Psychological Experience of Caregivers of COVID-19 Patients date = 2020-04-08 keywords = SARS; nurse; psychological; study summary = Previous studies have shown that during sudden natural disasters and infectious diseases, nurses will sacrifice their own needs to actively participate in the anti-epidemic work and make selfless contributions out of moral and professional responsibility [7] . Previous studies have shown that when nurses are in close contact with patients with emerging infectious diseases such as SARS [9] , MERS-Cov [10, 11] , Ebola [12] , H1N1 [13] , they will suffer from loneliness, anxiety, fear, fatigue, sleep disorders, and other physical and mental health problems. This study explored the psychological experience of caregivers of patients with COVID-19 using phenomenological methods and we summarised our findings into four themes: significant amounts of negative emotions at an early stage, self-coping styles, growth under stress, and positive emotions that occur simultaneously or progressively with negative emotions. doi = 10.1016/j.ajic.2020.03.018 id = cord-325452-2sywbgje author = Sun, Pengfei title = Understanding of COVID‐19 based on current evidence date = 2020-03-05 keywords = SARS summary = A study by Wang et al 12 In the absence of effective treatments, the best way to deal with the SARS-CoV-2 epidemic is to control the sources of infection. 9 According to the official Chinese data, the case fatality rate among the SARS-CoV-2-infected patients was much lower than that of SARS and MERS. These studies will help further reduce the case fatality and transmission rates among SARS-CoV-2-infected patients. Moreover, super-spreaders were reported during the SARS and MERS epidemics. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health-the latest 2019 novel coronavirus outbreak in Wuhan, China Updated understanding of the outbreak of 2019 novel coronavirus (2019-nCoV) in Wuhan Clinical features of patients infected with 2019 novel coronavirus in Wuhan Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 Clinical characteristics of 2019 novel coronavirus infection in China doi = 10.1002/jmv.25722 id = cord-346677-20ky3t6y author = Sun, Pengfei title = Clinical characteristics of hospitalized patients with SARS‐CoV‐2 infection: A single arm meta‐analysis date = 2020-03-11 keywords = China; SARS summary = OBJECTIVE: We aim to summarize reliable evidence of evidence‐based medicine for the treatment and prevention of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) by analyzing all the published studies on the clinical characteristics of patients with SARS‐CoV‐2. Since December 2019, the epidemic of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infectious pneumonia in Wuhan, China. To acquire more accurate conclusions on the clinical characteristics and mortality of patients with SARS-CoV-2 infection, we searched the relevant literatures and carried out single-arm metaanalysis. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 17 hospitalized patients with 2019 novel coronavirus infections outside Wuhan, China. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical characteristics of hospitalized patients with SARS-CoV-2 infection: A single arm meta-analysis doi = 10.1002/jmv.25735 id = cord-312305-ll29frwc author = Sun, Shihui title = Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date = 2020-11-11 keywords = COVID-19; CoV-2; Fig; SARS; mouse summary = Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. We further characterized the in vivo replication dynamics of MASCp6 in both young and aged mice, and the results from qRT-PCR showed that high levels of SARS-CoV-2 subgenomic RNAs were persistent in the lung and tracheas till 4 day post infection (dpi) in aged mice (Fig. 1E) . The skewed age distribution of COVID-19 disease was reproduced in the MASCp36 infected mouse model where more severe symptoms were observed in aged mice when compared to young mice. In addition to the age-related skewed distribution of COVID-19, gender-related differences in distribution of COVID-19 disease is also recapitulated in this MASCp36 infected mouse model with increased susceptibility and enhanced pathogenicity observed in male mice when compared to their female counterparts. doi = 10.1101/2020.11.10.377333 id = cord-272019-4uua0zgp author = Sun, Wei title = Changes in coagulation and fibrinolysis of post-SARS osteonecrosis in a Chinese population date = 2006-03-18 keywords = III; SARS summary = The purpose of this study was to detect changes in coagulation and fibrinolysis of post-severe acute respiratory syndrome (SARS) Chinese patients with osteonecrosis, investigate the aetiology of post-SARS osteonecrosis (ON), and select the sensitive molecular markers for identifying the susceptible population. Of 88 patients with post-SARS, 78 (88.64%) were found to have at least one coagulopathy versus 36.54% of controls (p<0.01); PC, APC-R, AT-III, PAI, and PLG were significantly different between the two groups (Tables 1 and 2 ). [28] studied risk factors for pulmonary emboli after total hip or knee arthroplasty, 21 serological measures and five genes associated with thrombophilia and/or hypofibrinolysis were assessed: 13 of 27 (48%) in the control group also had at least one abnormality. In this study, we did not detect any coagulation abnormalities in a small proportion of the patients; this may reflect limitations in our understanding of the causes of thrombosis and hypofibrinolysis. Risk factors potentially activating intravascular coagulation and causing nontraumatic osteonecrosis doi = 10.1007/s00264-005-0067-6 id = cord-326666-melz5fq4 author = Sun, Weitao title = The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date = 2020-09-03 keywords = HGS; SARS summary = title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. 578 shown with special markers at the top of colored blocks representing ORFs. Mutation 623 10818G>T in ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which 624 results in amino acid M37F mutation in transmembrane protein nsp6. ORF1ab (codon TTG>TTT) occurred in populations with high HGS, which results in amino 631 acid M37F mutation in transmembrane protein nsp6. doi = 10.1101/2020.09.03.280727 id = cord-267735-y3832u9e author = Sun, Wuping title = Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date = 2020-09-24 keywords = SARS; covid-19 summary = title: Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic It has been reported that hyper-immunity individuals have received treatment with immunosuppressive or modulatory agents; these approaches may increase the possibility of SARS-CoV-2 infection (Cai et al., 2020) . These results demonstrated that SARS-CoV-2 infection-induced immune alteration in COVID-19 patients. These studies suggested that SARS-CoV-2 infection-induced immune alteration could further result in the concurrence of chronic pain since it affects the nervous system. Acquired immune deficiency syndrome (AIDS) is associated with various infection symptoms, and peripheral neuropathic pain is the most common and severe neurological manifestation that has been reported in HIV-positive, immunocompromised individuals (Amaniti et al., 2019) . Chronic pain patients have received limited treatment and discounted services during the COVID-19 outbreak due to limit the spread of SARS-CoV-2 infection. Chronic pain patients may also have increased infection risks to SARS-CoV-2 due to complicated reasons. doi = 10.3389/fmicb.2020.572318 id = cord-333018-2h8y118z author = Sun, Xingxing title = Safety Considerations for Neuraxial Anaesthesia in Parturients with COVID-19 date = 2020-05-14 keywords = SARS summary = To decide the mode of anaesthesia for parturients with COVID-19, one should evaluate neurological symptoms in addition to respiratory symptoms. Angiotensin-converting enzyme 2 (ACE2) is the functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); 7 it is expressed in the cell membrane of various tissues and organs including lung, small intestine, and brain. When deciding on anaesthetic strategy for patients with COVID-19, we think that one should consider the possible deleterious effects on the nervous system by neuraxial anaesthesia. For patients with apparent central or peripheral nervous system symptoms, although direct evidence is still lacking, general anaesthesia might be an acceptable alternative. However, general anaesthesia can impair the blood-brain barrier 10 , which might facilitate the invasion of SARS-CoV-2 into the central nervous system. Emergency Caesarean delivery in a patient with confirmed coronavirus disease 2019 under spinal anaesthesia doi = 10.1016/j.bja.2020.05.005 id = cord-318364-5bmdzgla author = Sun, Xinjuan title = Cytokine storm intervention in the early stages of COVID-19 pneumonia date = 2020-04-25 keywords = COVID-19; IFN; SARS summary = In a retrospective study of 41 patients with COVID-19, most patients with SARS-CoV-2 infection developed mild symptoms, whereas some patients later developed aggravated disease symptoms, and eventually passed away because of multiple organ dysfunction syndrome (MODS), as a consequence of a severe cytokine storm. In view of the severe morbidity and mortality of COVID-19 pneumonia, we review the current understanding of treatment of human coronavirus infections from the perspective of a dysregulated cytokine and immune response. In support of the above observations, a retrospective study of 41 patients with COVID-19 2 showed that most SARS-CoV-2 infected patients present clinically with mild symptoms, while a minority of patients progressively declined from the infection and eventually died of acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MOD). Severe pneumonia caused by pathogenic human coronaviruses (HCoV) are often associated with induced hypercytokinemia, also termed cytokine storm, in immunocompetent individuals; uncontrolled overproduction of inflammatory cytokines contributes to acute lung injury and acute respiratory distress syndrome (ARDS). doi = 10.1016/j.cytogfr.2020.04.002 id = cord-301227-ica5x0r1 author = Sun, Yi-Sheng title = A SARS-CoV-2 variant with the 12-bp deletion at E gene date = 2020-10-29 keywords = SARS summary = In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. In this paper, we isolated two SARS-CoV-2 strains with both wild-type and mutant E genes from the same sample using plaque purification. To explore whether other clinical samples contained a similar SARS-CoV-2 strain lacking a 12-bp sequence in the E gene, we used RT-PCR to detect the mutant E gene specifically. Our results indicated that both the F8 and 8X strains can infect Vero cells, however, the S protein content of the F8 viral culture was higher than that of 8X. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. In conclusion, we report an E gene mutant and a wild type SARS-CoV-2 strain isolated from the same clinical sample by plaque purification. doi = 10.1080/22221751.2020.1837017 id = cord-336093-ic6q6ke8 author = Sun, Ying title = Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date = 2014-02-11 keywords = Fig; RNA; SARS; yeast summary = Abbreviations: SARS, severe acute respiratory syndrome; SARS-CoV, SARS coronavirus; nsp, nonstructural protein; N7-MTase, guanine-N7-methyltransferase; 2 0 -O-MTase, 2 0 -O-methyltransferase; AdoMet, S-adenosyl-L-methionine; AdoHcy, S-adenosyl-L-homocysteine; ATA, aurintricarboxylic acid; IC 50 , inhibitory concentration at 50% activity. A single transformed colony of the YBS40 strain containing plasmids expressing human N7-MTase (MT-Human), SARS-CoV N7-MTase (MT-SARS), N7-MTases of other coronaviruses (MT-MHV, MT-TGEV, and MT-IBV), and the pMceK294A vector as control (representing the yeast N7-MTase [MT-Yeast]), were inoculated separately into 5 ml of a basic medium (Min SD Base) lacking tryptophan and incubated at 30°C for 21-24 h until reaching a similar final cell density in the stationary phase (0.5-1.0 Â 10 8 cells/ml) (Chrebet et al., 2005) . Although AdoHcy, ATA and sinefungin, were previously reported to be inhibitors of coronavirus RNA MTases in vitro , only sinefungin significantly suppressed the growth of the MT-yeast, MT-human, and MT-SARS yeast cells (Fig. 3 ). doi = 10.1016/j.antiviral.2014.02.002 id = cord-330715-olypwdoq author = Sun, Zeyu title = Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications date = 2020-08-30 keywords = HCoV-19; SARS; protein summary = title: Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications In this study, we report a comprehensive N-glycosylation profile-as well as other PTMs-of the HCoV-19 S protein and hACE2, elucidated by high-resolution mass spectrometry (MS) analyses. To resolve glycan camouflage on the surface of the HCoV-19 S protein and hACE2, intact glycopeptides derived from protease digestion and fractionated by HILIC were directly subjected to LC-MSMS analysis specifically designed to detect peptides with extra molecular weight due to N-glycan attachment. Fig. 2 (c) provides a summary of the most dominant N-glycan composition and predicted structure for each site of the HCoV-19 spike protein and hACE2. When the spike proteins from HCoV-19 and SARS-CoV were compared, it was noticeable that the majority of differences in the glycosylation sites occurred in the distal S1 subunit, resulting in a significant difference in the glycan profile in the outermost canopy of the virus formed by spike trimer clusters. doi = 10.1016/j.eng.2020.07.014 id = cord-352909-s11tpfoq author = Sun, Zhiping title = Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions date = 2020-08-14 keywords = COV-2; SARS summary = Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions Zhiping Sun 1 , Xia Cai 1 , Chenjian Gu 2 , Rong Zhang 2 , Wendong Han 1 , Yun Qian 1 , Yuyan Wang 2 , Wei Xu 2 , Yang Wu 2 , Xunjia Cheng 2 , Zhenghong Yuan 2 , Youhua Xie 2 and Di Qu 1, 2 Dear Editor, The pneumonia caused by a novel coronavirus was first reported in December 2019 in Wuhan of China, and since then has become a pandemic 1, 2 . Here, we first investigated the infectivity of SARS-COV-2 using a plaque-purified strain nCoV-SH01 isolated from a patient in Shanghai (GenBank MT121215) 6 , studied subsequently its stability in liquid medium, on dry filter paper, and under acidic condition (pH2.2) at RT. doi = 10.1038/s41421-020-00191-9 id = cord-351651-6dbt99h0 author = Sun, Zhong title = Potential Factors Influencing Repeated SARS Outbreaks in China date = 2020-03-03 keywords = China; SARS; SARS-2; Wuhan summary = Thus, if bats were the natural hosts of SARS-CoVs, cold temperature and low humidity in these times might provide conducive environmental conditions for prolonged viral survival in these regions concentrated with bats. A study on the genome sequence of diseased pangolins smuggled from Malaysia to China found that pangolins carry coronavirus, suggesting that pangolins may be intermediate hosts for SARS-COV-2 [35] . However, the only source of bats that have been publicly identified as carrying virus phylogenetically close to SARS-CoV-2 is far away from Wuhan in Zhoushan, Zhejiang. However, to confirm this scenario, it is necessary to find wild bats in Wuhan and its neighboring areas that carry CoVs identical to those isolated from various SARS-2 patients. This mini-review evaluated the common epidemiological patterns of both SARS epidemics in China and identified cold, dry winter as a common environmental condition conducive for SARS virus infection to human beings. doi = 10.3390/ijerph17051633 id = cord-278457-yrm5hi3v author = Sung, Heungsup title = Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea date = 2020-10-17 keywords = Allplex; EQA; SARS summary = EQAs using pooled respiratory samples spiked with inactivated cultured SARS-CoV-2 had indicated the possible effects of these variations on assay performance, thereby allowing External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. doi = 10.3201/eid2610.202551 id = cord-303934-8gh3q7p3 author = Sungnak, Waradon title = SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways date = 2020-03-13 keywords = ACE2; SARS; TMPRSS2 summary = To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA-sequencing (scRNA-seq) datasets from healthy individuals generated by the Human Cell Atlas consortium. To clarify the expression patterns of ACE2 and TMPRSS2 and analyze the expression of the other potential genes associated with SARS-CoV-2 pathogens at cellular resolution, we interrogated single-cell transcriptome expression data from published scRNA-seq datasets from healthy donors generated by the Human Cell Atlas consortium 24 . While we cannot rule out the possibility that the virus uses alternative proteases for entry in such contexts, or that lung fetal tissue expresses the relevant genes, these results are at least consistent with early reports that fail to detect evidence of intrauterine infection through vertical transmission in women who develop COVID-19 pneumonia in late pregnancy 38 . doi = 10.1038/s41591-020-0868-6 id = cord-330779-mso2zfom author = Sunkari, Emmanuel Daanoba title = Sources and routes of SARS-CoV-2 transmission in water systems in Africa: Are there any sustainable remedies? date = 2020-09-09 keywords = Africa; SARS; water summary = Hence, it is proposed that governments in Africa must put measures like improved WASH facilities and public awareness campaigns, suburbanization of wastewater treatment facilities, utilizing low-cost point-of-use water treatment systems, legally backed policy interventions, and Community-Led Total Sanitation (CLTS). Overall, since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water is very high and thus, the sources and routes of community spread of the virus, which is currently being reported must be critically re-examined. Since most of the people living in Africa, especially those dwelling in rural and peri-urban settlements depend on surface and groundwater resources for their domestic water supply, the risk of contracting COVID-19 through SARS-CoV-2 contaminated water from wastewater systems is very high. doi = 10.1016/j.scitotenv.2020.142298 id = cord-354773-u86bdmvf author = Suo, Tao title = ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date = 2020-06-07 keywords = PCR; SARS summary = To improve the diagnostic accuracy of nucleic acid detection of SARS-Cov-2 in low viral load samples using droplet digital PCR, we compared the dynamic range and the limit of detection (LoD) with a 95% repeatable probability between ddPCR and RT-PCR in laboratory, and tested the clinical samples from 77 patients by both ddPCR and RT-PCR for head to head comparison. Throat swab samples of each patient were firstly collected for official approved RT-PCR diagnosis in hospitals and blinding laboratory RT-PCR and ddPCR tests simultaneously with the same primers/probe sets approved by Chinese CDC. As shown in Figure 3 , throat swab samples of each suspected outpatient were firstly collected for laboratory RT-PCR, ddPCR tests and official approved RT-PCR diagnosis in hospitals simultaneously with the same primers/probe sets approved by Chinese CDC (Table 1) . In this study, two throat swab samples of each supposed convalescent were collected for laboratory RT-PCR, ddPCR and official approved RT-PCR tests simultaneously with the same primers/probe sets (Table 2) . doi = 10.1080/22221751.2020.1772678 id = cord-023865-6rafp3x3 author = Surjit, Milan title = The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date = 2009-07-22 keywords = RNA; SARS; protein summary = Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese''s laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells doi = 10.1007/978-3-642-03683-5_9 id = cord-316880-hbw6jbz5 author = Sutton, Melissa title = Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 date = 2020-08-14 keywords = SARS summary = title: Notes from the Field: Seroprevalence Estimates of SARS-CoV-2 Infection in Convenience Sample — Oregon, May 11–June 15, 2020 to the Oregon State Public Health Laboratory for testing with the Abbott Architect Laboratories SARS-CoV-2 IgG immunoassay. Antibodies to SARS-CoV-2 were detected in nine of 897 specimens, yielding an unadjusted seroprevalence of 1.0% (95% confidence interval = 0.2%-1.8%). The estimated seroprevalence of SARS-CoV-2 antibodies in a convenience sample of adult Oregonians was approximately 10 times the measured cumulative COVID-19 incidence obtained by nucleic acid testing, consistent with results from seven other U.S. states and geographic areas (4). Population point prevalence of SARS-CoV-2 infection based on a statewide random sample-Indiana Estimated community seroprevalence of SARS-CoV-2 antibodies-two Georgia counties Seroprevalence of antibodies to SARS-CoV-2 in 10 sites in the United States All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. doi = 10.15585/mmwr.mm6932a4 id = cord-285944-8lapwnuw author = Suwanwongse, Kulachanya title = Hyperpyrexia in COVID‐19 patients date = 2020-06-10 keywords = COVID-19; SARS summary = We propose three possible underlying mechanisms based on our current knowledge: 1) direct brain injury from SARS-CoV-2, 2) persistent immune dysfunction and dysregulation of cytokines, and 3) vascular thrombosis. According to our case series, the lack of normal daily temperature variation in patient 4 and 5, and the presence of hypothermia in patient 1 and 5 support the hypothesis that direct brain injury from SARS-CoV-2 leads to hyperpyrexia. SARS-CoV-2 may cause injury to the brain-stem respiratory center explaining why COVID-19 patients often report lesser perception of dyspnea than the actual degree of hypoxia and the extent of lung pathology [15] . Our case series also highlights the need to determine underlying mechanisms of hyperpyrexia in COVID-19 patients as each cause requires different management. The underlying mechanisms of hyperpyrexia in COVID-19 are unknown but may be a result of SARS-CoV-2 related brain injury, exuberant immune response, and thrombus formation. doi = 10.1002/jmv.26154 id = cord-302786-ibt7mupq author = Suwanwongse, Kulachanya title = Fatal Outcome in a Kidney-Pancreas Transplant Recipient With COVID-19 date = 2020-06-18 keywords = SARS; covid-19 summary = Despite a growing report on clinical characteristics and prognosis of patients with COVID-19, the data in the special population, including transplant recipients, is still limited. We proposed that the pre-existing T-cell dysfunction from the long-term use of immunosuppressive agents in organ transplant recipients adversely affects COVID-19 prognosis and worsens COVID-19 mortality. However, impaired immune functions may paradoxically protect transplant patients from the hyper-inflammatory response to SARS-CoV-2 and thus dampen the disease severity. Long-term immunosuppressive therapy in organ transplant recipients may alter clinical features and outcomes of COVID-19. The long-term use of immunosuppressive medications in organ transplant recipients is associated with the decrease in T-cell number and function; TAC and MMF preferentially inhibit T-cell response. However, in this report, immunosuppressive agents were discontinued in patients with severe disease, presumably with high mortality risks. Preexisting T-cell immune response deficits from long-term use of immunosuppressive agents may worsen the prognosis of COVID-19 in transplant recipients. doi = 10.7759/cureus.8691 id = cord-308279-gsk4qel5 author = Suzuki, Yuichiro J. title = The viral protein fragment theory of COVID-19 pathogenesis date = 2020-09-11 keywords = SARS summary = I herein propose the viral protein fragment theory of COVID-19 pathogenesis based on my observations in cultured human vascular cells that SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I hypothesize that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling without the rest of the viral components. This hypothesis is based on my experimental observations in cultured human vascular cells that the recombinant full length S1 subunit of SARS-CoV-2 spike protein can activate cell signaling events without the rest of the viral components. I propose a scenario that, as humans are infected with SARS-CoV-2, the virus releases a fragment of the spike protein that can target host cells for eliciting cell signaling. doi = 10.1016/j.mehy.2020.110267 id = cord-313805-6mnclfeg author = Suzuki, Yuichiro J. title = SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date = 2020-10-12 keywords = MEK; SARS summary = Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. Our results showing that SARS-CoV-2 spike protein is capable of activating the MEK/ERK pathway in pulmonary artery smooth muscle and endothelial cells suggest that cell growth signaling may be triggered in the pulmonary vascular walls in response to SARS-CoV-2. The major finding of this study is that the SARS-CoV-2 spike protein without the rest of the virus can elicit cell signaling, specifically the activation of the MEK/ERK pathway, in human host lung vascular smooth muscle and endothelial cells. doi = 10.1101/2020.10.12.335083 id = cord-275199-y7b12vml author = Suárez-Fariñas, Mayte title = Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date = 2020-09-25 keywords = ACE2; IBD; SARS; TMPRSS2; figure summary = The RISK cohort 18 : ACE2 and TMPRSS2 in treatment-free pediatric CD (<17 years of age) patients was studied using RNA-seq expression profiles from GSE57945, which includes ileal biopsies from endoscopically defined inflamed samples (n=160), non-inflamed (n=53) and non-IBD controls (n=42). Genes differentially expressed in blood 22 , lung NHBE/A549 23 or human small intestinal organoids 24 (hSIO) following SARS-CoV-2 infection; IBD inflammation; or response to medications were separately projected onto various BGRNs allowing for 1 or 2 nearest neighbors depending on the signature sizes. The expression of ACE2 and TMPRSS2 was similar when comparing active smokers to non-smokers, either between healthy controls or IBD patients (data not shown) and no significant interactions with inflammation status, region or other covariates were found. We observed that genes: up-regulated with inflammation, or positively associated with macroscopic or microscopic measures of disease, or associated with the risk of IBD, were significantly enriched with genes up-regulated by SARS-CoV2 infection of lung epithelial cells ( Figure S10e ). doi = 10.1053/j.gastro.2020.09.029 id = cord-327912-wfjdxgxh author = Swann, Heather title = Minimal system for assembly of SARS-CoV-2 virus like particles date = 2020-08-24 keywords = SARS summary = Here we demonstrate that non-infectious SARS-CoV-2 virus like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells. Non-infectious virus like particles (VLPs) displaying essential viral proteins can be used to study the structural properties of the SARS-CoV-2 virions and due to their maximum immunogenicity are also vaccine candidates 2, 3 . Similarly, expression of M, E and S proteins are shown to result in release of morphologically identical particles to wild type SARS-CoV virus 9, 10 . We then tested the structural integrity of the SARS-CoV-2 VLPs attached to dry glass using Atomic Force Microscopy (AFM), since SARS-CoV-2 virions have been reported to survive on solid surfaces in dry conditions for many hours 13 . SARS-CoV-2 M, S and E protein genes were identified from the full genome sequence of the virus 1 , these genes were then humanized and inserted in CMV driven mammalian expression vectors (see supplement for complete plasmid sequences). doi = 10.1101/2020.06.01.128058 id = cord-299565-shlhreve author = Sweileh, Waleed M. title = Global research trends of World Health Organization’s top eight emerging pathogens date = 2017-02-08 keywords = Congo; East; Ebola; SARS summary = According to WHO, the list of pathogens, which required urgent attention for research and development pertaining to preparedness, included "Crimean Congo haemorrhagic fever, Ebola virus, Marburg, Lassa fever, Middle East respiratory syndrome (MERS) and Severe acute respiratory syndrome (SARS) coronavirus diseases, Nipah, and Rift Valley fever" [1] . ( TITLE ( "Crimean-Congo" OR ebola OR "Middle East Respiratory Syndrome" OR "Severe acute respiratory syndrome" OR lassa OR nipah OR "Rift valley" OR marburg OR mers OR merscov OR sars OR ebolavirus OR crimean ) AND TITLE-ABS ( virus OR viral OR fever OR hemorrhagic OR haemorrhagic OR corona* OR coronavirus OR infection OR infectious ) AND TITLE ( vaccin* ) ) AND PUBYEAR > 1995 AND PUBYEAR < 2016 AND ( LIMIT-TO ( SRCTYPE , "j" ) ) AND ( EXCLUDE ( DOCTYPE , "er" ) ) N = 472 doi = 10.1186/s12992-017-0233-9 id = cord-033901-itj6v1jl author = Syambani Ulhaq, Z. title = Recurrent positive SARS-CoV-2 RNA tests in recovered and discharged patients() date = 2020-10-17 keywords = SARS summary = The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic remains a global concern that requires a comprehensive approach to reduce rapid transmission, starting from case detection, inpatient care, as well as post-hospital management. However, concerns have risen over recent reports of increasing re-detectable positive (RP) SARS-CoV-2 RNA tests observed among recovered and discharged patients 1-2 . Aiming to summarize the current evidence, a meta-analysis was performed to estimate the prevalence of RP SARS-CoV-2 RNA tests among recovered patients, in addition to the days of RNA-positive conversion since last negative/discharge. A comprehensive literature search was conducted through an electronic database dated up to May 2020, with search terms such as "recovered/discharged patients", "coronavirus 2019/COVID-19", "SARS-CoV-2", "positive PCR" used in combination without language restriction. 1. Observational studies or case reports that described some RP SARS-CoV-2 RNA tests among recovered/discharged patients. Positive SARS-Cov-2 test in a woman with COVID-19 at 22 days after hospital discharge: A case report doi = 10.1016/j.rceng.2020.06.005 id = cord-279106-3ffa9djf author = Syatila Ab Ghani, Nur title = Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: the case for COVID-19 date = 2020-10-21 keywords = COVID-19; PDBID; SARS; drug; protein summary = In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed. 33 In this work, amino acid side chain similarity searching was utilized to propose alternative target sites in 34 SARS-CoV-2 protein structures for drug repositioning. doi = 10.1016/j.csbj.2020.10.013 id = cord-354538-vqi67h6a author = Sydney, Elana R. title = Antibody evidence of SARS-CoV-2 infection in healthcare workers in the Bronx date = 2020-08-26 keywords = SARS summary = 5. What is the prevalence of antibodies in those healthcare workers with self-reported positive and negative SARS-CoV-2 PCR tests? In total, 1,700 healthcare workers were tested for SARS-CoV-2 IgG antibody between April 28 and May 4, 2020. We analyzed the data by looking at those healthcare workers that had positive antibodies and stratified it based on department, presence or absence of symptoms, and previously reported positive PCR. Notably, 12% of those who tested positive for the presence of IgG reported a negative SARS-CoV-2 PCR result. As expected, 92% of individuals that reported a positive PCR test developed IgG antibodies. A small number of individuals, representing 1% of those reporting a positive SARS-CoV-2 PCR test prior to being tested, had a negative antibody test. 6 Our results reflect a higher overall rate of SARS-CoV-2 antibody development among healthcare workers in the Bronx compared to reported rates in NYC healthcare workers. doi = 10.1017/ice.2020.437 id = cord-255631-516epnjw author = Syeda, H. B. title = The Role of Machine Learning Techniques to Tackle COVID-19 Crisis: A Systematic Review. date = 2020-08-25 keywords = August; COVID-19; SARS; preprint summary = Results: The 128 publications selected were classified into three themes based on ML applications employed to combat the COVID-19 crisis: Computational Epidemiology (CE), Early Detection and Diagnosis (EDD), and Disease Progression (DP). This study focused on peer-reviewed publications, as well as, preprints that applied ML techniques to analyze and address COVID-19 crisis on different scales including diagnostics, prognostics, disease spread forecast, omics, and drug development. We identified forty studies that primarily focused on diagnosing COVID-19 in patients with suspected infection mostly using chest radiological images such as Computed Tomography (CT), X-Radiation (X-Ray), and Lung Ultrasound (LUS). In our review, we identified one study by Roy et al [126] who used a deep learning model on annotated LUS COVID-19 dataset to predict disease severity. The goal of the study was to develop a decision support tool that integrates readily available lab results from EHRs. The novel coronavirus (COVID-19) pandemic has strained global healthcare systems, especially ICUs, due to hospitalized patients having higher ICU transfer rates [133] . doi = 10.1101/2020.08.23.20180158 id = cord-344213-j3yextjl author = Sze, Shirley title = The need for improved discharge criteria for hospitalised patients with COVID-19—implications for patients in long term care facilities date = 2020-09-19 keywords = COVID-19; SARS summary = In the COVID-19 pandemic, patients who are older and residents of long term care facilities (LTCF) are at greatest risk of worse clinical outcomes. We reviewed discharge criteria for hospitalised COVID-19 patients from ten countries with the highest incidence of COVID-19 cases as of 26th July 2020. We recommend a unified, simpler discharge criteria, based on current studies which suggest that most SARS-CoV-2 loses its infectivity by 10 days post-symptom onset. This represents a practical compromise between unnecessarily prolonged admissions and returning highly infectious patients back to their care facilities, and is of particular importance in older patients discharged to LTCFs, residents of which may be at greatest risk of transmission and worse clinical outcomes.  Current evidence suggests that most patients are non-infective 10 days post symptom onset or after first positive PCR result COVID-19 is a global pandemic. doi = 10.1093/ageing/afaa206 id = cord-252687-7084pfqm author = Szelenberger, Rafal title = Ischemic Stroke among the Symptoms Caused by the COVID-19 Infection date = 2020-08-19 keywords = COVID-19; SARS; cell; patient; stroke summary = Many clinical studies have shown an association between SARS-CoV-2 infection and hypercoagulability diagnosed on the basis of abnormal coagulation parameters, including activated partial thromboplastin time, prothrombin time, fibrinogen, D-dimer and C-reactive protein level. In this review, the potential mechanism and the effect of the SARS-CoV-2 viral infection on the development of ischemic stroke in COVID-19 patients were carefully studied. study, in which most non-survivor COVID-19 patients'' (71.4%) blood tests showed prolonged prothrombin time and an increased D-dimer levels, which indicated the state after activation of the plasma coagulation system [14] . The accumulation of immune cells in the vascular wall in response to the viral infection, especially among patients with ischemic risk factors, induces endothelial dysfunction, migration and proliferation of cells, activation of coagulation cascade and production of fibrous plaques. doi = 10.3390/jcm9092688 id = cord-262454-bccrvapy author = Szente Fonseca, Silvia Nunes title = Risk of Hospitalization for Covid-19 Outpatients Treated with Various Drug Regimens in Brazil: Comparative Analysis date = 2020-10-31 keywords = COVID-19; HCQ; SARS; patient summary = With all that, we developed a protocol for early recognition and treatment of high-risk patients (in our population, age greater than 40 years because of generally poorer health standards, or with comorbidities) who would come to our outpatient network of emergency rooms with influenza-like symptoms: fever, cough, myalgia and headache, among others, and receive early treatment, provided to patients at the first doctor visit, using physician discretion from among HCQ, azithromycin, ivermectin, oseltamivir, zinc sulfate, nitazoxanide and prednisone (the last starting on day-6 of symptoms). On March 28, 2020, the FDA issued an emergency use authorization for remdesivir and HCQ for patients in both clinical trials and with severe hospitalized disease (31) . We found early outpatient use of HCQ and prednisone, both as individual prescriptions and used together, to lower the risk of hospitalization in symptomatic high-risk COVID-19 patients presenting for primary care at the emergency rooms of our large HMO in Brazil. doi = 10.1016/j.tmaid.2020.101906 id = cord-349721-wdjlr4z4 author = Szpiro, L. title = Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection date = 2020-08-25 keywords = SARS; surface summary = To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. In an attempt to better understand and thus better control the transmission of SARS-CoV-2 behind the recent and ongoing pandemic, the impact of body fluid secretions, from coughing or sneezing corresponding to an artificial mixture containing nasal mucus and saliva, on the surface stability of SARS-CoV-2 and the virucidal efficiency of disinfectant were tested. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers (according to the EN14476 standard suspension test) and 1 surface chemical disinfectant (according to the virucidal surface quantitative EN16777 test) against SARS-CoV-2, HCoV-229E and FCoV was then measured. The virucidal activity of three commercial hand rub products against SARS-CoV-2, HCoV-229E and FCoV was determined using the quantitative suspension test according to EN 14476, comparing standardized interfering substance (clean condition, 0.3 g/l BSA) and our artificial mucus/saliva mixture. doi = 10.1101/2020.08.22.20180042 id = cord-251581-8ubyveyt author = Szymkowiak, Andrzej title = In-store epidemic behavior: scale development and validation date = 2020-05-04 keywords = SARS; consumer; covid-19; epidemic; store summary = All identified factors significantly correlated with the in-store infection threat which reiterates the importance of providing information revealing the true scale of the pandemic and not leaving space for individuals to create subjective probability judgments. Nonetheless, one must also bear in mind that grocery stores are a place for possible transmission of many bacterial and viral pathogens (Bell et al., 2009; Dalton, New, & Health, 2006; Sinclair, Fahnestock, Feliz, Patel, & Perry, 2018) , causing consumers to undertake various behavioral changes in their approach to shopping. Based on the analysis of this limited quantity of research related to consumer behavioral changes in response to epidemics, it is clear that there is a gap in research on how the fear of contagion and not budgetary limitations can impact consumer willingness to shop at stationery stores. Moreover, the questionnaire was performed during the outbreak of the COVID-19 pandemic which limits the possibility of comparing the results for in-shop behaviors with a time from before the epidemic. doi = nan id = cord-292874-6zjqflhz author = SØRENSEN, MORTEN DRÆBY title = Severe Acute Respiratory Syndrome (SARS): Development of Diagnostics and Antivirals date = 2006-05-10 keywords = SARS; antibody summary = abstract: The previously unknown coronavirus that caused severe acute respiratory syndrome (SARS‐CoV) affected more than 8,000 persons worldwide and was responsible for more than 700 deaths during the first outbreak in 2002–2003. As part of the Sino‐European Project on SARS Diagnostics and Antivirals (SEPSDA), an immune phage‐display library is being created from convalescent patients in a phagemid system for the selection of single‐chain fragment variables (scFv) antibodies recognizing the SARS‐CoV. In February 2003, the new and previously unknown deadly coronavirus causing severe acute respiratory syndrome (SARS-CoV) was brought to the attention of the World Health Organization (WHO) by Dr. Carlo Urbani and his colleagues. Creation of immune phage-display libraries for immunized donors has shown a particular efficiency in selecting neutralizing antibodies (NABs) against different viruses, for example, rabies, 39 varicella-zoster, 40 hepatitis A 41 and E, 42 measles, 43 and respiratory syncytial virus. doi = 10.1196/annals.1354.072 id = cord-288051-wp8v2mc5 author = Sánchez-González, Álvaro title = What Should Be Known by a Urologist About the Medical Management of COVID-19’s Patients? date = 2020-09-01 keywords = COVID-19; SARS; day; patient summary = Seven days after the clinical onset, the risk of transmission decreases in mildsymptomatic patients, but it may be extended over 24 days in severe cases [11•, 15] . The clinical spectrum of SARS-CoV-2 infection varies widely, including asymptomatic infection, mild upper respiratory tract illness, severe viral pneumonia with respiratory failure, and even death [9, 11•] (Fig. 1) . Corticosteroids are recommended in the treatment of septic shock, exacerbation of chronic obstructive respiratory disease and these COVID-19''s patients with respiratory deterioration and quick radiological progression associated with sings of cytokine storm (cytopenia, maintained fever, an increase of inflammatory reactants: D-dimer > 1000 ng/mL, ferritin > 1000 ng/mL, fibrinogen > 100 ng/mL, IL-6 > 40 pg/mL) [6, 23••] . Results from 237 patients, 158 assigned to remdesivir, showed no differences in time to clinical improvement, 28day mortality, oxygen support, hospitalization, or viral load. Clinical management of severe acute respiratory infection (SARI) when COVID-19 disease is suspected. Effective treatment of severe COVID-19 patients with tocilizumab doi = 10.1007/s11934-020-00995-y id = cord-332013-bl5d4xkc author = Sánchez-Álvarez, J. Emilio title = Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) date = 2020-04-27 keywords = Registry; SARS; patient summary = title: Status of SARS-CoV-2 infection in patients on renal replacement therapy Report of the COVID-19 Registry of the Spanish Society of Nephrology (SEN) Conclusions SARS-CoV-2 infection already affects a significant number of Spanish patients on RRT, mainly those on ICH, hospitalization rates are very high and mortality is high; age and the development of pneumonia are factors associated with mortality. As of April 11, data from 868 patients on RRT with documented SARS-CoV-2 coronavirus infection had been entered into the Registry. The analysis of data collected during the first three weeks of the Covid-19 Registry of SEN shows that the SARS-CoV-2 infection affects a significant number of Spanish patients on RRT, mainly those that are in HDC . Nevertheless our registry show that , hydroxychloroquine and other commonly used drugs in the SARS-CoV infection-2 are used more frequently in transplant than in dialysis patients. doi = 10.1016/j.nefroe.2020.04.002 id = cord-297381-1upz6dsy author = Sánchez‐Duque, Jorge A. title = Are we now observing an increasing number of coinfections between SARS‐CoV‐2 and other respiratory pathogens? date = 2020-05-29 keywords = SARS summary = Then, we would like to take the opportunity to discuss some of them, 1-10 as there are not yet reviews on this emerging issue of Currently, the evidence suggests that the coinfection rates between SARS-CoV-2 and other respiratory pathogens would be higher than initially expected, which represents a challenge for the diagnosis and treatment. Of patients with confirmed SARS-CoV-2 infection, 20.7% (n=24) were positive for one or more additional pathogens, of which the most common were rhinovirus/enterovirus (6.9%; n=8), respiratory syncytial virus (5.2%; n=6) and other Coronaviruses (4.3%; n=5). 2 Another study by Ding et al., 3 included 115 patients with SARS-CoV-2 infection, 4.35% (n=5) had influenza coinfection (3 for influenza A; 2 for influenza B) 9 . 6 Arashiro et al., 4 published a case report of a patient who debuted with severe acute respiratory distress associated with This article is protected by copyright. doi = 10.1002/jmv.26089 id = cord-280528-7ivw72l0 author = TUFAN, Abdurrahman title = COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs date = 2020-04-21 keywords = COVID-19; HCQ; IL-6; SARS; cell summary = In this review, to gain better information about appropriate anti-inflammatory treatments, mostly used in rheumatology for COVID-19, we have focused the attention on the structural features of SARS-CoV-2, the host immune response against SARS-CoV-2 and its association with the cytokine storm. The effective antiviral responses of the host innate and adaptive immunity, including the production of various proinflammatory cytokines, the activation of T cells, CD4 and CD8+ T cells, are essential for controlling the viral replication, limiting the spread of virus, inflammation and cleaning the infected cells [31, 32] . Few retrospective studies have revealed that the lung injury reported with Murray score is strongly associated with the level of IL-1α, IL-1ra, IL-2, IL-7, IL-10, IL-17, IFN-ɣ, inducible interferon protein (IP)-10, G-CSF, and MCP-3 and these cytokines and chemokines excluding MCP-3 are positively related to SARS-CoV-2 viral load 2 [7] . doi = 10.3906/sag-2004-168 id = cord-253987-83h861lp author = Tada, Takuya title = A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date = 2020-09-17 keywords = ACE2; SARS; figure; protein summary = The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. In SARS-CoV-2 entry, the virus attaches to the target cell through the interaction of the spike glycoprotein (S) with its receptor, the angiotensin-converting enzyme 2 (ACE2) (Li, 2015; Li et al., 2005; Li et al., 2003) , a plasma membrane protein carboxypeptidase that degrades angiotensin II to angiotensin-(1-7) [Ang-(1-7)] a vasodilator that promotes sodium transport in the regulation of cardiac function and blood pressure (Kuba et al., 2010; Riordan, 2003; Tikellis and Thomas, 2012) . To determine the relative antiviral activity of soluble ACE2 and the ACE2 microbody proteins, we tested their ability to block the infection SARS-CoV-2 Δ19 S protein pseudotyped GFP/luciferase reporter virus. doi = 10.1101/2020.09.16.300319 id = cord-343712-gn7fw891 author = Taglauer, Elizabeth title = Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads date = 2020-08-25 keywords = COVID-19; SARS summary = title: Consistent localization of SARS-CoV-2 spike glycoprotein and ACE2 over TMPRSS2 predominance in placental villi of 15 COVID-19 positive maternal-fetal dyads Parenchymal changes of placentas from COVID-19 infected mothers have been reported by several groups, but the localization and relative abundance of SARS-CoV-2 viral proteins and cellular entry machinery has not been fully characterized within larger placental tissue cohorts. Overall this study provides an important basis for the ongoing evaluation of SARS-CoV-2 physiology in pregnancy and highlights the importance of the placenta as a key source of primary human tissue for ongoing diagnostic and therapeutic research efforts to reduce the global burden of COVID-19. While ACE2 was consistently found in the sTB layer of all tissues 148 surveyed (COVID-19 Maternal and controls), TMPRSS2 expression was absent in both groups of 149 placentas (Fig. 3 A,B) . Vertical transmission of COVID-19: SARS-CoV-2 RNA on the fetal side of 301 the placenta in pregnancies with COVID-19 positive mothers and neonates at birth doi = 10.1016/j.placenta.2020.08.015 id = cord-287497-93oiiqqi author = Tagliamento, Marco title = Italian survey on managing immune checkpoint inhibitors in oncology during COVID‐19 outbreak date = 2020-06-14 keywords = SARS; covid-19; patient summary = The objectives of this survey were to examine the impact of COVID-19 outbreak on the perception of Italian physicians involved in the administration of ICIs about SARS-CoV-2 related risks in cancer patients receiving these therapies, and their attitudes towards the management of ICIs in oncology. The perception of respondents regarding the potential increased risk of severe events related to SARS-CoV-2 infection in cancer patients treated with ICIs is displayed in Figure 1B . 17 Moreover, besides the overlapping between cancer-related signs/symptoms or side effects of oncological treatments (including irAEs) and COVID-19 manifestations, additional issues could emerge from the differential diagnosis between radiological findings of lung involvement from SARS-CoV-2 and pneumonitis induced by ICIs. 9, 24 To the best of our knowledge, this is the first study exploring the perception of physicians towards these unsolved issues, and whether the outbreak has modified the clinical practice in managing the treatment with ICIs in oncology. doi = 10.1111/eci.13315 id = cord-337595-0p5f5o5v author = Tagliamento, Marco title = Call for ensuring cancer care continuity during COVID-19 pandemic date = 2020-05-07 keywords = SARS summary = On 11 March 2020, WHO declared the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to be a pandemic, and the related syndrome was then named coronavirus disease 2019 (COVID-19). At a median follow-up of 15 days since the confirmed diagnosis of SARS-CoV-2 infection, the case fatality rate was 24%: four patients out of 17 died due to severe COVID-19, two of whom were on oncological follow-up (ie, off therapy). Widespread testing for SARS-CoV-2 among patients with cancer and their healthcare providers could also help to control the potential negative consequences of this outbreak on cancer care. With the current uncertainty, the important aim behind this decision is to ensure continuity of care to those selected patients who can reasonably receive oncological treatments in spite of SARS-CoV-2 positivity, balancing the risks associated with the infection and the disruption of proper antineoplastic strategies. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan doi = 10.1136/esmoopen-2020-000783 id = cord-302414-g5onwhg1 author = Tahir ul Qamar, Muhammad title = Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2 date = 2020-09-16 keywords = MESV; SARS; epitope; protein; table summary = Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast Band Tcell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. The purpose of this study was to pinpoint the potential T-cell and B-cell epitopes from SARS-CoV-2 structural proteins which can be further joined through adjuvant and linkers to design a multiepitope-based subunit vaccine (MESV). Here, we explored the development of epitope-based vaccines targeting the structural proteins (S, M, and E) of the SARS-CoV-2. Taken together, we characterized SARS-CoV-2 structural proteins (S, E, and M) for antigenic epitopes and proposed a potential MESV utilizing various immunoinformatics and computational approaches. doi = 10.1186/s40249-020-00752-w id = cord-273614-qmp2tqtb author = Tahir, Faryal title = Cardiac Manifestations of Coronavirus Disease 2019 (COVID-19): A Comprehensive Review date = 2020-05-08 keywords = AMI; COVID-19; SARS; patient summary = However, multiple studies that highlight the clinical features, laboratory findings, and prognosis of acute myocardial injury (AMI) in COVID-19-affected individuals have been published. The study concluded that severe respiratory illness with 2019n-CoV infection with deteriorating complications was associated with ICU admission and a higher mortality rate [24] . This study concluded that patients with very severe COVID-19 have a higher percentage of increased cTnI levels and their mortality rate can be improved by protecting them from myocardial injury [40] . The study concluded that cardiac injury is a prevalent condition among hospitalized patients with COVID-19 in Wuhan, China, and it is associated with a higher risk of in-hospital mortality [41] . Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study (Epub ahead of print) Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China (Epub ahead of print) doi = 10.7759/cureus.8021 id = cord-280050-fktc778q author = Tahir, Shumaila title = Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan date = 2020-06-17 keywords = COVID-19; Pakistan; SARS summary = Methods We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. The primary aim of this retrospective observational study was to report the epidemiological features and statistics of individuals infected with COVID-19 from February 26 to April 24 from East Karachi, Pakistan, and contribute towards an accurate collection of figures from the country. The suspected or confirmed cases were clinically classified as asymptomatic, mild, moderate, severe, and critical, according to the National Institute of Health, Pakistan guidelines and are defined below in Table 1 [9]. Candidates with fever, symptoms of lower respiratory illness, and a travel history to Wuhan, China or other countries with uncontrolled COVID-19 cases or who have been in contact with an individual suspected of COVID-19 or with laboratory-confirmed COVID-19 in the preceding 14 days should be isolated and tested for the infection promptly [19] . doi = 10.7759/cureus.8679 id = cord-335118-oa9jfots author = Taka, E. title = Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date = 2020-09-21 keywords = ACE2; RBD; SARS summary = By performing all-atom Molecular Dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Initial studies have constructed a homology model of SARS-CoV-2 RBD in complex with ACE2, based on the SARS-CoV crystal structure (8, 14) and performed conventional MD (cMD) simulations totaling 10 ns (15, 16) and 100 ns (17, 18) in length to estimate binding free energies (15, 16) and interaction scores (18) . In this study, we performed a comprehensive set of all-atom MD simulations totaling 16.5 µs in length using the recently-solved structure of the RBD of the SARS-CoV-2 S protein in complex with the PD of ACE2 (7) . In 20 SMD simulations (each 15 ns, totaling 300 ns in length, table S1), the average work applied to unbind RBD from PD was 71.1 ± 12.7 kcal/mol (mean ± s.d.), demonstrating that the S protein binds stably to ACE2 (Fig. 3B) . doi = 10.1101/2020.09.21.305490 id = cord-312414-g5px0b65 author = Takagi, Akira title = An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date = 2020-09-19 keywords = CD8; SARS summary = As shown in Fig. 2 , the intracellular cytokine staining (ICS) assay showed that 173 significant numbers of IFN--producing CD8+ T cells were elicited in mice immunized 174 with 18 liposomal peptides including pp1a-38, -52, -84, -103, -445, -597, -641, -1675, 175 -2785, -2884, -3083, -3403, -3467, -3583, -3662, -3710, -3732, and -3886, revealing that 176 these 18 peptides are HLA-A*02:01-restricted CTL epitopes derived from SARS-CoV-2 177 pp1a. However, any of 18 185 epitopes are not found in the amino acid sequence of either MERS-CoV or the four 186 common cold human coronaviruses involving HCoV-OC43, In the 18 positive peptides, 10 peptides including pp1a-38, -84, -641, -1675, -2884, 189 -3467, -3583, -3662, -3710, and -3732 were selected for the following analyses because 190 of the high ratios of IFN- + cells in CD8 + T cells (Fig. 2) . At first glance, the graphs of CD107a ( Taken together, 10 peptides differed significantly in their ability to induce 226 SARS-CoV-2 pp1a-specific CTLs when mice were immunized with the mixture of 10 227 peptides in liposomes. doi = 10.1101/2020.09.18.304493 id = cord-339670-lq46nj8j author = Takahashi, Nozomi title = Clinical course of a critically ill patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-06-16 keywords = ICU; SARS summary = Although several studies have reported on the clinical and epidemiological characteristics of the patient with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinical course of the most severe cases requiring treatment in ICU have been insufficiently reported. A 73-year-old man traveling on a cruise ship with history of hypertension and dyslipidemia developed high fever, dyspnea and cough after 7 days of steroid treatment for sudden sensorineural hearing loss, and tested positive for SARS-CoV-2 in sputa polymerase chain reaction (PCR) examination. The sustained excessive inflammatory cytokines in the present case might have led to the exacerbation of the disease, requiring vigorous organ support therapies to allow for survival and recovery from the rapid progression of multiple organ dysfunctions and severe respiratory failure. (SARS-CoV-2), who developed multiple organ dysfunctions, treated with artificial organ supports including mechanical ventilation, extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT). doi = 10.1007/s10047-020-01183-y id = cord-315849-e16lln3f author = Takayama, Kazuo title = In vitro and Animal Models for SARS-CoV-2 research date = 2020-05-30 keywords = COVID-19; SARS summary = An in vitro cell model for SARS-CoV-2 research is essential for understanding the viral life cycle, for amplifying and isolating the virus for further research and for preclinical evaluation of therapeutic molecules. This section lays out the cell lines used to replicate and isolate SARS-CoV-2, as well as organoids that can be used to examine the effects of SARS-CoV-2 infection on specific human tissues (Table 1A, Figure 1 ). They showed that their organoids were permissive to the SARS-CoV-2 infection and could evaluate anti-viral effects of COVID-19 candidate therapeutic compounds including camostat [17] . who conducted SARS-CoV-2 infection experiments using HeLa cells that expressed ACE2 proteins taken from multiple animal species from mice to humans [11] . The team found that such mice after SARS-CoV-2 infection, showed weight loss, virus replication in the lungs, and interstitial pneumonia [25] . Human ACE2 transgenic mice After SARS-CoV-2 infection, the mice show weight loss, virus replication in the lungs, and interstitial pneumonia. doi = 10.1016/j.tips.2020.05.005 id = cord-352557-l7sahv5t author = Takla, Michael title = Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety date = 2020-11-13 keywords = COVID-19; HCQ; SARS; patient summary = In contrast, only 58% of observational studies employing an endpoint specific to efficacy recorded no significant difference in the attainment of outcomes, such as duration of hospital stay, need for mechanical ventilation, and probability of transfer to an intensive care unit (ICU), between COVID-19 patients given a range of CQ and/or HCQ doses, and the control groups. Indeed, of the remaining papers, 60% found evidence of a higher probability of discharge rate (Sbidian et al., 2020) , viral clearance and shorter symptom duration (Huang et al., 2020a) in a therapeutic context, and a lower incidence of SARS-CoV-2 infection in a prophylactic context (Bhattacharya et al., 2020 Although 60% of clinical trials found evidence of higher mild adverse drug-related events in the treatment group, none of those specifically focusing on cardiac-side effects discovered any significant difference relative to the control. doi = 10.1016/j.jsps.2020.11.003 id = cord-333092-78vo7i6v author = Taksande, Amar title = Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age date = 2020-08-11 keywords = SARS summary = title: Myocardial dysfunction in SARS-CoV-2 infection in infants under 1 year of age The authors studied the SARS-CoV-2 infection in infants under 1 year of age in Wuhan City, China. [2] reported that the prevalence of malnutrition in elderly patients with coronavirus disease 2019 (COVID-19) was high, and nutritional support should be strengthened during treatment. Have the authors used any cardiac biomarkers, such as troponin-T or echocardiography (tissue Doppler imaging), to assess myocardial function in the infants? The authors found that 61.11% of infants have bilateral pneumonia and that 41.67% have received antibiotics treatment. This means that procalcitonin is a better indicator of inflammation than CRP in infants with SARS-CoV-2 infection. To my knowledge, this is the best study of the SARS-CoV-2 infection in infants under 1 year of age carried out by the author. SARS-CoV-2 infection in infants under 1 year of age in Wuhan City doi = 10.1007/s12519-020-00384-y id = cord-316432-xemz7zn9 author = Talaie, Haleh title = Is there any potential management against COVID-19? A systematic review and meta-analysis date = 2020-08-18 keywords = COVID-19; SARS; clinical; patient summary = METHODS: Pubmed, Embase, Scopus, Cochrane, and Scholar databases were searched from inception to July 1, 2020, to identify studies reporting the current treatment process and medications (e.g. hydroxychloroquine, antiviral therapy, convalescent plasma, and immunomodulatory agents) for COVID-19. Zhong et al., provided a systematic review and meta-analysis including the therapies for severe acute respiratory syndrome (SARS), Middle Eastern respiratory syndrome (MERS) mainly besides COVID-19 and assessed their safety and efficacy profiles [31] . All types of studies i.e. randomized controlled trials (RCTs), prospective or retrospective cohort studies, and the case series that investigated clinical outcomes and/or viral clearance among adult patients were included to conduct this study. In agreement with previous researches, our meta-analysis results showed that the administration of immunomodulatory agents (especially tocilizumab and anakinra) significantly decreased the mortality rate and ameliorate clinical symptoms in patients with COVID-19 [113, 114] . Virological and clinical cure in COVID-19 patients treated with hydroxychloroquine: a systematic review and meta-analysis doi = 10.1007/s40199-020-00367-4 id = cord-267511-tb69dwg8 author = Talebian, Sepehr title = Why Go NANO on COVID-19 Pandemic? date = 2020-09-02 keywords = COVID-19; SARS summary = This will be essential to find viral particles in an efficient way and target them for destruction by developing NANOvaccines involved in host cell protection and immune and immunity response and/or anti-viral NANOagents, involved in inhibiting viral attachment, cell entry, and systemic infection (Figure 1 ). 6 Hence, one could imagine the realization of an oral multi-modal NANOvaccine for targeted delivery of a synthetic mRNA of the virus to the respiratory tract, with the purpose of enhancing the immunostimulatory activity of the vaccine, by simply including antibodies or small molecules that could target the interaction sites between ACE2 and SARS-CoV. Considering that viruses could be phylogenetically unrelated and structurally different, and given that most vaccines are virus specific, a promising approach would be that of developing broad-spectrum anti-viral NANOparticles to fight COVID-19 and future pandemics. Potential Therapeutic Approaches by which NANOtechnology Can Contribute against COVID-19 doi = 10.1016/j.matt.2020.08.005 id = cord-296232-6zj99nuw author = Talukdar, Jayanta title = Potential of natural astaxanthin in alleviating the risk of cytokine storm in COVID-19 date = 2020-10-16 keywords = ASX; COVID-19; IL-6; PPAR; SARS summary = We present reports where ASX is shown to prevent against oxidative damage and attenuate exacerbation of the inflammatory responses by regulating signaling pathways like NF-ĸB, NLRP3 and JAK/STAT. Studies including human trials have shown that ASX effectively regulates immunity and disease etiology, suggesting its wide array of potential therapeutic and nutritional support in prevention and treatment of various pathogenic diseases and metabolic disorders, all of which have elements of oxidative stress and/or inflammation in the pathogenesis [8, 10, 17] . [9] found that the administration of ASX provides both preventive and curative anti-inflammatory effects against LPS-induced inflammation in the human gingival keratinocyte line NDUSD-1 by suppressing the production of IL-6 via inhibiting activation of the NF-ĸB signaling pathway. Evidence from these studies suggest that ASX is a potent antioxidant and a natural anti-inflammatory compound having efficient immunomodulatory action that exerts potential therapeutic benefits against oxidative and inflammation induced tissue damage. doi = 10.1016/j.biopha.2020.110886 id = cord-322980-rembksdr author = Talwar, Shivangi title = Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020 date = 2020-10-22 keywords = Ayurveda; COVID-19; SARS; coronavirus; treatment summary = The severe acute respiratory syndrome coronavirus (SARS-CoV-2019) emerged in 2019 in the month of December in Wuhan city of China, which again made the life of humans miserable with numerous fatal health issues and slowly and gradually this virus entrapped the whole world [2, 3] . Before the doctors, scientists, and researchers could study and come up with a cure for treatment, this virus had already infected more than lakhs of people across the world with the human coronavirus pathogens, i.e., HCoV-22E and HCoV-OC43, which affects the upper respiratory tract. Because of broad reach, presently, remdesivir and its in vitro studies against coronavirus help in treating SARS-CoV-2 with EC50 and EC90 estimations of 0.77 μM and 1.76 μM, respectively, and are proved to be a fruitful expected treatment for COVID-19 [ doi = 10.1007/s40495-020-00245-2 id = cord-294718-n3gx862b author = Tam, Patrick C K title = Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date = 2020-05-30 keywords = RNA; SARS summary = title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. doi = 10.1093/cid/ciaa673 id = cord-281571-vob1bu9c author = Tam, Theresa W.S title = The Canadian Pandemic Influenza Plan: an evolution to the approach for national communicable disease emergencies date = 2004-06-30 keywords = SARS; health summary = The general concepts incorporated into the CPIP may be utilised in the contingency planning for a bioterrorism event or other communicable disease emergencies, including: a national, coordinated approach in planning; an emergency management structure to conduct the response; the use of common terminology to facilitate communication and response coordination, and the establishment of specific technical, communications and operational response groups and networks in advance. After the Hong Kong influenza A/H5N1 incident in 1997, the pandemic plan evolved to include a more comprehensive approach, incorporating the following key components: surveillance, vaccine programs, and use of antivirals, health services, emergency services, public health measures and communications. The general concepts incorporated into the CPIP that may be utilised in the contingency planning for other infectious disease emergencies include: a national, coordinated approach to planning; an emergency management structure to coordinate and conduct the response; the need for common terminology (e.g. using the same response phases), and the need to have specific technical, communications and operational response groups and networks formed in advance. doi = 10.1016/j.ics.2004.01.036 id = cord-350328-wu1ygt6w author = Tambyah, P. A. title = SARS: responding to an unknown virus date = 2004-07-14 keywords = Hong; SARS; Singapore summary = The severe acute respiratory syndrome (SARS) is an emerging infection caused by a novel coronavirus which first appeared in southern China at the end of 2002. The severe acute respiratory syndrome (SARS) is a newly recognized coronavirus infection that emerged in southern China [1] with subsequent global spread to 29 countries [2] [3] [4] [5] . The newly infected individuals traveled onward to their homes or next destinations in the USA, Canada, Singapore, Hong Kong and Ireland sparking off epidemics of varying degrees of severity in each of those countries, mainly in hospitals but also in their respective communities. A directive had gone out from the Hong Kong Department of Health on 21 February 2003 to maintain strict infection control with droplet precautions for all cases of "atypical" community-acquired pneumonia because of concerns that highly pathogenic avian influenza might be easily transmissible from person to person. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.1007/s10096-004-1175-8 id = cord-264924-ds6jv5ek author = Tambyah, Paul A title = Severe acute respiratory syndrome from the trenches, at a Singapore university hospital date = 2004-11-30 keywords = SARS; Singapore; TTSH; patient summary = Summary The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The epidemiology and virology of severe acute respiratory syndrome (SARS) have been written about many times and several guidelines on the infection control and public health measures believed necessary to control the spread of the virus have been published. The severe acute respiratory syndrome (SARS) coronavirus is a novel pathogen that emerged in southern China at the end of 2002 and because of a single event in a hotel in Hong Kong one night in February 2003, spread to three continents. Mild illness associated with severe acute respiratory syndrome coronavirus infection: lessons from a prospective seroepidemiologic study of health-care workers in a teaching hospital in Singapore doi = 10.1016/s1473-3099(04)01175-2 id = cord-351283-1y9dfobn author = Tan, Bai‐Hong title = The possible impairment of respiratory‐related neural loops may be associated with the silent pneumonia induced by SARS‐CoV‐2 date = 2020-06-11 keywords = SARS summary = As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID‐19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit stay for those requiring invasive mechanical ventilation. In view of the findings for H5N1 influenza virus, the silence of pneumonia induced by SARS-CoV-2 may be due to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. As compared to many other viral pulmonary infections, there existed several peculiar manifestations in the COVID-19 patients, including the "silence" of pneumonia in both mild and severe cases and a long intensive care unit (ICU) stay for those requiring invasive mechanical ventilation. Therefore, we propose that the peculiar manifestations in COVID-19 patients may be attributed to the possible impairment of peripheral chemosensitive reflexes as well as the damage to the respiratory-related central neurons. doi = 10.1002/jmv.26158 id = cord-269939-8nvrt5y7 author = Tan, Boon Fei title = Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore date = 2020-04-23 keywords = SARS; Singapore summary = title: Personal View: Managing The Covid-19 Pandemic As A National Radiation Oncology Centre In Singapore Abstract COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. On 23 January 2020, Singapore reported its first imported case of the novel coronavirus infection, officially named COVID-19, [AQ1]which was later declared a global pandemic by the World Health Organization (WHO) [1] . The division serves about 61% of the country''s population who require radiotherapy, treating about 280-300 patients per day, including inpatients from SGH and other hospitals within the healthcare cluster. Should any patient who is quarantined for 14 days due to close contact with confirmed COVID-19 cases or those with a Stay Home Notice (SHN) due to recent entry from abroad as of 20 March 2020 require radiotherapy, it will be conducted in a highly controlled manner with close collaboration with the Ministry of Health. doi = 10.1016/j.clon.2020.04.006 id = cord-309934-kcyao9i9 author = Tan, Emily L.C. title = Inhibition of SARS Coronavirus Infection In Vitro with Clinically Approved Antiviral Drugs date = 2004-04-17 keywords = CPE; SARS; Vero summary = Here we report that certain interferon subtypes exhibit in vitro inhibitory activity against SARS-CoV and are candidates for follow-up studies in animal models and patients to determine their efficacy in vivo. A collection of 19 antiviral drugs was tested in the SARS-CoV CPE inhibition assay ( Table 2) . Because the criteria for ascertaining anti-SARS-CoV activity in this screen were set at 100% inhibition of CPE, and as high doses of interferons may result in severe clinical side effects, we chose to conduct further evaluations only in the interferons that showed complete inhibition from initial screen, namely, Wellferon, Multiferon, Betaferon, and Alferon. Betaferon, Alferon, Multiferon, Wellferon, and ribavirin inhibited CPE in SARS-CoV-infected Vero E6 cells, in decreasing order of potency. Ribavirin, a drug widely used in initial efforts to manage SARS infections, inhibited CPE completely at 500-5,000 µg/mL at virus loads of 100-10,000 PFU per well. doi = 10.3201/eid1004.030458 id = cord-346335-el45v0a5 author = Tan, H.S. title = Fourier spectral density of the coronavirus genome date = 2020-08-11 keywords = SARS; Spike; genome summary = We uncover an interesting, new scaling law for the coronavirus genome: the complexity of the genome scales linearly with the power-law exponent that characterizes the enveloping curve of the low-frequency domain of the spectral density. An example of a seminal paper in this subject is that of Voss in [2] where the author found that the spectral density of the genome of many different species follows a power law of the form 1/k β in the low-frequency domain, with the exponent β potentially related to the organism''s evolutionary category. We develop a few models to characterize the typical spectrum, and in the process stumble upon a linear scaling law between a measure of the complexity of each genome and the power-law exponent that describes the enveloping curve of the low-frequency domain. doi = 10.1101/2020.06.30.180034 id = cord-268718-tt07cwrf author = Tan, Heng Wee title = Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date = 2020-06-30 keywords = ACE2; COVID-19; CoV-2; RNA; SARS summary = 54 Virus infectivity study has indicated that the SARS-CoV-2 is able to utilize ACE2 of human, Chinese horseshoe bats, civet, and pig but was not able to use mouse ACE2. The roles of ACE2 expression in SARS-CoV-2 pathogenesis and human COVID-19 susceptibility are largely unknown. B, ACE2 expression in lung cancer patients with different smoking histories analyzed using similar methods as described previously 106 other symptoms in addition to respiratory symptoms, suggesting that SARS-CoV-2 could perhaps infect other organs (Figure 3 ). 118 In addition to sputum, SARS-CoV-2 RNA has been detected in the stools of a COVID-19 patient, 119 F I G U R E 3 Tissue distribution of angiotensin-converting enzyme 2 (ACE2) expression and potential COVID-19 susceptibility. Expression of elevated levels of proinflammatory cytokines in SARS-CoV-infected ACE2 + cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS doi = 10.1002/rmv.2122 id = cord-311383-1aqt65cc author = Tan, Jinzhi title = The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes date = 2009-05-15 keywords = ADP; Nsp3; SARS; SUD summary = However, within the large Nsp3 (1922 amino-acid residues), the structure and function of the so-called SARS-unique domain (SUD) have remained elusive. The SARS-CoV genome is devoid of G-stretches longer than 5–6 nucleotides, but more extended G-stretches are found in the 3′-nontranslated regions of mRNAs coding for certain host-cell proteins involved in apoptosis or signal transduction, and have been shown to bind to SUD in vitro. In this communication, we describe the crystal structures at 2.2 Å and 2.8 Å resolution (monoclinic and triclinic form, respectively) of the core of the SARS-unique domain (SUD core , Nsp3 residues 389-652). One potential binding site for G-quadruplexes might be in a cleft between two consecutive SUD core dimers as they occur in both the monoclinic and triclinic crystal forms ( Figure S2B ), but for confirmation, any of these models will have to await crystallographic determination of the complex. doi = 10.1371/journal.ppat.1000428 id = cord-275888-6u1o6414 author = Tan, Kian Teo title = N95 acne date = 2004-06-29 keywords = SARS; porokeratosis summary = 1 The giant porokeratosis lesion on the left hand of our patient was totally excised and grafted. A diagnosis of sarcoidosis involving the central nervous system, lacrimal gland, nasal septum, vocal cord, lung and scalp was made, and the patient was treated with 20 mg of methylprednisone on alternate days with intralesional triamcinolone injection for skin lesions. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. Both were healthcare assistants working in the Singapore General Hospital throughout the severe acute respiratory syndrome (SARS) crisis, had worn N95 masks continuously for about 3 months whilst on the wards, and had suffered an outbreak of acne of the skin occluded by the mask. doi = 10.1111/j.1365-4632.2004.02338.x id = cord-301079-n1nytr6k author = Tan, Li title = Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date = 2020-07-27 keywords = HCP; SARS; patient summary = Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. doi = 10.1016/j.ijid.2020.07.027 id = cord-267971-xgwmda8e author = Tan, Shing Cheng title = Clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) patients date = 2020-04-07 keywords = SARS; covid-19 summary = Background: Numerous groups have reported the clinical and epidemiological characteristics of Coronavirus Disease 2019 (COVID-19) cases; however, the data remained inconsistent. Understanding the clinical and 46 epidemiological characteristics of the disease is important for informing public health decision 47 making, which would enable improvement of surveillance and effective planning of treatment. (4) found that the male-to-female ratio among the 81 patients included 56 was close to 1:1, indicating that both genders were equally susceptible to 57 the World Health Organization (WHO) has declared COVID-19 a global pandemic and the 58 contagion shows no sign of slowing down (13). In this 60 study, a systematic review and pooled analysis was performed to characterize the clinical and 61 epidemiological features of COVID-19 patients. In this work, a systematic review and pooled analysis was 137 performed to combine data from 69 previous reports, in order to yield a more accurate summary 138 of the clinical and epidemiological characteristics of COVID-19 patients. doi = 10.1101/2020.04.02.20050989 id = cord-023473-ofwdzu5t author = Tan, Wei‐Jiat title = Managing threats in the global era: The impact and response to SARS date = 2006-06-26 keywords = Asia; China; Kong; SARS; firm; risk summary = doi = 10.1002/tie.20107 id = cord-339303-feiy6xed author = Tan, Xiaodong title = Severe Acute Respiratory Syndrome epidemic and change of people''s health behavior in China date = 2004-10-17 keywords = SARS; acute summary = title: Severe Acute Respiratory Syndrome epidemic and change of people''s health behavior in China Severe Acute Respiratory Syndrome (SARS) has become a new worldwide epidemic whose origin was until recently unknown. This study presents an inquiry into people''s knowledge and self-reported changes in behavior in response to the epidemic. Most respondents took action to avoid being infected by SARS, including, most commonly, efforts to improve indoor ventilation, to disinfect the indoor environment and to increase hand-washing frequency. Severe Acute Respiratory Syndrome (SARS) is a new flu-like disease that made its appearance in late 2002 and spread to over 30 countries by mid-2003. The adoption of these measures, due to the initially unclear nature of SARS transmission, actually increased panic among the Chinese people who began wearing masks, reducing the chances of outdoor activities, disinfecting the environment and washing their hands. Seven questions about health behavior change in the previous 2 weeks addressed recent preventive measures generally and hand-washing specifically. doi = 10.1093/her/cyg074 id = cord-317123-0tdfvlqd author = Tan, Xiaotian title = Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date = 2020-04-21 keywords = ELISA; SARS summary = Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. In this work, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, and sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen -S protein, both of which are spiked in serum, as a model system. For the anti-S1 IgG detection experiments (see Figure S2 (B) for the detailed protocol), various concentrations of monoclonal antibodies were prepared by diluting the stock solutions with 50 times diluted human serum (the serum was diluted with 1× reagent diluent, which correlates to 1% BSA). doi = 10.1101/2020.04.20.052233 id = cord-332276-gs80celr author = Tan, Yee‐Joo title = Regulation of cell death during infection by the severe acute respiratory syndrome coronavirus and other coronaviruses date = 2007-08-20 keywords = SARS; Vero; cell summary = In two independent studies, it was demonstrated that the inhibition of apoptosis, either by caspase inhibitors or by overexpression of the Bcl-2 protein, did not affect SARS-CoV replication in Vero cells (Ren et al., 2005; Bordi et al., 2006) , suggesting that apoptosis does not play a role in facilitating viral release. The mechanisms for induction of apoptosis by these SARS-CoV proteins are unclear, although in some cases, it could be related to their abilities to interfere with cellular functions, such as blocking cell cycle progression, altering membrane permeability, activating signal transduction pathways, upregulating transcription factors and other regulatory genes (Table 1 ). (2007) The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) gene 7 products contribute to virus-induced apoptosis. Over-expression of 7a, a protein specifically encoded by the severe acute respiratory syndrome (SARS) -coronavirus, induces apoptosis via a caspase-dependent pathway doi = 10.1111/j.1462-5822.2007.01034.x id = cord-321315-bzmokdzk author = Tanacan, Atakan title = The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey date = 2020-07-30 keywords = COVID-19; SARS summary = title: The Rate of SARS-CoV-2 Positivity in Asymptomatic Pregnant Women Admitted to Hospital for Delivery: Experience of A Pandemic Center in Turkey OBJECTIVE: To investigate the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. CONCLUSION: Healthcare professionals should be cautious in the labor and delivery of high-risk pregnant women during the pandemic period and universal testing for COVID-19 may be considered in selected populations. The aim of this study is to investigate the rate of SARS-CoV-2 positivity in asymptomatic pregnant women admitted to hospital for delivery in a Turkish pandemic center. Maternal age, gravidity, parity, number of previous miscarriages, body mass index (BMI) (kg/m2), gestational age at birth, birth weight, 1st-5th minute Apgar scores, route of delivery (spontaneous vaginal deliver yor cesarean section) and SARS-CoV-2 positivity rates were compared between the healthy and high-risk pregnant women. doi = 10.1016/j.ejogrb.2020.07.051 id = cord-301811-ykpiorgo author = Tanaka, Takuma title = Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date = 2020-10-28 keywords = Hokkaido; SARS; patient summary = title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing We estimated the numbers of undiagnosed symptomatic patients and the lower bound of the number of total infected individuals per diagnosed patient before and after the declaration of the state of emergency in Hokkaido, Japan. The present analysis uses the distributions of the cluster size and patients'' time from onset to diagnosis, which are released by the health officials, to estimate the model parameters. At the same time, the nodes in the connected component containing the diagnosed node are also removed from the network, which corresponds to the contact tracing of the infected individuals (Fig 2, gray open circles) . In this paper, we have formulated a model to describe the spreading of infection and the quarantine of infected individuals, and estimated the number of undiagnosed symptomatic and asymptomatic COVID-19 patients in Hokkaido. doi = 10.1371/journal.pone.0241170 id = cord-322051-89wgv100 author = Tanasa, Ingrid Andrada title = Anosmia and ageusia associated with coronavirus infection (COVID-19) - what is known? date = 2020-05-28 keywords = CoV-2; SARS; olfactory summary = This study summarizes the existing data regarding the association of anosmia and ageusia with the SARS-CoV-2 infection. In a retrospective observational study, Klopfenstein et al (20) reported that 54 patients (47%) with confirmed SARS-CoV-2 infection developed anosmia, 4.4 (±1.9) days after infection onset, and that was the third symptom to manifest in 38% (22/52) of the cases. Some authors reported three mechanisms for anosmia in COVID-19 patients: i) local infection of support cells and vascular pericytes in the nose and olfactory bulb that may affect the function of bipolar neurons or mitral cells; ii) damage to support cells in the sensory epithelium that may indirectly influence the signaling pathway from sensory neurons to the brain; and iii) damage to sustentacular cells and Bowman''s gland cells that could lead to diffuse morphological damage to the olfactory sensory epithelium and altering of smell perception (28, 29) . Further research is needed to demonstrate the association between anosmia and ageusia with SARS-CoV-2 infection, the clinical manifestations determined by variants of ACE2 receptor, and recovery rates of olfactory and gustative dysfunction, and specific treatment protocols of these manifestations. doi = 10.3892/etm.2020.8808 id = cord-260407-jf1dnllj author = Tang, Catherine So-kum title = Factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult Chinese in Hong Kong date = 2004-06-11 keywords = Health; Model; SARS summary = This study aimed to determine factors associating with individuals'' practice of the target SARS preventive behavior (facemask wearing). Three of the five components of the Health Belief Model, namely, perceived susceptibility, cues to action, and perceived benefits, were significant predictors of facemask-wearing even after considering effects of demographic characteristics. Overall, perceived benefits, perceived barriers, and perceived susceptibility are the three most powerful components of the Health Belief Model in influencing whether individuals practice different preventive behaviors [21, 29, 30] . A logistic regression with odds ratios was conducted to test the efficacy of the Health Belief Model in predicting the wearing of facemasks to prevent SARS. Similar to previous research [15 -26] , this study found the Health Belief Model useful in identifying major determinants of the wearing of facemasks to prevent contracting and spreading SARS. The remaining two components of the Health Belief Model, perceived severity and perceived barriers, were found to be nonsignificant determinants of the target SARS preventive behavior in this study. doi = 10.1016/j.ypmed.2004.04.032 id = cord-024614-6bu3zo01 author = Tang, Daxing title = Prevention and control strategies for emergency, limited-term, and elective operations in pediatric surgery during the epidemic period of COVID-19 date = 2020-03-26 keywords = COVID-19; Health; SARS; patient summary = Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period. Based on the "Technical Guidelines for the Prevention and Control of New Coronavirus Infection in Medical Institutions (First Edition)," 17 "Diagnosis and Treatment Plan on the New Coronavirus inflicted pneumonia (Sixth trial edition, revised)" 2 (both released by the National Health Commission of China), "Recommendations for the Prevention and Control of General Surgery in the Background of New Coronavirus Outbreak," 6 and other relevant latest reports, we propose the following control measures and practical strategies for pediatric surgery practice during the COVID-19 epidemic. doi = 10.1136/wjps-2020-000122 id = cord-344967-t88pedeb author = Tang, Hon Lok title = Severe acute respiratory syndrome in haemodialysis patients: a report of two cases date = 2003-10-17 keywords = SARS; patient summary = A 49-year-old male, who had end-stage renal failure and was receiving chronic haemodialysis twice weekly, was admitted to the Princess Margaret Hospital on April 6, 2003, because of fever, chills, rigors and cough for 1 day. In view of his contact history with SARS patients, he was put on anti-viral therapy with i.v. ribavirin on day 5. Despite ribavirin treatment, the patient ran a persistently low-grade fever and a chest radiograph on day 21 revealed new shadows over the right lower zone. We report two cases of SARS occurring in end-stage renal failure patients. The diagnosis of SARS was based on his strong contact history, chest radiograph shadows and the second RT-PCR assay for coronavirus of his throat and nasal swabs on day 24. The optimal ribavirin dose for treating SARS in patients with end-stage renal failure and in those receiving haemodialysis is unknown. doi = 10.1093/ndt/gfg454 id = cord-255252-md0avnqg author = Tang, Julian W. title = Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date = 2007-07-02 keywords = GAPDH; RNA; SARS summary = SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. Post-mortem tissues were collected with great care from the major organs including heart, kidney, liver, spleen, lung, small bowel, psoas (skeletal) muscle, and bone marrow. Figures 1-6 show the results, using semi-log plots, for each organ: heart, kidney, liver, spleen, lung, and small bowel, respectively, for SARS-CoV, GAPDH and the SARS-CoV/GAPDH RNA ratio. In the organspecific viral load results, the overall picture made up from the data points from the seven different patients with different durations of SARS illness, generally, the SARS-CoV/GAPDH RNA ratio never reached above one in heart, kidney, liver, and spleen tissue for all x-axis parameters analyzed. doi = 10.1002/jmv.20873 id = cord-353099-38bz0acw author = Tang, Mei San title = Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date = 2020-07-02 keywords = SARS summary = Methods 67 specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Results The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46 respectively. Conclusion COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. The correlation of the SARS-CoV-2 neutralizing titer with the ratio reported by the 162 Roche, Abbott, and EI assays was 0.29, 0.47, and 0.46 respectively (Figure 2A-C) . Increased neutralizing antibody titers were also higher in patients that were intubated, 201 had cardiac injury, or AKI relative to those with milder COVID-19 symptoms ( Figure 202 4B-D). doi = 10.1101/2020.07.01.182220 id = cord-277278-lg38l5gh author = Tang, Olive title = Outcomes of nursing home COVID-19 patients by initial symptoms and comorbidity: Results of universal testing of 1,970 residents date = 2020-10-14 keywords = SARS; resident summary = Residents who were positive for COVID-19 and had multiple symptoms at the time of testing had the highest risk of mortality (HR 4.44; 95% CI: 2.97, 6.65) and hospitalization (SHR 2.38; 95% CI: 1.70, 3.33), even after accounting for comorbidity burden. Of 52 SARS-CoV-2 positive residents who were asymptomatic at the time of testing and were closely monitored for 14 days at one facility, only 6 (11.6%) developed symptoms. Conclusions and Implications Asymptomatic infection with SARS-CoV-2 in the nursing home setting was associated with increased risk of death suggesting a need for closer monitoring of these residents, particularly those with underlying cardiovascular and respiratory comorbidities. A 78 cohort of all residents at one facility who were asymptomatic at the time of testing were closely 79 monitored by nursing home staff for development of symptoms over a 14 day period; this was 80 documented in a dedicated line list and included as a sub-analysis. doi = 10.1016/j.jamda.2020.10.011 id = cord-338041-gl65i3s0 author = Tang, Qin title = Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition date = 2015-11-26 keywords = SARS; SVM summary = Both the support vector machine (SVM) model and the Mahalanobis distance (MD) discriminant model achieved high accuracies in leave-one-out cross-validation of training data consisting of 730 representative coronaviruses (99.86% and 98.08% respectively). Based on the data matrix of nucleotide composition, the MD and SVM were applied to predict hosts of coronaviruses. The data matrix with 19 factors as columns and 730 samples as rows was fitted to SVM and MD models, all predictions in leave-one-out cross-validations were listed in Supplementary Table S2 and summarized in Table 1 according to host species. Cross-host evolution research of SARS-CoV in palm civet and humans indicated that the variations in spike genes seemed to be essential for the transition of coronavirus from animal-to-human transmission to human-to-human transmission 25 . The MD correctly predicts bats as the natural hosts of the three viruses, and the SVM indicates that Rs3367 and SL-CoV-WIV1 are harmful to humans. doi = 10.1038/srep17155 id = cord-352768-16vgnq14 author = Tang, Qingquan title = Application of siRNA Against SARS in the Rhesus Macaque Model date = 2008 keywords = Fig; RNA; SARS; SCV summary = Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen''s genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. A pair of siRNAs showing prominent prophylactic and therapeutic activities in the cell culture study (29), referred to as siSC2 and siSC5, were further evaluated in vivo, first in mice using a reporter gene assay and subsequently using a clinically acceptable intranasal administration in the recently established rhesus macaque SARS model (23-26). doi = 10.1007/978-1-59745-191-8_11 id = cord-104081-a3fx8tyd author = Tang, Tiffany title = Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date = 2020-10-05 keywords = SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Our results demonstrate that S1/S2 pre-cleavage is essential for plasma membrane entry into Calu-3 cells, a model lung epithelial cell line, but not for endosomal entry Vero E6 cells, a model cell culture line, and that other proteases in addition to furin are responsible for processing SARS-CoV-2 S1/S2. dec-RVKR-CMK treatment had no significant impact on SARS-CoV S mediated infection of Vero E6 and Calu-3 cells (Figure 6A and 6B) , suggesting that dec-RVKR-CMK impacts on SARS-CoV-2 S is due to inhibiting the S1/S2 pre-cleavage and not due to some general effect on protein expression. Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2 Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells doi = 10.1101/2020.10.04.325522 id = cord-269275-b7xxk48t author = Tang, Xiaojia title = Neurological manifestations in COVID-19 and its possible mechanism date = 2020-09-27 keywords = COVID-19; China; CoV-2; SARS; patient summary = SARS-CoV-2 has been reported to be associated with Guillain-Barré syndrome, rhabdomyolysis, acute cerebrovascular disease, central nervous system infections and other neurological diseases. Four formal reports have described neurological problems in SARS patients, including polyneuropathy [35] , myopathy and rhabdomyolysis [36] , large artery ischemic stroke [37] and central nervous system infections [38] . In a study by Mao et al., 214 patients diagnosed with COVID-19 were enrolled, and six (2.80%) of them developed acute cerebrovascular disease (five cases of ischemic stroke and one case of cerebral hemorrhage). Strokes are not uncommon in critically ill patients with multiple comorbidities, so SARS-CoV-2 infections in humans may increase the risk of stroke. Since some COVID-19 patients have complained of headaches, nausea etc, care providers should be alert for central nervous system infections caused by SARS-CoV-2 if such patients also exhibit symptoms such as a fever, epilepsy and disturbances of consciousness. doi = 10.18632/aging.103732 id = cord-015503-j99cgsjt author = Tang, Xiaolu title = On the origin and continuing evolution of SARS-CoV-2 date = 2020-03-03 keywords = CoV-2; SARS; type summary = Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Further, the genomic sequences of SARS-CoV-2 viruses isolated from a number of patients share sequence identity higher than 99.9%, suggesting a very recent host shift into humans [1] [2] [3] . doi = 10.1093/nsr/nwaa036 id = cord-353887-f4yd7guj author = Tang, Yujun title = Cytokine Storm in COVID-19: The Current Evidence and Treatment Strategies date = 2020-07-10 keywords = COVID-19; IL-6; SARS; TNF; cell; clinical; cytokine summary = Besides, corticosteroids, programmed cell death protein (PD)-1/PD-L1 checkpoint inhibition, cytokine-adsorption devices, intravenous immunoglobulin, and antimalarial agents could be potentially useful and reliable approaches to counteract cytokine storm in COVID-19 patients. In this review, we referred COVID-19 associated cytokine storm as the patients who are severely ill along with a high concentration of pro-inflammatory cytokines. The innate and adaptive immune responses activated by SARS-CoV-2 infection lead to uncontrolled inflammatory responses and ultimately cause the cytokine storm (14) . MERS-CoV infects the cells mentioned above to induce delayed (but increased) levels of pro-inflammatory cytokines (e.g., IL-2) and chemokines (e.g., CCL2, CCL3) (27, 30) . Although SARS-CoV is abortive in macrophages and DCs, the virus induces an increase in levels of pro-inflammatory cytokines and chemokines (31, 32) . A comment and a meta-analysis, which mainly bases on the evidence of SARS and MERS (64, 65) , stated that corticosteroid would increase mortality and delayed clearance of viral in coronavirus infection diseases. doi = 10.3389/fimmu.2020.01708 id = cord-308994-4nljzm8a author = Tang, Zhongmin title = Insights from nanotechnology in COVID-19 treatment date = 2020-11-04 keywords = SARS; drug; nanomaterial summary = We focus specifically on SARS-CoV-2 and the detailed role that nanotechnology can play in addressing this pandemic, including i) using FDA-approved nanomaterials for drug/vaccine delivery, including further exploration of the inhalation pathway; ii) introducing promising nanomaterials currently in clinical trials for drug/vaccine delivery; iii) designing novel biocompatible nanomaterials to combat the virus via interfering in its life cycle; and iv) promoting the utilization of nanomaterials in pneumonia treatment. To summarize, the advantages of nanotechnology in antiviral research include the following: 1) promotes the delivery of water-insoluble drugs; [39] 2) enhances the circulation time of drugs in vivo; [40] 3) achieves co-delivery of drugs; [40] 4) improves drug utilization efficiency and reduce side effects through targeting antibody modification; [41] 5) protects DNA and mRNA vaccines, overcoming bottlenecks for in vivo applications; [42] and 6) the physicochemical properties of nanomaterials can also be employed directly against viruses. doi = 10.1016/j.nantod.2020.101019 id = cord-286466-scokdxp2 author = Tani, Hideki title = Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date = 2020-08-23 keywords = CRNT; SARS summary = The neutralization values of the serum samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative donors against the pseudotyped virus infection evaluated by the CRNT were compared with antibody titers determined from an immunofluorescence assay (IFA). The neutralization values of the serum 31 samples collected from hospitalized patients with COVID-19 or SARS-CoV-2 PCR-negative 32 donors against the pseudotyped virus infection evaluated by the CRNT were compared with 33 was designated as pCAG-SARS-CoV-2. Vero cells were treated with serially diluted sera or whole blood of convalescent patients with 145 COVID-19 or PCR-negative donors and then inoculated with Sfullpv, St19pv, or VSVpv. To 146 remove hematopoietic cells from whole blood samples, centrifugation was performed at 2,000 × g 147 for 5 min. To determine the specificity of infection of Sfullpv and St19pv, a neutralization assay of the 183 pseudotyped viruses was performed using sera of two hospitalized COVID-19 patients. doi = 10.1101/2020.08.21.262295 id = cord-352073-rdhjj72g author = Taniwaki, S.A title = Resource optimization in COVID-19 diagnosis date = 2020-06-26 keywords = SARS summary = The emergence and rapid dissemination worldwide of a novel Coronavirus (SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This manuscript reports on the optimization of the Charité and the CDC RT-qPCR protocols for SARS-CoV-2 detection regarding concentration and volumes of reagents for both probe and intercalant agent-based platforms, as well as on the substitution of rayon swabs for cotton swabs for sample collection. Performance of E and RdRp genes of SARS-CoV-2 RT-qPCRs, based on final reaction volume of 10 µL with 2 µL of RNA (Table 1) , were verified with a relative standard curve built with 10 -2 to 10 -8 dilutions of positive RNA control. Tabela 4 -Probe-based RT-qPCR to the E gene of serial dilutions of SARS-CoV-2 sampled with cotton and rayon swabs. doi = 10.1101/2020.06.25.172528 id = cord-254777-h8hw4m9f author = Tanner, Tamara title = Hyperinflammation and the utility of immunomodulatory medications in children with COVID-19 date = 2020-07-29 keywords = COVID-19; IL-6; SARS; patient summary = Cytokine storm syndromes include various entities, depending on the inciting factor: primary Hemophagocytic Lymphohistiocytosis [HLH] in children with specific genetic mutations; secondary HLH due to infection or malignancy, macrophage activation syndrome due to rheumatologic disease and cytokine release syndrome (CRS) when hyperinflammation is due to CAR T-cell therapy. Although still under investigation, ADE has been proposed as a potential mechanism underlying the newly described MIS-C, based on the observation that a majority of the patients have evidence of existing antibodies to SARS-CoV-2 and the inflammatory condition seems to lag behind the COVID-19 infection peak by approximately 4-6 weeks. The rationale for use of IL-6 blockade in serious COVID-19 infections is based on the observation that for the subset of patients with severe manifestations, IL-6 is most likely one of the drivers of the cytokine storm, and elevated levels of IL-6 have been consistently shown [14] . doi = 10.1016/j.prrv.2020.07.003 id = cord-288818-6uvb4qsk author = Tanveer, Faouzia title = Ethics, pandemic and environment; looking at the future of low middle income countries date = 2020-10-15 keywords = SARS; country; covid-19; health; pandemic summary = From the restrictions on public freedom and burgeoning socio-economic impacts to the rationing of scarce medical resources, the spread of COVID-19 is an extraordinary ethical dilemma for resource constrained nations with less developed health and research systems. International regimes are on high alert to stop its spread, however, as far as the global scenario is concerned, countries and governments are clueless in stopping the expanding pandemic as not much is known about SARS-CoV-2, while left only with implementing nationwide lock downs and curfews which opened new economic fronts and social challenges. COVID-19 has presented itself as a test case for the humanity in terms of global fraternity, decision making, technology and expertise sharing, rapid pandemic response mechanisms, stability, crises management and policy making. doi = 10.1186/s12939-020-01296-z id = cord-293059-2iwzieqm author = Tao, Huaqiang title = Dysimmunity and inflammatory storm: Watch out for bone lesions in COVID-19 infection date = 2020-10-06 keywords = SARS; covid-19 summary = It has been approved that inflammation-induced pathogenesis in COVID-19 infection has a strong correlation with incidence of cardiovascular metabolic diseases and gastrointestinal injury (1) . However, studies on the correlation between pro-inflammatory cytokine responses and bone metabolism in COVID-19 patients are still lacking. In this special background, will inflammatory disorder and immune imbalance affect bone metabolism after COVID-19 infection? Simultaneously, hypoxia inducible factor (HIF-1) was proven to facilitate osteoclast differentiation by overexpressing RANKL and nuclear factor of activated T cells cytoplasmic 1 (NFATc1) (14) . As osteoblasts and osteoclasts exist in approach with immune cells in medullary cavity, it''s no wonder that immune system shares massive regulatory cytokines, signaling molecules and transcription factors with bone biology. Apart from that, NF-κB and AP-1 stimulate the expression of many elements which required for inflammatory cytokines, driving up osteoclast activity and usually implicated inhibition on proliferation and differentiation of osteoblasts (22) . doi = 10.1016/j.mehy.2020.110332 id = cord-103662-a4ok5wqc author = Tarek, M. title = Custommune: a web tool to design personalized and population-targeted vaccine epitopes date = 2020-04-29 keywords = ACE2; Custommune; HIV-1; HLA; SARS summary = When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. doi = 10.1101/2020.04.25.20079426 id = cord-306832-w8s282nq author = Tarragón, Blanca title = FRACASO RENAL AGUDO EN PACIENTES HOSPITALIZADOS POR COVID-19 date = 2020-10-09 keywords = COVID-19; FRA; SARS summary = La mediana de estancia fue de 12 días (RIC 9-23), y el 22% fallecieron-Los pacientes que desarrollaron FRA durante el ingreso presentaron valores más altos de proteína C-reactiva, LDH o dímero D, una afectación pulmonar más grave, más necesidad de ingreso en UCI, más tratamiento con lopinavir/ritonavir y fármacos biológicos y mayor necesidad de TSR. Además, esta afectación en pacientes COVID-19 no es uniforme según lo comunicado por los hospitales chinos y puede estar condicionada por la estrategia de detección de casos de cada sistema de salud, la política de ingresos de cada hospital, la definición de daño renal e incluso los factores genéticos y ambientales de las diversas poblaciones afectadas. El FRA se ha definido como factor de peor pronóstico y mayor mortalidad en pacientes ingresados con infección por SARS-Cov-2 9,10 . doi = 10.1016/j.nefro.2020.08.005 id = cord-296031-r6iqiy1n author = Tattan-Birch, H. title = COVID-19, smoking, vaping and quitting: A representative population survey in England date = 2020-06-30 keywords = COVID-19; NRT; SARS summary = Aims: To explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home. Conclusions: In a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In this study, we will use a representative population sample of adults in England to estimate: 1) associations between suspected SARS-CoV-2 infection and smoking status, e-cigarette use and NRT use; . https://doi.org/10.1101/2020.06.29.20142661 doi: medRxiv preprint A1: Logistic regression was used to estimate the association between suspected SARS-CoV-2 infection and (i) smoking status, (ii) e-cigarette use and (iii) NRT use, with and without adjustment for potential confounders. doi = 10.1101/2020.06.29.20142661 id = cord-299999-jra1yu6a author = Tattar, R. title = COVID PDPs date = 2020-05-22 keywords = COVID-19; SARS summary = However, a structure needs to be developed to account for the disruption in training COVID-19 has caused and facilitate the progression of the trainees without compromising the quality and integrity of the respected specialities. The New England Journal of Medicine case report of the first COVID-19 patient in the USA detected high SARS-CoV-2 viral load in their stool sample. At present, PDPs are not a routine part of the undergraduate curricula 3 and as such, newly qualified dentists will be faced with the new challenge of having to proactively plan their CPD to fulfil outstanding competencies from their current training course. Whilst CPD cycles are five years, the need to complete certain key foundation skills to ensure adequate competence and baseline knowledge to facilitate progression through postgraduate training pathways will result in trainees having to meet such objectives sooner. Urgent dental care for patients during the COVID-19 pandemic Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic doi = 10.1038/s41415-020-1696-2 id = cord-262598-zk192s0x author = Tatu, Laurent title = Guillain–Barré syndrome in the COVID-19 era: another occasional cluster? date = 2020-06-23 keywords = SARS summary = entitled ''Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster?'' [1] . The authors reported an unusual cluster of seven patients affected by Guillain-Barré syndrome (GBS) in an Italian region (Friuli Venezia-Giulia), which coincided with the descending curve of the COVID-19 pandemic. In the public health crisis of March-April 2020, we encountered an unusually high number of GBS cases, admitting seven patients. Some authors report a possible correlation between acute symptomatic COVID-19 infection and GBS [4, 5] . Nevertheless, the issue raised by Gigli''s cases and those in this series is different: an abnormally high frequency of GBS amid the SARS-CoV-2 pandemic in patients without a COVID infection. Guillain-Barré syndrome in the COVID-19 era: just an occasional cluster? Guillain-Barré syndrome associated with SARS-CoV-2 infection: causality or coincidence? Guillain-Barré syndrome related to COVID-19 infection doi = 10.1007/s00415-020-10005-3 id = cord-274841-rcdoewwv author = Tay, Matthew Zirui title = The trinity of COVID-19: immunity, inflammation and intervention date = 2020-04-28 keywords = ACE2; COVID-19; CoV-2; SARS summary = Monoclonal antibodies targeting the When severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects cells expressing the surface receptors angiotensin-converting enzyme 2 (ACE2) and TMPRSS2, the active replication and release of the virus cause the host cell to undergo pyroptosis and release damageassociated molecular patterns, including ATP, nucleic acids and ASC oligomers. While there are no clinical trials specifically testing these drugs against COVID-19 at the time of writing, when camostat mesylate was tested on SARS-CoV-2 isolated from a patient, it prevented entry of the virus into lung cells 44, 50 . Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Neutralizing antibodies in patients with severe acute respiratory syndrome-associated Nature reviews | Immunology coronavirus infection doi = 10.1038/s41577-020-0311-8 id = cord-255734-038xu4hq author = Taylor, Deborah R. title = Obstacles and advances in SARS vaccine development date = 2006-02-13 keywords = SARS; respiratory; vaccine; virus summary = The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets doi = 10.1016/j.vaccine.2005.08.102 id = cord-018441-r6wwpfcy author = Taylor, Milton W. title = Emerging Viruses date = 2014-07-22 keywords = Ebola; SARS; virus summary = Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). doi = 10.1007/978-3-319-07758-1_20 id = cord-102456-6jt4ksha author = Taylor-Cousar, Jennifer L. title = How I Do It: Restarting Respiratory Clinical Research in the Era of the COVID19 Pandemic date = 2020-11-13 keywords = COVID-19; PPE; SARS; research summary = However, now that we have navigated the initial surge of SARS-CoV-2 cases, many are considering how to reintroduce non-COVID-19 clinical research conduct while protecting participants, staff and ensuring data integrity. Here we review key considerations and suggest a step-wise approach for resuming clinical research including observational research, registry trials, and interventional trials, as well as potential data confounding related to COVID-19 infections that are important to consider as research studies restart and data are analyzed. In the spirit of "Do No Harm", it is critical that institutional policies and processes are in place to ensure that there is no significant additional risk of contracting viral respiratory or other infections in the normal course of participation in research studies; now during the COVID-19 pandemic, these principles are even more critical. Throughout the subject''s participation in clinical research during the pandemic, she expressed her appreciation for the opportunity to continue in the study from which she believed she was benefiting, with minimal risk of exposure to infection from SARS-CoV-2. doi = 10.1016/j.chest.2020.11.001 id = cord-344383-7s4gnxs4 author = Tee, Augustine K.H. title = Atypical SARS in Geriatric Patient date = 2004-02-17 keywords = Hospital; SARS summary = We describe an atypical presentation of severe acute respiratory syndrome (SARS) in a geriatric patient with multiple coexisting conditions. On the basis of epidemiologic data (contact tracing linking her to one of the three original index cases in Singapore) (12) , the index patient''s cause of death was determined to be SARS (Figure 3 ). Since the issue of a global alert on atypical pneumonia by the World Health Organization on March 12, reported cases of SARS increased daily and appeared in other countries, including Canada, the United States, Europe, and Africa. Our case serves to highlight atypical signs and symptoms of SARS, especially the resolving fever, delay in establishing a positive contact history, and the nonspecific chest radiographic appearance that could be affected by concurrent coexisting conditions, such as cardiac failure. A cluster of cases of severe acute respiratory syndrome in Hong Kong Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.3201/eid1002.030322 id = cord-302813-963ypqow author = Tegally, H. title = Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown. date = 2020-10-30 keywords = Africa; SARS; South summary = Through the unprecedented sharing of SARS-CoV-2 sequences during this pandemic, including from one of the first cases in Wuhan, China (MN908947.3) 2 , genomic epidemiology investigations globally are playing a major role in characterizing and understanding this emerging virus [4] [5] [6] [7] [8] [9] . The profile of SARS-CoV-2 epidemiological progression in South Africa was largely influenced by the implementation of lockdown measures in the early phases of the epidemic and the subsequent easing of these measures. We focused on the three largest monophyletic lineage clusters (C.1, B.1.1.54, B.1.1.56,) that spread in South Africa during lockdown and then grew into large transmission clusters during the peak infections phase of the epidemic (Fig 1C) . Our analysis therefore shows that a number of SARS-CoV-2 lineages, each with unique mutations, emerged within localized epidemics during lockdown even as the introduction of new lineages from outside South Africa was being curbed. doi = 10.1101/2020.10.28.20221143 id = cord-331825-dwi350c0 author = Teherani, Mehgan F title = Burden of illness in households with SARS-CoV-2 infected children date = 2020-08-11 keywords = SARS; child summary = We investigated the dynamics of illness among household members of SARS-CoV-2 infected children that received medical care (n=32). To address this knowledge gap, we utilized a prospective registry of laboratory-confirmed pediatric COVID-19 cases and conducted contact tracing of household members to characterize the presumed transmission before and after the child''s diagnosis. We defined the suspected index case as the first person (child or adult) to report symptoms or test positive for SARS-CoV-2 in the household, documented 14 days prior to, during, or after symptoms of other family members. Because pediatric patients are more likely to be asymptomatic or show mild symptoms, it has been challenging to define their role in SARS-CoV-2 household transmission, which this study aimed to address. In our study of child-to-adult transmission cases, children were symptomatic for at least 4 days prior to seeking care, the time period when they were most likely to be infectious to other household members 5,9 . doi = 10.1093/jpids/piaa097 id = cord-016844-lq2bgu7a author = Teksam, Ozlem title = Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective date = 2013-05-29 keywords = H1N1; NIV; SARS summary = title: Noninvasive Mechanical Ventilation in Patients with High-Risk Infections and Mass Casualties in Acute Respiratory Failure: Pediatric Perspective Invasive mechanical ventilation (IMV) is a critical intervention in many cases of acute respiratory failure (ARF), but there are absolute risks associated with endotracheal intubation (ETI). Additionally, the World Health Organization''s interim guidelines on the prevention and control of acute respiratory diseases associated with health care have included NIV among the aerosol-generating procedures in which there is possibly an increased risk of respiratory pathogen transmission [ 11 ] . Nonetheless, after the most important two viral pandemics during the last decade, especially the last one with infl uenza A(H1N1), most of the societies including above-mentioned and the European Respiratory Society, European Society of Intensive Care Medicine, and The American Association for Respiratory Care have recommended that NIV not be used to treat ARF due to H1N1, particularly in severely ill patients. doi = 10.1007/978-3-7091-1496-4_29 id = cord-350352-wgppovfx author = Temmam, Sarah title = Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus date = 2020-08-29 keywords = CoV-2; SARS; cat summary = In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others (n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc.) compatible with COVID-19 infection. We investigated the presence of SARS-CoV-2 infection of domestic cats (n = 9) and dogs (n = 12) living in close contact with a cluster of French veterinary students, their owners (n = 18), whose median age was 23 years (21-28 years). Although based on a small cluster of 21 domestic pets, our cross-sectional study based on the antibody response one month after exposure to the index case points to J o u r n a l P r e -p r o o f Journal Pre-proof undetectable interspecific transmission of the SARS-CoV-2 virus between COVID-19 patients and domestic dogs or cats under natural exposure conditions. doi = 10.1016/j.onehlt.2020.100164 id = cord-269568-vwkawh6x author = Ten Hulzen, Richard D. title = Impact of Hearing Loss and Universal Face Masking in the COVID-19 Era. date = 2020-08-03 keywords = SARS; mask summary = Abbreviations: COVID-19 = coronavirus disease 2019; dB = decibel; ED = Emergency Department; FFP = filtering face piece; FM = frequency modulation; Hz = Hertz; ICU = Intensive Care Unit; N95 mask = a particulate-filtering face mask that filters at least 95% of airborne particles; PPE = personal protective equipment; PSAPs -personal sound amplification products; SARS-CoV-2 = severe acute respiratory syndrome-coronavirus-2. We''d like to call attention to the negative impacts of universal masking and social distancing in both health-care and community settings for individuals with hearing loss. Social Healthcare professionals should recognize that, with the loss of visual cues (i.e., lip reading) and support systems (e.g., family members), current COVID-19 policies such as universal masking, social distancing, and unaccompanied patients may "unmask" significant hearing loss-related issues that previously had been diminished or ignored. doi = 10.1016/j.mayocp.2020.07.027 id = cord-313082-n3bo9jw1 author = Tenenbein, Paul title = The case for routine screening for SARS-CoV-2 before surgery date = 2020-06-03 keywords = COVID-19; SARS; patient summary = Herein, we focus on one specific aspect of this question, namely whether all surgical patients should, in addition to detailed clinical screening (i.e., exposure risk and symptoms) for COVID-19, undergo routine preoperative testing for SARS-CoV-2 with nasopharyngeal swabbing and nucleicacid-based testing. Dans cet éditorial, nous nous intéressons à un aspect en particulier de cette question : faudrait-il faire passer un test préopératoire systématique pour dépister le SARS-CoV-2 à l''aide d''un écouvillon nasopharyngé et d''un test d''amplification des acides nucléiques à tous les patients chirurgicaux, en plus du dépistage clinique détaillé (c.-à-d. É tant donné le risque que la COVID-19 pose aux patients chirurgicaux, il est conseillé de remettre toute intervention qui peut être retardée en toute sécurité ou d''envisager des options thérapeutiques non chirurgicales, le cas échéant, pour tout patient positif au SARS-CoV-2. doi = 10.1007/s12630-020-01730-4 id = cord-289719-64ugdvfe author = Tenforde, Mark W. title = Characteristics of Adult Outpatients and Inpatients with COVID-19 — 11 Academic Medical Centers, United States, March–May 2020 date = 2020-07-03 keywords = COVID-19; SARS; patient summary = During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. During April 15-May 24, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had positive reverse transcription-polymerase chain reaction (RT-PCR) test results for SARS-CoV-2 in outpatient and inpatient settings at 11 U.S. academic medical centers in nine states. To explore the spectrum of illness across health care settings and potential community SARS-CoV-2 exposures after issuance of national social distancing guidelines on March 16, 2020 (4), 11 academic medical centers in nine states conducted telephone-based surveys of a sample of patients with positive SARS-COV-2 test results during April 15-May 24, 2020 (testing dates = March 31-May 10, 2020). doi = 10.15585/mmwr.mm6926e3 id = cord-290863-f0wpsaip author = Tenforde, Mark W. title = Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 date = 2020-07-31 keywords = COVID-19; SARS summary = During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. At 14-21 days from the test date, CDC personnel interviewed the randomly sampled patients or their proxies by telephone to obtain self-reported baseline demographic, socioeconomic, and underlying health information, including the presence of chronic medical conditions. doi = 10.15585/mmwr.mm6930e1 id = cord-325324-kh2aal5n author = Teng, Shaolei title = ACE2 Enhance Viral Infection or Viral Infection Aggravate the Underlying Diseases date = 2020-08-06 keywords = ACE2; COVID-19; CoV-2; SARS summary = SARS-CoV-2 spike protein (S) is cleaved by the human furin enzyme to generate S1, which binds to the host receptor, ACE-2. It is possible that the released free spike or the cleaved S1 protein in the blood might bind to cellular membrane ACE2 of heart, artery and alveolar lung cells to block the conversion of Angiotensin II to Ang-(1-7) and/or Angiotensin I to Ang-(1-9), which is consistent with a previous experimental result on SARS-CoV-1 (59) . Therefore, our hypothesis, as shown in the right side of Fig. 1 as "Viral aggravating existing diseases", is that comorbidities in COVID-19 patients are aggravated by the infection of SARS-CoV-2 to causes higher fatalities because the viral S protein interacts with ACE2 to inhibit ACE2 function. The claims that COVID-19 disproportionately affects the individuals of minority groups and aged people are not only supported by reported data but also by our hypothesis that SARS-CoV-2 infection generates spike protein that interacts with ACE2 to either exhaust ACE2 or inhibit ACE2 function or both so that the comorbidities are aggravated (Figure 1 ). doi = 10.1016/j.csbj.2020.08.002 id = cord-315760-9g8901v6 author = Teng, Xufei title = Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date = 2020-08-30 keywords = SARS summary = Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. We have further examined the compositional subtleties among the clades and clusters with 304 a focus on G+C and purine content variability as both contents appear drifting toward optima 305 in SARS-CoV-2 and its relatives ( Figure 5C and 5D). doi = 10.1101/2020.08.26.267781 id = cord-328695-nptfd6c2 author = Tengs, Torstein title = A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date = 2020-06-29 keywords = SARS summary = title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. The presence of s2m in the SARS-CoV-2 genome (GenBank accession MN908947, position 29727-29768) and other members of this group is probably the result of a single horizontal transfer event, predating the divergence of the SARS-related viruses (Tengs, et al. The insect species that contain s2m (and the associated protein) are distantly related, indicating either a deep evolutionary origin with multiple losses or that this genetic construct is also a mobile element, perhaps using viruses as a vector . doi = 10.1101/2020.06.29.177030 id = cord-264970-232stxxo author = Testa, Sophie title = Switch from oral anticoagulants to parenteral heparin in SARS-CoV-2 hospitalized patients date = 2020-04-15 keywords = DOAC; SARS summary = The development of COVID-19 syndrome in anticoagulated patients, and especially their admission to intensive-care units with acute severe respiratory syndrome (SARS-CoV-2), expose them to specific problems related to their therapy, in addition to those associated with the acute viral infection. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral heparin to avoid the risk of over/under treatment. In consideration of the pharmacological characteristics of oral anticoagulant drugs, the multiple pharmacological interactions due to the treatment of acute disease, and the possible necessity of mechanical ventilation with hospitalization in intensive-care units, we suggest replacing oral anticoagulant therapies (VKA and DOAC) with parenteral low-molecular-weight heparin (LMWH) or unfractionated heparin (UH) to avoid the risk of over/under treatment. doi = 10.1007/s11739-020-02331-1 id = cord-302075-ctd9sutv author = Tetro, Jason A. title = Is COVID-19 receiving ADE from other coronaviruses? date = 2020-02-22 keywords = SARS summary = One of the most perplexing questions regarding the current COVID-19 coronavirus epidemic is the discrepancy between the severity of cases observed in the Hubei province of China and those occurring elsewhere in the world. ADE also requires prior exposure to similar antigenic epitopes, presumably circulating in local viruses, making it a possible explanation for the observed geographic limitation of severe cases and deaths. Notably, these observations in COVID-19 patients are similar to those who suffered from severe acute respiratory syndrome (SARS) during the 2003 epidemic [4] . Based on this information and the similarity of symptoms to SARS, COVID-19 appears to constitute a major threat to human health justifying the World Health Organization''s declaration of a Public Health Emergency of International Concern. Cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis Anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a pH-and cysteine protease-independent FcgR pathway doi = 10.1016/j.micinf.2020.02.006 id = cord-336938-03366q9t author = Thacker, Vivek V title = Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date = 2020-08-10 keywords = Fig; SARS; cell summary = title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model A combination of qRT-PCR, RNAscope, immunofluorescence, and ELISA measurements are used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 delivered to the apical surface of the epithelial face maintained at an air-liquid interface. We therefore establish a human lung-on-chip model for SARS-CoV-2 infections, and probe the viral growth kinetics, cellular localization and responses to a low dose infection using qRT-PCR, ELISA, RNAscope, immunofluorescence and confocal imaging (Fig. 1J) . Nevertheless, total RNA extracted from the apical and vascular channels of an infected LoC without macrophages at 1 dpi revealed >10 4 genomes in both epithelial and endothelial cells (Fig. 2C ) and genome copy numbers exceeded those for cellular housekeeping gene RNAseP (Fig. 2D ). Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors doi = 10.1101/2020.08.10.243220 id = cord-322503-fynprt6f author = Thakur, Aarzoo title = Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date = 2020-08-07 keywords = HIV; SARS summary = Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. To address this possibility, we utilized physiologically-based pharmacokinetic (PBPK) modeling to simulate the unbound lung concentration of lopinavir achieved by 400/100 mg twice daily dose of lopinavir/ritonavir in both Caucasians and Chinese populations. 14, 15 Therefore, we derived unbound EC 50 (EC 50,unbound ) values against SARS-CoV-2 from various literature reports and compared it against the predicted C u,lung values to determine if clinically used doses of 400/100 mg twice a day would reach efficacious lung concentrations in Caucasian and Chinese populations. The impact of protein binding on PK/PD assessments were then assessed by comparing the predicted total and unbound lung concentrations of 400/100 mg twice daily lopinavir/ritonavir with EC 50 and EC 50,unbound values of lopinavir against SARS-CoV-2 respectively. doi = 10.1002/cpt.2014 id = cord-345929-z7yfegr5 author = Thakur, Suman S. title = Proteomics and Its Application in Pandemic Diseases date = 2020-11-06 keywords = COVID-19; CoV-2; SARS summary = found that the antimalarial drug metaquine and anti-HIV antiretroviral saquinavir interact with four SARS-CoV-2 receptors, including Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S protein), interacting with human ACE2; therefore, they may be repurposed for COVID-19 treatment. Furthermore, Maffucci and Contini used an in silico approach to find drug candidates against the main proteinase and spike protein of SARS-CoV-2. suggested that the antigenic peptides generated from the S1 spike glycoprotein of SARS-CoV-2 using aminopeptidases ERAP1, ERAP2, and IRAP might be helpful in selecting better epitopes for immunogenic studies and the design of a vaccine for COVID-19. Interestingly, a computational method was used to find an allosteric site on the SARS-CoV-2 spike protein by Di Paola et al., as its detection would weaken the spike−ACE2 interaction and thereby reduce the viral infection. doi = 10.1021/acs.jproteome.0c00824 id = cord-277907-x6387i7b author = Tham, Sai Meng title = Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020 date = 2020-11-17 keywords = SARS summary = Coronavirus disease (COVID-19) and tuberculosis (TB) developed in 4 foreign workers living in dormitories in Singapore during April–May 2020. Clinical manifestations and atypical radiographic features of COVID-19 led to the diagnosis of TB through positive interferon-gamma release assay and culture results. Pleural fluid analysis revealed a lymphocytic exudative effusion with an adenosine deaminase (ADA) level of 130 U/L (reference range <40 U/L), but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 112 U/L and interleukin-6 (IL-6) level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. Pleural fluid analysis revealed a lymphocytic exudative effusion with an ADA level of 62 U/L and an IL-6 level of >1,000 pg/mL, but the fluid was negative for SARS-CoV-2 by RT-PCR. tuberculosis and SARS-CoV-2 in patients with atypical radiographic features of COVID-19. doi = 10.3201/eid2611.202752 id = cord-277496-9ss09g6h author = Thaweerat, Wajana title = Current evidence on pancreatic involvement in SARS-CoV-2 infection date = 2020-05-27 keywords = SARS summary = SARS-CoV-2, the infectious agent of COVID-19, attached to angiotensin-converting enzyme 2 (ACE2) at cell surface which act as a receptor for viral entry into host cells. 5 Chinese case series reported 9 patients with mild elevation of pancreatic enzymes less than triple of upper limit of normal which does not reach the cut-point for diagnosis and did not provide other supported evidence to fulfill the criteria of diagnosing acute pancreatitis such as characteristics of abdominal pain or imaging findings. 8 Acute pancreatitis in severe COVID-19 patients may result from direct attack of SARS-CoV-2 to pancreatic acinar cells or uncontrollable systemic inflammatory response from cytokine storm syndrome leading to multi-organ dysfunction including pancreatic injury. 14 Therefore, further autopsy of COVID-19 cases still required to provide histological evidence of SARS-CoV-2 infection in pancreatic cells. In conclusion, current evidence of pancreatic manifestation in COVID-19 patients are limited which further investigation is essential to unravel consequences of SARS-CoV-2 infection to both endocrine and exocrine function of pancreas. doi = 10.1016/j.pan.2020.05.015 id = cord-026111-pb3r74uq author = Thede, Christian title = Mögliche Therapiestrategien bei Covid-19-Erkrankungen mit chinesischen Arzneimitteln date = 2020-06-05 keywords = Dekokt; Feuchtigkeit; Hitze; SARS; Schleim; lunge; und; von summary = Abschließend werden vorläufige Behandlungsvorschläge mit chinesischen Arzneimitteln für das offenbar zentrale Dysharmoniemuster -eine Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) und der Transformation von Flüssigkeiten im Rahmen einer Akkumulation von humor ("Feuchtigkeit", shi) mit Toxischem − für die sich bei schweren Verläufen entwickelnde Pneumonie vorgestellt. Wie in den meisten anderen Rezepturen aus diesem Therapieprotokoll findet sich auch hier Ephedrae herba (Mahuang) in Kombination mit aromatischen Arzneien sowohl zur Elimination der Akkumulation von humor ("Feuchtigkeit", shi) als auch der Entfaltung des qi pulmonale (Qi des Fk "Lunge", feiqi). Obwohl das Krankheitsmuster "yidu" (Epidemisch-Toxisches) genannt wird, wird auch hier primär die Kombination von "Dekokt mit Ephedra, Prunus armeniaca, Gypsum und Glycyrrhiza" (Maxing shigan tang) mit aromatischen und diuretischen Arzneien zur Lösung der humor-Akkumulation ("Feuchtigkeit", shi) und somit der Blockade des qi pulmonale (Qi des Fk "Lunge", feiqi) eingesetzt. doi = 10.1007/s00052-020-0260-0 id = cord-034021-6h5h3zow author = Thede, Christian title = COVID-19 – Therapiemöglichkeiten mit chinesischen Arzneimitteln in der Akutphase und Rekonvaleszenz date = 2020-10-20 keywords = Medizin; SARS; der; und summary = Wenngleich diese Berichte noch mit einer gewissen Vorsicht zu betrachten sind und die Ergebnisse erster kontrollierter randomisierter Studien zum Einsatz von CAM bei COVID-19 noch ausstehen, kann der Einsatz chinesischer Medizin eine Bereicherung des zur Zeit noch sehr kargen Spektrums an Therapiemöglichkeiten bei SARS-CoV-2-Infektionen darstellen. In der vorliegenden Arbeit sollen, basierend auf dem in China entwickelten Konsens zum dominierenden Krankheitsmechanismus und der daraufhin unter der Ägide der staatlichen Gesundheitsbehörden entwickelten Therapieprotokolle [5] , Therapieoptionen für ausgewählte Krankheitsphasen einer COVID-19-Erkrankung vorgestellt werden: zum einen für die Phase der beginnenden Pneumonie, also für spätambulante bis frühstationäre Stadien, und zum anderen für mögliche Entwicklungen nach überstandener Akuterkrankung, also poststationäre Stadien mit klinischen Problemen. Dazu gehören persistierende restriktive Ventilationsstörungen oder eine Fatigue-Symptomatik, die angesichts der zunehmenden Zahl von Personen, die eine COVID-19-Erkrankung durchgemacht haben, wachsende Bedeutung erlangen und für welche die etablierte Medizin bisher keine Lösungen gefunden hat. Während coronavirusassoziierte Fatigue-Symptomatik bisAngesichts der persistierenden SARS-CoV-2-Pandemie und noch immer mangelnder Therapieoptionen werden in der vorliegenden Arbeit Therapiemöglichkeiten mit chinesischen Arzneimitteln erörtert, die sich in ersten Beobachtungsstudien als Erfolg versprechend erwiesen haben. doi = 10.1007/s42212-020-00316-x id = cord-352796-6einbent author = Theodore Coroneo, Minas title = The eye as the discrete but defensible portal of coronavirus infection date = 2020-05-21 keywords = ACE2; SARS; eye; ocular; surface summary = The virus may bind to corneal and conjunctival angiotensin converting enzyme 2 (ACE2) receptors and potentially to the lipophilic periocular skin and superficial tear film with downstream carriage into the nasopharynx and subsequent access to the lungs and gut. A combination such as hydroxychloroquine, azithromycin and zinc, all of which have previously been used topically in the eye and which work at least in part by blocking ACE2 receptors, may offer a safe, cost-effective and resource-sparing intervention. At the height of the 1918 world influenza epidemic, a landmark paper appeared, proposing transmission of acute respiratory infections via the eye and lacrimal-nasal pathway (5) (Figure 1) . Table 2 summarises the drugs that have been identified as potential treatments for coronavirus infection, their efficacy (in vitro and in vivo) and for which there is data (for that agent or a related compound) for previous topical ocular surface usage. doi = 10.1016/j.jtos.2020.05.011 id = cord-342951-nirue1x4 author = Theophanous, Christos title = Bell’s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-09-04 keywords = Bell; SARS summary = title: Bell''s palsy in a pediatric patient with hyper IgM syndrome and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) This is the first reported pediatric case of Bell''s palsy in the setting of SARS-CoV-2 infection. [5, 6] There are limited reports of an association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and Bell''s palsy in adults but this seems to be rare with only two cases reports at the time of this report. Herein, we report the first case of a pediatric patient presenting with acute onset Bell''s Palsy in the setting of SARS-CoV-2 infection. To our knowledge, this is the first report of an association between Bell''s palsy and SARS-CoV-2 in a pediatric patient. Few cases of Bell''s palsy in the setting of SARS-CoV2 infection have been reported in adults and appear to be very infrequent [9, 10] . Our patient''s history of hyper-IgM syndrome may complicate his response to a SARS-CoV-2 infection. doi = 10.1016/j.braindev.2020.08.017 id = cord-340415-6fte7krp author = Thevarajan, Irani title = Clinical presentation and management of COVID‐19 date = 2020-07-17 keywords = COVID-19; SARS; clinical; patient summary = In the face of high health care demand during the peak of a pandemic, safe management of low risk patients in the community will likely be essential to preserve hospital capacity for the more severely ill. This position is endorsed by the Australasian Society for Infectious Diseases interim guidelines for the clinical management of COVID-19 in adults, 20 guidelines for the clinical care of people with COVID-19, 19 which state that even where conditional recommendations for use of disease modifying agents are made, whenever possible these should be administered in the context of randomised trials with appropriate ethical approval. 37, 38 However, given the current lack of evidence of clinical benefit and reports of significant limitations of supply of hydroxychloroquine for patients with rheumatological conditions, in March 2020, the Pharmaceutical Society of Australia and the Australasian Society for Infectious Diseases called for immediate cessation of prescribing and dispensing of hydroxychloroquine for indications relating to COVID-19, outside use in approved clinical trials. Specific antiviral therapy in the clinical management of acute respiratory infection with SARS-CoV-2 (COVID-19). doi = 10.5694/mja2.50698 id = cord-275960-1m6poddy author = Thieme, C. J. title = The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity date = 2020-05-16 keywords = CD4; SARS summary = Analyzing a cohort of COVID-19 patients with moderate, severe, and critical disease severity, we show that overlapping peptide pools (OPP) of all three proteins can activate SARS-CoV-2-reactive T-cells with a stronger response of CD4+ compared to CD8+ T-cells. Accordingly, very recent studies identified SARS-CoV-2 S-protein reactive T cell responses in patients suffering from moderate, severe, and critical COVID-19 4, 10 . Surprisingly, and in contrast to the endemic SARS-CoV infection, we detected the highest magnitude of CD4 + and CD8 + T cells reactive to S-, M-, and N-proteins in critical COVID-19 (Fig. 3) . Polyfunctional T cells showed higher frequencies in critical COVID-19 patients compared to moderate and severe cases (Fig. 3e ,f,n,o). In line with data showing an association between polyfunctionality and the stage of phenotypic differentiation 17 , we observed higher frequencies of CD8 + T cells with effector memory (TEM)/TEMRA phenotype in critical COVID-19 patients compared to moderate and severe cases (Fig S4) . doi = 10.1101/2020.05.13.20100636 id = cord-282821-qvtvpnrr author = Thijsen, Steven title = Elevated nucleoprotein-induced interferon-γ release in COVID-19 patients detected in a SARS-CoV-2 enzyme-linked immunosorbent spot assay date = 2020-06-12 keywords = SARS summary = (2) (3) (4) The objective of the present study was to determine the functional T-cell responses to SARS-CoV-2 antigens (mosaic surface protein and nucleoprotein), by using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay, in patients with RT-PCR confirmed COVID-19 (n=27) and healthy controls (n=16). Our results show that the SARS-CoV-2-specific T-cell response measured in the ELISpot versus the dps induced by the mosaic surface protein and the nucleoprotein showed different patterns. In all but one of the 27 COVID-19 cases the T-cell response against the mosaic surface protein was absent or weak, as shown by the ELISpot results which were lower than 20 spot forming cells (SFC). In contrast, the Tcell response against the nucleoprotein measured by the ELISpot assay was elevated (10-150 SFC) in 12 of 19 patients (63%) that were sampled at ≥14 dps ( Fig. 1b) . doi = 10.1016/j.jinf.2020.06.015 id = cord-309323-yflng8m3 author = Thomas, T. title = COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status date = 2020-05-16 keywords = IL-6; SARS; covid-19; figure; patient; preprint summary = Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). The current study provides the first comprehensive targeted and untargeted metabolomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to inflammatory markers and renal function. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint described impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients (44), though they also described that progressive increases in disease severity, from mild to severe to critical, correlated with the levels of transcripts for JAK1, STAT1 and 2, interferon alpha 2, interferon alpha receptors 1 and 2, and interferon regulatory factors 1, 4, 5 and 7. . https://doi.org/10.1101/2020.05.14.20102491 doi: medRxiv preprint Serum levels of free fatty acids and acylcarnitines were significantly different when comparing COVID-19positive patients and controls. doi = 10.1101/2020.05.14.20102491 id = cord-309629-7jtnhn65 author = Thomas, Viju title = International society for gynecologic endoscopy (ISGE) guidelines and recommendations on gynecological endoscopy during the evolutionary phases of the SARS-CoV-2 pandemic date = 2020-08-26 keywords = COVID-19; ISGE; SARS; surgery summary = We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports'' closure (such as using gas filters and smoke evacuation systems). We recommend, during minimal access surgeries, to use strategies to reduce production of bioaerosols (such as minimal use of energy, experienced surgeon), to reduce leakage of smoke aerosols (for example, minimizing the number of ports used and size of incisions, as well as reducing the operating pressures) and to promote safe elimination of smoke during surgery and during the ports'' closure (such as using gas filters and smoke evacuation systems). did assess the risk of open and laparoscopic surgery to be the same provided the gas/smoke was evacuated safely and water lock filters were used or if gasless laparoscopy was performed [24] . doi = 10.1016/j.ejogrb.2020.08.039 id = cord-333487-zem2d4y6 author = Thomaz Ugliara Barone, Mark title = The Impact of COVID-19 on People with Diabetes in Brazil date = 2020-07-03 keywords = Brazil; COVID-19; SARS; diabetes summary = Methods In a convenience sampling study, data were collected from 1701 individuals, aged 18 or above; 75.54% female participants; 60.73% T1D and 30.75% T2D, between April 22nd and May 4th, using an anonymous and untraceable survey containing 20 multiple choice questions (socio-demographic; health status and habits of life during COVID-19 pandemic). Conclusions This study provides a firsthand revelation of the severity of COVID-19 on individuals with diabetes in Brazil, altering their habits, which impacted their glycemia, potentially increasing their risk of poor outcomes if infected by SARS-CoV-2. This also harmed adjustments to continue the proper follow-up and management of other diseases, including both communicable and NCDs. For these reasons, the present study aims to investigate challenges encountered by people living with diabetes in Brazil during the COVID-19 pandemic. doi = 10.1016/j.diabres.2020.108304 id = cord-048335-5fl0rk90 author = Thompson, Alison K title = Pandemic influenza preparedness: an ethical framework to guide decision-making date = 2006-12-04 keywords = SARS; decision; ethical; framework summary = The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The incorporation of ethics into pandemic planning can be helped by senior hospital administrators sponsoring its use, by having stakeholders vet the framework, and by designing or identifying decision review processes. The significance of this ethical framework is a) in the unique collaborative approach taken to its development that involved ethicists with different areas of expertise and a variety of health care stakeholders, and b) that it fills an important need in pandemic planning for an ethical framework to guide decision-making that has been unmet in most pandemic planning processes world wide. The second part of the framework identifies ten key ethical values that should inform the pandemic influenza planning process and decision-making during an outbreak. doi = 10.1186/1472-6939-7-12 id = cord-351278-nm2bq717 author = Thompson, Craig title = Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors - a pilot study of the value of serology to determine population exposure date = 2020-04-17 keywords = SARS; preprint summary = title: Neutralising antibodies to SARS coronavirus 2 in Scottish blood donors a pilot study of the value of serology to determine population exposure We performed a serological study of recent blood donors in Scotland to detect antibodies to SARS-CoV-2 as a marker of past infection. Serial follow up studies are needed to track infection and seroconversion in this and other similar populations However, these data indicate that sero-surveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic like the current SARS-CoV-2 outbreak. Since the first reports in December, 2019, infections with SARS-CoV-2 have been reported from an increasing number of countries worldwide, with particularly high incidence of diagnosed infections and associated deaths from respiratory disease initially in China but more recently in Italy, Iran, Spain, France and the USA (https://www.who.int/emergencies/diseases/novel-coronavirus-2019). doi = 10.1101/2020.04.13.20060467 id = cord-287499-zcizdc7s author = Thompson, Hayley A title = SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China date = 2020-08-24 keywords = SARS; Wuhan summary = title: SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China Highlight: We estimated SARS-CoV-2 infection prevalence in cohorts of repatriated citizens from Wuhan to be 0.44% (95% CI: 0.19%-1.03%). Although not representative of the wider population we believe these estimates are helpful in providing a conservative estimate of infection prevalence in Wuhan City, China, in the absence of large-scale population testing early in the epidemic. By focusing on flights where all passengers were tested for SARS-CoV-2 infection with real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR), regardless of symptoms, a more accurate estimate of infection prevalence can be obtained compared to relying on symptomatic surveillance testing alone. 8 The repatriation flights we considered represent a globally diverse population of foreign nationals who were residing in Wuhan City leading up to the outbreak for variable periods of time and for a variety of reasons: students, work-related travel, visiting friends and families and tourism. High prevalence of SARS-CoV-2 infection in repatriation flights to Greece from three European countries doi = 10.1093/jtm/taaa135 id = cord-303651-fkdep6cp author = Thompson, Robin N. title = Key questions for modelling COVID-19 exit strategies date = 2020-08-12 keywords = COVID-19; SARS; datum; epidemic; estimate; model; transmission summary = This leads to a roadmap for future research (figure 1) made up of three key steps: (i) improve estimation of epidemiological parameters using outbreak data from different countries; (ii) understand heterogeneities within and between populations that affect virus transmission and interventions; and (iii) focus on data needs, particularly data collection and methods for planning exit strategies in low-to-middle-income countries (LMICs) where data are often lacking. Three key steps are required: (i) improve estimates of epidemiological parameters (such as the reproduction number and herd immunity fraction) using data from different countries ( §2a-d); (ii) understand heterogeneities within and between populations that affect virus transmission and interventions ( §3a-d); and (iii) focus on data requirements for predicting the effects of individual interventions, particularly-but not exclusively-in data-limited settings such as LMICs ( §4a-c). doi = 10.1098/rspb.2020.1405 id = cord-333099-hy4nmy7l author = Thoms, Matthias title = Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 date = 2020-07-17 keywords = Fig; Nsp1; SARS summary = Here, we show that Nsp1 from SARS-CoV-2 binds to the 40S ribosomal subunit, resulting in shutdown of mRNA translation both in vitro and in cells. To elucidate the molecular interaction of SARS-CoV-2 Nsp1 with human ribosomes, we reconstituted a complex from purified, recombinant Nsp1 and purified human 40S ribosomal subunits and determined its structure by cryo-EM at an average resolution of 2.6 Å (Fig. 2, A and B , and figs. To characterize the ribosomal targets and the mode of interaction of Nsp1 in human cells, we expressed N-terminally 3xFLAG tagged Nsp1 in HEK293T cells and affinity purified associated native complexes for analysis by cryo-EM and mass spectrometry (Fig. 2E , figs. The second major population of Nsp1-bound 80S ribosomes (Fig. 2 , M and N) lacked CCDC124, but contained the cell growth regulating nucleolar protein LYAR, which has been implicated in processing of pre-rRNA and in negative regulation of antiviral innate immune responses (34, 35) . doi = 10.1126/science.abc8665 id = cord-321166-nvphu1fm author = Thomson, Emma C. title = The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity date = 2020-11-05 keywords = CoV-2; N439; RBD; RBM; SARS; d614; figure summary = We find that the N439K mutation is associated with a similar clinical spectrum of disease and slightly higher viral loads in vivo compared with isolates with the wild-type N439 residue, and that it results in immune escape from polyclonal sera from a proportion of recovered individuals and a panel of neutralizing mAbs. N439K provides a sentinel example of immune escape, indicating that RBM variants must be evaluated when considering vaccines and the therapeutic or prophylactic use of mAbs. Long term control of the pandemic will require systematic monitoring of immune escape variants and selection of strategies that address the variants circulating in targeted populations. Fitness of this variant, N439K, was demonstrated by repeated emergence by convergent evolution, spread to multiple countries and significant representation in the SARS-CoV-2 sequence databases, the fact that the N439K RBD retains a high affinity interaction with the hACE2 receptor, efficient viral replication in cultured cells, and no disease attenuation in a large cohort of infected individuals. doi = 10.1101/2020.11.04.355842 id = cord-328505-5fkpnbdb author = Thornton, Jeanine Rempe title = Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab date = 2020-06-26 keywords = SARS summary = title: Negative SARS-CoV-2 antibody testing following COVID-19 infection in Two MS patients treated with ocrelizumab We report a series of two MS patients who developed COVID-19 while on Ocrelizumab therapy and subsequently exhibited negative SARS-CoV-2 serology. The sensitivity may be diminished by inadequate timing of testing following an infection, but the most recent literature suggests that the vast majority of patients with symptomatic COVID-19 produce antibodies within the first two to three weeks after symptom onset (Long et al., 2020) . In MS, a possible concern is the impact of certain DMTs, such as CD-20 monoclonal antibodies In this article, we report serology results from the first two patients at our center to have undergone SARS-CoV-2 antibody testing after developing COVID-19 while on Ocrelizumab therapy. In this case series, we present negative results from the first two MS patients at our site who underwent SARS-CoV-2 antibody testing after developing PCR-confirmed COVID-19 while on Ocrelizumab. doi = 10.1016/j.msard.2020.102341 id = cord-331910-s474ecvk author = Thota, Sai Manohar title = Natural products as home‐based prophylactic and symptom management agents in the setting of COVID‐19 date = 2020-08-17 keywords = SARS; TGF; acute; covid-19; fibrosis; pulmonary summary = Natural products like ginger, turmeric, garlic, onion, cinnamon, lemon, neem, basil, and black pepper have been scientifically proven to have therapeutic benefits against acute respiratory tract infections including pulmonary fibrosis, diffuse alveolar damage, pneumonia, and acute respiratory distress syndrome, as well as associated septic shock, lung and kidney injury, all of which are symptoms associated with COVID‐19 infection. In this context, this review highlights the potential beneficial effects of natural products that are actively used in alternative/ traditional medicines to treat many of the acute pulmonary infections, routinely seen in COVID-19 patients. Importantly, these pre-clinical studies highlight the efficacy of garlic in mitigating pulmonary fibrosis, lung injury, and sepsis-associated organ failure, all of which are symptoms observed in patients with advanced COVID-19 infection. Taken together, preclinical and clinical studies suggest that vitamin-C could have promising therapeutic benefits in individuals with pulmonary fibrosis, pneumonia, ARDS, sepsis, acute lung injury, and multiple organ dysfunction all of which are observed in advanced COVID-19 patients. doi = 10.1002/ptr.6794 id = cord-317928-doj39520 author = Thum, Thomas title = SARS-CoV-2 receptor ACE2 expression in the human heart: cause of a post-pandemic wave of heart failure? date = 2020-05-14 keywords = ACE2; SARS summary = A number of pre-clinical studies have shown various organ systems to express the primary SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2). Potentially, the COVID-19 outbreak will also lead to an increase of long-term complications of patients with CVD such as heart failure in both patients infected with SARS-CoV-2 and those that are not infected but that were treated suboptimally during the ongoing pandemic ( Figure 1 ). In conclusion, Nicin and co-workers report here an important observation with future implications in both research and, potentially, treatment of SARS-CoV-2-infected cardiovascular patients. These novel data at least suggest that it will be important to monitor SARS-CoV-2-infected patients for cardiovascular complications and assess the impact of ARB/ACE inhibitor therapy in more detail. Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 doi = 10.1093/eurheartj/ehaa410 id = cord-300272-95o8yd7h author = Thépaut, Michel title = DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date = 2020-08-10 keywords = SARS; SIGN summary = In the context of the current COVID-19 pandemic, attention is now focused on the SARS-CoV-2 virus Zhou et al., 2020) .Coronaviruses use a homotrimeric glycosylated spike (S) protein protruding from their viral envelope to interact with cell membranes and promote fusion upon proteolytic activation. Additionally, in the case of SARS-CoV-2, a new paradigm is needed to untangle the complex clinical picture, resulting in a vast range of possible symptoms and in a spectrum of disease severity associated on one hand with active viral replication and cell infection through interaction with ACE2 along the respiratory tract, and, on the other hand, to the development of excessive immune activation, i.e. the so called "cytokine storm", that is related to additional tissue damage and potential fatal outcomes. These observations prompted us to investigate the potential interaction of C-type lectins receptors, notably DC/L-SIGN with SARS-CoV-2, through glycan recognition of the spike envelope glycoprotein, as well at their potential role in SARS-CoV-2 transmission. doi = 10.1101/2020.08.09.242917 id = cord-355395-rckzi8vz author = Tian, Dandan title = Hepatic complications of COVID‐19 and its treatment date = 2020-05-21 keywords = COVID-19; SARS; liver summary = SARS‐CoV‐2 can cause liver injury through systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia‐reperfusion injury, side effects of treatment drugs, and underlying liver disease and can attack liver cells directly via ACE2. Considering limited number of autopsy cases in patients with COVID-19 studied and the relatively low expression of ACE2 in liver, liver damage directly caused by SARS-CoV-2 infection of hepatocytes deserves further investigation. It was speculated that in addition to the virus itself causing liver injury, immune injury, systemic inflammatory response syndrome (SIRS), cytokine storms, ischemia and hypoxia reperfusion injury, and drug-induced injury may be the main mechanisms that cause secondary liver injury in patients with COVID-19 [11] [12] 14, 27 . Patients with COVID-19 have varying degrees of hypoxemia, with more than 40% requiring oxygen therapy 5 Drug hepatotoxicity( Figure 2) In China, the incidence of drug-induced liver injury is second only to viral hepatitis and fatty liver disease (including alcoholic and non-alcoholic). doi = 10.1002/jmv.26036 id = cord-297826-2nruf2g7 author = Tian, Jing-Hui title = SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date = 2020-06-30 keywords = Matrix; NVX; SARS summary = In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). Mice 171 immunized with 10 μg dose of NVX-CoV2373/Matrix-M induced antibodies that blocked 172 hACE2 receptor binding to S-protein and virus neutralizing antibodies 21-28-days after 173 a single priming dose ( Fig. 4B and 4C ). Importantly, we found the frequency 254 of IFN-γ + , TNF-α + , and IL-2 + cytokine-secreting CD4 + and CD8 + T cells was 255 significantly higher (p <0.0001) in spleens from the NVX-CoV2373/Matrix-M immunized 256 mice compared to mice immunized without adjuvant ( Fig. 6B and 6C) . Anti-S protein IgG titers were detected within 21-days of a single priming immunization 288 in animals immunized with NVX-CoV2373/Matrix-M across all the dose levels (GMT = 289 1,249-19,000). doi = 10.1101/2020.06.29.178509 id = cord-270665-z4l3lq39 author = Tian, Qing title = Endoscopic mask innovation and protective measures changes during the COVID‐19 pandemic: experience from a Chinese hepato‐biliary‐pancreatic unit date = 2020-07-23 keywords = SARS; patient summary = However, due to the distinctive epidemiological characteristics of SARS‐CoV‐2 (the virus causing COVID‐19), healthcare providers are exposed to the patient''s respiratory and gastrointestinal fluids, rendering endoscopy a high risk for transmitting a nosocomial infection. This article introduces preventive measures for endoscopic treatment enacted in our medical center during COVID‐19, including the adjustment of indications, the application of endoscope protective equipment, the design and application of endoscopic masks and splash‐proof films, and novel recommendations for bedside endoscope pre‐sterilization. During the COVID-19 pandemic, due to the distinctive epidemiological characteristics of SARS-CoV-2, endoscopy poses a high risk of nosocomial infection, since healthcare providers are exposed to the patient''s respiratory and gastrointestinal fluids 6 . 6) All medical personnel who a) have fever or respiratory symptoms, b) had contact with suspected or confirmed COVID-19 patients, c) live in or had contact with individuals residing in areas where the disease is prevalent, or d) recently returned from a high-pandemic area or country should undergo self-isolation for 14 days. doi = 10.1111/den.13799 id = cord-314574-3e6u4aza author = Tian, Xiaolong title = Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody date = 2020-02-17 keywords = RBD; SARS summary = Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3] , CR3014 [4] , CR3022 [5] , as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15] , and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)) . doi = 10.1080/22221751.2020.1729069 id = cord-267509-w7nfbnbb author = Tian, Yuan title = Review article: gastrointestinal features in COVID‐19 and the possibility of faecal transmission date = 2020-03-31 keywords = China; SARS summary = METHODS: We have reviewed gastrointestinal features of, and faecal test results in, COVID‐19 from case reports and retrospective clinical studies relating to the digestive system published since the outbreak. 7, 11, 17 Gastrointestinal symptoms were also present in critically ill children, 28 Early studies indicated that individuals infected with SARS-CoV-2 might shed and spread the virus while they were pre-symptomatic or asymptomatic. Manifestations of digestive system in hospitalized patients with novel coronavirus pneumonia in Wuhan, China: a single-center, descriptive study Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1111/apt.15731 id = cord-282635-ffq8kpij author = Tierraseca, Melody Sánchez title = MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) date = 2020-05-11 keywords = SARS summary = title: MANIFESTACIÓN GASTROINTESTINAL EXCLUSIVA COMO FORMA DE PRESENTACIÓN DE INFECCIÓN POR CORONAVIRUS (COVID-19) Como se describe en el manuscrito al que hace referencia el título, así como series publicadas desde enero de 2020, la mayoría de los niños infectados por SARS-CoV-2 presentan clínica respiratoria leve 2,3 . Aún no disponemos de suficiente información de la clínica gastrointestinal exclusiva por SARS-CoV-2 y los protocolos actuales están dirigidos al manejo de las manifestaciones respiratorias quedando muchas incógnitas sobre otras manifestaciones. Sin embargo, se ha descrito la posibilidad de su transmisión por la excreción fecal 2,3 por la detección del ARN viral en las heces de pacientes infectados, incluso varias semanas tras su negativización en muestras respiratorias. Actualización de la situación epidemiológica de la infección por SARS-CoV-2 en España. Infección por coronavirus(COVID-19) en Anales de Pediatría Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and doi = 10.1016/j.anpedi.2020.04.021 id = cord-297842-hkr1wm3k author = Tilley, Kimberly title = A Cross-Sectional Study Examining the Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in a University Student Population date = 2020-10-15 keywords = CoV-2; SARS; student summary = PURPOSE: The aim of the study was to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in a university student population. METHODS: This was a cross-sectional survey study based on the World Health Organization population-based seroepidemiological investigational protocol for SARS-CoV-2 conducted between April 29, 2020, and May 8, 2020, examining SARS-CoV-2 antibody prevalence among 790 university students in Los Angeles, CA. With the goal of having the sample distributions match distributions in the population, these strata were selected based on internal university data, indicating that females are more likely to participate in health-related research projects compared with males, and fewer undergraduates (36.4%) spent the end of the Spring 2020 semester in Los Angeles relative to graduate students (76.5%). Seroprevalence of SARS-CoV-2 antibodies in a Los Angeles university student population as of May 8, 2020, was estimated to be 4.0%. doi = 10.1016/j.jadohealth.2020.09.001 id = cord-264974-hspek930 author = Timmis, Kenneth title = The COVID‐19 pandemic: some lessons learned about crisis preparedness and management, and the need for international benchmarking to reduce deficits date = 2020-05-03 keywords = COVID-19; SARS; crisis; health; pandemic; system summary = If, despite the explicit warning of the World Health Organization in 2011 that ''The world is ill-prepared to respond to a severe influenza pandemic or to any similarly global, sustained and threatening public-health emergency'' (https://apps.who.int/gb/ebwha/pdf_files/WHA64/A64_10en.pdf), it was not apparent to those in charge, and to the general public-i.e., those suffering from COVID-19 infections and the funders of health services (tax/insurance payers)-that existing health systems had inherent vulnerabilities which could prove to be devastating when seriously stressed, the SARS-CoV-2 pandemic (e.g., see Brüssow, 2020 ) has brutally exposed it now. International benchmarking is mandatory, because it has become clear that there is a wide range of effectiveness in the ability of different countries with developed economies to respond to this crisis (and probably others), and the tax-paying public has no compelling reason to tolerate perpetuation of factors underlying poor responses to crises. doi = 10.1111/1462-2920.15029 id = cord-337430-c2vdnml7 author = Timpka, Toomas title = Sports Health During the SARS-Cov-2 Pandemic date = 2020-05-02 keywords = Cov-2; SARS; covid-19 summary = In December 2019, the Chinese city of Wuhan reported an outbreak of SARS-Cov-2 (severe acute respiratory syndrome coronavirus-2) infection that causes the Covid-19 disease, an atypical pneumonia [1] . The national public health agencies choose social distancing regulations based on an overall assessment of how critical certain activities are for society as a whole and whether motivation to comply with the rules can be assumed. During the SARS-Cov-2 pandemic, effectively all population-level interventions include the recommendation that social contacts with the elderly, and especially the senior elderly, are to be reduced to an absolute minimum. Sports organisations should develop a pandemic response strategy that addresses the needs of its athletes and coaches, while complying with the regulations and recommendations issued by the government and national public health agency. The temporary frameworks for organised sports practice and competitions must be developed based on the social distancing and quarantine protocols activated during the pandemic. doi = 10.1007/s40279-020-01288-7 id = cord-255440-ls1l2mlg author = Tindle, Courtney title = Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date = 2020-10-18 keywords = ALI; COVID-19; Fig; SARS; at2; cell summary = Besides the approaches described so far, there are a few more approaches used for modeling COVID-19-(i) 3D organoids from bronchospheres and tracheospheres have been established before (Hild and Jaffe, 2016; Rock et al., 2009; Tadokoro et al., 2016) and are now used in apical-out cultures for infection with SARS-COV-2 (Suzuki et al., 2020); (ii) the most common model used for drug screening is the air-liquid interphase (ALI model) in which pseudo-stratified primary bronchial or small airway epithelial cells are used to recreate the multilayered mucociliary epithelium (Mou et al., 2016; Randell et al., 2011) ; (iii) several groups have also generated 3D airway models from iPSCs or tissue-resident stem cells (Dye et al., 2015; Ghaedi et al., 2013; Konishi et al., 2016; McCauley et al., 2017; Miller et al., 2019; Wong et al., 2012) ; (iv) others have generated AT2 cells from iPSCs using closely overlapping protocols of sequential differentiation starting with definitive endoderm, anterior foregut endoderm, and distal alveolar expression (Chen et al., 2017; Gotoh et al., 2014; Huang et al., 2014; Jacob et al., 2017; Jacob et al., 2019; Yamamoto et al., 2017) . doi = 10.1101/2020.10.17.344002 id = cord-281561-r10y2sgb author = Tiwari, Nidhi title = Novel β-Coronavirus (SARS-CoV-2): Current and Future Aspects of Pharmacological Treatments date = 2020-08-27 keywords = COVID-19; SARS; drug; patient; treatment summary = Another invitro study reported that Ribavirin, analogue of guanosine nucleotide having wide spectrum of antiviral activity, used along with LPV/RTV to treat SARS-COV-2 viral infection in china (ChiCTR2000029387) . reported remdesivir shows possible efficacy better as compared to placebo group in hospitalized patients for the treatment of SARS-CoV-2 virus. The effectiveness and safety concern of darunavir/cobicistat combination is being evaluated under development of clinical trials phase 3 by enrolling 30 COVID-19 patients and estimated completion of study on December 31, 2020. Recently, retrospective cohort study showed high dose of anakinra (5 mg/kg, BD,iv) produces beneficial and efficacious effects in 72% Covid-19 infected patients associated with ARDS (Cavalli et al., 2020) . Based on case study of patients with SARS-CoV2 infection and also confirmed severe pneumonia and ARDS treated with i.v. infusion of eculizumab along with anticoagulant therapy (Enoxaparin 4000 IU/day s.c), antiviral therapy (LPV 800 mg/day + RTV 200 mg/day), hydroxychloroquine 400 mg/day, ceftriaxone 2 g/day IV, vitamin C 6 g/day for 4 days. doi = 10.1016/j.jsps.2020.08.015 id = cord-291987-zpkzzldu author = To, Kelvin KW title = False-positive SARS-CoV-2 serology in three children with Kawasaki disease date = 2020-07-17 keywords = SARS summary = Recent reports showed that children with KD-like disease from KD low prevalence regions had positive SARS-CoV-2 serology despite a negative SARS-CoV-2 polymerase chain reaction (PCR) in respiratory samples. To describe three paediatric Kawasaki Disease patients with false positive SARS-CoV-2 serology. We aim to describe three paediatric Kawasaki Disease patients diagnosed during the COVID-19 outbreak with false positive SARS-CoV-2 serology. Blood (5 mL) was collected from each patient and serum was obtained for the detection of IgG against SARS-CoV-2 nucleoprotein (NP) and spike protein receptor binding domain (RBD) using a microsphere-based antibody assay as described previously. Three Chinese children, who had no epidemiological links with COVID-19 patients were diagnosed with typical KD during the peak of COVID-19 outbreak in Hong Kong (Table 1) 10 11 We believe the false positive SARS-CoV-2 serology results were unrelated to the administration of IVIG for treating KD. doi = 10.1016/j.diagmicrobio.2020.115141 id = cord-254478-scc9wee0 author = To, Kelvin Kai-Wang title = Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date = 2020-03-23 keywords = SARS; load; patient; viral summary = title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. We present findings of an observational cohort study of the temporal profile of viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from posterior oropharyngeal saliva samples and serum antibody responses, dated by symptom onset and correlated with clinical findings. doi = 10.1016/s1473-3099(20)30196-1 id = cord-269973-sntnmqqd author = To, Kelvin Kai-Wang title = Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date = 2020-08-05 keywords = Kong; SARS summary = However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. doi = 10.1093/cid/ciaa1119 id = cord-295525-emrwcx0m author = To, Kelvin Kai-Wang title = Consistent Detection of 2019 Novel Coronavirus in Saliva date = 2020-02-12 keywords = SARS; saliva summary = The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. doi = 10.1093/cid/ciaa149 id = cord-325614-e9hnhzfg author = Todorov, German title = A Possible Path towards Rapid Development of Live-Attenuated SARS-CoV-2 Vaccines: Plunging into the Natural Pool date = 2020-10-14 keywords = CoV-2; SARS; attenuated summary = Our proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, which may lead to a shorter cycle of vaccine development, as well as higher vaccine effectiveness. The proposed approach is based on screening for, identifying, analyzing and selecting naturally attenuated yet highly immunogenic SARS-CoV-2 strains, potentially leading to a more rapid cycle of vaccine development, as well as higher vaccine effectiveness. If the candidate attenuated SARS-CoV-2 strain is easily transmissible, we would need to evaluate whether a live-attenuated virus that causes a very mild form of infection but is easy to transmit can be considered sufficiently safe for use as a vaccine, or whether it needs to be further attenuated in the lab, which could slow down the development of the vaccine. All in all, at present there are too many unknowns to predict how much screening of suitable individuals in high-risk subpopulations will be required to find naturally-evolved candidate strains for the development of live-attenuated vaccines. doi = 10.3390/biom10101438 id = cord-312509-m3p9fuq0 author = Tohidinia, Maryam title = Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 date = 2020-08-21 keywords = SARS; cell summary = title: Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19 The main aim of the 91 current is to use of bioinformatics tool to identify potential B-and T-cell epitope(s) of S protein with high 92 antigenicity that could be used to develop promising vaccines [20] . In 161 addition, Bcepred server at http://www.imtech.res.in/raghava/bcepred/ [32] was employed to predict linear B-162 cell epitopes in a protein sequence. Therefore, the usage of several tools to predict linear B-168 cell epitopes in protein sequences are more reliable. Ellipro at http://tools.immuneepitope.org [33] was used to 169 predict linear and discontinuous antibody epitopes based on a protein antigen''s 3D structure. The spike protein on the surface of the viral particle plays key roles in the binding of the cell receptor and 459 membrane fusion, by which the host range is firmly determined. doi = 10.1016/j.micpath.2020.104459 id = cord-252049-rgdynmla author = Tomar, Sakshi title = Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CL(pro)): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS date = 2015-06-08 keywords = 3CL; CoV; Fig; MERS; SARS; pro summary = All coronaviruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the proteolytic activity of the nsp5 protease (also known as 3C-like protease, 3CL(pro)) during virus replication, making it a high value target for the development of anti-coronavirus therapeutics. Therefore, we determined the dependence of the enzymatic activity of MERS-CoV 3CL pro on the total enzyme concentration and compared it with other 3CL pro enzymes from HKU4, HKU5, and SARS coronaviruses (Fig. 2) . The kinetic data for all four 3CL pro enzymes, MERS-CoV, HKU4-CoV, HKU5-CoV, and SARS-CoV, fit well to this model, and the resulting values for the monomer-dimer equilibrium dissociation constant, K d , and apparent turnover number, k cat , for each enzyme are provided in Table 2 . Compound 11 also forms two direct and one water-mediated hydrogen bond interactions with amino acids in the MERS-CoV 3CL pro active site (Fig. 6E) . doi = 10.1074/jbc.m115.651463 id = cord-271551-bj2db91j author = Tomczyk, Samuel title = Social Distancing and Stigma: Association Between Compliance With Behavioral Recommendations, Risk Perception, and Stigmatizing Attitudes During the COVID-19 Outbreak date = 2020-08-11 keywords = SARS; compliance summary = Latent class analysis examined patterns of compliance, and subsequent multinomial logistic regression models tested sociodemographic (age, gender, country of origin, level of education, region, and number of persons per household) and psychosocial (knowledge about preventive behaviors, risk perception, stigmatizing attitudes) predictors. However, to our knowledge, only one study applied latent class analysis to population behaviors following a novel virus outbreak [i.e., influenza A (H7N9)] in Hong Kong (Liao et al., 2015) , despite the method''s statistical advantages in modeling behavioral patterns (e.g., flexibility, integration of measurement error). Via an online survey, a community sample of 157 German adults [80% female; M (SD) age = 27.82 (11.01)] provided information about their knowledge of preventive measures, risk perception, intentions to comply with official behavioral recommendations and guidelines as well as their stigmatizing attitudes toward people suffering from COVID-19. doi = 10.3389/fpsyg.2020.01821 id = cord-008841-r17qhfsj author = Tomlinson, Brian title = SARS: experience at Prince of Wales Hospital, Hong Kong date = 2003-05-03 keywords = Hong; SARS summary = THE LANCET • Vol 361 • May 3, 2003 • www.thelancet.com COMMENTARY The Prince of Wales Hospital (PWH) has been at the forefront of the outbreak of severe acute respiratory syndrome (SARS) in Hong Kong. Three major reasons for spread of infection to health-care workers have been: failure to apply isolation precautions to cases not yet identified as SARS, breaches of procedure, and inadequate precautions. "Super-spreaders" may be prone to carry a high viral load because of defects in their COMMENTARY SARS: experience at Prince of Wales Hospital, Hong Kong immune system, as could be the case in the patient with end-stage renal failure implicated in the Amoy Gardens outbreak and another with renal failure at the centre of an outbreak in Singapore. Case definitions for surveillance of severe acute respiratory syndrome (SARS) A cluster of cases of severe acute respiratory syndrome in Hong Kong doi = 10.1016/s0140-6736(03)13218-7 id = cord-315972-5g2hnk1x author = Tong, Suxiang title = Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya date = 2009-03-17 keywords = SARS; bat summary = The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans. Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identifi ed from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species (6) (7) (8) (9) (10) (11) . To characterize the overall diversity of CoV sequences, in this study a phylogenetic tree (Figure 2 ) of the 121-bp fragment of RdRp was generated from 39 coronaviruses from bats in Kenya and 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database based on the Bayesian Monte Carlo Markov Chain method (14) . bats (location 17) were closely related to a SARS-like CoV cluster, including 1 sequence shown in Figure 2 (BtKY15) and another (BtKY16) that was 1 of the 3 low-quality sequences excluded from the tree. doi = 10.3201/eid1503.081013 id = cord-332537-rtdu4jae author = Tong, Tommy R. title = Airborne Severe Acute Respiratory Syndrome Coronavirus and Its Implications date = 2005-05-01 keywords = SARS summary = Airborne transmission of the severe acute respiratory syndrome (SARS) coronavirus (CoV) has been the favored explanation for its transmission on an aircraft [1] and appeared to explain a large community outbreak of SARS in the Amoy Gardens in Hong Kong [2] . in this issue of the Journal of Infectious Diseases [3] suggests that airborne dissemination of SARS-CoV may also occur in the health-care setting. However, if SARS-CoV is naturally airborne (produced by breathing and coughing), as was shown by Booth et al., then there is sufficient concern that it can be transmitted successfully by air. Acknowledgment of the fact that SARS-CoV can be aerosolized justifies the actions of those who have already committed resources for providing a safer environment in terms of preventing airborne transmission of infectious diseases and might provide the needed pressure for others to follow suit. Evidence of airborne transmission of the severe acute respiratory syndrome virus doi = 10.1086/429637 id = cord-294385-6dlgv3tb author = Tong, Xin title = Surveillance of SARS‐CoV‐2 infection among frontline health care workers in Wuhan during COVID‐19 outbreak date = 2020-08-20 keywords = SARS; Wuhan summary = The radiological analysis revealed that there was no typical chest CT scan of COVID‐19 among 222 HCWs. Consistently, anti‐SARS‐CoV‐2 IgM or IgG was also found to be negative among 191 HCWs. CONCLUSIONS: There was no nosocomial infection of SARS‐CoV‐2 among our cohort of the frontline HCWs, suggesting that zero occupational infection is an achievable goal with appropriate training, strict compliance, and psychological support for the frontline HCWs. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging infectious disease, first described in Wuhan, China, has rapidly spread throughout worldwide. 2 The ever-increasing number of COVID-19 cases, overwhelming workload, the depletion of personal protection equipment (PPE), physical fatigue, and psychological stress during the early outbreak has resulted in at least 22 073 cases of COVID-19 among HCWs. 3 A study from China Center for Disease Control and Prevention (CDC) showed that as of 17 February 2020, 3.8% confirmed COVID-19 cases were among HCWs. 4 A report from Italy revealed 11% of COVID-19 cases were HCWs. 5 All the evidence suggested a high risk of occupational infection of SARS-CoV-2. doi = 10.1002/iid3.340 id = cord-274536-fv7mltj7 author = Tong, Yongqing title = Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date = 2020-11-02 keywords = RNA; SARS summary = RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn''t be detected in other types of specimen in this study. Firstly, we analyzed the possible sites of infection in hospitalized patients with COVID-19 by detecting viral RNA with 12 different types of specimens, including nasopharyngeal swab, oropharyngeal swab, sputum, bronchoalveolar lavage fluid (BALF), stool, anal swab, urine, peritoneal dialysis fluid (PDF), blood, sweat, cerebrospinal fluid (CSF) and corneal secretion. The 20 discharged cases of COVID-19, the criteria [12] for which was the SARS-CoV-2 virus RNA detection negative in two consecutive respiratory specimens (at least 1 day of time interval of sampling) for patients who have reached the standards of isolation period (14 days) after clinical cured, during the isolation period were selected to detect SARS-CoV-2 RNA with multiple specimens including nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and blood. doi = 10.1186/s12967-020-02580-w id = cord-283786-d65njv7b author = Toptan, Tuna title = Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date = 2020-06-20 keywords = PCR; SARS summary = The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). The alignment of over 4300 full-length SARS-CoV2 genomes including FFM1-7 isolates revealed single nucleotide polymorphisms (SNPs) in 13 different positions for RdRP (total 0.33%) and eight positions for the M-gene (total 0.61%) within the primer/probe binding sites ( Figure S3 , Table S4 ). Therefore, we additionally compared the performance of two research kits (New England Biolabs, Ipswich, MA, USA) and one In conclusion, our M-gene-based qRT-PCR detection of SARS-CoV-2 RNA was at least as specific as the RdRP PCR recommended for confirmation by the WHO but showed a significantly higher sensitivity. doi = 10.3390/ijms21124396 id = cord-325479-2r4oomdp author = Torii, Shotaro title = Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date = 2020-10-17 keywords = MS2; RNA; SARS summary = This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. This study aims (1) to compare the combination of primary concentration (UF, EMV, and PEG) and RNA extraction (QIAamp Viral RNA Mini Kit and TRIzol) for the whole process recovery of nonenveloped and enveloped virus surrogates and (2) to test the applicability of the method providing the highest φ6 recovery to detect SARS-CoV-2 doi = 10.1016/j.scitotenv.2020.143067 id = cord-266150-wox7pnkr author = Torres, Juan Pablo title = SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date = 2020-07-10 keywords = PCR; SARS; covid-19 summary = Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. doi = 10.1093/cid/ciaa955 id = cord-356150-ivso91ln author = Torretta, Sara title = Diagnosis of SARS-CoV-2 by RT-PCR Using Different Sample Sources: Review of the Literature date = 2020-08-31 keywords = COVID-19; NPS; SARS summary = 2 Despite suboptimal detection rates, 3 collection of secretions from the upper airway by means of NPS/OPS still represents the first-line diagnostic modality to test patients and otherwise asymptomatic population for COVID-19, provided that it is early and adequately performed after onset of symptoms. 2 As a fact, reduced detection rates reflect analytical sensitivity of RT-PCR test and the epidemiologic characteristics of COVID-19, given that a false negative RT-PCR result could be possibly obtained both in the initial phase of the disease (ie, a few days before symptom onset) and at the ''''tail end'''' of SARS-CoV-2 infection (ie, from 20 days after symptom onset) due to a low viral load and a viral shedding below analytical RT-PCR sensitivity threshold. 3 On the basis of the reported detection rates, 4 the US Center for Disease Control and Prevention (US-CDC) has recommended the collection of sole upper respiratory NPS, 2 but the US Food and Drug Administration pointed out that a negative RT-PCR test result does not completely rule out SARS-CoV-2 infection and it shall not be used as a single element for patient management decisions. doi = 10.1177/0145561320953231 id = cord-270064-hidirfkv author = Tort, Fernando L. title = A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date = 2020-04-12 keywords = CAI; SARS; codon summary = In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. In order to gain insight into the emergence, evolution, adaptation and spread of the SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. To gain insight into the biology and evolution of emerging SARS-CoV-2, a comprehensive analysis of genome composition, codon and amino acid usage of βCoV strains isolated in China from humans, bats, civets and ferret hosts was performed, including SARS-CoV-2 strains recently isolated from current outbreak. The results of these studies revealed that SARS-CoV-2 strains enrolled in these analyses have a distinct genome composition in relation to other βCoV strains isolated from human (SARS-CoV), bats, civets and ferrets (see Fig. 1 ). doi = 10.1016/j.virusres.2020.197976 id = cord-260981-647wfa8z author = Torti, Lorenza title = Impact of SARS CoV-2 in Hemoglobinopathies with Immune Disfunction and Epidemiology. A Protective Mechanism from Beta Chain Hemoglobin Defects? date = 2020-07-01 keywords = SARS; patient summary = A novel coronavirus (SARS-CoV-2) has rapidly overspread infecting in few months all continents and representing a medical emergency, with 20% of patients with severe clinical manifestations. 2 The transcribed, non-structural SARS-CoV-2 proteins ORF 8, 3a, and 10 play critical roles during infection (viral replication) and disease pathogenesis (stimulate NF-kB mediated inflammation and immune responses). Of the 105 patients who were in contact with the infected staff, only 7 reported symptoms, all mild, in the two months surveillance, and only 1 of the 7 tested positive on the swab. The SARS-CoV-2 positive patient, a female aged 59 with Beta-Thalassemia Major(TM)(IVS-6/745) received a transfusion on March 5, and after being notified, called the hospital on March 21 reporting mild temperature (37 o C). So, our case of SARS-CoV-2 infection in TM patient was revealed during an endemic outbreak, which involved 24 symptomatic HCPs out of a staff of 52. Recently a multicentric Iranian experience of 18350 Beta-thalassemic patients (only fifteen confirmed cases) reported mild to moderate disease of COVID-19. doi = 10.4084/mjhid.2020.052 id = cord-256300-emsvxxs5 author = Tortorici, M. Alejandra title = Structural insights into coronavirus entry date = 2019-08-22 keywords = MERS; SARS summary = We review here our current understanding of the mechanism used by CoVs to infect host cells based on recent structural and biochemical studies of S glycoprotein ectodomains in prefusion and postfusion states as well as complexes with known receptors or neutralizing antibodies. Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al., 2017; Kirchdoerfer et al., 2018; Song et al., 2018; Walls et al., 2019; Yuan et al., 2017) . Major antigenic determinants of MHV and SARS-CoV S overlap with the fusion peptide region (Daniel et al., 1993; Zhang et al., 2004) and binding of neutralizing antibodies to this site could putatively prevent fusogenic conformational changes, as proposed for influenza virus hemagglutinin or HIV envelope (Corti et al., 2011; Kong et al., 2016; Lang et al., 2017) . doi = 10.1016/bs.aivir.2019.08.002 id = cord-321742-cstub5zz author = Tovar, Isabel title = Rationale for the Use of Radiation-Activated Mesenchymal Stromal/Stem Cells in Acute Respiratory Distress Syndrome date = 2020-09-02 keywords = ANXA1; SARS; cell; msc; stem summary = We have previously shown that the combination of radiotherapy with human umbilical-cord-derived mesenchymal stromal/stem cells (MSCs) cell therapy significantly reduces the size of the xenotumors in mice, both in the directly irradiated tumor and in the distant nonirradiated tumor or its metastasis. Knowing the role of annexin A1 in the control of hypoxia and inflammation that is characteristic of acute respiratory-distress syndrome (ARDS), we designed a hypothetical therapeutic strategy, based on the transplantation of mesenchymal stromal/stem cells stimulated with radiation, to alleviate the symptoms of patients who, due to pneumonia caused by SARS-CoV-2, require to be admitted to an intensive care unit for patients with life-threatening conditions. Supposedly a vectorized signaling system, we now believe that the exosomes released from radiation-activated-MSCs cells can reach other organs different from the lungs, where they will be up-taken after intravenous injection and thus extend the anti-inflammatory and antimicrobiological effects of the treatment, to cover systemic problems such as the treatment of patients with septic shock in general and for COVID-19 at this particular time. doi = 10.3390/cells9092015 id = cord-346445-hgqohdct author = Toyoshima, Yujiro title = SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date = 2020-07-22 keywords = HLA; SARS summary = Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. doi = 10.1038/s10038-020-0808-9 id = cord-258435-lhn34tc4 author = Tracy, C Shawn title = Public perceptions of quarantine: community-based telephone survey following an infectious disease outbreak date = 2009-12-16 keywords = SARS; Toronto; public summary = CONCLUSION: To engender strong public support for quarantine and other restrictive measures, government officials and public health policy-makers would do well to implement a comprehensive system of supports and safeguards, to educate and inform frontline public health workers, and to engage the public at large in an open dialogue on the ethical use of restrictive measures during infectious disease outbreaks. In view of the evidence of potential adverse effects on individual well-being and psychosocial health, and owing to the critical necessity of high compliance in the event of a major infectious disease outbreak, it is increasingly important to understand how quarantine is perceived by the general public. The data reported in this paper are derived from a subset of 15 survey items specifically designed to measure public attitudes towards the use of quarantine during infectious disease outbreaks. doi = 10.1186/1471-2458-9-470 id = cord-266450-g9vihgbk author = Tran, Michael title = SARS-CoV-2 and pulmonary embolism: who stole the platelets? date = 2020-09-03 keywords = SARS; patient summary = Careful attention to his daily platelet count suggested the possibility of immune mediated heparin-induced thrombocytopenia (HIT) which was confirmed by laboratory testing and resolved when anticoagulation was switched to a direct thrombin inhibitor. CONCLUSIONS: Since excessive platelet activation and in situ thrombosis occur in HIT, this case underscores the need to consider that thrombocytopenia in patients with SARS-CoV-2—most of whom receive heparinoids—may be unrecognized HIT. Emerging reports suggest the possibility of HIT developing in SARS-CoV-2 patients receiving heparin anticoagulation [4, 5] . The patient''s platelet count decreased from 487 k/uL to a nadir of 91 k/uL over the following 4 days, raising the concern for heparin induced thrombocytopenia (HIT) with an intermediate pretest probability by the 4Ts score of 4 ( Table 1 ). Platelet count and time points for anticoagulation administration and laboratory testing COVID-19 patients receiving heparin-involved treatment. doi = 10.1186/s12959-020-00229-8 id = cord-329971-09ubsq2k author = Tranoulis, Anastasios title = Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic date = 2020-06-30 keywords = SARS summary = title: Challenges and management options of tubo-ovarian cancer during the SARS-CoV-2 pandemic To date, there is no clear evidence concerning the impact of SARS-CoV-2 on tubo-ovarian cancer care. Generally, cancer patients are seemingly at increased risk of SARS-CoV-2 infection owing to the underlying immunosuppression. According to the cases treated using the ''do no harm'' principle, we believe that the following situations should be considered for surgery: (1) To conclude, the effects of SARS-CoV-2 pandemic can be mitigated to a certain degree for patients with ovarian cancer, by adopting a careful and individualised triage and treatment management. A rigorous counseling concerning the risk of undergoing surgery during SARS-CoV-2 pandemic should be done, whilst the national and international health bodies recommendations will supportively guide clinicians prioritise ovarian cancer care. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan doi = 10.1016/j.ejso.2020.06.043 id = cord-334988-brumg6jh author = Traugott, Marianna title = Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in Different Stages of Infection: Comparison of Commercial Enzyme-Linked Immunosorbent Assays and Rapid Tests date = 2020-05-30 keywords = SARS; Wantai summary = We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction–confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. We comparatively assessed sensitivities and specificities of 4 commercial enzyme-linked immunosorbent assays (ELISAs) and 2 rapid tests in 77 patients with polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 infection, grouped by interval since symptom onset. In the current study, we compared the diagnostic ability of 4 enzyme-linked immunosorbent assays (ELISAs), which assess SARS-CoV-2-specific antibodies of different immunoglobulin (Ig) classes (Euroimmun SARS-CoV-2 IgA and IgG and Wantai SARS-CoV-2 IgM and total antibody), and 2 rapid tests (Wantai SARS-CoV-2 Ab Rapid Test and Hangzhou AllTest Biotech 2019-nCoV IgG/IgM Rapid Test) in 77 patients with symptomatic SARS-CoV-2 infection. Of the 77 patients with PCR-confirmed SARS-CoV-2 infection, 30 individuals (12 female, 18 male; median age, 58 years; age range, 15-83 years) provided serum/plasma samples that were obtained at symptom onset or 1-5 days after the onset of disease (group 1). doi = 10.1093/infdis/jiaa305 id = cord-289535-srrfr1es author = Tregoning, J. S. title = Vaccines for COVID‐19 date = 2020-10-18 keywords = COVID-19; CoV-2; MERS; RNA; SARS; dna; phase; vaccine summary = One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial doi = 10.1111/cei.13517 id = cord-345405-ngpsgn63 author = Tremiliosi, Guilherme C. title = Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date = 2020-06-26 keywords = SARS; fabric; nanoparticle; polycotton summary = An adaptation of ISO 18184 Determination of antiviral activity of textile products Standard Method [23] was used as a reference for a quantitative method to evaluate the treated polycotton''s ability to inactivate the SARS-CoV-2 virus particles (SARS-CoV-2/human/BRA/SP02cc/2020 -MT350282), under the tested conditions, at two different time intervals (2 and 5 minutes of contact time). The antiviral activity test was designed to determine the inactivation of viral particles upon short exposure to the products, which in this case were the Ag-based treated polycotton samples incubated in liquid media. Table 6 shows the number of copies of the control media without any fabric sample, non-treated polycotton, and the two Ag-based treated polycotton samples at the two different tested time periods. Application of silver nanoparticles to cotton fabric as an antibacterial textile finish Fibers Polym Antibacterial properties of cotton fabric treated with silver nanoparticles doi = 10.1101/2020.06.26.152520 id = cord-328122-nfvbog77 author = Tresoldi, Ilaria title = SARS‐COV‐2 and infectivity: Possible increase in infectivity associated to integrin motif expression date = 2020-04-10 keywords = SARS summary = It has been proposed that SARS-COV-2 has acquired the spike glycoprotein RGD (KGD in SARS-CoV) 1 integrin-binding site which is considered significant for the virus transmission efficiency. The most common of these motifs is the minimal peptide sequence for binding integrins, RGD, which is known for its role in virus infection via its ability to interact with over half of the more than 20 known integrins. 4 Besides the fibronectin binding motif RGD, other integrinbinding sites are specifically expressed in SARS-COV-2, and, particularly, a change from a LDV to a LDI motif is likely significant. 5 We investigated the protein sequence of the human coronavirus and compared it to SARS and bat coronavirus to identify any eventual overexpression of other integrin-binding sites. Orf1ab polyprotein has many integrin-binding motifs implicated in cell adhesion with binding sites on Fibronectin, Tenascin_C, and VCAM. doi = 10.1002/jmv.25831 id = cord-274416-bmvazgj7 author = Trevisanuto, Daniele title = Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan date = 2020-04-24 keywords = COVID-19; Coronavirus; SARS summary = title: Neonatal Resuscitation Where the Mother Has a Suspected or Confirmed Novel Coronavirus (SARS-CoV-2) Infection: Suggestion for a Pragmatic Action Plan This perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed COVID-19 infection. Although it is unlikely that neonates born from SARS-CoV-2-infected mothers require an intensive care management related to the maternal infection [18, 19] , coronaviruses may result in adverse outcomes for the fetus and infant (intrauterine growth restriction, preterm delivery, admission to the neonatal intensive care unit (NICU), spontaneous abortion and perinatal death) [16, 17, 25] . Our designated approach for the management of women with suspected or confirmed CO-VID-19 and their infants before, during, and after delivery provides cues to reduce the chance of neonatal infection and therefore potential negative outcomes in the newborn. doi = 10.1159/000507935 id = cord-284429-d7qxfo6d author = Trezza, Alfonso title = An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors date = 2020-08-17 keywords = ACE2; Lumacaftor; SARS; Simeprevir summary = We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein – ACE2 interaction inhibitor. By combining molecular dynamics simulations (MD), Supervised MD (SuMD), Steered MD (SMD) and interaction energy calculations, we showed that Simeprevir and Lumacaftor bind RDB with high affinity and prevent ACE2 interaction. In order to identify possible PPI inhibitors the transient pocket that contained key residues involved in hACE2 recognition and binding (Fig. 1A ) was selected and used for the virtual screening of 1582 FDA-approved drugs. In order to understand if Simeprevir and Lumacaftor are able to interfere and prevent the binding between the S glycoprotein and ACE2, we ran a Supervised Molecular Dynamics (SuMD) simulations. Using SuMD it is possible to simulate the full binding process of ACE2 to RBD in presence of Simeprevir or Lumacaftor in an unbiased way (i.e. independently from starting relative positions), taking into account hydration patterns and drug binding-unbinding events. doi = 10.1038/s41598-020-70863-9 id = cord-327511-e3idvknz author = Trifan, G. title = Characteristics of a Diverse Cohort of Stroke Patients with SARS-CoV-2 and Outcome by Sex date = 2020-09-11 keywords = COVID-19; SARS; stroke summary = CONCLUSION: In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this cohort of SARS-CoV-2 stroke patients, most had clinical evidence of coronavirus infection on admission and preexisting VRFs. Severe in-hospital complications and worse outcomes after ischemic strokes were higher in males, than females. In this multicenter study of patients with stroke and SARS-CoV-2 infection admitted to comprehensive stroke centers in the Chicagoland area, males were more likely than females to have severe COVID-19 manifestations and worse ischemic stroke outcome at hospital discharge. doi = 10.1016/j.jstrokecerebrovasdis.2020.105314 id = cord-253422-m18ngwbt author = Trimarchi, Hernán title = COVID-19 and acute kidney injury in pediatric subjects: is there a place for eculizumab treatment? date = 2020-09-29 keywords = SARS summary = One of the reasons we found this case of particular interest is that it reminds us of a similar experience by one of the authors who observed a dramatic effect of eculizumab in a 4-year-old child with diffuse proliferative lupus nephritis who developed complement-mediated TMA and AKI [6] . She fully recovered but needed chronic eculizumab treatment for atypical hemolytic uremic syndrome (aHUS). In both cases the initial disease was a severe multisystem inflammatory syndrome due to SARS-CoV-2 or systemic lupus erythematosus. He was admitted with severe diffuse bilateral SARS-CoV-2 pneumonia [9] and elevated D-dimer and fibrinogen concentrations, suggesting a pro-coagulant state due to pulmonary microthrombosis, as described in autopsies of subjects with COVID-19 infections [1] , despite ongoing chronic eculizumab treatment. However, while waiting for further follow-up, the present report deserves our utmost interest because it highlights the role of the complement system activation in SARS-COV-2 infection and the pharmacological interventions to attenuate the micro-thrombotic complications associated with COVID-19. Eculizumab, SARS-COV-2 and atypical hemolytic uremic syndrome doi = 10.1007/s40620-020-00859-1 id = cord-329853-kf3kh26y author = Trimarchi, Hernán title = Eculizumab, SARS-CoV-2 and atypical hemolytic uremic syndrome date = 2020-09-27 keywords = COVID-19; SARS summary = Complement activation is thought to contribute to endothelial injury and there are at least seven ongoing clinical trials testing six different anti-complement strategies for coronavirus disease 2019 (COVID-19), including eculizumab. We herein report on a kidney transplant patient with aHUS on chronic eculizumab therapy that developed severe COVID-19 despite eculizumab administration early in the course of the disease. Although eculizumab was unable to prevent the development of severe endothelial cell injury, as assessed by increasing D-dimer levels from 292 to 10 586 ng/mL, the patient eventually recovered following dexamethasone and convalescent plasma administration. To our knowledge, this is the first report of a kidney transplant recipient with aHUS on eculizumab therapy who developed SARS-CoV-2 infection. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: a report of five cases doi = 10.1093/ckj/sfaa166 id = cord-305091-tfn2pyc6 author = Tripathi, Praveen Kumar title = Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2 date = 2020-12-01 keywords = 3CL; Pro; SARS; Teicoplanin summary = We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL(Pro) of SARS-CoV-2. COVID-19 is an infectious disease caused by a newly discovered positive-sense single-stranded RNA virus called the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The involvement of H-bond donors and acceptors around hydrophobic sites compel the Teicoplanin molecule to interact within the inhibitor binding pocket of the 3CL Pro protease. In a recent MD simulation study, it was reported that Teicoplanin in complex with SARS-CoV-2 main protease has stable ligand-protein complex and intermolecular interactions during the simulated trajectory [21] . We report Teicoplanin as an effective drug against 3CL Pro which works at a micromolar concentration of 1.5 µM (Fig. 2) and acts by blocking the active site of the protease (Fig. 4F) . doi = 10.1016/j.ijbiomac.2020.08.166 id = cord-319983-e4f2sfl4 author = Tripathi, Shweta title = The COVID-19: Current understanding date = 2020-09-26 keywords = COVID-19; China; Coronavirus; SARS summary = Till the date of writing this article (August 15, 2020), a total number of 2526192+65002 laboratory-confirmed cases of COVID-19 from 35 states and Union Territories, out of which 1,915,580 (71.91%) recovered, while 50,924 (1.93%) deaths are reported in India [8, 10] . According to the Ministry of Family and Health Welfare of India; a suspected case is defined as a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, and shortness of breath) and a history of travel to or residence in a location reporting community transmission of COVID-19, 14 days prior of the beginning of symptoms. However, more clinical trials are needed to prove the safety and effectiveness of convalescent plasma transfusion in SARS-CoV-2 infected patients [48] . Epidemiological and clinical characteristics of 99 cases of 2019 novel Coronavirus pneumonia in Wuhan, China: A descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel Coronavirus-infected pneumonia in Wuhan, China doi = 10.14202/vetworld.2020.1998-2005 id = cord-333234-yvixy77x author = Triposkiadis, Filippos title = Renin-angiotensin-system inhibition in the context of corona virus disease-19: experimental evidence, observational studies, and clinical implications date = 2020-09-01 keywords = ACE2; SARS; covid-19 summary = While the potential for benefit with the use of renin-angiotensin-aldosterone system inhibitors (RAASi) and the risks from stopping them is more evident, potential harm by RAΑSi may also be caused by the increase in the activity of the ACE2 receptor, the inefficient counter regulatory axis in the lungs in which the proinflammatory prolyloligopeptidase (POP) is the main enzyme responsible for the conversion of deleterious angiotensin (ANG) II to protective ANG [1–7] and the proinflammatory properties of ACE2(+) cells infected with SARS-CoV-2. In a recent statement of the European Medicinal Agencies (EMA), it is emphasized (10 June 2020 EMA/284513/2020): "Recent observational studies of angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs, also called sartans) have not shown an effect of these medicines on the risk of becoming infected with severe acute respiratory syndrome coronavirus 2 (the virus causing COVID-19) and do not indicate a negative impact on the outcome for patients with COVID-19 disease. doi = 10.1007/s10741-020-10022-4 id = cord-317067-u90zkjk9 author = Trottein, François title = Potential causes and consequences of gastrointestinal disorders during a SARS-CoV-2 infection date = 2020-07-03 keywords = SARS summary = Intensive research on the pathogenic mechanisms used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed – notably in order to identify potential drug targets. Here, we review gastrointestinal disorders in patients with COVID-19, suggest hypothetical mechanisms leading to gut symptoms, and discuss the potential consequences of gastrointestinal disorders on the outcome of the disease. Lastly, we discuss the role of the gut microbiota during respiratory viral infections and suggest that targeting gut dysbiosis may help to control the pathogenesis of COVID-19. In this review, Trottein & Sokol present hypothetical mechanisms leading to gut symptoms in patients with COVID-19 and discuss their potential consequences on disease severity. They also discuss the role of the gut microbiota in disease and the potential interest of targeting it to improve COVID-19 pathogenesis. Clinical characteristics of 138 hospitalized patients with 2019 novel 589 coronavirus-infected pneumonia in Wuhan, China doi = 10.1016/j.celrep.2020.107915 id = cord-283895-1p5uog38 author = Trottier, J. title = Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date = 2020-07-09 keywords = RNA; SARS summary = Indeed, several reports indicate that SARS-CoV-2 RNA was readily detected in wastewater, and it is proposed that such approach could anticipate the occurrence of novel COVID-19 outbreaks in low prevalence regions , La Rosa et al., 2020 , Medema et al., 2020 , Orive et al., 2020 , Randazzo et al., 2020 . First, we showed that the Ebola standard (Ebo Std) primer/probe set was not detecting RNA from SARS-CoV-2-infected Vero E6 cells (Table 1) . . https://doi.org/10.1101/2020.07.08.20148882 doi: medRxiv preprint Next, we measured the SARS-CoV-2 RNA levels using N1 and N3 primer/probe sets in wastewater collected upstream of the main WWTP of the Montpellier metropolitan area on May 7 th , 18 th , 26 th , June 4 th , 15 th and 25 th (Figure 2A ). This intriguing result is reminiscent of a recent Spanish study, in which the authors could detect SARS-CoV-2 RNA in wastewater weeks before the first COVID-19 cases were reported (Randazzo et al., 2020) . doi = 10.1101/2020.07.08.20148882 id = cord-339152-wfakzb6w author = Trovato, Maria title = Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date = 2020-09-03 keywords = MERS; Nile; SARS; West; Zika; dna; vaccine; virus summary = Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. doi = 10.3389/fimmu.2020.02130 id = cord-323685-gjocoa60 author = Tsai, Shang-Jui title = Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination date = 2020-11-06 keywords = LSNME; SARS; cell summary = The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Conclusion Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins. These antigen-responsive CD4+ and CD8+ populations were present nearly two months after the final boost injection, indicating that LSNME/S W1 vaccination had elicited a sustained cellular immune response to both of these SARS-CoV-2 structural proteins. As for the future development of the LSNME/S W1 vaccine, we anticipate that follow-on studies in larger animal models at doses comparable to other mRNA vaccines will demonstrate a desirable combination of safety, balanced immune responses, and when challenged, protection against SARS-CoV-2 infection and/or disease. doi = 10.1101/2020.11.06.371419 id = cord-292337-74c69z28 author = Tsai, Shin-Han title = Transporting Patient with Suspected SARS date = 2004-07-17 keywords = SARS; Taiwan summary = Because medical facilities are limited on these islands, the Department of Health authorized the National Aeromedical Consultation Center (NACC), a physician-based 24-hour control center that coordinates all aeromedical transport of critically ill or injured patients within Taiwan, to coordinate transporting these patients to designated SARS hospitals in Taipei. When leaving the pre-isolation room, the physician and the PIU were sprayed with a sodium hypochloride solution before the first layer of personal protective equipment was removed. Although one report by Christopher and Eitzen (2) suggested the value of an aeromedical team to evacuate patients with suspected lethal, infectious diseases, limited evidence supported a safer means of transportation that would possibly reduce transmission of SARS to persons taking part in the mission. Interim guidance: air medical transport for severe acute respiratory syndromes (SARS) patients doi = 10.3201/1007.030608 id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 keywords = HIV; SARS; infection; treatment; virus summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial doi = 10.1177/1759720x20947296 id = cord-354948-q5eouyi2 author = Tsao, Kuo‐Chien title = False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome date = 2005-09-19 keywords = HTLV; SARS summary = title: False positive antibody results against human T‐cell lymphotropic virus in patients with severe acute respiratory syndrome An earlier serum collected from the same patient on the 3rd day after disease onset was retested, and it was found that the results were negative for both SARS-CoV and HTLV antibodies. It was speculated that some SARS-CoV peptides common to HTLV might be responsible for the false positive results observed in HTLV antibody detection. These four common peptides were synthesized and tested the cross-reactivity of antibodies in the sera of SARS versus HTLV-infected patients. These four common peptides were synthesized further and tested for crossreactivity of antibodies in the sera of SARS versus HTLV infected-patients. This finding suggests that among the antibodies in the sera of SARS patients, those with cross-reactivity with HTLV peptides might disappear Six SARS coronavirus genomes are TW1/ay291451, CUHK-W1/ay278554, TOR2/nc_004718, CUHK-Su10/ay282752, BJ01/ay278488, and Urbani /ay278741. doi = 10.1002/jmv.20460 id = cord-349827-0trvostt author = Tse, Alan C.B. title = Crisis management and recovery: how restaurants in Hong Kong responded to SARS date = 2005-01-29 keywords = SARS; crisis; restaurant summary = This article reviews a typology of crises, examines the crisis response of restaurants in Hong Kong, illustrates how local restaurants deal with this unprecedented situation and develop strategies for management and recovery. Restaurants in Hong Kong have already been put under great pressure to survive in the harsh market environment resulting from the Asian financial crisis of 1997, but the Severe Acute Respiratory Syndrome (SARS) outbreak in March 2003 was a death sentence to the industry. The SARS instance in Hong Kong had indirectly generated crises of the social environment because many restaurants experienced liquidity problems after the outbreak, and had to lay off thousands of staff or force them to take no-pay leave. In the SARS outbreak, for example, restaurant managers'' attempt to lay off staff without proper compensation to improve their cash flow position may lead to confrontation with the labour, which may subsequently cause a crisis of the social environment type. doi = 10.1016/j.ijhm.2004.12.001 id = cord-348071-0zlzblwi author = Tseng, Jen-Yu title = Potential implications of SARS-CoV-2 on pregnancy date = 2020-05-13 keywords = SARS summary = The Wuhan Coronavirus (recently named SARS-CoV-2) has been making headline news around the world as there are over 60,000 confirmed cases and a total of over 1300 deaths in China alone since the start of the outbreak [1]. In a review of previous coronavirus infections in pregnancy, there were 13 cases of SARS-CoV and 11 cases of MERS-CoV reported in the literature [3, 4] . Maternal outcome of the 13 cases: 4 cases had miscarriage, 2 opted for termination of pregnancy, 2 succumbed to SARS, 2 required mechanical ventilation, and 3 were treated conservatively. Maternal outcome of the 11 MERS-CoV cases: 2 were asymptomatic, 3 succumbed to MERS, 2 required mechanical ventilation, 3 were treated conservatively, and 1 refused treatment. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature doi = 10.1016/j.tjog.2020.03.025 id = cord-303880-zv4nbz9p author = Tsikala Vafea, Maria title = Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19 date = 2020-06-24 keywords = COVID-19; SARS; patient; vaccine summary = RESULTS: Key focus areas include the applications of artificial intelligence, the use of Big Data and Internet of Things, the importance of mathematical modeling for predictions, utilization of technology for community screening, the use of nanotechnology for treatment and vaccine development, the utility of telemedicine, the implementation of 3D-printing to manage new demands and the potential of robotics. The technologies in this review include: artificial intelligence (AI), machine learning and deep learning, nanomedicine, novel technologies for vaccines development and therapeutics, novel mathematical modeling, big data, internet of things (IoT), telemedicine, robots, and 3D printing technology. Mei et al proposed an AI system based on machine learning and deep learning models that combines demographic (age, sex) and clinical information (laboratory test results, reported symptoms, history of exposure etc.) with chest imaging findings for rapid identification of patients with COVID-19. doi = 10.1007/s12195-020-00629-w id = cord-264013-8jnae6ig author = Tsilingiris, Dimitrios title = Telomere length, epidemiology, and pathogenesis of severe COVID‐19 date = 2020-08-09 keywords = SARS; telomere summary = Cohen et al reported that in a relatively selected population of healthy adults aged between 18 and 55 years, following experimental exposure to Rhinovirus 39 (a single-stranded RNA virus), a shorter telomer length in PBMCs, total lymphocytes, as well as CD4+ and CD8+ Tlymphocyte subsets was associated with an increased probability of upper respiratory infection 23 . A diminishing telomere length in human lymphocytes is related to the process of their replicative senescence (or biological "aging") 26 . 29 Conversely, CD8+ lymphocyte senescence associated with critical telomere shortening induces a state of "hyper-function" with evasion of apoptosis, increased secretion of pro-inflammatory cytokines such as Tumor Necrosis Factor-alpha and interleukin-6 and loss of surface CD28, a co-stimulatory receptor necessary for the mobilization of targeted T-cell immune responses. We further speculate that this observation is driven by a complex immune dysregulation tracing back to immune cell senescence associated with telomere shortening, leading to increased susceptibility to infection and clinical disease (particularly pneumonia) by SARS-CoV-2, as well as unfavorable disease progression potentially marked by cytokine storm syndrome. doi = 10.1111/eci.13376 id = cord-289716-nleql08z author = Tsitsilonis, Ourania E. title = Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report date = 2020-09-21 keywords = CoV-2; NKUA; SARS summary = Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. According to the manufacturer''s package insert, Elecsys ® Anti-SARS-CoV-2 exhibits high overall clinical specificity of 99.81% with no cross-reactivity to the common cold coronaviruses; clinical sensitivity, determined by testing a total of 204 samples from 69 symptomatic patients with a PCR-confirmed SARS-CoV-2 infection, is 100% for samples collected ≥14 days after PCR confirmation in this collective; these values were verified in our study by measuring 25 RT-qPCR SARS-CoV-2 positive and 25 negative samples. doi = 10.3390/life10090214 id = cord-331930-w2055c42 author = Tso, Eugene Y. K. title = Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date = 2004-05-01 keywords = SARS summary = title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. doi = 10.1086/383580 id = cord-314124-yk4y0kea author = Tsou, Ian Y. title = Severe acute respiratory syndrome (SARS) in a paediatric cluster in Singapore date = 2003-08-20 keywords = SARS; child summary = BACKGROUND: Severe acute respiratory syndrome (SARS) is a major infectious disease pandemic that occurred in early 2003, and one of the diagnostic criteria is the presence of chest radiographic findings. Severe acute respiratory syndrome (SARS) is a new form of atypical pneumonia, and is an infectious disease which has caused a pandemic with significant public health concerns. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Materials and methods: The chest radiographs of four related children ranging in age from 18 months to 9 years diagnosed as having SARS were reviewed for the presence of air-space shadowing, air bronchograms, peribronchial thickening, interstitial disease, pleural effusion, pneumothorax, hilar lymphadenopathy and mediastinal widening. Chest radiographic findings of a case of severe acute respiratory syndrome (SARS) in Singapore doi = 10.1007/s00247-003-1042-2 id = cord-330908-402eb8wg author = Tsuji, Motonori title = Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease date = 2020-05-29 keywords = SARS summary = title: Potential anti‐SARS‐CoV‐2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease Additional docking simulations for predicted compounds with high binding affinity with M(pro) suggested that 28 bioactive compounds may have potential as effective anti‐SARS‐CoV‐2 drug candidates. Additional docking simulations for predicted compounds with high binding affinity with M pro suggested that 28 bioactive compounds may have potential as effective anti-SARS-CoV-2 drug candidates. In this study, I performed stepwise structure-based virtual screenings using two different docking simulations in order to discover potential drugs that target M pro using the ChEMBL database [4] , which mainly lists drugs and known bioactive compounds. Structure-based virtual screenings were performed using RDOCK (2013) [11] and AUTODOCK VINA version 1.1.2 [12] ; both interfaces are available in Docking Study with HYPER-CHEM (DSHC) software [5, 13] , and the resulting docking modes filtered by the RDOCK score threshold were more precisely simulated using AUTODOCK VINA. doi = 10.1002/2211-5463.12875 id = cord-274205-e2r38v29 author = Tsunetsugu-Yokota, Yasuko title = Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen date = 2007-11-28 keywords = SARS summary = title: Large-Scale Preparation of UV-Inactivated SARS Coronavirus Virions for Vaccine Antigen In general, a whole virion serves as a simple vaccine antigen and often essential material for the analysis of immune responses against virus infection. In order to develop an effective vaccine and diagnostic tools, we prepared UV-inactivated SARS coronavirus on a large scale under the strict Biosafety Level 3 (BSL3) regulation. We have demonstrated that subcutaneously administered UV-inactivated SARS-CoV elicits a high level of IgG-type neutralizing antibodies and weak T-cell responses in mice (4). Here we describe our protocol for the largescale preparation of UV-inactivated SARS-CoV virion under the strict Biosafety Level 3 (BSL3) regulation. In order to increase the safety of this UV-inactivated SARS-CoV, we inactivated the virion vaccine using both UV and formalin. Severe acute respiratory syndrome (SARS) coronavirus: application of monoclonal antibodies and development of an effective vaccine doi = 10.1007/978-1-59745-181-9_11 id = cord-338333-yvm3d6xy author = Tu, Danna title = Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 date = 2020-07-25 keywords = SARS summary = title: Immunological detection of serum antibodies in pediatric medical workers exposed to varying levels of SARS-CoV-2 • Pediatric healthcare workers are at risk for SARS-CoV-2 transmission from children and aerosols increase SARS-CoV-2 infection rate. Here we would like to share our finding about the serum antibodies analyzed in a special group of pediatric medical workers exposed to varying levels of SARS-CoV-2 after Wuhan severe epidemic of COVID-19. The overall positive rate for SARS-CoV-2 IgG and IgM antibodies in the pediatric medical workers was 43.08 and 5.85%, respectively. This research revealed that pediatric medical workers are a high-risk group for infection by SARS-CoV-2, and the higher the exposure levels to COVID-19 patients and aerosol production, the greater chance of being infected. Table 1 Test results of serum antibodies in pediatric medical workers exposed to different levels of SARS-CoV-2 High SARS-CoV-2 antibody prevalence among healthcare workers exposed to COVID-19 patients doi = 10.1016/j.jinf.2020.07.023 id = cord-282433-p6jl9gxf author = Tu, Xinyi title = Functional polymorphisms of the CCL2 and MBL genes cumulatively increase susceptibility to severe acute respiratory syndrome coronavirus infection date = 2015-03-27 keywords = CCL2; MBL; SARS summary = RESULTS: Both the high-CCL2-producing GG genotype and the low-MBL-producing B allele were consistently associated with increased risks of SARS-CoV infection in all 4 case–control populations (joint P = 1.6 × 10(−4) and 4.9 × 10(−8), for CCL2 and MBL respectively), with no interaction between polymorphisms could be detected. 3À10 In particular, our previous two independent association studies have implicated that a functional polymorphism at codon 54 in exon 1 (rs1800450, G230A, denoted as A/B variant) of mannose binding lectin (MBL), which encodes a protein belonging to the family of collectin and plays a critical role in the innate immune response, conferred a significantly increased susceptibility to SARS-CoV infection. Taken together, the large size of the investigation, the consistency of the observations in 4 independent caseecontrol series and the low P values distinguish our study from previous studies investigating the influence of different other polymorphisms on the development of SARS, and strengthen the association between the CCL2 G-2518A and MBL codon 54 variant (A/B) and susceptibility to SARS-CoV infection. doi = 10.1016/j.jinf.2015.03.006 id = cord-278467-c0jw9dkw author = Tulchinsky, Mark title = The American College of Nuclear Medicine Guidance on Operating Procedures for a Nuclear Medicine Facility During COVID-19 Pandemic date = 2020-05-01 keywords = SARS summary = During the COVID-19 pandemic, 5 scheduling of examinations should be judicious, equipment disinfection should be practiced before each patient, medical service sustainability should be optimized, all aerosol-generating tests must be avoided, and time of staff-patient contact should be minimized for each test in order to contain the contagion. 3. Provide to the patient and/or guardian as much information as possible by phone in advance of arrival to an NMF, including screening questions for COVID-19 risk and explanation of the test or therapy to be performed, in order to minimize the time spent in close in-person contact. Although the outlined principles are universal, their practical applications and implementation are dependent on prevalence dynamics of COVID-19 at specific locations and resources available to individual NMFs. A novel coronavirus from patients with pneumonia in China Incidental findings suggestive of COVID-19 in asymptomatic patients undergoing nuclear medicine procedures in a high-prevalence region doi = 10.1097/rlu.0000000000003146 id = cord-304176-yloqrblw author = Tunesi, S. title = Prescribing COVID-19 treatments: what we should never forget date = 2020-05-13 keywords = SARS summary = authors: Tunesi, S.; Bourgarit, A. COVID-19-induced proinflammatory status looks to trigger most severe SARS-CoV-2 forms (2). Many drugs have been hypothesized to be directly active against COVID-19 only because of a supposed antiviral activity: remdesivir, a molecule originally tested against Ebola virus, shows in vivo activity against MERS-CoV (5) but there is actually no real evidence of in vivo activity against COVID-19; lopinavir/ritonavir, a well-known protease inhibitor used in HIV treatment, has been widely used before randomized clinical trials showed his inefficacy in mortality reduction (6); chloroquine and hydroxychloroquine, which are largely used in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) treatment, show modest antiviral effects, but mortality due to QT elongation-related cardiac events is a matter of concern (7). Conversely, preliminary data about a potential role of ACE inhibitors in favouring the onset of severe forms of SARS-CoV-2 infection induced a massive change in antihypertensive drugs prescription that caused the onset of severe cardiovascular events (9). doi = 10.1016/j.jinf.2020.05.018 id = cord-028363-7pmro8bu author = Tung-Chen, Yale title = Acute pericarditis due to COVID-19 infection: An underdiagnosed disease? date = 2020-07-10 keywords = SARS; acute summary = 4 Gradually a therapeutic scheme is being established that would include hydroxychloroquine and azithromycin 5 (or in other cases lopinavir/ritonavir) in the early stages of moderate disease that does not require treatment in ICU (Intensive Care Unit) but given the analytical indication (elevation of ddimer) and imaging (thrombosis in CTPA) in many cases, should be evaluated the early inclusion of low molecular weight heparin (LMWH) at doses of at least high-risk prophylaxis in all these patients without thrombopenia <20,000 platelets or acute bleeding and manifesting high d-dimer. 5 In another study, 83 patients with severe and critical COVID-19 infection underwent a CT scan, 6 chest pain was reported in 6% of the patients and pericardial effusion was found in 4.8%, which suggests that acute pericarditis could be an under diagnosed pathology, and therefore, not correctly managed and treated. This is the first case report to describe an acute pericarditis episode due to SARS-CoV-2, which might be an under diagnosed condition in this pandemic, and therefore not correctly managed. doi = 10.1016/j.medcle.2020.06.001 id = cord-351559-az4pgi9k author = Turjya, Rafeed Rahman title = Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date = 2020-06-29 keywords = RNA; SARS; protein summary = Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. doi = 10.1101/2020.06.29.177204 id = cord-317423-3nkzp1z2 author = Turk, Can title = In vitro analysis of the renin–angiotensin system and inflammatory gene transcripts in human bronchial epithelial cells after infection with severe acute respiratory syndrome coronavirus date = 2020-06-03 keywords = ACE2; RAS; SARS summary = RESULTS: The whole-genome expression data of the lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were analyzed, and a total of 15 RAS family and 29 immune genes were found to be highly correlated with the exposure time to the virus in the studied groups. 13, 21 The main purpose of this present in silico genomic study was to assess how the expressions of the RAS gene family changes after cellular infection with SARS-CoV in the lung epithelial cell culture. The whole normalized gene expression data of lung epithelial cells infected with SARS-CoV for 12, 24, and 48 hours were compared between different groups in order to determine significantly and differentially expressed RAS family genes. Based on our results, in this phase, as the exposure time to SARS-CoV increases, EGFR and IGF2R, two receptors with key roles in the RAS signaling pathway, were significantly down-regulated in the infected human bronchial epithelial cells. doi = 10.1177/1470320320928872 id = cord-306760-05my504t author = Turner, Dan title = Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date = 2020-03-31 keywords = COVID-19; IBD; Porto; SARS summary = METHODS: An electronic reporting system of children with IBD infected with SARS-CoV-2 has been circulated among 102 PIBD centres affiliated with the Porto and Interest-group of ESPGHAN. Standard IBD treatments including biologics should continue at present through the pandemic, especially in children who generally have more severe IBD course on one hand, and milder SARS-CoV-2 infection on the other. In light of the hyperinflammatory immune response seen in patients with COVID-19 it is highly relevant that blockade of IL-6R with tocilizumab resulted in clinical improvement associated with normalisation of fever, lymphocyte counts, and CRP in a retrospective group of 21 adults with severe SARS-CoV-2 infection (20) . Therefore, uninfected children should generally continue their medical treatment, including immunomodulators and biologic therapies, as the risk of a disease flare outweighs any estimated risk of SARS-CoV2 infection. doi = 10.1097/mpg.0000000000002729 id = cord-339241-e2nl766y author = Turriziani, Ombretta title = SARS‐CoV‐2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period date = 2020-08-02 keywords = China; SARS summary = The study retrospectively included 6565 subjects tested for SARS‐CoV‐2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. This analysis allowed to gather comprehensive information on SARS‐CoV‐2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown. In this scenario this paper aims to take a snapshot of the epidemiological characteristics of the population resulted positive for SARS-CoV-2 at Sapienza University Hospital "Policlinico Umberto I" in Rome starting from 6 March until 4 May. This study includes all individuals (n = 6565) who have been tested 2.1 | Statistical analysis χ 2 Test was used to analyze the differences in positivity between groups. doi = 10.1002/jmv.26332 id = cord-274824-kaefedl1 author = Turski, Waldemar A. title = AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date = 2020-09-24 keywords = IDO1; SARS; ahr; covid-19; infection summary = as pro viral factor TiPARP, and to the modulation of cytokine gene expression, specifically, interleukin 1␤ (IL-1␤), IL-10, and TNF-␣ ( Fig. 1) , which is consistent with the role for AhR activation in the host response to CoV infection Grunewald, Shaban, Mackin, Fehr, & Perlman, 2020; Neavin, Liu, Ray, & Weinshilboum, 2018) . Since CoV persistently activate AhRs, this may lead to up-regulation of multiple sets of downstream effectors resulting in different pathologies (Fig. 2) depending on time after infection, individuals overall state of health, comorbidities, and environmental factors affecting AhRs. We believe it is therefore appropriate to describe this disease as a systemic AhR activation syndrome (SAAS), which can manifest in an acute (current pandemic), and perhaps later, in a chronic form, in survivors. doi = 10.3233/rnn-201042 id = cord-280068-rszu1c48 author = Twomey, Julianne D. title = COVID-19 update: The race to therapeutic development date = 2020-10-24 keywords = ACE2; COVID-19; CoV-2; SARS summary = We highlight two major lines of therapeutic strategies for COVID-19 treatment: 1) repurposing the existing drugs for use in COVID-19 patients, such as antiviral medications (e.g., remdesivir) and immunomodulators (e.g., dexamethasone) which were previously approved for other disease conditions, and 2) novel biological products that are designed to target specific molecules that are involved in SARS-COV-2 viral entry, including neutralizing antibodies against the spike protein of SARS-COV-2, such as REGN-COV2 (an antibody cocktail) and LY-COV555, as well as recombinant human soluble ACE2 protein to counteract SARS-COV-2 binding to the transmembrane ACE2 receptor in target cells. The current review highlights the potential therapeutic strategies for the treatment of COVID-19, including small molecule drugs and therapeutic proteins to target the SARS-CoV-2 viral entry, viral amplification or the host immune responses. doi = 10.1016/j.drup.2020.100733 id = cord-252305-rstxyofq author = Tyan, Kevin title = Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting date = 2020-08-31 keywords = SARS summary = We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. While this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. Some products on List N do not have an emerging viral pathogen claim but have been included because they 1) demonstrate efficacy against another human coronavirus similar to SARS-CoV-2 or 2) are EPA-approved against select viruses that are harder-to-kill [5] . The publication of the EPA List N was an important step in providing a resource for selecting disinfectants against SARS-CoV-2 and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability. doi = 10.1093/ofid/ofaa396 id = cord-269723-gm65p1op author = Tzeng, Nian-Sheng title = What could we learn from SARS when facing the mental health issues related to the COVID-19 outbreak? A nationwide cohort study in Taiwan date = 2020-10-06 keywords = SARS; Taiwan; disorder summary = There were several studies about the psychiatric and mental health issues related to the severe adult respiratory syndrome (SARS) outbreak in 2003, however, the association between SARS and the overall risk of psychiatric disorders and suicides has, as yet, to be studied in Taiwan. A total of 285 patients with SARS and 2850 controls without SARS (1:10) matched for sex, age, insurance premium, comorbidities, residential regions, level of medical care, and index date were selected between February 25 and June 15, 2003 from the Inpatient Database Taiwan''s National Health Insurance Research Database. To the best of our knowledge, this is the first study on the association between SARS and increased risk in developing psychiatric disorders and suicide, in a 12-year follow-up, from a nationwide, population-based database. doi = 10.1038/s41398-020-01021-y id = cord-338436-0z828org author = Tzou, Philip L. title = Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds date = 2020-09-09 keywords = COVID-19; CoV-2; MERS; SARS; cell; compound summary = Results: As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. Figure 4 displays EC 50 values for many of the directly acting antiviral compounds currently in clinical trials for the treatment of COVID-19 including six polymerase inhibitors (remdesivir, EIDD-2801, favipiravir, ribavirin, galidesivir, and sofosbuvir), three HIV-1 protease inhibitors (lopinavir, atazanavir, and darunavir), and three entry inhibitors (receptor binding monoclonal antibodies, soluble recombinant human ACE2, and umifenovir). Viruses 2020, 12, x FOR PEER REVIEW 11 of 22 Table 4 describes a set of the most promising compounds for the treatment of SARS-CoV-2 based on the following criteria: (i) act by a validated direct or indirect antiviral mechanism, (ii) display submicromolar activity in vitro and/or inhibitory activity in an animal model, and (iii) have a record of safety and favorable pharmacokinetics in human subjects. doi = 10.3390/v12091006 id = cord-335492-od3c25qg author = UGUREL, Osman Mutluhan title = An updated analysis of variations in SARS-CoV-2 genome date = 2020-06-21 keywords = SARS summary = In this study; we have used these data to analyse the mutations on SARS-CoV-2 genome using a software based on multiple sequence alignment (Strategy Based Local Alignment Tool: ODOTool) that have been originally developed for bacterial SNP determination in our studies. Now, we targeted to analyse the mutations that have emerged in at least 10% of SARS-CoV-2 genomes in all 30366 sequences submitted in GISAID by May 20th, 2020 using the ODOTool in terms of date and location they occurred, the relationship with each other and their effect on the primary protein structure. Despite the Strategy Based Local Alignment Tool (ODOTool) used in this study was originally developed by our group for bacterial single nucleotide polymorphism (SNP) determination, it was reasonable to test the abilities of the tool using a different dataset with the emergence of SARS-CoV-2 causing COVID-19 pandemic and this is applied in the present study to analyse variations in viral genome. doi = 10.3906/biy-2005-111 id = cord-305632-xbji6g5x author = Uccelli, Matteo title = COVID-19 and Obesity: Is Bariatric Surgery Protective? Retrospective Analysis on 2145 Patients Undergone Bariatric-Metabolic Surgery from High Volume Center in Italy (Lombardy) date = 2020-10-31 keywords = COVID-19; Italy; SARS summary = There are also emerging data indicating that obesity is an independent predictor of intensive care unit (ICU) admission, mechanical ventilation, and death [6, 11, 12] , and in a recent report from a large cohort of COVID-19 patients in New York, obesity was found to be one of the most common associated comorbidities in hospitalized patients [13, 14] . We therefore analyzed a significant number of patients to evaluate the spread and the effects of the SARS-CoV-2 infection in a population of patients who had undergone bariatric surgery. Therefore, our data are encouraging, considering that these patients were obese: bariatric surgery and the consequent weight loss seem to significantly lower the risk of serious consequences due to COVID infection. Bariatric surgery, therefore, can be considered a protective factor with respect to the onset of severe respiratory disease resulting from infection with SARS-CoV-2. doi = 10.1007/s11695-020-05085-z id = cord-328856-1l7x72j7 author = Ucciferri, Claudio title = Pidotimod in Paucisymptomatic SARS-CoV2 Infected Patients date = 2020-07-01 keywords = Pidotimod; SARS summary = Several studies on COVID-19 are focusing on severe forms; however, the most frequent SARS-CoV-2 clinical presentation is a mild disease with or without pneumonia in about 80% of patients. Notwithstanding immune response appeared fundamental for SARS infection resolution, SARS-Cov-2 disease present increased levels of plasma pro-inflammatory mediators, as a consequence of an induced dysregulated cytokine storm. We enrolled SARS-CoV2 positive patients (Brescia-COVID Respiratory Severity Scale 0), with fever and cough without acute respiratory failure or sign of pneumonia from March to April 2020 at the Infectious Diseases Clinic, University ''G. 9 In our study, in the outpatient population affected by SARS-CoV2 infection, pidotimod appears as a valid option to reduce the duration of symptoms in patients, as an earlier defervescence of fever and it could prevent the cytokine cascade activation. In conclusion, in ambulatorial adult patients with SARS-Cov2 infection without pneumonia, pidotimod could be considered an option, well tolerated and associated with a rapid reduction of systemic symptoms of disease. doi = 10.4084/mjhid.2020.048 id = cord-331243-0u65qguq author = Ucciferri, Claudio title = Role of monoclonal antibody drugs in the treatment of COVID-19 date = 2020-10-06 keywords = COVID-19; SARS summary = Evidence suggests that elevated cytokine levels, reflecting a hyperinflammatory response secondary to SARS-CoV-2 infection, are responsible for multi-organ damage in patients with COVID-19. These studies suggest that tocilizumab may be a candidate to improve the outcome of patients with severe COVID-19 infections. Recent data on anakinra showed that, in a cohort of patients with COVID-19 and Acute respiratory distress syndrome managed with non-invasive mechanical ventilation, treatment with highdose anakinra was safe and associated with clinical improvement [16, 17] . Currently available data on SARS-CoV-2 infection show that the extent of the inflammatory response correlates with disease progression and subsequent organ damage. Tocilizumab for the treatment of severe COVID-19 pneumonia with hyperinflammatory syndrome and acute respiratory failure: A single center study of 100 patients in Interleukin-1 blockade with high-dose anakinra in patients with COVID-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study doi = 10.12998/wjcc.v8.i19.4280 id = cord-269283-jm18lj5t author = Uddin, Md Bashir title = Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date = 2020-07-01 keywords = COVID-19; China; SARS summary = Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. As the outbreak of the 2019 novel coronavirus (COVID-19 [SARS-CoV-2]) is expanding rapidly, analysis of epidemiological data of COVID-19 is necessary to explore the measures of burden associated with the disease and to simultaneously gather information on determinants and interventions. Moreover, the conservancy study of immunogenic peptides predicted from the SARS-CoV-2 proteins was also compared against other human coronavirus strains (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1 and MERS-CoV). Cross-checked conservancy analysis of COVID-19 antigenic epitopes with SARS-CoV proteins showed that conservancy when crosschecked with other coronaviruses, including BufCoV-HKU26 of Bangladesh origin, was not significant ( Table 3) . doi = 10.1016/j.meegid.2020.104440 id = cord-299711-m5gb03is author = Udrea, Ana-Maria title = Laser irradiated phenothiazines: New potential treatment for COVID-19 explored by molecular docking date = 2020-08-15 keywords = CPZ; SARS summary = In this study we predict, using molecular docking, the binding affinity of 15 phenothiazines (antihistaminic and antipsychotic drugs) when interacting with the main protease (M(pro)) of SARS-CoV-2. For identifying a treatment of COVID-19 disease, we used molecular docking procedure to predict the inhibitory activity (against SARS-CoV-2) M pro of some compounds from phenothiazines drug class. To simulate the interaction between SARS-CoV-2 and drugs from the class of phenothiazines including TZ and CPZ photoproducts we have used the virus M pro from RCSB Protein Data Bank: PDB code 6LU7 [15] . The 2D/3D chemical structure of compounds from Phenothiazines class and TZ and CPZ photoproducts that resulted during laser irradiation; 2D chemical structure, lowest EFEB (kcal/mol) for each compound resulted after 100 runs using molecular docking simulation, predicted KI (nM) and pKI values are also presented. Our results suggest that TZ and TZ photoproducts obtained by laser irradiation, have significant biological activity on SARS-CoV-2 M pro and could be used in a potent treatment in COVID-19 disease. doi = 10.1016/j.jphotobiol.2020.111997 id = cord-035026-2qcsfd87 author = Ugwueze, Chidiebere V. title = COVID-19 and Diabetes Mellitus: The Link and Clinical Implications date = 2020-10-23 keywords = ACE2; COVID-19; DPP4; SARS; patient summary = The effect of glucocorticoids and catecholamines, invasion of the pancreatic islet cells, drugs used in the treatment of COVID-19, and the lockdown policy may impact negatively on glycemic control of diabetic patients. [40] showed that the clinical outcomes in COVID-19-positive patients with coexisting diabetes and hypertension who use ACE inhibitor or angiotensin II receptor blocker were comparable to those not using the drugs. A clinical trial (NCT04318418) was designed to determine the effect of ACE inhibitors and angiotensin II type 1 receptor blockers on the severity of COVID-19 infection [41] . Some authors have considered the rapidity of worsening glycemic control in stable diabetic patients with CO-VID-19 requiring the use of high insulin dose and suggested the possibility of pancreatic invasion by the SARS-CoV-2 [57, 58] . Once the entry of the virus is established, there is a downregulation of ACE2 receptor and a corresponding Ugwueze/Ezeokpo/Nnolim/Agim/ Anikpo/Onyekachi Dubai Diabetes Endocrinol J 6 DOI: 10.1159/000511354 activation of renin-angiotensin-aldosterone system, which is responsible for the cardiac and pulmonary complications of COVID-19 infection [75] . doi = 10.1159/000511354 id = cord-319540-kivk3h1k author = Uhe, Tobias title = Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy date = 2020-07-13 keywords = Fig; SARS summary = title: Collateral damage: Fear from SARS-CoV2-infection causing Takotsubo cardiomyopathy An 84-year-old male patient with known ischemic cardiomyopathy was admitted to the emergency department of Leipzig University Hospital with typical signs and symptoms of an acute coronary syndrome in the midst of the SARS-Cov2 pandemic on April 22, 2020. Echocardiography (Fig. 2) showed wall motion abnormalities with apical septal dyskinesis, mid ubiquitous akinesia and basal septal and anterior hypokinesis. Due to media reports, she was highly afraid of SARS-CoV2 infections for her husband and herself, because age and hypertension were communicated as high risk for a severe course of COVID-19. Her condition acutely and severely exacerbated when her husband was admitted to the hospital, which she felt would place him at a high risk of death, and because she was not allowed to visit him due to the SARS-CoV2-specific regulations. The patient was provided with psychological support and the SARS-CoV2-negative couple was allowed to meet. doi = 10.1007/s00392-020-01706-w id = cord-263279-afdmegq0 author = Uhteg, Katharine title = Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date = 2020-04-26 keywords = PCR; SARS summary = Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. doi = 10.1016/j.jcv.2020.104384 id = cord-019076-4qu9j953 author = Ulferts, Rachel title = Expression and Functions of SARS Coronavirus Replicative Proteins date = 2009-07-22 keywords = MHV; RNA; SARS summary = doi = 10.1007/978-3-642-03683-5_6 id = cord-313541-fpqwzf9k author = Ulloa, S. title = A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date = 2020-08-22 keywords = RNA; SARS summary = The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Thus, the four different media used in this study (UTM, PBS 1x solution, Hanks medium and DNA/RNA Shield TM ) did not affect analytical results, because all precipitated samples were able to be detected by rRT-PCR using the whole viral panel (Orf1ab, N and S genes) and the internal control gene. Here, a simple protocol to detect SARS-CoV-2 from NPSs using rRT-PCR after a heat inactivation and a precipitation/concentration step is proposed. doi = 10.1016/j.jviromet.2020.113960 id = cord-032552-rjuug7er author = Umviligihozo, Gisele title = Sub-Saharan Africa preparedness and response to the COVID-19 pandemic: A perspective of early career African scientists date = 2020-07-08 keywords = COVID-19; SARS; SSA; african summary = As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. As a group of early career scientists and the next generation of African scientific leaders with experience of working in medical and diverse health research fields in both SSA and resource-rich countries, we present a unique perspective on the current public health interventions to fight COVID-19 in Africa. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. We documented public health interventions implemented in seven SSA countries including Uganda, Kenya, Rwanda, Cameroon, Zambia, South Africa and Botswana, the existing gaps and the important components of disease control that may strengthen SSA response to future outbreaks. doi = 10.12688/wellcomeopenres.16070.1 id = cord-017463-repm1vw9 author = Ungchusak, Kumnuan title = Public Health Surveillance: A Vital Alert and Response Function date = 2018-07-27 keywords = Health; SARS; disease; public; surveillance summary = We examine networks that contribute to global surveillance systems and highlight the role of social media and information technology in providing data to monitor new events of international importance. The IHR 2005 require countries to develop core capacities in public health, including surveillance systems and epidemiology services, that can analyse and act on surveillance information to detect and respond to diseases where and when they occur so that their potential to spread internationally is decreased. Surveillance and response teams detect early stage public health threats while control programmes gather disease (or condition) specific information to plan activities. These networks depend on cooperation of governments, public health workers and scientists to report cases, provide specimens and share information so that specific diseases can be controlled globally. doi = 10.1057/978-1-137-54984-6_10 id = cord-345628-a4c46m2w author = Unudurthi, Sathya D. title = Cardiac inflammation in COVID-19: Lessons from heart failure date = 2020-09-21 keywords = COVID-19; SARS; cell; patient summary = Autopsies of COVID-19 patients reveal an infiltration of inflammatory mononuclear cells in the myocardium, confirming the role of the immune system in mediating cardiovascular damage in response to COVID-19 infection and also suggesting potential causal mechanisms for the development of new cardiac pathologies and/or exacerbation of underlying CVDs in infected patients. Myocyte damage and lymphocytic myocarditis have also been independently confirmed by recent autopsies carried out on multiple COVID-19 patients from Seattle and Germany (Bradley et al., 2020; Wichmann et al., 2020) Recently, SARS-CoV-2 viral particles have been identified in cardiac macrophages, suggesting that these cells can be directly infected by the virus, potentially transmitting the disease systemically to multiple tissues (Tavazzi et al., 2020) . doi = 10.1016/j.lfs.2020.118482 id = cord-340323-xz6v95yy author = Urbach, Horst title = Notfällige Neurointerventionen, Covid-19 und Thorax-CT: SOP und Literaturübersicht date = 2020-05-07 keywords = COVID-19; SARS summary = Bei Schlaganfall-und anderen Notfallpatienten kann das Ergebnis einer RT-PCR zum Nachweis von SARS-CoV-2, dem Erreger der COVID-19, aus einem Abstrich in der Mehrzahl der Fälle nicht abgewartet werden. Ein solcher Patient wird also wie ein COVID-19-Verdacht betrachtet, auch wenn die Wahrscheinlichkeit, dass er mit SARS-CoV-2 infiziert ist, eher gering erscheint. Das wünschenswerte Szenario ist nun, dass der Patient die Bereiche Computertomographie (CT), Angiographie und Intensivstation wie ein COVID-19-Patient durchläuft sowie Isolierung und Verdacht nach negativem RT-PCR-Ergebnis aufgehoben werden [1] [2] [3] . V. eine Umfrage darüber gestartet, welche diagnostischen und Schutzmaßnahmen in den einzelnen Kliniken bei Patienten mit möglicher SARS-CoV-2-Infektion getroffen werden. Das unterschiedliche Vorgehen neuroradiologischer Abteilungen in Deutschland spiegelt die Unsicherheit im Umgang mit Schlaganfallpatienten und möglicher "coronavirus disease 2019" (COVID-19) wider. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 doi = 10.1007/s00062-020-00911-4 id = cord-351492-8jv7ip67 author = Urwin, S. G. title = FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date = 2020-10-20 keywords = COVID-19; PCR; SARS summary = Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. In this systematic review and pooled analysis of IPD, we found that the FebriDx LFD had a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) for COVID-19 across two studies performed within acute hospitals in the UK when compared to RT-PCR on nose and throat swabs during the first wave of the SARS-CoV-2 pandemic. doi = 10.1101/2020.10.15.20213108 id = cord-257802-vgizgq2y author = Uttamchandani, Mahesh title = Applications of microarrays in pathogen detection and biodefence date = 2008-11-12 keywords = SARS; dna; microarray; pathogen; protein summary = Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] . doi = 10.1016/j.tibtech.2008.09.004 id = cord-348342-iqq8kmn0 author = Uyoga, S. title = Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors date = 2020-07-29 keywords = July; SARS summary = Methods We measured anti-SARS-CoV-2 spike IgG prevalence by ELISA on residual blood donor samples obtained between April 30 and June 16, 2020. National seroprevalence was estimated using Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and region, adjusted for assay performance. Based on these data, we defined anti-SARS-CoV-2 IgG seropositivity as an OD ratio >2 and selected the spike ELISA for this study; the sensitivity and specificity of this threshold was 83% (95% CI: 59-96%) and 99.0% (95% CI 98.1-99.5%), respectively (Table 1, Figure S3 panels A & B). The Bayesian population-weighted and test-adjusted seroprevalence for Kenya was 5.2% (95% CI 3.7-7.1%, Table 3 ) and the posterior sensitivity and specificity estimates were 82.5% (95% CI 69.6-91.2%) and 99.2 (95% CI 98.7-99.6%), respectively. In this anti-SARS-CoV-2 IgG seroprevalence study of blood donors in Kenya, the crude prevalence was 5.6% and the population-weighted test-adjusted seroprevalence was 5.2%. doi = 10.1101/2020.07.27.20162693 id = cord-311673-z4hkw17g author = Uzzan, Mathieu title = Why is SARS-CoV-2 infection more severe in obese men? The gut lymphatics - lung axis hypothesis date = 2020-06-23 keywords = COVID-19; SARS; patient summary = As the visceral fat possesses an intense immune activity, is involved in metabolic syndrome and is at the crossroad between the intestines, the systemic circulation and the lung, we hypothesized that it plays a major role in severe forms of SARS-CoV-2 infection. Several factors may increase intestinal permeability including, direct enterocyte damage by SARS-CoV2, systemic inflammatory response syndrome (SIRS) and epithelial ischemia secondary to SARS-CoV2associated endothelial dysfunction. This increase permeability further leads to translocation of microbial components such as MAMPS (microbial-associated molecular pattern), triggering an inflammatory immune response by TLR-expressing cells of the mesentery fat (mostly macrophages and adipocytes). As the increased volume of mesentery fat in overweight men play a key role in the occurrence of metabolic syndrome [8] , we hypothesized that the visceral adipose tissue plays a central role in severe forms of COVID-19. doi = 10.1016/j.mehy.2020.110023 id = cord-323618-d09b65gd author = Vabret, A. title = Coronavirus humains (HCoV) date = 2008-05-05 keywords = NL63; SARS; coronavirus; des; les summary = La survenue récente, en 2002 à 2003, de l''épidémie de SRAS (ou syndrome respiratoire aigu sévère), et l''identification de l''agent pathogène responsable, un coronavirus émergent dans la population humaine, ont conduit à un vif regain d''intérêt et une intensification importante des recherches sur ces virus. Certaines données expérimentales sont inattendues : malgré des séquences en aminoacides conservées au niveau de la protéine S1 des HCoV 229E et NL63, ces deux coronavirus humains utilisent des récepteurs différents (APN et ACE2, respectivement) ; par ailleurs, le SARS-CoV utilise le même récepteur cellulaire que NL63 alors que les séquences S1 sont éloignées, cependant le RBD des deux virus semble proche et il est absent chez les SL-CoV. Une des conséquences biologiques de cette grande délétion est le changement de tropisme du virus qui, d''entérique pour le TGEV, est devenu respiratoire pour le PRCV [36] De nombreuses études ont été menées à la recherche du réservoir animal du SARS-CoV. doi = 10.1016/j.patbio.2008.02.018 id = cord-253077-61fmul8c author = Vabret, Nicolas title = Immunology of COVID-19: current state of the science date = 2020-05-06 keywords = CD4; COVID-19; Coronavirus; IFN; MERS; SARS; cell; patient; severe summary = Lastly, Nonhuman primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific IgG responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into pro-inflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012; Liu et al., 2019) . Collectively, these data suggest that cross-talk with monocytes might impair NK cell recognition and killing of SARS-CoV-2infected cells, and antibodies targeting IL-6 and TNF-signaling may benefit enhanced NK cell functions in COVID-19 patients ( Figure 2 ). However, these CD4 T cells lacked phenotypic markers of activation and were specific for C-terminal S protein epitopes that are highly similar to endemic human coronaviruses, suggesting that crossreactive CD4 memory T cells in some populations (e.g., children and younger patients that experience a higher incidence of hCoV infections) may be recruited into an amplified primary SARS-CoV-2-specific response (Braun et al., 2020) . doi = 10.1016/j.immuni.2020.05.002 id = cord-259185-qg4jwbes author = Vadlamani, B. S. title = Functionalized TiO2 nanotube-based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date = 2020-09-09 keywords = RBD; SARS summary = In this work, we report the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor and its efficacy for rapid detection of spike glycoprotein of SARS-CoV-2 by examining S-RBD protein as the reference material. Our manuscript reports the synthesis of a cheap yet highly sensitive cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical biosensor for rapid detection of spike glycoprotein of SARS-CoV-2. . https://doi.org/10.1101/2020.09.07.20190173 doi: medRxiv preprint asymptomatic individuals are needed, which is feasible only after the development of a simple, portable and rapid point-of-use sensor for the detection of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data showed that cobalt functionalized TNTs could selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~ 30 secs. doi = 10.1101/2020.09.07.20190173 id = cord-344180-v8xs5ej8 author = Vadlamani, Bhaskar S. title = Functionalized TiO(2) Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2 date = 2020-10-17 keywords = RBD; SARS; TNT summary = In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO(2) nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. In the current work, we have determined the potential of Co-functionalized TiO2 nanotubes (Co-TNTs) for the electrochemical detection of S-RBD protein of SARS-CoV-2. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. Our data shows that cobalt functionalized TNTs can selectively detect the S-RBD protein of SARS-CoV-2 using the amperometry electrochemical technique in ~30 s. In this study, we developed a Co-metal functionalized TNT as a sensing material for electrochemical detection of SARS-CoV-2 infection through the detection of the receptor binding domain (RBD) of spike glycoprotein. doi = 10.3390/s20205871 id = cord-355422-c4odhdql author = Vaira, Luigi Angelo title = Potential pathogenesis of ageusia and anosmia in COVID‐19 patients date = 2020-04-27 keywords = SARS summary = From the first reports, ageusia and anosmia appear to be frequent clinical features in coronavirus disease 19 (COVID‐19) patients. 3 We report our survey of the literature up to April 14, 2020 , analyzing the possible causes of these chemosensory alterations, which may be useful as a starting point for specific future studies. Moreover, the Middle East Respiratory Syndrome (MERS) coronavirus may bind to the sialic acid receptors 9 , an ability which has also recently been described for SARS-CoV-2 10 . In such a way, SARS-CoV-2 could therefore occupy the binding sites of sialic acid on the taste buds, accelerating the degradation of the gustatory particles. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): a multicenter European study Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia doi = 10.1002/alr.22593 id = cord-293544-nemw29r7 author = Valdivia, Arantxa title = Qualitative assessment of SARS‐CoV‐2‐specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay date = 2020-08-02 keywords = SARS summary = Here, we carried out qualitative assessment of SARS‐CoV‐2‐specific antibody avidity using an urea (6M) dissociation test performed on a lateral flow immunochromatographic IgG/IgM device. 2 Although serology testing is mainly aimed at identifying individuals who have previously been exposed to SARS-CoV-2, it may also aid in diagnosis of ongoing COVID-19, particularly in RT-PCR negative patients who present at relatively late times after infection. 3 Knowledge of the precise timing of infection may be of clinical and epidemiological relevance as viral shedding in the upper respiratory tract seems to continue up to 7 to 9 days after onset of symptoms in patients presenting with mild or moderate COVID-19. T A B L E 2 Qualitative assessment of SARS-CoV-2-specific antibody avidity in serial serum samples from patients with COVID Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay doi = 10.1002/jmv.26344 id = cord-331002-7uojryqz author = Valent, Francesca title = Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date = 2020-09-06 keywords = SARS summary = METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. The main finding of our study is the long duration of SARS-CoV-2 positivity in a population 133 including patients ranging from asymptomatic to acute respiratory distress syndrome requiring ICU 134 care. SARS-CoV-2 Viral Load in Upper 236 Respiratory Specimens of Infected Patients doi = 10.1016/j.cmi.2020.08.041 id = cord-310061-nro623aa author = Valitutto, Marc T. title = Detection of novel coronaviruses in bats in Myanmar date = 2020-04-09 keywords = Myanmar; SARS; bat; sample summary = Historically, bats have been linked to highly pathogenic viruses that pose a serious threat to human health, including the coronaviruses responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), the hemorrhagic ebola and Marburg filoviruses, and paramyxoviruses such as Nipah virus [10, 11, [13] [14] [15] [16] [17] [18] . The 2002-2003 SARS epidemic, the emergence of MERS in people in 2012, and the ongoing COVID-19 pandemic have prompted substantial interest in detecting coronaviruses of bat origin due to public health concern and their pandemic potential [10, [13] [14] [15] [16] [17] [18] . In addition to human-associated CoVs, bats are also hosts of coronaviruses that infect production animals, and have been implicated in the emergence and origin of swine acute diarrhea syndrome (SADS), transmissible gastroenteritis virus (TGEV) in pigs, and porcine epidemic diarrhea (PED), which can cause considerable losses [23] [24] [25] [26] . doi = 10.1371/journal.pone.0230802 id = cord-327653-2gn9h4i2 author = Vallinoto, Antonio Carlos Rosário title = The challenges of COVID-19 in the Brazilian Amazonian communities and the importance of seroepidemiological surveillance studies date = 2020-08-15 keywords = COVID-19; SARS summary = Since the elimination of beta-coronavirus circulation requires a minimum herd immunity (indications 50-66%) [7] , the information for which is still unknown at the local, national or global levels, conducting seroepidemiological and surveillance studies on SARS-CoV-2 in geographic areas such as the Amazon is extremely important, as it will allow for the assessment of the prevalence and titre of antibodies anti-SARS-CoV-2, mortality and case fatality rates and the epidemiological aspects of risk of exposure in communities from different population strata, such as riberinhos (riverain communities), quilombola (Afro-descendant communities) and indigenous peoples, providing an improvement in the decisionmaking of future epidemics. doi = 10.1186/s12939-020-01256-7 id = cord-283485-xit6najq author = Van Damme, Wim title = The COVID-19 pandemic: diverse contexts; different epidemics—how and why? date = 2020-07-27 keywords = COVID-19; China; Health; SARS; disease; epidemic; transmission summary = Since its emergence in Wuhan, China, in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 4 It was soon discovered that the virus is easily transmitted, can cause Summary box ► Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has spread to nearly all countries of the world in only a few months. 88 Box 2 On the use of mathematical models during epidemics A dominant way of studying the transmission dynamics of an infectious disease such as COVID-19, and predicting the amplitude and peak of the epidemic in a population (city, province, country) and analysing the effect of control measures is using mathematical models. doi = 10.1136/bmjgh-2020-003098 id = cord-344751-i4qnrtjq author = Van Praet, Jens T. title = Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date = 2020-09-10 keywords = PCR; SARS summary = Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. To evaluate the specificity of the immuno-assays, we used a set of serum samples from control patients with recent respiratory viral or atypical bacterial infections. To this end, we tested for cross-reactivity with sera of patients with other respiratory viral or atypical bacterial infections, including common coronavirus infections, since these may present with clinical and radiological findings similar to Covid-19. Our study focused on the clinical sensitivity and specificity of four commercial immuno-assays for anti-SARS-COV-2 IgG in the subset of patients presenting with negative RT-PCR and suspect CT findings. In summary, we found good clinical sensitivity of anti-SARS-Cov-2 IgG immunoassays for Covid-19 in the subset of patients with negative RT-PCR 14 days after onset of symptoms. doi = 10.1007/s15010-020-01523-3 id = cord-326148-9wpxm5of author = Van Walle, I. title = Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date = 2020-09-18 keywords = COVID-19; SARS; test summary = title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Studies containing potentially usable data on clinical performance of SARS-CoV-2 nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. doi = 10.1101/2020.09.16.20195917 id = cord-243806-26n22jbx author = Vandelli, Andrea title = Structural analysis of SARS-CoV-2 and prediction of the human interactome date = 2020-03-30 keywords = Fig; RNA; SARS; protein summary = Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5'' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . doi = nan id = cord-297652-ut6e1ysz author = Vanden Eynde, Jean Jacques title = COVID-19: A Brief Overview of the Discovery Clinical Trial date = 2020-04-10 keywords = Discovery; MERS; SARS summary = The study is entitled "Trial of Treatments for COVID-19 in Hospitalized Adults (DisCoVeRy)" (NCT04315948) [4] . In a MERS-CoV mouse model, the combination lopinavir/ritonavir/interferon β-1a, used as prophylactic and curative treatments, revealed no significant decrease in the viral load [9] . The results of an ongoing clinical trial (NCT Pharmaceuticals 2020, 13, 65 5 of 8 02845843 [4]), entitled "MERS-CoV infection treated with a combination of lopinavir/ritonavir and interferon Beta-1b", are eagerly awaited, but will not be disclosed before 2021. On March 28, the FDA issued an Emergency Use Authorization for use of hydroxychloroquine and chloroquine for patients who do not have access to the drugs via clinical trials [36] . The first cases of COVID-19 emerged in Wuhan, China, in late 2019, and to date there is no approved specific drug to cure patients infected by SARS-CoV-2. In Vitro Antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) doi = 10.3390/ph13040065 id = cord-335932-0phqok4g author = Vanhems, Philippe title = Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit date = 2020-03-30 keywords = SARS summary = title: Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit Lyon Study Group on Covid19 infection (Geriatric sectionAlphabetic order): Adrait, A, Benoist F, Castel-Kremer E, Chuzeville M, Dupin AC, Doh S, Kim B, Favrelle L, Hilliquin D, Kanafer N, Marion E, Martin-Gaujard G, Moyenin Y, Paulet-Lafuma H, Ricanet A, Saadatian-Elahi M, Vanhems P. To the Editor-SARS-CoV2 nosocomial transmission has been reported among healthcare professionals and patients. The nasal swab previously collected was retested on March 6 and confirmed positive for SARS-CoV2 by RT-PCR. Strict infection control measures and close monitoring of suspected cases of patients and healthcare professionals were subsequently performed to contain the intraunit transmission of the SARS-Cov-2 virus. The rapid spread of nosocomial COVID-19 in this ward confirms the contagiousness of SARS-CoV-2 in healthcare settings and the high mortality rates in this population. Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit doi = 10.1017/ice.2020.99 id = cord-300763-3ateeei3 author = Vannabouathong, Christopher title = Novel Coronavirus COVID-19: Current Evidence and Evolving Strategies date = 2020-05-06 keywords = COVID-19; China; People; Republic; SARS summary = The term PHEIC is defined as 27 : "an extraordinary event which is determined to constitute a public health risk to other States through the international spread of disease; and to potentially require a coordinated international response." Also, according to the WHO 28 , "This definition implies a situation that is serious, unusual, or unexpected; carries implications for public health beyond the affected state''s national border; and may require immediate international action." Eleven days later, on February 10, 2020, there were, cumulatively, 40,554 confirmed cases and 910 deaths globally across 25 countries, and the majority were identified in the People''s Republic of China 29 . In a cross-sectional analysis that included 1,023 COVID-19-related deaths in the People''s Republic of China, the Novel Coronavirus Pneumonia Emergency Response Epidemiology Team 43 found that >80% were patients ‡60 years of age; when extending this range to those who were ‡50 years of age, this number increased to >90% 44 . doi = 10.2106/jbjs.20.00396 id = cord-296109-kco85lqn author = Vanuytsel, Kim title = Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date = 2020-05-19 keywords = BMC; PCR; SARS summary = Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. In the United States, significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate COVID-19 patient care and public health management of the pandemic (Sharfstein et al., 2020) , impacting the timely mapping of the dynamics of viral spread in the general population, and more topically, the conservation of personal protective equipment. Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). doi = 10.1016/j.medj.2020.05.001 id = cord-265724-fdt00qw1 author = Varadarajan, Saranya title = EMMPRIN/BASIGIN as a biological modulator of oral cancer and COVID-19 interaction: novel propositions date = 2020-07-09 keywords = EMMPRIN; SARS summary = Apart from ACE-2, recently EMMPRIN, has been regarded as a target for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attachment and entry into the host cell. Since one of the routes of entry for the virus is the oral cavity, it becomes imperative to percept oral comorbidities such oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMDs) in terms of EMMPRIN as a target for SARS-CoV-2. 1 Angiotensin-Converting Enzyme 2 (ACE-2) on the host cells is the attachment protein for the spike receptor present on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). [4] [5] [6] Apart from ACE-2, recently extracellular matrix metalloproteinase inducer (EMMPRIN), which is also called BASIGIN/CD147, has been regarded as a target for SARS-CoV-2 attachment and its entry into the host cell. OSCC, by the virtue of upregulation of EMMPRIN expression (potential and alternative site for ''S'' receptor), increases the susceptibility to SARS-CoV-2 infection. doi = 10.1016/j.mehy.2020.110089 id = cord-257766-z7vcdtcq author = Varadhachary, Atul title = Salivary anti-SARS-CoV-2 IgA as an accessible biomarker of mucosal immunity against COVID-19 date = 2020-08-11 keywords = August; BRAVO; COVID-19; IgA; SARS; international summary = To minimize risk to lab personnel of exposure to SARS-CoV-2, our clinical study was limited to salivary samples collected from individuals who were at least a month post-symptom onset, so we cannot report on when IgA levels first appear in saliva, though that work is currently underway. Individual Immunity and Clinical Implications: Our observations that (i) we see a large variation in salivary IgA titer, even in pre-COVID-19 samples; (ii) elevated IgA levels appear to persist for at least 2-3 months; and (iii) individuals may develop mucosal IgA without an overt SARS-CoV-2 infection, each raise intriguing questions. . https://doi.org/10.1101/2020.08.07.20170258 doi: medRxiv preprint Community Surveillance and Herd Immunity: Reports that systemic IgA may be detectable earlier than IgG or IgM, 22,23 as early as two days after symptom onset are consistent with the early-response role played by IgA, as well as with our anecdotal observations that individuals can muco-convert to positive salivary IgA contemporaneously with viral detection by PCR. doi = 10.1101/2020.08.07.20170258 id = cord-329363-kaw3h5xm author = Vardeny, Orly title = Applying the Lessons of Influenza to COVID-19 During a Time of Uncertainty date = 2020-05-26 keywords = COVID-19; SARS summary = For patients with underlying cardiovascular disease, other opportunities for minimizing complications from infection include remaining up to date on other immunizations, including influenza vaccine, which is available and effective, and pneumococcal vaccine, as secondary bacterial infections often lead to hospitalizations among those with primary viral infections. Because viral illness has been shown to exacerbate underlying cardiac illness and can lead to acute events such as acute myocardial infarction or decompensated heart failure, efforts should be made to optimize guideline-directed treatment strategies that have been shown to improve clinical status in high-risk patients, and thus reduce the risk of worsening symptoms or acute events in case of infection. In patients without known or suspected COVID-19, this includes all evidence-based therapies in cardiovascular disease, such as aspirin, statins, and β-blockers for secondary prevention in patients with coronary disease, and guideline-directed medical therapy in those with heart failure. doi = 10.1161/circulationaha.120.046837 id = cord-296095-onereai5 author = Vardhan, Seshu title = In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19 date = 2020-07-28 keywords = ACE2; SARS; phytochemical summary = Considering the published literature on medicinal importance, 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). In this manuscript, 154 phytochemicals from limonoids and triterpenoids were selected by considering their known medicinal importance to search potential hits for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). Our recent molecular docking study on searching inhibitors for COVID-19 revealed that the phytochemical limonin known for inhibiting the replication of retroviruses like HTLV-I and HIV-1 showed the higher dock score towards the protein targets RdRp and ACE2 of SARS-CoV-2, and comparatively higher than the drug hydroxychloroquine [17] . doi = 10.1016/j.compbiomed.2020.103936 id = cord-272681-u3p0hsla author = Vargas-Gandica, Jair title = Ageusia and anosmia, a common sign of COVID-19? A case series from four countries date = 2020-07-14 keywords = COVID-19; SARS summary = As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to evolve, novel signs and symptoms continue to emerge and expand the clinical manifestations of coronavirus disease 2019 (COVID-19) (Rodriguez-Morales et al. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. Herein, we present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries. As we observed in our patients, deficits in olfactory and taste function were usually of acute onset and at early stages of the disease, presenting for most cases as the initial clinical manifestation throughout the first days (Beltran-Corbellini et al. Anosmia as a presenting symptom of SARS-CoV-2 infection in healthcare workers -a systematic review of the literature, case series, and recommendations for clinical assessment and management doi = 10.1007/s13365-020-00875-8 id = cord-274802-7ioiwsd8 author = Varghese, Praveen Mathews title = Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies date = 2020-08-19 keywords = COVID-19; China; CoV-2; Coronavirus; SARS; Syndrome; acute; cell; clinical; patient; severe; study summary = Proteomic and transcriptomic studies on bronchoalveolar lavage (BAL) samples from COVID-19 patients have also revealed considerable insights into the expression of SARS-CoV-2 receptors, co-receptors, immune responses, as well as risk factors for severe disease e.g. age and co-morbidities. Furthermore, treatment with a recombinant C5a antibody on 2 male COVID-19 patients aged 54 and 67 years showed significant benefit in suppressing complement hyperactivation, which contributes to the excessive immune response causing aggravated inflammatory lung injury, a hallmark of SARS-CoV-2 pathogenesis and lethality (242) . Consistent with endothelial injury, the significantly elevated levels of von Willebrand factor found in the patient with severe COVID-19 has led to the idea that the infection of the ACE2 expressing endothelium by SARS-CoV-2 induces injury and activates the complement , which sets up a feedback loop that maintains a state of inflammation (243, (268) (269) (270) . Initial clinical studies in China involving 100 SARS-CoV-2 infected patients, who were treated with Chloroquine, showed amelioration of pneumonia, shortened disease progression, increased resolution of lung lesions on CT, and a better virus-negative conversion (313, 314) . doi = 10.1016/j.imbio.2020.152008 id = cord-323185-n0rubc72 author = Varshney, Bhavna title = SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date = 2012-01-12 keywords = ERK; IL2; SARS; runx1 summary = Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. In this study, we confirmed the putative interaction of 3b and RUNX1b and observed in vivo recruitment of 3b on the RUNX1 binding element on the IL2 promoter in transiently transfected human T, jurkat cells. We next determined the positive effect of 3b-RUNX1b interaction on the expression of RUNX1b regulated chemokine MIP-1a, reported to be upregulated in SARS-CoV infected monocyte derived dendritic cells. To investigate whether 3b-RUNX1b interaction leads to the recruitment of 3b on RUNX1 binding elements on the endogenous IL2 promoter, ChIP assays were performed in RUNX1b/CBFb endogenously expressing jurkat cells that are abortively infected by SARS-CoV. To investigate the effect of SARS-CoV 3b protein on the RUNX1b transcriptional activity, reporter gene assays were performed using the mouse IL2 promoter. doi = 10.1371/journal.pone.0029542 id = cord-318625-hf7fgtnp author = Vashi, Yoya title = Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens date = 2020-05-27 keywords = SARS summary = The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. The potential epitope regions were predicted using the sequence of the S protein of SARS-CoV-2 that showed the least variability (GenBank accession number NC_045512). We identified 18 linear epitopes, predicted by ElliPro (IEDB), which contained regions from 19 of our selected peptides (highlighted in red in Table 2 ). The study could help us to use the predicted peptide as an immunogen for the development of diagnostics and vaccines against SARS-CoV-2. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2. doi = 10.1016/j.meegid.2020.104382 id = cord-265322-3854ddb9 author = Vavougios, George D. title = A data-driven hypothesis on the epigenetic dysregulation of host metabolism by SARS coronaviral infection: potential implications for the SARS-CoV-2 modus operandi date = 2020-04-23 keywords = CoV-2; SARS summary = Based on both structural and syndromic similarities with SARS-CoV, a hypothesis is formed on SARS-CoV-2 potential to affect the host''s metabolism as part of its lifecycle. In the literature, SARS-CoV has been known to cause de novo diabetes by ACE2-dependent uptake on pancreatic isle cells, and furthermore dysregulate lipid autophagy in favor of the viral lifecycle. Their study provided the foundation for a hypothesis put forth by Fang and colleagues indicating that diabetic and hypertensive patients exposed to ACE2 inhibitors may be at an increased risk of more severe COVID-19 (7) . In another study, SARS-CoV was shown to cause diabetes by ACE2-dependent infection of pancreatic isle cells (10) . Future studies should determine SARS-CoV-2 interaction and effect on the human transcriptome, further identifying drug targets using pharmacogenomic enrichment analyses. Natural small molecules as inhibitors of coronavirus lipid-dependent attachment to host cells: a possible strategy for reducing SARS-COV-2 infectivity? doi = 10.1016/j.mehy.2020.109759 id = cord-035203-dnoc0xcv author = Vaňková, Eva title = Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic date = 2020-10-29 keywords = Fig; PLA; SARS; mask summary = Complete decontamination of PLA surfaces from externally applied Staphylococcus epidermidis, Escherichia coli, Candida albicans and SARS-CoV-2 was achieved using all disinfectants tested, and human adenovirus was completely inactivated by sodium hypochlorite-containing disinfectant. In the present study, we have investigated FDM 3D-printed PLA structure and porosity after exposure to common chemical disinfectants including ethanol, isopropanol and a commercial disinfectant containing sodium hypochlorite, which are easily accessible. In addition, we examined the efficiency of PLA disinfection after artificial contamination with bacteria (Staphylococcus epidermidis, Escherichia coli), a yeast fungus (Candida albicans), viruses (SARS-CoV-2 and human adenovirus -HAdV) or natural contamination by wearing the masks. The effect of immersing in three chemical disinfectants (96% ethanol, 70% isopropanol and the commercial disinfectant and bleach SAVO Original, Unilever ČR s.r.o., Czech Republic containing 0.85% sodium hypochlorite diluted with water (2:9)) was tested by repeated (5 × 15 min) cycles and long-term (24 h) exposure. Effect of ethanol, isopropanol and sodium hypochlorite on disinfection of PLA material contaminated with bacteria, yeast fungus or viruses doi = 10.7717/peerj.10259 id = cord-326514-7plamtl8 author = Veerus, Piret title = Seroprevalence of SARS‐CoV‐2 antibodies among pregnant women in Estonia: a call for epidemiological studies date = 2020-09-24 keywords = SARS summary = On April 7, 2020 Mehreen Zaigham and Ola Andersson published a systematic review of maternal and perinatal outcomes in 108 pregnancies with Covid‐19 concluding that careful monitoring of such pregnancies and is warranted.(1) We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS‐CoV‐2) causing Covid‐19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. 1 We would like to emphasise the need to assess objectively the impact of the novel Severe Acute Respiratory Coronavirus Type 2 (SARS-CoV-2) causing Covid-19 disease on pregnancy and perinatal outcomes by conducting epidemiological studies among pregnant women. In comparison with available data from Spain, 9 seroprevalence of SARS-CoV-2 antibodies among pregnant women in Estonia was 10 times lower than among the general population in Spain indicating the possibility of regional differences in the incidence of COVID-19 across Europe. doi = 10.1111/aogs.13995 id = cord-343757-e4hmo4yc author = Velavan, Thirumalaisamy P. title = The COVID‐19 epidemic date = 2020-02-16 keywords = China; SARS summary = The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People''s Republic of China, has spread to many other countries. The initial clinical sign of the SARS-CoV-2-related disease COVID-19 which allowed case detection was pneumonia. A combination of the antiretroviral drugs lopinavir and ritonavir significantly improved the clinical condition of SARS-CoV patients [17] and might be an option in COVID-19 infections. Repurposing these available drugs for immediate use in treatment in SARS-CoV-2 infections could improve the currently available clinical management. Given the fragile health systems in most sub-Saharan African countries, new and re-emerging disease outbreaks such as the current COVID-19 epidemic can potentially paralyse health systems at the expense of primary healthcare requirements. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Clinical characteristics of 2019 novel coronavirus infection in China. doi = 10.1111/tmi.13383 id = cord-303054-s1clwunc author = Velly, Lionel title = Guidelines: Anaesthesia in the context of COVID-19 pandemic date = 2020-06-05 keywords = COVID-19; N95; SARS; infection; patient; risk; surgery summary = Operating theatre 12 R1.3.1 -Experts suggest that healthcare professionals involved in airway management (intubation, extubation, supraglottic airway insertion and/or removal…), or those who could be brought to do so in some given situations, wear a fit tested respirator mask (Respirator N95 or FFP2 standard, or equivalent) in addition to a disposable face shield or at least, in the absence of the latter, safety goggles, regardless of the patient''s COVID-19 status (Table 1) The presence of major (i.e., very frequent or relatively characteristic) and/or minor (i.e. more inconsistent and/or less specific) symptoms allows to orient the preoperative COVID-19 status assessment, and then to estimate the benefit/risk balance of maintaining or postponing the surgery, taking into account the risk of contamination of health personnel and others patients within the care structure. doi = 10.1016/j.accpm.2020.05.012 id = cord-255178-mb784dam author = Velu, P. title = Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution date = 2020-06-08 keywords = June; SARS summary = NP and sputum samples were tested on the altona RealStar® rRT-PCR 145 assay to ensure the absence of SARS-CoV-2 and pooled for use as a matrix for spiking 146 in RNA for LOD studies and accuracy studies. Probit analysis was applied to the NP data after an additional five replicates 187 of testing were performed at 0.8, 0.6, 0.5, 0.4, and 0.2 gene copies/reaction, and 188 narrowed the LOD to 2.7 gene copies/reaction at 95% detection rate (Figure 2) The in silico analysis for inclusivity that was performed by the manufacturer of the kit 197 found 100% homology of the E gene and S gene forward and reverse primers and probes 198 with 563 whole-genome sequences of SARS-CoV-2 published in GISAID and NCBI as of 199 3/16/2020 [9] . doi = 10.1101/2020.06.05.20109637 id = cord-309876-l0xginsa author = Vena, Antonio title = Prevalence of Antibodies to SARS-CoV-2 in Italian Adults and Associated Risk Factors date = 2020-08-27 keywords = CoV-2; SARS summary = A generalized estimating equations model showed that the main risk factors associated with SARS-CoV-2 seroprevalence were the following: an occupational exposure to the virus [Odd ratio (OR) = 2.36; 95% CI 1.59–3.50, p = 0.001], being a long-term care facility resident (OR = 4.53; 95% CI 3.19–6.45, p = 0.001), and reporting previous symptoms of influenza-like illness (OR = 4.86; 95% CI 3.75–6.30, p = 0.001) or loss of sense of smell or taste (OR = 41.00; 95% CI 18.94–88.71, p = 0.001). In the present observational study performed on a large sample of subject in northern Italy, we found the following: (1) the overall seroprevalence of anti-SARS-CoV-2 antibodies (IgG and/or IgM) was 11.0%; (2) occupational exposure to the virus, long-term care facility residency, as well as previous symptoms of influenza-like illness or loss of sense of smell or taste were independently associated with anti-SARS-CoV-2 positivity. doi = 10.3390/jcm9092780 id = cord-284950-qqje5s04 author = Venkataraman, Thiagarajan title = The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis date = 2017-07-31 keywords = EGFR; SARS; TGF; fibrosis summary = In this article, we summarize pulmonary fibrotic changes observed after a SARS-CoV infection, discuss the extent to which other respiratory viruses induce fibrosis, describe available animal models to study the development of SARS-CoV induced fibrosis and review evidence that pulmonary fibrosis is caused by a hyperactive host response to lung injury mediated by epidermal growth factor receptor (EGFR) signaling. In this article, we summarize observations of pulmonary fibrosis during and after the SARS epidemic, note the extent to which fibrosis occurs after other pulmonary viral infections, describe efforts to recapitulate fibrotic changes in mouse models of SARS, and review evidence that the condition represents a hyperactive response to lung injury, driven by proinflammatory mediators acting through epidermal growth factor receptor (EGFR) signaling. After an illness lasting 1e2 weeks, most patients resolve the infection, however about one-third develop severe pulmonary complications leading to acute lung injury and acute respiratory distress syndrome (ARDS), resulting in intubation and prolonged hospitalization (Tsui et al., 2003) . doi = 10.1016/j.antiviral.2017.03.022 id = cord-297671-3d3gcn6k author = Venn, April M.R. title = A case series of pediatric croup with COVID-19 date = 2020-09-15 keywords = NRE; SARS summary = We describe three previously healthy children, admitted from our emergency department (ED) to our free-standing children''s hospital, as the first documented cases of croup as a manifestation of SARS-CoV-2 infection. All three cases (ages 11 months, 2 years, and 9 years old) presented with non-specific upper-respiratory-tract symptoms that developed into a barky cough with associated stridor at rest and respiratory distress. The novel 2019 coronavirus SARS-CoV-2, responsible for COVID-19 disease, commonly presents in children with fever, cough or shortness of breath. [7] After an electronic health record database review, we describe this ca 1 se series of our ED''s only three cases, between March 1, 2020 and July 31, 2020, of children who received nebulized racemic epinephrine (NRE) and had a positive SARS-CoV-2 infection. [15] Pediatric croup patients who received ≥3 NRE in one children''s hospital were more likely to need intensive care management. doi = 10.1016/j.ajem.2020.09.034 id = cord-334300-hnrmaytm author = Ventura Fernandes, Bianca H title = Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date = 2020-10-20 keywords = SARS; covid-19 summary = Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. Based on the advantages of using zebrafish as a model in research, herein we suggest doing this to test the safety of the putative vaccine candidates and to study immune response against the virus. Based on the in vivo and in silico results presented here, we propose the zebrafish as a model for translational research into the safety of the vaccine and the immune response of the vertebrate organism to the SARS-CoV-2 virus. 169 In the global task to develop the vaccine and possible therapeutic approaches for 170 COVID-19, several animal models have been proposed, such as mice 10 , hACE2 171 transgenic mice 11 , alpaca 12 , golden Syrian hamsters, ferrets, dogs, pigs, chickens, and 172 cats 9 , and species of non-human primates 10 . doi = 10.1101/2020.10.20.346262 id = cord-280821-kc0ut4oy author = Venturini, Elisabetta title = Treatment of children with COVID-19: position paper of the Italian Society of Pediatric Infectious Disease date = 2020-09-24 keywords = COVID-19; Cov-2; SARS; day; patient summary = The Italian Society of Pediatric Infectious Diseases steering and scientific committee developed a position paper on treatment of children with COVID-19, reviewing the current literature on this topic and providing indications based on the available literature data. Currently, American guidelines on COVID-19 treatment published in May 2020, recommend both in children and adults to use lopinavir/ritonavir only in the context of clinical trials, given the lack of effectiveness reported now in literature [9, 12] . The latest Chinese guidelines on SARS-Cov-2 pneumoniae do not recommend the use of a specific antiviral for the treatment of COVID-19, and nevertheless include lopinavir/ritonavir among the available therapeutic options for hospitalized patients [29] . In May 2020, following an assessment of the emergency use authorization criteria and available scientific evidence, the FDA issued an emergency use authorization allowing for the administration of remdesivir intravenously by health care providers for the treatment of COVID-19 suspected or laboratoryconfirmed in adults and pediatric patients hospitalized with severe disease [34] . doi = 10.1186/s13052-020-00900-w id = cord-275004-qzg03dvg author = Veras, Flavio Protasio title = SARS-CoV-2–triggered neutrophil extracellular traps mediate COVID-19 pathology date = 2020-09-14 keywords = Fig; SARS; covid-19; net; patient summary = The concentration of NETs was augmented in plasma, tracheal aspirate, and lung autopsies tissues from COVID-19 patients, and their neutrophils released higher levels of NETs. Notably, we found that viable SARS-CoV-2 can directly induce the release of NETs by healthy neutrophils. The well-known similarities between sepsis and key events involved in the COVID-19 pathophysiology, such as cytokine overproduction (Mehta et al., 2020) , microthrombosis (Magro et al., 2020; Dolhnikoff et al., 2020) , and acute respiratory distress syndrome (Lai et al., 2020) , led us to hypothesize that NETs are triggered during SARS-CoV-2 infection and might contribute to tissue injury in COVID-19 patients. In summary, in the present study, we demonstrated that in COVID-19 patients, circulating and lung-infiltrating neutrophils are releasing higher levels of NETs. We also showed that SARS-CoV-2 directly stimulates neutrophils to release NETs in mechanisms dependent on ACE2 and serine protease activity axis and effective viral replication. doi = 10.1084/jem.20201129 id = cord-322148-sfr9twfa author = Verbeek, P. Richard title = Loss of Paramedic Availability in an Urban Emergency Medical Services System during a Severe Acute Respiratory Syndrome Outbreak date = 2008-06-28 keywords = SARS summary = Objectives: To describe the loss of paramedic availability to Toronto Emergency Medical Services during a biphasic (SARS‐1 and SARS‐2) outbreak of severe acute respiratory syndrome (SARS). [3] [4] [5] Ontario 8, 9 In response to the SARS outbreak, a program of contact tracing, quarantine, and medical surveillance of paramedics was implemented by Toronto Emergency Medical Services (EMS) and base hospital of Sunnybrook and Women''s College Health Sciences Centre. Paramedics were advised to wear gloves, mask, and gown for patients with ''''an acute Home quarantine (HQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital or to a patient with suspect/probable SARS under home observation for ten days from the last known exposure date. Work quarantine (WQ) was defined as keeping asymptomatic paramedics with a history of unprotected exposure to a SARS-affected hospital during the SARS-2 outbreak on duty while wearing PPE at all times. doi = 10.1197/j.aem.2004.03.021 id = cord-286015-oonfpa0c author = Verbeure, Birgit title = Patent pools and diagnostic testing date = 2006-01-27 keywords = SARS; genetic; patent; pool summary = Recent studies have reported on the licensing practices of the owners of patents for genetic inventions [3] [4] [5] [6] , and concerns have been raised that patent thickets, resulting in royalty stacking (see Glossary), block access to patented technology through the accumulated license fees that a downstream inventor has to pay to upstream patent holders. In the late 1990s, several patent pools were formed in the electronics and telecommunications industries, starting with the moving picture experts group (MPEG)-2 pool in 1997 for inventions relating to the MPEG-2 standard (see Klein [15] and the Guidelines on the Application of Article 81 of the EC Treaty to Technology Transfer Agreements [16] . The Organization for Economic Co-operation and Development (OECD; www.oecd.org) considers the concept of a patent pool to be an interesting one for biotechnology but has some doubts as to whether the technologies and markets for genetic inventions are amenable to patent pools [20] . doi = 10.1016/j.tibtech.2006.01.002 id = cord-266558-vd41u2t1 author = Verdecchia, Paolo title = The pivotal link between ACE2 deficiency and SARS-CoV-2 infection date = 2020-04-20 keywords = ACE2; SARS; receptor summary = Clinical reports of patients infected with SARS-CoV-2 show that several features associated with infection and severity of the disease (i.e., older age, hypertension, diabetes, cardiovascular disease) share a variable degree of ACE2 deficiency. The entry of SARS-CoV-2 into cells is mediated by the efficient binding of the spike (S) viral protein, a 1273 amino acid long protein which belongs to the viral envelope and protrudes outwards with a ''corona'' like appearance, to the angiotensin converting enzyme 2 (ACE2) receptors. In the current pandemic of SARS-CoV-2 infection with associated pulmonary inflammation and Acute Respiratory Distress Syndrome (ARDS), it is interesting to note that angiotensin II also interferes with adaptive immunity by activating machrophages [24] and other cells of the immune system, with consequent increased production of IL-6, [25] TNFα and other inflammatory citokynes. The authors found that even the isolated spike viral protein induced down-regulation of ACE2 receptors with concomitant increase of angiotensin II in the lung tissue and precipitation of severe pulmonary inflammatory lesions. doi = 10.1016/j.ejim.2020.04.037 id = cord-291356-df5n5v09 author = Verma, Saguna title = ACE2 receptor expression in testes: implications in coronavirus disease 2019 pathogenesis date = 2020-05-19 keywords = ACE2; SARS summary = Expression of angiotensin-converting enzyme 2, receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is high in the testes, therefore SARS-CoV-2 infection and its association with male reproductive health should be investigated in male coronavirus disease 2019 patients. SARS-CoV-2 infection is robust in cells expressing angiotensinconverting enzyme 2 (ACE2) receptor, a type I integral membrane protein that controls cardiac and kidney functions by negatively regulating renin-angiotensin systems [2] . High ACE2 expression may augment virus infection in the lung, heart, and small intestine that might explain the pathophysiology of acute lung and myocardial injury, and gastrointestinal symptoms reported in COVID-19 patients [1] . Cytokines and chemokines induced by SARS-CoV-2 entry into the LC and SC may recruit peripheral immune cells including macrophages and virus-specific T cells that may further potentiate inflammation and orchitis in accordance with reported symptoms from 19% of patients in study by Pan et al. doi = 10.1093/biolre/ioaa080 id = cord-303585-8py6joh6 author = Verma, Surjeet title = Anti-SARS-CoV Natural Products With the Potential to Inhibit SARS-CoV-2 (COVID-19) date = 2020-09-25 keywords = 3CL; COVID-19; SARS summary = The objective of this review was to collate information regarding the potential of plants and natural products to inhibit coronavirus and targets associated with infection in humans and to highlight known drugs, which may have potential activity against SARS-CoV-2. Finally, this review discusses the potential use of Southern African medicinal plants, which have traditionally been used for the treatment of symptoms related to respiratory viral infections, and influenza, to inhibit SARS-CoV-2. The selective index (SI) values of compounds 1-6 were found to be 58, >510, 111, 193, 180 , and >667, respectively, indicating that these plants were able to inhibit viral replication without having a cytotoxic effect on the host cells. A chalcone, xanthoangelol E (8), isolated from the ethanolic leaf extract of Angelica keiskei (Miq.) Koidz., showed inhibitory activity against SARS-CoV 3CL pro and a papain-like protease (PL pro ) with IC 50 values of 11.4 and 1.2 µM, respectively, using cell-free assays. doi = 10.3389/fphar.2020.561334 id = cord-305703-ypeibwje author = Veronese, Nicola title = Use of Corticosteroids in Coronavirus Disease 2019 Pneumonia: A Systematic Review of the Literature date = 2020-04-24 keywords = ARDS; COVID-19; SARS summary = For each article, we extracted data regarding authors, year of publication, country, city or region in which the study was conducted, the period of observation, how the diagnosis of COVID-19 was obtained, the stage of COVID-19 infection (asymptomatic forms, pneumonia, acute respiratory distress syndrome (ARDS), requiring intensive care unit, ICU; convalescent), sample size included, number of males and females, mean age and its standard deviation (or similar information such as median and range), the percentage of people treated with corticosteroids in the sample as a whole, and, if possible, the route of administration and type of corticosteroid considered. Overall, two studies reported negative findings regarding these medications, one reported no significant association between corticosteroids and clinical outcomes, and one concluded that methylprednisolone was associated with a significant reduction of mortality in patients with COVID-19 pneumonia developing ARDS. doi = 10.3389/fmed.2020.00170 id = cord-286901-whvq8y1p author = Vidali, Sofia title = D-dimer as an indicator of prognosis in SARS-CoV-2 infection: a systematic review date = 2020-07-13 keywords = ARDS; COVID-19; SARS summary = This study aims to highlight the correlation between elevated D-dimer (an indirect thrombosis marker) and the increased rate of poor prognosis-associated conditions, and to introduce D-dimer-labelled anticoagulant administration as a potentially useful tool to prevent complications and positively influence coronavirus disease 2019 (COVID-19) course. The keywords and their variants (differently combined) used for the search were "COVID-19", "2019-nCoV", "2019 novel coronavirus", "SARS-CoV-2", "D-dimer", "coagulation", "hypercoagulative state", "laboratory analysis", "ARDS", "haemostasis", "thrombosis", "pulmonary embolism", "disseminated intravascular coagulation (DIC)", "heparin" and "anti-coagulation". The alterations of coagulation factors during SARS-CoV-2 infection and specifically that of D-dimer are, as documented in the clinical experiences described here, severe, constant and correlated with prognosis, complications and CEP rates. Among the factors that were demonstrated to be connected to the clinical outcome of COVID-19 patients, the presence of comorbidities may represent a confounding factor for the interpretation of D-dimer and other coagulation parameter alterations, especially considering the heterogeneous aetiology of thrombotic and thrombophilic states. doi = 10.1183/23120541.00260-2020 id = cord-330690-cupy89gl author = Vierucci, Francesco title = How COVID-19 Pandemic Changed Children and Adolescents Use of the Emergency Department: the Experience of a Secondary Care Pediatric Unit in Central Italy date = 2020-09-23 keywords = March; SARS summary = During phase 1 (national lockdown period, March 9th-May 3rd, 2020) the Italian Ministry of Health recommended to avoid direct access to the emergency department (ED) in case of fever and/or cough or other respiratory symptoms, favoring home care or phone consultation for ill patients without compromised general conditions [10] . The aims of this study were to (1) evaluate the impact of COVID-19 pandemic on the activity of a secondary care Italian Pediatric Unit assessing, in particular, the characteristics of pediatric ED consultations performed in 2020 before and after the beginning of lockdown; (2) evaluate the prevalence of SARS-CoV-2 infection in children and adolescents referred to ED; and (3) compare pediatric ED activity during the same period of 2019 and 2020. doi = 10.1007/s42399-020-00532-5 id = cord-325320-v9e2axf4 author = Vigil‐De Gracia, P. title = Pregnancies recovered from SARS‐CoV‐2 infection in the second and third trimesters: obstetric evolution date = 2020-09-30 keywords = SARS summary = However we do not know the maternal and perinatal results of pregnant women recovered from SARS-CoV-2 infection continuing the pregnancy. This first report of pregnant women infected with COVID-19 and recovered allows us to know that the patient continues to be at high obstetric risk, especially due to the PROM and labor before 39 weeks. A study of 16 placentas from SARS-CoV-2 patients reports an increase in the rates of maternal and fetal vascular malperfusion features; two cases were more than 30 days after the appearance of symptoms and these placentas showed fetal vascular malperfusion (clustered avascular villi, hipercoiled umbilical cord, chorangiosis) 3 . In our opinion, in pregnant patients infected and recovered with SARS-CoV-2, there is a "placental inflammatory syndrome" characterized by spontaneous onset of labor, premature births, premature rupture of membranes, alteration in the cardiotocograph trace, fetal distress, death and placental alterations. Fetal deaths in pregnancies with SARS-CoV-2 infection in Brazil: A case series. doi = 10.1002/uog.23134 id = cord-316702-dj2fo8sn author = Vignesh, Ramachandran title = Is Herd Immunity Against SARS-CoV-2 a Silver Lining? date = 2020-09-30 keywords = COVID-19; CoV-2; SARS summary = Since many studies from different geographical locations are documenting preexisting immunity to SARS-CoV-2, it will be important to define specificities of these T and B cell immune response carefully to assess their association with COVID-19 disease severity. This preexisting cross-reactive T and B cell immunity to SARS-CoV-2 may have wide implications as this could explain differential clinical outcomes in COVID-19 patients, disease severity, vaccine development, and important in accessing herd immunity for SARS-CoV-2 viral infection/COVID-19 disease. Several studies have provided strong evidence for the importance of SARS-CoV-2 specific CTLs, and T helper cells in mild and moderate patients compared to severe COVID-19 disease (27, 28, (31) (32) (33) . Several studies have provided strong evidence for the importance of SARS-CoV-2specific neutralizing antibodies in association with less disease severity in COVID-19 patients (38, 39) . A recent modelling study has estimated that about one in five individuals worldwide would be at increased risk of severe COVID-19, upon infection with SARS-CoV-2, owing to the underlying conditions. doi = 10.3389/fimmu.2020.586781 id = cord-320266-7gzx6ljt author = Vigneshwar, Navin G. title = Positive tracheal SARS-CoV-2 RNA test after three negative SARS-CoV-2 RNA tests in a patient with COVID-19 date = 2020-06-12 keywords = SARS summary = Perioperative guidelines for patients with suspected coronavirus disease (COVID-19) often rely on nasopharyngeal swab testing for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Herein, we report the case of a patient with three consecutive negative nasopharyngeal swab tests followed by a positive tracheal aspirate test for SARS-CoV-2 RNA (Figure 1 ). On admission, a viral respiratory panel and two nasopharyngeal swab SARS-CoV-2 RT-PCR tests separated by four hours were negative. On hospital day 1, the patient''s hypoxia improved, and results from a repeat SARS-CoV-2 RT-PCR test from a nasopharyngeal swab were negative. During the novel influenza A (H1N1) pandemic, approximately 10% of patients showed positive RT-PCR test results in respiratory secretions after intubation when prior tests on nasopharyngeal swab gave negative results. Following further deterioration of the patient''s respiratory status and endotracheal intubation, a tracheal sample was positive for SARS-CoV-2 RNA. doi = 10.1007/s12630-020-01742-0 id = cord-343604-v986m9jd author = Vijayakumar, Balaji Gowrivel title = In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date = 2020-08-06 keywords = RNA; SARS summary = title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. Coronavirus main 403 proteinase (3CLpro) structure: basis for design of anti-SARS drugs Structural basis for inhibition 675 of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir doi = 10.1016/j.ejphar.2020.173448 id = cord-221611-eeybl35x author = Vijayan, Ramachandran title = Structure-based inhibitor screening of natural products against NSP15 of SARS- CoV-2 revealed Thymopentin and Oleuropein as potent inhibitors date = 2020-07-28 keywords = NSP15; SARS; Thymopentin summary = Here, we screened Selleckchem Natural product database of compounds against the NSP15, Thymopentin and Oleuropein showed highest binding energies. The structure of SARS-CoV-2 NSP15 protein is very similar to other Coronavirus NSP15 monomers, consisting of mainly three regions: the N-terminal domain, a subsequent middle domain, and a catalytic C-terminal nidoviral RNA uridylate-specific endoribonuclease domain. In order to design specific inhibitors against the Non-structural protein 15 (NSP15), Libraries of Selleckchem Natural products (https://www.selleckchem.com/screening/natural-productlibrary.html) were chosen for Virtual screening [24] [25] [26] . After the docking studies, the Molecular dynamic simulation [25] [26] [27] was performed for the top five screened compounds (Thymopentin, Ginsenoside, Oleuropein, Akebia Saponin D and Keampferitrin), to understand the binding stability of the docked complexes. In this study, structure based virtual screening followed by the validation through Molecular dynamic simulation approaches were carried out to find antiviral leads against NSP15 of SARS-CoV-2. doi = nan id = cord-259267-trpo5w11 author = Vilibic-Cavlek, Tatjana title = Severe acute respiratory syndrome coronavirus 2 seroprevalence among personnel in the healthcare facilities of Croatia, 2020 date = 2020-08-26 keywords = SARS; covid-19 summary = From April 25 to May 24, 2020, when the COVID-19 epidemic curve was approaching the end of the first wave in Croatia, a total of 592 serum samples from HCWs and allied/auxiliary HCWs were tested for the presence of SARS-CoV-2 antibodies. Two studies from the United Kingdom showed that 18% of symptomatic HCWs 6 and 3% of asymptomatic HCWs tested RT-PCR-positive for SARS-CoV-2 7 . Data are limited on the seroprevalence of COVID-19 among HCWs. In this study, using ELISA, SARS-CoV-2 IgG antibodies were detected in 2.7% of participants, while neutralizing antibodies were detected in 1.5% of participants, indicating a low seroprevalence among HCWs in Croatia. In the present study, three seropositive HCWs reported experiencing COVID-19-consistent clinical symptoms, while six were asymptomatic. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients doi = 10.1590/0037-8682-0458-2020 id = cord-344798-q34j4zxu author = Villalba, María Caridad Montalvo title = Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients date = 2020-08-29 keywords = IFN; RANTES; SARS; TGF summary = title: Interferon gamma, TGF-β1 and RANTES expression in upper airway samples from SARS-CoV-2 infected patients The aim of this study was evaluate inflammatory response using the expression of immune mediators with antiviral, immunosuppression and chemotactic functions in the primary site of SARS-CoV-2 replication, at early stage of infection. J o u r n a l P r e -p r o o f Taking into account that Ct value has a correlation with the amount of RNA present in the samples, it was found that medians and IQR of SARS-CoV-2 viral titer was similar in asymptomatic (33.00, 29.00-37.00) and symptomatic (30, 27 .00-37.00) cases; and comparison between groups did not show difference (p=0.4373). As show our results, SARS-CoV-2 infection induced high IFN-γ expression in swabbed cells from upper airway; its expression was higher in symptomatic patients in comparison with asymptomatic individuals. Also, positive correlation between IFN-γ and TGF-β1 provided evidence of immune response control could determinate the asymptomatic presentation of SARS-CoV-2 infection. doi = 10.1016/j.clim.2020.108576 id = cord-331375-tbuijeje author = Villalobos, Carlos title = SARS-CoV-2 Infections in the World: An Estimation of the Infected Population and a Measure of How Higher Detection Rates Save Lives date = 2020-09-25 keywords = SARS; covid-19; detection; number summary = This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This paper provides an estimation of the accumulated detection rates and the accumulated number of infected individuals by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). By weighting the age-stratified IFRs by the country population agegroups shares in each country, it is possible to obtain countryspecific IFRs. The relevance of this study is 3-fold: Firstly, the estimation of the true number of infections includes not only confirmed cases but COVID-19 undetected cases, as well as SARS-CoV-2infected individuals without the disease, or in a pre-symptomatic stage. In order to provide reliable estimates of the number of SARS-CoV-2 infections and of the cumulative detection rates, it is necessary that governments provide real-time information about the number of COVID-19 deaths. doi = 10.3389/fpubh.2020.00489 id = cord-292173-95t89yee author = Villani, Federico Alcide title = COVID-19 and Dentistry: Prevention in Dental Practice, a Literature Review date = 2020-06-26 keywords = COVID-19; N95; SARS; dental; mask summary = Several authors have highlighted the importance of telephone triage and/or clinic questionnaires, body temperature measurement, usage of personal protective equipment, surface disinfection with ethanol between 62% and 71%, high-speed instruments equipped with an anti-retraction system, four-handed work, and large-volume cannulas for aspiration. The aim of this narrative review is to investigate preventive measures in dental practice by assessing the operator and patient health protection during the new COVID-19 emergency by considering past experiences in terms of prevention, as the virus was only recently discovered. In addition, a second search was made: "masks" OR "disinfectants" OR "PPE" OR "dental equipment" AND "Covid-19" OR "coronavirus" OR "SARS-CoV-2". instead obtained diametrically opposing results; they showed, through a randomized controlled clinical study on 3591 subjects, that health workers who used N95 masks continuously during the shift or in situations considered to be at high risk, presented an 85% chance of not contracting a viral infection transmitted via droplets [36] . doi = 10.3390/ijerph17124609 id = cord-354612-7f91l0n9 author = Villar, Livia Melo title = USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS date = 2020-07-23 keywords = SARS summary = title: USEFULNESS OF SALIVA SAMPLES FOR DETECTING SARS-CoV-2 RNA AMONG LIVER DISEASE PATIENTS A total of four individuals (two hepatitis cases and two without liver disease) were negative to SARS CoV-2 in NPS and saliva (100% of specificity). Positive concordant results in NPS and saliva were observed in seven individuals (two hepatitis cases and 5 without liver disease) until 7 days after onset of symptoms (100% of sensitivity). This is the first report of SARS CoV-2 detection in saliva samples among liver disease patients showing best results until 7 days of beginning of symptoms. In addition, there is no information regarding the usefulness of saliva for detecting SARS CoV-2 RNA in individuals presenting comorbidities, such as liver disease. Since saliva can be collected easily, SARS CoV-2 RNA detection in saliva can be useful strategy to increase the access of sample collection for the diagnosis of COVID-19 in patients with liver disease. doi = 10.1016/j.jinf.2020.07.017 id = cord-281281-knelqmzx author = Villas-Boas, Gustavo R. title = The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date = 2020-09-07 keywords = ACE2; COVID-19; China; CoV-2; RNA; SARS; figure; virus summary = The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. doi = 10.3390/molecules25184086 id = cord-263803-0n41gylj author = Villoutreix, Bruno O. title = Prevention of COVID-19 by drug repurposing: rationale from drugs prescribed for mental disorders date = 2020-06-25 keywords = SARS; drug summary = We also compared these 18 drugs with published molecules known to have in vitro antiviral activities [1, 2] using various chemoinformatics strategies (e.g., computation of molecular descriptors and compounds clustering carried out on J o u r n a l P r e -p r o o f about 300 molecules with in vitro antiviral activities on various viruses including SARS-CoV-2). Overall, our analysis suggests that the most commonly prescribed psychotropic drugs, including some antihistamine agents used as anxiolytics, possess in vitro antiviral activity ( Table 1 ). In summary, we propose that some of the drugs commonly prescribed to psychiatric patients could protect them from SARS-CoV-2 infection via the modulation of the endo-lysosomal pathway, membrane fusion and yet to be characterized interactions with specific receptors (e.g., nAChR, ACE2 and Sigma receptors, Fig. 1 ). Based upon the above analysis, we suggest that one of these CAD molecules or a combination could be used as preventive treatment against SARS-CoV-2 infection, especially drugs with reduced adverse effects (e.g., low dosage nicotine patch associated with an antihistamine agent). doi = 10.1016/j.drudis.2020.06.022 id = cord-286168-019rcbpg author = Vindegaard, Nina title = COVID-19 pandemic and mental health consequences: systematic review of the current evidence date = 2020-05-30 keywords = COVID-19; SARS; health summary = Out of these, only two studies evaluated patients with confirmed COVID-19 infection, whereas 41 evaluated the indirect effect of the pandemic (2 on patients with preexisting psychiatric disorders, 20 on medical health care workers, and 19 on the general public). 23, 24 We aimed to systematically review the literature in order to provide an overview of the psychiatric complications to COVID-19 infection (direct effect) and how COVID-19 are currently affecting mental health among psychiatric patients and general public (indirect effect) alongside with factors altering the risk of psychiatric symptoms in both groups. A variety of factors were associated with higher risk of psychiatric symptoms and/or low psychological well-being of the general public including female gender, front-line health care workers, and poor self-rated health. From previous studies of the SARS CoV-1 epidemic it is known that health care workers are at risk of anxiety and depressive symptoms, which the current studies indicate also is the case of COVID19 . doi = 10.1016/j.bbi.2020.05.048 id = cord-343766-hlg7t5i5 author = Vinken, Mathieu title = A putative AOP for pneumonia related to COVID-19 date = 2020-07-20 keywords = SARS; covid-19 summary = In order to further encourage research in this direction, an updated version of the putative AOP for pneumonia linked to COVID-19 is proposed, which encompasses new knowledge that is rapidly accumulating (Fig. 1) . One of the major MIEs in this AOP is the binding of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor at the plasma membrane surface of type II pneumocytes lining the alveoli in lung. Such AOP network should comprise the mechanisms driving the multi-organ failure frequently observed in severe COVID-19 patients, for which the causes (i.e. MIEs) are as yet not entirely clear or delineated. Thus, liver failure may be caused by the direct binding and actions of SARS-CoV-2 in hepatocytes or cholangiocytes, but could also be an indirect consequence of the systemic inflammatory response syndrome associated with COVID-19. A putative AOP for pneumonia linked to COVID-19 doi = 10.1007/s00204-020-02860-w id = cord-279439-h4ji0ttm author = Viotti, Manuel title = HUMAN PRE-IMPLANTATION EMBRYOS ARE PERMISSIVE TO SARS-COV-2 ENTRY date = 2020-09-30 keywords = SARS summary = DESIGN: Assessment of expression levels of SARS-CoV-2 entry mediators in human embryo biopsies by RNAseq analysis, and infection of cultured embryos with SARS-CoV-2 Spike glycoprotein pseudotyped reporter virions expressing green fluorescent protein (GFP). MATERIALS AND METHODS: Trophectoderm biopsies from blastocyst-stage embryos (n¼24) were processed for RNAseq using a commercial kit and sequenced; results were analyzed for expression of factors implicated in SARS-CoV-2 cellular entry. For viral infection experiments, blastocyst-stage embryos (n¼94) were hatched from zonas mechanically, and infected by spinoculation with GFP-reporter virions pseudotyped with the SARS-CoV-2 Spike glycoprotein (required for SARS-CoV-2 entry). RESULTS: Cells collected from blastocyst-stage embryos robustly expressed the canonical SARS-CoV-2 entry receptor ACE2 and the putative activator protease TMPRSS2, in addition to other reported entry factors. Embryos exposed to reporter virions pseudotyped with SARS-CoV-2 Spike glycoprotein displayed robust GFP signal, often in numerous cells with cytoplasmic localization. CONCLUSIONS: Our results indicate that cells present in preimplantation embryos are permissive to the canonical Spike-ACE2 viral entry mechanism utilized by SARS-CoV-2. doi = 10.1016/j.fertnstert.2020.09.127 id = cord-006890-81wv1s33 author = Viret, Jean-Francois title = Development of a SARS vaccine: an industrial perspective on the global race against a global disease date = 2014-01-09 keywords = SARS; vaccine summary = The high profile of SARS in the international news media contributed to early public disease awareness but also caused fear in both affected and unaffected populations, placing additional political and economic pressure on authorities to act on the threat despite of an insufficient basis for informed decisions. Once the global scale of the outbreak became fully apparent, the scientific community, supported by the WHO, committed to ''...the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models and correlates of protection in humans.'' an unparalleled collaborative effort. More specifically, in spite of the fortunate capability to propagate the SARS-CoV on a well-accepted cell substrate (VERO), the development of a vaccine against the pathogen is severely impeded by the current fragmentary information on viral pathogenicity and the lack of adequate animal models of persistent infection and correlates of protection in humans. doi = 10.1586/14760584.2.4.465 id = cord-296426-upwsdgso author = Virmani, Sarthak title = Identifying a Kidney Transplant Recipient COVID Phenotype to Aid Test Utilization in the Setting of Limited Testing Availability - Does One Exist? date = 2020-06-20 keywords = COVID-19; CoV-2; SARS summary = While it is true that other non-novel viruses tend to cause more severe disease in immunocompromised patients [1] , no conclusive data is available to suggest an increased susceptibility or severity of SARS-Cov-2 infection in immunosuppressed kidney transplant recipients (KTRs). This was a single center, retrospective chart review performed as a QAPI project to assess similarities in kidney transplant recipients who tested positive for SARS-CoV-2 as compared to those who tested negative, and guide testing recommendations in the setting of limited testing availability during the COVID-19 pandemic. We did not observe any significant association between patient gender, level of education, or history of diabetes on the SARS-CoV-2 test result. Our cohort of KTRs showed no significant difference in ALC between patients who tested positive and negative for SARS-CoV-2 (Table 3 ). Though statistically significant in our small patient cohort, larger studies of KTRs with COVID-19 disease and a history of BKV will be required to confirm and better understand this association. doi = 10.1016/j.transproceed.2020.05.033 id = cord-346055-7fa57pmf author = Visani, Giuseppe title = SARS-CoV-2 impact in a community-based hematological ward in an Italian Red Zone date = 2020-06-13 keywords = SARS summary = Initial reports from China suggested that patients with cancer had an estimated two-fold increased risk of contracting SARS-CoV-2 than the general population and, if infected, also had a higher risk of either ICU admission, invasive ventilation, or death, compared to patients without cancer [2] . Up to now, 5924 cases resulted SARS-CoV-2 positive in Marche Region (out of 30,543 test done), with a rhythm of infection and death toll five times superior those of China [4] ; 845 patients died (452 in Pesaro Area) due to Covid-19, with high case-fatality rate (14%). Finally, we implemented testing with nasopharyngeal swabs and a quantitative polymerase-chain-reaction test to detect SARS-CoV-2 infection in patients admitted for chemotherapy/stem cell transplantation. Thirty-five HCPs, working exclusively at our Center, were tested: none of them resulted SARS-CoV-2 positive by nasopharyngeal swab. Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China doi = 10.1007/s00277-020-04116-0 id = cord-317000-bfc51e0m author = Visci, G. title = Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date = 2020-10-27 keywords = PCR; SARS summary = In the present study we aimed to analyze the prevalence of positive serology testing following positive RT-PCR or the appearance of symptoms suggestive of Covid-19 among high-risk HCWs employed in public hospitals of Bologna, Northern Italy, an area at high incidence of infection with SARS-CoV-2 and mortality from Covid-19, and to compare the sensitivity of different types of serological tests, including chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA). An additional group of healthcare workers who developed symptoms related to Covid-19, but did not have a positive RT-PCR result, was included in the surveillance program (based on clinical diagnostic criteria). Based on the results reported in Table 2 , and sensitivity of LFIA test equal to 75.2%, we estimated that 73.4% of HCWs with Covid-19 related symptoms, who were not tested with RT-PCR, were not infected with SARS-CoV-2. doi = 10.1101/2020.10.25.20219113 id = cord-253665-1dn3ek34 author = Vishnubalaji, Radhakrishnan title = Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response date = 2020-07-07 keywords = CoV-2; SARS; covid-19; figure; nhbe summary = Coronavirus disease 2019 , caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared a global pandemic by the World Health Organization (WHO) on Phenomenal changes in ncRNA expression are also seen within host cells, which can play a major role in respiratory virus pathogenesis, with long non-coding RNAs (lncRNAs) exhibiting higher tissue specificity than coding genes [30] . Disease and function analysis on the differentially expressed genes revealed the most significant enrichment in pathways related to reactive oxygen species, induction of apoptosis and necrosis, as well as activation of neutrophils in SARS-CoV-2 infected NHBE cells (Figure 3a,b) . The top ten activated upstream regulator networks (CST5, IFNG, IFNL1, IFNA2, SPI1, RNY3, PRL, TGM2 , miR-122 and miR-122-5p) in lung tissue derived from COVID-19 patient based on transcriptome and IPA analyses, revealed the enrichment of functions related to immune system associated JAK-STAT cascade, type 1 interferon receptor binding, cytokine receptor binding, and MHC 1 biosynthesis (Figure 6a and Supplementary Table S10 ). doi = 10.3390/genes11070760 id = cord-341783-e7xz4utr author = Vistisen, Simon T. title = Risk and prognosis of COVID-19 in patients treated with renin–angiotensin–aldosterone inhibitors date = 2020-07-06 keywords = COVID-19; SARS summary = 2 Because ACE2 plays an important role in the renin-angiotensin system and also acts as a receptor for SARS-CoV-2 cell entry, hypotheses about an association between ACEi/ARBs and COVID-19 outcomes were rapidly generated. Nevertheless, based on these initial observational findings, there seems to be no increased risk of SARS-CoV-2 infection for ACEi/ARB users. Four studies examined the prognosis of COVID-19 patients and uniformly found that risk of severe outcomes was not higher for the collapsed group of ACEi and ARB 740 Vistisen et al. The transmembrane angiotensin-converting enzyme 2 receptor allows SARS-CoV-2 entry and leads to virus replication, activation of innate immune system/complement, cytokine formation followed by neutrophils/lymphocytes in the lung and development of acute respiratory distress syndrome (ARDS). Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China doi = 10.1097/eja.0000000000001277 id = cord-303959-e1654g5j author = Vitiello, Antonio title = COVID-19 Patients with Pulmonary Fibrotic Tissue: Clinical Pharmacological Rational of Antifibrotic Therapy date = 2020-08-27 keywords = COVID-19; SARS summary = In this direction, the use of a pharmacological approach to reduce or prevent fibrotic status, with antifibrotic agents such as pirfenidone, used with demonstrated clinical efficacy in idiopathic pulmonary fibrosis [4] can be a valuable aid in the prevention of serious or fatal complications from COVID-19 in patients with ongoing infection, or in those already healed with residual fibrotic lung lesions [5] . Although many patients who develop SARS-CoV-2 respiratory distress syndrome survive the acute phase of the Fig. 1 Antifibrotic therapy, pleiotropic effects of Pirfenidone disease, data have shown that some of them die from progressive pulmonary fibrosis [19] . Several reports suggest, however, that there are differences between IPF and COVID-19-induced pulmonary fibrosis, diversity in the rapid evolution of the fibrotic and inflammatory state, and a highly developed procoagulant effect in SARS-CoV-2 viral infection [22, 23] . doi = 10.1007/s42399-020-00487-7 id = cord-332778-rf47ptj6 author = Vivarelli, Silvia title = Cancer Management during COVID-19 Pandemic: Is Immune Checkpoint Inhibitors-Based Immunotherapy Harmful or Beneficial? date = 2020-08-10 keywords = COVID-19; CoV-2; SARS; cancer; patient summary = It was demonstrated that cancer patients have an increased risk of developing a worse symptomatology upon severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV-2) infection, often leading to hospitalization and intensive care. Given their immune-compromised status, cancer patients infected by SARS-CoV-2 might be at a higher risk of developing severe and critical consequences upon COVID-19, including ARDS, septic shock and acute myocardial infarction [29] [30] [31] . Nevertheless, cancer patients, when infected by SARS-CoV-2 might develop more severe outcomes, if anti-cancer treatments induce a weakening of the host immune health [38] . Since the beginning of this pandemic, nine independent clinical studies have been published about the risks possibly related to SARS-CoV-2 infection in patients with cancer. In line with this concept, three additional independent clinical studies are currently enrolling non-cancer COVID-19 patients to test the efficacy of administering ICIs to reshape the impaired immune system of SARS-CoV-2 infected individuals (i.e., NCT04268537; NCT04356508 and NCT04413838). doi = 10.3390/cancers12082237 id = cord-332278-2p64ab2z author = Vivas, David title = Recomendaciones sobre el tratamiento antitrombótico durante la pandemia COVID-19. Posicionamiento del Grupo de Trabajo de Trombosis Cardiovascular de la Sociedad Española de Cardiología date = 2020-06-19 keywords = LMWH; SARS; patient summary = Thus, even patients who are not infected with SARS-CoV-2 are being affected by the pandemic, which is having a strong influence on the optimization of antithrombotic therapy due to the current health care situation. Its aim is to summarize the available information and provide simple guidelines for the use of antithrombotic drugs in order to guarantee optimal care for patients infected by the SARS-CoV-2 virus. Patients with SARS-CoV-2 infection are at increased risk of thromboembolic events, especially VTE, which is associated with the critical situation and immobilization entailed by this disease. Figure 2 shows an algorithm for the treatment approach to patients with prior oral anticoagulation therapy admitted for COVID-19 infection, in which a change to parenteral anticoagulation is proposed (mainly due to the severe situation or to interactions with COVID-19 drugs). doi = 10.1016/j.rec.2020.04.025 id = cord-336373-xb3jrg75 author = Vivas, Esther X. title = COVID19 and Otology/Neurotology date = 2020-08-22 keywords = SARS; covid-19 summary = The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), responsible for the worldwide COVID-19 pandemic, has caused unprecedented changes to society as we know it. In the following text I will review some of the changes to the practice of otology and neurotology in the US, in the context of the COVID-19 pandemic. In general, it is safe to say that while N95s have been used extensively, the role of CAPR and PAPR is limited for routine otologic and neurotologic procedures, but may be necessary on COVID-19 positive patients. Another change to standard operating procedures has been the implementation of pre-operative COVID-19 testing for all patients undergoing surgery. The COVID-19 pandemic has required otologists and neurotologists to implement several changes into our practice. doi = 10.1016/j.otc.2020.08.003 id = cord-286655-5vorrnq3 author = Vivek-Ananth, R.P. title = In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection date = 2020-08-22 keywords = SARS; TMPRSS2; figure summary = Lastly, we filtered the subset of phytochemicals whose binding energy in the best docked pose with TMPRSS2 (respectively, cathepsin L) is ≤−8.5 kcal/mol (respectively, ≤−8.0 In the third stage, we performed protein-ligand docking using AutoDock Vina [34] . Finally, in the fifth stage, for the top three inhibitors of TMPRSS2 namely, T1 (qingdainone), T2 (edgeworoside C) and T3 (adlumidine), and of cathepsin L namely, C1 (ararobinol), C2 ((+)-oxoturkiyenine) and C3 (3α,17α-cinchophylline), their respective protein-ligand complexes were analyzed using 180 ns MD simulation (Section 3; Figures 8 and 9; Supplementary Figures S1 and S2) and their interaction binding energy was computed using MM-PBSA method (Section 3; Table 3 ). As mentioned above, we have identified 96 potential natural product inhibitors of TMPRSS2 by computational screening of 14,011 phytochemicals produced by Indian medicinal plants, and these 96 compounds labelled T1-T96 are listed in Supplementary Table S1 along with their PubChem identifier, common name, IUPAC name and structure in SMILES format. doi = 10.3390/molecules25173822 id = cord-304306-rxjahqwh author = Vlachakis, Dimitrios title = Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date = 2020-10-08 keywords = COVID-19; CoV-2; RNA; SARS; protein summary = The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response doi = 10.1016/j.fct.2020.111805 id = cord-264515-nle4axad author = Vlachos, J. title = School closures and SARS-CoV-2. Evidence from Sweden''s partial school closure date = 2020-10-14 keywords = SARS; school summary = To study the broad impact of school closures on the transmission of the virus, we estimate differences in infection rates between parents exposed to lower and upper secondary students. We estimate differences in infections among parents, teachers, and teachers'' partners who were differently exposed to lower (open) and upper (online) secondary schools using linear probability models (OLS) and logistic regressions. We find that parental exposure to open rather than closed schools is associated with a somewhat higher rate of PCR-confirmed SARS-CoV-2 infections The positive association for PCR-confirmed cases could partly reflect other behavioral differences between households with slightly younger and older children, but if treated as a causal the estimates indicate that a hypothetical closure of lower secondary schools in Sweden would have resulted in 341 fewer detected cases among the 312 575 parents in our sample. doi = 10.1101/2020.10.13.20211359 id = cord-303787-dx1n8jap author = Vonck, Kristl title = Neurological manifestations and neuro‐invasive mechanisms of the severe acute respiratory syndrome coronavirus type 2 date = 2020-05-16 keywords = COVID-19; SARS; patient; report summary = RESULTS: Neurological manifestations potentially related to COVID‐19 have been reported in large studies, case series and case reports and include acute cerebrovascular diseases, impaired consciousness, cranial nerve manifestations and auto‐immune disorders such as Guillain‐Barré Syndrome often present in patients with more severe COVID‐19. Neurological symptoms were more common in patients with severe infection according to their respiratory status (45.5% vs 30.2% in non-severe cases) and fell into 3 categories: central nervous system (CNS) manifestations (dizziness, headache, impaired consciousness, acute cerebrovascular disease, ataxia, and seizure), cranial and peripheral nervous system manifestations (taste impairment, smell impairment, vision impairment, and neuropathy), and skeletal muscular injury manifestations. This is illustrated by a recent report of a COVID-19 patient with an acute necrotizing encephalopathy, a rare complication observed in infections with viruses including influenza, and related to a cytokine storm in the brain without direct viral invasion 26 . doi = 10.1111/ene.14329 id = cord-337674-mb6ue2hl author = Voulgaris, Athanasios title = Sleep medicine and COVID-19. Has a new era begun? date = 2020-07-17 keywords = SARS; SDB; covid-19; pap summary = This is especially important for the treatment of patients with sleep disordered breathing (SDB) since the application of positive airway pressure (PAP) can induce spread of aerosol and increase substantially the risk of infection [6] . A group of experts in SDB from the Chinese Thoracic Society provided feedback on the management of patients with OSA and suggested that sleep studies and initiation of PAP application should be continued only in regions with low incidence of COVID-19, preferably with the use of home sleep apnea tests (HSAT) [19] . In case where in-laboratory sleep studies are necessary, especially for PAP titration or insurance demands, these could be performed only after patients'' negative screening for COVID-19, according to local recommendations and hospital guidelines, with the personnel using all necessary personal protective equipment (PPE) and keeping safe distances, as previously mentioned and according to WHO infection prevention and control guidance [34] . doi = 10.1016/j.sleep.2020.07.010 id = cord-263031-cco2vh0f author = Vultaggio, Alessandra title = Considerations on Biologicals for Patients with allergic disease in times of the COVID‐19 pandemic: an EAACI Statement date = 2020-06-05 keywords = SARS; patient; severe summary = We discuss immunological and clinical considerations for patients on biologic agents (biologicals)targeting the type 2 inflammatory response due to difficult-to-treat allergic diseases in the context of COVID-19. In other coronavirus infections such as severe acute respiratory syndrome (SARS), type I IFN are critical for the initiation of immune response and virus clearance. In line with a paucity of mechanistic data on COVID-19 in the context of type 2 inflammation, knowledge on the disease course in patients treated with biologicals targeting type 2 inflammation due to severe asthma or other atopic diseases, such as CSU, AD and CRSwNP, is scarce to absent. In the past years, new biological therapies for severe asthma, atopic dermatitis (AD), chronicrhinosinusitis with nasal polyps (CRSwNP) and chronic spontaneous urticaria (CSU) have been developed targeting different aspects of the type 2 immune response. doi = 10.1111/all.14407 id = cord-314947-fy1lqk00 author = WU, Xiao Dong title = The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells date = 2004-10-17 keywords = SARS summary = title: The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells In order to investigate the maturation and proteolytic processing of the S protein of SARS CoV, we generated S1 and S2 subunit specific antibodies (Abs) as well as N, E and 3CL protein-specific Abs. Our results showed that the antibodies could efficiently and specifically bind to their corresponding proteins from E.coli expressed or lysate of SARS-CoV infected Vero-E6 cells by Western blot analysis. When S2 Ab was used to perform immune precipitation with lysate of SARS-CoV infected cells, a cleaved S2 fragment was detected with S2-specific mAb by Western blot analysis. Furthermore, antibodies against S1, S2, N protein could detect their corresponding proteins from the lysates of SARS-CoV infected Vero E6 cells. To First, S2-specific mAb was directly used to detect native S2 fragment or full length of S protein in the lysate of SARS-CoV infected Vero E6 cells. doi = 10.1038/sj.cr.7290240 id = cord-342765-rw8valjp author = Wacharapluesadee, Supaporn title = Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19 date = 2020-05-13 keywords = SARS summary = Additionally, NT specimens with PCR cycle threshold (Ct) greater than 35 were pooled to determine the limit of detection and sensitivity of pooling samples to test for SARS-CoV-2. Previously positive specimens with high and low-concentrations of RNA, as determined by PCR Ct values at the time of detection, were selected to determine the effect of viral load on pooling to ensure that the sensitivity and accuracy of the assay was maintained (Table 1) The fifteen 1X (L>35) pools were tested by performing duplicate (replicates I and II) qPCR assays to determine the limit of detection of specimen pooling when compared to individual testing. This study demonstrates that specimen pooling (either 1X or 2X pooling ratios) does not compromise the sensitivity of detecting SARS-CoV-2 provided the Ct value of the individually tested sample is lower than 35. doi = 10.1002/jmv.26005 id = cord-263002-f3itn0sb author = Wagener, Frank A. D. T. G. title = Targeting the Heme-Heme Oxygenase System to Prevent Severe Complications Following COVID-19 Infections date = 2020-06-19 keywords = HO-1; Heme; SARS; covid-19 summary = Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. Dimethyl fumarate (DMF) is a clinically used Nrf2 activator [86] that could possibly be used to prevent the many heme-induced complications during SARS-CoV-2 infection, such as edema, inflammation, and thrombosis and fibrosis by induction of the versatile HO-1 enzyme. These predisposing conditions, and inflammation in general, downregulate HO-1 expression and activity [67, 74, [100] [101] [102] [103] [104] [105] [106] , further supporting that this compromised protection and diminished tolerance against inflammatory and oxidative stress promotes adverse clinical outcome in COVID-19 patients. Since dexamethasone reduces hemolysis and induces HO-1 in macrophages [113] , it is tempting to speculate that this increased protection against free heme attenuates the severity of disease in COVID-19 patients. doi = 10.3390/antiox9060540 id = cord-289079-m417oxpc author = Waggershauser, Constanze H. title = Letter: immunotherapy in IBD patients in a SARS‐CoV‐2 endemic area date = 2020-08-14 keywords = SARS summary = Editors, With interest, we read the article of Taxonera et al on symptoms and the risk of COVID-19 in inflammatory bowel disease (IBD). 1 We would like to provide data from our IBD centre during the outbreak of SARS-CoV-2 concerning patients receiving immunotherapies. 2 Therefore, soon two questions raised great concern: are IBD patients who receive immunotherapies more susceptible to SARS-CoV-2 infections than the general population and are infected patients exposed to a more severe course? Since the estimated number of silent SARS-CoV-2 infections is high 7 and most individuals show only moderate symptoms of respiratory tract infection, we called or invited our patients to fill-in a questionnaire, 8 Our data confirm the recommended practice that immunotherapies should not be stopped or delayed during the COVID-19 crisis. Daniel Szokodi has served as a speaker for Pfizer. 2019 novel coronavirus disease (COVID-19) in patients with inflammatory bowel diseases doi = 10.1111/apt.15897 id = cord-284102-rovyvv45 author = Wagner, Teresa R. title = NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date = 2020-09-28 keywords = ACE2; RBD; SARS summary = Here we identified 11 unique nanobodies (Nbs) with high binding affinities to the SARS-CoV-2 spike receptor domain (RBD). Considering that Nbs targeting diverse epitopes within the RBD:ACE2 interface are beneficial 201 in both reducing viral infectivity and preventing mutational escape, we next combined the most 202 potent inhibitory and neutralizing candidates derived from Nb-Set1 (NM1226, NM1228) and 203 We incubated our previously generated color-coded beads 232 comprising RBD, S1 domain or homotrimeric spike with serum samples from patients or non-233 infected individuals, in addition to dilution series of the combinations NM1226/ NM1230 or 234 NM1228/ NM1230 and used this to detect patient-derived IgGs bound to the respective 235 antigens. As a result, we modified our previously described multiplex immunoassay 303 (MULTICOV-AB, 20 ) and developed a novel diagnostic test called NeutrobodyPlex to monitor 304 the presence and the emergence of neutralizing antibodies in serum samples of SARS-CoV-2 305 infected individuals. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block 681 interaction with ACE2 doi = 10.1101/2020.09.22.308338 id = cord-348301-bk80pps9 author = Wahl, Angela title = Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801 date = 2020-09-24 keywords = CoV-2; Fig; SARS; human summary = Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Human lung tissues of LoM were inoculated with SARS-CoV-2 and titers of replication competent virus determined 2, 6, and 14 days post-exposure (Fig. 1c , Extended Data Table 2 ). Collectively, our results indicate that LoM re ect the pathogenic effects in icted by SARS-CoV-2 on the human lung and demonstrate their utility as a single in vivo platform to evaluate and compare the replication and pathogenesis of past, present, and future pre-emergent, epidemic, and pandemic coronaviruses accelerating the development and testing of pre-exposure prophylaxis agents such as EIDD-2801. doi = 10.21203/rs.3.rs-80404/v1 id = cord-275894-puwaty70 author = Wajnberg, A. title = SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months date = 2020-07-17 keywords = July; SARS summary = Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. In order to determine if antibodies induced against the spike protein exert neutralizing activity, we 111 performed a well-established, quantitative microneutralization assay (18) based on authentic 112 SARS-CoV-2 with 120 samples of known ELISA titers ranging from ''negative'' to 1:2880. . https://doi.org/10.1101/2020.07.14.20151126 doi: medRxiv preprint with authentic SARS-CoV-2 virus, and the vast majority of individuals with antibody titers of 1:320 167 or higher show neutralizing activity in their serum. doi = 10.1101/2020.07.14.20151126 id = cord-262328-q7mt0xve author = Wajnberg, Ania title = Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date = 2020-09-25 keywords = CoV-2; PCR; SARS summary = In this observational study, we ran an outreach programme in the New York City (NY, USA) area, including parts of Connecticut and New Jersey, to identify people who had recovered from SARS-CoV-2 infection for nasopharyngeal PCR (cobas 6800; Roche Diagnostics, Indianapolis, IN, USA) and serum IgG titre measurement (ELISA; Icahn School of Medicine at Mount Sinai, New York, NY, USA). We did not find reports of ELISA antibody assays as large as this one from areas with major COVID-19 hotspots, and found mixed and growing reports of IgG response to and PCR positivity for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over time. In the 584 participants for whom both nasopharyngeal PCR testing and serum antibody testing was available, SARS-CoV-2 RNA was detected in 249 (43%) at a median of 20 days (IQR 18-23) from symptom onset and 12 days (9-14) from symptom resolution. doi = 10.1016/s2666-5247(20)30120-8 id = cord-015181-875gf11z author = Walgate, Robert title = SARS escaped Beijing lab twice date = 2004-04-27 keywords = SARS summary = Email: Walgate@scienceanalysed.com The latest outbreak of severe acute respiratory syndrome (SARS) in China, with eight confirmed or suspected cases so far and hundreds quarantined, involves two researchers who were working with the virus in a Beijing research lab, the World Health Organization (WHO) said on Monday (April 26). "We suspect two people, a 26-year-old female postgraduate student and a 31-year-old male postdoc, were both infected, apparently in two separate incidents," Bob Dietz, WHO spokesman in Beijing, told us. China has level three research guidelines and rules in place for handling the SARS virus, which are "of acceptable quality" to WHO, Dietz told us. They are going to go into the labs with Ministry of Health people and find out what happened here," Dietz said. " We''ve been told we''ll have full access, be able to test all the surfaces, interview people who worked there, and look at documentation to find out what was being done," Dietz said. doi = 10.1186/gb-spotlight-20040427-03 id = cord-015183-1eytelxn author = Walgate, Robert title = Latest SARS evidence date = 2003-04-07 keywords = SARS summary = The outbreak of SARS (Severe Acute Respiratory Syndrome) that originated in China is, with "95-97% certainty," caused by a completely new type of coronavirus, according to Julie Hall, who is responsible for the World Health Organization''s Global Alert, Response and Operations Network. In patients, we''d also like to see the curves of IgM [specific to this virus], to show people have an acute response, and then IgG, which takes two to three weeks to level up, and stays with you, to show that it wasn''t just a passing extraneous infection." Moreover "We have lots of blood samples to test this in now," Hall said, so the results should not be long coming. Günther said he and Drosten had isolated three short DNA sequences from the coronavirus in a tissue sample from the "index case" (first case) of SARS in Germany, by a random amplification, lowstringency PCR approach. doi = 10.1186/gb-spotlight-20030407-01 id = cord-326198-6okk3u49 author = Walker, A. title = Genetic structure of SARS-CoV-2 in Western Germany reflects clonal superspreading and multiple independent introduction events date = 2020-04-30 keywords = Heinsberg; SARS summary = An analysis (Supplementary Text) of other publicly available SARS-CoV-2 sequences did not reveal an obvious origin of the Heinsberg outbreak (Supplementary Table S4 ); the Heinsberg isolates are not related to early sequences from other German outbreak areas (Bavaria, Baden Wuerttemberg), and, despite intense Dutch viral sampling efforts (585 available viral genomes from the Netherlands at the time of analysis), our analysis identified only 2 closely related isolates from the Netherlands (one collected on 21 st March, the other with undefined collection date). A minimum spanning tree analysis of unambiguously resolved viral sequences ( Figure 1 ) showed that there were at least 5 clusters of viral haplotypes circulating in the Düsseldorf area; the number of variant positions relative to the SARS-CoV-2 reference genome in the Düsseldorf samples varied between 2 and 13 (Supplementary Table 2 ). doi = 10.1101/2020.04.25.20079517 id = cord-314107-x6e1jhcd author = Walker, M. title = SARS-CoV-2 Infection and Stroke: Coincident or Causal? date = 2020-07-29 keywords = SARS summary = Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Consistent with global reports, we observed a regional reduction in overall stroke volume during the COVID-19 pandemic peak. Surprisingly, less than 0.1% of patients suffered coincident SARS-CoV-2 infection and ischemic stroke. We also found no association between SARS-CoV-2 infection and stroke in younger patients. Similarly, a retrospective review in the UK during this same period [4] failed to identify a causal relationship in six patients with large vessel strokes and coincident SARS-CoV-2 infection because competing vascular risk factors were present. Regional data from five U.S. states suggests that among patients who sought care or were hospitalized during the peak of COVID-19, acute ischemic stroke in the setting of SARS-CoV-2 infection is rare and may be coincident. Large-Vessel Stroke as a Presenting Feature of Covid-19 in the Young doi = 10.1101/2020.07.17.20156463 id = cord-293382-uyat0w58 author = Walker, Susanne N. title = SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients date = 2020-10-21 keywords = ACE2; AUC; Fig; SARS summary = title: SARS-CoV-2 Assays To Detect Functional Antibody Responses That Block ACE2 Recognition in Vaccinated Animals and Infected Patients The first assay is surface plasmon resonance (SPR) based and can quantitate both antibody binding to the SARS-CoV-2 spike protein and blocking to the Angiotensin-converting enzyme 2 (ACE2) receptor in a single experiment. The second assay is enzyme-linked immunosorbent assay (ELISA) based and can measure competition and blocking of the ACE2 receptor to the SARS-CoV-2 spike protein with antispike antibodies. Four of the six guinea pigs immunized against SARS-CoV-2 spike showed statistically significant ACE2 blocking, and importantly, the pooled sera was comparable to the average AUC from all six serum samples (Fig. 3F, Fig. S2D ). First, we showed that an ELISA-based assay could be employed to measure receptor blocking antibodies in animals vaccinated with the SARS-CoV-2 spike protein. doi = 10.1128/jcm.01533-20 id = cord-318938-7d731q65 author = Wallentin, Lars title = Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation date = 2020-09-27 keywords = ACE2; SARS; covid-19 summary = In unadjusted analyses and after adjustment for clinical variables and medical treatment, male sex, diabetes, congestive heart failure, prior myocardial infarction, and age were consistently associated with higher sACE2 levels in both cohorts ( Figure 3A ; Supplementary material online, Table S2 ). The results showed that higher levels of sACE2 were associated with male sex, cardiovascular disease, diabetes, and older age, which are also the main risk factors for complications and mortality of COVID-19 infections. The indication that male sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes might be associated with a specific mechanism leading to higher risk of more severe SARS-CoV-2 infection might be useful for risk stratification concerning COVID-19. The close association between biomarkers and the sACE2 level suggests that biological ageing and cardiovascular disease and dysfunction might lead to increased ACE2 expression and a potentially higher risk for SARS-CoV-2 binding and more severe COVID-19 infection. doi = 10.1093/eurheartj/ehaa697 id = cord-310195-am3u7z76 author = Waller, J. title = Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date = 2020-05-10 keywords = SARS; risk; test summary = Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. This study was designed to test two hypotheses: describing a test indicating the presence of antibodies using the term Immunity (vs Antibody), and describing test results as Passports or Certificates (vs Test), increases the likelihood that those with this test result erroneously perceive they have no risk of becoming infected in the future with coronavirus. . https://doi.org/10.1101/2020.05.06.20093401 doi: medRxiv preprint Primary outcome Proportion of participants perceiving an antibody-positive test result to mean no risk of catching coronavirus in the future, assessed in response to a question with four response options. doi = 10.1101/2020.05.06.20093401 id = cord-322834-rl6yum7n author = Wallinga, Jacco title = Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures date = 2004-09-15 keywords = SARS summary = The available epidemic curves for SARS show marked differences between the affected regions with respect to the total number of cases and epidemic duration, even for those regions in which outbreaks started almost simultaneously and similar control measures were implemented at the same time. In this paper, we interpret the observed epidemic curves with regard to disease transmission potential and effectiveness of control measures, and we compare the epidemiologic profiles of SARS outbreaks in Hong Kong, Vietnam, Singapore, and Canada. The model uses values of k t = 0.18 for cases with a symptom onset date before March 12, 2003 , and k t = 0.08 for cases with a symptom onset date on or after March 12, 2003 ; these values correspond to the distribution of the number of secondary infections per case as observed during the severe acute respiratory syndrome (SARS) outbreak in Singapore (4). doi = 10.1093/aje/kwh255 id = cord-308428-zw26usmh author = Walter, Justin D. title = Highly potent bispecific sybodies neutralize SARS-CoV-2 date = 2020-11-10 keywords = ACE2; Fig; RBD; S-2P; SARS; Sb#15; Sb#68 summary = Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. We identified a sybody pair (Sb#15 and Sb#68) that can bind simultaneously to the RBD, and block ACE2 binding, thereby neutralizing pseudotyped and live SARS-CoV-2 viruses. However, binders of the isolated RBD may not effectively engage the aforementioned pre-fusion conformation of the spike protein, which could account for the poor neutralization ability of recently described single-domain antibodies that were raised against the RBD of SARS-CoV-2 spike protein [29] . Since Sb#15 and Sb#68 can bind simultaneously to the RBD and the full-length spike protein, we mixed Sb#15 and Sb#68 together to investigate potential additive or synergistic neutralizing activity of these two independent sybodies. To gain structural insights into how Sb#15 and Sb#68 recognize the RBD, we performed single particle cryo-EM analysis of the spike protein in complex with the sybodies. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.11.10.376822 id = cord-318444-sgm24q1i author = Walter, Justin D. title = Sybodies targeting the SARS-CoV-2 receptor-binding domain date = 2020-05-16 keywords = ECD; ELISA; RBD; SARS; TBS summary = Two independently prepared RBD constructs were used for in vitro sybody selections, and resulting single clones that could bind the full spike ectodomain were sequenced, expressed, and purified. Six unique sybodies show favorable binding affinity to the SARS-CoV-2 spike, and five of these were also found to substantially attenuate the interaction between the viral RBD and human ACE2. While this purified pre-fusion spike (PFS) had not yet been available for binder selections and characterization by grating-coupled interferometry, it was used to conduct ELISAs in order to identify selected sybodies which recognize the RBD in the pre-fusion context (see below). Since virulence of SARS-CoV-2 is dependent on the ability of the viral RBD to bind to human ACE2 (hACE2), we sought to determine which of the 57 selected sybodies that were well-behaved upon purification could inhibit interaction between the isolated RBD and purified hACE2. doi = 10.1101/2020.04.16.045419 id = cord-255940-chb4iuis author = Walton, David A. title = Facility-Level Approaches for COVID-19 When Caseload Surpasses Surge Capacity date = 2020-06-26 keywords = SARS; covid-19 summary = We present two COVID-19 treatment center designs that leverage lessons learned from previous outbreaks of communicable infectious diseases and provide potential solutions when caseload exceeds existing capacity, with and without access to SARS-CoV-2 testing. These designs are intended for settings in which health facilities and testing resources for COVID-19 are surpassed during the pandemic, are adaptable to local conditions and constraints, and mitigate the likelihood of nosocomial transmission while offering an option to care for hospitalized patients. To respond to the immediate crisis facing health workers and patients, we propose a COVID-19 treatment center design ( Figure 1 ) that harnesses lessons learned from other outbreaks and adheres to infection prevention and control principles recommended by the WHO for the novel coronavirus. The design assumes that two thresholds have been reached: first, the health center no longer has space to individually isolate COVID-19 patients, and second, laboratory capacity is limited or surpassed, such that rapid, accurate testing for COVID-19 may not be available, as is the reality facing our colleagues in Haiti. doi = 10.4269/ajtmh.20-0681 id = cord-257142-q79yy6o5 author = Wambier, Carlos Gustavo title = Androgen sensitivity gateway to COVID‐19 disease severity date = 2020-05-15 keywords = COVID-19; SARS; TMPRSS2 summary = Similarly, we believe that shorter CAG repeats in the androgen receptor gene may be associated with increased COVID-19 disease severity and mortality. A spectrum of androgenic activity would imply in polar pauciviral COVID-19 (e.g., children < 7), with null airway/fecal transmission potential, women with normal androgen activity would have low transmission potential (borderline pauciviral COVID-19), male teenagers and adults would have high transmission potential (borderline multiviral , and infected individuals with abnormally high androgen receptor activity (genetic or acquired) would represent the multiviral COVID-19 pole of the spectrum, with extremely high transmission To further test this hypothesis, it would be interesting to observe for severe COVID cases in female patients who present with increase androgens, for example, females with metabolic syndrome, or whom are using birth control methods with progestogen hormones that bind to androgen receptor. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is likely to be androgen mediated doi = 10.1002/ddr.21688 id = cord-352934-ypls4zau author = Wan, Jinkai title = Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection date = 2020-07-03 keywords = RBD; SARS summary = title: Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection We screened sera samples from 11 patients recently recovered from COVID-19, and 119 found all individuals showed certain levels of serological responses, with #507 and 120 #501 being the weakest, to SARS-CoV-2 Spike RBD and S1 proteins ( Figure 1A ). We 121 also found that 10 sera, except for 507, showed neutralization abilities against 122 SARS-CoV-2 pseudoviral infection of HEK293T cells stably expressing human ACE2 123 ( Figure 1B ). In order to screen for SARS-CoV-2 spike antigen specific monoclonal antibodies, we 143 used two primary assays based on ELISA (enzyme linked immunosorbent assay) and 144 FCA (flow cytometry assay), respectively. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin 561 converting enzyme 2 receptor A potent neutralizing human antibody reveals the N-terminal domain of the 564 Spike protein of SARS-CoV-2 as a site of vulnerability Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific 612 human monoclonal antibody doi = 10.1016/j.celrep.2020.107918 id = cord-305263-fgwf6wy3 author = Wang, Ben X. title = The yin and yang of viruses and interferons date = 2012-02-07 keywords = HCV; IFN; SARS; response; virus summary = IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. doi = 10.1016/j.it.2012.01.004 id = cord-306486-y6a4u0vh author = Wang, Bin title = Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients date = 2020-05-05 keywords = SARS summary = 5 To fulfill the pressing need, we examined antibody generation and virus clearance in 26 patients with SARS-CoV-2-induced COVID-19. Thus, this is the first report to state that innate immunity plays an essential role in SARS-CoV-2 clearance, which The disease severity and fatality were increased with age in COVID-19 patients, which may be explained by the augmentation of proinflammatory responses and the reduction of antiviral cytokines in elder individuals. Taken together, we showed that SARS-CoV-2 could coexist with virus-specific IgG antibodies in COVID-19 patients for an unexpectedly long time and, without adaptive immunity, innate immunity may still be powerful enough to eliminate SARS-CoV-2. The long-term coexistence of IgG with SARS-CoV-2 in the human body raises the question of whether patients with antibodies are still at risk for reinfection, which may make COVID-19 "immunity passports" Long-term coexistence of SARS-CoV-2 with antibody response in COVID-19 patients doi = 10.1002/jmv.25946 id = cord-274668-lh7c9izt author = Wang, Chaofu title = Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients date = 2020-06-20 keywords = China; SARS; covid-19; fig summary = BACKGROUND: The novel coronavirus pneumonia COVID-19 caused by SARS-CoV-2 infection could lead to a serious of clinical symptoms and severe illness, including acute respiratory distress syndrome (ARDS) and fatal organ failure. INTERPRETATION: Infection of Alveolar macrophage by SARS-CoV-2 might be drivers of the "cytokine storm", which might result in damages in pulmonary tissues, heart and lung, and leading to the failure of multiple organs . One case report showed the pathological characteristics of a patient who died from severe infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by postmortem biopsies. Moreover, type II alveolar epithelial cells and macrophages in alveoli and pulmonary hilum lymphoid tissue were infected by SARS-CoV-2, as revealed by immunohistochemistry using Rp3-NP specific antibodies (Figs. [10] In the case of COVID-19, the viral infection of aggregated alveolar macrophages was obvious from early phase to the late stage, according to our study and the results in recent reports of pulmonary pathology [17, 20] . doi = 10.1016/j.ebiom.2020.102833 id = cord-253035-tijcxtwx author = Wang, Chen title = A novel coronavirus outbreak of global health concern date = 2020-01-24 keywords = Health; SARS summary = Early in the SARS coronavirus outbreak, frontline health workers became infected, which amplified transmission to patients in hospitals where outbreaks were occurring. 4 Early evidence from the initial MERS outbreaks suggested that health workers were likewise being infected, but that their infections were less severe than those of patients in hospitals who became infected and had comorbidities such as diabetes or chronic respiratory disease. 3 In The Lancet, Chaolin Huang and colleagues 7 report clinical features of the first 41 patients admitted to the designated hospital in Wuhan who were confirmed to be infected with 2019-nCoV by Jan 2, 2020. Considering that substantial numbers of patients with SARS and MERS were infected in health-care settings, precautions need to be taken to prevent nosocomial spread of the virus. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected. doi = 10.1016/s0140-6736(20)30185-9 id = cord-349656-baoqgu8v author = Wang, Chen title = Intrauterine vertical transmission of SARS‐CoV‐2: what we know so far date = 2020-04-07 keywords = SARS summary = [2] In a study by Chen et al., [3] paired neonatal pharyngeal swab samples and placental tissues of three pregnant women with COVID-19 were used as samples to evaluate the potential risk of intrauterine vertical transmission, and all samples tested negative for SARS-CoV-2 RNA. Notably, a neonate born to a pregnant woman with COVID-19 tested positive for SARS-CoV-2 RNA in the pharyngeal swab sample at 36 hours after birth was subsequently confirmed that the qRT-PCR testing of the placenta and cord blood was negative for SARS-CoV-2, suggesting that intrauterine vertical transmission might not have occurred. Furthermore, in a cohort study by Zeng et al., [13] 3 of 33 (9%) infants were diagnosed with neonatal early-onset infection with SARS-CoV-2 based on positive qRT-PCR results of the nasopharyngeal and anal swabs in two consecutive tests at day 2 and 4 of age. Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn. doi = 10.1002/uog.22045 id = cord-351115-dy81dtnk author = Wang, Chen title = Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date = 2020-10-20 keywords = CoV-2; RNA; SARS; site summary = This study addresses both by utilizing evolutionary information from SARS-CoV-2 sequence and structural data to search for actionable functional sites for each protein in the SARS-CoV-2 genome. Here we systematically suggest potential drug target sites for most SARS-CoV-2 proteins based on evolutionary information. This relative ranking re ects the variation entropy of each sequence position within and across the branches of an associated phylogenetic tree, revealing evolutionary pressure points that correspond to functional and structural determinants, and the protein sites at which they often cluster (30) . As in our approach to discover ET drug sites, we combined ET residue ranking information with sequencing data from SARS-CoV-2 isolates to arrive at linear peptides along the proteome that are evolutionarily important and also show little variation in the current outbreak ( Figure S6 , Dataset S5). The data include, for example, multiple sequence alignments, precalculated ET ranks, and predicted epitopes (both linear and structural) for all SARS-CoV-2 proteins. doi = 10.21203/rs.3.rs-95030/v1 id = cord-259935-xyo2pe4g author = Wang, Ching-Ying title = SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date = 2017-05-02 keywords = Fig; SARS; TGF; type summary = To examine the association of SARS-CoV PLpro-induced TGF-β1 production with the collagen up-regulation, A549 lung epithelial cells transiently transfected with pcDNA3.1 and pSARS-PLpro were analyzed the production of TGF-β1 and type I collagen using Western blot, realtime RT-PCR and Sirius red staining assays (Fig. 1) . To examine whether SMAD-dependent pathways involve in TGF-β1mediated up-regulation of Type I collagen in response SARS-CoV PLpro, subcellular localization of receptor-regulated SMAD3 and inhibitory SMAD7 in transfected cells were detected using the immunofluorescent and DAPI staining (Fig. 4) . To examine the possible pathways involved in TGF-β1-dependent up-regulation of Type I collagen by SARS-CoV PLpro, the profiles of ubiquitin-conjugated proteins in transfected cells with vector control and pSARS-PLpro were determined using immune-precipitation and nanoLC-MS/MS. Subcellular localization analysis demonstrated that SMAD3 was predominant in cytoplasmic, but not in the nucleus in transfected cells with pSARS-PLpro compared to vector control (Fig. 4) , revealing that canonical Smad-dependent signaling pathway was not involved in PLpro-induced TGF-β1-dependent upregulation of Type I collagen. doi = 10.1016/j.virusres.2017.04.008 id = cord-320788-ln8ddyuj author = Wang, Chun-Hua title = Persistence of lung inflammation and lung cytokines with high-resolution CT abnormalities during recovery from SARS date = 2005-05-11 keywords = CD8; HRCT; SARS; patient summary = BACKGROUND: During the acute phase of severe acute respiratory syndrome (SARS), mononuclear cells infiltration, alveolar cell desquamation and hyaline membrane formation have been described, together with dysregulation of plasma cytokine levels. In the current study, we conducted a study to examine HRCT changes in patients who recovered from the acute phase of SARS at days 60 and 90, and measured the associated inflammatory profiles directly by examining bronchoalveolar lavage fluid (BALF). At 60 days, compared to normal subjects, there was a significant increase in total cell counts in BAL fluid from SARS patients (Table 3 ) with a significant increase in alveolar macrophages (AM) and lymphocytes., The proportion of CD8+ T cells was increased to a greater extent than CD4+ T cells, leading to a significant decrease in CD4/CD8 ratio (Table 4 ). Coronavirus infected cells were not detected in any of SARS patients with low HRCT score or in normal subjects (Table 1) . doi = 10.1186/1465-9921-6-42 id = cord-283127-jetmocvk author = Wang, Denong title = Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date = 2015-03-12 keywords = HIV-1; SARS; Tri; gna summary = In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). One intriguing question is whether human viruses of distinct phylogenetic origins, such as HIV-1 and SARS-CoV, may display conserved glycan targets that are suitable for broad virus neutralization. Subsequently, we performed a comparative carbohydrate microarray analysis to characterize the glycan-binding profiles of 2G12 and GNA and to pinpoint specific glyco-epitopes they recognize. To support exploration of the potential GNA glyco-epitopes in this study, we produced a set of comprehensive antigen microarrays, which include a large-panel of carbohydrates, lipids/liposomes, and protein antigens (Supplementary Table S1 ). Using carbohydrate microarrays and ELISA-based viral glycan-profiling analysis, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and lectin GNA. doi = 10.3390/molecules20034610 id = cord-294212-nlekz39f author = Wang, Dongliang title = Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date = 2020-07-03 keywords = CoV-2; HLA; SARS summary = Linear B-cell epitopes of the SARS-CoV-2 S protein were predicted by BepiPred 2.0 in IEDB (BepiPred 2.0., Immune Epitope Database and Analysis Resource, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA) with a threshold of 0.55 (corresponding specificity > 0.817 and sensitivity < 0.292), and only the epitopes with more than 8 residues were considered for subsequent antigenicity analysis. Discontinuous B-cell epitopes were predicted via the DiscoTope 2.0 server tool in IEDB with a default threshold of −3.7 (corresponding specificity > 0.75 and sensitivity < 0.47), based on the 3-dimensional (3D) structures of the SARS-CoV-2 S protein (PDB ID: 6VYB, B chain) and the SARS-CoV-2 S protein RBD (PDB ID: 6M0J, B chain). It is worth noting that one epitope ( 786 QILPDPLKPTKRSFIEDLLFNKVTLA 811 ) located in the S2 subunit of the SARS-CoV S protein is an important linear B-cell epitope capable of eliciting the production of a neutralizing antibody (NAb) identified in patients who recovered from SARS-CoV infection (Table S2 ) [13] . doi = 10.3390/vaccines8030355 id = cord-254469-7q6xi2xx author = Wang, Fuzhou title = An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development date = 2020-05-05 keywords = COVID-19; CoV-2; SARS; vaccine summary = In March 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US). However, on March 16 2020, the first phase I clinical trial of a novel lipid nanoparticle (LNP)-encapsulated mRNA-based vaccine, mRNA-1273, which encodes the spike protein (S protein) of SARS-CoV-2, began in the United States (US), conducted by Moderna and the Vaccine Research Center (VRC) of the National Institute of Allergy and Infectious Diseases (NIAID) [12, 13] . Although mRNA vaccines are commencing human clinical trials, due to the rapid global spread of this new viral pandemic, it may not be possible to develop a safe and effective vaccine for SARS-CoV-2 in time to prevent the increasing number of deaths due to this novel RNA virus. doi = 10.12659/msm.924700 id = cord-320417-01l27d99 author = Wang, Hai-Long title = The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date = 2020-10-14 keywords = SARS; SNP; clade summary = I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intraand inter-viral clades. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination. SARS-CoV-2 is an RNA virus with limited genome length, but its high mutation rate and homologous genetic recombination nonetheless gave rise to exponentially increased variants. This is why all previously reported recombination events of SARS-Cov-2 have relied on clade-defining SNPs. The 2D co-occurring variant mapping is a simple way to display inter-clade hybrid lineages, and it can be used to directly compare distributions of populations for intra-and inter-clade from different geographic locations or the same location but at a different time point. I downloaded ~18,000 SARS-CoV-2 genome sequences from NCBI (on September 2 nd ) and used the same criterion as before to search for inter-clade co-occurring SNP pairs (see method for details). doi = 10.1101/2020.10.13.338038 id = cord-339976-tg2jkss7 author = Wang, Haibin title = Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date = 2004-07-01 keywords = PCR; RNA; SARS summary = title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient''s clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome doi = 10.1373/clinchem.2004.031237 id = cord-322212-8xrehbd1 author = Wang, Hanyin title = Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock date = 2020-04-23 keywords = Ang-2; SARS summary = title: Unexpected BP Sensitivity to Angiotensin II in a Patient With Coronavirus Disease 2019, ARDS, and Septic Shock We report the case of an 88-year-old man with coronavirus disease 2019 (COVID-19) who presented with ARDS and septic shock. 1 An estimated 5.0% of patients with coronavirus disease 2019 (COVID-19) required ICU admission, 2.3% underwent mechanical ventilation, and 1.1% had septic shock. 2 Angiotensin II (Ang-2) is a synthetic vasopressor that received US Food and Drug Administration approval in 2017 for treatment of refractory vasodilatory shock. We report our experience with Ang-2 for septic shock in a critically ill patient with COVID-19. He became hypotensive and required ABBREVIATIONS: ACE = angiotensin-converting enzyme; ACE2 = angiotensin-converting enzyme 2; Ang-2 = angiotensin II; COVID-19 = coronavirus disease 2019; SARS-CoV = severe acute respiratory syndrome-related coronavirus; SARS-CoV-2 = 2019 novel coronavirus On ICU day 2, the SARS-CoV-2 polymerase chain reaction result was positive. doi = 10.1016/j.chest.2020.04.015 id = cord-273373-5elel6qo author = Wang, Haofeng title = Recent progress in the discovery of inhibitors targeting coronavirus proteases date = 2016-02-19 keywords = SARS summary = The CoV proteases, which play pivotal roles in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, are attractive targets for drug design. Structural analyses revealed that the substrate-binding pockets of various CoV M pro s are highly conserved, which led to the concept of "widespectrum inhibitors" for targeting all CoVs. Through a structure-based drug design, we have identified a lead compound named N3 with potent inhibitory activity against all M pro s tested ( Figure 2D) . Structurebased design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome-coronavirus papain-like protease Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Papain-like protease 2 (PLP2) from severe acute respiratory syndrome coronavirus (SARS-CoV): expression, purification, characterization, and inhibition doi = 10.1007/s12250-015-3711-3 id = cord-271505-eot38721 author = Wang, Hongliang title = Molecular pathogenesis of severe acute respiratory syndrome date = 2006-09-28 keywords = ACE2; CoV; SARS; SIGN summary = demonstrated that the angiotensin-converting enzyme 2 (ACE2) is a functional cellular receptor of SARS-CoV, by using coimmunoprecipitation of the virus glycoprotein (S1) with lysates from cells that are susceptible to virus infection (Vero E6 cells) followed by mass spectrometry analysis [7] . In the case of SARS, apoptosis was observed in patients'' lung epithelial cells; thus, SARS-CoV induced apoptosis would certainly have a deleterious pathogenic role, leading to severe tissue damage [26] . This model system allowed us to avoid possible secondary effects resulting from viral replication or infections in vivo and to directly test whether SARS-CoV spike protein might adversely affect acute lung injury through modulation of ACE2. SARS-CoV infection or spike protein treatment can down-regulate the expression of ACE2, and thus aggravate lung injury. Nabel, pH-dependent entry of severe acute respiratory syndrome coronavirus is mediated by the spike glycoprotein and enhanced by dendritic cell transfer through DC-SIGN doi = 10.1016/j.micinf.2006.06.012 id = cord-260508-z11exbyu author = Wang, Hongru title = Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date = 2020-10-12 keywords = CoV-2; GD410721; SARS summary = Phylogenetic analyses (Fig. 2 ) in genomic regions with all recombination tracts 6 (Supplementary Table 5 ) masked using Maximum-likelihood (Fig. 2a) and Neighbor-joining 7 based on synonymous (Fig. 2b ) or non-synoymous (Fig. 2c ) mutation distance metrics, 8 consistently support RmYN02 as the nearest outgroup to human SARS-CoV-2, in contrast to 9 previous analyses before the discovery of RmYN02, which instead found RaTG13 to be the 10 nearest outgroup ). Notice that the divergences 14 between human SARS-CoV-2 and the bat viral sequences, RaTG13 and RmYN02, in most 15 regions of the genome, are quite low compared to the other comparisons. While the overall divergence in the S gene encoding the spike protein could suggest the 10 presence of recombination in the region, previous study ) reported that the tree 11 based on synonymous substitutions supported RaTG13 as the sister taxon to the human SARS-12 doi = 10.1101/2020.04.20.052019 id = cord-034354-4xu97je3 author = Wang, Hongye title = SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution date = 2020-10-21 keywords = CoV-2; SARS; figure summary = The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. Using the SARS-CoV-2 proteome microarray, we screened IgM and IgG antibodies in the serum of 10 COVID-19 patients who were in the early stage of infection (days of symptoms onset, 3.0 ± 5.92) (Supporting Information, Table S2 ) to construct a landscape of humoral responses to the SARS-CoV-2 proteome (Figure 2 ). Sixty-one (61) IgG and IgM antibody epitopes were identified in seven SARS-CoV-2 proteins (M, N, S, Orf1ab, Orf3a, Orf7a, and Orf8) with a Z-score higher than 3 in at least one COVID-19 patient (Table 1) . Furthermore, we constructed the first landscape of B-cell epitopes of serum IgM and IgG antibodies, representing the comprehensive antibody response of COVID-19 patients to SARS-CoV-2 infection (Figures 2−4) . doi = 10.1021/acscentsci.0c00742 id = cord-291388-tt9eq7e0 author = Wang, Jann-Tay title = Clinical Manifestations, Laboratory Findings, and Treatment Outcomes of SARS Patients date = 2004-05-17 keywords = SARS; disease; patient summary = Previous reports have described some major clinical findings of SARS, including the temporal progression of clinical symptoms and chest radiography, the outcomes, suggested treatment protocol, and risk factors for death (4, 5) . We report on the clinical features of our SARS patients with pneumonia, with emphasis on temporal progression of laboratory findings, treatment outcome, and risk factors for poor prognosis. Methylprednisolone was usually administered in the second week of the disease if any of the following occurred: a flare of fever, progression of clinical symptoms (such as dyspnea or diarrhea), a surge or resurge of CRP level, or rapid deterioration of chest radiographic findings (development of new infiltration). A previous study reported the temporal progression of clinical and radiologic findings in SARS patients and indicated that several parameters would become more severe in the second and third week of disease (5). doi = 10.3201/eid1005.030640 id = cord-277816-ncdy9qgb author = Wang, Ji-gan title = Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis date = 2020-10-20 keywords = COVID-19; China; SARS summary = title: Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis In order to understand the clinical manifestations and incidence of gastrointestinal symptoms of coronavirus disease (COVID-19) in children and discuss the importance of fecal nucleic acid testing.We retrospectively analyzed studies on gastrointestinal symptoms and fecal nucleic acid detection in pediatric COVID-19 patients from January 1, 2020 to August 10, 2020, including prospective clinical studies and case reports. Stata12.0 software was used for meta-analysis.The results showed that the most common gastrointestinal symptoms in children with COVID-19 were vomiting and diarrhea, with a total incidence of 17.7% (95% Cl 13.9–21.5%). At present, there is no relevant study on whether there is a difference in the positive rate of fecal nucleic acid testing in COVID-19 children with and without diarrhea. Clinical features of 33 cases in children infected with SARS-CoV-2 in Anhui Province, China: a multi-center retrospective cohort study. doi = 10.1038/s41598-020-74913-0 id = cord-296362-9vi8xwu7 author = Wang, Jian-Min title = Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function date = 2008-09-12 keywords = CoV; SARS summary = title: Construction of a non-infectious SARS coronavirus replicon for application in drug screening and analysis of viral protein function Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. Based on the infectious cDNA clone of rSARS-CoV-DE, in which the E gene has been deleted, a safe non-infectious replicon was constructed by replacing the S gene with the enhanced green fluorescent protein (eGFP) gene. For in-depth study of functions of different viral proteins and regulatory sequence elements by reverse genetics, full-length infectious cDNA clones have been established using various techniques including bacterial artificial chromosome (BAC) vector [23] [24] [25] and SARS-CoV replicon cell lines [26] , which can also be used for antiviral drug screening. Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis doi = 10.1016/j.bbrc.2008.06.129 id = cord-258859-iaiosjlu author = Wang, Jiao title = Mask use during COVID-19: A risk adjusted strategy() date = 2020-06-25 keywords = COVID-19; SARS; mask summary = In the context of Coronavirus Disease (2019) (COVID-19) cases globally, there is a lack of consensus across cultures on whether wearing face masks is an effective physical intervention against disease transmission. This study 1) illustrates transmission routes of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); 2) addresses controversies surrounding the mask from perspectives of attitude, effectiveness, and necessity of wearing the mask with evidence that the use of mask would effectively interrupt the transmission of infectious diseases in both hospital settings and community settings; and 3) provides suggestion that the public should wear the mask during COVID-19 pandemic according to local context. The mask is generally used 278 by general public, while the respirator or a filtering face piece, which is designed to 279 protect the wearer from exposure to airborne contaminants, is mainly used by health care 280 workers especially during AGP (European Centre for Disease Prevention and Control, 281 2020). doi = 10.1016/j.envpol.2020.115099 id = cord-300532-4d6fnjt8 author = Wang, Jiao title = Disinfection technology of hospital wastes and wastewater: Suggestions for disinfection strategy during coronavirus Disease 2019 (COVID-19) pandemic in China date = 2020-04-24 keywords = China; SARS; disinfection; hospital; waste summary = For each ward and restroom of an infectious disease hospital or the infectious disease area of a general Table 1 Comparison of Disinfection technologies for hospital wastewater (Fan et al., 2017; Kühn et al., 2003; Kleinb€ ohl et al., 2018; Messerle et al., 2018; Yu et al., 2013 The ability of decoloring and deodorizing and quick decomposition of microorganisms High operation costs and hazardous by-products hospital, 1 kg of bleaching powder containing 25% of available chlorine per 10 beds should be added 3 to 4 times before further disinfection. From the perspective of investment and operation costs as well as economic and social benefits, high temperature incineration is still one of the most valuable hospital waste disinfection technology in China. Recently, RNA of SARS-CoV-2 has been found in feces of patients, which triggered concern to the disinfection of wastes and wastewater of designated hospitals during COVID-19 pandemic in China. doi = 10.1016/j.envpol.2020.114665 id = cord-302409-40ktyt5q author = Wang, Jie title = SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date = 2020-04-18 keywords = RNA; SARS summary = OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs'' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. doi = 10.1016/j.ijid.2020.04.024 id = cord-304379-4mfyxp6h author = Wang, Jin title = Mathematical models for COVID-19: applications, limitations, and potentials date = 2020-06-25 keywords = COVID-19; SARS summary = (5) conducted computational modeling of potential epidemic trajectories to estimate the outbreak size in Wuhan, China, and their results indicated that control measures need to block well over 60% of transmission to be effective in containing the outbreak. Incorporating such an environment-tohuman route into mathematical modeling may better characterize the transmission dynamics of COVID-19 and potentially gain deeper understanding of its epidemic patterns. For example, many countries (China in particular) implemented strong disease control measures, including large-scale quarantine, intensive tracking of movement and contact, strict isolation of infected individuals, expanded medical facilities, and social distancing, which can effectively (and, in some places, rapidly) reduce the transmissibility of the virus. Mathematical epidemic models are well positioned to incorporate the economic impact of COVID-19, to quantify the interaction of epidemiological and economic factors, and to suggest an optimal balance between the pandemic control and economic development. doi = 10.21037/jphe-2020-05 id = cord-281161-u896icp9 author = Wang, Jing title = The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date = 2012-05-17 keywords = ASP-1; SARS; adjuvant; mouse; rOv summary = We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. As shown in Table 2 , similar IgG1 and IgG2a humoral immune responses against the influenza viruses were induced in the mice vaccinated previously with rRBD plus rOv-ASP-1 adjuvant and those administered with PBS only. As shown in Table 3 , all of the NHPs vaccinated with rRBD protein plus 50 mg (n = 2), 100 mg rOv-ASP-1 (n = 2) or 500 mg CpG (n = 1) as the adjuvant developed RBDspecific IgG antibody response with increasing antibody level after each boost. Secondly, using two concentration of the rOv-ASP-1 adjuvant, 50 or 100 mg, and rRBD as the vaccine antigen, we were able to induce after three immunizations high titers of neutralizing antibodies (1:3,500-1:6,392) that much exceed what is needed for protection against SARS-CoV infection in vivo (.1:500) [56] . doi = 10.1371/journal.pone.0037019 id = cord-325449-fl6ob5ja author = Wang, Jing title = COVID-19 and diabetes: the contributions of hyperglycemia date = 2020-10-01 keywords = SARS; covid-19 summary = Thus, following SARS-CoV-2 infection, poor-controlled blood glucose in diabetes patients may promote macrophage inflammation and antigen presentation impairment in DCs, resulting in a great increase in the secretion of inflammatory cytokines and chemokines from immune cells and ultimately cytokine storm and increased mortality (Figure 1) . The exact mechanisms linking diabetes and COVID-19 remain to be further elucidated, but available clinical/laboratory observations suggest that hyperglycemia-induced immune dysfunction, cytokines storm, and elevated lactate levels may play critical roles in the severity of COVID-19 in patients with pre-existing diabetes. A large body of evidence shows that hyperglycemia or diabetes may impair immune response mediated by macrophages, monocytes, and DCs, weaken T-cell function, and promote cytokine storm, ultimately resulting in increased susceptibility of SARS-CoV-2 infection and COVID-19-associated mortality. Hyperglycemia may also increase lactate production via HIF-1α, which suppresses the innate immune RLR signaling by targeting MAVS, leading to delayed clearance of SARS-CoV-2 and thus severe outcomes in diabetes patients with COVID-19, including ARDS, septic shock, and MODS. doi = 10.1093/jmcb/mjaa054 id = cord-337208-6rs1sgx1 author = Wang, Jingbo title = Enlightenments of Asymptomatic Cases of SARS-CoV-2 Infection date = 2020-06-30 keywords = SARS summary = They both had normal lymphocyte counts and CT scans, without clinical symptoms; however, their qRT-PCR results of throat swabs and sputum samples both showed positive for SARS-CoV-2. The wife, daughter, and son-in-law of Case 1 were successively diagnosed with novel coronavirus-infected pneumonia, all of which were common types, and all had clinical symptoms such as fever, cough, sore throat, decreased lymphocyte count, and the CT examination of both lungs showed typical ground-glass and patchy shadows, and qRT-PCR results of pharyngeal brush and sputum specimens were positive for SARS-CoV-2. Among them, infected patients 1, 2 and 3 had clinical symptoms (fever, cough, sore throat, etc.), lymphocyte count decreased, lung CT scan showed typical ground-glass and patch shadows, and qRT-PCR tests of pharyngeal swabs and sputum specimens revealed positive for SARS-CoV-2. On February 2, Case 2 had tested positive for SARS-CoV-2 by qRT-PCR of pharyngeal swabs, and was hospitalized in isolation. doi = 10.2478/jtim-2020-0017 id = cord-262268-gm99cadh author = Wang, Jingqiang title = Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus date = 2003-12-01 keywords = ELISA; SARS; protein summary = Consequently, we thoroughly investigated the immunoreactivities with patient sera of a series of synthesized peptides from SARS-coronavirus structural proteins. Results: Four epitopic sites, S599, M137, N66, and N371-404, located in the SARS-coronavirus S, M, and N proteins, respectively, were detected by screening synthesized peptides. The peptides representing the COOH terminus of the N protein, in particular N371 and N385, had high absorbance/cutoff value ratios with the highest positive detection rate and the lowest hydrophobicity score among all of the synthesized peptides (Fig. 1C, and Fig. 3 in the online Data Supplement). The other 17 peptides reacted only slightly with the sera from SARS patients and gave low detection rates, suggesting that the regions of the S protein covered by these peptides have no epitopic site. The patient sera preincubated with 4 mg/L S599 or N385 gave a 25-30% lower response in the ELISA (data not shown), suggesting that the two peptides could compete with SARS coronavirus for binding to the antibodies in SARS serum. doi = 10.1373/clinchem.2003.023184 id = cord-269718-e1mxmo3a author = Wang, Jingquan title = Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China date = 2020-11-13 keywords = SARS summary = title: Impact of hydrological factors on the dynamic of COVID-19 epidemic: A multi-region study in China Considering the live SARS-CoV-2 was detected and isolated from the excrement and urine of infected patients, the potential public health risk of its waterborne transmission should be paid broad and close attention. The purpose of the current study is to investigate the associations between COVID-19 incidences and hydrological factors such as lake area, river length, precipitation and volume of water resources in 30 regions of China. Based on the results of descriptive analysis and nonlinear regression analysis, positive associations with COVID-19 confirmed numbers were observed for migration scale index (MSI), river length, precipitation and volume of water resources, but negative associations for population density. length, precipitation and volume of water resources, but negative associations for 21 population density. Impact of meteorological factors on the COVID-19 transmission: 435 A multi-city study in China Water transmission oF SARS-CoV-2 doi = 10.1016/j.envres.2020.110474 id = cord-007581-nu1shltl author = Wang, Jiun-Ling title = Rhabdomyolysis associated with probable SARS date = 2003-10-01 keywords = SARS summary = Four type II patients were treated with angiotensin-converting enzyme (ACE) inhibitors when they had the first angioedema attack, as compared with none with type I disease. Previous studies have pointed out that patients with probable SARS may have abnormal laboratory examination results, including elevated creatine kinase levels (2-4). We report 3 patients with probable SARS who developed rhabdomyolysis. The first patient was a 38-year-old woman who suffered from probable SARS during a nosocomial outbreak in Taiwan (5) . Serum creatine kinase level increased from 378 to 7659 U/L from April 24 to 30, and renal failure developed. Elevated serum creatine kinase levels of up to 3000 U/L have been noted in previous patients with SARS. We conclude that rhabdomyolysis-associated renal failure may be another unusual but severe presentation of SARS. Patients with SARS should have their creatine kinase levels monitored carefully, even if initial levels are only slightly elevated. doi = 10.1016/s0002-9343(03)00448-0 id = cord-288862-upcsvjuo author = Wang, Junmei title = Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study date = 2020-04-21 keywords = PBSA; SARS summary = Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson–Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Flexible docking and MM-PBSA-weighted solvent-accessible surface area (WSAS) were applied as the first and second filters, respectively, to improve the efficiency and accuracy of HVS in inhibitor identification for SARS-CoV-2 main protease. MD simulations were first performed for a docking hit for two purposes: (1) studying the relative stability of the ligand residing in the binding pocket; (2) sampling a set of conformations for MM-PBSA-WSAS binding free energy calculations and MM-GBSA residue−ligand binding free energy decomposition analysis. doi = 10.1021/acs.jcim.0c00179 id = cord-333688-bykbyojs author = Wang, Junxue title = Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report date = 2020-08-21 keywords = SARS; patient summary = RATIONALE: Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. We report the case of a patient with mild symptoms of coronavirus disease (COVID-19), who achieved clinical recovery but showed persistently positive SARS-CoV-2 nucleic acid test results until Day 92 after disease onset. The third scenario is that the COVID-19-related symptoms have disappeared and the patient has entered the convalescent phase, but SARS-CoV-2 nucleic acid test results are positive for a long period of time. [4] In this study, we report the case of a patient with COVID-19 who achieved clinical recovery but showed persistently positive results on the SARS-CoV-2 nucleic acid test for up to 92 days after disease onset. Recently, patients with COVID-19 who showed persistently positive SARS-CoV-2 nucleic acid test results despite resolved clinical symptoms have attracted a lot of attention. doi = 10.1097/md.0000000000021865 id = cord-278491-cnqxsno8 author = Wang, K. title = Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date = 2020-07-17 keywords = July; SARS summary = Methods Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. 9, 10 However, the dynamics and roles of SARS-CoV-2specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Our study may provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases and aid in the development of vaccines against SARS-CoV-2. 15, 16 The short-term humoral immune response in COVID-19 patients is also highly consistent with that observed in patients infected with SARS-CoV and MERS-CoV, 17, 18 who show a rapid decrease in virus-specific antibody titers within 3-4 months. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. doi = 10.1101/2020.07.14.20151159 id = cord-279550-7u2hksxm author = Wang, Kai title = Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date = 2020-08-03 keywords = SARS; covid-19; patient summary = METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. Thus, serological testing, especially to detect NAbs, is essential in determining the onset of the serological immune response, evaluating the potential capacity of the host body for viral clearance, and identifying donors for passive antibody therapy trials. 12, 13 However, the dynamics and roles of SARS-CoV-2-specific NAbs and their correlation with antibody responses have not been explored in COVID-19 patients more than two months after symptom onset. Furthermore, to determine if there was a statistical correlation between NAb levels and virus-specific IgG levels in COVID-19 patients, serum samples were grouped by time (weeks) after symptom onset. In summary, we determined the dynamics of NAb titers within 3 months after symptom onset in 30 SARS-CoV-2-infected patients and found a positive correlation between NAb titers and IgG antibodies. doi = 10.1093/cid/ciaa1143 id = cord-349392-r71g2e9y author = Wang, L. -F. title = Bats, Civets and the Emergence of SARS date = 2007 keywords = China; SARS; animal summary = Virological and serological studies indicated that masked palm civets ( Paguma larvata ), together with two other wildlife animals, sampled from a live animal market were infected with SARS-CoV or a closely related virus. Here, we review studies by different groups demonstrating that SARS-CoV succeeded in spillover from a wildlife reservoir (probably bats) to human population via an intermediate host(s) and that rapid virus evolution played a key role in the adaptation of SARS-CoVs in at least two nonreservoir species within a short period. Recently, two groups independently demonstrated that bats in the genus Rhinolophus are natural reservoirs of SARS-like viruses , providing strong evidence that SARS-CoV is indeed a new zoonotic virus with a wildlife origin. (2003) , SARS-CoV-like viruses were isolated from palm civets and a raccoon dog in a live animal market in southern China and serologic evidence indicted that a third species, the Chinese ferret-badger, was also infected by a similar virus. doi = 10.1007/978-3-540-70962-6_13 id = cord-309302-n6cd2fc3 author = Wang, Li title = Clinical management of lung cancer patients during the outbreak of COVID-19 epidemic date = 2020-09-23 keywords = COVID-19; China; SARS; cancer; patient summary = In this review, we focus on the epidemiological characteristics, early diagnosis, patient management and mental health of lung cancer patients during the COVID-19 epidemic. According to China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), drugs with potential antiviral effects should be used early in the course of the disease, and it is recommended to focus on patients with high risk factors for severe illness patients. However, hydroxychloroquine or combined azithromycin is not recommended for COVID-19 patients base on China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). In addition, convalescent plasma is suitable for patients with rapid disease progression, severe and critically ill patients base on China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8). According to China''s New Coronavirus Pneumonia Diagnosis and Treatment Plan (Trial Version 8), Tocilizumab can be tried for patients with extensive lung disease and elevated IL-6 levels in the laboratory. doi = 10.1186/s13027-020-00322-7 id = cord-258160-v08cs51n author = Wang, Lin-Fa title = Review of Bats and SARS date = 2006-12-17 keywords = China; SARS; bat summary = Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Although in 1 live animal market, 3 species were found to be infected by viruses related to SARS-CoV (9), all subsequent studies have focused mainly on palm civets, possibly because the rate of detection was higher in civets or because the number of civets traded in southern People''s Republic of China exceeds that of other wildlife groups. doi = 10.3201/eid1212.060401 id = cord-277309-kelebqr6 author = Wang, Lin-Fa title = Viruses in bats and potential spillover to animals and humans date = 2019-01-18 keywords = Pteropus; SARS; bat; human; virus summary = doi = 10.1016/j.coviro.2018.12.007 id = cord-277759-zbmzjsvs author = Wang, Luwen title = Coronavirus Disease 19 Infection Does Not Result in Acute Kidney Injury: An Analysis of 116 Hospitalized Patients from Wuhan, China date = 2020-03-31 keywords = AKI; CKD; SARS summary = BACKGROUND: Whether the patients with coronavirus disease 19 (COVID-19) infected by severe acute respiratory syndrome (SARS)-CoV-2 would commonly develop acute kidney injury (AKI) is an important issue worthy of clinical attention. This study aimed to explore the effects of SARS-CoV-2 infection on renal function through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. As shown in Table 2 , 111 COVID-19-confirmed patients without CKD did not develop obvious abnormal renal function after infection with SARS-CoV-2 and during the treatment of pneumonia. SARS-CoV-2 RNA in urine sediments of COVID-19-confirmed 53 patients, including 5 CKD cases, enrolled in this study was examined by real-time RT-PCR. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. In this study, the effects of SARS-CoV-2 infection on renal function were explored through analyzing the clinical data of 116 hospitalized COVID-19-confirmed patients. doi = 10.1159/000507471 id = cord-332672-fbwz8oxp author = Wang, Manli title = Bats as animal reservoirs for the SARS coronavirus: Hypothesis proved after 10 years of virus hunting date = 2013-10-30 keywords = SARS summary = It was suggested that the previously known bat SL-CoV stains cannot jump from bats to civets or humans owing to the significant differences between their RBDs (Li F, 2013); 2) although SL-CoVs have been identified from different bat species, isolation of a live SL-CoVs from bats never succeed; 3) no native SL-CoV from bats could use ACE2 as receptors and infect human cells, only when its RBD is replaced with the counterpart from a human SARS-CoV strain (Li W, et al, 2003; Becker M M, et al, 2008; Ren W, et al, 2008) . The residue 479 is known to be an asparagine only in human SAR-CoVs, but not in the previously identified bat SL-CoVs or civet SAR-CoVs. It is proposed that an asparagine at position 479 has a higher binding affinity with human ACE2 and is likely to determine whether the virus can infect humans (Li F, 2013) . doi = 10.1007/s12250-013-3402-x id = cord-349545-w7c2tu5a author = Wang, Mengmeng title = Analytical performance evaluation of five RT‐PCR kits for severe acute respiratory syndrome coronavirus 2 date = 2020-10-27 keywords = SARS summary = BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT‐PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS‐CoV‐2 infection. 8 Pan et al found that thermal inactivation adversely affected the efficiency of RT-PCR for SARS-CoV-2 detection samples with low viral loads. In the work, we presented the analytical performance evaluations of five RT-PCR kits using nasopharyngeal swabs samples from patients with confirmed SARS-CoV-2 infection, and negative nasopharyngeal swabs samples ( Figure 1 ). To further confirm the detection ability of the five kits, a positive clinical specimen (Ct: ORF1ab 26.99, N: 28.19) was diluted with 5-fold using RNase-free water, and the resulting dilution is considered as Level 1. No positive result was obtained in testing of 30 negative clinical samples by using five kits for ORF1ab and N gene. doi = 10.1002/jcla.23643 id = cord-318387-s4d442kx author = Wang, Ming title = Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses date = 2020-03-06 keywords = NTS; SARS; preprint summary = COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. https://doi.org/10.1101/2020.03.04.20029538 doi: medRxiv preprint read numbers of the test sample to those of the negative control (with "0" in the negative control 129 calculated as "1"), we defined that a ratio of ≥10 indicates a positive result for that fragment, 130 scoring 1; ≥3 to 10 fold is inconclusive, scoring 0.4; and <3 is negative, scoring 0. The 4 h sequencing output data (Fig. 4a ) revealed that all 153 19 samples defined as positive by qPCR were recognized SARS-CoV-2-infected by NTS, 154 doi = 10.1101/2020.03.04.20029538 id = cord-327124-kzavc4ez author = Wang, Ming title = SARS-CoV Infection in a Restaurant from Palm Civet date = 2005-12-17 keywords = SARS; civet summary = Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003–2004 were a waitress at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant a short distance from animal cages. Only 5 signature nt variations (SNVs) were observed in the 5 complete S gene sequences from palm civets determined in this study, indicating that SARS-CoV sequences from civets at the restaurant were not different from those of the original animal SARS source. These most recent SARS patients were therefore infected by SARS-CoV that is most closely related to virus isolates from palm civets at the restaurant (Figure) (6) . When the complete genomes of SARS-CoV from palm civets at the restaurant were compared with sequences of human isolates, 62 SNVs were identified. However, when the complete genome was compared with sequences of virus isolated from palm civets from animal markets in the 2003 epidemic, only 37 SNVs were identified. doi = 10.3201/eid1112.041293 id = cord-299148-uge5uodk author = Wang, Qiang title = A Method To Prevent SARS-CoV-2 IgM False Positives in Gold Immunochromatography and Enzyme-Linked Immunosorbent Assays date = 2020-05-26 keywords = ELISA; SARS summary = We set out to investigate the interference factors that led to false-positive novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgM detection results using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions. GICA and ELISA were used to detect SARS-CoV-2 IgM in 86 serum samples, including 5 influenza A virus (Flu A) IgM-positive sera, 5 influenza B virus (Flu B) IgM-positive sera, 5 Mycoplasma pneumoniae IgM-positive sera, 5 Legionella pneumophila IgM-positive sera, 6 sera of HIV infection patients, 36 rheumatoid factor IgM (RF-IgM)-positive sera, 5 sera from hypertensive patients, 5 sera from diabetes mellitus patients, and 14 sera from novel coronavirus infection disease 19 (COVID-19) patients. At a urea dissociation concentration of 4 mol/liter and with affinity index (AI) levels lower than 0.371 set to negative, SARS-CoV-2 IgM results were positive in 3 mid-to-high-level-RF-IgM-positive sera and in 14 COVID-19 patient sera detected using ELISA. doi = 10.1128/jcm.00375-20 id = cord-297332-rzf0cw1x author = Wang, Qidi title = Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates date = 2016-04-11 keywords = ADE; CoV; DPI; SARS; USA; figure summary = 15 Other observations include evidence of ADE reported here for the first time induced by an inactivated SARS-CoV vaccine in rhesus macaques ( Figure 1 ) and by antisera from SARS patients (Table S1) , as well as ADE in other coronavirus infections. Herein, we discovered that a peptide of the viral sequence simultaneously elicits the antibodies of disparate functions in protection and enhancement against SARS-CoV infection by the studies with host Vero E6 cells in vitro and in non-human primates. In contrast, the immunized monkeys in the Vac3 group had a strongly increased ability to control SARS-CoV infection in association with induction of high levels of anti-S 604−625 antibodies ( Figure 7E ). 44 This study demonstrates for the first time that an antibody (mAb43-3-14) targeting a specific linear epitope (S 597−603 ) of the SARS-CoV spike protein can mediate enhancement of virus infection both in vitro and in non-human primates via an epitope sequence-dependent mechanism. doi = 10.1021/acsinfecdis.6b00006 id = cord-291076-p350i54m author = Wang, Renxi title = The role of C5a in acute lung injury induced by highly pathogenic viral infections date = 2015-05-06 keywords = ALI; H5N1; SARS; TNF summary = Unregulated complement activation is likely to play a crucial role in the pathogenesis of acute lung injury (ALI) induced by highly pathogenic virus including influenza A viruses H5N1, H7N9, and severe acute respiratory syndrome (SARS) coronavirus. [1] [2] [3] In addition, the complement system has been implicated in the development of acute lung diseases induced by highly pathogenic viruses including influenza A virus H1N1, 4 H5N1, 5 H7N9, 6 severe acute respiratory syndrome coronavirus (SARS-Cov), 7 Middle East respiratory syndrome coronavirus (MERS-Cov). C5a-mediated release of reactive oxygen species C5a is a strong chemoattractant for neutrophils and monocytes; it then activates these cells to generate oxidative burst with release of 10 A study demonstrated that ROS are primary pathogenic molecules in pneumonia from mice infected with influenza virus. Inhibition of Complement Activation Alleviates Acute Lung Injury Induced by Highly Pathogenic Avian Influenza H5N1 Virus Infection doi = 10.1038/emi.2015.28 id = cord-193489-u6ewlh16 author = Wang, Rui title = Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine date = 2020-04-29 keywords = CoV-2; SARS; SNP; protein summary = Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. Genetic identification and characterization of the geographic distribution, intercontinental evolution, and global trends of SARS-CoV-2 is the most efficient approach for studying COVID-19 genomic epidemiology and offer the molecular foundation for region-specific SARS-CoV-2 vaccine design, drug discovery, and diagnostic development [10] . We use K-means methods to cluster SARS-CoV-2 mutations, which provides the updated molecular information for the region-specific design of vaccines, drugs, and diagnoses. Table 5 presents the statistics of single mutations on various SARS-CoV-2 proteins that occurred in the recorded genomes between January 5, 2020, and April 24, 2020. Specifically, nucleocapsid protein has both the highest number of mutations per residues of 0.56 and the highest h-index of 27, suggesting that it is the most non-conservative protein in SARS-CoV-2 genomes. doi = nan id = cord-206006-8l7hrany author = Wang, Rui title = Mutations on COVID-19 diagnostic targets date = 2020-05-05 keywords = COVID-19; SARS summary = Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on the genotyping of 7818 SARS-CoV-2 genome samples collected up to May 1, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have had mutations. We further show that SARS-CoV-2 has the most devastating mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been unfortunately used by countries around the world to diagnose COVID-19. It is interesting to note that N-China-F [10] is the most inefficient reagent among all primers/probes and its SARS-CoV-2 target has eight mutations involving samples in all five clusters, which may explain many media reports about the inefficiency of certain COVID-19 diagnostic kits made in China. doi = nan id = cord-277774-kec1o4ys author = Wang, Shangqian title = The need for urogenital tract monitoring in COVID-19 date = 2020-04-20 keywords = COVID-19; SARS summary = Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, which invades a cell through binding to the ACE2 receptor and TMPRSS2 priming. Most patients with severe COVID-19 present with pneumonia-related symptoms, but some patients with severe disease could develop serious urinary complications including acute kidney injury (AKI), which requires continuous renal replacement therapy (CRRT) 1 . Furthermore, male reproductive systems are vulnerable to infection; dramatic changes in sex hormones in patients with COVID-19 have been observed, suggesting gonadal function impairment 2 . Similar findings were also observed in autopsy kidney samples from patients with MERS-CoV infection 4 , which showed degeneration of the renal tubules, including ectasia changes and necrosis, sloughing, and loss of brush surface in the proximal tubular epithelial cells. Human kidney is a target for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection doi = 10.1038/s41585-020-0319-7 id = cord-296250-7ln7p715 author = Wang, Sheng-Fan title = The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date = 2020-05-20 keywords = ACE2; CoV-2; RNA; SARS summary = Increasing evidence showed potential therapeutic agents directly acting against SARS-CoV-2 virus, such as interferon, RNA-dependent RNA polymerase inhibitors, protease inhibitors, viral entry blockers, neuraminidase inhibitor, vaccine, antibody agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitor. Increasing evidence reveals potential therapeutic agents acting directly against SARS-CoV-2, such as interferon (IFN), RdRp inhibitors, protease inhibitors, coronaviral protease inhibitor, viral entry blocker, neuraminidase inhibitor, vaccine, antibody, agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitors. The novel specific anti-SARS-CoV-2 agents might comprise inhibitors interfering with the viral replication cycle, antibody targeting the host receptor and virus S protein, and inhibitors of host cellular proteases involved in the virus endocytosis pathway. 33, 34 Moreover, evidence showed that diarylheptanoids, the natural products derived from Japanese alder (Alnus japonica), can inhibit the papain-like protease and restore the host innate immunity response against SARS-CoV through maintaining the function of IFNs. 31 Therefore, specific coronaviral proteases might be good candidate targets for developing new drugs to fight COVID-19. doi = 10.1097/jcma.0000000000000353 id = cord-311610-uniz8tuc author = Wang, Shi-Yi title = The impact on neonatal mortality of shifting childbirth services among levels of hospitals: Taiwan''s experience date = 2009-06-08 keywords = SARS; hospital summary = This evidence indicates that the neonatal mortality rate in areas with large hospitals was significantly lower than predicted, despite the shift of childbirth services to local community hospitals during the SARS epidemic. Furthermore, this study''s large sample size of 1,848 observations allows us to demonstrate clearly that the shifting of childbirth services among hospitals associated with the SARS epidemic did not increase the risk of neonatal deaths. Although it has not been documented conclusively whether or not advanced hospitals provide better care for normal birthweight deliveries than small maternity units [7] [8] [9] [10] [11] [12] [13] [14] [15] , this study has demonstrated that childbirth outcomes were not influenced by the shift in maternity services to local community hospitals during the SARS epidemic in Taiwan. doi = 10.1186/1472-6963-9-94 id = cord-321564-6950p8i9 author = Wang, Shiu‐Mei title = Severe acute respiratory syndrome coronavirus spike protein counteracts BST2‐mediated restriction of virus‐like particle release date = 2019-07-10 keywords = BST2; SARS summary = BST2 is a component of innate immune response in the form of restricted enveloped virion release, and many viruses have evolved specific antagonists to counteract BST2 antiviral activity: HIV-1 Vpu, HIV-2 Env, simian immunodeficiency virus (SIV) Nef and Env, Ebola and Sendai virus GP, Kaposi''s sarcoma-associated herpesvirus K5, and influenza virus neuraminidase are all capable of antagonizing BST2. 23 We also found that the SARS-CoV spike (S) protein is capable of downmodulating BST2, thus mitigating the BST2-mediated restriction of virus-like particle (VLP) release, and suggesting that SARS-CoV and other enveloped viruses are capable of evolving additional anti-BST2 factors. BST2, bone marrow stromal antigen 2; SARS-CoV, severe acute respiratory syndrome coronavirus SARS-CoV virion release is mitigated by SARS-CoV S, it is possible that a number of enveloped viruses have developed supplementary anti-BST2 factors over time-note that in addition to Vpu, HIV-1 Nef is capable of overcoming BST2 restrictions on virus release under certain conditions. doi = 10.1002/jmv.25518 id = cord-346669-7n75m669 author = Wang, Shixin title = Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: A case-control study date = 2008-02-29 keywords = SARS; TNF summary = This study was to investigate the relationship between tumor necrosis factor (TNF)-α gene polymorphisms with the occurrence of SARS-CoV infection and its role in prognosis of patients with lung interstitial fibrosis and femoral head osteonecrosis. METHODS: The association between genetic polymorphisms of TNF-α gene and susceptibility to severe acute respiratory syndromes (SARS) was conducted in a hospital-based case-control study including 75 SARS patients, 41 health care workers and 92 healthy controls. Relationships of TNF-α gene polymorphisms with interstitial lung fibrosis and femoral head osteonecrosis were carried out in two case-case studies in discharged SARS patients. In this paper, we aimed to study whether polymorphisms in TNF-α promoter region were associated with SARS-CoV infection, development, and progression of interstitial lung fibrosis and femoral head necrosis in cure SARS patients. Considered that the progression of interstitial lung fibrosis or femoral head necrosis may be affected by hormone therapy, hormone using dosage, method and lasting period were considered in this study when analyzing the associations between gene polymorphisms with disease. doi = 10.1186/1471-2334-8-27 id = cord-269862-krcu3hfa author = Wang, Shui-Mei title = APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date = 2009-05-25 keywords = HIV-1; SARS summary = We previously demonstrated that HIV-1 Gag mutants containing severe acute respiratory syndrome coronavirus nucleocapsid (SARS-CoV N) coding sequences as NC substitutes can effectively assemble VLPs . Given that SARS-CoV N possesses a RNA-binding property, it is likely that assembly-competent chimeras containing a replacement of HIV-1 NC by an SARS-CoV N sequence may support the incorporation of hA3G into VLPs. Here we demonstrate that the carboxyl-terminal half of the SARS-CoV or human coronavirus 229E (HCoV-229E) N protein not only enables efficient VLP production, but also confers the ability to efficiently package human APOBEC3G (hA3G) when substituted for HIV-1 NC. As the results in Fig. 6B indicate, the carboxyl-terminal half of HCoV-229E N (which also contains a putative self-association domain) (Tswen-Kei Tang, 2005) was capable of replacing the HIV-1 NC function with respect to VLP assembly and hA3G packaging-that is, substantial amounts of VLPs and hA3G were detected in NC(229EN2) transfectant supernatant (lane 4). doi = 10.1016/j.virol.2009.03.010 id = cord-296672-i267t23m author = Wang, Shui-Mei title = Severe acute respiratory syndrome coronavirus nucleocapsid protein confers ability to efficiently produce virus-like particles when substituted for the human immunodeficiency virus nucleocapsid domain date = 2008-07-01 keywords = SARS; VLP summary = We replaced the HIV-1 nucleocapsid (NC) domain with different N-coding sequences to test SARS-CoV nucleocapsid (N) self-interaction capacity, and determined the capabilities of each chimera to direct virus-like particle (VLP) assembly. Each mutant was transiently transfected into 293T cells and subjected to Western immunoblotting to determine its ability to assemble and release VLPs. As shown in Fig. 2b , chimeric proteins with predicted molecular weights corresponding to Pr55 gag containing a SARS-CoV N coding sequence insertion in the NC region were readily detected. The above results suggest that HIV-1 Gag containing a large sequence of approximately 200-400 residues inserted into the NC region is still capable of assembling and releasing VLPs. Since the cultured 293T transfectant supernatant was centrifuged through 20% sucrose cushions for 40 min, we believe the recovered viral proteins in the pelleted medium are virus-associated. doi = 10.1007/s11373-008-9265-8 id = cord-335619-t3yv5y7h author = Wang, Song-mi title = Screening of SARS-CoV-2 in 299 Hospitalized Children with Hemato-oncological Diseases: A Multicenter Survey in Hubei, China date = 2020-08-07 keywords = COVID-19; SARS summary = A cross-sectional study was performed to investigate the clinical characteristics, lung CT scan, SARS-CoV-2 nucleic acid test and serum antibodies of hospitalized children with hemato-oncological diseases from January 23 to April 24, 2020. A cross-sectional study was performed to inves-tigate the SARS-CoV-2 infection status of children with hemato-oncological diseases hospitalized in three medical institutions from January 23 to April 24, 2020. The findings of this study showed that the SARS-CoV-2 infection rate in enrolled children with hematological malignancies was 0.33%. Zhang [3] reported that 53.6% of COVID-19infected cancer patients had serious clinical events, with a mortality rate of 28.6%. Therefore, for patients with hematological malignancies, the possibility of COVID-19 cannot be ruled out by negative antibody detection, which needs to be combined with multiple nucleic acid test, epidemiological history, and lung imaging to assist in the diagnosis. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.1007/s11596-020-2228-7 id = cord-268193-xwptzgvl author = Wang, Tzong-Luen title = Establishing a clinical decision rule of severe acute respiratory syndrome at the emergency department() date = 2003-12-29 keywords = SARS; system summary = Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Study objective: In the absence of reliable rapid confirmatory tests during severe acute respiratory syndrome (SARS) endemics, we designed a 2-phase cohort study to establish a scoring system for SARS and to evaluate whether it could improve the sensitivity and specificity of the World Health Organization (WHO) criteria. Methods: According to the clinical characteristics and initial laboratory findings of 175 suspected cases defined by the WHO criteria (20 confirmed as cases of SARS) in 3 university teaching hospitals in Taipei between March 1 and April 20, 2003, the scoring system for SARS was designed by multivariate analysis and stepwise logistic regression as the simple arithmetic sum of point values assigned to 7 parameters. doi = 10.1016/j.annemergmed.2003.08.002 id = cord-344364-vu389d88 author = Wang, Wei title = Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date = 2020-06-02 keywords = HLA; SARS summary = Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. doi = 10.1111/tan.13941 id = cord-354394-zojhdnlu author = Wang, Wei-Kung title = Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date = 2004-07-17 keywords = CoV; RNA; SARS summary = We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. Using a quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay and fractionation experiment, we investigated the load of SARS-CoV in these samples and different components of the throat wash. As shown in Table 1 , SARS-CoV RNA was detected in the cell-associated component of the throat wash from all 16 specimens examined. doi = 10.3201/eid1007.031113 id = cord-348526-g3asp1ps author = Wang, Wenjun title = WeChat, a Chinese social media, may early detect the SARS-CoV-2 outbreak in 2019 date = 2020-02-26 keywords = China; SARS summary = We plotted daily data on the frequencies of keywords related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from WeChat, a Chinese social media. Using WeChat Index, we obtained daily data from Nov 17, 2019 to Feb 14, 2020 for the keywords related to the SARS-Cov-2 disease such as "SARS", "Feidian (Chinese abbreviation for severe acute respiratory syndrome)", "pneumonia", "fever", "cough", "shortness of breath", "dyspnea", "fatigue", "stuffy nose", "runny nose", "diarrhea", "coronavirus", "novel coronavirus", and "infection" (see the raw data in Appendix A). By exploring daily data from WeChat, a Chinese social media, we found that the frequencies of several keywords related to the SARS-Cov-2 disease behaved abnormally during a period ahead of the outbreak in China, 2019. Gathering and analyzing data from social media, Internet search queries, news wires and web sites represents a novel approach to early warning and detection of disease outbreaks and is a supplementary to traditional surveillance systems [6] . doi = 10.1101/2020.02.24.20026682 id = cord-338790-rvdoq616 author = Wang, Xiaowen title = Be aware of acute kidney injury in critically ill children with COVID-19 date = 2020-08-26 keywords = AKI; COVID-19; SARS summary = BACKGROUND: Acute kidney injury (AKI) is a common complication of critically ill adult patients with COVID-19. METHODS: By extracting data from electronic medical records, we conducted a retrospective observational study of kidney involvement in confirmed pediatric COVID-19 cases in Wuhan Children''s Hospital during the coronavirus outbreak, from January 24 to March 20, 2020. The AWARE (Assessment of Worldwide Acute Kidney Injury, Renal Angina, and Epidemiology) study, which enrolled ICUs in 32 hospitals in Asia, Australia, Europe, and North America, showed that the overall incidence of AKI in 4683 critically ill children was 26.9%, and the incidence of severe AKI (KDIGO stage 2 or 3) was 11.6% [8, 14] . The correlation between IL-6 titer and serum creatinine level in our patients suggests that cytokine storm might play a more important role in critically ill COVID-19 children with AKI, in addition to the prerenal and intrarenal injuries. doi = 10.1007/s00467-020-04715-z id = cord-336711-bnb62wa6 author = Wang, Xiaoyang title = CT findings of patients infected with SARS-CoV-2 date = 2020-06-23 keywords = SARS summary = BACKGROUND: We aimed to describe the chest CT findings in sixty-seven patients infected by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The typical CT findings in hospitalized patients with SARS-CoV-2 infection were ground glass opacities (42/54), lesions located in the peripheral area (50/54), multiple lesions (46/54), and lesions located in the lower lobes (42/54). There were less typical CT findings, including air bronchogram (18/54), pleural thickening or pleural effusion (14/54), consolidation (12/54), lesions in the upper lobes (12/54), interlobular septal thickening (11/54), reversed halo sign (9/54), single lesion (8/54), air cavities (4/54), bronchial wall thickening (3/54), and intrathoracic lymph node enlargement (2/54). The chest CT image shows ground glass opacities occupying the left lower lobe (blue arrow) Fig. 4 A female patient infected with SARS-CoV-2. Chest CT images showed the enlargement of ground glass opacity (red arrows) and intrathoracic lymph node (blue arrows) after 10-day treatment found in the patients infected with SARS-CoV-2 ( Table 2 ). doi = 10.1186/s12880-020-00471-6 id = cord-277113-pykf7iw1 author = Wang, Xingyu title = The Clinical Features and Outcomes of Discharged Coronavirus Disease 2019 Patients：A Prospective Cohort Study date = 2020-05-22 keywords = SARS summary = By gathering detailed information of symptoms and treatments, reexamined outcomes, distribution of quarantine locations and close contact history post hospitalization, we aimed to track the course of clinical outcomes of COVID-19 patients after discharge, and to evaluate their transmissibility during the period of observation, therefore to make improvement on post-discharge management if necessary. All of the discharged COVID-19 patients met the discharge criteria as follows: afebrile for at least three days, respiratory symptoms significantly improved, improvement in the radiological abnormalities on chest radiograph or CT, and two consecutive negative SARS-CoV-2 tests more than 24 hours apart [6] . However, the clinical characteristics of Patient 2 was not in line with other 7 patients, who retested with positive SARS-CoV-2 but were only associated with mild symptoms as dry cough or intermittent fever and ultimately pronounced negative tests and improved chest CT during 4 weeks of follow-up period. doi = 10.1093/qjmed/hcaa178 id = cord-280627-dfnc9g2c author = Wang, Xiong title = Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date = 2020-04-18 keywords = China; SARS summary = The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). doi = 10.1016/j.ijid.2020.04.023 id = cord-279476-h7zi82a8 author = Wang, Xueliang title = Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) date = 2020-04-13 keywords = SARS summary = title: Limits of Detection of Six Approved RT–PCR Kits for the Novel SARS-coronavirus-2 (SARS-CoV-2) To cope with the COVID-19 epidemic, the China National Medical Products Administration (NMPA) approved six RT-PCR kits for SARS-CoV-2, and some of which subsequently received CE marking. To verify its applicability, the viral RNA was tested with the six kits provided by Shanghai Liferiver Bio-tech Co., Ltd, Wuhan Huada Bio-tech Co., Ltd, Shanghai GeneoDx Biotech Co., Ltd, DAAN Gene Co., Ltd of Sun Yat-sen University, Sansure Biotech Inc., and Shanghai BioGerm Medical Co., Ltd. The different target genes ( Table 1 ) produced typical S-shaped amplification curves, indicating that the RNA could be used in the six kits to evaluate their LoDs. The viral RNA concentration was determined with RT-droplet digital PCR (RT-ddPCR), which allows the absolute quantification of viral RNA by counting single molecules, without reference to an external standard curve. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR We acknowledge the six manufacturers for providing the SARS-CoV-2 RT-PCR detection kits. doi = 10.1093/clinchem/hvaa099 id = cord-305223-go75cs6r author = Wang, Yafei title = Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China date = 2020-08-25 keywords = SARS; severe summary = title: Clinical Characteristics of Patients with Severe Pneumonia Caused by the SARS-CoV-2 in Wuhan, China OBJECTIVES: The aim of this study was to explore the clinical characteristics and risk factors of severe pneumonia caused by the SARS-CoV-2 in Wuhan, China. SPSS was used for data analysis to explore the clinical characteristics and risk factors of patients with severe pneumonia caused by SARS-CoV-2. Statistical analysis showed that advanced age, increased D-Dimer, and decreased lymphocytes were characteristics of the patients with severe pneumonia. Severe pneumonia usually progresses rapidly, and many clinical indicators can change in a short time, especially lymphocyte count, D-Dimer and serum albumin values, and chest CT manifestations. The result suggests that advanced age, lymphocyte decline, and D-dimer elevation are independent risk factors for patients with severe COVID-19. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China doi = 10.1159/000507940 id = cord-304718-w469n0o8 author = Wang, Yan title = Lack of association between polymorphisms of MASP2 and susceptibility to SARS coronavirus infection date = 2009-05-01 keywords = MASP2; MBL; SARS summary = One case-control study has reported an association between susceptibility to SARS and mannan-binding lectin (MBL) in China. As the downstream protein of MBL, variants of the MBL-associated serine protease-2 (MASP2) gene may be associated with SARS coronavirus (SARS-CoV) infection in the same population. RESULTS: There is no significant association between alleles or genotypes of the MASP2 tagSNP and susceptibility to SARS-CoV in both Beijing and Guangzhou populations. A few case-control studies have reported an association between SARS susceptibility and human leucocyte antigen (HLA) and MBL [8] [9] [10] [11] . With regard to SARS-CoV infection, the codon 54 variant of the MBL gene has been shown to be associated with infection susceptibility but not with disease severity [11] . As the downstream protein of MBL, variants of the MASP2 gene may be associated with SARS-CoV infection. Genomic DNA from 30 individuals with SARS was chosen for analysis of MASP2 gene polymorphisms. doi = 10.1186/1471-2334-9-51 id = cord-258113-mnou31j3 author = Wang, Yaping title = Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date = 2020-05-19 keywords = SARS; Wuhan; patient summary = title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. [5] studied the clinical features of 99 patients with COVID-19 and found that SARS-Cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ARDS). Among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, PCT, LDH, CK, ALB, AST, and D-dimer were associated with disease severity. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1093/ofid/ofaa187 id = cord-346015-bzeqs5oh author = Wang, Yeming title = Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial date = 2020-04-29 keywords = COVID-19; SARS; patient; remdesivir summary = Although several approved drugs and investigational agents have shown antiviral activity against SARS-CoV-2 in vitro, 6, 7 at present there are no antiviral therapies of proven effectiveness in treating severely ill patients with A multicentre, open-label, randomised controlled trial (RCT) of hydroxychloroquine involving 150 adults admitted to hospital for COVID-19 reported no significant effect of the drug on accelerating viral clearance. This was an investigator-initiated, individually randomised, placebo-controlled, double-blind trial to assess the effectiveness and safety of intravenous remdesivir in adults (aged ≥18 years) admitted to hospital with severe COVID-19. Our study is the first randomised, double-blind, placebocontrolled clinical trial assessing the effect of intravenous remdesivir in adults admitted to hospital with severe COVID-19. Future studies of remdesivir, including earlier treatment in patients with COVID-19 and higher-dose regimens or in combination with other antivirals or SARS-CoV-2 neutralising antibodies in those with severe COVID-19 are needed to better understand its potential effectiveness. doi = 10.1016/s0140-6736(20)31022-9 id = cord-252671-uf96jgig author = Wang, Yi title = The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism date = 2016-02-09 keywords = Fig; IFN-; SARS summary = title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. The result of a dual-luciferase assay using the Renilla luciferase gene as a transfection control demonstrated that the SARS-CoV M gene rather than the S and E genes markedly increased IFN-␤ promoter activity (Fig. 1D) , whereas the valineto-alanine alteration at residue 68 of M protein completely abolished this induction, indicating that the specificity of M gene products played a role in this process. Taken together, our data indicate for the first time that SARS-CoV M protein may function as a novel cytosolic PAMP to activate IFN-␤ induction through an intracellular TLR-related signaling pathway in a TRAF3-independent manner. doi = 10.1128/mbio.01872-15 id = cord-027650-pl6qsojf author = Wang, Yijin title = SARS-CoV-2 infection in liver-Author’s reply date = 2020-06-23 keywords = ACE2; SARS summary = In light of the low percentage of hepatocytes expressing ACE2, but not absolute absence, it is not surprisingly that SARS-CoV-2 is capable of causing liver injury directly. It is therefore assumed that viral direct effect in liver might not operate absolutely through ACE2 expression, and other receptors could not be excluded. Alternatively, the finding of up-regulated ACE2 expression in hepatocytes in cirrhotic liver inspired us to speculate that SARS-CoV-2 infection might induce compensatory hyperplasia of hepatocytes, which are possibly derived from highly expressed ACE2 cholangiocytes [16] . All in all, our data fully support a direct role of SARS-CoV-2 in COVID-19 related hepatic impairment. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2+ cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway doi = 10.1016/j.jhep.2020.06.028 id = cord-317647-vcktnsv8 author = Wang, Yinhua title = Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis date = 2020-09-18 keywords = MERS; SARS summary = title: Assessment of the efficacy and safety of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19): A protocol for systematic review and meta-analysis We plan to systematically review the use of ribavirin in patients with coronavirus-related pneumonia and meta-analyze the data with updated studies. Therefore, we aim to systematically review the use of ribavirin on coronavirus-related pneumonia (SARS, MERSS, and COVID-19) and meta-analyze the data with the results of the updated RCTs to provide advanced evidence. We aim to assess the safety and efficacy of Ribavirin in treatment of coronavirus-related pneumonia (SARS, MERS and COVID-19). Our systematic review and meta-analysis will include these updated results and re-assess the efficacy and safety of ribavirin in patients with coronavirus-related pneumonia. Efficacy and safety of antiviral treatment for COVID-19 from evidence in studies of SARSCoV-2 and other acute viral infections: a systematic review and meta-analysis doi = 10.1097/md.0000000000022379 id = cord-292236-eudcs9t2 author = Wang, Yishan title = Asymptomatic cases with SARS‐CoV‐2 infection date = 2020-05-22 keywords = SARS summary = On 31 March 2020, Chinese Health Authorization announced that numbers of asymptomatic cases with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection will be made to the public daily. Currently, asymptomatic cases are not included in the confirmed patients in everyday-report according to the "Novel Coronavirus Pneumonia Diagnosis and Treatment Protocol (7th edition, trial)." Another study reported that the asymptomatic ratio was estimated at 30.8% among evacuees tested positive for SARS-CoV-2 using the information on Japanese nationals that were evacuated from Wuhan, China. Studies from single-center reported 4% to 6% cases with SARS-CoV-2 did not develop any symptom during the course of the disease. Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data. Alert for non-respiratory symptoms of Coronavirus Disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Epidemiological and clinical features of asymptomatic patients with SARS-CoV-2 infection doi = 10.1002/jmv.25990 id = cord-323481-uz6usokd author = Wang, Yixuan title = Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures date = 2020-03-29 keywords = China; SARS; Wuhan summary = title: Unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (COVID‐19) implicate special control measures By 27 February 2020, the outbreak of coronavirus disease 2019 (COVID‐19) caused 82 623 confirmed cases and 2858 deaths globally, more than severe acute respiratory syndrome (SARS) (8273 cases, 775 deaths) and Middle East respiratory syndrome (MERS) (1139 cases, 431 deaths) caused in 2003 and 2013, respectively. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China The guidelines for diagnosis and treatment of novel coronavirus (2019-nCoV) infected pneumonia (the sixth edition draft) issued by the National Health Commission of China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection doi = 10.1002/jmv.25748 id = cord-266914-3eatplc2 author = Wang, Yongjin title = Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date = 2010-06-02 keywords = IFN; NL63; SARS summary = The group II coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis coronavirus (MHV) encode a number of proteins that antagonize host innate immunity. Innate immune signal transduction was stimulated by NDV infection in cells transfected with plasmids-expressing nsp1 from HCoV-229E, HCoV-NL63 or SARS-CoV, or with a control plasmid. Luciferase reporter assays showed that synthesis of the innate immune promoter IFN-band ISG15-driven genes was suppressed by 5-20-folds in HCoV-229E and HCoV-NL63 nsp1-expressing 293 cells (Fig. 4A) . Synthesis of non-immune promoter-driven genes, including for SV40, HSV-TK and CMV promoters, was inhibited to a similar extent by the two group I coronavirus nsp1 proteins (Fig. 4B) . These results indicate that group I coronaviruses have evolved a mechanism strikingly similar to SARS-CoV for antagonizing host cell proliferation and innate immunity using nsp1. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells doi = 10.1016/j.meegid.2010.05.014 id = cord-294558-cqa58db8 author = Wang, Yubo title = Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date = 2020-05-22 keywords = SARS summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. doi = 10.1093/cid/ciaa629 id = cord-299082-s8bm40vy author = Wang, Yueying title = Cardiac arrhythmias in patients with COVID‐19 date = 2020-07-26 keywords = COVID-19; SARS; clinical; patient summary = 5, 6, 9, 10, [12] [13] [14] [15] Several investigators have reported cardiac function and structural abnormalities in patients with SARS-CoV-2 infection, including acute heart failure (HF), 3,10,16 takotsubo syndrome, 17 ,18 viral myocarditis, 19 and acute myocardial infarction. In addition to exacerbating the previous cardiomyopathy and conduction disorders, inducing arrhythmia events, SARS-CoV-2 may also induce electrophysiological abnormalities in patients with no previous history of heart disease under a variety of mechanisms. Clinical features and mechanism of heart injury in patients suffered from severe acute respiratory syndrome. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial Risk of QT interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease 2019 (COVID-19) doi = 10.1002/joa3.12405 id = cord-282142-76jr4p7n author = Wang, Yun title = Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date = 2020-08-07 keywords = COVID-19; CoV-2; SARS; infection summary = Pregnant women are susceptible to respiratory pathogens and the development of severe pneumonia, suggesting the urgent need to assess the potential maternal and infant outcome of pregnancy with COVID-19. Therefore, the effect of SARS-CoV-2 infection on maternal and infant outcomes needs to be explored, especially the intrauterine vertical transmission potential of COVID-19. SARS-CoV infection during pregnancy was associated with a risk of adverse maternal and neonatal complications, including intrauterine growth restriction, preterm delivery, spontaneous miscarriage, severe maternal illnesses, such as, admission to the intensive care unit (ICU), renal failure, and disseminated intravascular coagulopathy, and death (4, 6, 13, (42) (43) (44) (45) (46) . The samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples from six patients tested negative for SARS-CoV-2 (5), suggesting no intrauterine vertical transmission of SARS-CoV-2 in the nine pregnant COVID-19 patients. doi = 10.3389/fped.2020.00511 id = cord-312278-rin733w4 author = Wang, Yung‐Chih title = Current diagnostic tools for coronaviruses–From laboratory diagnosis to POC diagnosis for COVID‐19 date = 2020-08-13 keywords = COVID-19; SARS; dna summary = 22 For detecting the presence of novel infectious diseases, the gold standard method has been the use of qRT-PCR for the detection of 29 Saliva has also been approved as a noninvasive specimen for detecting SARS-CoV-2. Another well-known test is the Vivalytic COVID-19 test (Bosch, Germany), which delivers results in less than 2.5 hr using multiplex PCR and μArray-detection to identify SARS-CoV-2. All of these tests employ PCR to detect the presence of SARS-CoV-2 RNA, and can provide results within 72 hr. Second, all of these at-home kits are designed to detect SARS-CoV-2 RNA during early-stage infection, but they are not used to determine the presence of antibodies. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using fieldeffect transistor-based biosensor Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis doi = 10.1002/btm2.10177 id = cord-343566-epvswt7f author = Wang, Zhao-Hua title = Critically Ill Patients with Coronavirus Disease 2019 in a Designated ICU: Clinical Features and Predictors for Mortality date = 2020-07-20 keywords = SARS; covid-19; patient; sofa summary = CONCLUSION: Critically ill COVID-19 patients aged higher than 70, arrhythmia, or a SOFA score above 4 have a high risk of mortality, and need prior medical intervention. In the present study, we present details of 59 critically ill patients with SARS-CoV-2 infection, admitted to the intensive care unit (ICU) of Caidian Branch of Tongji Hospital, and then identified prognostic factors for mortality of these critically ill patients. 3, 4 According to the WHO interim guidance and Diagnostic and Treatment Program of COVID-19 (Version 7.0) published by the National Health Commission of the People''s Republic of China, all patients were diagnosed with severe pneumonia induced by SARS-CoV-2 infection who required mechanical ventilation, had inspiratory oxygen fraction (FiO₂) ≥60%, or had the shock or organ failure. doi = 10.2147/rmhp.s263095 id = cord-312991-ypgrw78s author = Wang, Zhi-Gang title = Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV date = 2005-09-12 keywords = SARS summary = In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. According to 5 polymorphism sites, 63 SARS-CoV genomes were divided into early, middle and late phase genotype groups [19] . Key mutation loci are shown in Table 3 (identified by using nucleotide-nucleotide BLAST program at NEBI and Clustalw 1.83), and the phylogenetic tree of 174 loci ( Fig. 1) showed that, according to the polymorphism sites of C9404T, C9479T, G17564T, G19838A, A21721G, C22222T, G22517A, G23823T, T27243C and C27827T, the SARS-CoV genomes of the first epidemic can be divided into two genotypes, genotype C and T. among the genotypes and the groups The genetic characteristics of the genotypes were further analyzed based on the sequence polymorphism of the spike protein genes ( Table 4 ). SARS-CoV GD03T0013 was from the patient with ''''mild clinical symptoms'''', and its genome sequence was similar to that of the sub-genotype C1. doi = 10.1016/j.febslet.2005.07.075 id = cord-253990-m75xwrz9 author = Wang, Zhiguo title = Covid‐19: From structure to therapeutic targeting in studying approved drugs and local DNA vaccination date = 2020-10-29 keywords = COVID-19; SARS summary = The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represent one of the major challenges in controlling the disease severity, keeping to pose a huge threat to the global health. The current lack of specific and effective therapies for the COVID-19, and the continuous spread of coronavirus SARS-CoV-2 across many parts of the world, represents one of the major challenges in controlling the disease severity and consequences, posing a huge threat to the global health. In this article, we highlight several previously approved drugs for potential effect on combating SARS-CoV-2 coronavirus infection, and modulating pulmonary inflammation and immune response. Despite unprecedented efforts to contain the virus spread and prevent infection, SARS-CoV-2 pneumonitis can still rapidly strike to incapacitate the lung causing severe acute respiratory distress syndrome (ARDS), resulting in severe disease aftermath and sometimes death. doi = 10.1111/1440-1681.13409 id = cord-332832-kjppd6uz author = Ward, B. J. title = Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants date = 2020-11-06 keywords = IL-4; November; SARS; dose; preprint summary = (ClinicalTrials.gov number NCT04450004) Methods: The study was a randomized, partially-blinded, prime-boost 21 days apart, dose-escalation Phase 1 study intended to assess the safety, tolerability, and immunogenicity of CoVLP at three dose levels (3.75 microgram, 7.5 microgram, and 15 microgram) unadjuvanted or adjuvanted with either CpG 1018 or AS03 in 180 SARS-CoV-2 seronegative healthy adults 18 to 55 years of age. We report here the results of a Phase 1 study initiated in July 2020 evaluating the safety, 203 tolerability and immunogenicity of two doses, 21-days apart of 3.75, 7.5 or 15 µg of a virus-204 like-particle vaccine candidate for Covid-19 produced in plants (hereafter called CoVLP). ; https://doi.org/10.1101/2020.11.04.20226282 doi: medRxiv preprint Like any early-phase clinical trial, this study has several limitations beyond the obvious 459 concern regarding small group size when testing multiple dose levels and formulations 460 (n=20/group). doi = 10.1101/2020.11.04.20226282 id = cord-316617-8cqxz3wi author = Ward, Michael P. title = SARS‐CoV‐2, where to now? date = 2020-06-19 keywords = COVID-19; SARS summary = (2020) present the results of a SARS-CoV-2 serological survey in 35 animal species in China, including the dog of a COVID-19 patient and an additional two in-contact dogs. Tests available for the detection of SARS-CoV-2 are comprehensively described in this issue of Transboundary and Emerging Diseases (Li & Ren, 2020) . In addition to the publication of new knowledge about SARS-CoV-2 in this issue of Transboundary and Emerging Diseases, new ideas are also presented. A key enabler of such a shift in our thinking and approach to disease emergence and spread is a One Health workforce capable of undertaking integrated monitoring, surveillance, risk assessment and response activities. The COVID-19 pandemic could be a catalyst for such a seismic shift in how we approach emerging infectious diseases and One Health. We can be sure, even when the current COVID-19 pandemic is resolved, that the need for surveillance, response and prevention of transboundary and emerging diseases will remain. doi = 10.1111/tbed.13654 id = cord-333326-n9ifhw5s author = Wardell, Hanna title = Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Febrile Neonates date = 2020-07-09 keywords = COVID-19; CoV-2; SARS summary = Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in pediatric patients are mild or asymptomatic. We report a case series of 4 full-term neonates hospitalized with fever and found to have SARS-CoV-2 infection with a spectrum of illness severities. Herein we present a case series of 4 full-term neonates who were hospitalized with fever and found to be infected with SARS-CoV-2. Due to the concern for end-organ involvement with possibly evolving acute myocardial injury as well as a supplemental oxygen requirement, the patient was initiated on therapy with remdesivir on inpatient day 4 via an expanded-access program from the manufacturer after approval from the US Food and Drug Administration and local institutional review board, with informed consent. In this report, we present 4 febrile neonates hospitalized with SARS-CoV-2 infection with favorable outcomes. SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress doi = 10.1093/jpids/piaa084 id = cord-258681-66ct8nod author = Warnock, David G. title = Clinical Trials during the SARS-CoV-2 Pandemic date = 2020-04-14 keywords = SARS summary = The primary outcome measures of this trial include the incidence of active COVID-19-related disease at 14 days post-enrollment, and a COVID-19 Disease Severity Scale self-reported by participants at 14 days post-enrollment: no COVID-19-related disease (score of 1); COVID-19-related disease with no hospitalization (score of 2); or COVID-19-related disease with hospitalization or death (score of 3).The goal is to enroll and randomize 1,500 subjects into each of the active-drug and placebo arms, followed by a 6-day treatment course with hydroxychloroquine. Secondary outcome measures include 14-day incidence of hospitalization, 14-day incidence of confirmed SARS-CoV-2 infection, the number of participants in each arm who discontinue or withdraw from the protocol, and 90-day incidence of death related to COVID-19-related disease. The trial includes a chartered Data Safety Monitoring Board with defined stopping rules for clinical futility or statistically significant improvement in the primary outcome measures comparing the active-drug group to the placebo group (personal communication, March 22, 2020: covid19faq COVID-1-Post-Exposure Prophylaxis FAQ Account). doi = 10.1159/000507582 id = cord-315440-he7sm7nj author = Wassie, Gizachew Tadesse title = Incubation period of SARS-CoV-2: A systematic review and meta-analysis date = 2020-10-11 keywords = COVID-19; SARS; period summary = Since there is no effective COVID-19 vaccine available yet, it is increasingly important to understand the average incubation period of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to design appropriate preventive and control strategies. Therefore, this systematic review and meta-analysis was designed to estimate the pooled average incubation period of SARS-CoV-2. We included peer-reviewed research studies written in the English language on the incubation period of SARS-CoV-2 using pre-defined quality and inclusion criteria. With regard to studies published in peer-reviewed journals or found in grey literature, all observational study designs (i.e. cross-sectional, case-control, and cohort), studies involving humans, and studies reporting the incubation period of SARS-CoV-2 were eligible for inclusion in this systematic review and meta-analysis. Studies with no accessible full text after using all the PRISMA-P search strategies and studies not reporting a specific incubation period for SARS-CoV-2 were excluded from this systematic review and meta-analysis. doi = 10.1016/j.curtheres.2020.100607 id = cord-263452-y2ral8nx author = Watanabe, Yasunori title = Site-specific glycan analysis of the SARS-CoV-2 spike date = 2020-05-04 keywords = HIV-1; SARS summary = To resolve the site-specific glycosylation of SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo-electron microscopy (cryo-EM) structure, albeit without glycan processing blockade using kifunensine (4). The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27) , influenza HA (28, 29) , and LASV GPC (24). For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34) . This suggests that SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies. SARS-CoV-2 spike site-specific N-linked glycan analysis doi = 10.1126/science.abb9983 id = cord-317786-iv1br2oj author = Waterfield, T. title = Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study. date = 2020-09-02 keywords = CoV-2; SARS; September summary = Discussion In this study children demonstrated similar antibody titres in response to SARS-CoV-2 irrespective of age. The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. Participants and their parents provided information at enrollment relating to age, sex, previous health and potential predictors of SARS-CoV-2 infection including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/antibody testing. Seroprevalence of SARS-CoV-2 antibodies in children of healthcare workers-A prospective multicentre cohort study protocol -Accepted for publication doi = 10.1101/2020.08.31.20183095 id = cord-326706-75mjs6vm author = Waterfield, Thomas title = Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study date = 2020-11-10 keywords = CoV-2; SARS summary = Following multivariable analysis four independent variables were identified as significantly associated with SARS-CoV-2 seropositivity: known infected household contact OR=10.9 (95% CI 6.1 to 19.6); fatigue OR=16.8 (95% CI 5.5 to 51.9); gastrointestinal symptoms OR=6.6 (95% CI 3.0 to 13.8); and changes in sense of smell or taste OR=10.0 (95% CI 2.4 to 11.4). The objective of this study was to report the presence, and titres, of SARS-CoV-2 antibodies in healthy children of healthcare workers across the UK and to report the symptomatology of infection including the asymptomatic rate. This multicentre observational prospective cohort study was designed to determine the seroprevalence of SARS-CoV-2 antibodies in healthy children, and report the symptomatology of infection. 26 Participants and their parents provided information at enrolment relating to age, sex, previous health and potential predictors of SARS-CoV-2 seropositivity including; known contact with individuals with COVID-19, contact with individuals who have been symptomatic and/or self-isolating and results of any diagnostic testing such as RT-qPCR testing/ antibody testing. doi = 10.1136/archdischild-2020-320558 id = cord-282964-dmc8mlxu author = Wathore, Roshan title = Understanding air and water borne transmission and survival of coronavirus: Insights and way forward for SARS-CoV-2 date = 2020-08-04 keywords = SARS; covid-19 summary = This has spurred efforts to characterize the coronavirus and understand the factors impacting its transmission and survival such as aerosols, air quality, meteorology, chemical compositions and characteristics of particles and surfaces, which are directly or indirectly associated with coronaviruses infection spread. Nonetheless, many peer-reviewed articles have studied these aspects but mostly in isolation; a complete array of coronavirus survival and transmission from an infected individual through airand water-borne channels and its subsequent intractions with environmental factors, surfaces, particulates and chemicals is not comprehensively explored. Finally, this study outlines probable air and water borne routes and suggest a way forward highlighting the need for investigating the effect of particulate matter characteristics on survival and transmission of SARS-CoV-2 due to the prominent presence of PM in ambient, spaces, and on the surfaces. doi = 10.1016/j.scitotenv.2020.141486 id = cord-282133-5dzzm9s8 author = Watzky, Manon title = Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry date = 2020-10-15 keywords = ACE2; SARS; TMPRSS2 summary = In here, exploiting a large panel of publicly available genome-wide data, we investigated whether the human receptor ACE2 and human proteases TMPRSS2, FURIN and CATHEPSINs (B, L and V), which are involved in SARS-CoV-2 cell entry, are transcriptionally regulated by environmental cues. We queried the comparative toxicogenomics database (CTD) to identify studies reporting changes in expression levels of human genes encoding receptor and proteases J o u r n a l P r e -p r o o f important for SARS-CoV-2 cell entry upon chemical exposure (Davis et al., 2019) . Using these criteria, we identified several chemical exposures regulating the expression of receptor ACE2 and human proteases TMPRSS2, FURIN and Cathepsins genes in human cells and tissues (Figure 2; Supplementary Table S2 ). Our analysis suggests that expression of human receptor and proteases of SARS-CoV-2 spike S glycoprotein are not directly regulated by cigarette smoke at the transcriptional level in lung cells, nor that PIR and ACE2 are coregulated upon cigarette smoke exposure. doi = 10.1016/j.envres.2020.110317 id = cord-327616-uu9uygic author = Wazny, Vanessa title = Vascular underpinning of COVID-19 date = 2020-08-27 keywords = ACE2; CD147; COVID-19; SARS; cell summary = Coronavirus disease 2019 (COVID-19) case study reports have called attention to the overrepresentation of cardiovascular diseases, in addition to respiratory diseases, among patients at risk of critical illness and mortality following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection [1] [2] [3] [4] [5] [6] [7] [8] . Initial concerns were also raised regarding the medical treatment of hypertension with adverse COVID-19 outcomes, as studies in animals have shown that the use of renin-angiotensin system blockers-angiotensin-converting enzyme inhibitors and angiotensin receptor blockers result in the upregulation of angiotensin-converting enzyme 2 (ACE2) expression, which is an entry factor for SARS-CoV-2 [13] . Collectively, these case reports of confirmed COVID-19 hospitalized patients strongly indicate a strong association between underlying cardiovascular diseases and diabetes with severe health outcomes and fatality following SARS-CoV-2 infection. In COVID-19 research, nasal and alveolar epithelial cells are generally believed to be the primary sites of viral infection due to the high expressions of SARS-CoV-2 entry factors [51] . doi = 10.1098/rsob.200208 id = cord-262760-mf1pn587 author = Weber, Stefanie title = Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date = 2020-09-24 keywords = China; SARS; Table summary = By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). doi = 10.1016/j.virusres.2020.198170 id = cord-315585-bjij8ds7 author = Wee, Liang En title = Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore date = 2020-05-08 keywords = COVID-19; RSW; SARS summary = METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. 15 Here, we report our experience with a novel concept, a respiratory surveillance ward (RSW), which was introduced as a strategy for admission, triage and disposition of patients presenting with respiratory syndromes during a SARS-CoV-2 outbreak. Respiratory surveillance wards (RSWs): Admissions criteria, layout, infection control, and transfer criteria At our institution, high-risk patients that fulfilled suspect case criteria for COVID-19 were admitted to an isolation ward with 37 negative-pressure rooms. During an outbreak of SARS-CoV-2 with local transmission, an RSW to cohort all inpatients admitted from the community with respiratory symptoms may enhance case detection and reduce the potential of nosocomial transmission. doi = 10.1017/ice.2020.207 id = cord-310594-i0586vfw author = Weemaes, Matthias title = Laboratory information system requirements to manage the COVID-19 pandemic: a report from the Belgian national reference testing center date = 2020-04-29 keywords = COVID-19; LIS; SARS summary = OBJECTIVE: To describe the development, implementation and requirements of laboratory information system (LIS) functionality to manage test ordering, registration, sample flow, and result reporting during the COVID-19 pandemic. RESULTS: We outline the design, implementation and requirements of LIS functionality related to managing increased test demand during the COVID-19 crisis, including tools for test ordering, standardized order sets integrated into a computerized provider order entry module, notifications on shipping requirements, automated triaging based on digital metadata forms, and the establishment of databases with contact details of other laboratories and primary care physicians to enable automated reporting. DISCUSSION: Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turn-around-time of SARS-CoV-2 testing. During the early stages of the COVID-19 outbreak, our laboratory was the only SARSNotably, the large majority of our expanded work force (30 of the 38 additional FTE) was assigned to help with administrative tasks (sample reception, triaging, patient registration, result validation and reporting, and epidemiological studies), and not directly involved in expanding analytical capacity (i.e. PCR analysis) ( Figure 2 ). doi = 10.1093/jamia/ocaa081 id = cord-315652-hct9yh3n author = Wehbe, Zena title = Molecular Insights Into SARS COV-2 Interaction With Cardiovascular Disease: Role of RAAS and MAPK Signaling date = 2020-06-03 keywords = ACE2; CVD; MAPK; SARS summary = As such, a thorough understanding of the signaling pathways common to the pathogenesis of CVD and SARS-CoV-2 infection is necessary to identify crucial sites of crosstalk and direct future investigation of potential therapeutic interventions mitigating both COVID-19 complications in CVD patients as well as short-and long-term viral-induced cardiovascular impairment. The chronic nature and gradual development timeframe of these diseases might argue that the crosstalk among increased MAPK signaling cascades and SARS-CoV-2 pathogenesis leads to increased infection severity and complications in patients with established CVD rather than being involved in viraltriggered cardiovascular involvement. This raises the possibility for a beneficial effect of eplerenone or other aldosterone receptor antagonists in reducing risk of severe COVID-19 infection in CVD patients or to mitigate the cardiovascular burden of SARS-CoV-2 infection. doi = 10.3389/fphar.2020.00836 id = cord-345603-mirsz6m8 author = Wehrhahn, Michael C. title = Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic date = 2020-05-04 keywords = SARS summary = Self-collected swabs in the community for SARS-CoV-2, the agent of COVID-19, and for other respiratory viruses offers potential significant benefit in the current pandemic by J o u r n a l P r e -p r o o f reducing requirement for PPE, limiting exposure of patients and staff to infection, increased convenience and access for patients and timeliness of a sample receipt. 9 Recent reports on SARS-CoV-2 in respiratory specimens indicate early high viral loads in symptomatic and asymptomatic patients in a variety of clinical specimens including nasal and throat swabs, sputum and saliva samples. The aim of this study was to compare prospectively the performance of HC with separate SC nasal (SCN) and throat swabs (SCT) and the combination of the two (SCNT) for respiratory viruses including SARS-CoV-2. doi = 10.1016/j.jcv.2020.104417 id = cord-256940-yuja99jg author = Wei, Bo title = Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date = 2020-07-20 keywords = RNA; SARS summary = title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. However, some COVID-19 patients have been reported to have long-term positivity for SARS-CoV-2 ribonucleic acid (RNA). On April 5, after three consecutive negative nucleic acid test results, he was discharged and transferred to another hospital for further treatment of comorbidities. Thus, DNVr may be a potential antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. doi = 10.1590/0037-8682-0372-2020 id = cord-310201-70fj4fhr author = Wei, D.-Q. title = Anti-SARS drug screening by molecular docking date = 2006-05-22 keywords = Chou; Mpro; SARS summary = (2003) and Chou (2004) found the fitting problem of AG7088 to the binding pocket of SARS CoV Mpro, and they suggested its derivative KZ7088 as a better starting point. Furthermore, the intermolecular hydrogen bonds and electrostatic interaction, whose effects have already been counted in the binding energy, were also investigated in order to find useful information for drug design. In contrast, if ranking the docking results according to the binding free energy which includes the torsional term as shown in Rank 2 of Table 1 , it was found that most of the top-20 ligands interacted quite well with the receptor in the pocket. A comparison of the results between Ranks 1 and 2 suggests that the binding free energy is more reliable as a criterion for the virtual screening via molecular docking. Hydrogen bonds between ligand 4 and the involved residues of SARS CoV Mpro. doi = 10.1007/s00726-006-0361-7 id = cord-276402-ymxvtyll author = Wei, Jia title = SARS-CoV-2 infection in immunocompromised patients: humoral versus cell-mediated immunity date = 2020-07-29 keywords = SARS; car summary = BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic placed unprecedented pressure on various healthcare systems, including departments that use immunotherapies such as chimeric antigen receptor (CAR) T-cell therapy and immunosuppression therapy in organ transplantation units. The true impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on immunocompromised CAR T-cell therapy recipients and kidney transplant recipients (KTRs) has not yet been established. His virus clearance failure and life-threating cytokine storm during SARS-CoV-2 infection suggested that any decision to proceed CAR T-cell therapy during COVID-19 pandemics will require extensive discussion of potential risks and benefits. 3 Coronavirus disease 2019 (COVID-19) is a heterogeneous disease population, of which most patients exhibit mild to moderate symptoms, however approximately 15% progress to severe pneumonia, while 5% were eventually admitted to intensive care units (ICU) due to the resultant acute respiratory distress syndrome (ARDS), septic shock and/or multiple organ failure. doi = 10.1136/jitc-2020-000862 id = cord-335338-wzxjn5ip author = Wei, Lan title = Pathology of the thyroid in severe acute respiratory syndrome() date = 2006-09-25 keywords = SARS; patient; thyroid summary = To further investigate the effects of SARS associated coronavirus (CoV) on the thyroid, we have undertaken a detailed study of the thyroid gland with special attention to the pattern of cellular and architectural alterations on parafollicular and follicular cells. In contrast to normal thyroid, the thyroid glands from patients with SARS consistently showed destruction of the follicular epithelium and exfoliation of epithelial cells into the follicle. Our study has demonstrated that thyroid glands in patients with SARS were significantly affected by the disease with extensive injury to the follicular epithelial cells and the parafollicular cells. The extent of morphological injury and the large quantity of cells undergoing apoptosis that we observed in the thyroid follicular epithelium provide an explanation for the diminished serum T3 and T4 levels in patients with SARS. Evaluation and observation of serum thyroid hormone and parathyroid hormone in patients with severe acute respiratory syndrome The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells doi = 10.1016/j.humpath.2006.06.011 id = cord-268065-mxvbbkc4 author = Wei, Maoti title = Epidemiology of Coronavirus Disease 2019 (COVID-19) Caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-05-18 keywords = COVID-19; China; SARS summary = Shortly after the virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the epidemic of coronavirus disease 2019 (COVID-19) broke out, and an information storm occurred. Based on information of SARS, Middle East respiratory syndrome (MERS), and COVID-19, the components of the epidemic (the sources, the routes of infection, and the susceptible population) will be discussed, as well as the role of natural and social factors involved. S ince the end of 2019, a novel coronavirus, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID19) , appeared in Wuhan, Hubei Province, China. Recent results showed that SARS-CoV-2 persists longer with a higher viral load and peaks later in the respiratory tissue of patients with severe disease; this phenomenon highlights the need for the prevention and control of the epidemic. Some experts commented that people with mild or asymptomatic SARS-CoV-2 infection were not identified by epidemic prevention measures, thus accelerating the spread of the disease. doi = 10.1017/dmp.2020.155 id = cord-304254-67brxejx author = Wei, Ping title = The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase date = 2006-01-20 keywords = 3CL; SARS summary = As we have reported previously, the peptide cleavage assay shows that the specific activity for proteolysis decreases linearly with the decrease of enzyme concentration, suggesting that the dimer is the major form for biological activity and that the dimeric interface could be targeted for structural-based drug design against SARS 3CL proteinase [18] . The crystal structure of SARS 3CL proteinase indicates that the N-finger fragment plays an important role in the dimerization and maintenance of the active form of the enzyme [16] . The dimer dissociation constants of the SARS 3CL proteinase and N-terminal mutants were determined by sedimentation velocity and equilibrium methods. In summary, we have carried out a mutational study on the N-finger of SARS 3CL proteinase and determined the dimer dissociation constants for the wild-type protein and the mutants using sedimentation velocity and equilibrium techniques. doi = 10.1016/j.bbrc.2005.11.102 id = cord-323389-8vp57c1o author = Wei, S. title = Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2. date = 2020-06-16 keywords = SARS summary = We developed an assay that detects single copies of SARS-CoV-2 virus directly from saliva and swab samples in 30 min using a simple, one-step protocol that utilizes only a heat block and microcentrifuge tube prefilled with a mixture containing the necessary reagents and has a sensitivity and specificity of 97% and 100%, respectively. To determine which primer set was most sensitive and specific to SARS-CoV-2, we tested the eight primer sets that we designed, along with previously published primer sets 9, 10 , using serial dilutions of 500 to 0.5 copies of SARS-CoV-2 RNA standard spiked into a 25 μ L RT-LAMP reaction ( Figure 1C ). . https://doi.org/10.1101/2020.06.13.20129841 doi: medRxiv preprint necessary for testing clinical samples ( Figure 1D ). In summary, we developed HP-LAMP, which enables rapid detection of SARS-CoV-2 directly from saliva in 30 min using a simple one-step protocol with a LoD of 2 viral copies per μ L of saliva and a sensitivity and specificity of 97% and 100%, respectively. doi = 10.1101/2020.06.13.20129841 id = cord-262796-syu4wbpi author = Wei, Xiao-Shan title = Diarrhea is associated with prolonged symptoms and viral carriage in COVID-19 date = 2020-04-18 keywords = SARS; patient summary = Abstract Background & Aims We compared clinical, laboratory, radiological, and outcome features of patients with SARS-CoV-2 infection (COVID-19) with pneumonia, with vs without diarrhea. Methods We performed a retrospective, single-center analysis of 84 patients with SARS-CoV-2 pneumonia in Wuhan Union Hospital, China, from January 19 through February 7, 2020. Of 76 patients with a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039). On admission to hospital, all confirmed COVID patients were tested for SARS-CoV-2 RNA from stool samples. Of 76 COVID-19 patients who had a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P=.039) ( Table 5) . doi = 10.1016/j.cgh.2020.04.030 id = cord-138439-wvynetna author = Wei, Xiyi title = Sex Differences in Severity and Mortality Among Patients With COVID-19: Evidence from Pooled Literature Analysis and Insights from Integrated Bioinformatic Analysis date = 2020-03-30 keywords = ACE2; COVID-19; SARS; patient summary = Objective: To conduct a meta-analysis of current studies that examined sex differences in severity and mortality in patients with COVID-19, and identify potential mechanisms underpinning these differences. Methods: We performed a systematic review to collate data from observational studies examining associations of sex differences with clinical outcomes of COVID-19. Conclusions: This meta-analysis detected an increased severity and mortality rate in the male populations with COVID-19, which might be attributable to the sex-based differences in cellular compositions and immunological microenvironments of the lung. However, whether the sex difference is related to the risk factors for infection, severity, and mortality of COVID-19 is still lacking a comprehensive analysis based on the integration of new studies. ACE2 as a receptor of SARS-CoV and spike protein can be primed by TMPRSS2 are exploited to entry into target cells, which play an vital role in coronavirus pneumonia infection. doi = nan id = cord-332109-ont0tqpn author = Wei, Yufeng title = Substance Use Disorder in the COVID-19 Pandemic: A Systematic Review of Vulnerabilities and Complications date = 2020-07-18 keywords = ACE2; BBB; CNS; COVID-19; HPA; IL-6; SARS; immune; increase summary = The immunosuppression reduces antibody production, cytotoxicity, and T cell-mediated immune responses, and is linked to higher incidences of pathogen infections, slowed recovery, and severe disease progression in COVID-19. Due to compromised immune responses, cocaine abusers have considerably high incidences of viral infections, including human immunodeficiency virus (HIV), influenza, and potentially SARS-CoV-2. Cardiac arrhythmias and acute MI; oxygen imbalance; microvascular diseases and thrombosis [122] [123] [124] [125] [126] [127] [129] [130] [131] [132] Increased severity and mortality [12, 37, 38] Immune system Stimulating HPA axis; immunosuppression; defects in antibody formation, lymphocyte proliferation, macrophage and NK activation [141, 142] High incidence of viral infection [142] CNS Increased BBB permeability due to loss of tight junction proteins; rearrangement of cytoskeleton structure [143] [144] [145] [146] Endotheliitis and CNS infection [53, [55] [56] [57] Amphetamine, METH, MDMA doi = 10.3390/ph13070155 id = cord-327520-qj7coqfr author = Wei, Yulong title = Coronavirus genomes carry the signatures of their habitats date = 2020-06-13 keywords = Fig; SARS summary = Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Here we compared the CpG and U content 327 of these coronaviruses and found that viruses that regularly infect AVP-rich tissues tend to Based on global sequence comparison, figure 4a shows that most SNPs are C->U substitutions. doi = 10.1101/2020.06.13.149591 id = cord-014938-7evmiuv5 author = Wei-ming, Yan title = Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model date = 2008-01-13 keywords = SARS summary = title: Expression of prothrombinase/fibroleukin gene fg12 in lung impairment in a murine severe acute respiratory syndrome model To evaluate the role of murine fibrinogen like protein 2 (mfgl2) /fibroleukin in lung impairment in Severe acute respiratory syndrome (SARS), a murine SARS model induced by Murine hepatitis virus strain 3 (MHV-3) through trachea was established. In a separate experiment, tissues including lungs, spleen, liver, kidneys, intestine, heart, brain were collected at a series of time points from Balb/cJ mice infected with MHV-3 through trachea. Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung The clinical pathology of severe acute respiratory syndrome (SARS): a report from China Lung pathology of severe acute respiratory syndrome (SARS): a study of 8 autopsy cases from Singapore Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR A novel coronavirus associated with severe acute respiratory syndrome doi = 10.1007/s12250-007-0020-5 id = cord-261470-sqxdwu6j author = Weichmann, Franziska title = Projected supportive effects of Pycnogenol® in patients suffering from multi-dimensional health impairments after a SARS-CoV2 infection date = 2020-10-09 keywords = COVID-19; Pycnogenol; SARS; patient summary = Two London based hospitals also found increasing numbers of patients with Kawasaki-like symptoms in communities with high rates of COVID 19, which was provisionally called pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) [68] [70] . Another double-blind, placebo-controlled study reported similar effects when supplementing type II diabetes and hypertensive patients, taking ACE inhibitor medication together with 125 mg Pycnogenol ® daily for 3 months. Regarding endotheliitis, Pycnogenol ® studies offer good evidence for potential beneficial effects for patients suffering from COVID-19 by improving endothelial function. As Pycnogenol ® offers antioxidant and anti-inflammatory activities and positively influences endothelial cell function as well as microcirculation and platelet reactivity, a supplementation might support the management of COVID-19 patients. We hypothesize possible additional beneficial effects of Pycnogenol ® in patients infected with the new coronavirus SARS-CoV2 and those who suffer from abiding health problems, when complemented to the standard treatment also upon the first day of symptoms or infection. doi = 10.1016/j.ijantimicag.2020.106191 id = cord-339508-nf6ov39g author = Weil, Ana A. title = Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle date = 2020-09-01 keywords = SARS; SNF; employee summary = In this study, we describe the results of cross-sectional resident and employee SARS-CoV-2 testing, and infection control and personnel policies associated with 16 Seattle area SNFs. Through two testing strategies, a total of 16 SNFs offered testing to either residents, employees, or both. For employees tested through the Seattle Flu Study, data included participant date of birth, date of testing, race and ethnicity, location and nature of work, new symptoms experienced during the last 7 days, and history of SARS-CoV-2 testing (Appendix 1 in the Supplementary Material). For employees, positive or inconclusive SARS-CoV-2 test results were reported directly to participants by phone within 48 h and to the Washington State Department of Health. We report the results of a large cross-sectional study evaluating SARS-CoV-2 prevalence in skilled nursing facilities (SNFs) in the Seattle area during the spring 2020 peak of the COVID-19 pandemic. doi = 10.1007/s11606-020-06165-7 id = cord-277210-xaj2623u author = Weinkove, Robert title = Managing haematology and oncology patients during the COVID‐19 pandemic: interim consensus guidance date = 2020-05-13 keywords = COVID-19; SARS; cancer; patient; risk summary = • Adopt measures within cancer centres to reduce risk of nosocomial SARS-CoV-2 acquisition; support population-wide social distancing; reduce demand on acute services; ensure adequate staffing; and provide culturally safe care. Patients with cancer could be at elevated risk of severe COVID-19, while delivery of cancer therapies could be disrupted by quarantines, social distancing measures, and interruption of routine health care delivery by the pandemic. 38 Community spread of COVID-19 has the potential to diminish the donor pool, to threaten the capacity of cancer services to provide routine transfusion support, and to increase the risks that transfusion-dependent patients will come into contact with other individuals with SARS-CoV-2. We present interim guidance for clinicians caring for patients with cancer who may be particularly vulnerable both to severe COVID-19 and the potential impact of the pandemic on the provision of cancer investigations and treatment. doi = 10.5694/mja2.50607 id = cord-300793-tuq8z6gm author = Weiss, Robin A title = Social and environmental risk factors in the emergence of infectious diseases date = 2004 keywords = AIDS; HIV; SARS; disease; human; infection summary = About 30 new diseases have been identified, including Legionnaires'' disease, human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS), hepatitis C, bovine spongiform encephalopathy (BSE)/variant Creutzfeldt-Jakob disease (vCJD), Nipah virus, several viral hemorrhagic fevers and, most recently, severe acute respiratory syndrome (SARS) and avian influenza. Emerging infectious diseases in humans comprise the following: first, established diseases undergoing increased incidence or geographic spread, for example, Tuberculosis and Dengue fever; second, newly discovered infections causing known diseases, for example, hepatitis C and Helicobacter pylori; and third, newly emerged diseases, for example, HIV/AIDS and SARS. Although some of the apparent increase in infectious disease may be attributable to better diagnostic methods and surveillance, there seems little doubt that more incidents are occurring, and have the potential to spread more widely than 50 years ago, as outbreaks and spread of infections like Nipah virus and SARS would not have passed unnoticed. doi = 10.1038/nm1150 id = cord-321938-pda4a5n7 author = Weisshoff, Hardy title = Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date = 2020-11-02 keywords = HRFYRLAN; RNA; SARS summary = We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). In the Spike protein of SARS-CoV-2, several sequences which are highly susceptible to interaction with DNA (multiple amino acids with positive charged side chains) were identified, in particular at the angiotensin I-converting enzyme 2 (ACE2)-receptor binding domain (RBD): YRLFRK (SARS-CoV-2 specific from protein data bank (PDB) data base entry PBD ID: 6VXX, source: [23] ), as well as NRKRISN (PBD ID: 6VXX) and KIKRMK (PDB ID: 5X5B source: [24] ). This enabled us to exploit NMR-spectroscopy to investigate whether the selected peptide-sequences from SARS-CoV-2 proteins bind to this clinically advanced aptamer (BC 007), forcing it into its well described quadruple structure just by molecular interaction. doi = 10.1016/j.heliyon.2020.e05421 id = cord-297197-klr208kp author = Weizman, Yehuda title = Use of Wearable Technology to Enhance Response to the COVID-19 Pandemic date = 2020-07-01 keywords = SARS; bracelet summary = ABSTRACT Introduction As part of the COVID-19 outbreak response, numerous technology-based solutions have been created to enable contact tracing, track movements of the population and ensure social control. The bracelet would facilitate 3 functions; screening on a population level, digital contact tracing and real-time immunity status tracking. The bracelet would employ the IoT to transfer data over a network to an interactive web-based dashboard that tracks COVID-19 in real-time. If an individual then tested positive for SARS-CoV-2, the database could automatically trace back anyone they had come in contact with in the past 14 days using a GPS feature (described below). In this instance, the biometric bracelet''s GPS feature would continuously track movements of individuals within a geographical area and communicate back to the Covid-19 database platform saving input on the population whereabouts at each timepoint. As the coronavirus pandemic continues to spread, some Privacy Commissioners are lifting data restrictions for health officials to keep track of the outbreak. doi = 10.1016/j.puhe.2020.06.048 id = cord-256982-t6urqus7 author = Wellinghausen, Nele title = Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date = 2020-09-16 keywords = PCR; SARS summary = The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. A comparison of five commercial immunoassays in serum samples taken at least ten days after onset of symptoms from 51 PCR-confirmed COVID-19 outpatients revealed an overall sensitivity of the assays from 74.5% to 88.2%. doi = 10.3205/id000066 id = cord-308256-jy20xtwx author = Wells, P. M. title = Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date = 2020-07-30 keywords = COVID-19; SARS summary = Methods: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. doi = 10.1101/2020.07.29.20162701 id = cord-322812-9u3ptqjs author = Wells, Philippa M. title = Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England date = 2020-10-15 keywords = App; COVID-19; SARS summary = METHODS: We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. We undertook a population-based study of the humoral immune response to SARS-CoV-2, with regards to longitudinal clinical symptoms collected through a mobile phone app in a population-based sample of 431 TwinsUK volunteers. For three months prior to the visit, the majority of participants had completed regular logging of symptoms, via the C-19 Covid Symptom Study app 5 , enabling measurement of antibody response to COVID-19 with regards to clinical symptoms. doi = 10.1016/j.jinf.2020.10.011 id = cord-260925-puuqv6zk author = Wen, Feng title = Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 date = 2020-03-05 keywords = SARS summary = title: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 The sequences NC_004718.3 of SARS coronavirus 6 genes were utilized to define the protein products of SARS-CoV-2. First, the protein sequences of SARS-CoV-2 were compared with RaTG13, human SARS (NC_004718.3), bat SARS (DQ022305.2), and human MERS (NC_019843.3) by calculating the similarity in a given sliding window ( Fig. 1 A) . These results suggested that there had probably been no hyper-variable genomic hotspot in the SARS-CoV-2 population until now. The hyper-variable genomic hotspot has been established in the SARS-CoV-2 population at the nucleotide but not the amino acid level, suggesting that there have been no beneficial mutations. mutations in nsp1, nsp3, nsp15, and gene S that identified in this study would be associated with the SARS-CoV-2 epidemic and was worthy of further study. The genome sequence of the SARS-associated coronavirus doi = 10.1016/j.jinf.2020.02.027 id = cord-033406-xoyt7esk author = Wen, Wen title = Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient date = 2020-09-11 keywords = SARS summary = title: Next-generation sequencing revealed influenza and Chlamydia infection in recurrent pneumonia in a recovered COVID-19 patient The patient presented to Anqing Municipal Hospital (Anhui province) with a positive result on nasopharyngeal swabs for SARS-CoV-2 and discharged in good clinical condition after consecutive negative results On February 9, 2020. 3 In our report, the patient recovered from COVID-19 and developed a lung infection with GGO 82 days later after being discharged from hospital. This study is part of the project of "Construction of a bio-information platform for novel coronavirus pneumonia Chest computed tomography show completely absorbed lesion when he was discharged on May 28, 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing doi = 10.1093/pcmedi/pbaa033 id = cord-259033-op94wuy4 author = Wendling, Daniel title = Can SARS-CoV-2 trigger reactive arthritis? date = 2020-10-27 keywords = COVID-19; SARS summary = The potential mechanisms at the origin of arthritis in a context of viral infection by SARS-CoV-2 remain at the hypothesis stage. The mechanism of reactive arthritis is plausible, due to the clinical presentation, the delay between the onset (or diagnosis) of COVID and the onset of rheumatological manifestations, the usual negativation of nasopharyngeal RT-PCR at the time of onset of rheumatological involvement. However, cases of symptomatic SARS-CoV-2 infection have been reported in patients treated with an anti IL-17 monoclonal antibody for spondyloarthritis [19] . Arthritis may be reactive to a masked pulmonary or digestive infection as a consequence of COVID [13] , or it may be a non-specific consequence of the "cytokine storm" that accompanies the symptomatic forms of the disease [20] . This new infectious disease may induce rheumatological manifestations, with the possibility of reactive arthritis. Patient-reported Disease Activity in an Axial Spondyloarthritis Cohort during the COVID-19 Pandemic. A Case of Reactive Arthritis Secondary to Coronavirus Disease 2019 Infection Case of acute arthritis following SARS-CoV-2 infection doi = 10.1016/j.jbspin.2020.105086 id = cord-318766-vx0dnnxh author = Wendt, Ralph title = Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany date = 2020-06-03 keywords = Germany; SARS summary = title: Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2–positive physician among patients and healthcare workers in Germany We investigated potential transmissions of a symptomatic SARS-CoV-2–positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. We tested all 254 potential contacts of the symptomatic SARS-CoV-2-positive index physician, including 67 patients, and 187 nurses and doctors, technical and medical assistants, and other healthcare staff, on day 5 after the exposure by specific RT-PCR from nose and throat swabs or pharyngeal lavage, irrespective of reported symptoms. We tested a large number of possible contact persons of a symptomatic SARS-CoV-2-infected physician among HCWs and patients on day 5 after exposure; all were negative. 6 For further analysis and confirmation of our results, we investigated the serum of all high-risk contacts (n = 23) on days 15 or 16 and 22 or 23 for SARS-CoV-2-specific antibodies. doi = 10.1017/ice.2020.268 id = cord-258281-gxwk8jq9 author = Wenling, Yao title = Pregnancy and COVID-19: management and challenges date = 2020-08-31 keywords = COVID-19; MERS; SARS; clinical summary = Based on recently published literature and official documents, this review provides an introduction to the pathogenesis, pathology, and clinical features of COVID-19 and has focused on the current researches on clinical features, pregnancy outcomes and placental histopathological analysis from pregnant women infected with SARS-CoV-2 in comparison with SARS-CoV and MERS-CoV. Although there is no unequivocal evidence to support the fetal infection by intrauterine vertical transmission of SARS, MERS and SARS-CoV-2 so far, more and more articles began to report maternal deaths due to COVID-19. There were no cases of vertical transmission identified among pregnant women infected with SARS 44-49 so far, but SARS during pregnancy is associated with high incidences of spontaneous miscarriage, preterm delivery, intrauterine growth restriction, endotracheal intubation and admission to the neonatal intensive care unit [44] [45] [46] . This is a review on pregnant women infected by SARS-CoV-2, SARS, and MERS, including their pathogenesis, clinical manifestations and pregnancy outcomes. Middle East respiratory syndrome coronavirus (MERS-CoV) infection during pregnancy: report of two cases & review of the literature doi = 10.1590/s1678-9946202062062 id = cord-320455-doup2bqq author = Werion, Alexis title = SARS-CoV-2 Causes a Specific Dysfunction of the Kidney Proximal Tubule date = 2020-08-10 keywords = ACE2; COVID-19; IQR; SARS summary = Coronavirus disease 2019 (COVID-19) is commonly associated with kidney damage, and the angiotensin converting enzyme 2 (ACE2) receptor for SARS-CoV-2 is highly expressed in the proximal tubule cells. At the structural level, kidneys from patients with COVID-19 showed prominent tubular injury, including in the initial part of the proximal tubule, with brush border loss, acute tubular necrosis, intraluminal debris, and a marked decrease in the expression of megalin in the brush border. Thus, our data establish that SARS-CoV-2 causes specific manifestations of proximal tubule dysfunction and provide novel insights into COVID-19 severity and outcome. The angiotensin converting enzyme 2 (ACE2), the receptor mediating the entry of SARS-CoV-2 in human cells, is expressed in the lung, heart, intestine and kidney, providing a rationale for the systemic manifestations of the disease [4] [5] [6] [7] . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection doi = 10.1016/j.kint.2020.07.019 id = cord-304487-ycvu5l5f author = Wertheim, Joel O title = A glimpse into the origins of genetic diversity in SARS-CoV-2 date = 2020-03-04 keywords = SARS summary = Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. doi = 10.1093/cid/ciaa213 id = cord-252922-cdhnlvxv author = West, Erin A. title = Corona Immunitas: study protocol of a nationwide program of SARS-CoV-2 seroprevalence and seroepidemiologic studies in Switzerland date = 2020-10-24 keywords = Corona; Immunitas; SARS; Switzerland; study summary = We describe here the protocol of Corona Immunitas, a centrally coordinated research program consisting of repeated cross-sectional and longitudinal seroprevalence and seroepidemiological studies conducted across several regions and populations in Switzerland, whose aim is to generate reliable data to inform policy-making. Specific aims are to: (1) estimate the number of individuals infected with SARS-CoV-2 in the population with or without symptoms at several points in time; (2) compare the seroprevalence between the general population and specific subpopulations; (3) investigate the characteristics, duration, and extent of immunity after infection; (4) assess the association between participant characteristics and behaviors with their risk of infection; and (5) quantify the association between the pandemic and participants'' mental and physical health. Corona Immunitas is a research program coordinated by SSPH?, conducting longitudinal, population-based seroprevalence studies covering a number of Swiss Cantons as well as several seroepidemiological studies in specific subpopulations. doi = 10.1007/s00038-020-01494-0 id = cord-309856-flkjl1dm author = Westblade, Lars F. title = SARS-CoV-2 Viral Load Predicts Mortality in Patients with and Without Cancer Who Are Hospitalized with COVID-19 date = 2020-09-15 keywords = SARS summary = For data generated using the cobas assay, we used viral load cutoffs based on C T values for the 123 ORF1ab gene target that were previously shown to correlate with in-hospital mortality among 124 hospitalized patients with COVID-19: high, C T value <25; medium, C T value 25-30, low, C T value 125 >30 (Magleby et al., 2020) . In the overall cohort, using assay-specific C T value cutoffs, 38.8% of patients with a high viral 156 load died during their hospitalization, compared to 24.1% of patients with a medium viral load, active cancer that adjusted for age and need for supplemental oxygen within 3 hours of 169 presentation to the ED (Table 4) , we found that having a high viral load was independently 170 associated with increased in-hospital mortality (aOR 5.00; 95% CI: 1. In conclusion, using two different diagnostic platforms, we found that admission SARS-CoV-2 277 viral load, as assessed by C T values that are generated by routine RT-PCR diagnostic assays, 278 was highly associated with in-hospital mortality in COVID-19 patients with and without cancer. doi = 10.1016/j.ccell.2020.09.007 id = cord-310606-msmh7d8m author = Westerhuis, B. M. title = Severe COVID-19 patients display a back boost of seasonal coronavirus-specific antibodies date = 2020-10-12 keywords = October; SARS summary = . https://doi.org/10.1101/2020.10.10.20210070 doi: medRxiv preprint All patients mounted a strong SARS-CoV-2 immune response shown by rising IgG titers against 174 SARS2-SECTO, SARS2-S1 and SARS2-SRBD which peaked around 4 weeks post onset of clinical 175 symptoms ( Figure 1A and Supplementary figure 1A for individual patients). Besides the SARS-CoV-2 IgG response, serum IgG reactivity towards various, but not 183 all seasonal CoV antigens, increased in longitudinally analyzed COVID-19 patients ( Figure 1A is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint However, cross-reactivity 282 between OC43-SECTO and SARS-CoV-2 S antigens showed significant weak negative 283 correlations (range R=-0.038 --0.088, range p=4,7x10 -6 -0.014) suggesting that OC43-S ECTO 284 specific clones are unlikely to cross-react with SARS-CoV-2 S in severe COVID-19 patients 285 ( Figure 3B ). doi = 10.1101/2020.10.10.20210070 id = cord-258595-bk35vxlr author = Westhaus, Sandra title = Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date = 2020-08-18 keywords = CoV-2; RNA; SARS; wastewater summary = Inoculation of differentiated Caco-2 cells for ten days with purified and concentrated wastewater (P2, P5, P11, and P12) did not result in the production of infectious SARS-CoV-2 particles (data not shown), which suggests that treated sewage appears to be non-infectious even though viral RNA fragments can be detected. Inter-comparing these nine catchment areas, we plotted the estimated cumulative and the acute prevalence against the measured SARS-CoV-2 load (Figure 8 ), the latter calculated from RT-qPCR measured M-gene copy concentration ( Figure 4 ) and the actual wastewater flow Q actual on the day of sampling (Table 2) . In contrast, plotting the incidence against SARS-CoV-2 concentration did not yield a conclusive correlation (not shown), likely because the precision of the qPCR employed was not sufficient to discriminate relatively minor differences in the incidence prevailing in the studied catchment areas at the time of sampling, ranging from 30 to 174 cases per 100,000 residents (less than an order of magnitude, Figure 8C and D). doi = 10.1016/j.scitotenv.2020.141750 id = cord-293991-x5zdo8t2 author = Wheatley, A. K. title = Evolution of immunity to SARS-CoV-2 date = 2020-09-10 keywords = Fig; SARS; September; preprint summary = While SARS-CoV-2 specific B and T cell responses are readily induced by infection, the longitudinal dynamics of these key memory populations remains poorly resolved. We find that binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection, as expected, with a similar decline in S-specific CD4+ and circulating T follicular helper (cTFH) frequencies. Serum inhibition of RBD-ACE2 binding and S1-specific IgG 106 responses in early infection were also well correlated with neutralisation titre in late 107 convalescence (Spearman rho=0.79, 0.81, respectively; Extended Data Fig 3) . S-specific cTFH and conventional CD4+ 152 and CD8+ memory T cells (Tmem), were quantified using activation induced marker 153 (AIM) assays 19,22 (Methods) following stimulation with overlapping S (split into S1 154 or S2) peptide pools (Fig. 3A, 3B ). SARS-CoV-2 infection induces sustained humoral immune 623 responses in convalescent patients following symptomatic COVID-19. doi = 10.1101/2020.09.09.20191205 id = cord-275128-620wf0pb author = White, J. R. title = PI3K/mTOR and topoisomerase inhibitors with potential activity against SARS-CoV-2 infection date = 2020-09-03 keywords = ACE2; SARS summary = We performed a statistical evaluation of in vitro gene expression profiles reflecting exposure to 1,835 drugs, and found topoisomerase inhibitors and PI3K/mTOR pathway inhibitors among the strongest candidates for reduced expression of ACE2, a host gene associated with SARS-CoV-2 infection. We next performed a retrospective review of clinical records to evaluate the frequency of SARS-CoV-2 infection in patients on these ACE2-associated antineoplastics. Retrospective data was obtained from an IRB-approved study of adult cancer patients tested for SARS-CoV-2 receiving active antineoplastic therapy at Memorial Sloan Kettering Cancer Center (MSKCC) during the COVID-19 epidemic period (n=4,040 patients; Table S2 ). Patients receiving ACE2-associated therapies demonstrated a lower univariate odds ratio (0.65, 95% CI 0.00-0.98, P=0.04) for a positive SARS-CoV-2 test during active antineoplastic therapy compared to patients on other agents (Table S3) . Cancer patients taking these potential ACE2-associated agents showed lower rates of a positive SARS-CoV-2 test compared to patients taking other forms of active antineoplastic therapy. doi = 10.1101/2020.09.02.20186783 id = cord-354720-fu19u2b0 author = White-Dzuro, Gabrielle title = Multisystem effects of COVID-19: a concise review for practitioners date = 2020-11-04 keywords = ACE2; COVID-19; SARS; infection; patient summary = It is important that clinicians managing critically ill COVID-19 patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. It is important that clinicians managing these critically ill patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. The indirect effects of the virus result from the host''s response to the viral infection, and are associated with a cytokine storm characterized by very high circulating levels of pro-inflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukins, granulocyte-colony stimulating factor, and chemokines [9] . include direct viral damage of nervous tissue, injury resulting from the excessive inflammatory response, unintended host immune response effects after the acute infection (e.g., Guillain-Barré syndrome as reported in a case series of four patients [24] ), and injury resulting from the effects of systemic illness. doi = 10.1080/00325481.2020.1823094 id = cord-284791-bgodmbru author = Whitworth, Carrie title = Persistence of Bacteriophage Phi 6 on Porous and Nonporous Surfaces and the Potential for Its Use as an Ebola Virus or Coronavirus Surrogate date = 2020-08-18 keywords = EBOV; Ebola; SARS summary = The persistence of phi 6 was evaluated as a surrogate for Ebola virus (EBOV) and coronaviruses on porous and nonporous hospital surfaces. Under these laboratory-simulated Western indoor hospital conditions, we assessed the suitability of phi 6 as a surrogate for environmental persistence research related to enveloped viruses, including EBOV and coronaviruses. This study evaluated the persistence of phi 6 in the presence of artificial test soil (ATS) as a potential surrogate for EBOV or coronaviruses at two absolute humidity (AH) conditions on four potential fomites: nonporous stainless steel (SS) and plastic (PL) and two types of porous hospital curtain fabrics. found that the Phi 6 was shown here in the current study to be a conservative surrogate for EBOV in a laboratory-simulated Western hospital room condition of 3.0 g/m 3 AH, persisting longer than the Makona-C05 variant (AH ϭ 3.3 g/m 3 ), with decay rates of 0.06 log 10 /d and 0.79 log 10 /h, respectively (Table 1 ). doi = 10.1128/aem.01482-20 id = cord-267124-8efdzlc0 author = Wichmann, Dominic title = Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date = 2020-05-06 keywords = COVID-19; RNA; SARS; patient summary = In response to the pandemic spread of SARS-CoV-2, the authorities of the German federal state of Hamburg ordered mandatory autopsies in all patients dying with a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR). During autopsy, tissue samples for histology were taken from the following organs: heart, lungs, liver, kidneys, spleen, pancreas, brain, prostate and testes (in males), ovaries (in females), small bowel, saphenous vein, common carotid artery, pharynx, and muscle. In this autopsy study of 12 consecutive patients who died of COVID-19, we found a high incidence of deep venous thrombosis (58%). In studies that examined deceased patients with COVID-19 without relying on autopsy, no increased rates of pulmonary embolism were observed clinically. To our knowledge, only 3 case reports have been published on patients with COVID-19 who have undergone complete autopsy and a few more in which only lung tissue was examined (7, 8) . doi = 10.7326/m20-2003 id = cord-264031-0y7xbgun author = Wierbowski, Shayne D. title = A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date = 2020-10-13 keywords = CoV-2; SARS; human; interface; protein summary = title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. Further, we explore the utility of our interactome modeling approach in identifying key 99 interactions undergoing evolution along viral protein interfaces, highlighting population variants on 100 human interfaces that could modulate the strength of viral-host interactions to confer protection from or 101 susceptibility to COVID-19, and prioritizing drug candidates predicted to bind competitively at viral-102 human interaction interfaces. doi = 10.1101/2020.10.13.308676 id = cord-276995-b003vcdc author = Wiese, Andrew D title = Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date = 2020-06-20 keywords = SARS summary = And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. doi = 10.1093/cid/ciaa834 id = cord-291677-zcbyhsf1 author = Wilamowski, M. title = Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date = 2020-08-16 keywords = Nsp16; RNA; SAM; SARS; nsp10/16 summary = To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex doi = 10.1101/2020.08.14.251421 id = cord-022473-l4jniccw author = Wilder-Smith, Annelies title = As Travel Medicine Practitioner during the SARS Outbreak in Singapore date = 2009-11-16 keywords = SARS; Singapore; hospital summary = In the first week after our first cases, the WHO named the disease "SARS", and they sent out global alerts. In Singapore, the outbreak was initially only hospital based, but in April the news was out that SARS had affected a large vegetable market. The news of the death of Carlo Urbani, the Italian WHO doctor who was instrumental in the control of SARS in Vietnam, sent our hospital staff into depression. In total, we lost a total of five healthcare workers to SARS in Singapore: 2 doctors, 1 nursing officer, 1 nursing aide and 1 hospital attendant. Two to three weeks into the epidemic it became clear, that infection control measures were effective; no more new cases occurred amongst the staff of our hospital. The SARS outbreak in Singapore can be traced to the first imported case. New imported SARS cases therefore need not lead to major outbreaks if systems are in place to identify and isolate them early. doi = 10.1016/b978-0-08-045359-0.50041-5 id = cord-252292-qz9msrl7 author = Wilder-Smith, Annelies title = Experience of Severe Acute Respiratory Syndrome in Singapore: Importation of Cases, and Defense Strategies at the Airport date = 2006-03-08 keywords = SARS; Singapore summary = METHODS: Information on imported cases of SARS and measures taken at entry points to Singapore was retrieved from the Ministry of Health and the Civil Aviation Authority of Singapore. The large outbreaks in Hong Kong, Toronto, Singapore and Vietnam were initiated by cases that were imported before this new disease had been identified and before appropriate measures had been put in place to prevent transmission. Information on measures taken at the national airport (Changi Airport), seaports and road entry points to reduce the importation of further cases was obtained from the Civil Aviation Authority of Singapore (CAAS) and from the websites of the Ministry of Health, Singapore (http://www.moh.gov.sq/sars/news/chronology.html; accessed 15 June). She became very unwell and breathless on her return flight from Beijing to Singapore on 26 March, but no precautions were taken on the airplane,as her diagnosis was not known.Immediately after arrival, her mother took her in a taxi to Tan Tock Seng Hospital,where she was isolated in the Intensive Care Unit. doi = 10.2310/7060.2003.2676 id = cord-279001-l5ogbl5p author = Wilder-Smith, Annelies title = Can we contain the COVID-19 outbreak with the same measures as for SARS? date = 2020-03-05 keywords = COVID19; China; SARS summary = COVID-19 differs from SARS in terms of infectious period, transmissibility, clinical severity, and extent of community spread. Even if traditional public health measures are not able to fully contain the outbreak of COVID-19, they will still be effective in reducing peak incidence and global deaths. In November, 2002, the severe acute respiratory syn drome coronavirus (SARSCoV) emerged in China causing global anxiety as the outbreak rapidly spread, and by July, 2003, had resulted in over 8000 cases in 26 countries. In the absence of vaccines and specific treatment, the only available public health tools to control persontoperson transmittable diseases are isolation and quarantine, social distancing, and community containment measures. Isolation, quarantine, social distancing and community containment: pivotal role for oldstyle public health measures in the novel coronavirus (2019nCoV) outbreak Public health measures to control the spread of the severe acute respiratory syndrome during the outbreak in Toronto doi = 10.1016/s1473-3099(20)30129-8 id = cord-295061-58tj4csz author = Wilder‐Smith, Annelies title = Short communication: Low risk of transmission of severe acute respiratory syndrome on airplanes: the Singapore experience date = 2003-10-22 keywords = SARS summary = The risk of transmission of severe acute respiratory syndrome (SARS) on airplanes is of major concern to the public and airline industry. Seven airplanes with nine passengers on board later diagnosed as suffering from probable SARS (based on WHO criteria) arrived in Singapore between 25 February and 31 May 2003: three were from Hong Kong (with five cases of SARS), one from Beijing, one from New York, one from East Malaysia and one from Indonesia. However, only three airplanes (with four passengers) had symptomatic cases of SARS on board, whereas the passengers of the other flights developed symptoms within the first 2 days after arrival in Singapore. The third flight with one passenger with severe symptoms of SARS (fever, cough, shortness of breath) arrived after the Infectious Disease Act had been invoked: all crew members and 46 of 47 passengers were contactable and quarantined with active surveillance for 10 days; none developed SARS. doi = 10.1046/j.1360-2276.2003.01133.x id = cord-323980-rcyjthze author = Willems, Laurent M. title = SARS-CoV-2-related rapid reorganization of an epilepsy outpatient clinic from personal appointments to telemedicine services: A German single-center experience date = 2020-10-06 keywords = COVID-19; SARS; patient; telemedicine summary = METHODS: Documentations of telephone contacts and telemedicine consultations at the Epilepsy Center Frankfurt Rhine-Main were recorded in detail between March and May 2020 and analyzed for acceptance, feasibility, and satisfaction of the conversion from personal to telemedicine appointments from both patients'' and medical professionals'' perspectives. The aim of this study was to analyze the acceptance, feasibility, and satisfaction of the SARS-CoV-2-related conversion from face-to-face to telemedicine appointments from the perspectives of both patients and medical professionals. General understanding and acceptance of cancelations of elective face-to-face ambulatory visits and of the option to have telemedicine consultations during the SARS-CoV-2 pandemic in Germany was high, especially in patients with very urgent or urgent appointment priority. doi = 10.1016/j.yebeh.2020.107483 id = cord-315424-i3nnennw author = Willer, Brittany L. title = The otolaryngologist’s and anesthesiologist’s collaborative role in a pandemic: a large quaternary pediatric center’s experience with COVID-19 preparation and simulation date = 2020-06-10 keywords = COVID-19; SARS; patient summary = Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be intimately familiar with strategies to mitigate the high-risk periods of viral contamination that are posed to the environment and healthcare personnel during tracheal intubation and extubation procedures. Since both the pediatric otolaryngologist and anesthesiologist are directly involved in emergency airway interventions, both specialties impact the safety of caring for COVID-19 patients and are a part of overall hospital pandemic preparedness. The pediatric otolaryngologist and anesthesiologist will encounter the COVID-19 patient in a variety of clinical settings (perioperative/operative, intensive care unit, emergency department, and radiology suite) and situations (emergent airway management, urgent or emergent surgical intervention, diagnostic or interventional radiology, and critical care resuscitation). Because of the aerosolization inherent in airway management, the pediatric otolaryngologist and anesthesiologist should be welleducated in and familiar with strategies to mitigate these high risk periods of viral contamination that are posed to the environment and healthcare personnel during endotracheal intubation and extubation procedures [9] . doi = 10.1016/j.ijporl.2020.110174 id = cord-264052-uph136sn author = Wilson, Mitchell P title = Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature date = 2020-04-23 keywords = COVID-19; SARS summary = title: Coronavirus disease (COVID-19) in neurology and neurosurgery: A scoping review of the early literature A search of MEDLINE, J o u r n a l P r e -p r o o f EMBASE, Scopus, and the Cochrane Library (including the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and the Cochrane Special Collections) from inception to April 7, 2020 was performed in order to identify articles evaluating both COVID-19 and neurology or neurosurgery. A total of 10 articles including 4 articles discussing clinical symptomatology and/or the neuroinvasive potential of SARS-CoV-2 (5-8) and 6 articles discussing recommendations for modified neurosurgical (9-11), stroke (12) , and spine (13) (14) practices during the COVID-19 crisis. Thus far, early experience and recommendations in neurosurgical (9) (10) (11) 33) , stroke (12) , and spine (13, 14) practices have been reported (Table 2) As an early scoping review of available literature to date, this study has certain limitations. doi = 10.1016/j.clineuro.2020.105866 id = cord-331927-b7pfm3i0 author = Winn, Soe P title = Diabetic Ketoacidosis in Coronavirus Disease Patients With Type 2 Diabetes Mellitus date = 2020-08-14 keywords = DKA; SARS summary = Since the emergence of the coronavirus disease (COVID-19) pandemic, we have seen many cases and studies on the underlying pathophysiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia with or without respiratory failure. We have also learned that the angiotensin-converting enzyme receptor is one of the major entry sites of SARS-CoV-2 infection, and it might be one of the causes that predispose patients to DKA. also stated that the human pancreas also expresses ACE2, and therefore, patients with diabetes are more vulnerable to SARS-CoV-2 infection than the general population [9] . In our cases, the transient damage of pancreatic beta-cell function leading to reduced levels of serum C peptide may be the reason for our patients experiencing acute insulin-dependent DKA for a brief period during the course of COVID-19. COVID-19 may cause DKA by increasing insulin requirement induced by ACE2-mediated destruction of pancreatic beta cells, as evidenced by reversible decreased serum C peptide levels or other unexplored mechanisms. doi = 10.7759/cureus.9731 id = cord-310946-rjwyirld author = Wiseman, Jessica title = False negative SARS-CoV-2 PCR - A case report and literature review date = 2020-07-06 keywords = PCR; SARS summary = The first case of the novel Coronavirus Diseases (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected in Wuhan, China in December 2019. A nasopharyngeal SARS-CoV-2 PCR was obtained on day 1 of his admission and was negative. This case highlights multiple negative nasopharyngeal SARS-CoV-2 PCR swabs in a patient with high clinical suspicion for SARS-CoV-2, who ultimately tested positive when deep sputum was sent for PCR nine days into his admission (10 days after respiratory symptoms started). Therefore, to improve the odds of making a definitive diagnosis, additional testing methods such as sputum for PCR and serology testing should be considered in patients with a high clinical suspicion of COVID-19 who have a negative nasopharyngeal PCR. Subsequently [7] , conducted a study on 127 patients in Beijing Ditan Hospital comparing RT-PCR versus droplet digital PCR (ddPCR) testing, which is reported as being more sensitive in virus detection, in addition to assessing viral load with disease progression. doi = 10.1016/j.rmcr.2020.101140 id = cord-309869-gk0svt2f author = Wiwanitkit, Viroj title = SARS-CoV-2 in Semen date = 2020-10-23 keywords = SARS summary = key: cord-309869-gk0svt2f cord_uid: gk0svt2f Dear Editor, I would like to discuss the publication "Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection" [1] . [1] concluded that "although all semen samples were obtained in the acute stage of the infection when the nasopharyngeal swab test was positive, we did not detect SARS-CoV-2 in semen." In fact, there are some previous reports showing no existence of pathogen in semen samples [2, 3] . Nevertheless, a recent meta-analysis still noted that there is still a requirement for caution on the possibility of COVID-19 transmission via sexual contact [4] . Investigation of SARS-CoV-2 in semen of patients in the acute stage of COVID-19 infection Italian males recovering from mild COVID-19 show no evidence of SARS-CoV-2 in semen despite prolonged nasopharyngeal swab positivity Atypical modes of COVID-19 transmission: how likely are they? doi = 10.1159/000511616 id = cord-348010-m3a3utvz author = Wolff, Michael title = On build‐up of epidemiologic models—Development of a SEI(3)RSD model for the spread of SARS‐CoV‐2 date = 2020-10-13 keywords = Paragraph; SARS; model; person summary = (Adequate contacts, reproduction and contact numbers) (i) A contact is called adequate (also effective), if it leads to a transmission of the pathogen from an infectious person to another one, and, if the affected individual is susceptible, then an infection is provoked. In the case of concrete models one uses generally contact and replacement numbers, and , which reflect the current infection behaviour. (i) (Closed-population model) An assumed constant number of community members (see Remark 2.2) seems to be justified, if the infection spreads quickly, approximately within a year, and/or, if there is a balance between births, migration and non-disease-related deaths. (Using , there arise difficulties with the dot indicating the time derivation.) If the model is to be to take a latent period into account, the class of infected is divided into subclasses in the following way. doi = 10.1002/zamm.202000230 id = cord-313754-f4sq45gy author = Wong, Chi-Yan title = Practice of habitual and volitional health behaviors to prevent severe acute respiratory syndrome among Chinese adolescents in Hong Kong date = 2005-03-31 keywords = HBM; SARS; health summary = Abstract Purpose To explore factors relating to the practice of habitual and volitional health behaviors against the severe acute respiratory syndrome (SARS) among Chinese adolescents in Hong Kong. Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy). Pearson correlation analyses were conducted to examine associations among SARS preventive health behaviors, demographic characteristics, and six components of the HBM (i.e., perceived threat, perceived benefits, perceived barriers, environmental cues, knowledge, and self-efficacy) ( Table 1) . For volitional health behaviors of facemask-wearing to prevent SARS, environmental cues, practice of habitual health behaviors, and perceived threat were positive correlates (r ϭ .40, .38, and .27, respectively; p Ͻ .05). This study showed that among six components of the HBM, perceived threat and cues to action were more salient correlates of SARS preventive health behaviors among Chinese adolescents. doi = 10.1016/j.jadohealth.2004.02.024 id = cord-296517-414grqif author = Wong, Gary title = MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease date = 2015-10-14 keywords = EBOV; MERS; SARS summary = In September 2012, Middle East Respiratory Syndrome coronavirus (MERS-CoV) emerged as a novel virus that can result in severe respiratory disease with renal failure, with a case fatality rate of up to 38%. Notably, between May and July 2015, an outbreak of MERS-CoV centered in South Korea killed 36 people out of 186 confirmed cases (Promedmail.org, 2015) , with thousands quarantined as health authorities attempted to control virus spread. The 2015 MERS-CoV outbreak in South Korea began from an imported case, a 68-year-old male with a recent travel history to several Middle Eastern countries, including Bahrain, the United Arab Emirates, Saudi Arabia, and Qatar. Thus, the MERS-CoV outbreak in South Korea was driven primarily by three infected individuals, and approximately 75% of cases can be traced back to three super-spreaders who have each infected a disproportionately high number of contacts ( Figure 1A ). doi = 10.1016/j.chom.2015.09.013 id = cord-272633-2vmdf9j6 author = Wong, Gary W.K. title = Out of the East – Emerging infections date = 2006-06-05 keywords = H5N1; SARS summary = Severe Acute respiratory syndrome (SARS) originated from southern China and rapidly spread to many countries in early 2003 with over 8000 cases worldwide. 1 Human infection due to a highly pathogenic avian influenza A (H5N1) virus was first described in a mini-outbreak from Hong Kong in 1997. The first outbreak of human disease of avian influenza occurred in 1997 with 18 cases and 6 deaths. 2 Unlike SARS, human disease of avian influenza has a high mortality in both adults and children. Epidemiology of severe acute respiratory syndrome (SARS): adults and children Avian influenza virus infections in humans Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus Outbreak of avian influenza A (H5N1) virus infection in Hong Kong in 1997 Pathology of fatal human infection associated with avian influenza A H5N1 virus doi = 10.1016/j.prrv.2006.04.194 id = cord-282947-3hgku2e4 author = Wong, Hui Hui title = Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 date = 2017-12-30 keywords = Fig; IFN; IRF3; SARS summary = title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3 Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. Compared to wild type and rIBV8a/b, however, rIBV8b and rIBV8ab were observed to replicate significantly better and express higher levels of N protein in cells stimulated by poly (I:C) (Fig. 2a) . In view of the central role of IRF3 in regulating IFN activation during virus infection, 8b and 8ab with Flag epitope-tagged to their Ntermini were co-expressed with Myc-tagged IRF3 (Fig. 3a) in Cos-7 cells using the vaccinia/T7 expression system (Anderson et al., 1996; Lim and Liu, 2001) for co-immunoprecipitation assays to determine if there is any physical interaction between the proteins. doi = 10.1016/j.virol.2017.12.028 id = cord-319501-a2x1hvkk author = Wong, Lok-Yin Roy title = A molecular arms race between host innate antiviral response and emerging human coronaviruses date = 2016-01-15 keywords = IFN; MERS; RNA; SARS; rig summary = Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. This suggests SARS-CoV N may interfere with RNA recognition by host immune sensors such as RIG-I and MDA5 thus achieving suppressive role in IFN production. Our group demonstrated that MERS-CoV ORF4a interacts with PACT, a cellular dsRNA-binding protein that optimally activates RIG-Iand MDA5-induced type I IFN production, in an RNAdependent manner (Siu et al., 2014c) . Infection with SARS-CoV and MERS-CoV has been accompanied with suppression of innate immune response, most notably with the suppression of type I IFN production and signaling pathways. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses pact-induced activation of RIG-I and MDA5 in the innate antiviral response doi = 10.1007/s12250-015-3683-3 id = cord-257698-ed2tqn35 author = Wong, Raymond S.M. title = Index Patient and SARS Outbreak in Hong Kong date = 2004-02-17 keywords = Hong; SARS summary = During the global outbreak of severe acute respiratory syndrome (SARS) in 2003, treatment was empiric. We report the case history of the index patient in a hospital outbreak of SARS in Hong Kong. Other laboratory tests were performed, including blood, sputum, and urine cultures, nasopharyngeal aspirate for influenza and parainfluenza, indirect immunofluorescence for respiratory syncytial viral antigen detection, and atypical pneumonia titer (for adenovirus, Chlamydia psittaci, Q fever, influenza A and B, and Mycoplasma). Our patient was identified as the index case-patient 5 days after the onset of this large outbreak at the Prince of Wales Hospital, as he was the first patient who had the characteristic clinical, radiologic, and laboratory features of SARS and had epidemiologic links with other infected persons. Severe acute respiratory syndrome (SARS) in Singapore: clinical features of index patient and initial contacts doi = 10.3201/eid1002.030645 id = cord-312730-4ejjmab4 author = Wong, Rebecca S. Y. title = The SARS-CoV-2 Outbreak: an Epidemiological and Clinical Perspective date = 2020-09-29 keywords = COVID-19; China; SARS summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak started with the detection of an increasing number of pneumonia cases of unknown origin in Wuhan, China, since December 2019. In response to the rapidly growing number of confirmed cases and deaths, some measures taken by the Chinese authorities include the quarantine of millions of its citizens with the unprecedented lockdown of many cities, in an attempt to contain the virus and slow down the spread of the disease [3] . One study in China reported a young 22-year-old male who spread SARS-CoV-2 infection to his contacts (1 relative and 6 classmates, all of which were youngsters from 16 to 23 years) just after a few-hour contact during the incubation period, when he was totally asymptomatic [18] , suggesting that the disease is highly infectious during the incubation period. doi = 10.1007/s42399-020-00546-z id = cord-289947-z2dw2eaz author = Wong, River Chun-Wai title = Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay date = 2020-08-16 keywords = SARS summary = title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens. The overall performance of Xpert Xpress SARS-CoV-2 assay was satisfactory when tested with DTS and LRT specimens. To our knowledge, this is the first report to evaluate the use of PBS for sample homogenization of DTS prior to testing with Xpert Xpress SARS-CoV-2 assay. These procedures can minimize the mucus and viscous substances among non-validated specimen types and broaden the testing scope of Xpert Xpress SARS-CoV-2 assay. doi = 10.1016/j.jcv.2020.104593 id = cord-311604-qsc3nks6 author = Wong, River Chun‐Wai title = Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date = 2020-09-30 keywords = SARS summary = title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens This study aims to evaluate the diagnostic performance of PF assay for detection of SARS-CoV-2 in comparison to the TIB-Molbiol LightMix® SarbecoV E-gene assay (TIB-Molbiol assay) (TIB-Molbiol, Berlin, Germany) using DTS, NP and LRT specimens. Despite the manufacturer of TIB Miobiol regarded results with Ct <36 as positive, when use as an initial screening test in our laboratory, sample with any Ct value will be tested supplementary with Xpert Xpress assay. Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens doi = 10.1002/jmv.26574 id = cord-268750-kox3uah2 author = Wong, S. F. title = Measures to Prevent Healtcare Workers from Contracting Severe Acute Respiratory Syndrome During High-Risk Surgical Procedures date = 2004-01-08 keywords = HEPA; SARS summary = When the operations were performed, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga., USA) had not yet prepared guidelines for the prevention of SARS transmission during Caesarean sections. For the three Caesarean sections performed on mothers with SARS, the number of healthcare workers was limited to a minimum, with only those personnel essential to carry out the operation, neonatal resuscitation, and cleanup being involved (i.e., 2 senior obstetricians, 2 senior neonatologists, 1 senior anaesthetist, 1 theatre assistant, a team of 4 senior midwives, and 2 cleansing staff). The participating HCWs wore appropriate PPE according to the hospital''s guidelines prior to the arrival of the patient from the intensive care unit. In conclusion, the procedures described above were sufficient to prevent our healthcare workers from contracting SARS while performing these very high-risk operations. doi = 10.1007/s10096-003-1068-2 id = cord-022776-fz7m177w author = Wong, S.F. title = Severe Acute Respiratory Syndrome and pregnancy date = 2003-12-22 keywords = SARS; pregnancy summary = Severe Acute Respiratory Syndrome (SARS) has already had an enormous impact on society and medical practice but presents special problems in pregnancy. The following comments are based on the experience of those in Hong Kong caring for patients with SARS in pregnancy of which there have been 10 at the time of writing in May 2003. The risk of cross infection is particularly high at the time of vaginal or operative deliveries, especially when there is maternal viraemia. There have not been any fetal problems reported in the very few women given ribavarin in the second half of pregnancy 2,3 . Our own experience with SARS in Hong Kong is in keeping with the extra risk of pregnancy in viral illness. Therefore, it is tempting to recommend early delivery or termination of pregnancy in pregnant women who are seriously ill with SARS. doi = 10.1046/j.1471-0528.2003.03008.x id = cord-322603-8ajckhzc author = Wongsawat, Jurai title = Risk of novel coronavirus 2019 transmission from children to caregivers: A case series date = 2020-06-22 keywords = SARS summary = World Health Organization (WHO) characterised coronavirus disease 2019 (COVID-19) as a pandemic on 11 March 2020. [4] [5] [6] The potential risk of transmission from infected children to adults is of concern due to prolonged detection of the SARS-CoV-2 RNA in respiratory specimens and faeces. Children were allowed to be discharged when their swabs turned negative for SARS-CoV-2 RNA on 2 consecutive days; this happened on days 15, 23 and 27 of illness for cases 1, 2 and 3, respectively. 8, 9 While our study revealed no evidence of transmission from mildly ill, afebrile children to their caregivers despite prolonged positivity of the SARS-CoV-2 RNA in their respiratory specimens, our findings are consistent with WHO''s recommendations for alternatively managing patients with mild COVID-19 disease at home. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: An observational cohort study SARS-CoV-2 infection in children: Transmission dynamics and clinical characteristics doi = 10.1111/jpc.14965 id = cord-268572-uhak283t author = Woo, Marcel S. title = Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients date = 2020-07-11 keywords = SARS summary = title: Control of SARS-CoV-2 infection in rituximab-treated neuroimmunological patients However, few details about the effect of individual immunotherapies have been reported, which could instruct us about the immunological control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we report on two individuals with underlying neuroimmunological diseases who were under stable rituximab therapy-a B cell-depleting monoclonal antibody [6, 7] -when confirmed COVID-19 developed. Patient 2 was a 68-year-old female with neuromyelitis optica spectrum disorder (NMOSD, diagnosed 2014, EDSS 6.0), who was directly admitted to our intensive care unit (ICU) on March 29th, 2020 with progressive respiratory failure and infection of the urinary tract. She had a B cell count of 25/µL (Ref. 80-500/µL, Supplementary Table 2) at the day of admission and tested negative for SARS-CoV-2-specific antibodies (3.5 AU/mL; Ref. In summary, we report on two patients who developed COVID-19 while under treatment with rituximab due to neuroimmunological diseases. Antibody responses to SARS-CoV-2 in patients with COVID-19 doi = 10.1007/s00415-020-10046-8 id = cord-287210-sars5dmi author = Woo, Patrick C. Y. title = Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia date = 2005-12-01 keywords = HKU1; SARS; patient summary = However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia from 4 hospitals were subjected to reverse-transcription polymerase chain reaction, for detection of CoV-HKU1. All prospectively collected NPAs from patients with community-acquired pneumonia that were sent to the clinical microbiology laboratories of 4 hospitals in Hong Kong during a 12-month period (22 March 2003 [the beginning of the SARS epidemic in Hong Kong] to 21 March 2004) for detection of SARS-CoV and were found to be negative for SARS-CoV RNA, by reverse-transcription polymerase chain reaction (RT-PCR) [20] , were included in the study. Sequence analysis revealed 0%-2% nucleotide differences between the sequences of the fragments and the sequence of the pol gene from The epidemiological, clinical, and radiological characteristics of the 10 patients with CoV-HKU1-associated community-acquired pneumonia are summarized in table 2. doi = 10.1086/497151 id = cord-264968-ctx39vhi author = Woo, Patrick CY title = Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia date = 2004-03-13 keywords = CoV; ELISA; SARS summary = An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. An ELISA based on recombinant nucleocapsid protein for IgG detection was tested with serum from 149 healthy blood donors who donated 3 years previously and with serum positive for antibodies against SARS-CoV (by indirect immunofluorescence assay) from 106 patients with SARS-CoV pneumonia. Assessment of recombinant nucleocapsid protein ELISA Serum samples from 149 healthy blood donors who donated blood 3 years previously (aged 18 years or older) and 106 patients with pneumonia positive for antibodies against SARS-CoV detected by our indirect immunofluorescence assay 1 were used for the assessment of the ELISA-based IgG antibody test. doi = 10.1016/s0140-6736(04)15729-2 id = cord-276403-yomjm2gg author = Woo, Patrick CY title = Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections date = 2006-10-30 keywords = China; H5N1; SARS summary = title: Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections In this review, these two severe zoonotic viral infections transmitted by the respiratory route, with pandemic potential, are used as models to illustrate the role of Chinese wet-markets in their emergence, amplification and dissemination. The outbreak of avian influenza A H5N1 virus human infections in Hong Kong in 1997, with 18 cases and six deaths [6] , serves as another excellent example to illustrate the role of Chinese wet-markets in the emergence of zoonotic severe respiratory viral infections (Fig. 4) . China, with one-quarter of the world''s population, 16 of the 20 most polluted cities of the world and a huge diversity of animals closely associated with the human population, is one of the countries with the greatest potential for the emergence and spread of infectious diseases, such as SARS and avian influenza. doi = 10.1097/01.qco.0000244043.08264.fc id = cord-258725-z79gel8h author = Wood, R. title = Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland date = 2020-09-22 keywords = COVID-19; SARS summary = Methods Using a Scotland-wide record-linkage based occupational cohort comprising healthcare workers and members of their households, we examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalisation with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). Similar, but slightly stronger associations were found when the analysis was restricted to households where at least one member of staff had a patient-facing role (fully adjusted model, HR per child 0.83; 95% CI 0.68-1.02, Supplementary Table S3), a group with greater occupational exposure to SARS-CoV-2 than non-patient facing healthcare workers, although on formally testing for an interaction between patient facing and non-patient facing groups, the coefficient included the null, (P-value for interaction = 0.80). doi = 10.1101/2020.09.21.20196428 id = cord-265599-903w782b author = Woods, R. title = Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection date = 2020-10-21 keywords = October; SARS summary = title: Accuracy of Healthcare Professionals Nasopharyngeal Swab Technique in SARS-CoV-2 Specimen Collection Conclusion: Inaccurate specimen collection from poor swab technique could contribute to false negative rate of testing for SARS-CoV-2. 8, 9 A study was performed to assess nasopharyngeal swab technique of staff in a major academic institution. Accurate specimen collection is critical to ensure optimal sensitivity of testing for SARS-CoV-2 but depends on the skill of the person performing the swab.  There is little evidence on the accuracy of swabbing technique in peer-reviewed published medical literature  This study uses a novel tool to evaluate a crucial aspect of public health measures to control the spread of SARS-CoV-2  The low success rate of accurately swabbing the nasopharynx implies that better training is necessary  Better training may improve specimen collection and sensitivity of testing for SARS-CoV-2  Standardised training videos with description of the relevant anatomy would likely be useful to improve testing . doi = 10.1101/2020.10.19.20213140 id = cord-337673-1nau263l author = Wu, Chang-Jer title = Antiviral applications of RNAi for coronavirus date = 2006-01-24 keywords = RNA; SARS; viral; virus summary = Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . doi = 10.1517/13543784.15.2.89 id = cord-024613-yump76qu author = Wu, Chunxing title = Recommendations for control and prevention of infections for pediatric orthopedics during the epidemic period of COVID-19 date = 2020-04-23 keywords = COVID-19; SARS; medical summary = Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares, for clinical practices of pediatric orthopedics according to the physicochemical properties of SARS-CoV-2. Combined with our experience, we have consulted the relevant national regulations and the latest research advances and have formulated the prevention and control measures of SARS-CoV-2 infection, including outpatient, emergency, inpatient and surgical cares for pediatric orthopedics, pediatric surgery and others. reCommendAtion formAtion proCeSS Given the high demand of patients for medical treatment and the need to protect medical staff from infectious diseases, a recommendation working group "Recommendation Formulating Team for Pediatric Orthopedic Infection controls during the Epidemic''s Period of COVID-19" (including all authors) was formed to focus on relevant issues for protection of medical staff in pediatric surgery, pediatric orthopedics, infectious diseases department, anesthesiology department, and nursing department to hospital administrators. doi = 10.1136/wjps-2020-000124 id = cord-335859-k37jivp6 author = Wu, Daphne C. title = Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date = 2020-10-21 keywords = COVID; SARS summary = To understand the socio-demographic predictors of COVID symptoms, we conducted a logistic regression analysis where the outcome was self-reported symptoms suggestive of COVID infection which we defined in this study as the respondent reporting himself/herself and/or at least one member of the household having had a combination of fever (with or without hallucinations) and any of i) difficulty breathing/shortness of breath or ii) dry cough so severe that it disrupts sleep or iii) a loss of a sense of smell in the past month; and the explanatory variables were gender (male, female, or other), education level (high school and under, or some college/ university and higher), province, age, ethnicity (Indigenous, English and other European, or others), visible minority (defined as persons, other than Aboriginal peoples, who are nonwhite in race or colour) [6] , and number of household members. doi = 10.1371/journal.pone.0240778 id = cord-273675-0oiq44gl author = Wu, Di title = To alert coinfection of COVID-19 and dengue virus in developing countries in the dengue-endemic area date = 2020-05-04 keywords = SARS summary = At the meantime, dengue was endemic in the Southeast Asia and South America, and a part of the patients shared the same symptoms, so, we write this paper to alert the clinicians to distinguish these two diseases. 1 Gabriel Yan et al 2 reported 2 cases of COVID-19 patients coinfected with dengue fever in Singapore. Joob et al 3 also reported a patient coinfected with SARS-CoV-2 and dengue virus in Thailand. These 3 cases raise concern that patients with fever can be infected with both SARS-CoV-2 and dengue at the same time in dengue-endemic areas such as Singapore, Thailand, and Malaysia in Southeast Asia and Brazil in South America. Some patients present only with fever when infected with SARS-CoV-2. Therefore, measures should be taken to distinguish patients with fever and headache from dengue fever and COVID-19, and these atypical symptoms should trigger alerts, especially in developing countries with a high incidence of dengue fever, as in Southeast Asia and South American. doi = 10.1017/ice.2020.187 id = cord-277911-x916hsg6 author = Wu, Di title = Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) date = 2020-04-13 keywords = SARS summary = title: Coinfection of Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated from Wuhan in China and has now spread globally. However, despite the concern focused on SARS-CoV-2, influenza virus continues to circulate and cause disease. The SARS-COV-2 outbreak in late December of 2019 in Wuhan, China, has caused many infections and deaths globally. 1 In China, several respiratory viruses are also now active including influenza, parainfluenza virus, respiratory syncytial virus, adenovirus, and now SARS-COV-2. The current World Health Organization (WHO)/ECDC definition of suspected case is not focused on pediatric population. Considering the large number of patients referring to pediatric hospital because of acute respiratory infections in winter season, the strict adoption of WHO/ECDC criteria can lead to a congestion of our hospitals. Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia doi = 10.1097/inf.0000000000002688 id = cord-334973-jemeyudi author = Wu, Dingye title = Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center date = 2020-07-22 keywords = COVID-19; SARS summary = title: Analysis of the lymphocyte count in type 2 diabetic patients with coronavirus disease (COVID-19): A retrospective study in a centralized treatment center Hospitalization days, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid positive days, minimal lymphocyte count, and occurrence time were collected and comparatively analyzed. In addition, a multiple linear regression model was used to analyze the effect of diabetes on minimal lymphocyte count and its emergence time, patient''s hospitalization days, and SARS-CoV-2 nucleic acid positive days by adjusting for potential confounding factors including age; gender; BMI; SBP; DBP; and ALT, AST, and Cr levels. This single center, observational, retrospective study of patients with COVID-19 showed that, patients with T2DM have higher CRP, lower level and more rapid decline in lymphocyte count, and longer hospitalization time than those without T2DM. Our study found a decrease in lymphocyte count in patients with COVID-19, and the lower the lymphocyte count, the longer SARS-CoV-2 nucleic acid positive days and hospitalization days. doi = 10.1016/j.diabres.2020.108340 id = cord-308302-5yns1hg9 author = Wu, Gang title = A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings date = 2020-08-20 keywords = SARS; feature; model summary = We used machine learning for processing laboratory findings of 110 patients with SARS-CoV-2 pneumonia (including 51 non-survivors and 59 discharged patients). Thus it is feasible to establish an accurate prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings. Laboratory tests for SARS-CoV-2 pneumonia included: blood routine test, serum biochemical (including glucose, renal and liver function, creatine kinase, lactate dehydrogenase, and electrolytes), coagulation profile, cytokine test, markers of myocardial injury, infection-related makers, and other enzymes. 68 discharged patients with SARS-CoV-2 pneumonia whose age and gender matched the non-survivors were selected (46 male, median age 66 years). A number of laboratory features were compared between non-survivors and discharged patients with SARS-CoV-2 pneumonia. With machine learning methods previously used in radiomics, a prediction model combining seven out of thirty-eight laboratory features was built for predicting the outcome of SARS-CoV-2 pneumonia. doi = 10.1038/s41598-020-71114-7 id = cord-285865-1gsy43a0 author = Wu, Guang title = Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species date = 2004-12-09 keywords = SARS; spike summary = Randomly predictable present type of amino-acid pair with unpredictable frequency There are 84 alanines (A) in the spike glycoprotein from human SARS-CoV. In view of the unpredictable portion whose actual value is smaller than its predicted value (left panel), the spike glycoproteins have the largest percentages in both unpredictable type and frequency among different coronavirus proteins. With respect to the second line of evidence, we find that the spike glycoprotein has a larger percentage of unpredictable types and frequencies whose actual values are smaller than the predicted values in Fig. 2 . Comparison with the first nine proteins in Table 2 (columns V, VI, VII and VIII in Table 2 , similar to Fig. 3) shows that the difference between actual and predicted values is statistically larger in spike glycoproteins regarding unpredictable types and is statistically smaller regarding unpredictable frequency. doi = 10.1007/s00894-004-0210-0 id = cord-314102-8jf3fnqe author = Wu, Jie title = Advances in research on ACE2 as a receptor for 2019-nCoV date = 2020-08-11 keywords = ACE2; Ang; SARS; cell summary = Although 2019-nCoV and SARS-CoV are very similar viruses genomically and structurally, the huge number of severe cases and deaths now being caused by 2019-nCoV infections has understandably prompted intense research on the receptor used by it to enter human cells. Angiotensin converting enzyme 2 (ACE2), a functional receptor for SARS-CoV, now appears likely to mediate 2019-nCoV entry into human cells. Some recent studies have suggested Cellular and Molecular Life Sciences * Xiuhong Yang yangxiuhong@ncst.edu.cn 1 that 2019-nCoV may infect host cells through the ACE2 receptor, as has already been established for SARS-CoV [7] [8] [9] [10] . In this review, the latest advances in our understanding of the roles played by ACE2 in enzyme catalysis, CoV invasion, cellular expression changes after viral-host cell binding, and its relationships with viral transmission and population susceptibility are described in the context of the pathogenesis of COVID-19. Therefore, it is speculated that like SARS-CoV, 2019-nCoV infects host cells via the mediating effects of its S protein and ACE2 receptors on the surfaces of human cells. doi = 10.1007/s00018-020-03611-x id = cord-315656-asvf4roo author = Wu, Junjiao title = Revisiting the Immune Balance Theory: A Neurological Insight Into the Epidemic of COVID-19 and Its Alike date = 2020-10-15 keywords = ACE2; CNS; COVID-19; IL-6; SARS summary = However, in the central nervous system (CNS), the activation of resident immune cells including microglia and astrocytes may lead to chronic immune imbalance, which underlies the potential long-term effects in synaptic changes and neuropsychiatric impairments. (II) Multiple organ failure in severe COVID-19 is caused by the systemic acute immune responses, the cytokine storm, and unsurprisingly caused the brain inflammation and led to encephalitis. Apart from the direct infection of the brain, SARS-CoV-2 may cause neurological disorders indirectly by triggering an over-activated immune responses, characterized as cytokine storm. Although with exciting benefits, the inhibition of IL-6 pathway works mostly for severe cases, the long-term treatment strategy against the SARS-CoV-2 infection requires the rapid development of effective anti-viral drugs and, more importantly, vaccines. However, in addition to protective effects, microglia may also mediate hippocampal presynaptic membrane damage through complement system, resulting in long-term memory impairment and cognitive decline in patients with encephalitis, caused by coronavirus or human immunodeficiency virus (HIV) infection (69) . doi = 10.3389/fneur.2020.566680 id = cord-197818-asd39zbj author = Wu, Kai title = Magnetic Immunoassays: A Review of Virus and Pathogen Detection Before and Amidst the Coronavirus Disease-19 (COVID-19) date = 2020-07-09 keywords = COVID-19; GMR; NMR; SARS; detection; magnetic summary = In this review, magnetic biosensors'' application in virus and pathogen detection will be summarized and discussed based on the different working principle of the technologies. [69] The key take-away point here is that several experimental demonstrations of the magnetic assays for virus detection based on GMRs and the reported LOD indicate that GMR-based bioassay is one of the promising candidates for onsite, rapid, and sensitive detection of COVID-19. reported the volume-based MPS immunoassay platform utilizing the polyclonal antibodies induced cross-linking of MNPs for one-step, wash-free detection of H1N1 nucleoprotein molecules. In this section, we reviewed some representative works that use magnetic materials are auxiliary tools for high sensitivity virus and pathogen detections, as summarized in Table 3 . We reviewed the magnetic immunoassay literatures prior to COVID-19 and highlighted some promising tools for detecting pathogens as well as viruses with high specificity and sensitivity. Magnetic quantum dot based lateral flow assay biosensor for multiplex and sensitive detection of protein toxins in food samples doi = nan id = cord-327997-noqbcxua author = Wu, Kevin E. title = RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date = 2020-06-20 keywords = CoV-2; GPS; RNA; SARS; figure summary = We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5'' and 3'' viral untranslated regions contain the strongest, most distinct localization signals. As previously discussed, since much of the APEX-seq mitochondrial data used to train RNA-GPS actually consists of nuclear-encoded transcripts likely picked up as the APEX-COX4 fusion protein is transported to the mitochondria, we hypothesize that our predicted mitochondrial residency is alluding to similarity in localization pathways, rather than localization destination. To further validate the robustness of these results, we also trained a different predictive algorithm (a recurrent neural network, see STAR Methods for additional details) on the APEX-seq data and performed a similar set of experiments, comparing SARS-CoV-2 dominant subcellular residency predictions to human and coronavirus baselines ( Figure S3A /B). doi = 10.1016/j.cels.2020.06.008 id = cord-279616-8gtumtxb author = Wu, Kitty K. title = Posttraumatic Stress after SARS date = 2005-08-17 keywords = SARS summary = We used 2 Chinese self-report measures to examine features of PTSD, anxiety, and depression in 131 survivors of severe acute respiratory syndrome at 1 month and 3 months after discharge from the hospital. The first category included pre-SARS variables: sex, age, education level, family income, availability of emotional support as indicated by the number of persons with whom one could talk and share worries, and whether one was a healthcare worker. The measures used in the study include the Chinese versions of the Impact of Event Scale -Revised (IES-R) (7, 8) and the Hospital Anxiety and Depression Scale (HADS) (8) (9) (10) . Results of Pearson correlations (Table 2) showed that the level of SaO 2 , the number of persons with whom one could talk and share worries, and the rating on perceived threat were significantly related to various IES-R and HADS subscale scores. doi = 10.3201/eid1108.041083 id = cord-324938-2lu9z5b2 author = Wu, Li-Ping title = Duration of Antibody Responses after Severe Acute Respiratory Syndrome date = 2007-10-17 keywords = SARS summary = Among 176 patients who had had severe acute respiratory syndrome (SARS), SARS-specific antibodies were maintained for an average of 2 years, and significant reduction of immunoglobulin G–positive percentage and titers occurred in the third year. Both the OD readings (0.93) and positive percentages peaked at 90-120 days; however, the rate of reduction of the average OD readings was much faster, dropping by 22% (0.73) and 40% (0.54) at 1 and 2 years, respectively, after symptom onset (Figure 1) . Neutralizing antibodies in patients with severe acute respiratory syndrome-associated coronavirus infection Longitudinal profi le of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus Longitudinal analysis of severe acute respiratory syndrome (SARS) coronavirus-specifi c antibody in SARS patients doi = 10.3201/eid1310.070576 id = cord-308224-cqi1x92w author = Wu, Lianhua title = Clinical study on the related markers of blood coagulation in the patients with ANFH after SARS date = 2007-10-01 keywords = ANFH; SARS summary = The expression of CD31, CD61, CD62p, CD63 and PAC-1 on platelet membrane was measured respectively by flowcytometry, and the plasma prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and fibrinogen (Fbg) were measured by blood clotting instrument in 26 patients with ANFH after SARS and in 17 healthy adults. When patients experienced discomfort or pain at the site of hip-joint four to six months after administration of hormone, their blood samples were taken intravenously under the condition of fasting to measure CD31, CD61, CD62P, CD63, PAC-1 on platelet membrane and coagulation four indices including PT, APTT, Fbg and TT. It was found that, in these patients with ANFH after SARS, the expression of glycoprotein CD31, CD61, CD62P, CD63 and PAC-1 on platelet membrane decreased; coagulation four indices including PT, APTT and TT time were all normal. doi = 10.1007/s11684-007-0080-9 id = cord-332522-adul9nzf author = Wu, Qingfa title = Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date = 2004-04-02 keywords = PCR; SARS summary = In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. To compare the sensitivities of these 12 sets of nested primers, serial 10-fold di-lution genome cDNA of BJ01 that reverse transcribed with random primer was used as the template to carry out the nested PCR. doi = 10.1016/j.jviromet.2004.02.011 id = cord-354824-7fdcu2f0 author = Wu, Renyi title = An Update on Current Therapeutic Drugs Treating COVID-19 date = 2020-05-11 keywords = COVID-19; China; CoV-2; RNA; SARS; patient; treatment summary = Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. This estimated 20% of patients developing more severe disease with SARS-CoV-2 infection are most likely due to genetics, epigenetics, and or other factors, with dampened innate immune response to fight the virus coupled with enhanced viral load leading to cytokine storm, severe inflammatory/oxidative stress response, and severe lung injury secondary to ARDS. Chloroquine can inhibit the entry of SARS-CoV-2 and prevent virus-cell fusion by interfering with glycosylation of ACE2 receptor and its binding with spike protein, suggesting that chloroquine treatment might be more effective in the early stage of infection, before COVID-19 reduces ACE2 expression and activity [30, 38, 39] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, doubleblinded, phase IIb clinical trial (CloroCovid-19 Study) doi = 10.1007/s40495-020-00216-7 id = cord-331807-ooym5eh3 author = Wu, Tao title = A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) date = 2020-07-29 keywords = SARS summary = title: A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2. The minimum detection limit of real-time RAA assay was 10 copies / reaction. Use of a rapid 207 reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection Detection of 2019 novel coronavirus (2019-nCoV) by real-time 214 RT-PCR A rapid 235 and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA 236 extraction Development of a reverse 248 transcription recombinase-aided amplification assay for the detection of coxsackievirus A10 and 249 coxsackievirus A6 RNA doi = 10.1016/j.virol.2020.07.006 id = cord-301303-44sk478e author = Wu, Vin-Cent title = Renal hypouricemia is an ominous sign in patients with severe acute respiratory syndrome date = 2008-02-21 keywords = SARS summary = Conclusion: One fourth of patients with SARS developed hypouricemia, which might result from a defect in renal UA handling and was associated with a high serum IL-8 level. Serum levels of the proinflammatory cytokines IL-6, IL-8, and TNF-␣ were measured in 16 patients (6 hypouricemic, 10 normouricemic) during their UA excretion studies. The inverse correlation between serum UA level and FE UA indicates that the hypouricemia in patients with SARS resulted from an abnormal increase in UA excretion during SARS-CoV infection. 27 Our study showed that the lowest serum UA level occurred days 7 to 9 after fever onset, when the cytokine storm of patients with SARS usually occurred. 19 The present study shows that hypouricemic patients with SARS had a poor outcome, especially in terms of respiratory failure, compared with normouricemic patients. In summary, hypouricemia resulting from abnormal renal urate handling is not rare in patients with SARS-CoV infection and may reflect the severity of disease and predict poor patient outcomes. doi = 10.1053/j.ajkd.2004.09.031 id = cord-351269-xjy6chia author = Wu, Y title = Coronavirus disease 2019 among pregnant Chinese women: case series data on the safety of vaginal birth and breastfeeding date = 2020-05-26 keywords = SARS; woman summary = METHODS: We collected clinical data, vaginal secretions, stool specimens and breast milk from SARS‐CoV‐2‐infected women during different stages of pregnancy and collected neonatal throat and anal swabs. 2 Previous studies have suggested that SARS-CoV infection during pregnancy may carry severe complications including maternal death, spontaneous miscarriage, preterm delivery and intrauterine growth restriction; 3 and MERS has been associated with intrauterine fetal demise and stillbirth. All pregnant women with SARS-CoV-2 admitted to Renmin Hospital of Wuhan University in China between 31 We extracted demographic information, clinical course, laboratory indices and imaging results of infected pregnant women from the medical records, maternal throat swabs were collected upon admission. None of the newborns delivered in our study was infected, a result consistent with previous reports (e.g. negative tests for the novel coronavirus nucleic acid in pharyngeal swab samples from 19 neonates born to mothers with COVID-19 pneumonia, and for three placental samples 13, 14 ) . doi = 10.1111/1471-0528.16276 id = cord-303143-4sksz6xz author = Wu, Y. P. title = Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients date = 2009-03-19 keywords = SARS; SP‐D summary = title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients The diagnosis was further confirmed using the ELISA assay for plasma SARS-CoV protein N IgG measurement (described below). Anti-SARS-CoV N protein IgG levels were [median (95% CI)] 0.97 (0.81-1.58) versus 0.05 (0.04-0.06) and 0.05 (0.04-0.07) units (OD450) in patients with SARStype pneumonia, patients with CAP (S. A significant correlation between plasma SP-D and anti-SARS-CoV N protein IgG measured in SARS patients was observed using linear regression (r 2 = 0.5995, P = 0.02) (Fig. 5) . This was further confirmed by the measures of lung injury reported in the present study showing no significant differences in pulmonary infiltrate, chest radiographic score, thrombocytopenia and leucocytopenia between SARS patients and the bacterial-type pneumonia patients. Plasma surfactant protein levels and clinical outcomes in patients with acute lung injury doi = 10.1111/j.1365-3083.2009.02245.x id = cord-350130-c4u0gxp5 author = Wu, Yi-Chi title = The outbreak of COVID-19: An overview date = 2020-02-12 keywords = COVID-19; January; SARS summary = In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus#, emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The 2019-nCoV, SARS-CoV, and bat SARS-like CoV belong to Abstract: In late December 2019, a previous unidentified coronavirus, currently named as the 2019 novel coronavirus # , emerged from Wuhan, China, and resulted in a formidable outbreak in many cities in China and expanded globally, including Thailand, Republic of Korea, Japan, United States, Philippines, Viet Nam, and our country (as of 2/6/2020 at least 25 countries). The virus has a preferential tropism to human airway epithelial cells and the cellular receptor, The first confirmed nCoV case in Wuhan (no Huanan seafood market exposure) December 10 doi = 10.1097/jcma.0000000000000270 id = cord-354529-k8p2u7iq author = Wu, Yongran title = Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date = 2020-08-31 keywords = RNA; SARS summary = Clinical information of patients was collected from the electronic medical information system of Jinyintan Hospital, including the following factors: demographic data; date of symptom onset, admission, first CP infusion and discharge; laboratory data before and after infusion of CP, including white blood cell count, neutrophil count, lymphocyte count, liver and kidney function test, and inflammatory factors such as high sensitive C-reaction protein (HsCRP); results of SARS-CoV-2 test and cycle threshold value (Ct value) of quantitative reverse transcription-polymerase chain reaction; patients'' status and treatments before or after the CP therapy, including the vital signs, anti-virus therapy, oxygen therapy, and other treatments; total volume dose of CP; pulmonary imaging examination data; information on complications such as transfusion-related adverse reactions. Clinical Benefit and Outcome of Patients with Prolonged Positivity of SARS-CoV-2 RNA after CP Therapy As shown in Table 3 , the median and interquartile ranged total volume of CP transfusion was 400 (200-400) mL in EN group and 400 (400-800) mL in LN group. doi = 10.1007/s12250-020-00281-8 id = cord-302485-hhsa76k8 author = Wu, Yuntao title = SARS-CoV-2 is an appropriate name for the new coronavirus date = 2020-03-06 keywords = SARS summary = be significantly attenuated to the point of becoming a new low-pathogenic or non-patho genic virus, such attenuated viral isolates could be named as lowpathogenic human coronaviruses, such as LPH-CoV. We believe that the naming of SARS-CoV-2 by the Coronavirus Study Group is aligned with the goals of the International Committee on Taxonomy of Viruses to facilitate good practice and scientific exchange. We have read with great interest the Correspondence by Shibo Jiang and colleagues, 1 in which they propose a name change for the newly emerged coronavirus, 2 which was recently designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. 4 Through DivErsity pArtitioning by hieRarchical Clustering-based analyses, 5 the newly emerged coronavirus was deemed not sufficiently novel but is a sister virus to SARS-CoV, the primary viral isolate defining the species. doi = 10.1016/s0140-6736(20)30557-2 id = cord-268645-5op2m7pu author = Wu, Zhiqiang title = Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date = 2015-08-11 keywords = SARS; Supplementary; Table; bat; virus summary = However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . doi = 10.1038/ismej.2015.138 id = cord-288756-r96izsyq author = Wu, Zhiqiang title = ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus date = 2016-02-15 keywords = SARS summary = title: ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus Several lineage B betacoronaviruses termed severe acute respiratory syndrome (SARS)–like CoVs (SL-CoVs) were identified from Rhinolophus bats in China. The nucleotide sequences in the ORF1ab, E, M, and N genes in these bat-borne lineage B beta-CoVs are 89%-93% similar to those in the SARS-CoVs from humans. Furthermore, genetic evidence for the identical ORF8 is needed to trace the origin of SARS-CoVs to bat SL-CoVs. All genome sequences were submitted to GenBank. In this study, a systematic survey of bat-borne CoVs was performed using bat virome data from throughout China, described in our previous report [6] , to obtain genetic evidence indicating the source of SARS-CoVs. Fifteen SL-CoVs were identified from 9 bat species in 11 provinces ( Figure 1A ) [6] . sinicus have nearly identical ORF8s and similar backbone genes to those in SARS-CoVs in Yunnan and Guangxi provinces. doi = 10.1093/infdis/jiv476 id = cord-308576-iw8oobbe author = Wuxing, Dai title = Expression and purification of SARS coronavirus membrane protein date = 2004 keywords = SARS summary = To construct a recombinant plasmid Pet23a-M, the gene encoding severe acute respiratory syndrome (SARS) coronavirus membrane protein was amplified by RT-PCR and cloned into the expression plasmid Pet23a. To screen and prepare effective SARS virus vaccine and diagnostic antigens, we designed a pair of primers to amplify the gene encoding SARS coronavirus membrane protein and cloned it into an expression plasmid Pet23a. Coli BI.21 ( D E 3 ) and induced by I P T G , Western-blot showed that the expressed 27 kD protein which was characterized by SDS-PAGE and purified by metal chelated chromatography could react with antibodies in sera of SARS patients during convalescence, demonstrating the recombinant protein possessed the biological activity of membrane protein. doi = 10.1007/bf02831095 id = cord-348391-xytmq2f2 author = Wyganowska-Swiatkowska, Marzena title = Influence of Herbal Medicines on HMGB1 Release, SARS-CoV-2 Viral Attachment, Acute Respiratory Failure, and Sepsis. A Literature Review date = 2020-06-30 keywords = HMGB1; IL-6; LPS; SARS; TNF; extract; inflammatory summary = While long term proteinase and ACE-2 inhibition could be detrimental to cellular function and bodily homeostasis, targeted treatment partially reducing the effectiveness of coronavirus S protein attachment to the ACE2 or to the priming proteinase could have the potential to drop the SARS-CoV-2 viral load before a state of septic shock is reached at the peak of infection. Aspalathin and nothofagin extracted from Rooibos have been shown to effectively inhibit LPS-induced release of HMGB1, and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules [124] . The effect and mechanism of salidroside on sepsis-induced acute lung injury is mediated by the inhibition of inflammatory responses and HMGB1 production in bacterial LPS-treated macrophages and mice. Study has shown that pelargonidin (PEL) had effectively inhibited LPS-induced release of HMGB1 and suppressed HMGB1-mediated septic responses, such as hyperpermeability, adhesion and migration of leukocytes, and expression of cell adhesion molecules. doi = 10.3390/ijms21134639 id = cord-102842-51n5mnjb author = Węglarz-Tomczak, Ewelina title = Ebselen as a highly active inhibitor of PLProCoV2 date = 2020-05-17 keywords = SARS; pro summary = In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range. Here, we demonstrate that ebselen inhibits activity of the essential viral enzyme, namely, papain-like protease (PL pro ) from SARS-CoV-2 (PL pro CoV2) in low micromolar range. We applied ebselen as a possible inhibitor and, indeed, it suppresses PL Pro activity from CoV2 with inhibition constants approximately equal 2 μM (Table 1 and Figure 3 ). Our results were further illustrated by the use of molecular modeling to study the binding mode of ebselen with PL Pro SARS ( Figure 4 ) and PL Pro CoV2 (Figure 4 and 5) . This study confirmed our primary assumption that ebselen binds to the PL Pro CoV2 active site covalently and, thus, convinced us of our hypothesis about an irreversible mechanism of inhibition. doi = 10.1101/2020.05.17.100768 id = cord-355811-aq7p1uxo author = Węglarz-Tomczak, Ewelina title = Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date = 2020-05-21 keywords = SARS summary = A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). In recent studies, peptide analogues [11] and ebselen [12] have been identified as highly active inhibitors for PL pro . We show that some of them indeed possess higher activity than ebselen, that has been recently reported as PL pro CoV2 inhibitor [12] , and, thus, could be considered as novel potential drugs against COVID-19. In this work, we used the ebselen derivatives/analogues library and performed a comprehensive inhibition study of PL pro CoV2. In the case of PL pro SARS, none of the presented ebselen derivatives was able to block the enzyme. Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design Ebselen as a highly active inhibitor of PL pro CoV2 doi = 10.1101/2020.05.20.107052 id = cord-286130-4f7otdx1 author = Xavier, Joilson title = The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing date = 2020-08-11 keywords = Brazil; SARS summary = title: The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing To better understand the recent epidemic in the second most populous state in southeast Brazil Minas Gerais (MG) we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Initial phylogenetic analysis using the first two SARS-CoV-2 complete genomes isolated in São Paulo from travellers returning from Italy revealed two independent introductions into the country relative to the data set available at that time [13] . Herein, we present a summary of epidemiological data and the generation and analysis of 40 new SARS-CoV-2 genome sequences isolated from clinical samples of confirmed cases from MG. doi = 10.1080/22221751.2020.1803146 id = cord-317593-tajy3p9e author = Xi, AIqi title = Epidemiological and clinical characteristics of discharged patients infected with SARS-CoV-2 on the Qinghai plateau date = 2020-04-29 keywords = Qinghai; SARS summary = Since the outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, a series of confirmed cases of COVID-19 were found on the Qinghai-Tibet plateau. Coronavirus disease 2019 , caused by infection with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, Hubei, China in December 2019 [1] [2] [3] [4] and rapidly spread worldwide. For this retrospective study, we enrolled all 18 patients infected with SARS-CoV-2 from the hospitals designated for treatment by the Health Commission of Qinghai Province from Jan 21 to April 6, 2020. Convalescent plasma has been used to improve the survival rate of patients with severe acute respiratory syndrome (SARS) coronavirus infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China doi = 10.1101/2020.04.23.20077644 id = cord-355306-fj8utkfe author = Xia Chao, Yin title = The role of IgA in COVID-19 date = 2020-05-23 keywords = SARS summary = Secretory IgA plays a crucial role in the immune defense of mucosal surfaces, the first point of entry of SARS-CoV-2. Reported serology tests focus on IgM, IgG and total immunoglobulins although IgA is playing an important role in mucosal immunity. As an immune barrier, secretory IgA can neutralize SARS-CoV-2 before they reach and bind the epithelial cells (Figure1) . Mucosal vaccine targeting SARS-CoV-2 RBD given via oral or nasal targets to induce secretion of IgA within the mucosa may be a therapeutic strategy for preventing COVID-19 development. Plasma cells, which can be the target of mucosal vaccine, produce IgA and secreted into the mucus where they meet and neutralize the invaded virus through binding to the Spike protein on the surface of SARS-Cov-2. Other neutralization antibodies can also bind to SARS-Cov-2 to prevent it from infecting other cells. doi = 10.1016/j.bbi.2020.05.057 id = cord-280518-2tl0mtb8 author = Xia, Jianhua title = Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection date = 2020-03-12 keywords = SARS; coronavirus summary = title: Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection OBJECTIVE: This study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of SARS–CoV‐2‐infected patients. METHODS: A prospective interventional case series study was performed, and 30 confirmed novel coronavirus pneumonia (NCP) patients were selected at the First Affiliated Hospital of Zhejiang University from 26 January 2020 to 9 February 2020. Two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive RT‐PCR results. On 7 January 2020, the Chinese Center for Disease Control and Prevention isolated and confirmed this pathogen as a novel type of coronavirus through a throat swab. Study Group of the International Committee on Taxonomy of Viruses named 2019-nCoV severe acute respiratory syndrome-related coronavirus 2, or SARS-CoV-2. Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection doi = 10.1002/jmv.25725 id = cord-324926-3c5ab73l author = Xia, Shuai title = A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike date = 2019-04-10 keywords = EK1; Fig; HR1; HR2; MERS; OC43; SARS summary = Therefore, it is reasonable to speculate that HR1 could also be a good target for the development of fusion inhibitors against highly pathogenic HCoVs. We and others have reported that peptides derived from the HR2 regions of SARS-CoV and MERS-CoV S proteins can competitively inhibit viral 6-HB formation, thereby preventing viral fusion and entry into host cells (18, 27) . Moreover, structural studies of EK1 in complex with HR1s from different HCoVs explain the conserved basis for the HR1-EK1 interaction, further indicating that HR1 region could serve as a promising target site for the development of broad-spectrum pan-CoV fusion inhibitors. On the other hand, HR2P peptides derived from the two -HCoVs, i.e., 229E and NL63, showed potent and broad inhibitory activity against -HCoV S-mediated cell-cell fusion with IC 50 values ranging from 0.13 to 0.51 M or from 0.21 to 0.56 M, respectively, but no effective inhibitory activity against -HCoVs (including MERS-CoV, SARS-CoV, and OC43) S-mediated fusion ( Fig. 1D and table S1 ). doi = 10.1126/sciadv.aav4580 id = cord-329186-0eoz4npg author = Xia, Shuai title = The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin date = 2020-06-12 keywords = FCS; SARS summary = title: The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin It has been speculated that RRAR, a unique furin-like cleavage site (FCS) in the spike protein (S), which is absent in other lineage B βCoVs, such as SARS-CoV, is responsible for its high infectivity and transmissibility. Then, by calculating the ratio of the fused cells, we can assess the fusogenic capacity of the S protein in the presence or absence of exogenous trypsin or human airway trypsin-like protease (HAT). Next, we compared the fusogenic capacity of SARS-CoV-2-S, SARS-CoV-S and their mutants via an S-mediated cell-cell fusion assay in the absence of exogenous trypsin or human airway trypsin-like protease (HAT). © The Author(s) 2020 Fig. 1 The function of furin cleavage site in SARS-CoV-2-S mediated fusion. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion doi = 10.1038/s41392-020-0184-0 id = cord-298734-h286m32c author = Xia, Siyu title = Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury date = 2020-06-29 keywords = ACE2; SARS; cell summary = title: Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury In this study, we successfully established long term cultures of normal human kidney proximal tubule epithelial cells (KPTECs) in 2D and 3D culture systems using conditional reprogramming (CR) and organoids techniques. Due to the lack of specific detection of ACE2 mRNA and protein expression in human kidney tubule cells, it is hard to confirm the direct infection of SARS-CoV-2. In this study, we firstly established long term cell cultures of KPTECs using 2D CR and 3D organoids technologies, which maintained the lineage function, and the ability to differentiate and repair DNA damage. In terms of the questions above, we need model systems to study infection of SARS-CoVs in ACE2 expressing cell types, especially in kidney epithelial cells (Hamming et al. doi = 10.1007/s12250-020-00253-y id = cord-262844-qeheeqe3 author = Xia, Xuhua title = Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date = 2020-04-14 keywords = RNA; SARS; ZAP summary = The zinc finger antiviral protein (ZAP, known as ZC3HAV1 in mammals or hZAP in human), a key component in mammalian interferon-mediated immune response, binds specifically to CpG dinucleotides in viral RNA genomes via its RNA-binding domain (Meagher et al., 2019) . If a coronavirus infects a different host tissue with different ZAP abundance, then its RNA genome will experience different selection pressure against its CpG. The most striking pattern in Fig. 1 is an isolated but dramatic shift in the lineage leading to BatCoV RaTG13 which was reported (Zhou et al., 2020) (Theys et al., 2018) , but also in experimentally CpG dinucleotide-enriched viral genomes (Antzin-Anduetza et al., 2017; Burns et al., 2009; Fros et al., 2017; Trus et al., 2019; Tulloch et al., 2014; Wasson et al., 2017) . To search for a mammalian host with the potential to select viral lineages with low Poder, 2011; Pratelli, 2006) , have genomic ICpG and GC% values similar to those observed in SARS-CoV-2 and BatCoV RaTG13 (Fig. 3A) . doi = 10.1093/molbev/msaa094 id = cord-275250-ilmgy7ce author = Xia, Yong title = Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date = 2020-05-17 keywords = SARS summary = As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. doi = 10.1016/j.ijid.2020.05.042 id = cord-293503-e7be12qb author = Xiang, Chao title = CT Findings in a Novel Coronavirus Disease (COVID-19) Pneumonia at Initial Presentation date = 2020-08-15 keywords = SARS; covid-19 summary = COVID-19 leads to respiratory infections similar to those of SARS and MERS, causing pneumonia, severe acute respiratory syndrome, kidney failure, and even death. The CT image characteristics were recorded as follows: (a) lesion''s location (segment), (b) morphology (patchy, nodular, and linear), (c) distribution (single or multiple, peripheral or/and central), (d) type (ground-glass opacity, consolidation, and linear opacity), (e) pattern (reticulation, parenchymal bands, crazy-paving, and interlobular thickening), (f) atelectasis, (g) cavitation, (h) pleural effusion, (i) hilar or mediastinal lymphadenopathy, (j) bronchiectasis, and (k) air bronchogram. Although a patient with exposure history may be asymptomatic and obtained negative results of CT findings and viral nucleic acid test at initial presentation, the potential infection cannot be totally excluded, and performing repeating CT scan and coronavirus RNA test is needed. Ground-glass opacity and consolidation with multiple, bilateral, and lower lobe distribution are the main features of COVID-19 pneumonia at initial CT scan. doi = 10.1155/2020/5436025 id = cord-270474-jaurhjvr author = Xiang, Zhen title = Glucocorticoids improve severe or critical COVID-19 by activating ACE2 and reducing IL-6 levels date = 2020-06-27 keywords = ACE2; IL-6; SARS; covid-19 summary = We verified the efficacy of nine chemicals on regulating ACE2 expression in human GES-1, an upper digestive tract epithelial cell line, and THP-1, a human monocyte cell line, and found that several glucocorticoids imparted activating effects on ACE2 in both cell lines. We retrospectively analyzed the therapeutic efficacy of nine severe or critical patients from a cohort of 90 COVID-19 cases, who received medium to small doses of glucocorticoids from our integrated medical team in Wuhan. This study provides experimental and clinical evidence that medium-to-low-dose glucocorticoids may play a protective role in the respiratory and digestive systems by activating ACE2 and suppressing cytokine storm. Because the epithelial cells of the respiratory and digestive tracts are susceptible targets of SARS-CoV-2, we verified the regulatory effects of several candidate agonists of ACE2 expression on available normal human epithelial cells. Compared to the blank control, hydrocortisone revealed the strongest activating effect on ACE2 expression, followed by prednisolone, dexamethasone, and methylprednisolone. doi = 10.7150/ijbs.47652 id = cord-251995-nbqukjzv author = Xiao, Fei title = Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 date = 2020-08-17 keywords = Figure; SARS summary = title: Infectious SARS-CoV-2 in Feces of Patient with Severe COVID-19 S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged in China, causing a major outbreak of severe pneumonia and spreading to >200 other countries (1) . A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. A Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. The viral load was higher in feces than in respiratory specimens collected at multiple time points (17-28 days after symptom onset) (Appendix Figure, panel D) . We attempted to isolate SARS-CoV-2 virus from 3 of the viral RNA-positive patients. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient doi = 10.3201/eid2608.200681 id = cord-339752-o6atz33c author = Xiao, Li title = ACE2: The Key Molecule for Understanding the Pathophysiology of Severe and Critical Conditions of COVID-19: Demon or Angel? date = 2020-04-28 keywords = ACE2; Ang; SARS summary = According to a report based on 72,314 cases (test confirmed cases: 44,672 (62%) from the Chinese Center for Disease Control and Prevention, 81% of COVID-19 patients have cold-like symptoms and mild pneumonia, 14% have severe respiratory inflammation, and 5% have critical conditions including respiratory failure, septic shock, and/or multiple organ dysfunction or failure. Similar to SARS (severe acute respiratory syndrome, [2002] [2003] coronavirus (SARS-CoV) [3] , SARS-CoV-2 primarily uses the S protein to invade host cells through ACE2, an enzyme which is known to be important in the renin-angiotensin-aldosterone system (RAAS) [4, 5] . Since TMPRSS2 plays a very important role in SARS-CoV-2 cell entry and ACE2 dysfunction, blocking the activity of TMPRSS2 should be the primary strategy for preventing severe and critical conditions of COVID-19. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) doi = 10.3390/v12050491 id = cord-299491-8rfm0jxh author = Xiao, Shenglan title = Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date = 2017-07-20 keywords = File; SARS summary = Like many other respiratory viruses, the SARS-CoV is suspected to spread from an infected person to the susceptible via three basic transmission routes, i.e., the long-range airborne, close contact and fomite routes [14] [15] [16] , as shown in Fig 1. Several studies have proposed probable evidence for the airborne spread of the SARS-CoV based on the consistencies between bio-aerosol concentration distributions and reported attack rates [19] [20] [21] , but no mechanism-based investigations exist for the fomite route. To investigate the role the fomite route plays in SARS-CoV transmission, we conducted a detailed modelling study of the largest hospital outbreak in Hong Kong [20] , in which the distribution of reported attack rates of inpatients showed a statistically significant spatial pattern. A multi-agent model ( Fig 2) was developed to simulate the possible spread of the viruses from the index patient to the susceptible by air flow and surface touching, and to calculate the possible exposure doses and infection risks for each hypothesis. doi = 10.1371/journal.pone.0181558 id = cord-326721-2v5wkjrq author = Xiao, Wenlei title = A Cybernetics-based Dynamic Infection Model for Analyzing SARS-COV-2 Infection Stability and Predicting Uncontrollable Risks date = 2020-03-17 keywords = SARS; Wuhan summary = Distinguished with other epidemiological models, such as SIR, SEIR, etc., that compute the theoretical number of infected people in a closed population, CDIM considers the immigration and emigration population as system inputs, and administrative and medical resources as dynamic control variables. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint : Effective infectious increment (can be negative); : Total non-isolated cases (asymptomatic carriers); : Patient increment (symptom onset); : Total isolated cases (confirmed patients after symptom onset); Figure 4 : Basic principle of the cybernetics-based dynamic infection model be made. In the view of this, we used the data from Shanghai, a relatively well controlled city, to identify and calibrate the key parameters of the incubation period and the basic reproductive number. In Shanghai Model, there is no worry about the shortage of medical supplies, so a negative summation channel performs a direct control effect on the positive feedback infection loop, which is thus of paramount importance in reducing the number of total infectious cases. doi = 10.1101/2020.03.13.20034082 id = cord-325420-e9fjo7tl author = Xiao, Xia title = Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 date = 2020-07-06 keywords = SARS summary = Here we performed a high throughput screen of approximately 1700 US FDA approved compounds to identify novel therapeutic agents that can effectively inhibit replication of coronaviruses including SARS-CoV-2. These screens have identified 24 anti-SARS-CoV-2 drugs including previously reported compounds such as hydroxychloroquine, amlodipine, arbidol hydrochloride, tilorone 2HCl, dronedarone hydrochloride, and merfloquine hydrochloride. Positive compounds from the initial screen were tested for their antiviral 120 efficacy against SARS-CoV-2 in Vero cells. Our data show that 24 of these compounds show significant 124 efficacy in inhibiting SARS-CoV-2 replication with sub micromolar IC50 for many of these 125 drugs such as nilotinib, clofazimine and raloxifene. This screen identified five new compounds that 187 are highly efficacious in inhibiting the viral replication of SARS-CoV-2 with SI >600. The positively identified drugs from this screen were used to perform dose response curves 220 against OC43 on LLC-MK2 and against SARS-CoV-2 using Vero cells as described below. doi = 10.1101/2020.07.06.188953 id = cord-282895-85if4mnu author = Xiao, Xiaodong title = The SARS-CoV S glycoprotein: expression and functional characterization date = 2003-12-26 keywords = SARS; cell summary = Fragments containing the N-terminal amino acid residues 17–537 and 272–537 but not 17–276 bound specifically to Vero E6 cells and purified soluble receptor, ACE2, recently identified by M. Here we report cloning, expression, and characterization of the SARS-CoV fulllength S glycoprotein and various soluble fragments, demonstration of its fusogenic function at neutral pH, development of a quantitative cell fusion reporter gene-based assay, and localization of the RBD in the N-terminal 303-537 residues. We have not observed measurable cytopathic effects in cells transfected with any of the constructs we developed (data not shown) indicating the possibility that the full-length and soluble fragments of the S glycoprotein may not have direct cytopathic effects. In an attempt to localize the receptor-binding domain (RBD) of the S glycoprotein prior to the identification of the SARS-CoV receptor, we developed an assay based on the binding of various soluble fragments to receptor expressing Vero E6 cells. doi = 10.1016/j.bbrc.2003.11.054 id = cord-271243-8cfyen86 author = Xiao, Y. title = Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus date = 2008-05-31 keywords = CoV; SARS summary = title: Pathological Changes in Masked Palm Civets Experimentally Infected by Severe Acute Respiratory Syndrome (SARS) Coronavirus Summary Masked palm civets are highly susceptible to infection with the severe acute respiratory syndrome coronavirus (SARS-CoV). The present study describes the spectrum of histopathological changes in the lung, spleen, lymph node, liver, small intestine, kidney and cerebrum of civets infected experimentally with SARS-CoV. One animal from each group was sacrificed at 3, 13, 23, 34 and 35 days post-infection (dpi), and lung, spleen, lymph node, small intestine, kidney, trachea, cerebrum, pancreas, sex glands, stomach and heart were collected from each animal. In summary, the data presented in this study further corroborate previous findings (Wu et al., 2005) in demonstrating that civets are more susceptible to SARS-CoV infection than other animals, as implied by their clinical symptoms, pathological changes and virus distribution within tissues. doi = 10.1016/j.jcpa.2007.12.005 id = cord-279976-juz9jnfk author = Xie, Mingxuan title = Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date = 2020-04-01 keywords = China; MERS; SARS; Wuhan summary = METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". doi = 10.1016/j.ijid.2020.03.071 id = cord-343876-2inr4mcy author = Xie, Qin title = COVID-19 patients managed in psychiatric inpatient settings due to first-episode mental disorders in Wuhan, China: clinical characteristics, treatments, outcomes, and our experiences date = 2020-10-02 keywords = SARS; covid-19; disorder; patient summary = During the outbreak of COVID-19, the selection of an appropriate treatment setting for COVID-19 patients with mental disorders is a dilemma: in respiratory treatment settings these patients are more likely to not adhere with The main findings of this comparative study are 1) adjustment disorder and acute and transient psychotic disorders, with associated acute stress were the main clinical diagnoses in the COVID-19 group and some other disorders had their organic basis such as delirium due to infection and chloroquine-induced psychosis, while serious mental illnesses (SMIs) and alcohol use disorders were overrepresented in the control group, a common feature of inpatients of most Chinese psychiatric hospitals; 2) a wide range of psychiatric symptoms were found in COVID-19 patients with mental disorders on admission, including psychotic symptoms, aggressive behaviors, and anxiety symptoms; 3) the most common respiratory symptom of COVID-19 patients was cough, followed by fever, chills, and fatigue; and 4) mental disorders and COVID-19 of most patients were successfully treated after symptomatic and supportive treatments, including conventional psychotropic treatment and antiviral treatment, and, COVID-19 patients left the hospital earlier than psychiatric patients without COVID-19, on average by 16 days after admission. doi = 10.1038/s41398-020-01022-x id = cord-298899-lkrmg5qr author = Xie, Yewei title = Epidemiologic, clinical, and laboratory findings of the COVID-19 in the current pandemic: systematic review and meta-analysis date = 2020-08-31 keywords = COVID-19; China; SARS; Wuhan; clinical summary = To fill the research gaps mentioned above, this review article systematically summarizes global findings on the natural history, clinical spectrum, transmission patterns, laboratory findings, CT results, and risk factors of the COVID-19. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and risk factors for mortality of adult in patients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): a retrospective observational analysis of 193 confirmed cases in Thailand Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study doi = 10.1186/s12879-020-05371-2 id = cord-289134-ne3tjt5g author = Xing, Yue title = Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein date = 2020-07-17 keywords = SARS; cleavage summary = By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. From 45828 SARS-CoV-2 genome sequences available in the GISAID database as of June 13, 2020, 103 strains of SARS-CoV-2 1 https://www.ncbi.nlm.nih.gov/Class/Structure/aa/aa_explorer.cgi carried various DNA mutations including 25 unique ones that may affect the furin cleavage site located at the amino acid residual positions 680-689 (S1/S2 region) (Coutard et al., 2020; Wang et al., 2020; Zhang et al., 2020) of the SARS-CoV-2 spike protein (Figure 1 , Table 1, and Supplementary Table 1) . We uncovered 103 SARS-CoV-2 strains from multiple geographic regions, 81 of which carried 25 unique mutations that may affect the furin cleavage site in the spike glycoprotein. doi = 10.3389/fgene.2020.00783 id = cord-309577-438fotfd author = Xing, Yuhan title = Dynamics of faecal SARS-CoV-2 in infected children during the convalescent phase date = 2020-04-10 keywords = SARS summary = 1 We would like to share findings from our paediatric patients who were positive for nucleic acid testing for SARS-CoV-2 in stools up to 8-20 days after clearance of viral RNA in respiratory specimens. Surprisingly, we found SARS-CoV-2 remained detectable in faeces of paediatric patients for approximately 4 weeks, whereas negative conversion of viral RNA in respiratory specimens occurred within 2 weeks after disease onset. Two children showed negative results for faecal detection of SARS-CoV-2 20 days after clear-ance of viral RNA in the respiratory tract, while another child persistently tested positive on faecal samples even 8 days after respiratory samples turning negative. Faecal shedding of viral RNA has been constantly reported in patients infected with SARS-CoV-2. 7 -10 One study reported over half of the 17 patients had faecal samples positive for SARS-CoV-2 detection, although virus copies in stools were less than those in respiratory specimens. doi = 10.1016/j.jinf.2020.03.049 id = cord-345299-4k7qymqd author = Xiong, Hua-Long title = Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date = 2020-06-05 keywords = SARS; VSV summary = To identify drugs that are potentially used for the treatment of COVID-19, the potency of 1403 FDA-approved drugs were evaluated using a robust pseudovirus assay and the candidates were further confirmed by authentic SARS-CoV-2 assay. Four compounds, Clomiphene (citrate), Vortioxetine, Vortioxetine (hydrobromide) and Asenapine (hydrochloride), showed potent inhibitory effects in both pseudovirus and authentic virus assay. In this study, the anti-SARS-Cov-2 potentiality of 1403 FDA approved drugs were quantitatively evaluated by the pseudovirus-based assay. In the second round of screening, inhibition of VSV-SARS-CoV-2-Sdel18 virus infection and cell cytotoxicity were both detected (Supplementary Figure 1) . The robust assay based on VSV-SARS-CoV-2-Sdel18 pseudovirus screened out the potential drugs with high efficiency, then the inhibitory effect was confirmed by authentic SARS-CoV-2 assay. The relative value or inhibition rate of candidate drugs were calculated according to the decrease of GFP positive cell number (for pseudovirus-based assay) or cytopathic effect (for authentic SARS-CoV-2-based assay). doi = 10.1101/2020.06.05.135996 id = cord-345499-hq5um68k author = Xiong, Rui title = Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date = 2020-03-12 keywords = DHODH; Fig; S312; S416; SARS summary = title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. We identified that targeting DHODH offers broad-spectrum antiviral efficacies against various RNA viruses, including the DAA-resistant influenza virus and the newly emerged coronavirus SARS-CoV-2. doi = 10.1101/2020.03.11.983056 id = cord-337809-bxvgr6qg author = Xiong, Yong title = Family cluster of three recovered cases of pneumonia due to severe acute respiratory syndrome coronavirus 2 infection date = 2020-05-04 keywords = SARS; Wuhan summary = Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. Our observations suggest the importance of preventing family transmission and the efficacy of current integrated treatment for mild/ moderate pneumonia in COVID-19 cases. [2] [3] [4] [5] [6] [7] [8] This report describes the epidemiological and clinical features of coronavirus disease (COVID-19) among three members of a family following SARS-CoV-2 infection. On 10 and 11 January 2020, a family of three, comprising the father (65 years), the mother (61 years) and the son (38 years), were admitted to the Department of Infectious Disease at the Zhongnan Hospital of Wuhan University with symptoms of cough and fever. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1136/bcr-2020-235302 id = cord-321918-9jwma2y6 author = Xiu, Siyu title = Inhibitors of SARS-CoV-2 Entry: Current and Future Opportunities date = 2020-06-15 keywords = ACE2; CoV; CoV-2; MERS; RBD; SARS summary = The spike protein can be divided into two domains; S1 is responsible for angiotensin-converting enzyme II(ACE2) recognition, the recently identified host cell receptor, and S2 mediates membrane fusion (Figure 2 ). 98 99 On the basis of this approach, they identified two small molecules, TGG (12, Table 4 ) and luteolin (13) , that can bind avidly to the SARS-CoV S2 protein and inhibit viral entry of SARS-CoV into Vero E6 cells with IC 50 values of 4.5 and 10.6 μM, respectively. 113 A high-throughput screen (HTS) of a 1000-compound library that resulted in the identification of MDL28170 (17 , Table 4 ) by Bates et al., and in an antiviral activity assay, 17 specifically inhibited cathepsin L-mediated substrate cleavage and blocked SARS-CoV viral entry, with an IC 50 value of 2.5 nM and EC 50 value in the range of 100 nM. doi = 10.1021/acs.jmedchem.0c00502 id = cord-261877-4y37676n author = Xu, Cong title = Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date = 2020-06-30 keywords = ACE2; Fig; RBD; SARS summary = Recent cryoelectron microscopy (cryo-EM) studies on the stabilized ectodomain of SARS-CoV-2 S protein revealed a closed state of S trimer with three RBD domains in "down" conformation (Walls et al., 2020) , as well as an open state with one RBD in the "up" conformation, corresponding to the receptor-accessible state (Walls et al., 2020; Wrapp et al., 2020) . To gain a thorough picture on how the receptor ACE2 binding induces conformational dynamics of the SARS-CoV-2 S trimer and triggers transition towards the postfusion state, we determine the cryo-EM structure of SARS-CoV-2 S trimer in complex with human ACE2 PD domain to 3.8 Å resolution (termed SARS-CoV-2 S-ACE2, Figs. Based on the data, we put forward a mechanism of ACE2 binding-induced conformational transitions of SARS-CoV-2 S trimer from the tightly closed ground prefusion state transforming towards the postfusion state (Fig. 6) . Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding doi = 10.1101/2020.06.30.177097 id = cord-317523-idji1l0a author = Xu, Huanzhou title = SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date = 2020-10-27 keywords = SARS summary = With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. To assess if ORF3a also 135 mediates activation of other prominent inflammasomes including NLRP1 and NLRC4, we 136 depleted each of these molecules but were unable to block cleavage of pro-caspase 1 (Fig.2G) , 137 indicating that ORF3a predominantly activates the NLRP3 inflammasome. In summary, an essential viroporin required for release of SARS-CoV-2 from infected cells is also 178 able to prime and activate the NLRP3 inflammasome, the machinery responsible for much of the doi = 10.1101/2020.10.27.357731 id = cord-338973-73a7uvyz author = Xu, Jiabao title = Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV date = 2020-02-22 keywords = COVID-19; China; CoV-2; MERS; SARS summary = After the outbreak of the severe acute respiratory syndrome (SARS) in the world in 2003, human coronaviruses (HCoVs) have been reported as pathogens that cause severe symptoms in respiratory tract infections. Recently, a new emerged HCoV isolated from the respiratory epithelium of unexplained pneumonia patients in the Wuhan seafood market caused a major disease outbreak and has been named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The source of unexplained pneumonia was first discovered in Wuhan in Dec, 2019, and SARS-CoV-2, a new coronavirus, was isolated from the respiratory epithelium of patients. Hong Kong scholars found that, compared with ribavirin alone, patients treated with lopinavir/ritonavir and ribavirin had lower risk of acute respiratory distress syndrome (ARDS) or death caused by SARS-CoV [76, 77] . A high-resolution crystal structure of SARS-CoV-2 coronavirus 3CL hydrolase (Mpro) was announced after the outbreak of COVID-19 in the world [80] , and human coronaviruses (HCoVs) have been treated as severe pathogens in respiratory tract infections. doi = 10.3390/v12020244 id = cord-021055-ebcu3ywq author = Xu, Jianguo title = Inaugural editorial: Towards evidence-based biosafety and biosecurity date = 2019-02-20 keywords = SARS summary = China has experienced significant biosecurity and biosafety challenges and is the only nation that has been subjected to a bioweapon assault. 2 The SARS epidemic served as a timeous practical reminder to both China and the world that emerging infectious diseases could significantly threaten national and global safety and security. [3] [4] [5] [6] [7] The 2004 SARS outbreak in North China resulted from a series of flaws in the biosafety protocol at a national institute in Beijing, 5 resulting in infection of four laboratory workers. We propose that the scope of biosecurity and biosafety should include all relevant areas with the potential to cause death, social disruption and panic, economic breakdown, and/or national crisis (e.g. emerging infectious diseases, bioweapons, bioterror, laboratory biosafety, antibiotic-resistant bacterial super-strains, harmful invasive plant or animal species, misuse of synthetic biological technology, misuse of human genetic information, etc.). doi = 10.1016/j.jobb.2019.01.008 id = cord-252933-bu4oihem author = Xu, Jieqing Jessica title = Renal Infarct in a COVID‐19 Positive Kidney‐Pancreas Transplant Recipient date = 2020-06-01 keywords = COVID-19; SARS summary = The novel coronavirus disease 2019 (COVID‐19) is associated with increased risk of thromboembolic events, but the extent and duration of this hypercoagulable state remains unknown. We describe the first case report of renal allograft infarction in a 46‐year‐old kidney‐pancreas transplant recipient with no prior history of thromboembolism, who presented 26 days after diagnosis of COVID‐19. Since we are the first to report this complication, further investigation is required before making recommendations for thromboembolic prophylaxis in all solid organ transplant recipients with COVID-19. In summary, we present the case of a kidney-pancreas transplant recipient with moderate to severe COVID-19 complicated by late kidney allograft segmental infarction. This is the first case of a thromboembolic event in a SARS-CoV-2 positive solid organ recipient. High incidence of venous thromboembolic events in anticoagulated severe CoVID-19 patients Case report of CoVID-19 in a kidney transplant recipient: does immunosuppression alter the clinical presentation? doi = 10.1111/ajt.16089 id = cord-310331-29srzbuk author = Xu, Jiuyang title = 2019 novel Coronavirus outbreak: a quiz or final exam? date = 2020-03-20 keywords = China; SARS summary = Armed with experience from previous epidemics in the last two decades, clinicians, scientists, officials, and citizens in China are all contributing to the prevention of further 2019-nCoV transmission. The 2019 novel coronavirus (2019-nCoV) outbreak is currently bringing challenges to China and the whole world. Since direct human transmission and asymptomatic infection have been revealed for 2019-nCoV [3] , health authorities in China are facing an enormous challenge on disease management and control. Realizing the severity of SARS-CoV as a respiratory virus, the detection of pneumonia of unknown origin in 2019-nCoV outbreak enabled relatively early alarm from health authorities and raised awareness for medical staff to equip personal protection methods when dealing with suspected cases. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.1007/s11684-020-0753-1 id = cord-315056-ohyb6oa0 author = Xu, Juanjuan title = Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset date = 2020-10-29 keywords = COVID-19; China; SARS; patient summary = title: Clinical characteristics and outcomes of severe or critical COVID-19 patients presenting no respiratory symptoms or fever at onset This retrospective study presents the clinical, laboratory, and radiological profiles, treatments, and outcomes of atypical COVID-19 patients without respiratory symptoms or fever at onset. The study examined ten atypical patients out of 909 severe or critical patients diagnosed with COVID-19 in Wuhan Union Hospital West Campus between 25 January 2020 and 10 February 2020. Chest computed tomography (CT) scan and nucleic acid detection should be performed immediately on close contacts of COVID-19 patients to screen out those with atypical infections, even if the contacts present without respiratory symptoms or fever at onset. In this study, we aimed to describe the clinical, laboratory, and radiological characteristics, treatments, and outcomes of severe or critical COVID-19 patients who presented no respiratory symptoms or fever at onset. An atypical patient was defined as a patient with laboratory-confirmed COVID-19 but without characteristic fever or respiratory symptoms before hospital admission. doi = 10.1016/j.eng.2020.09.009 id = cord-266775-4npowkkz author = Xu, Jun title = Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date = 2005-10-15 keywords = Mig; SARS; patient summary = In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . doi = 10.1086/444461 id = cord-286121-ltaxmp3u author = Xu, Ke title = Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein date = 2009-06-05 keywords = SARS summary = In this study, we demonstrate that 9b protein is translated from bicistronic mRNA9 via leaky ribosome scanning and it is incorporated into both virus-like particles (VLPs) and purified SARS-CoV virions. The expression of 9b protein in SARS-CoV infected cells was confirmed by Western blot analysis with anti-9b monoclonal antibody. To confirm that 9b protein can be translated from an mRNA corresponding to the SARS-CoV subgenomic RNA9, the sequence encoding ORFN which contains ORF9b was cloned into the eukaryotic expression vector pCAGGS and transfected into 293T cells. As 9b protein is present in virions, it is advantageous to characterize the role of other SARS-CoV structural proteins in incorporation of 9b protein into VLPs. Cultures of 293T cells were transfected with the indicated plasmids, and pCAGGS vector was added to adjust the total amount of DNA to equivalent levels. 9b protein was immunoprecipitated by anti-9b polyclonal antibody from SARS infected FRhK-4 cell lysates in RIPA buffer, the mass spectrometry analysis of the corresponding gel slices detected a specific peptide that represents 9b protein. doi = 10.1016/j.virol.2009.03.032 id = cord-350317-a9qd3xdr author = Xu, Qiannan title = If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 date = 2020-11-05 keywords = SARS summary = title: If skin is a potential host of SARS-CoV-2, IL-17 antibody could reduce the risk of COVID-19 The expression of ACE2 is associated with the potential risk of making the target tissue susceptible to infection by SARS-CoV-2. Elevated ACE2 expression and detection of SARS-CoV-2 in the skin 4 of COVID-19 patients implied skin was a potential host of SARS-CoV-2. After IL-17 antibody treatment, the skin ACE2 expression was downregulated which meant IL-17 antibody could lower the risk of COVID-19 through lessening the cells which could interact with SARS-CoV-2. Additionally, IL-17 antibody could reverse the deteriorated barrier and inflammatory status in the skin of psoriasis patient which meant less microbe infection.Herein, the specific microbe could be SARS-CoV-2. Thus, whether IL-17 antibody could reduce the COVID-19 risk through reversing the inflammatory skin status with deteriorated barrier and preventing SARS-CoV-2 transmitting should be further discussed. Skin is a potential host of SARS-CoV-2: a clinical, single-cell transcriptome-profiling and histological study doi = 10.1016/j.jaad.2020.10.084 id = cord-298098-4dfqlebp author = Xu, Ruodan title = Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System date = 2020-07-30 keywords = SARS; VLP summary = In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Construction of SARS-CoV-2 VLPs was performed by co-transfecting cells with S, M, E, and N with molar ratio at 8:6:8:3 as shown in Figure 1 . To get better understanding of the secretory features of four SARS-CoV-2 structural proteins, we first transfected HEK-293T and Vero E6 cells with vectors expressing S, M, E, or N, respectively. In the current study, we described the efficient construction of SARS-CoV-2 VLPs by plasmid-driven transfection of viral structural proteins in mammalian cells. doi = 10.3389/fbioe.2020.00862 id = cord-034351-5br4faov author = Xu, Shuang-Fei title = Cross-Sectional Seroepidemiologic Study of Coronavirus Disease 2019 (COVID-19) among Close Contacts, Children, and Migrant Workers in Shanghai date = 2020-10-02 keywords = Coronavirus; Health; SARS summary = (1) Background: Along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of Coronavirus Disease 2019 (COVID-19) is warranted among key populations to determine the serum antibody against the SARS-CoV-2 and the carrying status of SARS-CoV-2 to identify potential asymptomatic infection and to explore the risk factors. Three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. Since the first known case of pneumonia infected with the novel coronavirus was reported in the city of Wuhan in late December of 2019, Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and announced by the World Health Organization on 11 February 2020, unexpectedly and quickly spread in China and many other countries with rapid geographical expansion and a sudden increase in the number of cases [1, 2] . doi = 10.3390/ijerph17197223 id = cord-332962-8y3t0r2d author = Xu, Xi title = Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2 date = 2020-02-28 keywords = SARS summary = We aimed to report the imaging and clinical characteristics of these patients infected with SARS-CoV-2 in Guangzhou, China. CONCLUSION: SARS-CoV-2 infection can be confirmed based on the patient''s history, clinical manifestations, imaging characteristics, and laboratory tests. Image analysis, focused on the lesion features of each patient, included (a) distribution characteristics, (b) number of lobes involved, (c) lobe of lesion distribution, (d) Fig. 1 A 49-year-old man with history of recent travel to Wuhan presented with fever and cough for 6 days. Our study showed some common CT imaging features in patients affected by SARS-CoV-2 pneumonia: bilateral, multifocal ground glass opacities, with peripheral distribution. In our study, few patients initially negative for SARS-CoV-2 nucleic acid test had bilateral ground glass opacities in chest CT scans. In a patient with a history of close contact with a SARS-CoV-2-infected patient, early manifestation of bilateral, multifocal, and peripheral ground glass opacities on a chest CT scan might be a sign of a 2019 novel coronavirus infection. doi = 10.1007/s00259-020-04735-9 id = cord-306373-61snvddh author = Xu, Xiao-Wei title = Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series date = 2020-02-19 keywords = Cov-2; SARS; Wuhan summary = OBJECTIVE: To study the clinical characteristics of patients in Zhejiang province, China, infected with the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) responsible for coronavirus disease 2019 (covid-2019). Since the outbreak of covid-19, strict precautionary measures have been implemented in Zhejiang province, including the creation of fever clinics that exclusively receive patients with suspected SARS-Cov-2 infection, defined as presenting with a fever or any respiratory symptoms, including dry cough, and especially in those with a history of travel to Wuhan or exposure to infected people within two weeks before the onset of illness since January 2020. The incubation period was defined as the time from exposure to the onset of illness, which was estimated among patients who could provide the exact date of close contact with individuals from Wuhan with confirmed or suspected SARS-Cov-2 infection. doi = 10.1136/bmj.m606 id = cord-255907-t7gpi2vo author = Xu, Yifei title = Unveiling the Origin and Transmission of 2019-nCoV date = 2020-02-24 keywords = SARS summary = A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Unveiling the Origin and Transmission of 2019-nCoV Yifei Xu 1, * A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. Regardless of its initial source, it is likely that 2019-nCoV was introduced into a small cluster of humans from a cluster of infected animals and, from there, the virus acquired the capacity for human-tohuman transmission, spreading in the city before the cluster of patients from the Huanan market was identified. doi = 10.1016/j.tim.2020.02.001 id = cord-266033-gbx48scp author = Xu, Yu-Huan title = Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2 date = 2020-02-25 keywords = NCP; SARS summary = Based on the fifth edition of the China Guidelines for the Diagnosis and Treatment Plan of Novel Coronavirus (2019-nCoV) Infection by the National Health Commission (Trial Version 5), 6 the NCP was classified into four types: mild with slight clinical symptoms but no imaging presentations of pneumonia; common with fever, respiratory symptoms and imaging presentations of pneumonia; severe type with any of the following: respiratory distress with RR > 30 times/minutes, oxygen saturation at rest < 93%, or PaO2/FiO2 < 300 mmHg (1 mmHg = 0.133 kPa); critically severe type with any of the following: respiratory failure needing mechanical ventilation, shock, or combination with other organ failure needing ICU intensive care. Fifty patients with NCP caused by infection of the SARS-CoV-2 virus were enrolled and had high-resolution pulmonary CT scanning, including mild type in nine, common in 28, severe in 10 and critically severe in the rest three ( Table 1 ). doi = 10.1016/j.jinf.2020.02.017 id = cord-032222-i6gfp4me author = Xue, Ling title = A quick look at the latest developments in the COVID-19 pandemic date = 2020-09-10 keywords = COVID-19; CoV-2; SARS summary = Later, the Coronavirus Study Group of the International Committee on Taxonomy of Viruses formally named this virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is a novel coronavirus, and an effective vaccine has yet to be developed. 51 A recombinant adenovirus type 5 vector vaccine, developed by Chen Wei''s team, showed good safety and immunogenicity in a phase I clinical trial, rapidly inducing both humoral and T-cell responses against SARS-CoV-2 in most participants. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia doi = 10.1177/0300060520943802 id = cord-279518-z3k7zaw4 author = Xue, Xiaotong title = High expression of ACE2 on the keratinocytes reveals skin as a potential target for SARS-CoV-2 date = 2020-05-23 keywords = ACE2; SARS summary = High ACE2 expression was identified in the type II alveolar cells (AT2), bronchial transient secretory cells, small intestinal epithelium cells and the oral epithelial cells in accordance with respiratory clinical manifestations and rare clinical manifestations such as gastrointestinal symptoms, suggesting the respiratory droplet, digestive ２ and fecal-oral transmission routes of SARS-CoV-2 (Lukassen et al., 2020; Liang et al., 2020; Xu et al., 2020a) . Therefore, we hypothesized that the expression and distribution of ACE2 in human organs and tissues could reflect the potential infection routes of SARS-CoV-2. However, scRNA-seq has not yet been applied to examine the ACE2 expression in the cells of skin tissues, and the transmission of this virus by percutaneous routes remains unclear. In conclusion, the high expression of ACE2 on keratinocytes in human skin indicated that percutaneous transmission might be a potential risk route for SARS-CoV-2 infection, especially in condition of skin barrier dysfunction. doi = 10.1016/j.jid.2020.05.087 id = cord-342091-xus5kxs0 author = YAVARIAN, Jila title = First Cases of SARS-CoV-2 in Iran, 2020: Case Series Report date = 2020-08-17 keywords = Feb; SARS summary = In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. Here we report the first cases of SARS-CoV-2 infections in Qom, central Iran in Feb 2020. Collectively seven patients'' residents of Qom City were positive for SARS-CoV-2 on Feb 19 in Iran. We identified the first cases of SARS-CoV-2 in Qom city, Iran with unclear transmission route. Futureresearch should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran. doi = 10.18502/ijph.v49i8.3903 id = cord-291627-5dqwyd9r author = Yadav, Rakhee title = SARS-CoV-2-host dynamics: Increased risk of adverse outcomes of COVID-19 in obesity date = 2020-07-21 keywords = COVID-19; China; SARS; obesity summary = 11 Many recent studies are now reporting obesity as one of the risk factors for severity of COVID-19 in USA, Brazil, UK, Italy, Spain and France [12] [13] [14] [15] [16] [17] [18] 67 (summarised in the In the current scenario, since USA has become the epi-centre of the COVID-19 pandemic; the dynamics of patient characteristics in terms of associated complications is showing a difference from the initial data put out by China. During the present pandemic, till now, it has been well established that cardiovascular diseases and diabetes are the major risk factors for poor outcomes but considering a higher BMI to be a forerunner for both these co-morbidities, the inclusion of obesity and overweight individuals as candidates for poor COVID-19 outcomes becomes very important. 58 Thus, the interaction between ACE2-RAS system, adipose tissue and the SARS-CoV-2 could, at least partially, explain the higher morbidity and mortality risk of COVID-19 in obese patients. doi = 10.1016/j.dsx.2020.07.030 id = cord-262783-uhfnv532 author = Yamamoto, Fumiichiro title = Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression date = 2020-09-23 keywords = ABO; SARS summary = title: Blood group ABO polymorphism inhibits SARS‐CoV‐2 infection and affects COVID‐19 progression The ABO blood group polymorphism was previously shown to influence the susceptibility to SARS with individuals in groups A and O having a higher and lower risk, respectively [6] . Since 11 March 2020, several papers reported the association between ABO blood groups and SARS-CoV-2/COVID-19. The authors compared ABO blood group distribution among 265 SARS-CoV-2-infected patients and 3,694 healthy controls. The SARS-CoV-2 viruses produced in individuals of groups A, B, AB and O express A, B, A and B antigens, and none, respectively. For example, SARS-CoV-2 viruses produced in group A individuals may express A antigens and infect group A or AB individuals without such antigen-antibody reactions. Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies Association between ABO blood groups and risk of SARS-CoV-2 pneumonia ABO blood groups and SARS-CoV-2 infection. doi = 10.1111/vox.13004 id = cord-352562-qfb478sf author = Yamamoto, Lidia title = SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date = 2020-09-04 keywords = ACE2; COVID-19; CoV-2; PCR; SARS summary = In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. They identified 191 cases in hospitalized patients younger than 21 years of age, reported by hospitals in the New York State with the diagnosis of Kawasaki disease, toxic shock syndrome, myocarditis, and suspected multisystem inflammatory syndrome associated with COVID-19 in children (MIS-C). The laboratory diagnosis of COVID-19 are based on the detection of viral RNA by real time amplifications (RT-PCR) 40 or the detection of antibodies (immunoglobulins) anti-SARS-CoV-2 from the classes IgM, IgA and IgG, produced by the host''s immune system. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review doi = 10.1590/s1678-9946202062065 id = cord-315576-bgcqkz0p author = Yamamoto, Naoki title = Apparent difference in fatalities between Central Europe and East Asia due to SARS-COV-2 and COVID-19: Four hypotheses for possible explanation date = 2020-08-05 keywords = Asia; COVID-19; East; Europe; SARS summary = The comparison of the numbers of cases and deaths due to SARS-CoV-2 / COVID-19 shows that people in Central Europe are much more affected than people in East Asia where the disease originally occurred. Trying to explain this difference, this communication presents four hypotheses that propose the following reasons for the observed findings: 1) Differences in social behaviors and cultures of people in the two regions; 2) Possible outbreak of virulent viruses in Central Europe due to multiple viral infection, and the involvement of immuno-virological factors associated with it, 3) Possibility of corona resistance gene mutation occurring among East Asians as a result of long-term co-evolution of virus and host, and 4) possible involvement of hygienic factors. For the analysis of the difference regarding the number of infected people and the death tolls due to COVID-19 between Central European and East Asian 5 countries, we have chosen Italy, Spain, France, Germany and UK from Central Europe and China, South Korea, Japan, and Taiwan from South East Asia. doi = 10.1016/j.mehy.2020.110160 id = cord-276361-77cylm1o author = Yamamoto, Norio title = HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus date = 2004-06-04 keywords = SARS; Vero summary = title: HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus Here we report that the HIV-1 protease inhibitor, nelfinavir, strongly inhibited replication of the SARS coronavirus (SARS-CoV). Experiments with various timings of drug addition revealed that nelfinavir exerted its effect not at the entry step, but at the post-entry step of SARS-CoV infection. We found that nelfinavir, a widely used HIV-1 protease inhibitor, could inhibit SARS-CoV replication efficiently. We screened our chemical library and found that nelfinavir could inhibit SARS-CoV replication in Vero E6 cells. Nelfinavir clearly inhibited the cytopathic effect (CPE) induced by infection with SARS-CoV (Fig. 1A) . Nelfinavir significantly inhibited SARS-CoV replication when used before infection (Figs. The other protease inhibitors including ritonavir had no effect on replication of SARS-CoV CC 50 , cytotoxic concentration of the compound that reduced cell viability to 50%. Our studies have clearly shown that nelfinavir can strongly inhibit the replication of SARS-CoV in Vero E6 cells. doi = 10.1016/j.bbrc.2004.04.083 id = cord-283818-4m9p717r author = Yan, Chao title = Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date = 2020-04-08 keywords = SARS summary = title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase 23 chain reaction (RT-PCR). The main findings of this study is that we established a rapid, sensitive, and 199 specific assay for SARS-CoV-2 detection by RT-LAMP. Rapid and sensitive detection of 311 novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated 312 isothermal amplification combined with a lateral-flow device A real-time 326 reverse transcription loop-mediated isothermal amplification assay for the rapid 327 detection of yellow fever virus doi = 10.1016/j.cmi.2020.04.001 id = cord-314932-edf9xjwr author = Yan, Junqiang title = Research Progress of Drug Treatment in Novel Coronavirus Pneumonia date = 2020-05-13 keywords = China; SARS; treatment summary = Studies have found that 2019-nCoV is a single-stranded RNA beta coronavirus similar to SARS and MERS (12) , so current treatment is mainly based on the treatment experience of these two diseases (13) and further development of new targeted drugs. Currently, the drugs studied for the treatment of 2019-nCoV mainly include antivirals, antimalarials, glucocorticoids, plasma therapy, biological agents, and traditional Chinese medicine, among which lopinavir/ritonavir, ribavirin, remdesivir, chloroquine phosphate, and interferon are the main drugs. Recent studies have shown that chloroquine can inhibit 2019-nCoV by increasing the endosome pH required for viral cell fusion (26) , and its antiviral and antiinflammatory activity considerations are also involved (36) . New research shows that interferon-α nebulization, injection of interferon-α2b (57) , and α-interferon combined with lopinavir/ritonavir drugs (58) may be applicable to the current treatment of 2019-nCoV infection. Current studies have shown that the drug treatment of 2019-nCoV-related pneumonia mainly includes antivirals, antimalarials, and interferon. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro doi = 10.1208/s12249-020-01679-z id = cord-339568-th2xmhb6 author = Yan, Meitian title = Analysis of the diagnostic value of serum specific antibody testing for coronavirus disease 2019 date = 2020-06-27 keywords = SARS; patient summary = The detection of antibodies produced during the immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has become an important laboratory method for the diagnosis of COVID‐19. In this study, retrospective analysis was used to explore the dynamic changes of serum IgM and IgG antibody and factors affecting diagnostic efficacy, so as to provide a theoretical basis for clinical diagnosis and treatment. Serum IgM antibodies against SARS-CoV can be detected 3-6 days after infection, but levels rapidly decrease thereafter. The positive rates of IgM and IgG antibodies in the non-severe group (71.62% and 71.14%, respectively) were higher than that in the severe group (28.38% and 28.86%, respectively), but these differences were not statistically significant (p > 0.05). Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis doi = 10.1002/jmv.26230 id = cord-342294-x18xmrji author = Yan, Nao title = Medium Term Follow-Up of 337 Patients With Coronavirus Disease 2019 (COVID-19) in a Fangcang Shelter Hospital in Wuhan, China date = 2020-07-03 keywords = COVID-19; SARS summary = Risk factors of nucleic acid re-positivity including the number of lobes infiltration (odds ratio[OR], 1.14; 95% CI, 1.09–1.19), distribution (OR, 0.16; 95% CI, 0.13–0.19), CT imaging feature of patchy shadowing accompanying with consolidation (OR, 9.36; 95% CI, 7.84–11.17), respiratory symptoms of cough accompanying with expectoration (OR, 1.39; 95% CI, 1.28–1.52), and chest congestion accompanying by dyspnea (OR, 1.42; 95% CI, 1.28–1.57). Considering the high infectious characteristics of the SARS-CoV-2 virus, all recovered patients continue to undergo 14 days postdischarge quarantine at designated locations, which is required by the diagnosis and treatment program for novel coronavirus pneumonia (Trial Version 6). All patients were detected to be SARS-CoV-2 nucleic acid positive by a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and classified as mild to moderate cases on admission based on the criteria issued by the National Health Commission (NHC) of the People''s Republic of China. doi = 10.3389/fmed.2020.00373 id = cord-309206-kq77whdx author = Yan, Victoria C. title = Advantages of the Parent Nucleoside GS-441524 over Remdesivir for Covid-19 Treatment date = 2020-06-23 keywords = GS-441524; Remdesivir; SARS summary = 13 Seeing that the enzymes involved in McGuigan prodrug hydrolysis are hardly expressed in the lungs undermines its utility in the context of a primarily respiratory disease such as Covid-19. 4−6 For the fleeting duration of time that remdesivir is in the blood (prior to hydrolysis to GS-441524), the expression of bioactivating enzymes for McGuigan prodrugs suggests that the highest concentrations of NTP formation by remdesivirrather than GS-441524 would occur in cell types with high expression of CES1/ CTSA/HINT1. 26 At the time of publication, a study by Agostini and colleagues is the only report that has compared the antiviral activities of GS-441524 and remdesivir in primary human airway epithelial (HAE) cells, the most clinically relevant in vitro model of the lung, infected with either SARS-CoV or MERS-CoV. 1 Above all else, premature hydrolysis of the McGuigan prodrug, followed by dephosphorylation in serum such that GS-441524 is the predominant metabolite 4,5,29 compels studies investigating its utility in patients with Covid-19. doi = 10.1021/acsmedchemlett.0c00316 id = cord-253006-r2a2ozrc author = Yan, Xiquan title = Duration of SARS-CoV-2 viral RNA in asymptomatic carriers date = 2020-05-24 keywords = SARS summary = title: Duration of SARS-CoV-2 viral RNA in asymptomatic carriers Notably, patient 2 carried SARS-CoV-2 viral for 32 days continuously after exposure to COVID-19 and tested positive for viral RNA in the respiratory sample for 13 days after first positive test onset. The results indicate that asymptomatic human can carry SARS-CoV-2 viral RNA after exposure to COVID-19, and the carriage seems long-lived. Further study is needed to determine the potential for and mode of contagion of asymptomatic carriers to develop more scientific control strategies. The long duration of asymptomatic infection with SARS-CoV-2 may warrant a reassessment of quarantine as the current outbreak. The US Centers for Disease Control and Prevention recommends that contacts of asymptomatic carriers self-isolate for 14 days [4] . Quarantine of asymptomatic carriers and identification of contacts are a crucial part of these control efforts. There is a great need for further studies on the mechanism by which asymptomatic carriers could acquire and carry SARS-CoV-2 that causes COVID-19. doi = 10.1186/s13054-020-02952-0 id = cord-318235-2e5er0x0 author = Yanai, Hidekatsu title = Adiposity is the Crucial Enhancer of COVID-19 date = 2020-08-01 keywords = SARS summary = A very recent study showed that patients with overweight and obesity admitted in a medical ward for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related pneumonia, despite their younger age, required more frequently assisted ventilation and access to intensive care units (ICUs) or semi-ICU than normal-weight patients [1] . Increased DPP4 expression was observed in vascular endothelial cells, adipose tissue and liver in obese people [8] , which can also make it easy for SARS-CoV-2 to enter human tissues. It has been proposed that the increase of secretion of interleukin-6 and tumor necrosis factor-alpha by adipose tissue in obesity-induced insulin resistance, could underlie the associations of insulin resistance with endothelial dysfunction and coagulopathy [9] . Elevation of inflammatory cytokines, endothelial dysfunction and procoagulant state already exist in obese people even before SARS-CoV-2 infection. In conclusion, obese people have various factors including high likelihood of entry of SARS-CoV-2 into human vital tissues, elevated cytokines, endothelial dysfunction and procoagulant state, which may enhance the severity of COVID-19. doi = 10.14740/cr1118 id = cord-259620-qigfstxt author = Yang, Chen title = Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date = 2020-10-10 keywords = ACE2; KIM1; SARS summary = Presently, it is generally recognized that SARS-CoV-2 initiates invasion through binding of receptor-binding domain (RBD) of spike protein to host cell-membrane receptor ACE2, however, whether there is additional target of SARS-CoV-2 in kidney remains unclear. Studies have indicated direct infection of SARS-CoV-2 in kidney in addition to lung 5, 31 , however, ACE2 remains the only confirmed receptor which may mediate this invasion. Notably, our results suggest that SARS-CoV-2-RBD binds KIM1 and ACE2 via two distinct pockets, implicating that KIM1 and ACE2 may synergistically mediate the invasion of SARS-CoV-2 in kidney cells; which may explain the strong renal tropism, as well as the high incidence of acute kidney injury in COVID-19 patients 5 . ACE2 is the most well-studied receptor for SARS-CoV-2 so far, yet it is not an ideal therapeutic target for COVID-19 since it is widely expresses in multiple organs, and plays crucial roles in regulating blood pressure and preventing heart/kidney injury 36, 37 . doi = 10.1101/2020.10.09.334052 id = cord-333999-k92fmnq7 author = Yang, Chih-Jen title = Remdesivir Use in the Coronavirus Disease 2019 Pandemic: A Mini-Review date = 2020-10-05 keywords = COVID-19; Remdesivir; SARS summary = In this mini-review, we summarize the current evidence on the efficacy and challenges of remdesivir for the treatment of coronavirus disease 2019 (COVID-19). J o u r n a l P r e -p r o o f Based on several clinical trials and reports on its compassionate use, remdesivir is considered by many to be the most promising drug for the treatment of COVID-19 [44] [45] [46] . First, to evaluate the efficacy and safety of remdesivir in patients with COVID-19, a randomized, placebo-controlled, double-blind, multicenter, phase 3 clinical trial was launched on February 5, 2020, in China 30, 60 . Clinically, common adverse drug reactions (ADRs) noted during the compassionate use of remdesivir in patients with COVID-19 reported by Grein et al. doi = 10.1016/j.jmii.2020.09.002 id = cord-310774-rpc8hrrx author = Yang, Chongtu title = Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia date = 2020-08-28 keywords = CEA; SARS summary = We designed this study to investigate the association between carcinoembryonic antigen (CEA) elevation and SARS-CoV-2 infection. METHODS: We retrospectively analyzed 177 patients with confirmed SARS-CoV-2 infection who received plasma CEA assays during hospitalization. CONCLUSION: SARS-CoV-2 infection might be another cause of CEA elevation, with nearly 20% of patients experienced transient and marked CEA increment during COVID-19 pneumonia. We found a portion of patients with COVID-19 pneumonia had raised serum of CEA, and we designed this study to investigate the association between CEA elevation and SARS-CoV-2 infection. However, as none of our participants had any clinical indication of malignancy, further studies are needed to investigate the role of CEA level in COVID-19 patients accompanied with colorectal cancer. In conclusion, SARS-CoV-2 infection might cause transient and marked CEA elevation especially in non-survivors, and this abnormal increment was not correlated with the severity of inflammation. doi = 10.1007/s00432-020-03350-3 id = cord-303171-u5jrbsii author = Yang, Gee-Gwo title = SARS-associated Coronavirus Infection in Teenagers date = 2004-02-17 keywords = SARS summary = On April 28, when a student (case-patient 1) visited the school nurse on the first day that he had a fever, an infection specialist from affiliated Tzu-Chi Medical Center immediately responded. All nine schoolmates underwent chest x-ray examinations and were tested for SARS-associated coronavirus (SARS -CoV) by reverse transcription-polymerase chain reaction (RT-PCR) (4) and DNA sequencing. Six schoolmates were positive for SARS-CoV by RT-PCR, confirmed later by DNA sequencing for replicase. No new cases of fever have occurred in Tzu-Chi High School in the 2 months since these patients'' isolation. Six schoolmates with fever were confirmed by real-time RT-PCR and DNA sequences to have SARS-CoV infection. Worldwide, SARS-CoV infection has been clinically severe, characterized by respiratory distress and a 15% average mortality rate (6) (7) (8) . Our teenagers with presumed SARS-CoV infection had very mild courses. The benign course of SARS-CoV infection in our teenage students supports the WHO finding of less-severe disease in younger persons. doi = 10.3201/eid1002.030485 id = cord-329069-ejdunj41 author = Yang, He S title = Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date = 2020-08-21 keywords = PCR; SARS summary = METHOD: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual''s SARS-CoV-2 infection status. CONCLUSION: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. In this study, we hypothesized that the results of routine laboratory tests performed within a short time frame as the RT-PCR testing, in conjunction with a limited number of previously identified predictive demographic factors (age, gender, race) (17), can predict SARS-CoV-2 infection status. Laboratory tests were selected to construct the input feature vectors of the prediction model based on the following criteria: 1) a result available for at least 30% of the patients two days before a specific SARS-CoV-2 RT-PCR test, and 2) showing a significant difference (P-value, P-value after Bonferroni correction, P-value after demographics adjustment all less than 0.05) between patients with positive and negative RT-PCR results. doi = 10.1093/clinchem/hvaa200 id = cord-351028-p5cq2is5 author = Yang, Jia-Wei title = Corticosteroid administration for viral pneumonia: COVID-19 and beyond date = 2020-06-27 keywords = SARS summary = IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Corticosteroid therapy for 386 critically ill patients with the Middle East respiratory syndrome: a multicenter 387 retrospective cohort study Epidemiological and clinical characteristics of 432 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive 433 study Clinical course and outcomes of critically ill patients 449 with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, 450 observational study doi = 10.1016/j.cmi.2020.06.020 id = cord-274280-x5s4l0pp author = Yang, Jinsung title = Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor date = 2020-09-11 keywords = ACE2; Fig; RBD; SARS summary = Here, we analyze the biophysical properties of the SARS-CoV-2 S-glycoprotein binding, on model surfaces and on living cells, to ACE2 receptors using force-distance (FD) curve-based atomic force microscopy (FD-curve-based AFM) (Fig. 1c) . used FD-curve-based AFM to evaluate at the single-molecule level the binding strength of the interaction established between the glycosylated S1 subunit and ACE2 receptors on model surfaces (Fig. 2a) . To investigate the properties of the binding complex, force-distance (FD) curves were recorded by repeatedly approaching and withdrawing the S1 subunit or RBD-functionalized tip from the ACE2 model surface (Fig. 2a, b) . To this end, we synthetized four different peptides (sequences provided in Supplementary Fig. 9 ), which have been selected to mimic the regions of ACE2 that interact with the S1 subunit as determined by the crystal structure 29 , and we tested their binding inhibition properties using our single-molecule force spectroscopy approach (Fig. 4a, b) . doi = 10.1038/s41467-020-18319-6 id = cord-270019-er70ehk4 author = Yang, Kunyu title = Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study date = 2020-05-29 keywords = COVID-19; China; SARS; patient summary = title: Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study METHODS: We did a retrospective, multicentre, cohort study of 205 patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and with a pathological diagnosis of a malignant tumour in nine hospitals within Hubei, China, from Jan 13 to March 18, 2020. Multivariable regression analysis showed that receiving chemotherapy within 4 weeks before symptom onset (odds ratio [OR] 3·51 [95% CI 1·16–10·59]; p=0·026) and male sex (OR 3·86 [95% CI 1·57–9·50]; p=0·0033) were risk factors for death during admission to hospital. 5 In particular, male sex and receiving chemotherapy within 4 weeks before symptom onset were identified as risk factors for death in patients with cancer who were diagnosed with COVID-19. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China doi = 10.1016/s1470-2045(20)30310-7 id = cord-256893-3sh87h2x author = Yang, Li title = COVID-19: immunopathogenesis and Immunotherapeutics date = 2020-07-25 keywords = COVID-19; SARS; patient summary = The recent novel coronavirus disease (COVID-19) outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is seeing a rapid increase in infected patients worldwide. SARS-CoV-2 not only activates antiviral immune responses, but can also cause uncontrolled inflammatory responses characterized by marked pro-inflammatory cytokine release in patients with severe COVID-19, leading to lymphopenia, lymphocyte dysfunction, and granulocyte and monocyte abnormalities. The number of people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is rapidly increasing worldwide. The effect of elevated cytokine production on clinical manifestations Increasing evidence shows that viral infection can induce severe syndromes of shock and organ failure; 8,57 this phenomenon was also investigated for COVID-19. Treg cell-based therapy The dysregulated inflammatory processes caused by SARS-CoV-2 in patients with severe COVID-19 are partially due to the dysfunction of Tregs, which are responsible for inhibiting inflammation. doi = 10.1038/s41392-020-00243-2 id = cord-295508-yhdj5m0e author = Yang, Li-Tao title = Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients date = 2006-06-16 keywords = IFN; SARS summary = title: Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients In this study, we found that memory T-cell responses against the spike (S) protein were persistent for more than 1 year after SARS-CoV infection by detecting the production of IFN-γ using ELISA and ELISpot assays. In this study, we analyzed CD4 + and CD8 + T-cell responses in peripheral blood of recovered SARS patients to a pool of 169 overlapping SARS-CoV S peptides and characterized the phenotype of memory T-cell subpopulations. In this study, we performed phenotypic characterization of antiviral T-cell responses specific for SARS-CoV S peptides on the basis of their ability to secrete IFN-g and the expression of CD45RO, CCR7 and CD62L. Consistent with observations in HIV infection, we showed that SARS-CoV S-specific CD8 + T cells produced IFN-g but not IL-2 and predominantly displayed CD45RO À CCR7 À phenotype which might represent terminally differentiated effector memory T cells [25] . doi = 10.1016/j.clim.2006.05.002 id = cord-293858-dk4snw9r author = Yang, Lin title = Comparison of influenza disease burden in older populations of Hong Kong and Brisbane: the impact of influenza and pneumococcal vaccination date = 2019-02-14 keywords = Hong; Kong; SARS summary = Annual excess rates of mortality or hospitalization associated with influenza in the older population were estimated for the pre-SARS (reference period), post-SARS and post-pandemic period, respectively. We constructed time series segmented regression models to estimate cause-specific mortality or hospitalization risks associated with influenza in the older population during the pre-SARS, post-SARS, and post-pandemic periods for Hong Kong and Brisbane. Compared to Hong Kong, during the study period Brisbane had higher mortality rates for all-cause (81.7 vs 66.5 per 100,000 population), cardiorespiratory diseases (CRD, 42.1 vs 33.8), stroke (9.5 vs 6.5) and ischemic heart diseases (IHD, 17.0 vs 7.5), but a lower rate for pneumonia and influenza (P&I, 2.8 vs 9.9), and a comparable rate for chronic obstructive pulmonary disease (COPD, 3.9 vs 4.2) (Additional file 1: Appendix 3). In this study, we estimated excess rates of mortality or hospitalizations attributable to influenza in different periods (pre-SARS, post-SARS, and post-pandemic) for two subtropical cities Hong Kong and Brisbane. doi = 10.1186/s12879-019-3735-7 id = cord-321468-nkl2mls8 author = Yang, Mo title = Thrombopoietin levels increased in patients with severe acute respiratory syndrome date = 2008-03-07 keywords = SARS; TPO summary = Using a ELISA method, we found an increase in thrombopoietin (TPO) levels in the plasma of convalesced SARS patients (290 ± 53 pg/ml) and active SARS patients (251 ± 23 pg/ml) comparing to that from normal control patients (228 ± 17 pg/ml). Severe Acute Respiratory Syndrome (SARS) is a recently emerged human disease caused by the infection of a novel coronavirus (SARS-CoV) [1] . In this study, TPO levels in plasmas from SARS patients, the effect of these plasmas on in vitro megakaryocytopoiesis, and whether SARS-CoV can directly infect hematopoietic stem cells and megakaryocytic cells are investigated. To study the correlation of platelet counts and the plasma TPO levels, linear regression analyses were carried out for the normal, convalesced SARS and active SARS patient groups respectively. The present study showed that there was an increase of TPO levels in the plasma of convalescence SARS patients comparing to those from normal control and active SARS patients. doi = 10.1016/j.thromres.2007.12.021 id = cord-299472-pmqqemku author = Yang, Naibin title = In-flight Transmission Cluster of COVID-19: A Retrospective Case Series date = 2020-03-30 keywords = March; SARS summary = No data were available about the risk of SARS-CoV-2 transmission on aircraft and clinical characteristics and outcomes of these COVID-19 patients. We conducted a retrospective study focused on the clinical characteristics of ten patients with COVID-19 successively admitted to Xiaoshan First People''s Hospital after having been on a flight. Epidemiology data were collected by interviewing each patient including exposure history, dates of illness onset, hospital admissions and All rights reserved. Patients were discharged from hospital when the results of two RT-PCR tests taken 24 hours apart were negative for SARS-CoV-2 and symptoms improved obviously according to China guidelines 10 . . https://doi.org/10.1101/2020.03.28.20040097 doi: medRxiv preprint SARS-CoV-2 transmission on aircraft were similar to those without in-flight history, as previously reported [4, 7, 14] . Notably, the symptoms of COVID-19 patients infected in this flight were relatively mild, outcomes were inclined to be better, and the risk to passengers was higher compared with transmission of SARS on aircraft [15-17]. doi = 10.1101/2020.03.28.20040097 id = cord-288670-1vlowf2n author = Yang, Naidi title = Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19 date = 2020-03-15 keywords = MERS; SARS summary = As a result, the endocytic pathway including endosome and lysosome has become important targets for development of therapeutic strategies in combating diseases caused by CoVs. In this mini-review, we will focus on the importance of the endocytic pathway as well as the autophagy process in viral infection of several pathogenic CoVs inclusive of SARS-CoV, MERS-CoV and the new CoV named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and discuss the development of therapeutic agents by targeting these processes. Further studies also demonstrated that either ATG5 or ATG7, two of the key autophagy proteins in control of autophagosome biogenesis, is not required for viral replication in cells infected by MHV [28, 29] or by SARS-CoVs [30] . Taken together, establishing the role of endocytic pathway in viral entry is a major breakthrough in the mechanistic understanding of the CoVs infection, which offers great opportunity in development of novel therapeutic strategies for treatment of diseases such as SARS and COVID-19. doi = 10.7150/ijbs.45498 id = cord-265877-dund6unq author = Yang, Q. title = Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis date = 2020-06-03 keywords = AKI; SARS; covid-19 summary = We extracted data from eligible studies to summarize the clinical manifestations and laboratory indexes of kidney injury on COVID-19 infection patients and further compared the prevalence of acute kidney injury (AKI) and the mean differences of three biomarkers between in ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint "SARS-CoV-2", "clinical", "laboratory", "kidney", "Acute Kidney Injury", "proteinuria" and "hematuria". To identify the risk factors for critical illnesses of COVID-19 patients, we then analyzed the relevance of the AKI and the three laboratory indexes with the clinical severity through comparing the incidences of AKI and mean differences of those biomarkers between ICU/severe and non-ICU/non-severe cases. . https://doi.org/10.1101/2020.05.28.20116400 doi: medRxiv preprint Due to the restriction of clinic information and most of the studies did not include in the death cases and the mortality of COVID-19, the association between kidney impairment and COVID-19-induced death was not be analyzed in our meta-analysis. doi = 10.1101/2020.05.28.20116400 id = cord-267887-ntwvquqz author = Yang, Ren title = Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro date = 2020-08-21 keywords = CoV-2; SARS summary = title: Development and effectiveness of Pseudotyped SARS-CoV-2 system as determined by neutralizing efficiency and entry inhibition test in vitro Previously, researchers had developed a pseudotyped virus system for SARS-CoV and MERS-CoV, based on HIV-1 core, bearing virus spike protein. Furthermore, the neutralization results for ppSARS-2 were consistent with those of live SARS-CoV-2 and determined using the serum samples from convalescent patients. In conclusion, we have developed an easily accessible and reliable tool for studying the neutralizing efficiency of antibodies against SARS-CoV-2 and the entry process of the virus in a BSL-2 laboratory. Development and optimization of a sensitive pseudovirus-based assay for HIV-1 neutralizing antibodies detection using A3R5 cells A safe and convenient pseudovirus-based inhibition assay to detect neutralizing antibodies and screen for viral entry inhibitors against the novel human coronavirus MERS-CoV Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig doi = 10.1016/j.bsheal.2020.08.004 id = cord-330873-hwbdreul author = Yang, Wan title = The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal date = 2020-07-07 keywords = SARS summary = title: The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal After infectious SARS-CoV-2 was isolated from COVID-19 patients'' feces and urines, the corresponding RNA in the wastewater and sewage sludge was also observed (Randazzo et al., 2020) , implying the possibility of transmission of SARS-CoV-2 through the wastewater treatment plants (WWTP). Therefore, it is imperative to understand the potential exposure and transmission risk of this virus in sludge for the sake of public health. While limited evidence was found that sludge would play an essential role in SARS-CoV-2 transmission, there is still a need to understand the fate of coronaviruses outside the human host, including their persistence and inactivation mechanisms in 5 sludge, which would help to reveal their potential risks during sludge treatment and disposal. Aerosol Transmission Figure 1 The potential exposure and transmission risk of SARS-CoV-2 through sludge treatment and disposal doi = 10.1016/j.resconrec.2020.105043 id = cord-292002-g0v0xc21 author = Yang, Wenjing title = The role of imaging in 2019 novel coronavirus pneumonia (COVID-19) date = 2020-04-15 keywords = COVID-19; China; SARS summary = Imaging features of multiple patchy areas of ground glass opacity and consolidation predominately in the periphery of the lungs are characteristic manifestations on chest CT and extremely helpful in the early detection and diagnosis of this disease, which aids prompt diagnosis and the eventual control of this emerging global health emergency. • Among the infected patients, characteristic findings on CT imaging include multiple, patchy, ground-glass opacity, crazy-paving pattern, and consolidation shadows, mainly distributed in the peripheral and subpleural areas of both lungs, which are very helpful for the frontline clinicians. The typical chest CT imaging characteristics of COVID-19 include multiple, peripheral, bilateral, patchy, sub-segmental, or segmental ground glass opacities and areas of consolidation, which are mostly distributed along the bronchovascular bundles and subpleural space. Furthermore, in the currently available reports, the most common chest CT findings in COVID-19 patients are the peripheral areas of ground glass opacity/consolidation (without subpleural sparing) which are bilateral in distribution [21] [22] [23] . doi = 10.1007/s00330-020-06827-4 id = cord-257876-nzjp1hrz author = Yang, Wenzhong title = Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality date = 2020-09-14 keywords = RBM; SARS; blast summary = Genomic annotation of the BLAST hits also showed that viruses from geographic regions with severe infections tended to have more dynamic genomic regions in the SARS-CoV-2 receptor-binding domain (RBD) and receptor-binding motif (RBM) of the spike protein (S protein). We collected all available raw sequencing data for SARS-CoV-2 from the four sequencing platforms (Illumina, BGI, Ion-Torrent and Nanopore) deposited in the National Center for Biotechnology Information (NCBI) Short Reads Archive (SRA) database as of 15 April 2020 (Supplementary Table S1 ). The BLAST hit score (BHS) is a metric based on the similarity between a high-quality read of a SARS-CoV-2 sample and each assembled genome in the coronavirus databases (Methods). To investigate the dynamic binding between RBM and ACE2, we implemented protein structure dockings between the modeled S proteins (with and without the ''hidden mutations'' in the alignments of 4I.C1) and human ACE2 protein using HDOCK [26] The threshold for the high-quality reads from BGI and Illumina platforms is 0.9 (marked by a dash line) and that for Ion-Torrent and Nanopore is 0.2 (marked by a dash line). doi = 10.1093/bib/bbaa208 id = cord-327690-di7hfghi author = Yang, Xiaobo title = Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study date = 2020-02-24 keywords = CoV-2; SARS; patient summary = title: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study METHODS: In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. In this study, we investigated critically ill patients with confirmed SARS-CoV-2 pneumonia who were admitted to Wuhan Jin Yin-tan hospital. The baseline SARS-CoV-2-associated morbidity and mortality data from this study will be of considerable value for the early identification of individuals who are at risk of becoming critically ill and who are most likely to benefit from intensive care treatment. During the outbreak of SARS-CoV-2 infection, the number of critically ill patients exceeded the capacity of ICUs. Therefore, two provisional ICUs were urgently established in Jin Yin-tan hospital and hence most mechanical ventilator settings and recordings were not recorded, except records of positive end-expiratory pressure in some cases. doi = 10.1016/s2213-2600(20)30079-5 id = cord-275862-1aqtqaod author = Yang, Xiaodong title = A case of COVID-19 patient with the diarrhea as initial symptom and literature review date = 2020-04-15 keywords = China; SARS summary = authors: Yang, Xiaodong; Zhao, Jie; Yan, Qiang; Zhang, Shangxin; Wang, Yigao; Li, Yongxiang Here we reported a case of 2019 novel coronavirus-infected patient (NCIP) with diarrhea as the initial symptom. Laboratory examination shows that the absolute number of leukocytes, neutrophils and lymphocytes decrease in most patients, while CRP increases significantly and procalcitonin is usually normal [7] . In our case, the patient suffered from diarrhea as the initial symptom, which was relatively rare in NCIP. In conclusion, we reported the clinic feature and laboratory examination of a NCIP patient with diarrhea as the initial symptom. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China doi = 10.1016/j.clinre.2020.03.013 id = cord-267579-gkvd0fol author = Yang, Xiaoyu title = Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period date = 2020-07-27 keywords = SARS summary = title: Asymptomatic Carrier Transmission of COVID-19 and The Multi-Point Aerosol Sampling to Assess Risks in OR During Pandemic Period The 2019 novel coronavirus disease (COVID-19) causing acute infectious pneumonia has widely spread in China and other countries in the world. Studies have documented that novel coronavirus spread through human-to-human transmission in hospital and family setting 2,3 . Nevertheless, the transmission of the novel coronavirus from an asymptomatic carrier should be considered as a source of the infection of COVID-19 as well 4 . Therefore, it is of significance to identify and isolate asymptomatic carriers as well as patients with mild symptoms to prevent the spread of the virus. Clinical Characteristics of Coronavirus Disease 2019 in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients doi = 10.1016/j.wneu.2020.07.144 id = cord-273751-61eeykj1 author = Yang, Zhenwei title = The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis date = 2020-04-10 keywords = SARS summary = title: The effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis The inclusion criteria in this meta-analysis were as follows: (1) subjects in each study were patients with coronavirus infection; (2) the patients were divided into the experimental group using corticosteroids and the control group not using corticosteroids; (3) the outcomes included the use of corticosteroids in critical and noncritical patients, mortality, length of stay (LOS) and adverse reactions to corticosteroids. We extracted the following variables: the authors, the publication year, the study design, viral type, population, treatment details (including corticosteroid use, types and doses of corticosteroids, and other treatments), and outcome measures such as the use of corticosteroids in critical and non-critical patients, mortality, LOS and adverse reactions to corticosteroids (including bacterial infection, hyperglycemia, hypocalcemia and hypokalemia). In this systematic review and meta-analysis, the result indicated that patients with severe conditions were more likely to require corticosteroids therapy. doi = 10.1016/j.jinf.2020.03.062 id = cord-282106-7k088cqv author = Yang, Zhi-yong title = A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice date = 2004 keywords = SARS; dna summary = Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Immunization and challenge were performed in mice as described previously 18 , and viral replication (mean log 10 TCID 50 per g tissue with standard error) in the lower (a) and upper (b) respiratory tract after challenge with SARS-CoV was measured for five immunized animals inoculated with SDCD, SDTM or empty plasmid vector control. doi = 10.1038/nature02463 id = cord-261688-njlxrxv6 author = Yang, Ziwei title = Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date = 2020-08-12 keywords = MDA5; NSP8; SARS summary = Melanoma differentiation-associated gene-5 (MDA5) acts as a cytoplasmic RNA sensor to detect viral dsRNA and mediates type I interferon (IFN) signaling and antiviral innate immune responses to infection by RNA viruses. Here, we report that SARS-CoV-2 nonstructural protein 8 (NSP8) acts as an innate immune suppressor and inhibits type I IFN signaling to promote infection of RNA viruses. Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. Our study contributes to our understanding of the direct immune evasion mechanism of SARS-CoV-2 by showing that NSP8 suppresses the most upstream sensor of innate immune responses involved in the recognition of viral dsRNA. Based on our existing experimental data, we propose a simple working model to illustrate how NSP8 218 negatively regulates innate immune responses by inhibiting MDA5 K63-linked polyubiquitination (Fig.5c) . doi = 10.1101/2020.08.12.247767 id = cord-350242-4u1iyf0p author = Yaniv, K. title = City-level SARS-CoV-2 sewage surveillance date = 2020-10-21 keywords = SARS summary = In this study we sampled an urban wastewater infrastructure in the city of Ashkelon, Israel, during the end of the first COVID-19 wave in May 2020 when the number of infections seemed to be waning. Using the linear equation, we calculated copy number of N1 gene in sewage samples reported in this study. If the sampling is extended to 24 hours, then the NVL can be expressed as number of SARS-CoV-2 RNA copies per 1,000 people per day. Ashkelon was chosen for surveillance of SARS-CoV-2 in sewage due to a relatively low COVID-19 prevalence during the time of study following a national lockdown period during Table S1 ). In conclusion, we present a proof-of-concept study demonstrating the feasibility of SARS-CoV-2 RNA detection in raw sewage originating from the city sewer system that reflects virus circulation in the assessed area. doi = 10.1101/2020.10.19.20215244 id = cord-102364-t5bt2eb4 author = Yao, Dehui title = Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date = 2020-06-08 keywords = RBM; SARS summary = In an effort of utilizing human ferritin as nanoplatform for drug delivery, we engineered a fusion protein by presenting receptor-binding motif (RBM) of SARS-CoV-2 virus spike glycoprotein on the N-terminus of ferritin subunits. The designed fusion protein with a cage-like structure, similar to that of corona virus, is a potential anti-SARS-CoV-2 vaccine. We hereby show the construction, preparation, and characterization of the fusion protein RBM-HFtn. Our initial affinity study confirmed its biological activity towards ACE2 receptor which suggests its mode of action against SARS-CoV-2 could be either through vaccine therapy or blocking the cellular entry of virus as antagonist of ACE2 receptor. Antibodies targeting the spike glycoprotein of SARS-CoV and MERS-CoV, especially its receptor-binding domain (RBD), was found to efficiently neutralize virus infection [1, 2] . In this work, we engineered a human ferritin heavy chain (HFtn) by fusing and presenting the RBM of its spike glycoprotein as potential vaccine of SARS-CoV-2. doi = 10.1101/2020.05.25.115618 id = cord-267426-3eu9umx5 author = Yao, Hangping title = Patient-derived mutations impact pathogenicity of SARS-CoV-2 date = 2020-04-19 keywords = April; SARS; preprint summary = Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously referred to as 32 2019-nCoV), associated with the ongoing outbreak of atypical pneumonia, has already 33 caused a global pandemic, despite China''s extensive systematic effort to contain the 34 All rights reserved. 75 To address this, we characterized 11 SARS-CoV-2 viral isolates from patients (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . https://doi.org/10.1101/2020.04.14.20060160 doi: medRxiv preprint 16 sequences and Taijima''s D is -2.8874 with a nucleotide diversity (π) of 0.000641 (p < 229 0.05 according to simulations performed in (Tajima, 1989) , indicating that the 230 SARS-CoV-2 genome has an excess of low-frequency alleles due to recent population 231 expansions, consistent with the repeated bottlenecking events during viral infections. doi = 10.1101/2020.04.14.20060160 id = cord-345103-b2wkm03g author = Yao, Hangping title = Molecular architecture of the SARS-CoV-2 virus date = 2020-09-06 keywords = RNP; SARS; figure summary = Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). The postfusion S observed on the SARS-CoV-2 virus may come from 1) products of occasional, spontaneous dissociation of S1 (Cai et al., 2020) , which was cleaved by host proteinases; 2) syncytium naturally formed on infected cells , when budding progeny virions carried a few residual postfusion S from the cell surface; 3) sample preparation procedure, as cryo-EM images of ßpropiolactone fixed viruses showed most spikes present on the virus are postfusion-like Gao et al., 2020) . Three representative SARS-CoV-2 virus (Figures 1B and 4D ) and a bundle of postfusion S ( Figure 3B ) were reconstructed by projecting all spikes and RNPs onto their refined coordinates and merging the structures using Jsubtomo (Huiskonen et al., 2014) . Structures and distributions of SARS-CoV-2 spike proteins on intact virions doi = 10.1016/j.cell.2020.09.018 id = cord-354868-pqn59ojj author = Yao, Hebang title = A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date = 2020-09-25 keywords = RBD; SARS; SR31 summary = title: A high-affinity RBD-targeting nanobody improves fusion partner''s potency against SARS-CoV-2 Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. A high-affinity RBD binder without neutralizing activity 85 Previously, we generated 99 sybodies from three highly diverse synthetic libraries by ribosome and phage display with in vitro selections against the SARS-CoV-2 RBD. Consistent with its inability to neutralize SARS-CoV-2 pseudovirus, SR31 did not affect RBD-ACE2 binding (Fig. 1C) . Most RBD-targeting neutralizing antibodies, including neutralizing nanobodies characterized so far (8, 13-15, 19, 20, 22-24, 26-28, 34, 35, 37) , engage the RBD at the receptor-binding motif (RBM) (Fig. 3A) , thus competing off ACE2 and preventing viral entry. Taken together, the structural data rationalize the high-affinity binding between SR31 and RBD, and its inability to neutralize SARS-CoV-2. Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2 doi = 10.1101/2020.09.24.312595 id = cord-322005-70snojec author = Yao, Pingping title = Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell date = 2020-06-19 keywords = SARS summary = title: Isolation and Growth Characteristics of SARS-CoV-2 in Vero Cell In a recent report, 149 mutations were found among 103 sequenced isolates of SARS-CoV-2 . To investigate whether our viruses show mutations different from other reported SARS-CoV-2, all the seven isolates were sequenced at the 3rd passage and the sequences were aligned with coding sequence (CDS) of SARS-CoV-2 Wuhan-Hu-1 (NC_045512). It is interesting to note that these seven patients infected with SARS-CoV-2 have high viral load in the early stage of clinical sign, which is consistent with previous reports (Kim et al. A The cytopathic effect was observed in Vero cells infected with the isolated viruses at 5 dpi. In conclusion, seven SARS-CoV-2 strains were isolated, sequenced and characterized in Vero cells, and a deletion mutation was identified after short passage in Vero cells. Viral load kinetics of SARS-CoV-2 infection in first two patients in Korea SARS-CoV-2 viral load in upper respiratory specimens of infected patients doi = 10.1007/s12250-020-00241-2 id = cord-353103-sdij1d90 author = Yao, Xueting title = In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-09 keywords = PBPK; SARS; chloroquine summary = title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug''s safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. doi = 10.1093/cid/ciaa237 id = cord-261472-qcu73sdu author = Yao, Yong Xiu title = Cleavage and Serum Reactivity of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein date = 2004-07-01 keywords = SARS; protein summary = Severe acute respiratory syndrome (SARS) coronavirus (SCoV) spike (S) protein is the major surface antigen of the virus and is responsible for receptor binding and the generation of neutralizing antibody. To investigate SCoV S protein, full-length and individual domains of S protein were expressed on the surface of insect cells and were characterized for cleavability and reactivity with serum samples obtained from patients during the convalescent phase of SARS. The possible use of insect cell-displayed S protein for diagnostic application was assessed by examining fragment reactivity with serum samples from patients infected with human CoV 229E and also with serum from a patient with suspected but clinically unconfirmed SARS (serum sample 3118). Of the 2 assay formats we used, nondenatured S protein present on the cell surface provided the most sensitive detection of antibodies, with clear shifts in fluorescence for serum samples from patients with suspected but clinically unconfirmed SARS. doi = 10.1086/421280 id = cord-289711-4ab3d00h author = Yarmarkovich, Mark title = Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date = 2020-06-08 keywords = HLA; SARS summary = Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 doi = 10.1016/j.xcrm.2020.100036 id = cord-253457-gawn4s9g author = Yau, Kevin title = COVID-19 Outbreak in an Urban Hemodialysis Unit date = 2020-07-15 keywords = CoV-2; SARS summary = Patients with SARS-CoV-2 infection including asymptomatic individuals were treated with droplet and contact precautions until confirmation of negative SARS-CoV-2 RT-PCR testing. Nasopharyngeal swabs were performed by physicians, nurse practitioners, and staff from the hospital''s COVID-19 Assessment Centre under droplet and contact precautions in the hemodialysis unit with curtains drawn around the dialysis station at which the patient was being swabbed. At the time of testing, six (55%) patients and six (55%) staff positive for SARS-CoV-2 were asymptomatic. Patients with confirmed SARS-CoV-2 infection including asymptomatic individuals were dialyzed in a dedicated room separate from the main hemodialysis unit for the duration of their infection and maintained on droplet and contact precautions. Five hemodialysis staff were allowed to return to work following symptom resolution and documentation of two negative SARS-CoV-2 nasopharyngeal swabs performed 14 days from symptom onset. Infection control authorities concluded that SARS-CoV-2 transmission during an outbreak at the St. Michael''s Hospital hemodialysis unit was likely to have originated from two index cases. doi = 10.1053/j.ajkd.2020.07.001 id = cord-270528-3rsv3jlh author = Yazdanpanah, Fereshteh title = The immune system and COVID-19: Friend or foe? date = 2020-06-02 keywords = COVID-19; SARS; cell; immune summary = The pathogenesis of this virus is not yet clearly understood, but there is evidence of a hyper-inflammatory immune response in critically ill patients, which leads to acute respiratory distress syndrome (ARDS) and multi-organ failure. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID19) , and has affected people''s lives globally, since first observed in Wuhan, China in the last days of 2019 (1, 2) . On the other hand, the hyper-inflammatory and cytokine release syndrome (CRS) typical of COVID-19 causes tissue damage to the lung epithelium and ARDS (32); therefore, immunosuppressive drugs may be useful as there is some evidence that an anti-IL-6 approach is effective in critically ill patients in the ICU (33) . Also, due to the overexpression of ACE2 in islet cells of the pancreas, SARS-CoV-2 may be a diabetogenic virus that causes severe instability in the blood glucose levels of diabetes patients, which worsens the inflammatory imbalance (37) . doi = 10.1016/j.lfs.2020.117900 id = cord-314111-bqmfmcfm author = Yazdanpanah, Yazdan title = Les antirétroviraux ont-ils une place dans le traitement du syndrome respiratoire aigu sévère ? date = 2006-01-31 keywords = SARS; VIH summary = Dans le traitement du syndrome respiratoire aigu sévère (SRAS) liés à severe acute respiratory syndrome-Coronavirus (SARS-CoV), l''évaluation de l''efficacité des anti-VIH était essentiellement motivée par l''absence d''alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Dans le traitement du SARS-CoV, l''évaluation de l''efficacité des anti-VIH, le virus pour lequel il existe le plus grand nombre de molécules, était essentiellement motivée par l''absence d''alternatives thérapeutiques devant un virus émergent, dans un contexte épidémique inquiétant. Compte tenu de ces observations, 2 hypothèses ont été proposées: l''interférence de l''infection par le VIH avec la réplication du SARS-CoV pouvant empêcher le développement du SRAS, et/ou un éventuel effet prophylactique des traitements antirétroviraux. Les auteurs ont observé un nombre significativement moins important de syndromes respiratoires aigus et de décès (2,4 %) chez 41 patients atteints de SRAS recevant dès l''admission un traitement par lopinavir/ritonavir (400/100 mg x 2/j) et ribavirine que dans une cohorte historique de 111 patients ayant reçu la ribavirine seule à leur admission (28,8 %). doi = 10.1016/s0755-4982(06)74531-6 id = cord-356005-zhwtlik6 author = Yazhini, Arangasamy title = D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date = 2020-11-02 keywords = SARS; d614 summary = Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ''closed'' and ''partially open'' conformations. Such changes in the local interaction energies enhance the thermodynamic stability of the spike protein trimer as free energy difference (ΔΔG) upon glycine substitution is −2.6 kcal/mol for closed conformation and −2.0 kcal/mol for open conformation. Our results on the structural and energetic basis of enhanced stability hint that G614 may confer increased availability of functional form of spike protein trimer and consequent in higher infectivity than the D614 variant. To study the effect of D614G variation on the thermodynamic stability of the spike protein trimer, we calculated free energy changes upon aspartate to glycine substitution using buildmodel function in FoldX (Schymkowitz et al., 2005) . The table contains details of frustration index of inter-residue contacts present at 614th position of spike protein trimer in closed and partially open conformations. doi = 10.1101/2020.11.02.364273 id = cord-291012-y0ufzx93 author = Ye, Qing title = SARS-CoV-2 infection causes transient olfactory dysfunction in mice date = 2020-11-10 keywords = SARS; figure summary = Robust viral nucleocapsid (N) protein was detected in the 89 lung from SARS-CoV-2 infected hACE2 mice, but not from the control animals 90 ( Figure S1B ). Remarkably, a significantly increased latency (152.8 s v.s. 81.8 s; p=0.022) to locate 103 food pellets was observed in SARS-CoV-2 infected mice as compared with the control 104 animals on 2 dpi ( Figure 1D ). Further RT-qPCR assay showed a dozen of 211 OR genes were significantly down regulated in response to SARS-CoV-2 infection 212 ( Figure 5E ), which may also attribute to the observed olfactory dysfunction. Interestingly, SARS-CoV-2 positive signals were also observed in mOSNs and HBCs 245 of infected animals, although we didn''t detect any hACE2 expression in these cells. A) Representative multiplex immunofluorescent staining shows SARS-CoV-2 674 (SARS-CoV-2 N protein-positive) infects sustentacular cells (CK8-positive, yellow 675 arrows), Bowman''s gland cells (Sox9/CK8-positive, white arrows), microvillar cells 676 (CD73/CK8-positive, cyan arrows), HBCs (CK5-postitive, gold arrows) and iOSNs 677 (GAP43-positive doi = 10.1101/2020.11.10.376673 id = cord-279766-s3ms5f56 author = Ye, Zhongde title = A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis date = 2008-07-28 keywords = ORF-6; SARS summary = title: A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis All these data suggest that ORF-6 induces apoptosis via Caspase-3 mediated, ER stress and JNK-dependent pathways. We observed that ORF-6 was able to induce apoptosis when overexpressed in Vero E6 and COS-7 cells (Fig. 1A and B) . The death rates were comparable to the rates caused by the overexpression of Bax, a well-known pro-apoptotic member of the Bcl-family, and ORF-7a, a SARS protein that has been shown to induce apoptosis [19] . Our observation suggests that overexpression of ORF-6 induced apoptosis via a Caspase-3-dependent pathway. One of the possible mechanisms for SARS protein-induced cell death is via the JNK pathway. Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells G0/G1 arrest and apoptosis induced by SARS-CoV 3b protein in transfected cells doi = 10.1016/j.bbagen.2008.07.009 id = cord-353704-lfndq85x author = Ye, Zi-Wei title = Zoonotic origins of human coronaviruses date = 2020-03-15 keywords = CoV; CoV-2; MERS; NL63; SARS summary = In contrast, SARS-CoV, MERS-CoV and the newly-identified SARS-CoV-2 are highly pathogenic, causing severe lower respiratory tract infection in relatively more patients with a higher chance to develop acute respiratory distress syndrome (ARDS) and extrapulmonary manifestations. The 2019 novel HCoV (2019-nCoV), which has subsequently been renamed SARS-CoV-2, is the causative agent of the ongoing epidemic of coronavirus disease 2019 (COVID19) , which has claimed more than 3,120 lives and infected more than 91,000 people as of March 3, 2020 [19] . All these four communityacquired HCoVs have been well adapted to humans and are generally less likely to mutate to cause highly pathogenic diseases, though accidents did occur for unknown reasons as in the rare case of a more virulent subtype of HCoV-NL63, which has recently been reported to cause severe lower respiratory tract infection in China [38] . Alternatively, whereas bat alpha-CoVs serve as the gene pool of HCoV-229E, alpacas and dromedary camels might serve as intermediate hosts that transmit viruses to humans, exactly as in the case of MERS-CoV [69] . doi = 10.7150/ijbs.45472 id = cord-266755-y2lf7ssp author = Yehualashet, Awgichew Shewasinad title = ACEIs and ARBs and Their Correlation with COVID-19: A Review date = 2020-09-16 keywords = ACE-2; ACE2; COVID-19; SARS summary = 21, 22 Both ACE-1 and ACE-2 cleave angiotensin peptides in that ACE-1 cleaves angiotensin I and generating angiotensin (Ang) II, which causes vasoconstriction, bronchoconstriction, increases vascular permeability, inflammation, and fibrosis and enhance the development of acute respiratory disease syndrome (ARDS) and lung failure in patients infected with SARS-CoV-2. 36 The probable rational proposed for the possible relation between the use of ACEIs/ARBs, and progression to ARDS in COVID-19 is the increased availability of ACE-2 attached to surface in the lung endothelium, an inherent effect of these two classes, leading to enhanced coupling of SARS-CoV2 to ACE-2 and its consequent cell entry. Based on prior animal studies, it was suggested that proposed ACEIs and ARBs can enhance ACE2 activity and thereby increase infectivity of COVID-19 virus. 48 In severe lung injury animal models, preclinical studies have showed that ACE2 is significantly downregulated and it has been shown that the inhibition of the angiotensin type 1 receptor by ARB like losartan reduces severe acute lung injury in mice administered with the spike glycoprotein of SARS-CoV. doi = 10.2147/idr.s264882 id = cord-301388-p3juk2vv author = Yen, Muh-Yong title = Recommendations for protecting against and mitigating the COVID-19 pandemic in long-term care facilities date = 2020-04-10 keywords = LTCF; SARS; covid-19 summary = 5, 6 It is therefore essential that the health care community develop infection control guidelines on prevention measures to address pandemic preparedness and response in LTCFs. 7, 8 Here we offer recommendations based on what we consider the "gold standard" for pandemic preparedness and response in LTCFs. However, we recognize that the ideal response we describe is likely not an option for LTCFs in the midst of the current COVID-19 pandemic. 18 Given the significant vulnerability of LTCF residents and staff to the COVID-19 pandemic, here we recommend adopting eTCB, and adapting it to LTCFs. Enhanced TCB protects LTCF staff and residents from droplet, contact and fomite transmission through a process including triage prior to entering the facility, separate zones of risk within the facility and checkpoint hand hygiene throughout. doi = 10.1016/j.jmii.2020.04.003 id = cord-033204-v17d98c9 author = Yen, Wei‐Ting title = Taiwan’s COVID‐19 Management: Developmental State, Digital Governance, and State‐Society Synergy date = 2020-09-23 keywords = COVID-19; China; SARS; Taiwan; government summary = The country''s success mainly lies in three factors: (1) reliance on the mask policy as the main disease prevention measure and the ability to quickly expand mask production capacity; (2) use of big data and technology to enhance effective implementation of disease prevention and detection measures; and (3) strong state‐society relations favoring transparency, communication, and collaboration. I then turn to the crisis management framework, discussing how the developmental state foundations and the democratic regime lead to Taiwan''s success on mask policy, digital governance, and strong state-society collaboration and communication. Moreover, the capacity of a government to define and communicate the uncertainty the crisis brings is also an essential element in an effective response because collective sense-making can help increase citizens'' voluntary compliance. Specifically, during COVID-19, digital governance helped improve disease detection through integrated databases of people''s health records and travel history, through more accurate contact tracing, and through active surveillance tracking for people under quarantine. doi = 10.1111/aspp.12541 id = cord-332292-n7k4va9k author = Yen, Yung-Feng title = Olfactory disorder in patients infected with SARS-CoV-2 date = 2020-08-20 keywords = SARS; covid-19 summary = Therefore, we conducted this cohort study to characterize the clinical course of olfactory disorder in COVID-19 patients in Taiwan. Two patients exhibited anosmia as the main symptom at the onset of SARS-CoV-2 infection, while one patient had hyposmia 4 days after the onset of COVID-19. 7 All patients with olfactory disorder in our study fully recovered their olfactory function before the RT-PCR results for SARS-CoV-2 turned negative. This cohort study was the first to characterize the clinical course of olfactory disorder in COVID-19 patients. 2 Limited COVID-19 cases in this study may preclude this J o u r n a l P r e -p r o o f analysis from estimating the precise prevalence of olfactory disorder in patients infected with SARS-CoV-2. However, consistent with a current report, 7 the findings of our study suggest that olfactory disorder is not an uncommon symptom in COVID-19 patients. Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study doi = 10.1016/j.jmii.2020.08.010 id = cord-275552-ijxxeo27 author = Yen, Zui-Shen title = How much would you be willing to pay for preventing a new dangerous infectious disease: A willingness-to-pay study in medical personnel working in the emergency department date = 2007-10-10 keywords = SARS; WTP summary = The objective of this study was to estimate the median amount of money ED personnel would be willing to pay for preventing nosocomial severe acute respiratory syndrome (SARS). 9 In this study, CVM was used to estimate the median amount emergency medical personnel would be willing to pay for a hypothetical vaccine to prevent developing nosocomial SARS. We used this study as an example to demonstrate that medical personnel would be willing to pay substantial monetary amounts to avert the risk of nosocomial SARS infection. However, we found that the median amount medical personnel in the ED would be willing to pay for a SARS vaccine was US $1,762, which was exceedingly high compared to the usual cost of a vaccine and equal to 14% of the 2002 Taiwan gross domestic product per capita (US $12,588). doi = 10.1016/j.ajic.2006.09.008 id = cord-355807-q3bngari author = Yepes-Pérez, Andres F. title = Uncaria tomentosa (cat’s claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling date = 2020-10-29 keywords = ACE-2; Proanthocyanidin; RBD; SARS summary = Molecular modeling was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (cat''s claw) focusing on the binding interface of the RBD–ACE-2 and the viral spike protein. tomentosa against focusing both on the binding interface of the RBD-ACE-2 and inside SARS-CoV-2 RBD spike protein, (2) simulations of ligand pathway of the best predicted compounds from step 1 to evaluate convenient entrance mechanism of the compounds to the binding site, (3) MD simulation to assess the stability of the best protein-ligand complexes from 1, (4) calculation of pharmacokinetics parameters for the most qualified compounds resulting from the previous parts of the docking protocol. Next, we used the cryo-EM structure of SARS-CoV-2 spike protein (PDB code: 6VYB) in their open state (Lipinski et al., 2012) to explore the potential inhibition of components of the cat''s claw, selecting ACE-2-binding pocket to this study. doi = 10.1080/07391102.2020.1837676 id = cord-351687-6otr8zl3 author = Yesilkaya, Umit Haluk title = Neuroimmune correlates of the nervous system involvement of COVID-19: A commentary date = 2020-05-27 keywords = SARS summary = • Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Strikingly, they postulated that enhanced inflammatory signalling and immune-mediated processes which are activated by SARS-CoV-2 might imitate the molecular architecture of self-directed immunity in the peripheral nervous system and might lead to Guillain Barre syndrome (GBS), an autoimmune disorder. It should be considered that neuropsychiatric manifestations related to human coronaviruses including SARS-CoV-2 might be associated with the involvement of both neuroimmune response and direct viral transmission.  Pathophysiological underpinnings of nervous system involvement of SARS-CoV-2 are yet to be elucidated  Neuropsychiatric manifestations related to COVID-19 might be associated with the involvement of both neuroimmune response and direct viral transmission. Severe Acute Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the Absence of Encephalitis in Mice Transgenic for Human ACE2 The neuroinvasive potential of SARS-CoV2 may be at least partially responsible for the respiratory failure of COVID-19 patients doi = 10.1016/j.jocn.2020.05.056 id = cord-253844-y6xdcf20 author = Yesudhas, Dhanusha title = COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics date = 2020-09-04 keywords = ACE2; CoV-2; SARS; human; protein; receptor summary = In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. SUMMARY: The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs. The sequence similarity between SARS-CoV-2 and SARS-CoV spike proteins explains the possibility of binding to the same receptor angiotensin converting enzyme 2 (ACE2) in the host cell [14] . In this review, we discuss the history of coronaviruses in both humans and animals, their transmissions, mechanism of host cell entry and the structural studies, explaining active and inactive receptor binding of spike protein and the key residues playing an important role in the receptor binding. During viral infection, spike protein (~ 1300 amino acid residues) is cleaved by host proteases into receptor binding subunit S1 and membrane fusion subunit S2. doi = 10.1007/s15010-020-01516-2 id = cord-305422-t8azymo7 author = Yi, Ye title = COVID-19: what has been learned and to be learned about the novel coronavirus disease date = 2020-03-15 keywords = COVID-19; China; Coronavirus; MERS; SARS; Wuhan; patient summary = The outbreak of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has thus far killed over 3,000 people and infected over 80,000 in China and elsewhere in the world, resulting in catastrophe for humans. The virus is highly homologous to the coronavirus (CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2003; thus, it was named SARS-CoV-2 by the World Health Organization (WHO) on February 11, 2020, and the associated disease was named CoV Disease-19 (COVID-19) [1] . Whenever possible, we will try to compare COVID-19 with SARS and another CoV-caused disease, Middle East respiratory syndrome (MERS, an outbreak in 2012). Due to the lack of experience with the novel CoV, physicians can mainly provide supportive care to COVID-19 patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other CoVs such as SARS-CoV and MERS-CoV and other viral diseases ( Table 2) . doi = 10.7150/ijbs.45134 id = cord-297918-840thddt author = Yilmaz, Umut title = COVID-19: neurologische Manifestationen: Was wir bisher wissen date = 2020-09-02 keywords = COVID-19; Fälle; SARS summary = So wurde in einer ersten Studie mit 214 COVID-19-Patienten aus Wuhan eine neurologische Beteiligung in 36,4 % der Fälle beschrieben [1] . Eine Studie mit 58 aufgrund eines akuten Lungenversagens ("acute respiratory distress syndrome", ARDS) intensivmedizinisch behandelten COVID-19-Patienten aus Straßburg berichtet von neurologischen Komplikationen in 84 % der Fälle. Im weiteren Verlauf der Pandemie sind in den letzten Monaten zahlreiche Fallberichte und Fallserien publiziert worden, die von unterschiedlichen neurologischen Manifestationen bei CO-VID-19-Patienten berichten. Daher wurden in einer aktuellen Metaanalyse von Fallberichten und Studien zu neurologischen Komplikationen standardisierte Falldefinitionen für die Wahrscheinlichkeit eines Zusammenhangs zur COVID-19-Infektion gefordert [7] . Eine PCR-Analyse des Liquors auf SARS-CoV-2 wurde in 4 Fällen durchgeführt und fiel bei einem Patienten positiv aus. In einer europäischen Studie mit 417 Patienten wird von Störungen des Geruchs-oder Geschmackssinnes in über 85 % der Fälle mit bestätigter Infektion berichtet [2] . Saggese und Kollegen berichten von einem 62-jährigen COVID-19-positiven Patienten mit multiplen vaskulären Risikofaktoren, der aufgrund eines Schlaganfalls behandelt wurde. doi = 10.1007/s00117-020-00748-5 id = cord-257403-jujrazsr author = Yin, Changchuan title = Genotyping coronavirus SARS-CoV-2: Methods and implications date = 2020-04-27 keywords = SARS; SNP summary = Abstract The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. In this study, we use the Jaccard distance of the SNP mutations of SARS-CoV-2 genomes to measure the dissimilarity of virus isolates. From the SNP profiles of SARS-CoV-2 strain, high-frequency mutations predominate in the virus isolations, therefore, these high-frequency mutations probably contribute to increased transmissibility. This study employs the substitutions variants in genotyping for understanding the evolution and transmission of SARS-CoV-2, however, structural variants including insertions, deletions, and copy number variation are critical for virus pathogenicity [40] and human pathology [41, 42] . In this study, the complete genomes of SARS-CoV-2 are used for SNP genotype calling. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1016/j.ygeno.2020.04.016 id = cord-283376-6wolrfvk author = Yin, M. title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study date = 2020-04-11 keywords = COVID-19; SARS; pregnant summary = For this retrospective cohort study, we reviewed clinical records, laboratory findings, and chest CT scans from 31 pregnant women and 35 non-pregnant women from Jan 28 to Feb 28, 2020 to evaluate the effects of SARS-CoV-2 infection during pregnancy. 4, [7] [8] [9] Although numerous studies have illuminated the clinical characteristics and outcomes of general population with COVID-19, 2, 8 little has been reported about the effects of SARS-CoV-2 infection on pregnant women. Considering that inflammatory cytokine storm was the main lethal factor of infectious pneumonia such as SARS and Middle East Respiratory Syndrome (MERS), 18-21 we compared the levels of interleukin (IL)-6 and some inflammatory indices including NLR, LMR, PLR, SII, ANRI and APRI, in pregnant and non-pregnant patients ( author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 12 However, we found a shorter interval from onset to hospitalization and severer COVID-19 in pregnant patients than non-pregnant patients with SARS-CoV-2 infection. doi = 10.1101/2020.04.07.20053744 id = cord-301978-9uu318tp author = Yin, Xiaoping title = A mild type of childhood Covid-19 - A case report date = 2020-03-27 keywords = SARS summary = This case is about a 9-year-old child diagnosed with COVID-19, with a history of epidemiology; SARS-CoV-2 nucleic acids testing was positive, while chest CT examination was negative. Because the child had lived in Wuhan two weeks before the onset of the disease and had a fever, SARS-CoV-2 infection was not excluded. Children and teenagers infected with SARS-CoV-2 have mild clinical symptoms and radiological manifestations [4] , and are rarely severe or critical. If children and adolescents have a history of living or traveling in epidemic areas within one to two weeks, or they have had contact with confirmed or suspected cases, or stay in an aggregated disease environment, the possibility of their infection with SARS-CoV-2 cannot be ruled out, even when their clinical symptoms are mild and there is no typical chest imaging manifestation. SARS-CoV-2 nucleic acid or gene testing is required for these patients. Preliminary study on clinical imaging features of 2019 novel coronavirus (2019-nCoV) pneumonia in Wuhan. doi = 10.1016/j.jrid.2020.03.004 id = cord-325172-a8ntxnmm author = Yip, Ming Shum title = Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus date = 2014-05-06 keywords = ADE; SARS; cell; infection; spike summary = More recently, we demonstrated that anti-Spike antibody potentiates infection of both monocytic and lymphoid immune cell lines, not only by SARS-CoVpp but also by replication-competent SARS-coronavirus [16] , thus providing evidence for a novel and versatile mechanism by which SARS-CoV can enter into target cells that do not express the conventional ACE2 virus receptor and are otherwise refractory to the virus. Finally, we have provided evidence that the intracellular signaling motifbut not the IgG binding motifof the FcγR is the key molecular determinant for triggering ADE of SARS-CoVpp. Our findings conclusively demonstrate that anti-spike serum promotes internalization of SARS-CoV by human macrophages. All the endodomain-truncated constructs (FcγRIIA-H.ΔIC, FcγRIIA-R.ΔIC and FcγRIIB.ΔIC, corresponding to constructs 2, 6, 11 respectively) were not susceptible to ADE of infection, indicating that binding of anti-Spike IgG-SARS-CoVpp immune complexes was not sufficient to mediate entry and that the signaling-competent endodomain was required. doi = 10.1186/1743-422x-11-82 id = cord-288692-v471648u author = Yip, Shea Ping title = Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date = 2005-10-01 keywords = PCR; SARS summary = title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus We designed a 1-step real-time quantitative RT-PCR assay for SARS-CoV with the use of 2 TaqMan probes, instead of 1 probe, hybridizing to the same PCR product to further improve the sensitivity. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Quantitation of severe acute respiratory syndrome coronavirus genome by real-time polymerase chain reaction assay using minor groove binder DNA probe technology Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested-polymerase chain reaction doi = 10.1373/clinchem.2005.054106 id = cord-261253-btwx2vxo author = Yip, Timothy T. C. title = Application of ProteinChip Array Profiling in Serum Biomarker Discovery for Patients Suffering From Severe Acute Respiratory Syndrome date = 2007 keywords = SARS; chip; serum summary = By protein chip array profiling technology, a number of serum biomarkers that might be useful in monitoring the clinical course of SARS patients were identified. The serum profiling spectra in SARS patients were acquired, baseline subtracted and analyzed in parallel with those from the control subjects by Ciphergen ProteinChip Software 3.0.2 with their peak intensities compared by a nonparametric two sample Mann-Whitney-U test. More than twelve peaks were differentially expressed in SARS patients with one at m/z of 11,695 (later identified to be serum amyloid A protein), which had increase in peak intensity correlating with the extent of SARS-coronavirus induced pneumonia as defined by a serial chest X-ray opacity score. In a recent article, the discovery of 12 upor downregulated serum biomarkers were reported in SARS patients by a novel protein chip array profiling approach (1014) with one biomarker appears to be useful in monitoring the extent of pneumonia (15) . doi = 10.1007/978-1-59745-304-2_20 id = cord-288398-vnra553x author = Yogeswaran, Athiththan title = Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study date = 2020-07-23 keywords = SARS summary = authors: Yogeswaran, Athiththan; Gall, Henning; Tello, Khodr; Grünig, Ekkehard; Xanthouli, Panagiota; Ewert, Ralf; Kamp, Jan C.; Olsson, Karen M.; Wißmüller, Max; Rosenkranz, Stephan; Klose, Hans; Harbaum, Lars; Lange, Tobias J.; Opitz, Christian F.; Waelde, Andrea; Milger, Katrin; Sommer, Natascha; Seeger, Werner; Ghofrani, Hossein Ardeschir; Richter, Manuel J. title: Impact of SARS-CoV-2 pandemic on pulmonary hypertension out-patient clinics in Germany: a multi-centre study This multi-centre study provides evidence for a negative influence of these restrictions on patient care in pulmonary hypertension expert referral centres. The impact of SARS-CoV-2 associated restrictions on PH out-patient departments in Germany, however, has not been systematically evaluated. This study provides evidence for the significant impact of SARS-CoV-2 and the related restrictions on the medical care of patients with (suspected and subsequently confirmed) PH in Germany. Of note, the relative fraction of patients with subsequently initiated PH-specific therapy remained constant during the SARS-CoV-2 pandemic. doi = 10.1177/2045894020941682 id = cord-310096-a242g5kg author = Yokota, I. title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-08-14 keywords = PCR; SARS summary = Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (self-collected saliva and NPS) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. doi = 10.1101/2020.08.13.20174078 id = cord-278045-hr3r17mz author = Yokota, Isao title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-09-25 keywords = NPS; SARS summary = METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (NPS and self-collected saliva) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. doi = 10.1093/cid/ciaa1388 id = cord-267476-j59tm40d author = Yong, Sarah Ee Fang title = Connecting clusters of COVID-19: an epidemiological and serological investigation date = 2020-04-21 keywords = COVID-19; Church; SARS summary = We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection. Serological testing had a crucial role in establishing a link between clusters, showing its use in identifying convalescent COVID-19 cases and supporting epidemiological investigations. In our epidemiological investigation, we used RT-PCR and serological testing to diagnose cases of COVID-19 and establish links between clusters. This investigation shows how SARS-CoV-2 serological analysis (ELISA detecting IgG and VNT detecting neutralising antibodies), in addition to use of traditional epidemiological methods, was important in establishing links among locally transmitted COVID-19 cases and tracing the transmission chain to an imported source. doi = 10.1016/s1473-3099(20)30273-5 id = cord-304101-b9na3yf6 author = Yong, Suh Kuan title = Molecular Targets for the Testing of COVID‐19 date = 2020-05-18 keywords = COVID-19; SARS summary = This diagnostic panel is working with Applied Biosystems 7500 Fast DX Real-Time PCR Instrument with SDS 1.4 software; 2) "New coronavirus nucleic acid assay" which targeted on ORF1ab and N genes was developed by Chinese National Institute for Viral Disease Control and Prevention; 3) Molecular test kits from four companies such as Seegene Inc., Kogene Biotech Co. Ltd., Sd Biosensor Inc., and Solgent Co. were approved by Ministry Food and Drug Safety and Korea Centers for Disease Control and Prevention which are now widely being used in South Korea. A probe, usually a specific antibody, is needed before a successful viral protein detection method can be developed. As aforementioned, the serology testing of COVID-19 is not targeting the virus itself but the antibodies such as immunoglobulin M (IgM) and immunoglobulin G (IgG) induced following viral infection. Serology testings targeting on viral-induced antibodies are given different information as those for viral RNA and proteins from SARS-CoV-2. doi = 10.1002/biot.202000152 id = cord-304550-6j1pb1pu author = Yongchen, Zhang title = Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients date = 2020-05-02 keywords = SARS; covid-19 summary = Here, we conducted a serial investigation on 21 individuals infected with SARS-CoV-2 in two medical centres from Jiangsu Province, including 11 non-severe COVID-19 patients, and 5 severe COVID-19 patients and 5 asymptomatic carriers based on nucleic acid test and clinical symptoms. In this respective study, we serially analysed the virus RNA test results in swab samples, along with anti-SARS-CoV-2 IgM and IgG responses among 21 COVID-19 patients at the Second Hospital of Nanjing and the Affiliated Hospital of Xuzhou Medical University in Jiangsu Province, China. Our serial SARS-CoV-2 RNA testing identified a prolonged viral shedding for asymptomatic cases compared to COVID-19 patients, suggesting the importance of early identification and timely quarantine for these asymptomatic carriers. It is possible that significantly high level of SARS-CoV-2 viral load observed in severe cases [8, 9] drives an early antibody response produced by immediate activation of extrafollicular B cells during acute infection [10, 11] . doi = 10.1080/22221751.2020.1756699 id = cord-289598-t8upoq9a author = Yoon, Jane C title = COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date = 2020-09-08 keywords = CoV-2; PEH; SARS summary = BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. Risk of SARS-CoV-2 infection, the virus that causes COVID-19, may be higher among people experiencing homelessness (PEH) because of challenges in preventing respiratory disease transmission in congregate shelter settings. Our finding of decreased prevalence in four shelters during repeat testing is consistent with reports from skilled nursing facilities and correctional facilities, supporting the use of universal (facility-wide) testing for early identification and isolation of those with positive SARS-CoV-2 as a strategy to interrupt transmission in congregate settings [23] [24] [25] . doi = 10.1093/cid/ciaa1340 id = cord-258792-4lakgpxp author = Yoon, Sung‐Won title = Sovereign Dignity, Nationalism and the Health of a Nation: A Study of China''s Response in Combat of Epidemics date = 2008-04-08 keywords = AIDS; China; Health; SARS; chinese; disease summary = Unless and until the Chinese leadership examines the nationalistic element embedded in their approach towards growing disease Sung-Won Yoon: Sovereign Dignity, Nationalism and the Health of a Nation epidemics and globalising health challenges, China''s ascendance to great power status will actually be harmed rather than helped. A major factor behind the government''s recent change in its attitude towards the AIDS epidemic seemed to be the outbreak of SARS in China in Studies in Ethnicity and Nationalism: Vol. 8, No. 1, 2008 2003, which exposed the dangers of not reacting to emerging infectious diseases. It is argued that global health governance may influence the nation''s response to the threats posed by emerging infectious diseases such as SARS or AIDS as a mode of building political compromises but does not considerably alter the nation''s behaviour, at least for China. doi = 10.1111/j.1754-9469.2008.00009.x id = cord-283249-pk5sc2ca author = Yoshida, Wataru title = Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers date = 2006-09-15 keywords = AES; SARS; dna summary = The structural change of the enzyme-inhibiting aptamer site induces a change in the inhibitory activity of the AES, which enables us to detect a target molecule by measuring the enzymatic activity of the whole aptameric complex in a homogeneous solution without bound/free separation. The stem-and-loop structure bearing the probe DNA sequence was inserted into the 3 0 -end T-T loop of the G-quartet structure of the 31-mer thrombin-inhibiting aptamer. We also inserted two additional T bases between the thrombin-inhibiting aptamer and the stem-and-loop structure in all AESs except AES 1, since the diameter of the DNA double helix is different from the distance between two Gs of the G-quartet structure (approximately 17 and 20 Å , respectively). For the measurement of the CD spectra of AES SARS 1, a stem-and-loop structure to be inserted into the 31-mer thrombin-inhibiting aptamer on AES SARS 1 was synthesized. doi = 10.1016/j.bbrc.2006.07.069 id = cord-321858-c5m4dj9m author = Yoshizawa, Shin-ichiro title = Evaluation of an octahydroisochromene scaffold used as a novel SARS 3CL protease inhibitor date = 2020-02-15 keywords = 3CL; SARS; Sharpless summary = The inhibitory activities of the diastereoisomerically-pure inhibitors (3a–d) strongly suggest that a specific stereo-isomer of the octahydroisochromene scaffold, (1S, 3S) 3b, directs the P1 site imidazole, the warhead aldehyde, and substituent at the 1-position of the fused ring to their appropriate pockets in the protease. To access whether the octahydroisochromene derivatives containing substituents at the 1-position of the ring system function as a novel inhibitor scaffold, the inhibitory activity of compounds 16a-d toward SARS 3CL pro was preliminary evaluated by the IC 50 values obtained using the procedure described below. To determine the configuration of each diastereomer (13a and 13b), the major product obtained after the asymmetric dihydroxylation reaction using (DHQ) 2 Pyr as the chiral ligand (Table 2, entry 3) was isolated and purified using preparative thin layer chromatography (PTLC). doi = 10.1016/j.bmc.2019.115273 id = cord-282372-nmii30mc author = Youk, Jeonghwan title = Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date = 2020-07-10 keywords = Data; Fig; RNA; SARS; cell summary = Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . doi = 10.1101/2020.07.10.194498 id = cord-345679-ydwcp75s author = Younas, Amber title = SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN date = 2020-08-24 keywords = SARS; blood summary = title: SEROPREVALENCE OF SARS-COV-2 ANTIBODIES AMONG HEALTHY BLOOD DONORS IN KARACHI, PAKISTAN Despite the prevailing pandemic, there are no recommendations available as yet for testing SARS-CoV-2 antibodies as part of blood screening. In our study, we conducted specific serological testing (total antibodies) to identify prevalence of SARS-2-CoV antibodies among the healthy blood donors who visited Blood Bank at our Institute.Their results were compared with specific serologic results of blood donors that came before the onset of pandemic(October, 2019). In July 2020, we tested 300 healthy blood donors, 113 donors (37.7%) were found to be reactive for anti-SARS-CoV-2antibodies. Another study in Northern France reported 25.8% of population positive for COVID-19 antibody(19)but they also did not exclude previously symptomatic cases. To conclude, seroprevalence of SARS-COV-2 antibodies has increased in Pakistan over a period of time and could help in recognizing the actual number of COVID-19 cases. The prevalence of antibodies to SARS-CoV-2 among blood donors in China.medRxiv doi = 10.1016/j.transci.2020.102923 id = cord-258724-1qhen1bj author = Young, Barnaby E title = Viral dynamics and immune correlates of COVID-19 disease severity date = 2020-08-28 keywords = PCR; SARS summary = METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). In this multi-pronged study, we describe the serologic evolution, inflammatory response and pattern of viral shedding and viability in patients with virologically confirmed COVID-19 in Singapore, and analyse the contributions these make to severe infections. Serum collected during the acute and convalescent phases of infection were tested for SARS-CoV-2 receptor binding domain specific IgM and IgG using capture ELISA (details in Supplementary Appendix). The central role of the immune response to SARS-CoV-2 in COVID-19 was evident from the strong correlation between disease severity and levels of IgG/IgM and inflammatory immune mediators in our cohort. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study doi = 10.1093/cid/ciaa1280 id = cord-300923-5cyxr98s author = Younger, David S title = Postmortem Neuropathology in Covid‐19 date = 2020-10-23 keywords = SARS summary = This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid‐19) due to severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) from among 250 reported patients succumbing to Covid‐19 illness (1‐7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid‐19 illness, and are important in the development of effective treatment strategies. This study concerns the clinicopathologic correlation of 50 decedents of 2019 coronavirus disease (Covid-19) due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from among 250 reported patients succumbing to Covid-19 illness (1-7) who underwent detailed postmortem neuropathological studies. These cases provide a more complete picture of Covid-19 illness, and are important in the development of effective treatment strategies. As shown in Table 1 , older age, male gender, increased serum cytokine and pro-coagulation markers, and critical care hospitalization for ≤10 days prior to death characterized the cohort. Neuropathologic features of four autopsied COVID-19 patients The spectrum of pathological findings in coronavirus disease (COVID-19) and the pathogenesis of SARS-CoV-2 doi = 10.1111/bpa.12915 id = cord-294335-qnu19ru5 author = Yousaf, Anna R title = A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date = 2020-07-28 keywords = PCR; SARS summary = We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . doi = 10.1093/cid/ciaa1072 id = cord-352256-qxdakdk0 author = Yousefi, Bahman title = A global treatments for coronaviruses including COVID‐19 date = 2020-05-11 keywords = ACE2; COVID-19; MERS; SARS summary = Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Chloroquine inhibits SARS-CoV entry, which exerts its inhibitory effect by altering glycosylation of the ACE2 receptor and spike protein. | 5 in a MERS-CoV rhesus macaque model were promising, with the results of the trial and the effect of ribavirin and IFN (either α2a or β1) on MERS-CoV infected patients it was different, however, ribavirin lowers hemoglobin concentrations in respiratory patients and therefore reduces its potential as an antiviral against SARS-CoV-2 (Arabi et al., 2017; Falzarano et al., 2013) . doi = 10.1002/jcp.29785 id = cord-298242-iuskpoug author = Yu, Alvin title = A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date = 2020-10-02 keywords = SARS; protein summary = Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. In this paper, we construct a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion from the currently available structural and atomistic simulation data on SARS-CoV-2 proteins. In this work, we detail several of our CG methods used to iteratively develop a CG model for the full SARS-CoV-2 virion, in which molecular interactions between CG particles are derived using a combination of phenomenological, experimental, and atomistic simulation approaches. In recent cryo-EM images of SARS-CoV-2 particles, the S1 domain of the S protein was found to transiently open and close in order to bind the ACE-2 receptor (3, 5) , which are subtle conformational changes that are difficult to sample in atomistic simulations. doi = 10.1101/2020.10.02.323915 id = cord-340635-8wki7noy author = Yu, Bin title = Innate and adaptive immunity of murine neural stem cell-derived piRNA exosomes/microvesicles against pseudotyped SARS-CoV-2 and HIV-based lentivirus date = 2020-11-13 keywords = NSC; SARS summary = Through testing pseudotyped SARS-CoV-2 and HIV-based lentivirus, this study reports that exosomes/microvesicles (Ex/Mv) isolated from murine hypothalamic neural stem/progenitor cells (htNSC) or subtype htNSCPGHM as well as hippocampal NSC have innate immunity-like actions against these RNA viruses. We then measured some of these piRNAs in NSC Ex/Mv (using htNSC PGHM and J o u r n a l P r e -p r o o f hpNSC as the representative) compared to the levels in MSC Ex/Mv. As shown in Fig. S2B and S3, most of these piRNAs were present in these NSC Ex/Mv but were much less detectable in MSC Ex/Mv. Our additional assays showed that htNSC PGHM were comparable or slightly stronger than htNSC in producing these piRNAs. Thus, based on the information from wildtype and pseudotyped SARS-CoV-2, NSC Ex/Mv contain piRNAs against the genomic sequences of both viruses, although these NSC were not previously exposed to either virus, suggesting that mouse species has evolved to establish large antiviral piRNA libraries in NSC Ex/Mv. We asked if an initial pre-exposure of a specific virus to NSC could lead to an enhancement or enrichment of specific antiviral piRNAs in NSC Ex/Mv. Thus, we treated these NSCs with pseudotyped SARS-CoV-2 virus for 2 generations, and then maintained them under normal culture for about 5 generations. doi = 10.1016/j.isci.2020.101806 id = cord-309517-yh4d414y author = Yu, Chao title = Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study date = 2020-08-12 keywords = SARS; asymptomatic; patient summary = In addition, some asymptomatic patients can develop symptoms during hospitalization [6] , and the characteristics of these presymptomatic patients and their independent risk factors have not been addressed yet. Therefore, in the present study, we investigated 79 asymptomatic patients to analyze their clinical characteristics, disease progression, and recurrence of positive SARS-CoV2 RNA after discharge. No intergroup differences were observed in other radiographic characteristics, and patchy shadowing was the most common abnormality Meanwhile, the asymptomatic carriers had normal levels of other markers related to liver damage, renal dysfunction, inflammation, and coagulation, which were comparable with those of the symptomatic patients. Although the presymptomatic patients developed symptoms during hospitalization, these patients had similar viral RNA shedding duration compared with the asymptomatic carriers (14 days [IQR 7-25 days] vs. In our study, the recurrence rate of positive SARS-CoV-2 nucleic acid in the asymptomatic carriers after discharge was lower than that in the symptomatic patients (10.12% vs. doi = 10.1080/21505594.2020.1802194 id = cord-265723-6k8196p2 author = Yu, Chengjun title = Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis date = 2020-06-25 keywords = IFN; SARS; study summary = title: Evaluation of safety, efficacy, tolerability, and treatment-related outcomes of type I interferons for Human coronaviruses (HCoVs) infection in clinical practice: An updated critical systematic review and meta-analysis Therefore, we conducted this updated systematic review and meta-analysis to recapitulate relevant studies to evaluate the safety, efficacy, tolerability and treatment-related outcomes of type I IFNs for coronavirus infection in clinical practice, with expectation to provide more robust evidence whether IFNs should be served as first-line agents for coronavirus infection, including the SARS-CoV-2. Each included article was thoroughly reviewed, and the following baseline information were extracted (Table 1) : first author, publication year, region, study type, participants, diagnostic method of coronavirus, data collection method, time from admission to treatment start, time from diagnosis to treatment start, primary endpoints, and treatment-related adverse effects. Critically ill defined as coronavirus-infected patients with other severe comorbidities, respiratory distress or failure, directly or indirectly transferred to ICU, needing intubation, mechanical ventilation, or extracorporeal membrane oxygenation (ECMO), when admitted to primary treatment. doi = 10.1016/j.intimp.2020.106740 id = cord-339934-g6ufz29l author = Yu, Hai-qiong title = Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients date = 2020-05-13 keywords = SARS summary = In the case of respiratory infection, while IgM and IgG isotypes have been the primary emphasis in characterizing immunity, mucosal and systemic IgA responses that may play a critical role in the disease pathogenesis, have received much less attention. This pattern of humoral immune response is different in case of SARS-CoV infection, in which IgM and IgA showed similar chronological profiles in terms of both seroconversion time and antibody titres [5] , in line with the knowledge that viremia is common in SARS. Upregulated IgA production may be the result of increased levels of TGF-β and IL-10 that promote antibody switching in SARS-CoV-2 infection. Considering the roles of mucosal and systemic IgA in COVID-19, inducing IgA production, e.g. using Lactoferrin to activate canonical TGF-β signaling [13] , or retinoic acid to enhance lactoferrin-induced IgA responses [14] , has been proposed as novel therapies for severe COVID-19. doi = 10.1183/13993003.01526-2020 id = cord-299122-djfj4262 author = Yu, Hua title = Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() date = 2007-03-15 keywords = SARS; cell; epitope summary = title: Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice() Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. Selection of SARS-Coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice ☆ Therefore, in the present study, we screened and identified specific B cell epitopes of SARS-CoV using phagedisplayed peptide library, Fab fragments from anti-SARS-CoV immunoglobulin G (IgG) and normal human IgG as targets, and an improved biopanning procedure. Splenic lymphocytes from mice on day 42 still exhibited significant proliferative responses to specific antigen, demonstrating that the four epitope-based peptides induced long-term immune responses (data not shown). doi = 10.1016/j.virol.2006.09.016 id = cord-281726-s1o5l7ns author = Yu, Ignatius T. S. title = Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date = 2005-05-01 keywords = March; SARS summary = We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Layout of the ward where the index case patient with severe acute respiratory syndrome (SARS) was hospitalized, showing the location of beds, air supply diffusers, and exhaust grilles. The relationships between SARS and bed location, date of exposure, duration of exposure, smoking To explore the possible roles of HCWs in the outbreak of infection, all nurses working on the ward during the study period were interviewed in person between 28 March and 8 April with a questionnaire to collect information on symptoms, contacts, and working practices. The analysis of the temporal-spatial spread of SARS from the index case patient to other inpatients in the ward suggested that airborne spread through virus-laden aerosols possibly played an important role. doi = 10.1086/428735 id = cord-338359-pd4bfjet author = Yu, J. title = Risk assessment of admission procedures for cancer patients during the convalescence of COVID-19 date = 2020-09-30 keywords = SARS; covid-19 summary = Conclusions: Unbiased proteomic profiling of COVID-19 patient serum identified a panel of candidate protein biomarkers that associate with tocilizumab treatment response as well as the ensuing course of the disease. Background: There are limited data on cancer patients (pts) and the novel coronavirus (SARS-CoV2) respiratory disease (COVID-19). We aim to evaluate the frequency of ILI in cancer pts during the pandemic, and to identify high-risk subjects to test for COVID-19. Results: Overall, 562 pts were enrolled: 13 (2%) pts had a positive SARS-CoV2 swab, none of which performed on the basis of triage procedures or questionnaires, rather detected through telephone communications and triage; 52 (9%) pts reported suspect symptoms and/or laboratory tests. The incidence of both COVID-19 diagnosis (2%), and SARS-CoV2 Ab positivity in pts tested on the basis of suspect symptoms (<1%), were similar to those observed in the general population. doi = 10.1016/j.annonc.2020.08.1759 id = cord-253179-pi5uq90z author = Yu, Jing title = SARS-CoV-2 transmission in cancer patients of a tertiary hospital in Wuhan date = 2020-02-25 keywords = SARS summary = Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Consequently, for cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. 3 Among the different disease types, cancer patients are often recalled to the hospital for treatment and disease surveillance, and therefore, they may be at an elevated risk of contracting SARS-CoV-2. https://doi.org/10.1101/2020.02.22.20025320 doi: medRxiv preprint real-time reverse transcription polymerase chain reaction assay for SARS-CoV-2 and eight by the clinical criteria of fever and radiological computed tomography changes; Table 1 ). For cancer patients who require treatment, proper isolation protocols must be in place to mitigate the risk of SARS-CoV-2 infection. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China doi = 10.1101/2020.02.22.20025320 id = cord-319337-w9zyshzb author = Yu, Jingyou title = DNA vaccine protection against SARS-CoV-2 in rhesus macaques date = 2020-05-20 keywords = Fig; SARS summary = Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. Following vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log(10) reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with sham controls. S3 and S4), including 1.92 and 2.16 log 10 reductions of median peak viral RNA in BAL and NS, respectively, in S vaccinated animals compared with sham controls (P = 0.02 and P = 0.04, two-sided Mann-Whitney tests) ( fig. Viral RNA assays were confirmed by PFU assays, which similarly showed lower infectious virus titers in S vaccinated animals compared with sham controls (P = 0.04, two-sided Mann-Whitney test) ( fig. In this study, we generated a series of prototype DNA vaccines expressing various S immunogens and assessed protective efficacy against intranasal and intratracheal SARS-CoV-2 challenge in rhesus macaques. doi = 10.1126/science.abc6284 id = cord-332300-5osg046o author = Yu, Luo title = Catching and killing of airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system date = 2020-07-07 keywords = Fig; SARS summary = Traditional air-conditioner filters based on fiberglass or aluminum (Al) mesh are difficult to heat or have large pores (about 1 centimeter in size), so they cannot effectively catch and kill the virus contained in aerosols (generally smaller than 5 µm in size) [23] or other airborne highly infectious agents, such as anthrax spores. In order to realize a filter for preventing the spread of SARS-CoV-2 and anthrax spores, here we designed and fabricated a filter device consisting of folded pieces of Ni foam in multiple compartments connected electrically in series to efficiently increase the resistance to a manageable level so that a temperature up to 250 was able to be achieved, and found that the filter device exhibits almost 100% ability to catch and kill aerosolized SARS-CoV-2 and anthrax spores in air passed once through the Ni foam heated up to 200 (temperature optimization will be addressed in a future study). doi = 10.1016/j.mtphys.2020.100249 id = cord-330324-4hqhty5o author = Yu, Meng title = Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species date = 2008-02-29 keywords = SARS; antibody; western summary = title: Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. In this study we identified and characterized the major immunodominant domains of the SARS-CoV N and S proteins recognized by different animal species, and then developed competition ELISAs based on these findings. The specificity of the antibody was further confirmed using Western blot against viral antigen (data not shown) and IFAT using SARS-CoV infected Vero cells. One of the main aims of this study was to assess the feasibility of developing a competition ELISA for detection of SARS-CoV antibodies from different animal species. Inhibition of binding of mono-specific chicken antibodies to SARS-CoV by sera from different species. doi = 10.1016/j.jim.2007.11.009 id = cord-333712-sdtxi8xw author = Yu, Ping title = Geographical structure of bat SARS-related coronaviruses date = 2019-02-06 keywords = SARS summary = In 2005, the discovery of novel CoVs related to human SARS-CoVs in Chinese horseshoe bats (genus Rhinolophus), named SARS-related coronaviruses (SARSr-CoVs), provided new clue that bats may be the natural host for SARS-CoV (Lau et al., 2005; Li et al., 2005) . SARS-CoV and SARSr-CoVs belong to lineage B of genus Betacoronavirus in the family Coronaviridae and share the same genomic organization with other coronaviruses, including genes coding for 16 nonstructural proteins (nsp, in ORF1ab domain), the structural proteins like spike protein (S), envelope (E), membrane (M), nucleocapsid (N) and other several genes (Perlman and Netland, 2009; Woo et al., 2009) . Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China doi = 10.1016/j.meegid.2019.02.001 id = cord-323882-127c5bve author = Yu, Wen-Bin title = Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data date = 2020-05-17 keywords = China; SARS; Wuhan summary = Of the 93 genomes of SARS-CoV-2, 39 (41.93%) were from infected patients in 11 countries outside China and encoded 31 haplotypes (H d =0.987±0.009 (SD), P i =0.16×10 -3 ± 0.01×10 -3 ), with 27 nationally/regionally private haplotypes. Three different datasets were used to infer evolutionary networks, which consistently supported H13 and H38 as the potentially ancestral haplotypes, i.e., the outgroup bat-RaTG13-CoV could connect to both H13 and H38, or H38 alone, or through a medium vector mv1 (an intermediate host or the first infected humans) connected to both H13 and H38 by single mutations at positions 18067 (S, synonymous substitution) and/or 29102 (S), referring to the numbering of the alignment length 29 910 bp ( Figure 5 ). To clarify the exact origins of these haplotypes outside China, we need more epidemiological investigative efforts and more SARS-CoV-2 genomic data from patients at the early stage of transmissions. doi = 10.24272/j.issn.2095-8137.2020.022 id = cord-330743-o11d0aa1 author = Yu, Xi title = Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date = 2020-05-25 keywords = DENV; SARS; ZIKV summary = Herein, we identified 2 secreted bacterial lipases from a Chromobacterium bacterium, named Chromobacterium antiviral effector-1 (CbAE-1) and CbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). Incubation of the culture supernatant but not the bacterial lysates resulted in significant suppression of DENV ( Figure 1B ) and ZIKV ( Figure 1C ) infectivity in Vero cells, indicating that an extracellular effector(s) secreted by Csp_BJ was responsible for viral inhibition. DENV, ZIKV, HSV-1 and SARS-CoV-2 virus stocks were diluted to 50 plaque-forming units (pfu) per ml and incubated untreated or with a serial dilution of the CbAEs in five-fold steps at 37°C for 1 hr before being added onto Vero cell monolayers for 2 hr of infection. doi = 10.1101/2020.05.22.109900 id = cord-295603-mk9oartb author = Yu, Xiaoqi title = Retrospective detection of SARS-CoV-2 in hospitalized patients with influenza-like illness date = 2020-07-05 keywords = SARS; covid-19 summary = However, it is unclear whether there has been cryptic transmission before these early officially confirmed cases, we therefore retrospectively screened for the SARS-CoV-2 RNA in 1271 nasopharyngeal swab samples, as well as the prevalence of IgM, IgG, and total antibodies against SARS-CoV-2 in 357 matched serum samples collected from hospitalized patients with influenza-like illness between 1 December 2018 and 31 March 2020 in Shanghai Ruijin Hospital. Additionally, among 6662 patients with influenza-like illness from 1 December 2017 to 31 March 2020, the overall number of patients positive for influenza and other respiratory viruses during the COVID-19 period decreased significantly when compared with that in the same period of the last two years, reflecting that public health interventions can effectively control the spread of common respiratory viruses. The nasopharyngeal swab samples for this study were collected from 1271 hospitalized patients with influenza-like illness from 1 December 2018 to 31 March 2020 in Ruijin Hospital (Shanghai, China). doi = 10.1080/22221751.2020.1785952 id = cord-295375-nakxfhxk author = Yu, Yang title = Assessment of the quality of systematic reviews on COVID‐19: A comparative study of previous coronavirus outbreaks date = 2020-04-28 keywords = MERS; SARS summary = In this comparative study, we investigated the present status of conducting SRs on COVID-19, MERS, and SARS, appraised the methodological quality of these SRs using the a measurement tool to assess systematic reviews (AMSTAR 2), and performed a preliminary examination of the potential risk factors associated with the quality of SRs, with the aim of providing suggestions from the aspects of methodological quality for conducting and using SRs during the COVID-19 pandemic. AMSTAR, a measurement tool to assess systematic reviews; MA, meta-analysis quality of most SRs is unsatisfactory, and those on COVID-19 have higher risks of poor quality, despite the rapid actions taken to conduct SRs. Teams that may want to conduct a SR should focus on the study design and focus on improving the quality of the SR. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis doi = 10.1002/jmv.25901 id = cord-282058-it0ojdk3 author = Yu, Yuanqiang title = Coronavirus Disease 2019 (COVID-19) in Neonates and Children From China: A Review date = 2020-05-15 keywords = COVID-19; China; CoV-2; SARS; Wuhan summary = References for this review were identified through searches of PubMed for articles published from January 1, 2003, to May 1, 2020, by use of the terms "coronavirus, " "neonate, " "children, " "COVID19, " and "SARS-CoV-2." Relevant articles published between 2003 and 2020 were identified through searches in the authors'' personal files. The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The World Health Organization (WHO) subsequently named the novel coronavirus pneumonia Coronavirus Disease 2019 (COVID-19) and named the virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The symptoms of COVID-19 appear to be less severe in infants and children than in adult patients, similar to the SARS-CoV infection (15) (16) (17) . Of the 34 pregnant women who were confirmed with the SARS-CoV-2 infection in multiple hospitals in Wuhan, including one pregnant woman with a negative nucleic acid test result, 30 had a fever and 16 had a cough (54) (55) (56) (57) . doi = 10.3389/fped.2020.00287 id = cord-317563-mu47vvma author = Yuan, Chunhui title = Viral loads in throat and anal swabs in children infected with SARS-CoV-2 date = 2020-06-09 keywords = SARS summary = Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay on anal swabs was recently reported to be persistently positive even after throat testing was negative during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Furthermore, viral loads detected on both throat and anal swabs also showed no significant difference (P = 0.9511) and correlation (Pearson r = 0.0434, P = 0.8406), and exhibited an inconsistent kinetic change through the course of SARS-CoV-2 infection. These findings revealed that RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune state in paediatric patients. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay has been widely used for clinical diagnosis and SARS-CoV-2 has been detected in specimens from multiple sites, including bronchoalveolar lavage fluid, sputum, nasal, anal, and throat swabs of patients with COVID-19 [2] . In conclusion, RT-PCR-testing on throat and anal swabs showed significant difference for monitoring SARS-CoV-2 infection and correlated with different immune states in paediatric patients. doi = 10.1080/22221751.2020.1771219 id = cord-273126-gceffbfp author = Yuan, Kehu title = Suppression of SARS-CoV entry by peptides corresponding to heptad regions on spike glycoprotein date = 2004-07-02 keywords = HR1; HR2; SARS summary = Subsequently, the highly conserved heptad repeat (HR) regions (HR1 and HR2) in the glycoprotein interact with each other to form a six-helix bundle structure, which facilitates the juxtaposition of the virus and cell membranes, leading to membrane fusion [9] . Based on the fusion mechanism described above, we used an approach that was successfully used for studying other enveloped viruses, such as HIV-1 and MHV, to identify the potent inhibitor for virus entry [16, 18, 19, 25] . Screened through the pseudotyped virus infection assay [7, [26] [27] [28] and validated with wild-typed virus infection, two peptides were identified, HR1-1 and HR2-18, which were able to inhibit the SARS-CoV entry process. Although we designed a series of peptides overlapping the HR2 region, only one peptide HR2-18 was identified to inhibit the entry of SARS-CoV with low inhibitor activity. doi = 10.1016/j.bbrc.2004.05.046 id = cord-330473-f03ka7bd author = Yuan, Meng title = A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date = 2020-03-14 keywords = SARS summary = In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. ONE SENTENCE SUMMARY Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain. A recent study has shown that CR3022, which is a human 49 neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4), Nonetheless, despite having a 70 high conservation in the epitope residues, CR3022 Fab binds to SARS-CoV RBD (K d = 1 71 nM) with a much higher affinity than to SARS-CoV-2 RBD (K d = 115 nM) (Table 1 Previous cryo-EM studies have also shown that the recombinant SARS-CoV S 121 protein is mostly found in the none-"up", single-"up", or double-"up" conformations (19, 122 21), but rarely in the triple-"up" conformation, even with ACE2 receptor bound (21, 22) . doi = 10.1101/2020.03.13.991570 id = cord-342902-y1v8wzxq author = Yuan, Shuofeng title = Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date = 2020-10-07 keywords = COVID-19; CoV-2; RNA; SARS; clofazimine; figure summary = Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. We found that co-application of clofazimine and remdesivir impacts SARS-CoV-2 replication in a manner that extends beyond the additive combinatorial activity predicted by the Bliss independence model (maximal Bliss Synergy Score of 44.28; Figure 5a , Extended Data Figure 2) , and indicates these two drugs harbor a synergistic antiviral relationship. doi = 10.21203/rs.3.rs-86169/v1 id = cord-351489-tzmev77c author = Yuan, Shuofeng title = Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date = 2020-06-10 keywords = AM580; IFN; RNA; SARS; antiviral summary = They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. In this primary screening, chloroquine, lopinavir, and remdesivir which were recently reported to have anti-SARS-CoV-2 activity, exhibited about 1.3-2.0 log10 copies/mL reduction in viral RNA load ( Figure 1 ). In comparison, recombinant IFN-β demonstrated the most potent anti-SARS-CoV-2 activity, with Avonex (IFN-β1a), Rebif (IFN-β1a), and Betaferon (IFN-β1b) each achieving about 3 log10 copies/mL reduction in viral load. In our primary screening using a fixed antiviral agent concentration and virus inoculum, we identified recombinant IFNs and lipogenesis modulators to be the most potent anti-SARS-CoV-2 agents among 22 broad-spectrum antivirals. doi = 10.3390/v12060628 id = cord-320054-wqpr8v3p author = Yuan, Xianlin title = The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date = 2020-08-24 keywords = SARS summary = In this study, we predict neutralizing antibody recognition sites (B cell epitopes) of the prototype S protein of SARS-COV2, along with several common variants using bioinformatics tools. To explore these questions, here we report 94 to used these immuno-bioinformatic tools from the IEDB and related resources to 95 predict the B cell epitopes of S protein from the prototype and mutated strains of 96 SARS-CoV-2 and compare the changes of the likely epitope sites from dominant and 97 rare mutations of S protein. The major variation sequences were available 409 from The Global Initiative for Sharing All Influenza Data (GISAID) [26] and GenBank 446 We used the sequence from early onset SARS-CoV-2 as the wildtype or prototype and 447 the recent variant virus as mutation strains to predict the B-cell epitopes of S protein. doi = 10.1101/2020.08.24.264895 id = cord-289377-2vqqabum author = Yubero, P. title = Evidence for immunity to SARS-CoV-2 from epidemiological data series date = 2020-07-24 keywords = COVID-19; SARS; immunity summary = We then estimate the capacity of EAKF techniques to infer the duration of this memory and then apply this approach to mortality time series from New York City, discerning immunity times against SARS-CoV-2 with reasonable accuracy. (B) The value of the synthetic infection rate β synth (dotted line) is captured by the protocol β model (blue) after some data assimilation steps, and prior to the pandemic peak. . https://doi.org/10.1101/2020.07.22.20160028 doi: medRxiv preprint uity of a strong reduction of the infection rate during the initial days of the epidemic in all data sets that we studied (results of Belgium, Spain and France are available in Fig. S4 ). In our case, the time-dependent state variables are the infection rate β , the immunity memory τ and the population in each compartment of the model. doi = 10.1101/2020.07.22.20160028 id = cord-252771-6kwfulqe author = Yue, Jing-Li title = Mental health services for infectious disease outbreaks including COVID-19: a rapid systematic review date = 2020-11-05 keywords = COVID-19; China; SARS; health; mental summary = Group-based cognitive behavioral therapy, psychological first aid, community-based psychosocial arts program, and other culturally adapted interventions were reported as being effective against the mental health impacts of COVID-19, Ebola, and SARS. Specifically, mental health professionals including psychiatrists, psychiatric nurses, and psychologists were deployed to provide psychological counseling and support for vulnerable populations (e.g. frontline healthcare workers, confirmed COVID-19 patients, suspected COVID-19 cases and their families) in China and for people in quarantine in South Korea. For example, group-based CBT (Waterman et al., 2018; Waterman et al., 2019) , PFA, PTL (Decosimo et al., 2019) , culturally adapted interventions such as SMART (Ng et al., 2006) , ultra-brief psychological interventions (Ping et al., 2020) and peer supports (Rastegar Kazerooni et al., 2020) have been reported to effectively mitigate the emotional impacts of COVID-19, EVD, and SARS outbreaks. Culturally-adapted and cost-effective mental health emergency systems based on evidence-based intervention methods integrated into public health emergency responses at the national and global levels are recommended to reduce the psychological impacts of infectious disease outbreaks, especially for COVID-19. doi = 10.1017/s0033291720003888 id = cord-009697-dq4y89ab author = Yuen, Eddie title = Role of absolute lymphocyte count in the screening of patients with suspected SARS date = 2003-07-25 keywords = SARS; patient summary = 3 This multicentre, placebo-controlled, randomized, double-blind trial in 6213 patients with acute ST-elevation myocardial infarct (STEMI) found that magnesium sulphate, (2 g intravenous bolus over 15 min followed by a 17 g infusion over 24 h), administered within 6 hours of onset of symptoms did not have any effect on the primary end-point of 30 day all-cause mortality when compared with placebo (15.3% 30 day mortality in the magnesium group vs 15.2% in the placebo group; odds ratio 1.0; 95% CI 0.9-1.2; P = 0.96). As the investigators point out in the discussion of their paper, this means that 68 684 patients have been studied over the past 22 years in 14 randomized trials of magnesium in myocardial infarction. Second, a multicentre, placebo-controlled, randomized, double-blind trial of intravenous magnesium sulphate in 248 patients with acute severe asthma was recently reported. doi = 10.1046/j.1442-2026.2003.00486_3.x id = cord-322877-jy1uvwre author = Yuen, Kenneth S.C. title = Ocular screening in severe acute respiratory syndrome date = 2004-03-30 keywords = IOP; SARS summary = To investigate the ocular manifestations of patients with severe acute respiratory syndrome (SARS) and to monitor the possible ocular complications arising from the treatment regimen with high-dose systemic corticosteroid drugs. In March 2003, Hong Kong was seriously affected by a massive outbreak of SARS, and we took that opportunity to conduct a prospective observational study to investigate the probable ocular manifestations arising from SARS and the possible short-term complications resulting from the pulse or high-dose corticosteroid therapy. Patients were assessed with a comprehensive ocular examination including best-corrected visual acuity, intraocular pressure (IOP) by noncontact tonometer ([NCT] Xpert Noncontact Tonometer Plus; Reichert Ophthalmic Instruments, New York, New York, USA), slit-lamp, and binocular indirect ophthalmoscopy at baseline and at 2 months and 3 months. 2 With the unremarkable ophthalmologic findings of this study, routine ocular screening in patients with SARS for diagnosis or for complications may not be worthwhile. doi = 10.1016/j.ajo.2003.09.060 id = cord-028525-0ckagrt1 author = Yung, Chee Fu title = Household Transmission of SARS-CoV-2 from Adults to Children date = 2020-07-04 keywords = COVID-19; SARS summary = Beginning on March 5, because of concern that infected children might not display symptoms, the Ministry of Health Singapore implemented screening for SARS-CoV-2 by real-time reverse transcriptase polymerase chain reaction from nasopharyngeal swabs for all pediatric household contacts (regardless of symptoms) of persons with laboratory-confirmed COVID-19. During March and April, among 137 households with a total of 223 adults (index patients) with laboratory-confirmed COVID-19, 213 children aged ≤16 years were tested for SARS-6 CoV-2; 13 cases were detected in seven households, for an attack rate of 6.1% among children and 5.2% of households with confirmed exposure to COVID-19 (Table) . Based on systematic surveillance and screening of children who were household contacts of persons with confirmed COVID-19, the attack rate of SARS-CoV-2 infection in children was 6.1%. The low attack rate suggests that strict compliance with infection control may be able to eliminate or reduce the risk of transmission from adults to children in household settings. doi = 10.1016/j.jpeds.2020.07.009 id = cord-269555-29t956ik author = Zaconeta, Alberto title = Letter to the editor“SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?” date = 2020-09-22 keywords = SARS summary = key: cord-269555-29t956ik title: Letter to the editor"SARS-CoV-2: What prevents this highly contagious virus from reaching the fetus?" journal: Placenta DOI: 10.1016/j.placenta.2020.09.063 cord_uid: 29t956ik transmission of SARS-CoV-2. After discussing anatomical and molecular differences between 36 the alveolar-capillary and syncytium-capillary barriers, the authors presented the well-37 considered hypothesis that the absence of caveolin expression in the syncytium is one of the 38 most important mechanisms preventing the transplacental passage of this virus (1) . their masterful analysis, we would like to extend the discussion to another important risk factor 40 for vertical transmission, namely viral load in blood. Factors preventing 55 materno-fetal transmission of SARS-CoV-2 Detection of SARS-CoV-2 in 58 different types of clinical specimens Clinical features of patients 61 infected with 2019 novel coronavirus in Wuhan SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not 65 associated with infectious virus The trinity of COVID-19: immunity, 68 inflammation and intervention doi = 10.1016/j.placenta.2020.09.063 id = cord-339506-pkusvf82 author = Zaki, N. title = The estimations of the COVID-19 incubation period: a systematic review of the literature date = 2020-05-23 keywords = COVID-19; SARS; incubation summary = One reason for this is that generally we can only discover the times when the patient was in contact with persons carrying the virus, and then assume that the incubation period runs from the earliest date of exposure to the appearance of clinical symptoms or medical diagnosis. et al [15] researched the early data regarding transmission dynamics for the virus in Wuhan, estimating the mean incubation period at 5.2 days (95% CI: 4.1-7.0), with the distribution''s 95 th percentile being 12.5 days. They took individual patient histories from COVID-19 subjects in China (not from Hubei Province) for estimating the distribution of the time for generation, incubation, and the time span between onset of symptoms and isolation/diagnosis. The researchers undertook analysis of clinical data for 34 subjects submitting to elective surgery during the COVID-19 incubation period at four Chinese hospitals (Renmin, Tongji, Zhongnan, and Central) in Wuhan between January 1 and February 5, 2020. doi = 10.1101/2020.05.20.20108340 id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 keywords = CMV; Fig; HSV; Nipah; SARS; cell; human; infection; pneumonia; respiratory; virus summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. doi = 10.1007/978-0-387-68792-6_11 id = cord-304115-xs54f295 author = Zamaniyan, Marzieh title = Preterm delivery in pregnant woman with critical COVID‐19 pneumonia and vertical transmission date = 2020-04-17 keywords = COVID-19; SARS summary = Given the patient''s history and fever and cough, two nasal and throat swab samples were taken and tested to be positive for SARS-CoV-2 with SuperScript III Platinum, Quantitive Real-time PCR system Kits (Invitrogen company, USA) 4 . The RT-PCR tests was positive for amniotic fluid and neonate, suggesting the infant might have been affected intrauterine by COVID-19; therefore, once more, it raised the concerns regarding possible vertical transmission of the virus in mothers with serious illness. In some previous studies, the authors reported 21 healthy babies delivered by infected mothers to COVID-19, but they could not detect the virus in any of the feto-maternal parts namely placenta, amniotic fluid and cord blood [9] [10] [11] . The current case study, once again, raises concerns regarding possible vertical transmission of COVID-19 in pregnant women infected by SARS CoV-2 in contrast to the findings reported in some small studies published previously. doi = 10.1002/pd.5713 id = cord-276061-7b8h2sjw author = Zammit, M title = A rise in facial nerve palsies during the coronavirus disease 2019 pandemic date = 2020-10-01 keywords = SARS; covid-19 summary = OBJECTIVE: An increase in spontaneous lower motor neuron facial nerve (VIIth cranial nerve) palsies was seen during the severe acute respiratory syndrome coronavirus 2 outbreak in our emergency clinic. • There was an increased incidence of spontaneous lower motor neuron facial nerve palsy in our emergency ENT clinic • Only two prior case reports have referenced an association between VIIth cranial nerve palsy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) • Facial nerve palsy incidence of 3.5 per cent was seen in clinic during 2020, 2.7 times higher than the previous year at 1.3 per cent • A SARS-CoV-2 incidence of 11.8 per cent was seen in our cohort, contrasting with that of the Liverpool population of 0.5 per cent • It is important for clinicians to be aware that facial nerve palsy may be an initial presentation of the disease doi = 10.1017/s0022215120002121 id = cord-347484-7vn93t58 author = Zamoto, Aya title = Identification of Ferret ACE2 and its Receptor Function for Sars-Coronavirus date = 2006 keywords = SARS summary = Severe acute respiratory syndrome associated coronavirus (SARS-CoV) was the causative agent of SARS, which occurred as an emerging pneumonic disease in 2002. Amplification of partial ACE2 gene by RT-PCR: RNAs were extracted from heart, lung, kidney, and small intestine of a ferret. Determination of nucleotide sequence of ferret ACE2 (feACE2): Two overlapping regions of feACE2 genes were amplified by RT-PCR from kidney RNA. The partial feACE2 gene was amplified from RNAs isolated from the lung, heart, kidney, and small intestine by RT-PCR. HeLa cells expressing feACE2 supported SARS-CoV replication to the same extent as those expressing human ACE2 (Fig. 3) . From these observations, it is postulated that animal species whose ACE2 functions as an efficient SARS-CoV receptor would be a susceptible in feACE2 expressing HeLa cells was over 10 times more efficient than that in mouse efficiently. Furthermore, transgenic mouse expressing ferret or human ACE2 may serve a useful animal model for SARS-CoV infection. doi = 10.1007/978-0-387-33012-9_93 id = cord-286001-pu1fetq7 author = Zang, Ruochen title = TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date = 2020-04-23 keywords = Fig; SARS; TMPRSS4 summary = In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. Importantly, we found that 160 expression of TMPRSS4 but not ST14 also resulted in a significant increase in the levels of viral RNA and infectious virus titers in the presence of ACE2 ( Fig. 3B and S3C) . Collectively, we have shown that TMPRSS2 and TMPRSS4 activate SARS-CoV-2 S and 187 enhance membrane fusion and viral endocytosis into host cells. Importantly, abrogating TMPRSS4 expression led 209 to a 4-fold reduction in SARS-CoV-2 chimera virus replication in human enteroid, even 210 more significant than TMPRSS2 knockout (Fig. 4B) , highlighting its importance in 211 mediating virus replication in primary cells. It is possible that in the 293 small intestine, whereas SARS-CoV-2 is relatively stable, additional proteases such as 294 trypsin likely enhance viral pathogenesis by triggering more robust IEC fusion (Fig. S2A) . doi = 10.1101/2020.04.21.054015 id = cord-258268-7ypq0t3d author = Zanin, Luca title = SARS-CoV-2 can induce brain and spine demyelinating lesions date = 2020-05-04 keywords = CoV-2; SARS summary = On January 24, 2020, a new virus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been identified, quickly gaining worldwide attention [21] . Similarly to other Coronavirus, SARS-CoV-2 can attack the olfactory bulb and then affect the central nervous system (CNS) through the olfactory tract in the early stages of infection [5] . Neurological impairment and demyelinating reaction appear as complications in case of severe Coronavirus Disease 2019 (COVID-19) [10] . Our patient showed symptoms consistent with a neurological involvement consequent to SARS-CoV-2 infection. In SARS-CoV-2 infection, neurological impairment was observed only in case of severe COVID-19 [10] . SARS-CoV-2 was not detected in the CSF probably because the neurological damage was sustained by a delayed immune response that occurred after the viremia. Sudden neurological impairment with seizures in COVID-19 patients may be sustained by CNS involvement and demyelinating lesions. Neurologic features in severe SARS-CoV-2 infection doi = 10.1007/s00701-020-04374-x id = cord-026806-pn4lwhr7 author = Zargar, Showkat Ali title = Gastrointestinal Endoscopy during COVID: Do Some, Leave Most date = 2020-05-16 keywords = COVID-19; SARS summary = Therefore, these guidelines cannot be applied uniformly all over India and more or less usual business can start with caveat of complete adherence to standard operating procedure of infectious control protocols in combination with adherence to social distancing, frequent hand washing, use of protective gears, and organization of endoscopy teams and space in green zones. Chinese data are testimony to the fact that in Wuhan, China-epicenter of COVID-19-that in the initial weeks HCWs accounted for large number of total cases which was significantly reduced following adherence to infectious control practices. The informed consent requires "detailed and transparent" discussion on issues as follows: (1) acquisition of infection by HCWs from asymptomatic COVID-19 patient and also patient may develop full-fledged infection in postprocedure period blaming the endoscopist; (2) chances of acquisition of infection despite of adherence to infectious control protocols; and (3) risks involved in postponing otherwise medically indicated, time-sensitive procedure and reasons for delaying it. doi = 10.1055/s-0040-1712337 id = cord-347548-h5fk64p8 author = Zarza, José title = Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection date = 2020-08-21 keywords = COVID-19; SARS summary = title: Evans syndrome associated with antiphospholipid antibodies in a patient with SARS-COV-2 infection Coronavirus disease 2019 (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which has sparked growing interest and concern in the international community. 1 We present a case of COVID-19 associated with Evans syndrome (hemolytic anemia plus thrombocytopenia, both with autoimmune causes) and antiphospholipid antibodies. With these findings, her diagnoses upon admission were SARS-COV-2 infection, SLE with associated antiphospholipid antibodies, and Evans syndrome. We present the case of a young patient who was apparently in good health but had a history of venous thrombosis of unknown cause in her childhood, which started with Evans syndrome and a high titer of antiphospholipid antibodies, in coincidence with a SARS-COV-2 infection. 4 Although the decreased platelet count is usually mild in COVID-19, some cases of severe thrombocytopenia have been reported in the context of disseminated intravascular coagulation in these patients. doi = 10.1016/j.htct.2020.08.003 id = cord-309931-cpzp33b3 author = Zawawi, Ayat title = The impact of COVID-19 pandemic on malaria elimination date = 2020-10-20 keywords = Africa; SARS; covid-19 summary = As lowand middle-income countries shift increasingly to focus on identifying and treating COVID-19, questions are emerging about the impact this shift in focus will have on ongoing efforts to control other infectious diseases, such as malaria. This review discusses how the spread of SARS-CoV-2 in lowand middle-income countries might impact these efforts, focusing in particular on the effects of co-infection and the use of antimalarial drugs used to treat malaria as therapeutic interventions for COVID-19. This review addresses this gap in the literature by discussing how the spread of SARS-CoV-2 in low-and middle-income countries might impact efforts to control malaria. Despite the CQ and HCQ treatment potential for COVID-19, the use of these two drugs could pose many challenges in low-and middle-income countries and not just in malaria-endemic areas. doi = 10.1016/j.parepi.2020.e00187 id = cord-328011-6lf3no6u author = Zayed, Hatem title = Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics date = 2020-08-14 keywords = COVID-19; SARS summary = title: Vaccine Development Against COVID-19 Prior to Pandemic Outbreaks, Using in vitro Evolution and Reverse Genetics Since coronaviruses are increasing alarmingly, there is an urgent need for a safe and effective vaccine to prevent the spread of the virus during pandemic outbreaks, and stop deaths associated with the virulent COVID-19. We now know that SARS-CoV-2 shares 88% identity with two SARS-like coronaviruses (bat-SL-CoVZXC21 and bat-SL-CoVZC45) that both originated in China, and use the same human angiotensin-converting enzyme 2 receptor for cell entry during the process of infection (3). In response to such forewarnings from scientists, a predictive vaccine could have been designed and developed for the potential virus pandemic. Thereafter, during the time of pandemic, suitable stored transgenic cell lines could be used, based on the Abbreviations: COVID-19, coronavirus disease 2019; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; VLP, virus-like particle; WHO, World Health Organization. doi = 10.3389/fimmu.2020.02051 id = cord-353628-f6ew980g author = Zayet, Souheil title = Encephalopathy in patients with COVID‐19: ‘Causality or coincidence?’ date = 2020-05-19 keywords = COVID-19; SARS summary = Since its discovery in December 2019, the novel coronavirus disease 2019 (COVID-19) has caused several clinical presentations: mainly respiratory, rarely gastrointestinal, and exceptionally neurological. In addition to the usual symptoms (general, respiratory and otorhinolaryngological) of the infection with SARS-CoV-2, several authors have described neurological manifestations as headache, nausea, and vomiting. These viruses can invade brainstem via a synapse-connected route from the lungs and airways 9 .Considering the high similarity between SARS-CoV-2 and others CoVs 10 , it is still not clearly known whether the potential neuro-invasion of SARS-CoV2 is partially responsible for respiratory failure in patients with COVID-19 9,11,12 . Therefore, in the context of COVID pandemic, it would be reasonable to perform a thoracic CT and a RT-PCR for SARS-CoV-2 in case of encephalopathy with normal lumbar puncture and brain imaging. The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients The neuroinvasive potential of SARS-CoV-2 may play a role in the respiratory failure of COVID-19 patients doi = 10.1002/jmv.26027 id = cord-305341-nokybn2a author = Zeng, Fanya title = Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments date = 2004-03-19 keywords = SARS summary = title: Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments Another interesting finding was that mouse antibodies elicited separately by plasmids encoding S1 and S2 subunits cooperatively neutralized SARS-CoV but neither the S1 nor S2 specific antibodies did, suggesting the possible role of both S1 and S2 subunits in host cell docking and entry. Animals vaccinated with DNA encoding secreting form of E2 glycoprotein of classical swine fever virus (CSFV) showed both CSFV specific antibody response and protection upon viral challenge though the native E2 was anchor membrane protein ( [28, 29] and Zeng et al., unpublished data). In the mice experiment, it was demonstrated that SARS-CoV specific antibodies could be induced by immunization with plasmids encoding S1, S2 and fragment of S1 subunit. The first paper on immunizing masques with structural genes of SARS-CoV, however, reported that co-delivery of three viral genes encoding S1, nucleocapsid (N), and membrane (M) protein could elicit a high titer of neutralizing antibody and T-cell response [24] . doi = 10.1016/j.bbrc.2004.01.166 id = cord-275185-9br8lwma author = Zeng, Hao title = The efficacy assessment of convalescent plasma therapy for COVID-19 patients: a multi-center case series date = 2020-10-06 keywords = COVID-19; RBD; SARS; patient summary = Following CP transfusion, six out of eight patients showed improved oxygen support status; chest CT indicated varying degrees of absorption of pulmonary lesions in six patients within 8 days; the viral load was decreased to a negative level in five patients who had the previous viremia; other laboratory parameters also tended to improve, including increased lymphocyte counts, decreased C-reactive protein, procalcitonin, and indicators for liver function. Herein, we performed a retrospective observational study involving eight critical or severe patients with COVID-19 from four designated hospitals in the southwest region of China, aiming to explore the potential efficacy and safety of CP therapy, and to provide more evidence for the quality control of donated plasma and reasonable clinical application of CP transfusion. 23 Assessing the effects of neutralizing activity of CP on the patients'' clinical efficacy, we found that patients treated by CP with high NAT50 (>1:640) had more obvious improvement than patients receiving low NAT50 value (≤1:640) of CP, including shorter negative conservation time of viral RNA, and higher increment of IgG level after CP transfusion. doi = 10.1038/s41392-020-00329-x id = cord-336752-cpxnof1b author = Zeng, Qi‐Qiang title = Radiomics‐based model for accurately distinguishing between severe acute respiratory syndrome associated coronavirus 2 (SARS‐CoV‐2) and influenza A infected pneumonia date = 2020-08-13 keywords = IAP; NCP; SARS summary = Patients were excluded if they met any of the following criteria: (a) history of American Society of Anesthesiologists (ASA) score of more than 2; (b) history of existing respiratory disease prior to outbreak of SARS-CoV-2; (c) pneumonia of etiology other than SARS-CoV-2 or influenza A virus by measuring nucleic acid by fluorogenic quantitative PCR of serum samples and/or oropharyngeal swab samples in conjunction to radiographic evidence and clinically established diagnosis; or (d) absent of obvious pulmonary lesions on radiographic imaging. Abbreviation: ASA score, American society of anesthesiologists score F I G U R E 2 Radiomics-based machine learning workflow, including computed tomography (CT) images acquisition and region-of-interest (ROI) segmentation of inflammatory lesions; radiomic feature extraction by LIFEx; features selection by least absolute shrinkage and selection operator (LASSO) with 10-fold cross-validation; radiomics prediction score and calibration; and nomogram development for a more clinicianfriendly application, and support vector machine (SVM) were used to distinguish these two kinds of diseases effectively drawn to compare the predicted outcome versus observed outcome of each patient in order to illustrate the probability of NCP. doi = 10.1002/mco2.14 id = cord-297324-me5ff1pb author = Zeng, Rong title = Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients() date = 2004-07-30 keywords = SARS; figure; protein summary = Analysis of the genomic organization of SARS-CoV showed that a gene locus containing ORF3a and 3b located between the S and E genes, 6 -8 is frequently found in different members of the coronavirus family (see Figure 4A ). According to the genomic sequence information for SARS-CoV, ORF 3a encoded a putative 31 kDa protein containing 274 amino acid residues. 6, 7 In order to confirm the result by shot-gun assay, the collected cytosol of SARS-CoV-infected Vero E6 cells was separated with SDS-PAGE, and then the gel slice around the 31 kDa region was excised and analyzed by capillary liquid chromatography electrospray tandem mass spectrometry (mLC-ESI-MS/MS). Interestingly, comparison with S protein sequences of the coronavirus family also shows a cysteinerich region overlapping the junction of the membrane-spanning domain and the cytoplasmic tail, which is a conserved motif of spike proteins in all analyzed coronaviruses (see Figure 3 of Marra et al. doi = 10.1016/j.jmb.2004.06.016 id = cord-256152-8wla6ne4 author = Zeng, Xiang title = Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? date = 2020-05-18 keywords = SARS summary = title: Conducting Research During the COVID-19 Pandemic: How Scientific Community Should be Prepared? Furthermore, scientists and researchers should always adhere to the conflict-of-interest guidelines during the crisis era. Finally, scientist and researchers need an unbiased interpretation of the findings. For example, while taking care of respiratory emergency is the priority, researchers were also concerned about the damage to the nervous system caused by SARS-CoV-2 infection. 5 Nonetheless, alterations of sex-related hormone levels in reproductive-aged men with SARS-CoV-2 infection may indicate a decline in gonadal function. Such proactive, forward-looking studies render a new perspective on comprehensive understanding of disease and get us prepared for drug discovery, and offer important references for the decision of public health policies. All in all, the scientific community is now taking on new challenges in the era of COVID-19 pandemic. Neurologic features in severe SARS-CoV-2 infection Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study doi = 10.14245/ns.2040212.106 id = cord-313268-j51zyodw author = Zeng, Xiangxiang title = Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning date = 2020-07-12 keywords = COVID-19; KGE; SARS; drug summary = Using Amazon''s AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. 10−12 Deep learning has also recently demonstrated its better performance than classic machine learning methods to assist drug repurposing, 13 −16 yet without foreknowledge of the complex networks connecting drugs, targets, SARS-CoV-2, and diseases, the development of affordable approaches for the effective treatment of COVID-19 is challenging. Via systematic validation using transcriptomics and proteomics data generated from SARS-CoV-2-infected human cells and the ongoing clinical trial data, we successfully identified 41 drug candidates that can be further tested in large-scale randomized control trials for the potential treatment of COVID-19. Using Amazon''s AWS computing resources, we identified 41 high-confidence repurposed drug candidates (including dexamethasone, indomethacin, niclosamide, and toremifene) for COVID-19, which were validated by an enrichment analysis of gene expression and proteomics data in SARS-CoV-2 infected human cells. doi = 10.1021/acs.jproteome.0c00316 id = cord-024319-isbqs7hg author = Zeng, Xin title = Isolation of a human monoclonal antibody specific for the receptor binding domain of SARS-CoV-2 using a competitive phage biopanning strategy date = 2020-04-30 keywords = ACE2; RBD; SARS summary = doi = 10.1093/abt/tbaa008 id = cord-253447-4w6caxwu author = Zeng, Xin title = Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date = 2020-04-20 keywords = ACE2; RBD; SARS summary = title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Several high-affinity antibodies targeting SARS-CoV-2 RBD and blocking its binding to ACE2 were isolated, and the top 1 lead exhibited a neutralization activity of SARS-CoV-2 pseudotyped VSV infection. A high-affinity antibody against the target protein can be screened from a phage display antibody library using the standard biopanning process, but its binding epitopes are identified by some extra steps, such as epitope mapping and competitive ELISA. doi = 10.1101/2020.04.19.049643 id = cord-320207-cwt7dswz author = Zeng, Yingchun title = The nucleocapsid protein of SARS-associated coronavirus inhibits B23 phosphorylation date = 2008-05-02 keywords = B23; SARS summary = B23 protein is also identified as one of the substrates of CDK2/cyclin E and plays a critical role in centrosome duplication during cell cycle progression, which is regulated by the phosphorylation of B23 at Thr199 [26, 27] . The overlayed result indicated that the SARS-CoV N protein co-localized with B23 protein in the perinuclear region of HeLa cells (Fig. 1f) . In our previous research, we found that SARS-CoV N protein contained three NLS motifs and a nuclear export signal, acting as a shuttle protein between nucleus and cytoplasm, and it could arrest the cell cycle progression [10] . B23 protein can bind NLS, facilitate protein nuclear import and play a role in centrosome duplication during cell cycle progression [20, 21, 26] . In our previous research, we have shown that the N protein of SARS-CoV can arrest cell cycle progression [10] , which is in accordance with the result of Surjit et al. doi = 10.1016/j.bbrc.2008.01.096 id = cord-293265-qqxlwpju author = Zeng, Yong title = Clinical characteristics of 9 cancer patients with SARS-CoV-2 infection date = 2020-05-14 keywords = SARS; chinese summary = D-dimmer rise, infection index rise, and chest CT(computed tomography) progression may be clinical warning indicators for severe patients, in our study, more 50% of patients had elevated levels of these indicators, but only 44% (including the dead) of patients had received treatment in the intensive care unit. Cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may be effective in the prevention and treatment of novel coronavirus-infected pneumonia (NICP). Studies [10] found that the combination of traditional Chinese medicine and western medicine was effective in the prevention and treatment of NICP in all stages, and the response rate of symptoms such as fever, cough and fatigue were significantly increased in ordinary patients after taking lianhua qingwen granules. By analyzing 9 cancer patients with SARS-CoV-2 infection, cancer comorbidity seems to have no direct relationship with severe events, and the combination of traditional Chinese medicine and western medicine may doi = 10.1186/s13020-020-00328-8 id = cord-270462-d9l3agr0 author = Zeng, Zhi title = Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion date = 2020-05-06 keywords = SARS; figure summary = title: Pulmonary Pathology of Early Phase COVID‐19 Pneumonia in a Patient with a Benign Lung Lesion The aim of this study was to explore pulmonary pathology of early phase COVID‐19 pneumonia in a patient with a benign lung lesion. METHODS AND RESULTS: We analyzed the pathological changes of lung tissue from a 55‐year‐old female patient with early phase SARS‐CoV‐2 infection. CONCLUSION: The results highlighted the pulmonary pathological changes of early phase SARS‐CoV‐2 infection and suggested a role of immune dysfunction in the pathogenesis of COVID‐19 pneumonia. [8] [9] [10] However, the pathological changes in the lungs caused by SARS-CoV-2, especially in the early stage of infection, have seldom been described. Combining epidemiological characteristics, clinical presentation, nucleic acid testing and intracytoplasmic viral-like inclusions, it is reasonable to speculate that this case represents an early stage of lung injury secondary to SARS-CoV-2 infection. Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer doi = 10.1111/his.14138 id = cord-281106-vzb5xzza author = Zerwes, S. title = COVID-19-Infektion – Risiko für thrombembolische Komplikationen date = 2020-09-01 keywords = COVID-19; SARS; die; patient summary = According to current data, the risk of thromboembolic events in hospitalized COVID-19 patients is significantly increased, making thrombosis prophylaxis with low molecular weight or unfractionated heparin necessary. Neben den bekannten Ursachen der Thromboseentstehung, wurden bei der COVID-Erkrankung spezielle Pathomechanismen beobachtet, die zur Bildung von Thrombosen sowohl im venösen als auch im arteriellen System beitragen können. Auch wenn die Mechanismen noch nicht in Ihrer Gesamtheit erfasst sind, so ist bereits jetzt ersichtlich, dass die thrombembolischen Komplikationen im Zusammenhang mit dem SARS-CoV-2-Virus auf eine exzessive Inflammationsreaktion, Veränderung von Blutflusseigenschaften, direkte virusbedingte Thrombozytenaktivierung und Endothelschädigung zurückzuführen sind [3] . Diese Hypothese wird von nahezu allen bisher publizierten Arbeiten zu thrombembolischen Ereignissen bei COVID-19-Patienten postuliert und könnte eine Erklärung für die deutlich erhöhte Anzahl von TVT bieten [1, 7, 17, 28, 39] . Eine einheitliche Nomenklatur besteht noch nicht, die Pu-blikationmitdergrößtenSerie benennt es als "Pediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2" (PIMS-TS) [36] . doi = 10.1007/s00772-020-00687-4 id = cord-339077-pxf2u68u author = Zerwes, Sebastian title = Erhöhtes Risiko für tiefe Beinvenenthrombosen bei Intensivpatienten mit CoViD-19-Infektion? – Erste Daten date = 2020-06-05 keywords = DVT; SARS; TVT summary = BACKGROUND: The incidence of deep vein thrombosis (DVT) in CoViD-19 patients in intensive care units (ICU) has so far been investigated in only a few studies. MATERIAL AND METHODS: In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. Es ist bekannt, dass intensivpflichtige Patienten per se ein erhöhtes Risiko für thrombembolische Ereignisse aufweisen: So treten bei Intensivpatienten Thrombosen je nach Grunderkrankung mit einer Wahrscheinlichkeit von 10-80 % auf; 10-15 % der Patienten entwickeln trotz Thromboseprophylaxe eine tiefe Beinvenenthrombosen (TVT; [8, 9] ). In this prospective single center study, which was conducted between 18 April 2020 and 30 April 2020, 20 SARS-CoV2 positive patients were compared with 20 non-CoVid-19 patients in the ICU with respect to the occurrence of DVT. doi = 10.1007/s00104-020-01222-7 id = cord-308310-wtmjt3hf author = Zha, Lisha title = Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date = 2020-05-14 keywords = RBD; SARS summary = Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro. The receptor binding domain (RBD) of the SARS spike protein binds to ACE2 and is an important target for neutralizing antibodies [5] [6] [7] . Hence, the RBD-CuMVTT vaccine candidate is able to induce high levels of SARS-CoV-2 neutralizing antibodies. Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine doi = 10.1101/2020.05.06.079830 id = cord-301324-2tyl1r2l author = Zhan, Jing title = Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() date = 2020-09-09 keywords = SARS summary = title: Environmental impacts on the transmission and evolution of COVID-19 combing the knowledge of pathogenic respiratory coronaviruses() The emergence of a novel coronavirus named by SARS-CoV-2 during December, 2019, has caused the global outbreak of coronavirus disease 2019 (COVID-19), which is officially announced to be a pandemic by the World Health Organization (WHO). Understanding the transmission, survival, and evolution of the virus in the environment will assist in the prevention, control, treatment and eradication of its infection. Herein, we aimed to elucidate the environmental impacts on the transmission and evolution of SARS-CoV-2, based on briefly introducing this respiratory virus. This review should be of great help to prevent and control the epidemics caused by emerging respiratory coronaviruses (CoVs). Summary: More knowledge on the transmission and evolution of SARS-CoV-2 in the environment is urgently needed. High infectivity and pathogenicity of influenza A 620 virus via aerosol and droplet transmission doi = 10.1016/j.envpol.2020.115621 id = cord-320860-qt84oicg author = Zhang, Aining title = Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date = 2020-09-15 keywords = COVID-19; SARS summary = title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis doi = 10.1016/j.ijid.2020.09.021 id = cord-259238-n2uuaof6 author = Zhang, Bao-Zhong title = SARS-CoV-2 infects human neural progenitor cells and brain organoids date = 2020-08-04 keywords = Fig; SARS summary = To explore the direct involvement of SARS-CoV-2 in the CNS in physiologically relevant models, we assessed SARS-CoV-2 infection in induced pluripotent stem cells (iPSCs)-derived human neural progenitor cells (hNPCs), neurospheres, and brain organoids. Importantly, extensive SARS-CoV-2 antigen was detected in the infected samples at 72 hpi (Fig. 1f) , indicating that SARS-CoV-2 directly infected the brain organoids. The results demonstrated SARS-CoV-2 RdRp gene copy number increased in a timedependent manner, suggesting active release of progeny virus particles from infected brain organoids (Fig. 1g, left) . Plaque assays performed on supernatant samples from brain organoids infected with SARS-CoV-2 showed that the infectious virus titer peaked at 24 hpi and were continuously detected at 48 and 72 hpi. h Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and TUJ1. i Representative images of SARS-CoV-2-infected human brain organoids immunostained for SARS-CoV-2-N and NESTIN. doi = 10.1038/s41422-020-0390-x id = cord-352020-9wxwktck author = Zhang, Baoshan title = A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone date = 2020-10-23 keywords = Fig; RSV; SARS summary = To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses. To improve protein solubility and expression, we added glycans to the surface of the nanoparticles, designing a panel of LuS and ferritin constructs with SpyTag and SpyCatcher (Table 1 and Supplementary Table S1 ). To demonstrate the versatility of our SpyTag-displaying nanoparticles in immunogen development, we conjugated them to three viral antigens of vaccine interest, the DS2-preF stabilized RSV F 33 , a DS2-stabilized version of PIV3 F 34 , and the 2P-stabilized version of SARS-CoV-2 spike 24 . doi = 10.1038/s41598-020-74949-2 id = cord-252288-klkoerfn author = Zhang, Bicheng title = Immune Phenotyping Based on the Neutrophil-to-Lymphocyte Ratio and IgG Level Predicts Disease Severity and Outcome for Patients With COVID-19 date = 2020-07-03 keywords = NLR; SARS; patient summary = This disease is initiated by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and uncontrolled cytokine storm, but it remains unknown as to whether a robust antibody response is related to clinical deterioration and poor outcome in COVID-19 patients. Immune response phenotyping based on the late IgG levels and neutrophil-to-lymphocyte ratio (NLR) was characterized to stratified patients into different disease severities and outcomes. Here, we evaluated antibody response within 35 days after symptom onset in laboratory-confirmed cases with COVID-19 as one component of an overall exaggerated immune activation in severe SARS-CoV-2 infection, and developed an immune phenotyping based on the late IgG response and NLR that could help determine disease severity and clinical outcome for COVID-19 patients. Using two immune responserelated indicators NLR and IgG levels detected in sera at late stage, we developed a combined immune response phenotype, which could predict disease severity and the outcome of COVID-19 patients. doi = 10.3389/fmolb.2020.00157 id = cord-327028-dbvucvy3 author = Zhang, Cantong title = Controversial treatments: An updated understanding of the coronavirus disease 2019 date = 2020-04-10 keywords = COVID-19; SARS summary = To reduce the case‐fatality rate among coronavirus disease 2019 patients, we should not ignore the complications, such as RNAaemia, acute respiratory distress syndrome, and multiple organ dysfunction. To help understand the advantages and limitations of differential treatments, we provide a timely review and discuss the complications and corresponding major treatments, especially controversial ones such as antiviral therapy (remdesivir, ribavirin, and chloroquine), glucocorticoid therapy, extracorporeal support including an artificial liver system, and extracorporeal membrane oxygenation based on available evidence. Furthermore, we list a table to conclude the mechanism, advantages, and limitations for different treatments mentioned in this review (Table 2) The mechanism of remdesivir against the virus showed that the drug effectively inhibited the Ebola virus RNA-dependent RNA polymerase (RdRp) complex. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China doi = 10.1002/jmv.25788 id = cord-030654-8yxa1r1c author = Zhang, Changhui title = Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date = 2020-08-20 keywords = Fig; RNA; SARS summary = This structure was revealed to be a horseshoe-like tetramer, which may play an essential role in nsp9 oligomerization and in the regulation of viral nucleic acid binding during the replication of the virus. The initial structure solved by molecular replacement showed that six SARS-CoV-2 nsp9 protomers form an OB-fold cluster in an asymmetric unit ( Supplementary Fig. 1a ). To obtain more information about the protein interfaces and the likely biological assemblies of the OB-fold cluster, we calculated the structure of SARS-CoV-2 nsp9 using PDBe-PISA [27] . These three contact surfaces in interface I b/c contribute a hydrophobic base with eight hydrogen bonds and one salt bridge, making the SARS-CoV-2 nsp9 tetramer extremely stable in the crystal structure. In this present study, we observed the nucleic acid-binding ability of SARS-CoV-2 nsp9, using the electrophoretic mobility The molecules in these two interfaces are shown as cartoons and colored and labeled as in Fig. 2a . doi = 10.1186/s43556-020-00005-0 id = cord-273349-penb65x7 author = Zhang, Chao title = Liver injury in COVID-19: management and challenges date = 2020-05-31 keywords = COVID-19; SARS summary = The severity, mortality, and incidence of complications in these patients, including secondary infection, hepatic encephalopathy, upper gastrointestinal bleeding, and liver failure, need to be examined in large-cohort clinical studies. As the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread from China to other countries, governments and the medical community are taking steps to prevent transmission, from common sense recommendations to radical quarantine measures. SARS-associated viral hepatitis caused by a novel coronavirus: report of three cases Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalised patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study doi = 10.1016/s2468-1253(20)30057-1 id = cord-253456-u9num2o9 author = Zhang, Che title = Clinical and epidemiological characteristics of pediatric SARS-CoV-2 infections in China: A multicenter case series date = 2020-06-16 keywords = COVID-19; SARS; patient summary = Suspected patients with clinical and/or radiological features of pneumonia were quarantined prior to SARS-CoV-2 nucleic acid detection according to WHO guidelines for cases with suspected infection [8] as well as the instructions from the Pediatric Branch of the Hubei Medical Association for pediatric cases [9] . Specifically, suspected cases of SARS-CoV-2 infection should meet 1 of the following criteria [10] : (1) at least 1 clinical symptom, including fever, expectation, tachypnea, lethargy, poor feeding, cough, vomiting, and diarrhea; (2) chest radiologic abnormalities consistent with viral pneumonia. Patients were discharged when all the following criteria were met [10] : (1) fever had recovered for at least 3 days; (2) upper respiratory symptoms were alleviated; (3) the exudative lesion was alleviated significantly according to radiological evidence; (4) negative results were obtained for SARS-CoV-2 nucleic acid detection in 2 consecutive tests performed with an interval of 24 hours. doi = 10.1371/journal.pmed.1003130 id = cord-327084-r12copka author = Zhang, Chenxi title = Survey of Insomnia and Related Social Psychological Factors Among Medical Staff Involved in the 2019 Novel Coronavirus Disease Outbreak date = 2020-04-14 keywords = SARS; covid-19; staff summary = A multiple binary logistic regression model revealed that insomnia symptoms were associated with an education level of high school or below (OR = 2.69, p = 0.042, 95% CI = 1.0–7.0), being a doctor (OR = 0.44, p = 0.007, 95% CI = 0.2–0.8), currently working in an isolation unit (OR = 1.71, p = 0.038, 95% CI = 1.0–2.8), is worried about being infected (OR = 2.30, p < 0.001, 95% CI = 1.6–3.4), perceived lack of helpfulness in terms of psychological support from news or social media with regard to COVID-19 (OR = 2.10, p = 0.001, 95% CI = 1.3–3.3), and having very strong uncertainty regarding effective disease control (OR = 3.30, p = 0.013, 95% CI = 1.3–8.5). doi = 10.3389/fpsyt.2020.00306 id = cord-104162-fe51v2pt author = Zhang, Chiyu title = Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date = 2020-11-02 keywords = HIV-1; RNA; SARS summary = Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). doi = 10.1101/2020.10.22.343673 id = cord-295850-nb6miso7 author = Zhang, Chuan-hai title = Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain date = 2005-05-02 keywords = CPE; Fig; SARS summary = title: Immune responses in Balb/c mice induced by a candidate SARS-CoV inactivated vaccine prepared from F69 strain The immunogenicity of a candidate-inactivated vaccine prepared from SARS-CoV F69 strain was evaluated in Balb/c mice. The present study was performed with the objective of determining the immunogenicity of a candidate-inactivated SARS-CoV vaccine made from F69 strain in Balb/c mice. In test groups, anti-SARS-CoV specific IgM antibodies were induced by the inactivated vaccine. The results showed that SARS-CoV F69 strain inactivated vaccine could induce potent humoral immune responses in Balb/c mice. In present study, the specificity of serum antibodies induced by F69 strain inactivated vaccine was identified by Western blot assay. A convalescent serum of SARS patient was used, and the same positive result was obtained (lane 3, Fig. 4) , which further demonstrated the specificity of the antibodies induced with the inactivated vaccine produced from F69 strain. doi = 10.1016/j.vaccine.2004.11.073 id = cord-293080-b4pxjrcj author = Zhang, Chunyan title = Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method date = 2020-09-18 keywords = SARS; covid-19 summary = Immunological diagnosis of COVID-19 is mainly achieved through testing specific antibody IgM and IgG responses after human infection with SARS-CoV-2 and is based on antigen-antibody capturemethods. Such methods include lateral flow assays and provide the advantages of easy operation, quick test results, no need of a special laboratory site with (complex) instruments, and high sensitivity and specificity, and is suitable for carrying out large-scale SARS-CoV-2 infection/screening as point-of-care sites [7] . Based on the process of SARS-CoV-2 infection and the production of specific antibody responses, a diagnostic IgG and IgM detection assay would be the most useful method to diagnosis the occurrence of COVID-19 and development of pulmonary disease. In the present study, the recombinant protein and test strip for detecting the SARS-CoV-2 antibody by the antigen capturing method, and its preparation method were provided, supporting a new method for SARS-CoV-2 infection screening, diagnosis, disease monitoring and prognosis evaluation. doi = 10.1080/22221751.2020.1811161 id = cord-256500-nlavfnpt author = Zhang, Dan title = COVID-19 infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome date = 2020-03-26 keywords = COVID-19; FSC; SARS summary = Background: Excessive monocyte/macrophage activation with the development of a cytokine storm and subsequent acute lung injury, leading to acute respiratory distress syndrome (ARDS) is a feared consequence of infection with COVID-19. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), also known as Corona Virus Disease-19 (COVID-19) is a new coronavirus, first identified in Wuhan, China in December 2019, which frequently induces fatal inflammatory responses and acute lung injury. Herein we describe novel observations in relation to changes in monocyte morphology and activation status, which correlate with the prognosis and severity of COVID-19 infection and which can be readily quantified by flow cytometry with the concurrent measurement of forward scatter (FSC) and (SSC), which measure cell size and complexity, respectively. We have shown that simple assessment of FSC by flow cytometry in the context of COVID-19 infection can rapidly identify those patients with an increasing proportion of large, activated, IL-6 and TNF secreting monocytes, who have severe disease and are at greatest risk of ICU admission. doi = 10.1101/2020.03.24.20042655 id = cord-338243-njkhwkwk author = Zhang, Dayi title = Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital date = 2020-06-23 keywords = CoV-2; SARS summary = title: Potential spreading risks and disinfection challenges of medical wastewater by the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral RNA in septic tanks of Fangcang Hospital In this study, we evaluated the presence of SARS-CoV-2 viral RNA in septic tanks of Wuchang Cabin Hospital and found a striking high level of (0.5–18.7) × 103 copies/L after disinfection with sodium hypochlorite. In septic tanks, disinfection achieved free chlorine > 6.5 mg/L for 1.5 hours when the dosage of sodium hypochlorite was 800 g/m 3 , meeting well with the guideline for emergency treatment of medical sewage containing SARS-CoV-2 suggested by China CDC. Septic tanks can behave as a long-term source J o u r n a l P r e -p r o o f to release SARS-CoV-2 viral RNA into waters when disinfection is not sufficient and challenges public health via potentially spreading viruses in drainage pipelines. doi = 10.1016/j.scitotenv.2020.140445 id = cord-103709-86hv27vh author = Zhang, Dong Yan title = Prefusion spike protein stabilization through computational mutagenesis date = 2020-06-19 keywords = SARS; SASA; protein summary = The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We subject the selected residues to computational redesign using Eris to find the stabilizing mutations by calculating the change in free energy ∆∆ = ∆ − ∆ , where ∆ and ∆ are the free energies of the mutant protein and wild type proteins correspondingly. After the designation of the mutation sites, the pipeline utilizes Eris to determine the changes in free energies of the mutants. We analyze the conservation score, RMSF, and SASA of residues in the spike protein through the pipeline. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes doi = 10.1101/2020.06.17.157081 id = cord-285755-zblitbo0 author = Zhang, F. title = Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study date = 2020-03-24 keywords = COVID-19; SARS; patient summary = [Results] A total of 110 patients with confirmed (n=80) or suspected (n=30) COVID-19 were screened and 48 patients (female 31.3%, mean age 70.58{+/-}13.38 year old) among them with high-sensitivity cardiac troponin I (hs-cTnI) test within 48 hours after admission were included, of whom 17 (17/48, 35.4%) died in hospital while 31 (31/48, 64.6%) were discharged or transferred to other hospital. [Conclusions] Cardiac injury defined by hs-cTnI elevation and elevated d-dimer on admission were risk factors for in-hospital death, while higher SpO2 could be seen as a protective factor, which could help clinicians to identify patients with adverse outcome at the early stage of COVID-19. Short-term prognosis of COVID-19 patients are discrepancy and in-hospital mortality risk are high in severe cases[1] [2] Although previous study had indicated that several risk factors were independently associated with short-term mortality, such as elevated d-dimer, older age and higher Sequential Organ Failure Assessment (SOFA) score [2] , few studies focused on cardiac injury with COVID-19 patients. doi = 10.1101/2020.03.21.20040121 id = cord-325348-yi6yu5l1 author = Zhang, G. title = Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD date = 2020-06-17 keywords = ACE2; SARS; SBP1 summary = Recent cryo-electron microscopy (cryo-EM) structural studies of the SARS-CoV-2 spike protein 68 receptor binding domain (RBD) in complex with full-length human ACE2 receptor revealed key 69 amino acid residues at the contact interface between the two proteins and estimated the binding 70 affinity at ~15 nM [7, 8] . The results of this MD simulation suggest 108 that SBP1 and SBP2 peptides derived from the ACE-PD α1 helix may alone potentially bind the 109 SARS-CoV-2 spike RBD protein with sufficient affinity to disrupt the associated PPI. However, competition was not observed when using non-biotinylated SBP1 pre-140 mixed in solution with Sino Biological insect-derived SARS-CoV-2-RBD, even with a 1000-fold 141 excess of the peptide (Fig. 3C, 3E ). In conclusion, a biotinylated peptide sequence derived from human ACE2 was found to 205 bind Sino Biological insect-derived SARS-CoV-2 spike protein RBD with micromolar affinity, but 206 did not associate with SARS-CoV-2-RBD variants obtained from other commercial sources. doi = 10.1101/2020.03.19.999318 id = cord-293082-fw7deem8 author = Zhang, Guangzhi title = Animal coronaviruses and SARS‐CoV‐2 date = 2020-08-16 keywords = CoV-2; Coronavirus; SARS summary = As of April 7, just four months since its first outbreak, more 48 than 3.4 million confirmed cases and 238,000 deaths have been recorded in 215 countries, areas, 49 and territories, and moreover it seems that severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2) that causes COVID-19 will probably continue to circulate around the globe 51 (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/). The health 52 authorities and governments of affected countries have paid attention to current pandemic and 53 have taken immediate measures to block COVID-19 transmission, including utilization of personal 54 protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis 55 and sharing, public health education, maintaining social distance, the creation of diagnostics, 56 therapeutics, and vaccines, etc (Xiao and Torok 2020) . Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain doi = 10.1111/tbed.13791 id = cord-349774-898tmq14 author = Zhang, Haiyang title = Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein date = 2020-06-16 keywords = SARS; protein summary = title: Proteasome activator PA28γ-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein Here, we report for the first time that the 11S proteasomal activator PA28γ regulates the intracellular abundance of the SARS-CoV-2 N protein (nCoV N). These results suggest that PA28γ binding is important in regulating 20S proteasome activity, which in turn regulates levels of the critical nCoV N nucleocapsid protein of SARS-CoV-2, furthering our understanding of the pathogenesis of COVID-19. The SARS-CoV-2 nucleocapsid protein (hereafter, referred to as nCoV N) accounts for the largest proportion of viral structure proteins and is the most abundant protein in virus-infected cells. PA28γ could be critical for degrading the SARS-CoV-19 nCoV N protein in the nucleus as part of the 20S proteasome, which acts to degrade proteins in a ubiquitin-independent manner, such as seen in the hepatitis C virus (HCV) core protein [11] . Interactions of SARS Coronavirus Nucleocapsid Protein with the host cell proteasome subunit p42 doi = 10.1016/j.bbrc.2020.06.058 id = cord-266324-uvsmbrbf author = Zhang, Hu title = Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases date = 2020-05-08 keywords = SARS; covid-19 summary = title: Clinical characteristics of Coronavirus Disease (COVID-19) patients with gastrointestinal symptoms: A report of 164 cases A cohort study of 140 COVID-19 patients showed that gastrointestinal symptoms were observed in 39.6% of the patients, including nausea (17.3%), diarrhoea (12.9%) and vomiting (5.0%) [4] . Therefore, we determined that a retrospective analysis of cases might be useful for clinicians to identify the clinical characteristics of COVID-19 patients with gastrointestinal symptoms. In this study, red and white blood cells were not identified in the faeces of patients who experienced gastrointestinal symptoms, a finding characteristic of viral infections. Second, this study was the lack of the result of SARS-CoV-2 RNA in the stool of COVID-19 patients, so we did not determine the hypothesis that the severity of gastrointestinal symptoms may be related to the presence of viral replication in stool. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan doi = 10.1016/j.dld.2020.04.034 id = cord-309513-dleo9rpl author = Zhang, Huilan title = Histopathologic Changes and SARS–CoV-2 Immunostaining in the Lung of a Patient With COVID-19 date = 2020-03-12 keywords = SARS summary = Biopsy lung sections were analyzed with hematoxylineosin staining, and immunostaining for SARS-CoV-2 was conducted as reported elsewhere (1) . In contrast, viral protein expression was minimally detectable on blood vessels ( Figure 2 , B, dashed black line) or in the interstitial areas between alveoli (Figure 2, B, bottom panel, blue arrows) . Immu-nostaining of Huh7 cells infected with SARS-CoV and of lung sections from an HIV-positive patient who died of fungal infection served as positive and negative staining controls, respectively (Figure 2, C) . A. Histopathologic examination revealing diffuse alveolar damage, organizing phase (A-1); denudation of alveolar lining cells (arrow 1), with presence of reactive type II pneumocyte hyperplasia (arrow 2) (A-2); intra-alveolar fibrinous exudates (arrow 3) and interstitial loose fibrosis with chronic inflammatory infiltrates (arrow 4) (A-3); and intra-alveolar loose fibrous plugs (arrow 5) (A-4). B. Immunostaining of SARS-CoV-2 in lung sections. doi = 10.7326/m20-0533 id = cord-317129-wa1j2f6b author = Zhang, Jia title = De Novo synthesis of PCR templates for the development of SARS diagnostic assay date = 2003 keywords = PCR; SARS summary = This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. This single-step sequential primer extension was expected to yield mainly final templates with no intermediate products. As shown in Figure 1 , DNA fragments in lengths of 182 and 204 bp were obtained from primers of set A and set B, respectively, by the single-step sequential primer extension where each reaction contained four partially overlapping a The expected products were extended from reverse primers (AR or BR) to the first forward primers. De novo synthesis of the PCR template complimentary to a viral genome provides a tool for the rapid development of early diagnostic assays for any new pathogen as soon as its sequence is known. doi = 10.1385/mb:25:2:107 id = cord-252980-1e28zj1d author = Zhang, Jiahao title = Insights into the cross-species evolution of 2019 novel coronavirus date = 2020-03-04 keywords = SARS summary = 5 Although humans and bats live in different environments, some wildlife species were susceptible to the novel coronaviruses in nature, highlighting that the need of tracing its origin of SARS-CoV-2 in wild animals. The similarity analysis of SARS-CoV-2 and the animal-origin coronaviruses demonstrated that recombination events were likely to occur in bat-and pangolin-origin coronaviruses (Supplementary Figure S1) . Although the S amino acid identities of pangolin-origin coronavirus exhibited lower amino acid identities with bat/RaTG13, it was noteworthy that six amino acids associated with the receptor binding preference of human receptor angiotensin converting enzyme II-464 L, 495F, 502Q, 503S, 510 N, and 514Y (SARS-CoV-2 numbering)-in the pangolin/1 coronavirus were the same as that of SARS-CoV-2 ( Fig. 2 ), but were distinct from that of the bat-origin coronaviruses. Besides, the PRRA-motif insertion was occurred in the S1/S2 junction of SARS-CoV-2; however, the PRRA-motif insertion in the pangolin-and bat-origin coronaviruses was missing (Supplementary Figure S4 ), suggesting that the convergent cross-species evolution of SARS-CoV-2-related coronaviruses. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus doi = 10.1016/j.jinf.2020.02.025 id = cord-285440-srtkqr13 author = Zhang, Jianguo title = Web-based electronic patient records for collaborative medical applications date = 2004-12-20 keywords = EPR; SARS summary = We developed a web-based system to interactively display electronic patient records (EPR), such as DICOM images, graphics, and structure reports and therapy records, for intranet and internet collaborative medical applications. Second, we present a new design of web-based interactive system architecture and its major components, which support EPR display and manipulation and operate in a central mode for collaborative applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. This paper also gives a new approach to create and manage image-based EPR from actual patient records, and also presents a novel method to use web technology and DICOM standard to build an open architecture for collaborative medical applications. doi = 10.1016/j.compmedimag.2004.09.005 id = cord-316623-tv5yyfak author = Zhang, Jianmin title = Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase date = 2008-03-04 keywords = 3CL; SARS summary = The product was purified by column chromatography (50:50 EtOAc/hexanes) to yield 12a as a solid (16 mg To a solution of 11a (10 mg, 0.045 mmol) in dry THF (5 mL) was added LiHMDS (0.1 mL, 1.0 M solution in THF, 0.1 mmol) over a period of 5 min. The mixture was stirred for 1 h at À78°C, and a solution of NFSi (32 mg, 0.1 mmol) in dry THF (3 mL) was added dropwise over 10 min. After 3 h of stirring at 20°C, the solvent was removed in vacuo and the product was purified by column chromatography on silica gel (25:75 EtOAc/hexanes) to yield 21 as a solid (1.35 g, 68%) Based on our previous modeling studies [10b,23], the three-ringed esters utilize a non-covalent and reversible mechanism of inhibition in a S4-S1 binding mode, by blocking entry of substrates into the active site of SARS-CoV 3CL pro . doi = 10.1016/j.bioorg.2008.01.001 id = cord-251943-jzaeaxam author = Zhang, Jian‐San title = A serological survey on neutralizing antibody titer of SARS convalescent sera date = 2005-08-24 keywords = ELISA; SARS summary = A seroepidemiologic study was conducted in North China in 2003 to determine the neutralizing antibody titer of severe acute respiratory syndrome (SARS) convalescent sera. A total of 99 SARS convalescent serum samples were collected from patients from the Inner Mongolia Autonomous Region, Hebei Province, and Beijing 35–180 days after the onset of symptoms. To gain a comprehensive understanding of the antibody to SARS-CoV, we report the anti-SARS antibody titer of 87 SARS convalescent sera determined by neutralization assay. These 87 serum samples were confirmed to be positive for anti-SARS antibodies with the combination of ELISA, neutralization, and Western blot, so they were pooled to form a convalescent sera database for the further analysis of neutralizing antibody titer. The anti-SARS neutralizing antibody titer of 87 positive convalescent sera was analyzed quantitatively by the neutralization assay. In our laboratory, a combination of ELISA, neutralization assay, and Western blot were performed on 99 SARS convalescent sera. doi = 10.1002/jmv.20431 id = cord-016120-pz2q62i7 author = Zhang, Jie title = Chai Jing: The Power of Vulnerability date = 2019-02-16 keywords = CCTV; Chai; China; Dome; SARS; chinese; news summary = This uneasiness with emotion, which is perceived to be opposite to journalistic objectivity, as well as the questioning of Chai''s sincerity, which is an innate paradox of the new documentary movement itself (some questioned whether the filmmakers are using the stories of the marginalized people for their own identity politics), provides a lens into the media consumption habits of the Chinese public in the first two decades of the twenty-first century. Chai left the CCTV in 2014 and returned to the public sphere in 2015 with her documentary Under the Dome, which uses a TED talk format to combine personal testimonials, graphs and data, animation, and interviews to investigate the causes of China''s air pollution. Chai''s embracing her own feelings of vulnerability, which dominated the beginning of her career, and using it to channel public feelings and drive news reporting has made her a distinctively controversial media personality. doi = 10.1007/978-981-13-5980-4_3 id = cord-316180-g3lfecp0 author = Zhang, Jingshu title = Membrane heist: Coronavirus host membrane remodeling during replication date = 2020-10-25 keywords = SARS summary = Here we review the current knowledge of the structure, lipid composition, function, and biogenesis of coronavirus-induced DMVs, highlighting the druggable viral and cellular factors that are involved in the formation and function of DMVs. Prior to the emergence of Coronavirus Disease-2019 (COVID-19) caused by severe 2 acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the outbreak of highly approximately 50 to 250 nm of these DMVs as described in detail elsewhere 9, 10 . Severe 503 acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 504 induce double-membrane vesicles Mutation in 521 murine coronavirus replication protein nsp4 alters assembly of double 522 membrane vesicles Expression and cleavage of middle east respiratory 537 syndrome coronavirus nsp3-4 polyprotein induce the formation of double-538 membrane vesicles that mimic those associated with coronaviral RNA 539 replication The N-terminal region of severe acute respiratory syndrome 546 coronavirus protein 6 induces membrane rearrangement and enhances virus 547 replication doi = 10.1016/j.biochi.2020.10.010 id = cord-324623-x6eom6kh author = Zhang, Jingyi title = Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review date = 2020-04-22 keywords = IVIG; SARS; topic summary = This rapid review aims to explore the clinical effectiveness and safety of IVIG in the treatment of children with severe COVID-19. Methods: We systematically searched the literature on the use of IVIG in patients with COVID-19, Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS), including both adults and children. Results: A total of 1519 articles were identified by initial literature search, and finally six studies, included one randomized controlled trial (RCT), four case series and one case report involving 198 patients. The risk of death was not associated with the use of IVIG in the patients with ARDS (31) .A case report of three adults with COVID-19 reported that a high dose IVIG (25 g/d for 5 days) administered at the appropriate point could successfully block the progression of disease cascade (result of the clinical symptoms, laboratory inspection indicators and chest CT scan), and finally improve the outcome of COVID 19 (32) . doi = 10.1101/2020.04.17.20064444 id = cord-319718-blqzi69t author = Zhang, L. title = Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route date = 2020-05-03 keywords = SARS summary = Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. In order to identify the evolutionary 28 relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are 29 currently used in different countries, we retrieved genomic sequences of 373 30 SARS-CoV-2 strains from multiple databases and performed genome-wide variation 31 analysis. . https://doi.org/10.1101 /2020 Based on the position and nucleotide variation of the phylogenetic tree, 104 we compared the evolutionary variation between SARS-CoV-2 representative 105 strains. doi = 10.1101/2020.04.27.20081349 id = cord-327005-7zgolyqf author = Zhang, Lan title = Clinical Features of 33 Cases in Children Infected With SARS-CoV-2 in Anhui Province, China–A Multi-Center Retrospective Cohort Study date = 2020-06-16 keywords = SARS; case summary = Here, we report 33 patients under the age of 19 years with confirmed COVID-19 infection from Anhui province, China, and describe the clinical features, laboratory, and radiological characteristics of a chest CT, treatment, and clinical outcome. Information recorded included demographic data, medical history, familial clustering, details of the confirmed patients, if any, in the family, whether they were residents of Wuhan, or traveled to Wuhan, whether they came in contact with confirmed patients, signs, and symptoms, including pharyngodynia, fever, cough, vomiting and diarrhea, fatigue, tightness in the chest, total WBC and lymphocyte percentages, levels of C-reactive protein (CRP), IL-6, liver function, CKMB, a marker of myocardial injury, chest CT, administration of INF a, lopinavir and ritonavir, ribavirin, or arbidol, and titers of Mp-IgM, anti-parainfluenza virus IgM, anti-influenza virus IgM, and anti-adenovirus IgM. A retrospective cohort study was used to analyze the epidemiological data, clinical symptoms, and signs, changes in WBC and total lymphocyte counts, chest CT, and the different treatments in children infected with SARS-COV-2. doi = 10.3389/fpubh.2020.00255 id = cord-299989-p59u6qa0 author = Zhang, Lei title = Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date = 2020-06-18 keywords = ACE2; SARS summary = title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. Interestingly, our finding that ACE2 was highly expressed in breast appears to be in contrast to a retrospective study on nine pregnant women with COVID-19 in the third trimester, in which the colostrum from six patients tested negative for SARS-CoV-2 (H. doi = 10.1016/j.meegid.2020.104428 id = cord-303917-2tu707ng author = Zhang, Lei title = Potential interventions for novel coronavirus in China: A systematic review date = 2020-03-03 keywords = COVID-19; MERS; SARS; coronavirus; vitamin summary = We suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children''s RNA‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. In addition, Semba et al 12 had reported that vitamin A supplementation reduced morbidity and mortality in different infectious diseases, such as measles, diarrheal disease, measles-related pneumonia, human immunodeficiency virus (HIV) infection, and malaria. 15 The mechanism by which vitamin A and retinoids inhibit measles replication is upregulating elements of the innate immune response in uninfected bystander cells, making them refractory to productive infection during subsequent rounds of viral replication. Remdesivir (RDV), a nucleoside analog GS-5734, had been reported to inhibit human and zoonotic coronavirus in vitro and to restrain severe acute respiratory syndrome coronavirus (SARS-CoV) in vivo. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1002/jmv.25707 id = cord-351512-h4vigeuy author = Zhang, Lin title = How scientific research reacts to international public health emergencies: a global analysis of response patterns date = 2020-06-09 keywords = COVID-19; China; Ebola; SARS; research summary = In the present paper, we attempt to characterise, quantify and measure the response of academia to international public health emergencies in a comparative bibliometric study of multiple outbreaks. From our analysis of six infectious disease outbreaks since 2000, including COVID-19, we find that academia always responded quickly to public health emergencies with a sharp increase in the number of publications immediately following the declaration of an outbreak by the WHO. Researches in the fields of virology, infectious diseases and immunology are the most active, and we identified two characteristic patterns in global science distinguishing research in Europe and America that is more focused on public health from that conducted in China and Japan with more emphasis on biomedical research and clinical pharmacy, respectively. From the perspective of countries and world regions, funding agencies in the USA, China, and the UK contributed most to supporting research in response to public health emergencies, as shown in Fig. 11 . doi = 10.1007/s11192-020-03531-4 id = cord-294831-pem059zk author = Zhang, Ling-Pu title = Focus on a 2019-novel coronavirus (SARS-CoV-2) date = 2020-06-11 keywords = COVID-19; China; CoV-2; MERS; SARS summary = A report of five patients in a family cluster who traveled to Wuhan and were infected with SARS-CoV-2 was the first report directly illustrating that the virus is capable of person-to-person transmission in hospital and family settings [23] . Xiao and colleagues showed that 53.42% of 73 hospitalized COVID-19 patients had SARS-CoV-2 RNA in stool specimens, and the duration time of positive stool results ranged from 1 to 12 days [27] . In a study published in The Lancet, 41 of 41 patients who were identified as positive for SARS-CoV-2 infection presented with pneumonia and abnormal chest computed tomography (CT) [6] . An article reported in Science shows that SARS-CoV-2 can replicate in the upper respiratory tract of ferrets, indicating that ferrets represent an ideal animal model for evaluating antiviral drugs or vaccine candidates against COVID-19 [64] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan doi = 10.2217/fmb-2020-0063 id = cord-298777-hit7rs6q author = Zhang, Linjie title = What we know so far about Coronavirus Disease 2019 in children: A meta‐analysis of 551 laboratory‐confirmed cases date = 2020-06-10 keywords = COVID-19; SARS summary = We conducted this systematic review and meta-analysis of currently available studies to summarize what we know so far about the epidemiological, clinical, radiological, and laboratory features, as well as therapeutic and prognostic aspects, of COVID-19 in children. To be included in this review, studies needed to meet the following criteria: (a) Study design: randomized trials, observational studies (cross-sectional, cohort and case-control), case series or case reports, and research letters; (b) Participants: children up to 18 years of age with laboratory-confirmed COVID-19; (c) Variables: epidemiological and demographic characteristics, clinical, radiological and laboratory findings, treatments, and prognosis. Thus, 46 articles [7] [8] [9] 14, 15, reporting 551 laboratory-confirmed cases of COVID-19 in children were included in the review (Figure 1 ). A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study doi = 10.1002/ppul.24869 id = cord-294931-a77g9rjo author = Zhang, Linqi title = Antibody responses against SARS coronavirus are correlated with disease outcome of infected individuals date = 2005-11-18 keywords = Nab; SARS summary = While there is no systematic evaluation of cytotoxic T-cell (CTL) activity in infected patients, there are some reports showing detection of binding antibodies to nucleocapsid (N) and spike (S) glycoprotein after about 2 weeks, remaining detectable for as long as 210 days after the onset of symptoms [Shi et al., 2003 Huang et al., 2004; Leung et al., 2004; Liu et al., 2004; Nie et al., 2004a; Temperton et al., 2005] . In this report, using both the ELISA-based and pseudotyped retrovirus-based neutralization systems, we characterized temporal changes in N protein-specific antibody and S glycoprotein-specific Nab responses in infected patients who have either recovered from or succumb to SARS-CoV infection. Since the 293/ACE2 cell line is the most susceptible to entry of the pseudotyped retrovirus bearing S glycoprotein, we chose this cell line for studies of neutralization antibody (Nab) activities of serum samples collected from SARS-CoV-infected patients. doi = 10.1002/jmv.20499 id = cord-261075-wqtxhiy8 author = Zhang, Meng title = The nervous system——a new territory being explored of SARS-CoV-2 date = 2020-10-28 keywords = ACE2; COVID-19; CoV-2; SARS summary = However, there is growing evidence that SARS-CoV-2 can result in a broad spectrum of neurologic diseases (6) (7) (8) (9) , which is not surprising, as neurological manifestations have been reported in other respiratory viral infections, including coronavirus, but the nervous system manifestations of COVID-19 are more common and disabling, raising the worldwide concerns about its potential long-term complications to humans (10, 11) . In particular, we focused on its neurological manifestations and specific pathogenesis, as well as its comparison with other viral respiratory infections.Finally, we further summarized the significance of the neuroinvasion and the follow-up issues that need to be paid attention to by scientists, so as to help neurologists understand the influence of SARS-CoV-2 on nervous system better and promote the accurate diagnosis and efficient treatment of COVID-19. doi = 10.1016/j.jocn.2020.10.056 id = cord-317085-qc8bfb9g author = Zhang, Nan title = Risk Factors for Poor Outcomes of Diabetes Patients With COVID-19: A Single-Center, Retrospective Study in Early Outbreak in China date = 2020-09-24 keywords = COVID-19; IQR; SARS; patient summary = In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In addition to general clinical characteristics of COVID-19, the severe events diabetes patients showed higher counts of white blood cells and neutrophil, lower lymphocytes (40, 76.9%), high levels of hs-CRP, erythrocyte sedimentation rate (ESR) and procalcitonin (PCT) as compared to the non-severe diabetes patients. In the present study, the clinical characteristics of 52 diabetic patients with COVID-19 from a designated hospital in Wuhan, China are described, and the risk factors associated with severe clinical events which were defined as the patients'' admission to ICU, the use of mechanical ventilation, or death are investigated. doi = 10.3389/fendo.2020.571037 id = cord-338152-e8e3lv79 author = Zhang, Peilin title = Detection of SARS-CoV-2 in placentas with pathology and vertical transmission date = 2020-08-03 keywords = SARS summary = We examined 364 consecutive placentas from the mothers tested in our facilities since the universal testing policy was adopted in March 2020 including 74 positive and 290 negative for SARS-CoV2 by nasopharyngeal swab PCR method as previously described [1] . One positive placenta for SARS-CoV2 by ISH was delivered by C-section at 35 weeks 6 days due to placental previa 4 associated with placental infarcts, and the newborn baby was tested positive by swab PCR at 24 hours, 48 hours and 7 days. The other positive placenta was from a mother with 40 week gestation associated with no significant clinical and pathological features, and the baby was tested negative for SARS-CoV2 by swab PCR method within the first 24 hours. The current study showed that SARS-COV2 viral particles are uncommon in placentas from PCR-positive mothers at late gestation. Neonatal testing for SARS-CoV2 by swab PCR also showed rare positive cases from positive mothers. doi = 10.1016/j.ajogmf.2020.100197 id = cord-268760-31i0mpvn author = Zhang, Qian title = Anosmia and Ageusia as the Only Indicators of Coronavirus Disease 2019 (COVID-19) date = 2020-05-01 keywords = COVID-19; SARS summary = There is currently a lack of published case reports describing COVID-19 patients with the sole symptoms of anosmia and ageusia in the United States of America. This case report details a 60year-old woman with the chief complaint of right-sided headache along with anosmia and ageusia but was eventually found to be SARS-COV-2 positive. The most common COVID-19 symptoms include fever (43.8% on initial presentation and 88.7% during hospitalization), cough (67.8%), nasal congestion (4.8%), nausea or vomiting (5.0%), and diarrhea (3.8%) based on a research study of 1099 patients from China. Our patient had a very low clinical suspicion of COVID-19 infection, as she was afebrile along with no respiratory symptoms despite having anosmia and ageusia in the setting of headache caused by trigeminal neuralgia. Awareness of a possible COVID-19 infection should be raised in patients with the sole presentation of anosmia and ageusia despite the lack of published case reports or research findings on its exact mechanisms of action. doi = 10.7759/cureus.7918 id = cord-254968-czrgzyr3 author = Zhang, Qiang title = A serological survey of SARS-CoV-2 in cat in Wuhan date = 2020-09-17 keywords = CoV-2; SARS; Wuhan summary = Here, we investigated the infection of SARS-CoV-2 in cats during COVID-19 outbreak in Wuhan by serological detection methods. Our data demonstrated that SARS-CoV-2 has infected cats in Wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of COVID-19. Here, we investigated the serological prevalence of SARS-CoV-2 in cats by an indirect ELISA and virus neutralization tests (VNT), and monitored the serum antibody dynamics of cats infected SARS-CoV-2, providing a basis for further understanding the infection of SARS-CoV-2 in cats. In this study, we detected the presence of SARS-CoV-2 antibodies in cats in Wuhan during the COVID-19 outbreak with ELISA, VNT and western blot. Virus neutralization test and Western blot assay of cat serum samples for SARS-CoV-2 (A) Cat#14, Cat#15 and Cat#4 sera were 3-fold serially diluted and mixed with SARS-CoV-2; after incubated at 37°C for 1 h, the mixture was used to infect Vero E6 cells, and replaced with semi-solid media 1 h later. doi = 10.1080/22221751.2020.1817796 id = cord-294199-o8w35pdy author = Zhang, Qiangzhe title = Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity date = 2020-06-17 keywords = SARS summary = Inspired by the fact that the infectivity of SARS-CoV-2 relies on its binding with the protein receptors, either known or unknown, on the target cells, we create cellular nanosponges as a medical countermeasure to the coronavirus. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) and CD147 expressed on the host cells, such as human alveolar epithelial type II cells, as receptors for cellular entry. To further verify that the inhibition was indeed due to epithelial cell or macrophage membrane coating, control nanosponges made from membranes of red blood cells (denoted "RBC-NS") were also tested in parallel for viral inhibition but were not effective in neutralizing SARS-CoV-2 infection of Vero E6 cells ( Figure 3C ). In principle, as long as the target of the virus remains the identified host cell, the nanosponges will be able to neutralize the infection, providing a broad-acting countermeasure resistant to mutations and protection against this and other emerging coronaviruses. doi = 10.1021/acs.nanolett.0c02278 id = cord-356154-ifb3qiz7 author = Zhang, Rong title = A Study of Two Cases Co-Infected with SARS-CoV-2 and Human Immunodeficiency Virus date = 2020-09-07 keywords = SARS summary = CT scan results in early February indicated lesions in bilateral lungs (Supplementary Table S1 ), but the result of the SARS-CoV-2 nucleic acid test was negative. However, the patient''s condition deteriorated again on February 20, and the nucleic acid test results were single positive for COVID-19 SARS-CoV-2. Notes: ND, no data; ?, positive; -, negative We assumed that HIV infection had damaged their immune systems; this could also explain why the patient tested negative for SARS-CoV-2 antibodies in the late stages of treatment when the disease became worse. In general, the blocking of the IL-6 receptor with tocilizumab has a particular effect on the treatment of COVID-19 patients with severe disease, but it may have little effect on patients with Fig. 1 The clinical courses of two cases co-infected with SARS-CoV-2 and HIV. COVID-19 patients with immunodeficiency disease may cause more severe illness and poor treatment response due to the destruction of the immune system. doi = 10.1007/s12250-020-00280-9 id = cord-321155-dty18esg author = Zhang, Rongxin title = Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date = 2020-06-05 keywords = RNA; SARS; SUD summary = We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. doi = 10.1101/2020.06.05.135749 id = cord-280961-fka8c69p author = Zhang, Rui title = CT features of SARS-CoV-2 pneumonia according to clinical presentation: a retrospective analysis of 120 consecutive patients from Wuhan city date = 2020-04-11 keywords = SARS; patient summary = METHODS: This was a retrospective analysis of the clinical and thoracic CT features of 120 consecutive patients with confirmed SARS-CoV-2 pneumonia admitted to a tertiary university hospital between January 10 and February 10, 2020, in Wuhan city, China. (c) Unenhanced axial CT images of a 27-year-old male doctor with a history of exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), nonproductive cough, dyspnea, and myalgia (c1) who progressed to a severe case requiring oxygen supplementation (c2). (d) Unenhanced axial CT images of a 52-year-old male doctor with asthma and exposure to confirmed SARS-CoV-2 patients, initially presenting with fever (39°C), non-productive cough, dyspnea, and myalgia who rapidly progressed to a severe form requiring mechanical ventilation. In this study, we reported the clinical characteristics and chest CT findings at presentation for all types of SARS-CoV-2 pneumonia severity. doi = 10.1007/s00330-020-06854-1 id = cord-320681-b3ui95vx author = Zhang, Rui title = COVID-19: Melatonin as a potential adjuvant treatment date = 2020-06-01 keywords = ALI; SARS; covid-19; melatonin summary = Based on clinical features, pathology, the pathogenesis of acute respiratory disorder induced by either highly homogenous coronaviruses or other pathogens, the evidence suggests that excessive inflammation, oxidation, and an exaggerated immune response very likely contribute to COVID-19 pathology. Herein, we review the evidence indicating that melatonin will have supportive adjuvant utility in treating COVID-19 induced pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In SARS-CoV and MERS-CoV infected animal model, marked inflammatory and immune responses may activate a "cytokine storm", and apoptosis of epithelial cells and endothelial cells; subsequently, vascular leakage, abnormal T cell and macrophages responses ensue and induce ALI/ARDS or even death [13] . The amplification of the inflammatory response would promote cellular apoptosis or We postulated that lungs infected by SARS-CoV-2, and a suppressed immune response, elevated inflammation and excessive oxidation stress proceed unabated, this results in the activation of the cytokine storm. doi = 10.1016/j.lfs.2020.117583 id = cord-298426-hhly45md author = Zhang, Shan-Yan title = Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China date = 2020-07-08 keywords = COVID-19; SARS; Zhejiang summary = title: Clinical characteristics of different subtypes and risk factors for the severity of illness in patients with COVID-19 in Zhejiang, China CONCLUSIONS: Clinicians should pay close attention to these features in patients with COVID-19 including older age, male, fever, cough, hemoptysis, gastrointestinal symptoms and hypertension to identify the severity of illness as early as possible. Hence, the aim of our study is to summarize the epidemiologic and clinical characteristics, laboratory and radiograph findings, treatments, and outcomes of different subtypes of patients with COVID-19 in Zhejiang Province. We conducted a retrospective study investigating on the epidemiological, clinical, laboratory, radiograph, treatments and outcomes characteristics of confirmed cases of COVID-19 in Zhejiang Province from 17 January to 12 February 2020. Several risk factors for the severity of illness in patients with COVID-19 were identified in our study including male, fever, cough, hemoptysis, gastrointestinal symptoms, hypertension, and higher age-grading. doi = 10.1186/s40249-020-00710-6 id = cord-302166-tah3jdw0 author = Zhang, Shen-Ying title = Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity? date = 2020-06-18 keywords = SARS; severe summary = We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. We suggest that these patients may become critically ill because of monogenic inborn errors that disrupt protective immunity to SARS-CoV-2. Studies since 1996 have identified a number of monogenic inborn errors of immunity (IEIs) underlying life-threatening infectious diseases, including specific viral diseases, in previously healthy patients 1,3-6 . The search for monogenic IEIs conferring predisposition to severe COVID-19 in previously healthy children and young or even middle-aged adults should therefore involve the genome-wide, agnostic testing of genetic hypotheses (see also COVID Human Genetic Effort) 10 . The discovery of monogenic IEIs to SARS-CoV-2 should help unravel the mechanistic basis of the immunopathogenesis of severe COVID-19 in young, previously healthy individuals. A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection doi = 10.1038/s41577-020-0373-7 id = cord-030535-8o7rzb98 author = Zhang, Sheng title = Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists date = 2020-08-12 keywords = SARS summary = The tutorial begins with the X-ray crystallographic structure of the main protease (Mpro) of the SARS coronavirus (SARS-CoV) bound to a peptide substrate and then uses the UCSF Chimera software to modify the substrate to create a cyclic peptide inhibitor within the Mpro active site. In this tutorial, we will use the X-ray crystallographic structure of the homologous SARS-CoV M pro bound to a protein substrate to recapitulate the design of a cyclic peptide inhibitor of the SARS-CoV-2 M pro . 8 We will first use the molecular modeling software UCSF Chimera to visualize the X-ray crystallographic structure of the SARS-CoV M pro bound to the protein substrate. In structure-based drug design, we would typically now synthesize the cyclic peptide inhibitor and evaluate its activity experimentally through studying its ability to block the cleavage of a fluorogenic peptide substrate by SARS-CoV-2 M pro . doi = 10.26434/chemrxiv.12791954 id = cord-294410-iy57tjx5 author = Zhang, Shengnan title = (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain date = 2010-12-23 keywords = SARS summary = title: (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain The main protease (M(pro)) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. Here, we reported the NMR assignments of the SARS-CoV M(pro) N-terminal domain alone, which are essential for its solution structure determination. The backbone resonance chemical shift assignments were based on 2D 1 H-15 N HSQC, 3D HNCA, HN(CO)CA, HNCACB, CBCA(CO)HN, HNCO, HN(CA)CO and HBHA(CO)NH NMR spectra. The side chain resonance chemical shift assignments were based on 3D HCCH-COSY, HCCH-TOCSY, (H)CCH-COSY, and (H)CCH-TOCSY NMR experiments data. Without its n-finger, SARS-CoV main protease can form a novel dimer through its C-terminal domain C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer doi = 10.1007/s12104-010-9287-9 id = cord-294392-a8s66g96 author = Zhang, Shuai title = Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date = 2020-09-07 keywords = SARS summary = title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. 12 Two studies showed that tracheal intubation procedure was related to increased risk of 120 transmission SARS-CoV-1 and SARS-CoV-2 to HCWs. 13,14 Face mask and eye protection especially 121 N95 respirators were most consistently with reduced COVID-19 infection among HCWs. 14,15 Face 122 mask was also reported to be associated with asymptomatic SARS-CoV-2 infection based on several 123 uncontrolled reports. The univariable logistic regression analysis showed worked in high-risk departments, 169 hand washing consistently and consistent use of isolation gown, N95 respirators, gloves, hair cover, 170 and eye protection were associated with an increased likelihood of asymptomatic infection (Table S1) . doi = 10.1016/j.cmi.2020.08.038 id = cord-332185-a96r1k7a author = Zhang, Shuyuan title = Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date = 2020-09-22 keywords = RBD; SARS summary = title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. Cryo-electron microscopy structures of the SARS-CoV spike 464 glycoprotein reveal a prerequisite conformational state for receptor binding Cryo-EM structure of the SARS 467 coronavirus spike glycoprotein in complex with its host cell receptor ACE2 Cryo-EM structures of MERS-CoV and SARS-CoV spike 495 glycoproteins reveal the dynamic receptor binding domains doi = 10.1101/2020.09.21.307439 id = cord-297236-wnuvofwr author = Zhang, Si title = SARS-CoV-2 binds platelet ACE2 to enhance thrombosis in COVID-19 date = 2020-09-04 keywords = ACE2; SARS; Spike; additional; covid-19; platelet summary = SARS-CoV-2 and its Spike protein directly enhanced platelet activation such as platelet aggregation, PAC-1 binding, CD62P expression, α granule secretion, dense granule release, platelet spreading, and clot retraction in vitro, and thereby Spike protein enhanced thrombosis formation in wild-type mice transfused with hACE2 transgenic platelets, but this was not observed in animals transfused with wild-type platelets in vivo. However, similar to the results from the SARS-CoV-2 virus experiments, we were able to demonstrate that the Spike protein dose-dependently enhanced platelet aggregation and ATP release (Additional file 1: Online Figure 6 ). In addition, the Spike protein potentiated platelet aggregation and ATP release in response to agonists in vitro and enhanced thrombosis formation in vivo on hACE2 transgenic mice, while it had no effect on wild-type mice ( Fig. 6c and Additional file 1: Online Figure 8 ). doi = 10.1186/s13045-020-00954-7 id = cord-327499-4aps0kvp author = Zhang, Wei title = Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes date = 2020-02-17 keywords = SARS; swab summary = It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Human samples, including oral swabs, anal swabs and blood samples were collected by Wuhan pulmonary hospital with the consent from all patients and approved by the ethics committee of the designated hospital for emerging infectious diseases. We conducted a molecular investigation to patients in Wuhan pulmonary hospital, who were detected as oral swabs positive for 2019-nCoV upon admission. We collected blood, oral swabs and anal swabs for 2019-nCoV qPCR test using previously established method [5] . We detected the virus in oral swabs, anal swabs and blood, thus infected patients can potentially shed this pathogen through respiratory, fecal-oral or body fluid routes. Above all, we strongly suggest using viral IgM and IgG serological test to confirm an infection, considering the unreliable results from oral swabs detection. doi = 10.1080/22221751.2020.1729071 id = cord-316126-j51dik7f author = Zhang, X. Sophie title = SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles date = 2020-10-28 keywords = COVID-19; CoV-2; N95; PPE; SARS; mask; study; transmission summary = title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles Since the beginning of the COVID-19 pandemic, there has been intense debate over SARS-CoV-2''s mode of transmission and appropriate personal protective equipment for health care workers in low-risk settings. This review attempts to summarize current cumulative data on SARS-CoV-2''s modes of transmission and identify gaps in research while offering preliminary answers to the question on everyone''s mind: is the airborne route significant and should we modify our COVID-19 PPE recommendations for frontline workers in low-risk settings? Given that substantial disagreement persists on the importance of natural aerosol generation by COVID-19 patients, and consequently, the necessary level of respiratory protection in non-AGP contexts, our review will focus on transmission and PPE in low-risk health care settings. doi = 10.1128/cmr.00184-20 id = cord-316525-uadfehr6 author = Zhang, X. W. title = Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date = 2004-10-11 keywords = IBV; SARS summary = Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). doi = 10.1007/s00705-004-0413-9 id = cord-263739-xoum5e0k author = Zhang, X.-Y. title = Analysis of the effect of proton pump inhibitors on the course of common COVID-19 date = 2020-06-09 keywords = June; SARS summary = In the proton pump inhibitors group and the control group, the duration of SARS-CoV-2 clearance were 7(6-9) and 7(6-11) days, and the duration of hospital stay was 21(16-25) and 20(15-26) days, respectively. Case exclusion criteria: (1) the patients used drugs to inhibit the secretion of 179 gastric acid within 30 days before admission; (2) Specimens used for SARS-CoV-180 2 nucleic acid testing were collected at an interval of more than 48 hours; (3) 181 The demographic and clinical data included age and sex of the patients, The nucleic acid test specimens of SARS-CoV-2 in this study were 209 The cumulative probability of SARS-CoV-2 clearance or discharge from 224 COVID-19 cases were conducted through Kaplan-Meier statistics, and the 225 difference was examined by Log-rank test. Cumulative probability of SARS-CoV-2 clearance and discharge in COVID-19 676 patients between PPIs group and control group by 1:1 PS-matching analysis doi = 10.1101/2020.06.07.20124776 id = cord-296375-gf0mgz5x author = Zhang, Xi title = Comparison of spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China date = 2020-10-30 keywords = COVID-19; SARS summary = CONCLUSIONS: COVID-19 and SARS outbreaks exhibited distinct spatiotemporal clustering patterns at the provincial levels in mainland China, which may be attributable to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms. Therefore, in this study, by collecting the daily numbers of newly confirmed COVID-19 and SARS cases during the two epidemics, we aimed to determine the spatial behavior and temporal features of the COVID-19 spread in mainland China and compared them with respective features from the SARS epidemic using spatiotemporal analysis. Incident cases infected by COVID-19 were extracted from the daily briefings on novel coronavirus cases from January 20 to March 4, 2020, provided on the official website of the National Health Commission of the People''s Republic of China [5] . Incident cases of SARS were extracted from daily situation reports for mainland China from April 21 to August 3, 2003 , which were posted by China.org.cn (in Chinese) and were also provided by the National Health Commission. doi = 10.1186/s12879-020-05537-y id = cord-353537-skeajydw author = Zhang, Xian title = Asymptomatic Subclinical Cases of Coronavirus Disease 2019 without Viral Transmission in Three Independent Families date = 2020-09-24 keywords = COVID-19; SARS summary = Their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected by SARS-CoV-2. Three medical staff diagnosed with asymptomatic SARS-CoV-2 infection by serological tests after returning to work and their family members were recruited for this study. The patients and their close contacts were systematically evaluated based on COVID-19-related symptoms, nucleic acid tests, serological tests, and chest computed tomography (CT) as needed to determine if they were infected with SARS-CoV-2. All their family members-including four old people, three young persons, and three children-showed no symptoms of COVID-19, and their nucleic acid and antibody tests were negative, indicating that they were not infected. During the following 2 months more, almost covering the whole disease process, from the incubation period to the recovery period, the indexes lived together with their family members, including a nasopharyngeal carcinoma patient who is theoretically vulnerable to SARS-CoV-2 infection due to impaired immune function as a result of radiotherapy or chemotherapy, without taking any protective measures. doi = 10.2147/idr.s261304 id = cord-300445-qzu4gz2d author = Zhang, Xiao-lei title = Pharmacological and cardiovascular perspectives on the treatment of COVID-19 with chloroquine derivatives date = 2020-09-23 keywords = COVID-19; SARS; chloroquine; patient summary = Chloroquine phosphate and its derivative hydroxychloroquine, which have been used in the treatment and prevention of malaria and autoimmune diseases for decades, were found to inhibit SARS-CoV-2 infection with high potency in vitro and have shown clinical and virologic benefits in COVID-19 patients. However, chloroquine phosphate and its derivative hydroxychloroquine, which have been used for decades in the treatment and prevention of malaria and chronic inflammatory diseases such as rheumatoid arthritis and systemic lupus erythematosus, were discovered to have a high inhibitory potency against SARS-CoV-2 infection in vitro [2] [3] [4] [5] and favorable clinical and virologic benefits in COVID-19 patients [6] [7] [8] [9] [10] , and they have emerged as important therapies for COVID-19 in several countries, including China, France, USA, and India, although the mechanisms of their anti-COVID-19 effects remain unclear. doi = 10.1038/s41401-020-00519-x id = cord-324727-bj8oei0v author = Zhang, Xiaomei title = Management of Digestive Disorders and Procedures Associated With COVID-19 date = 2020-06-03 keywords = COVID-19; SARS summary = The Chinese Gastroenterology Expert Group, comprising experts from the gastroenterology units and national medical aid teams of the epidemic region of Wuhan, along with the Chinese Society of Gastroenterology introduce and recommend this management consensus for digestive disorders in patients with COVID-19. Liver injury in patients with COVID-19 may be caused by either systemic inflammation or direct effects of SARS-CoV-2 on the angiotensin-converting enzyme 22 of cholangiocytes (13) . To prevent or control the transmission of SARS-CoV-2 in epidemic communities, gastroenterological procedures such as esophageal pH test, gastrointestinal motility, hydrogen breath test, fecal microbiota transplantation, Helicobacter pylori breath test, and stool antigen detection are recommended for suspension or postponement until the epidemic is under control. Don''t overlook digestive symptoms in patients with 2019 novel coronavirus disease (COVID-19) Digestive symptoms in COVID-19 patients with mild disease severity: Clinical presentation, stool viral RNA testing, and outcomes doi = 10.14309/ajg.0000000000000728 id = cord-276991-gv1k7u7j author = Zhang, Xu title = Strategies to trace back the origin of COVID-19 date = 2020-04-08 keywords = SARS summary = The recent outbreak of coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2, had raised great concern. Chinese authorities originally announced that the first infection case was reported on December 31, 2019, and many of the initial cases were linked directly to Huanan seafood market in Wuhan, in the Hubei province. The hypothesis that the outbreak originated at the market, with its initial transmission from live animals to human beings followed by rapid human-to-human transmission, is suggested to be most likely and convincing. Emergence of SARS-like coronavirus poses new challenge in China Novel coronavirus disease (Covid-19): the first two patients in the UK with person to person transmission Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Emergence of SARS-like coronavirus in china: an update doi = 10.1016/j.jinf.2020.03.032 id = cord-329707-89zyu8bl author = Zhang, Xue title = Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date = 2006-11-30 keywords = RNA; SARS summary = We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. doi = 10.1159/000097391 id = cord-336605-d4loia11 author = Zhang, Xue Wu title = Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs date = 2004-05-15 keywords = SARS; UC2 summary = To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Except four drugs (lopinavir, ritonavir, niclosamide and promazine), we also conducted the docking studies of two other molecules, PNU and UC2, for their molecular formulas are close to those of niclosamide and promazine, respectively (Fig. 2) , and they both are the inhibitors of HIV-1 reverse transcriptase. Figure 3 displays the overall structures of docking for four drugs (lopinavir, ritonavir, niclosamide and promazine) and two inhibitors (PNU and UC2) to SARS-CoV main proteinase. Thus, the four drugs and two inhibitors studied here can basically bind to the active site of SARS-CoV main proteinase, a cleft between domains I and II. doi = 10.1016/j.bmc.2004.03.035 id = cord-275216-dnt88ycw author = Zhang, Xue-Yan title = Biological, clinical and epidemiological features of COVID-19, SARS and MERS and AutoDock simulation of ACE2 date = 2020-07-20 keywords = ACE2; COVID-19; MERS; SARS summary = This review is intended to summarize the research on this new coronavirus, to analyze the similarities and differences between COVID-19 and previous outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and to provide guidance regarding new methods of prevention, diagnosis and clinical treatment based on autodock simulations. Given that the epidemic is still spreading and the evidence that there are similarities among the three coronaviruses in terms of their biological, clinical and epidemiological features, a comparison among the three is very helpful to guide the improvement of treatment and prevention measures, and the similarities and differences among the three are likely to provide the key to addressing the COVID-19 epidemic. In 2002-2003, SARS-CoV caused an epidemic of severe acute respiratory diseases in China; MERS-CoV was found in the Middle East in 2012 [9, 10] . doi = 10.1186/s40249-020-00691-6 id = cord-328187-9zd79gai author = Zhang, Yali title = Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date = 2020-07-22 keywords = CSBT; SARS; figure summary = The new system allows quantitative analyses of the inhibition potentials and detailed influence of COVID-19-convalescent human plasmas, neutralizing antibodies and compounds, providing a versatile tool for high-throughput screening and phenotypic characterization of SARS-CoV-2 entry inhibitors. 22 On 293T-ACE2iRb3 cells, both the SARS-CoV2-RBG and SARS-CoV2-STG 23 probes showed effective-binding to the cells, as membrane-bound and hACE2-24 mRuby3-colocalized mGam signals were observed after a 6-min incubation with the 25 cells ( Figure 2C ). Compared with 3 samples from healthy donors (n=40), all COVID-19-convalescent plasmas showed 4 significant cMFI inhibition on CSBT assay, whereas only 12 samples (37.5%) had 5 detectable CRBT activity ( Figure 3A ). Among the antibody titers derived from various assays, the 10 CSBT titer showed the best correlation with LVppNAT ( Figure 3D and Table S2, 11 r=0.832, p<0.001), and it also well correlated (r=0.959, p<0.001, Figure 3D ) with the 12 neutralization activity against authentic SARS-CoV-2 virus in 12 representative 13 samples (Table S3) . doi = 10.1101/2020.07.22.215236 id = cord-327721-y39751g4 author = Zhang, Yan title = Emotional “inflection point” in public health emergencies with the 2019 New Coronavirus Pneumonia (NCP) in China date = 2020-07-19 keywords = Hubei; Province; SARS; student summary = BACKGROUND: The outbreak of the new coronavirus pneumonia (NCP) in Wuhan, Hubei, has caused very serious consequences and severely affected people''s lives and mental health. METHODS: This study used self-designed questionnaires and artificial intelligence (AI) to assess and analyze the emotional state of over 30,000 college students during the outbreak period in January (T1) and home quarantine in February (T2). From these data, it indicated that during the period of home isolation, college students in Hubei Province showed more negative emotions due to their long-term exposure to the epidemic. There is also the stress symptom of "seeming as being infected" caused by too much browsing of the relevant news every day, which directly affects the emotions of students, they became more sensible and anxious to disease, this is a mental tension (Peng et al., 2019) . This survey found that there is an emotional "infection point" in February among college students, especially in the Hubei area. doi = 10.1016/j.jad.2020.07.097 id = cord-334378-dqtnj3y3 author = Zhang, Yi title = Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2 date = 2020-06-10 keywords = ACE2; SARS summary = How does RBD of the SARS-CoV-2 spike protein binds to the human receptor ACE2? The precise binding interface of the SARS-CoV-2 spike RBD and ACE2 can be dissected from the crystal structures of the complex determined by Shang et al. Analysis of the crystal structures of RBD from the SARS-CoV spike protein in complex with established SARS-CoV neutralizing human m396 and 80R antibodies reveals that the antibodies are bound in the same binding site as ACE2 9,10 , implying that their neutralizing mechanism is a direct blockage of receptor binding. Proteolytic cleavage of the SARS-CoV-2 spike protein by the human serine protease TMPRSS2 is a critical step in the virus entry through the plasma membrane fusion mechanism (Fig. 2) , as shown by Hoffmann et al. In addition to targeting components of the viral attachment and the membrane fusion machinery, other strategies to eliminate SARS-CoV-2 include impeding virus entry into the host cell through the endosomal pathway and disrupting activities of viral proteins. doi = 10.1038/s41467-020-16779-4 id = cord-268144-maa8c4a4 author = Zhang, Yuan title = Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization date = 2007-02-17 keywords = RBD; SARS summary = The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. As an envelope glycoprotein, the spike protein of severe acute respiratory syndrome coronavirus (SARS-CoV) plays a key role in the viral entry and neutralization (Bartlam et al., 2005; Denison, 2004; Lau and Peiris, 2005; Xu and Gao, 2004; Zhu, 2004) . Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1016/j.compbiolchem.2007.02.005 id = cord-316066-pge0vx04 author = Zhang, Zheng title = Longitudinal alteration of circulating dendritic cell subsets and its correlation with steroid treatment in patients with severe acute respiratory syndrome date = 2005-06-16 keywords = SARS summary = In this study, we found that 74 patients with severe acute respiratory syndrome (SARS) exhibited a rapid, dramatic decrease in numbers of circulating myeloid and plasmacytoid dendritic cells (mDCs and pDCs) during the first 2 weeks of illness (5.3and 28.4-fold reductions for mDCs and pDCs compared with 25 healthy individuals, respectively), with slow return to normal cell numbers during convalescence (weeks 5–7 of illness on average). A marked lymphocytopenia occurred in most patients during the acute phase of SARS, with CD4 and CD8 T-cell subsets particularly affected, and the degree of reduction of circulating T lymphocyte counts was found to be associated with disease severity, indicating that host immune functional changes are involved in the initiation and progression of SARS [3 -6] . In addition, our findings suggest that acute SARS-CoV infection may contribute to the rapid initial reduction of both circulating mDCs and pDCs. Subsequently, steroid administration, particularly at high doses over weeks, probably exacerbated and prolonged the decrease in numbers of DC subset as well as T-cell subsets. doi = 10.1016/j.clim.2005.04.015 id = cord-324518-a346cjx4 author = Zhang, Zhibin title = The outbreak pattern of the SARS cases in Asia date = 2004 keywords = SARS; case summary = The increase rate of SARS cases is expected to decrease with the cumulative SARS cases, as described by the traditional logistical model, which is widely used in population dynamic studies. The maximum instantaneous rate of increase, basic reproductive number, and maximum cumulative SARS cases were also calculated by using the logistic model. The outbreak pattern of cumulative SARS cases is likely of a logistic type because at the initial stage, it grows exponentially, later due to the increasing control effort by people and/or due to depletion of susceptible individuals, the infection will be slowed down. significant and negative linear "density dependency" of the instantaneous rate of increase on the cumulative cases of SARS indicates that the outbreak pattern of SARS can be well described by the logistic model( Fig. 1(a) and (b) ). doi = 10.1007/bf03183407 id = cord-310091-x31g02xw author = Zhang, Zhilan title = Pan-cancer analysis reveals that ACE2 is positively associated with immunotherapy response and is a potential protective factor for cancer progression date = 2020-09-02 keywords = ACE2; SARS; cancer summary = Using cancer genomics datasets from the Cancer Genome Atlas (TCGA) program, we performed computational analyses of associations between ACE2 expression and antitumor immunity, immunotherapy response, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in 13 cancer cohorts. A recent study [9] showed that ACE2 expression was associated with increased tumor immune infiltration and was a positive prognostic factor in uterine corpus endometrial and renal papillary cell cancers. Despite these previous studies, a systemic investigation into the association between ACE2 expression and antitumor immunity, oncogenic pathways, tumor progression phenotypes, and clinical outcomes in pan-cancer remains lacking. We also explored associations between ACE2 expression and multiple tumor phenotypes, including cell proliferation, stemness, epithelial-mesenchymal transition (EMT), oncogenic signaling, and clinical outcomes in these cancer cohorts. We found that ACE2 expression levels inversely correlated with the activity of cell cycle, mismatch repair, TGF-β, Wnt, VEGF, and Notch signaling pathways in 10, 7, 9, 7, 5, and 7 individual cancer types, respectively (Spearman''s correlation test, FDR < 0.05) ( Fig. 2A) . doi = 10.1016/j.csbj.2020.08.024 id = cord-265164-ybh5yljw author = Zhao, Bin title = Numerical study of the transport of droplets or particles generated by respiratory system indoors date = 2004-11-24 keywords = SARS; particle summary = The drift flux model, which considers the settling of particles or droplets under the effect of gravitational sedimentation, is adopted to simulate the droplets transport and distribution indoors during respiration and sneezing or coughing process, while the simplified model for solving the continuous fluid flow is combined. The results show that droplets or particles generated by normal breathing process transport a relatively short distance, while droplets or particles generated during coughing or sneezing may travel much longer distances, which may pose adverse effect on human bodies for defending the SARS or other infectious diseases. To calculate the three-dimensional and non-isothermal airflow inside ventilated rooms, a well validated simplified methodology combined with N-point air supply opening model [4] , a zero equation turbulence model [5] is applied. Numerical studies on the transport and distribution of particles or droplets generated by normal respiration and sneezing or coughing indoors result in the following conclusions: doi = 10.1016/j.buildenv.2004.09.018 id = cord-333140-cdikbi1l author = Zhao, Helong title = Imatinib is not a potent anti-SARS-CoV-2 drug date = 2020-09-30 keywords = SARS summary = We tested the effects of imatinib and asciminib, a highly specific and potent ABL inhibitor binding to the myristate pocket of the kinase domain [7] , on SARS-CoV-2 infection and replication in the naturally susceptible ACE2 + human Caco-2 cells [5] . We then performed the standard viral replication assay using the USA-WA1/2020 strain of SARS-CoV-2 to test imatinib and asciminib in a blinded fashion, including remdesivir as a positive control. Therefore, our data indicate that, within clinically achievable dose ranges, imatinib and asciminib have no significant effect on SARS-CoV-2 infection and replication. These data support additional prospective investigations into the potential beneficial effect of imatinib and possibly other ABL inhibitors on COVID-19, but provide insufficient evidence for the off-label use of imatinib in patients with COVID-19. Prevalence of COVID-19 diagnosis in Dutch CML patients during the 2020 SARS-CoV2 pandemic. Imatinib is not a potent anti-SARS-CoV-2 drug doi = 10.1038/s41375-020-01045-9 id = cord-347767-aq9niccc author = Zhao, Jie title = Yidu-toxicity blocking lung decoction ameliorates inflammation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome by eliminating IL-6 and TNF-a date = 2020-06-19 keywords = CD4; COV-2; IL-6; SARS summary = The present study investigates the differences in inflammatory agents alterations, immune function, and leukocyte differential count evaluation in severe pneumonia of SARS-COV-2 patients with Yidu-toxicity blocking lung syndrome after the recommended Chinese medicine prescription of Yidu-toxicity blocking lung decoction. A total of 40 patients with yidu-toxicity blocking lung syndrome, diagnosed as severe pneumonia of SARS-COV-2 following the latest Chinese national recommendations for the diagnosis and treatment of pneumonia caused by SARS-COV-2 (the 5th edition), were recruited. To characterize the effect of herbal medicine, immune function, and inflammatory agents, levels of white blood cells were detected for all patients according to the manufacturer''s instructions at the beginning and at the end of the two weeks. In conclusion, our study suggests that the 5th edition recommendation''s CM prescription, can be safely used in the treatment of severe pneumonia of SARS-COV-2 with yidu-toxicity blocking lung syndrome. doi = 10.1016/j.biopha.2020.110436 id = cord-316723-srenbxa7 author = Zhao, Jincun title = Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus date = 2004-11-23 keywords = ELISA; S450; SARS summary = Amino acid residues 450–650 of the spike (S) glycoprotein of SARS-CoV (S450-650) contains dominant epitopes for anti-viral antibodies (Abs) in patient sera. However, so far there is no enzyme-linked immunosorbent assay (ELISA) available for easier and more sensitive detection of anti-S Abs. Our computer-assisted analysis suggested that amino acid residues 450-650 of the S glycoprotein (S450-650) of SARS-CoV is largely solvent accessible and likely to contain dominant B cell epitopes. (2004) showing that residues 441-700 of the S protein of SARS-CoV contained dominant epitope(s) for anti-S Abs in patient sera, as determined in WB assays. All patient sera were tested for anti-SARS-CoV IgG Abs using an ELISA kit produced by Huada Institute (see below). Sera from three convalescent SARS patients and two healthy individuals were serial diluted and tested in the S450-650-based ELISAs, which detected anti-S IgG Abs in a specific and sensitive manner, with the reactivity end point from 1:400 to 1:800 diluted patient sera (Fig. 2) . doi = 10.1016/j.jcv.2004.09.024 id = cord-333515-llqpfhwg author = Zhao, Juanjuan title = Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date = 2020-03-03 keywords = RNA; SARS summary = Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. To mitigate this knowledge gap, and to provide scientific analysis on the benefit of antibody testing when used in combination with the current RNA testing, this study investigates the dynamics of total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 in serial blood samples collected from 173 confirmed COVID-19 patients and provides discussion on the clinical value of antibody testing. A total of 535 plasma samples collected during the hospitalization period of the 173 patients were tested for antibodies against SARS-CoV-2. In addition to the diagnosis value of Ab test, our study revealed a strong positive correlation between clinical severity and antibody titer since 2-week after illness onset, for the first time in COVID-19 patients. doi = 10.1101/2020.03.02.20030189 id = cord-298461-tyhtdawb author = Zhao, L. title = COVID-19: Effects of weather conditions on the propagation of respiratory droplets date = 2020-05-25 keywords = COVID-19; SARS; droplet; figure summary = This study investigates the influence of weather conditions including temperature, humidity and wind velocity, on the transmission of SARS-CoV-2-containing respiratory droplets. We suggest that the current pandemic may not ebb over the summer without continuous and proper public health intervention, because (1) in hot and dry weather, respiratory droplets more easily evaporate into aerosol particles capable of long-range transmission; (2) infectious PM2.5 that can infiltrate deeply into our lung has a longer suspension time in hot and dry weather; (3) many public spaces implement air-conditioning systems that can still operate at temperature and humidity setpoints that favor droplet transport. . https://doi.org/10.1101/2020.05.24.20111963 doi: medRxiv preprint Key parameters considered in the model include the distribution of initial droplet size d0, initial velocity v0, environmental temperature T ∞ , relative humidity RH, air velocity Vair, whose values are given here. doi = 10.1101/2020.05.24.20111963 id = cord-328686-5ik5em5a author = Zhao, L. title = First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date = 2020-08-21 keywords = RNA; SARS summary = In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint From the findings of this study, during the middle risk period, positive samples were detected both in 83 municipal and hospital wastewater systems. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Although SARS-CoV-2 RNA surveillance in wastewaters is a useful WBE drive, the public health risk associated 109 with water cycle is unclear since viral particles infectivity in sewage and faeces is yet to be determined in 110 addition to its probable fecal-oral transmission. doi = 10.1101/2020.08.19.20172924 id = cord-328040-5qd05e4r author = Zhao, Xin-Ying title = Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study date = 2020-04-29 keywords = COVID-19; SARS; patient summary = title: Clinical characteristics of patients with 2019 coronavirus disease in a non-Wuhan area of Hubei Province, China: a retrospective study Since December 2019, several cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were first reported the virus has caused an outbreak in a short time by human-to-human transmission throughout China, especially in Hubei Province. A considerable proportion of COVID-19 patients develop severe pneumonia, pulmonary edema, acute respiratory distress syndrome, and even multiple organ failure within a short time. Patients suspected of having COVID-19 were admitted and quarantined, and throat swab samples were collected and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative polymerase chain reaction assay (qPCR). Clinical data [age, previous chronic disease, epidemiological history, symptoms, vital signs, computed tomography (CT) images, virus load, laboratory tests, complications, and treatment process] of the 91 patients involved in this study were collected. doi = 10.1186/s12879-020-05010-w id = cord-324344-dxuabscn author = Zhao, Xuesen title = LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 date = 2020-04-05 keywords = LY6E; OC43; SARS summary = In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. In an effort to search for the host cellular protein(s) mediating the differential 29 susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and 30 LY6E, three cellular proteins with known activity of interfering virus entry, expressed at 31 significantly higher levels in HepG2 cells. Finally, the findings that LY6E inhibits human CoV entry cannot be evaded by ectopic 284 expression of membrane-associated serine protease TMPRSS2 and compromised by AmphoB 285 treatment strongly indicate that LY6E modulates virus entry via a distinct mechanism from that 286 IFITM proteins do (Figs. doi = 10.1101/2020.04.02.021469 id = cord-350627-4pgish5x author = Zhao, Yu title = Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date = 2020-01-26 keywords = ACE2; SARS summary = Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 RNA expression profile in the normal human lungs. These studies showed that in normal human lung, ACE2 is mainly expressed by type II and type I alveolar epithelial cells. In total, we analyzed 43,134 cells derived from normal lung tissue of To further understand the special population of ACE2-expressing AT2, we performed gene ontology enrichment analysis to study which biological processes are involved with this cell population by comparing them with the AT2 cells not expressing ACE2. Of note, the 2 male donors have a higher ACE2-expressing cell ratio than all other 6 female author/funder. We also noticed that the only Asian donor (male) has a much higher ACE2Altogether, in the current study, we report the RNA expression profile of ACE2 in the human lung at single-cell resolution. https://doi.org/10.1101/2020.01.26.919985 doi: bioRxiv preprint author/funder. doi = 10.1101/2020.01.26.919985 id = cord-339720-d1stzy8w author = Zhao, Yuan title = Susceptibility of tree shrew to SARS-CoV-2 infection date = 2020-04-30 keywords = SARS; shrew; tree summary = No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. In three young tree shrews (TS26, TS27 and TS28), we could detect viral RNA from only lungs in TS26 and TS27, but not in any tissue from TS28, although these animal had higher number of viral genomic copy numbers at the earlier stage of SARS-CoV-2 infection. Although SARS-CoV-2 infection didn''t cause severe disease in all three ages of tree shrews, viral replication and mild histopathological changes were still observed in this study. In conclusion, tree shrew is not as susceptible to SARS-CoV-2 infection as the reported animal models of COVID-19, though limited replication of SARS-CoV-2 and mild histopathology was detected and observed in some tissues. Young Old Adult 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Histopathological examination of affected tissues from SARS-CoV-2 infected tree shrews. doi = 10.1101/2020.04.30.029736 id = cord-290802-761wqgbe author = Zhao, Zheng title = Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date = 2020-09-18 keywords = RDRP; RNA; SARS; figure summary = title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. In sum, structurally, SARS-CoV-2 has high global/ core structural similarity to the RDRP catalytic domains of all other RNA viruses, which provides an opportunity for structure-based COVID-19 drug design and repurposing, noting that keys differences lie in the subtle details. According to the similarity of functionsite interaction fingerprints over all complexes, it was possible to divide the binding modes into four classes, where each class contains multiple PDB structures from different kinds of viruses (Table 1) . doi = 10.1021/acs.jproteome.0c00623 id = cord-340028-6oicmeam author = Zhavoronkov, Alex title = Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date = 2020-03-31 keywords = COVID-19; NAD; SARS; age; clinical; infection summary = Here we compare the expected benefit of treatments for elderly populations (60 years and older) that are currently in development, including standard preventative strategies such as vaccines and antivirals targeting SARS-CoV-2, and the potential added benefit of speculative geroprotective strategies such as rapalogs, NAD+ boosters, senolytics, and stem cell treatment. People >60 years of age with chronic medical conditions, such as type 2 diabetes or cardiovascular disease, direct immunosuppression from HIV, posttransplant or biologic treatment, pregnant individuals, or those with BMI>40, are believed to be at higher risk for influenza infection due to a weakened immune response [31] . As discussed in this paper, small clinical studies have shown that several geroprotective and senoremediative interventions, such as treatment with AGING sirolimus and rapalogs, can induce immunopotentiation, increase resistance to infection, and reduce disease severity in the elderly, without severe side effects. doi = 10.18632/aging.102988 id = cord-269488-7fy6exsd author = Zhen, Wei title = Development of a New Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection date = 2020-09-19 keywords = CDC; SARS summary = A LOD study with inactivated virus exhibited equal performance to the modified CDC assay with a final LOD of 1,301 ± 13 genome equivalents/ml for the Northwell Health Laboratories laboratory developed test (NWHL LDT) vs. The results demonstrate that the NWHL LDT multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and can be used as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2. The findings demonstrate that the NWHL LDT has comparable clinical performance for the specific detection of SARS-CoV-2 RNA in NP specimens and is more efficient and cost effective in comparison to the modified CDC assay. In summary, The NWHL LDT has comparable analytical sensitivity and accuracy for specific detection of SARS-CoV-2 RNA and also showed superior efficiency and cost-effectiveness when compared to the modified CDC assay. doi = 10.1016/j.jmoldx.2020.09.004 id = cord-332076-b0qtzzac author = Zhen, Wei title = Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date = 2020-07-23 keywords = Hologic; Molecular; SARS summary = In the present study, we evaluated the analytical sensitivity and clinical performance of the following four SARS-CoV-2 molecular diagnostic assays granted emergency use authorization by the FDA using nasopharyngeal swabs from symptomatic patients: the New York SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel (modified CDC) assay, the Simplexa COVID-19 Direct (Diasorin Molecular) assay, GenMark ePlex SARS-CoV-2 (GenMark) assay, and the Hologic Panther Fusion SARS-CoV-2 (Hologic) assay. In this study, we evaluated the analytical and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted EUA by the FDA, including the modified CDC, DiaSorin Molecular, GenMark, and Hologic assays. For workflow, TAT, and ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, and GenMark) outperformed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, and separate areas for processing and performing the test. doi = 10.1128/jcm.00743-20 id = cord-336720-2bf3xzni author = Zhen, Wei title = Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens date = 2020-04-22 keywords = Hologic; SARS summary = In the present study, we have evaluated the analytical sensitivity and clinical performance of four SARS-CoV-2 molecular diagnostic assays granted Emergency Use Authorization by the FDA using nasopharyngeal swabs from symptomatic patients. The LoD established by percent positive rate ranged from 1,000 copies/mL by both the GenMark and the 172 modified CDC assays to 50 copies/mL by the DiaSorin Molecular assay ( Table 2) . Overall turn-around time assessment, from sample to results, showed DiaSorin Molecular with the least 224 overall turn-around time to results, followed by GenMark, modified CDC assay and Hologic with the 225 greatest overall time ( Table 5) . DiaSorin 268 Molecular and GenMark showed 100% specificity, while Hologic and the CDC assay initially had two and 269 one discordant results, respectively. For workflow, TAT, and 298 ease of use, the three sample-to-answer platforms (DiaSorin Molecular, Hologic, GenMark) out-299 performed the modified CDC assay, which is a manual assay requiring many steps, specialized personnel, 300 doi = 10.1101/2020.04.17.20069864 id = cord-336836-54o9vjdl author = Zhen, Wei title = Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 date = 2020-07-23 keywords = SARS; Xpress summary = Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. In this study, our objective was to evaluate the analytical and clinical performance as well as the workflow of these three sample-to-answer platforms for SARS-CoV-2 detection in 108 nasopharyngeal (NP) swab specimens from symptomatic patients. We evaluated three sample-to-answer platforms currently in use in our health system for the detection of SARS-CoV-2, including Xpert Xpress and ID NOW, which are designed to be used in near-patient testing environments and outside the clinical laboratory environment. In summary, we evaluated three sample-to-answer platforms for the detection of SARS-CoV-2 using NP specimens, including two platforms that are designed to be used in the near-patient testing environment, Xpert Xpress and ID NOW. doi = 10.1128/jcm.00783-20 id = cord-341331-l24oe2pd author = Zheng, Baojia title = An increasing public health burden arising from children infected with SARS‐CoV2: a systematic review and meta‐analysis date = 2020-08-05 keywords = China; SARS; child summary = Therefore, it is valuable to perform a comprehensive analysis of the different published SARS-CoV2 pediatric cases recording clinical and epidemiological features, merging and This article is protected by copyright. The included studies were required to meet the following eligibility criteria: (1) studies focused on pediatric patients infected with SARS-CoV2 whose nucleic acid test or CT scan were positive; (2) retrospective observational studies, case reports or research articles describing the epidemiological, demographic, and clinical features of confirmed cases, which allowed stratification; and (3) a minimum size of patients (n>3) to conduct a meta-analysis. analysis, aiming to evaluate the features and situation of the children infected with SARS-CoV2 and their possibly increasing health burden on the public. In our study, we found that the proportion of asymptomatic infections in children was high; both males and females were susceptible to SARS-CoV2. doi = 10.1002/ppul.25008 id = cord-257265-lkzytud0 author = Zheng, Fang title = SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date = 2020-08-03 keywords = Lopinavir; Novaferon; SARS summary = According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. doi = 10.1016/j.ijid.2020.07.053 id = cord-322345-rq5gh710 author = Zheng, Fang title = A Novel Protein Drug, Novaferon, as the Potential Antiviral Drug for COVID-19 date = 2020-04-29 keywords = Novaferon; SARS summary = We aimed to determine the anti-SARS-CoV-2 effects of Novaferon in vitro, and conducted a randomized, open-label, parallel group study to explore the antiviral effects of Novaferon for COVID-19. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to the SARS-CoV-2 clearance in COVID-19 patients Results Novaferon inhibited the viral replication in infected cells (EC50=1.02 ng/ml), and protected healthy cells from SARS-CoV-2 infection (EC50=0.1 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher SARS-CoV-2 clearance rates on day 6 than the Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). We first determined whether Novaferon was able to inhibit SARS-CoV-2 at cellular level, and then conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in patients with COVID-19 by observing the SARS-CoV-2 clearance rates at different times during the treatment period. doi = 10.1101/2020.04.24.20077735 id = cord-291014-cfnoxhtd author = Zheng, Jian title = Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host date = 2018-02-28 keywords = IAV; MERS; SARS summary = In one example, our studies of mice infected with SARS-CoV showed that the severity of SARS correlated with the ability to develop a virus-specific immune response, while inhibitory alveolar macrophages and inefficient activation of dendritic cells (DCs) delayed this process and aggravated disease [1] . The CoV endonuclease, nsp15, efficiently prevented activation of host cell dsRNA sensors including melanoma differentiation-associated protein 5 (Mda5), 2 0 -5 0 oligoadenylate synthetase (OAS) and PKR [93, 94 ] , while coronavirus-encoded proteases countered innate immunity, including the IFN response, through diverse pathways [95] . Glycosylation of the HA protein not only mediated virus entry into host cells [115] [116] [117] , but also modulated IAV replication and transmission [118] , and the immune response against the virus [119] [120] [121] , thus representing a potential target for vaccine and drug development [122, 123 ] . doi = 10.1016/j.coviro.2017.11.002 id = cord-321358-plxz5mkg author = Zheng, Jun title = SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat date = 2020-03-15 keywords = China; CoV-2; SARS; Wuhan summary = An ongoing outbreak of pneumonia caused by a novel coronavirus, currently designated as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), was reported recently. In this review, we summarize the key events occurred during the early stage of SARS-CoV-2 outbreak, the basic characteristics of the pathogen, the signs and symptoms of the infected patients as well as the possible transmission pathways of the virus. CoVs have been identified in both avian hosts and various mammals, including bat, camels, dogs and masked palm civets, and are previously regarded as pathogens that only cause mild diseases in the immunocompetent people until the emergence of the coronavirus causing severe acute respiratory syndrome (SARS-CoV) in late of 2002 [3] [4] [5] [6] . doi = 10.7150/ijbs.45053 id = cord-279172-d2algx16 author = Zheng, Kewen title = Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme date = 2006-11-02 keywords = SARS summary = During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 Å, which agrees well with the experimental observations made by X‐ray crystallography; (ii) His163 and Glu166 form the "tooth" conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate‐binding pocket formed by loop 140–146 and loop 184–197 is large enough to accommodate the substrate analog. In this research, by comparing the process of the MD simulation of monomer with dimer, our aim is to (i) find the structural variations and dynamics of the active site residues in SARS M pro monomer in contrast to the dimer, which result in an inactive monomer and provide useful information for receptor based drug design; (ii) investigate the detailed specific interactions involving the two monomers within the dimer and its functional roles in maintaining the activity of the dimer, which provides insights for the design of specific protease inhibitors using the interface of the dimer as a new target. doi = 10.1002/prot.21160 id = cord-283912-ha2xwjzy author = Zheng, Meijuan title = Serum inflammatory factors are positively correlated with the production of specific antibodies in coronavirus disease 2019 patients date = 2020-09-22 keywords = SARS; covid-19 summary = 5 Thus, a detailed characterization of the associations between humoral immune responses and inflammatory factors could result in a better understanding of SARS-CoV-2-host interactions in COVID-19 patients. In the current study, the levels of RBD-specific IgG, RBD-specific IgA, and the frequencies of ASCs and ICOS+ T follicular helper (TFH) cells were found to be higher in severely affected COVID-19 patients than those in nonseverely affected patients. Collectively, these results indicated that severe COVID-19 illness induced strong humoral immune responses, which is consistent with previous studies showing higher IgG titers in severe patients than in nonsevere patients. Our study showed that the severely affected patients displayed higher levels of anti-RBD antibodies, increased frequencies of ASCs and ICOS + TFH cells, and elevated levels of CXCL13. Effective control of SARS-CoV-2 requires further investigation of the mechanism underlying the correlations between humoral immunity and inflammatory factors in severe COVID-19, and the results of such studies could be used to guide immunotherapy with passive antibodies while controlling hyperinflammation. doi = 10.1038/s41423-020-00551-1 id = cord-288500-ko4eda9w author = Zheng, Ruijun title = Prevalence and associated factors of depression and anxiety among nurses during the outbreak of COVID-19 in China: A cross-sectional study date = 2020-10-23 keywords = China; SARS; covid-19 summary = The results indicated that COVID-19-related stress, relationship quality with family, and demographic characteristics were associated with depression, anxiety, and perceived health status. A study reported that health care workers at high risk of contracting SARS were more likely to have a higher prevalence of depression and anxiety, and develop post-traumatic stress during the SARS epidemic (McAlonan et al., 2007) . In this study, we hypothesize that COVID-19-related stress, relationship quality with family, and perceived health status are associated with the risk of depression and anxiety. The questionnaire contained ten main items: unknown origin of COVID-19, fear of infection, lack of effective treatment, poor patient compliance, nursing workload, poor social support, parent-child relationship quality, couple relationship quality, relationship quality with other family members, and perceived health status. The main findings indicated that nurses experiencing COVID-19-related stress and poor relationship quality with family were more likely to develop depression and anxiety symptoms and have health concerns. doi = 10.1016/j.ijnurstu.2020.103809 id = cord-304871-gva617yp author = Zheng, Ting title = Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China date = 2020-06-08 keywords = SARS summary = title: Clinical characteristics and outcomes of COVID‐19 patients with gastrointestinal symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan, China The objective of this study is to compare clinical characteristics and outcomes between patients with and without GI symptoms admitted to Jianghan Fangcang Shelter Hospital in Wuhan. This retrospective study included 1320 patients with confirmed COVID-19 infection admitted to Jianghan Fangcang Shelter Hospital from February 5, 2020, to March 9, 2020. Multivariable logistic regression analysis showed Accepted Article that GI symptoms (p=0.045), male gender (p<0.001), and elevated CRP (p=0.008) were independent risk factors for patient transfer to a tertiary hospital ( Table 3) . Potential risk factors for developing GI symptoms, male gender, and increased CRP may help clinicians predict clinical worsening in COVID-19 patients. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms doi = 10.1002/jmv.26146 id = cord-308833-ei1faruy author = Zheng, Xiaohong title = Experimental investigation of integrated air purifying technology for bioaerosol removal and inactivation in central air-conditioning system date = 2004 keywords = SARS; air summary = In this research, high voltage static electricity and ultraviolet technologies were integrated to an air purifying device which can be used to trap and kill airborne bacteria and viruses in central air-conditioning systems. This provides a basis for using this particular phage strain as a viral simulant in place of SARS CoV and other airborne viruses in the tests for evaluation of bioaerosol removal and inactivation by different types of air purifiers. Fig. 4(a) shows that the plaques formed on a GSM plate were used to sample the airflow containing phage aerosol generated with a source suspension with 10 5 pfu/mL when the integrated air purifier was turned off. In addition to particle removal test, airborne bacteria were also sampled in the experimental room with the integrated air purifier. Based upon the integrated technology of high voltage electric field, ultraviolet ray, composite silver material, and activated carbon fibers, an air purifying device has been developed to prevent airborne bacteria and virus spread through central air-conditioning system. doi = 10.1007/bf03182817 id = cord-017108-vqbl0eov author = Zheng, Xiaolong title = Network-Based Analysis of Beijing SARS Data date = 2008 keywords = Beijing; SARS summary = Instead, a strategy that focuses on nodes (e.g., patients, locations, or occupations) with high degree and strength may lead to more effective outbreak control and management. A public health implication of this finding is that the traditional disease control approach based on random immunization (which has been shown to be effective in many epidemic outbreaks [8] ) may not be effective (unless, of course, the entire population can be treated), because untreated hubs, albeit small in number, can still lead to rapid and large-scale infections [8] . In this section, we analyze the SARS transmission patterns based on the weighted occupation network (WON) as shown in Fig. 7 . To better understand the SARS epidemic transmission patterns and evolution, we have studied three networks derived from the patient survey data, including a patient contact network, a weighted district network, and a weighted occupation network. doi = 10.1007/978-3-540-89746-0_7 id = cord-313639-qpt47sx2 author = Zheng, Yi title = Clinical characteristics of 34 COVID-19 patients admitted to intensive care unit in Hangzhou, China date = 2020-05-20 keywords = IMV; NIV; SARS summary = OBJECTIVE: This study summarizes and compares clinical and laboratory characteristics of 34 patients admitted to the intensive care unit (ICU) for complications from coronavirus disease 2019 (COVID-19) at the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China from Jan. 22 to Mar. 5, 2020. For this retrospective study, we analyzed data from patients admitted between Jan. 22 and Mar. 5, 2020, who had been diagnosed (according to the guidance of NHC (2020a)) with SARS-CoV-2 pneumonia in the ICU in the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. In this single-center case series of 34 ICU patients with SARS-CoV-2 infection in Hangzhou, China, 97.1% (33 cases) of patients had complications caused by ARDS, 44.1% (15) received IMV, 55.9% (19) only needed noninvasive respiratory support. doi = 10.1631/jzus.b2000174 id = cord-282795-kje7rn57 author = Zheng, Yue title = Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date = 2020-09-21 keywords = SARS summary = To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. Pseudotyped MLV viruses were tested on HEK293FT, HEK293T-ACE2, Huh7 and SupT1 cells. To test for specificity of neutralization, we asked whether neutralizing antibodies from SARSCoV-2 patients would exhibit cross-reactivity against a pseudotype expressing SARS-CoV-1 ( Figure 112 4). Characterization of 162 spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with 163 SARS-CoV Veesler D: Structure, Function, and 165 Antigenicity of the SARS-CoV-2 Spike Glycoprotein The 167 D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases 168 infectivity High-efficiency gene 170 transfer into CD34+ cells with a human immunodeficiency virus type 1-based retroviral 171 vector pseudotyped with vesicular stomatitis virus envelope glycoprotein G Pseudotyping Viral Vectors With Emerging Virus Envelope 177 Proteins doi = 10.1101/2020.07.17.207563 id = cord-290904-ngvhk0qy author = Zheng, Zhiqiang title = Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2 date = 2020-07-16 keywords = CoV-2; SARS; protein summary = In this study, we aim to verify if the sequence of the immunogen used to generate mAb 1A9, as well as three other mAbs, is conserved in different coronaviruses and if these mAbs bind to the S protein of SARS-CoV-2 expressed in mammalian cell lines. IF analysis performed on transiently transfected COS-7 cells showed binding of the four mAbs to this S protein fragment of SARS-CoV-2 ( Figure 2B ). Utility of monoclonal antibody 1A9 for detection of S protein in a sandwich ELISA format and in SARS-CoV-2 infected cells Based on indirect ELISA data, mAb 1A9 has the strongest binding to S protein when compared with the other three mAbs. Hence, a sandwich ELISA was performed to determine if it can be paired with the human mAb CR3022 which is known to bind to the S1 subunit of SARS-CoV-2. doi = 10.2807/1560-7917.es.2020.25.28.2000291 id = cord-276034-a8pixbuc author = Zhi, Yan title = Identification of murine CD8 T cell epitopes in codon-optimized SARS-associated coronavirus spike protein date = 2005-04-25 keywords = CD8; IFN; SARS summary = Overlapping peptides were used to identify major histocompatibility complex class I-restricted epitopes in mice immunized with vectors encoding codon-optimized SARS-CoV spike protein. The optimized recombinant adenoviral vaccine vectors encoding spike can generate robust antigen-specific cellular immunity in mice and may potentially be useful for control of SARS-CoV infection. Therefore, several versions of replication-defective adenoviral vectors expressing spike protein were created to induce spike-specific T cell responses in mice and to screen for CD8 T-cell epitopes using an overlapping peptide library spanning the entire spike protein in IFN-g ELISPOT and intracellular IFN-g staining assays. More importantly, a single administration of the optimized SARS-CoV spike vaccine vectors based on replication-defective human and simian adenovirus can generate strong spikespecific CD8 T-cell responses in mice. More importantly, a single administration of an optimized SARS-CoV spike vaccine vector based on a replication-defective simian adenovirus can generate strong spike-specific CD8 T-cell responses in mice. doi = 10.1016/j.virol.2005.01.050 id = cord-255774-ux3c3dzf author = Zhong, H. title = Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients date = 2020-07-05 keywords = SARS summary = Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Likewise, metatranscriptomics-detected bacterial or fungal respiratory co-infections were 6 3 defined if the respiratory specimens (at least one sample) of severe patients were mono-dominated (relative abundance >60%) by 6 4 pathogenic microbes known to cause nosocomial infections (appendix 2 p 9: TableS8). Sixty-seven serial 9 7 clinical specimens from the respiratory tract (RT) (n=47, sputum, nasal and throat swab) and gastrointestinal tract (GIT) (n=20, 9 8 anal swab and feces) of these patients were obtained during the same above period for comprehensive assessment of microbial non-rRNA transcripts) varied between different types of specimens, constituting a relatively high fraction of total high-quality 0 6 reads among RT specimens and a low fraction among GIT specimens (appendix 1 p 1: Supplementary figure 1 and appendix 2 0 7 p 4: TableS3). doi = 10.1101/2020.07.02.20143032 id = cord-214854-ck61ja2t author = Zhong, Jing title = Rapid and sensitive detection of SARS-CoV-2 with functionalized magnetic nanoparticles date = 2020-10-08 keywords = CoV-2; SARS summary = Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and sensitive detection of specific biomolecules, e.g. protein, DNA/RNA and virus. demonstrated the feasibility of wash-free, sensitive and specific assays for the detection of different viruses, e.g. orchid and influenza viruses, with antibody-functionalized MNPs by measuring the reduction in the ac susceptibility in mixed-frequency ac magnetic fields [23] [24] [25] . All these approaches have demonstrated that MNP-based homogeneous biosensing is a wash-free and mix-and-measure approach for rapid and sensitive detection of specific biomolecules. doi = nan id = cord-017715-99ri6x0y author = Zhou, Bo-Ping title = SARS date = 2015-07-25 keywords = SARS; patient; respiratory; severe summary = doi = 10.1007/978-94-017-7363-8_2 id = cord-327711-welf0eb1 author = Zhou, Daming title = Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date = 2020-06-13 keywords = Data; EY6A; Fig; RBD; SARS summary = Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19. A neutralisation test for EY6A based on quantitative PCR detection of virus in the supernatant bathing infected Vero E6 cells after 5 days of culture, showed a ~1000-fold reduction in virus signal (Methods, Extended Data Fig. 3 ) indicating that it is highly neutralising. To elucidate the epitope of EY6A, we determined the crystal structures of the deglycosylated SARS-CoV-2 RBD in complex with EY6A Fab alone and in a ternary complex incorporating a nanobody (Nb) which has been shown to compete with ACE2 (for data on a closely related Nb see Huo 2020, submitted), as a crystallisation chaperone. doi = 10.1101/2020.06.12.148387 id = cord-278169-elhz77ek author = Zhou, Dapeng title = Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics date = 2020-06-10 keywords = SARS summary = In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1–4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1. The receptor-binding domain region of the SARS-CoV-1spike protein is densely covered by glycans except FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ, which overlaps with a previously identified "Achilles heel" (i.e., vulnerable spot) for antibody binding (Berry, et al. Intranasal vaccination of recombinant adeno-associated virus encoding receptor-binding domain of severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein induces strong mucosal immune responses and provides long-term protection against SARS-CoV infection Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on Severe Acute Respiratory Syndrome Coronavirus Neutralization Escape and Fitness doi = 10.1093/glycob/cwaa052 id = cord-328687-clr1e9p6 author = Zhou, Fuling title = Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey date = 2020-09-15 keywords = COVID-19; SARS; Wuhan summary = BACKGROUND: Asymptomatic carriers were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without developing symptoms, which might be a potential source of infection outbreak. Recently, in order to avoid further nosocomial infection, all staff without clinical symptoms in our hospital participated in the physical examination before resumption of ordinary job, including chest CT, throat swab RT-PCR test and plasma COVID-19 IgM/IgG antibodies test. This study aims to analyze the examination results, understand the infection status of staff, track the infection related risk factors, as well as tracing of asymptomatic infection individual, so as to provide effective suggestions for other hospitals and non-medical institution in Wuhan, ensuring scientific and safe return to work. In our study, asymptomatic carrier refers to patients who have mild or non-symptoms but with positive test for viral nucleic acid of SARS-CoV-2 or with positive test for serum specific IgM antibody. doi = 10.1016/j.eclinm.2020.100510 id = cord-294363-bv6xa8v8 author = Zhou, Hong title = Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date = 2020-05-05 keywords = ACE2; China; CoV-2; RNA; SARS summary = Several studies demonstrated angiotensin converting enzyme 2 (ACE2) as an important therapeutic target of SARS-CoV-2 entry and infection, and many potential targets were subsequently proposed, such as the spike (S) protein and transmembrane serine protease 2 (TMPRSS2). Therefore, accelerating research for potential therapeutic target confirmation, promising drug discovery, and clinical verification development will speed up efforts to combat SARS-CoV-2. In addition to inhibiting the virus directly, ASOs are also expected to target the disease-related proteins involved in the inflammatory cytokine storm process, which could be considered a promising therapeutic strategy for combating SARS-CoV-2 . Although many strategies have been used to block the attachment, entry, replication and release processes to inhibit SARS-CoV-2 infection, how to prevent viral evasion from host immune responses and virus-induced cytopathic effects is considered one of the most urgent problems that need to be solved in SARS-CoV-2-induced pneumonia-associated respiratory syndrome (PARS) patients. doi = 10.1111/bph.15092 id = cord-318126-gg68o52z author = Zhou, Juan title = Observation and analysis of 26 cases of asymptomatic SARS-COV2 infection date = 2020-04-03 keywords = SARS summary = We read with interest the article in this journal which revealed that CT scanning provides important bases for early diagnosis and treatment of COVID-19 (Corona Virus Infection Disease 2019) which is caused by SARS-COV2 (Severe Acute Respiratory Syndrome Coronavirus 2). We observed and analyzed the phenotypic characteristics of asymptomatic individuals originating from the active detection of high-risk individuals who had close contacts with COVID-19 patients during isolated observation with viral nucleic acid positive. A total of 26 cases of asymptomatic infection were detected as SARS-COV2 positive through swab specimen between January 20 to February 30. These data showed that people of different ages are generally susceptible to SARS-COV2, but the average age of asymptomatic patients is lower than the reported age of COVID-19 patients which was 40-70 years old (propinquity 73%). These cases proved that asymptomatic SARS-COV2 carriers can also spread the virus before the https://doi.org/10.1016/j.jinf.2020.03.028 0163-4453/© 2020 The British Infection Association. doi = 10.1016/j.jinf.2020.03.028 id = cord-306598-xe0pq0ik author = Zhou, Mi title = Re-emergence of SARS-CoV2 in a discharged COVID-19 case date = 2020-04-02 keywords = SARS summary = title: Re-emergence of SARS-CoV2 in a discharged COVID-19 case Re-emergence of SARS-CoV2 in a discharged COVID-19 case Dear Editor: Since December 2019, novel coronavirus (SARS-CoV2) infected disease (now nominated as COVID-19) has soon emerged as a global health concern. Here we report a case of COVID-19 who met the criteria for discharge but was tested positive for SARS-CoV2 again 10 days after discharge. There her nasal swab was obtained, and SARS-CoV2 was tested positive with real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) assay targeting ORF1ab and N gene of virus genome. RT-PCR examination for SARS-CoV-2 was performed on day 10, 11 and 14, and all 3 tests were negative. Her symptom was not relieved on day 25, so her nasal swab was obtained and the test for SARS-CoV-2 was positive again. Previous study on SARS-CoV showed that virus load could be detected for more than 10 weeks after disease onset. doi = 10.1016/j.jmii.2020.03.031 id = cord-287222-wojyisu0 author = Zhou, Min title = Coronavirus disease 2019 (COVID-19): a clinical update date = 2020-04-02 keywords = COVID-19; China; MERS; SARS; Wuhan; patient summary = Of the first 99 laboratory-confirmed patients, 49 (49%) had been exposed to HSWM, which was reported to be the possible initial source of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [5] . New Coronavirus Infection Diagnosis and Treatment Scheme (Trial Version) published by Military Support Hubei Medical Team also put forward that for mild to moderate COVID-19 patients, corticosteroids should not be given principally and highdose corticosteroid pulse therapy was not recommended. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical pathology of critical patient with novel coronavirus pneumonia (COVID-19) doi = 10.1007/s11684-020-0767-8 id = cord-353012-rxhi8wd2 author = Zhou, Nan title = Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date = 2016-03-07 keywords = Ebola; Fig; HIV; SARS summary = Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Considering that the inhibitory dose of teicoplanin on the activity of cathepsin L is higher than that required for Ebola virus infection inhibition, a cell viability assay was performed to confirm that the inhibitory effect is not due to cytotoxicity (Fig. 6C) . Ebola trVLP system (28) , which can simulate the life cycle of wild-type Ebola viruses to a large extent, was applied to investigate whether teicoplanin and its glycopeptide antibiotic homologs dalbavancin, oritavancin, telavancin, and vancomycin can also inhibit the entry of Ebola trVLPs. Accordingly, the p4cis plasmid encoding Renilla luciferase, VP40, GP, and VP24 was transfected into HEK293T cells along with plasmids expressing T7 RNA polymerase, NP, VP35, VP30, and L viral proteins to produce Ebola trVLPs (Fig. 7A) . doi = 10.1074/jbc.m116.716100 id = cord-258167-jqm3qyfm author = Zhou, Peng title = Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date = 2009-09-18 keywords = HIV; SARS summary = Studies using wild bat sera revealed that it is highly likely that the immunodominant epitopes overlap with the major neutralizing sites of the SL-CoV S protein. Our previous studies showed that the SL-CoV and SARS-CoV shared similar genomic organization and highly conserved gene products, with the exception of the spike protein (S protein), which had a low sequence identity, especially in the receptor binding domain (RBD) located at the N-terminal region of the S proteins. In this study, the immunogenicity and immunodominant region of S SL was determined using sera generated from DNA immunization and naturally infected bats. Hyperimmune mouse sera were generated by DNA immunizations with plasmids pcDNA 3.1(+) containing the codon-optimized fulllength S gene of SARS-CoV BJ01, SL-CoV Rp3, and two chimeric plasmids CS 310-518 and CS 259-518 (see Fig. 1 for diagrams). In this study, DNA constructs expressing four different S proteins, SARS-CoV BJ01, SL-CoV Rp3 S and two chimeras, were used to generate hyperimmune sera in mice via DNA immunization. doi = 10.1016/j.bbrc.2009.07.025 id = cord-316493-wszoi6p2 author = Zhou, Weimin title = First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood date = 2013-09-16 keywords = IFA; SARS summary = BACKGROUND: Non-severe acute respiratory syndrome (non-SARS)-related human coronaviruses (HCoVs), including HCoV-229E, -HKU1, -NL63, and -OC43, have been detected in respiratory tract samples from children and adults. An S-protein-based indirect immunofluorescence assay (IFA) was then developed to detect anti-S IgG and IgM for the four individual HCoVs and applied to serum samples from a general asymptomatic population (218 children and 576 adults) in Beijing. To expand the epidemiological knowledge of four non-SARS-related endemic HCoVs in China, we expressed S proteins in a eukaryotic system and established an IFA for the detection of IgG or IgM antibodies against these four viruses. Our results showed that the S-based IFA enabled specific detection of IgG or IgM to four individual HCoVs. Using IFA, we investigated the natural seroprevalence of four non-SARS-related HCoVs in blood samples from a general population that comprised a variety of age groups. doi = 10.1186/1471-2334-13-433 id = cord-347208-leo0x10l author = Zhou, Y. title = Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study date = 2020-06-10 keywords = June; SARS summary = title: Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study . https://doi.org/10.1101/2020.06.09.20076646 doi: medRxiv preprint 9 time from illness onset to arbidol or interferon treatment, elevated C-reactive protein (CRP), elevated interleukin-4 (IL-4) and interleukin-6 (IL-6), elevated D-dimer and more lobes lesion in lung CT images were significantly associated with the prolonged viral shedding of COVID-19. The results of univariable regression analysis demonstrated that age older than 65 years, illness onset before January 31, the time from illness onset to first medical visitation, hypertension, arbidol combination with interferon, lobe lesions in lung computed tomography (CT) images, and the time from illness onset to arbidol or interferon initiation were significantly associated with the duration of SARS-CoV-2 RNA shedding by univariable regression analysis. doi = 10.1101/2020.06.09.20076646 id = cord-317435-4yuw7jo3 author = Zhou, Yadi title = Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2 date = 2020-03-16 keywords = Fig; MERS; SARS; drug; network summary = Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. The high druggability of HCoV-host interactome motivates us to develop a drug repurposing strategy by specifically targeting cellular proteins associated with HCoVs for potential treatment of 2019-nCoV/SARS-CoV-2. These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). doi = 10.1038/s41421-020-0153-3 id = cord-353572-b4mdiont author = Zhou, Yadi title = Network-based Drug Repurposing for Human Coronavirus date = 2020-02-05 keywords = SARS; drug; figure; international summary = Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs. Coronaviruses (CoVs) typically affect the respiratory tract of mammals, including humans, and lead to mild to severe respiratory tract infections [1] . These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs. To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). doi = 10.1101/2020.02.03.20020263 id = cord-321131-f8qeytxc author = Zhou, Yanchen title = Protease inhibitors targeting coronavirus and filovirus entry date = 2015-04-30 keywords = K11777; MERS; SARS; cell; protease summary = Abstract In order to gain entry into cells, diverse viruses, including Ebola virus, SARS-coronavirus and the emerging MERS-coronavirus, depend on activation of their envelope glycoproteins by host cell proteases. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. We report here that the cysteine protease inhibitor K11777, ((2S)-N-[(1E,3S)-1-(benzenesulfonyl)-5-phenylpent-1-en-3-yl]-2-{[(E)-4-methylpiperazine-1-carbonyl] amino}-3-phenylpropanamide) and closely-related vinylsulfones act as broad-spectrum antivirals by targeting cathepsin-mediated cell entry. Cell culture studies demonstrated that endosomal cysteine proteases, in particular cathepsin B (CTSB) and/or L (CTSL), can activate the glycoproteins of filoviruses, SARS-CoV, other coronaviruses, and NiV and Hendra (HeV) viruses to facilitate entry into certain cell lines. The notion that coronaviruses, including SARS-CoV, use both a cathepsin-dependent endosomal pathway and a direct cell-surface serine protease-mediated pathway for entry (Simmons et al., 2013) is supported by our finding that the combination of K11777 and camostat was superior to either compound alone. doi = 10.1016/j.antiviral.2015.01.011 id = cord-339951-how9cmw8 author = Zhou, Yaqing title = Clinical and Autoimmune Characteristics of Severe and Critical Cases of COVID‐19 date = 2020-05-14 keywords = China; SARS summary = The clinical, autoimmune, and laboratory characteristics of 21 patients who had laboratory‐confirmed severe and critical cases of coronavirus disease 2019 (COVID‐19) from the intensive care unit of the Huangshi Central Hospital, Hubei Province, China, were investigated. According to the sixth edition of Guidance for Corona Virus Disease 2019: Prevention, Control, Diagnosis and Management, issued by China''s National Health Commission, the diagnostic criteria for the clinical classification of COVID-19 are as follows: (i) mild-clinical symptoms are mild and no pneumonia manifestation can be found on imaging; (ii) ordinary-symptoms such as fever and respiratory tract symptoms and pneumonia manifestations can be seen on imaging; (iii) severe-any of the following: respiratory distress, respiratory rate (RR) ≥30 breaths/min, oxygen saturation <93% at rest, arterial partial pressure of oxygen (PaO 2 )/oxygen concentration (FIO 2 ) ≤300 mmHg (1 mmHg = 0.133 kPa), or >50% lesion progression within 24-48 hours on pulmonary imaging; and (iv) critical-any of the following: respiratory failure in which mechanical ventilation is required, shock occurs, or complications with another organ failure that require monitoring and treatment in the ICU. In this single-center and retrospective study, we have reported on the clinical and laboratory characteristics of 8 severe and 13 critical cases of SARS-CoV-2 in Huangshi, Hubei Province, China. doi = 10.1111/cts.12805 id = cord-266696-w9sb038q author = Zhou, Yi-Hua title = Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date = 2004-03-15 keywords = SARS summary = [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China doi = 10.1086/382081 id = cord-313458-ka02rsla author = Zhou, Yitian title = Single-cell transcriptional profile of ACE2 in healthy and failing human hearts date = 2020-09-01 keywords = ACE2; SARS summary = To explore the potential mechanisms contributing to this finding, we examined the expression of ACE2 in the different cells of the heart for heart samples from healthy individuals and heart failure patients and compared the results between these two groups. We found that the expression of ACE2 in cardiomyocytes was significantly increased compared to the other cells in the heart failure patients ( Figure 1L ). These results suggest that the cardiomyocytes of heart failure patients may be directly attacked by the virus and that this may contribute to the development of myocardial injury and severe conditions. We speculate that SARS-CoV-2 mainly attacks pericytes via ACE2, which leads to coronary microvascular disorder and myocardial injury in COVID-19 patients. This finding suggests that heart failure patients infected by the SARS-CoV-2 virus may suffer viral myocarditis and severe myocardial injury by direct attack on their cardiomyocytes. doi = 10.1007/s11427-020-1787-5 id = cord-300156-ags07bc5 author = Zhou, Yunyun title = Ocular Findings and Proportion with Conjunctival SARS-COV-2 in COVID-19 Patients date = 2020-04-21 keywords = SARS summary = The 1 patient with ocular symptoms and positive SARS-CoV-2 conjunctival swab results was classified as a severe or critical case. Two patients without ocular symptoms showed positive results for conjunctival SARS-CoV-2, with one of them classified as a severe or critical case and another classified as a mild or moderate case. Of 3 patients who showed positive results for conjunctival SARS-CoV-2, 2 were severe or critical cases and 1 was a mild or moderate case. The finding of ocular symptoms was not associated significantly with the results of conjunctival SARS-CoV-2 detection (Table S2, Our study has several limitations. In conclusion, this study characterizes the ocular symptoms in COVID-19 patients, reports the proportion of samples with positive conjunctival and nasopharyngeal RT-PCR results from patients with COVID-19, and incorporates the duration of disease into the analysis. The appearance of symptoms and penlight findings or the results of positive conjunctival swab analysis were not correlated significantly with the duration of disease. doi = 10.1016/j.ophtha.2020.04.028 id = cord-309930-zlzuoeh2 author = Zhou, Zhiming title = Coronavirus disease 2019: initial chest CT findings date = 2020-03-24 keywords = COVID-19; SARS summary = METHODS: We retrospectively reviewed the initial chest CT data of 62 confirmed coronavirus disease 2019 patients (34 men, 28 women; age range 20–91 years old) who did not receive any antiviral treatment between January 21 and February 4, 2020, in Chongqing, China. Since December 2019, an increasing number of pneumonia cases caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei, China, and subsequently, an outbreak of coronavirus disease 2019 (COVID-19) swept the globe [1] [2] [3] [4] . Hence, it is very necessary to systematically analyze the chest CT findings associated with this disease systematically, for the timely isolation, COVID-19 RT-PCR and respiratory care of patients, and early implementation of infection prevention and control measures. To fully understand and early discriminate the CT features of this disease in its early stages, we collected initial chest CT data from confirmed COVID-19 patients who did not receive any antiviral treatment mainly from Chongqing Three Gorges Central Hospital for analysis. doi = 10.1007/s00330-020-06816-7 id = cord-308501-z3eiac25 author = Zhu, Chengliang title = nBreastfeeding Risk from Detectable Severe Acute Respiratory Syndrome Coronavirus 2 in Breastmilk date = 2020-06-04 keywords = SARS summary = An emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) pandemic, imposes a great threat to global public health 1 . The transmission and pathophysiology of SARS-CoV-2 gradually known among various populations, but public health effects of COVID-19 on women and their outcomes should not be ignored 1, 2 . In pregnant and perinatal women, vertical transmission of SARS-CoV-2 from infected mother to her newborn is a controversial issue [2] [3] [4] . Here, we represent clinical characteristics of COVID-19 pneumonia in puerperal women and evidence of SARS-CoV-2 shedding in her breastmilk. Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records SARS-CoV-2 is not detectable in the vaginal fluid of women with severe COVID-19 infection. doi = 10.1016/j.jinf.2020.06.001 id = cord-304088-xkg0ylz8 author = Zhu, Han title = Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date = 2020-04-21 keywords = ACE2; COVID-19; SARS; infection summary = While limited data exist, potential mechanisms of cardiac injury include direct viral entry through the angiotensin-converting enzyme 2 (ACE2) receptor and toxicity in host cells, hypoxia-related myocyte injury, and immune-mediated cytokine release syndrome. The increased incidence of cardiac injury among those with severe systemic inflammatory response syndromes (SIRS) and shock in the setting of COVID-19 also highlights an important relationship between the immune response to the virus and the cardiovascular system. Of note, SARS-CoV-2 also contains an RNA-dependent RNA polymerase which is the target of the anti-viral agent remdesivir, currently being studied randomized clinical trials for use against COVID-19 disease [26] . A recent retrospective, multi-center study of 150 patients confirmed that inflammatory markers, including elevated ferritin (mean 1297.6 ng/ml in non-survivors vs 614.0 ng/ml in survivors, p < 0.001) and IL-6 (p < 0.0001) were associated with more severe COVID-19 infection, suggesting that systemic inflammation may be a significant driver of multi-organ damage [18, 64] . doi = 10.1007/s11886-020-01292-3 id = cord-319876-psilbis0 author = Zhu, Jian title = COVID-19 Epidemic: Clinical Characteristics of Patients in Pediatric Isolation Ward date = 2020-07-09 keywords = COVID-19; SARS summary = It was found that 55 cases (83.3%) had fever and 48 cases (72.7%) coughed in the isolated area, 31 cases (47%) had a history of exposure, 26 cases (39.4%) had a decrease in lymphocytes (LYM), more than half had an increase in lactate dehydrogenase and creatine kinase isoenzyme, 14 cases (21.2%) had positive SARS-CoV-2 nucleic acid, 58 cases (87.9%) had abnormal chest computed tomography (CT), and 11 cases (16.7%) had sinus arrhythmia. Therefore, for some suspected children with COVID-19, we can make a comprehensive judgment through clinical symptoms, epidemiological history, LYM number, myocardial enzyme spectrum, chest CT, and electrocardiogram; put these children in an isolation ward for treatment; and then transfer them to a general ward for treatment after excluding COVID-19. At present, some of COVID-19 are asymptomatic infection, 10, 11 which suggests that it is not only from the clinical symptoms to judge whether the children should be admitted to the isolation ward. doi = 10.1177/0009922820941228 id = cord-343455-v1648kng author = Zhu, Na title = Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells date = 2020-08-06 keywords = Fig; HAE; NL63; SARS summary = Here, we characterize the replication dynamics, cell tropism and morphogenesis of SARS-CoV-2 in organotypic human airway epithelial (HAE) cultures. SARS-CoV-2 replicates efficiently and infects both ciliated and secretory cells in HAE cultures. In this study, we compared the characteristics of the replication dynamics, cell tropism, and morphogenesis of SARS-CoV-2 and HCoV-NL63 in HAE cells, which express the shared receptor, to better understand the pathogenesis and transmission of SARS-CoV-2. As shown in Fig. 1a , HAE cells were highly susceptible to SARS-CoV-2 infection with peak virus production from apical wash at 48-72 h post infection (h pi) and remained at a high level from 3 to 6 days. As shown in Fig. 1c , virus particles were found on the apical surface of both ciliated cells and secretory cells; inclusion bodies formed by viral components were observed in the cytoplasm, which confirmed the infection of both cell types. doi = 10.1038/s41467-020-17796-z id = cord-301151-f6vya3qh author = Zhu, Xiaojuan title = Co-infection with respiratory pathogens among COVID-2019 cases date = 2020-05-11 keywords = SARS summary = In this study, the clinical features of COVID-19 patients were analyzed, then 39 respiratory pathogens in their throat swab were detected by specific real-time RT-PCR. 257 patients were diagnosed with the SARS-CoV-2 infection and their clinical severity was classified according to National Health Commission of the People''s Republic of China revised criteria for diagnosis and treatment of novel coronavirus infection pneumonia (trial version fifth, revised version). Below 15 years of age, a total of 11 (4.3 %) were diagnosed with the SARS-CoV-2 infection and there were no case in severe/critical category. In our study, 94.2 % of COVID-19 patients could be co-infected with one or more other pathogens, including 9 viruses, 11 bacteria and 4 fungi. Along with the course of disease, both the rates and pathogen species of co-infection among COVID-19 patients were decreased significantly, which may due to the treatment X. doi = 10.1016/j.virusres.2020.198005 id = cord-333420-qqyg9um9 author = Zhu, Xun title = idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date = 2020-10-09 keywords = SARS summary = title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. The on-going Coronavirus disease 2019 (Covid-19) pandemic has resulted in over 734,000 deaths, affect-20 ing more than 188 countries and territories (CSSE, 2020; Dong, et al., 2020) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV) 23 is the pathogenic cause of Covid-19 (Lescure, et al., 2020) . In order to quickly identify the clade of an isolate of SARS-Cov-2 given its sequencing FastQ files, 30 we have developed a bioinformatics pipeline and a user-friendly web interface. doi = 10.1101/2020.10.08.330456 id = cord-302584-fwdpzv85 author = Zhu, Ying title = Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date = 2005-01-01 keywords = CoV; SARS; WHU summary = title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates Despite the fact that the SARS-CoV can cause an atypical and fatal form of pneumonia, the genome structure, gene expression pattern, and protein profiles of the virus are similar to those of other conventional coronaviruses [17] , which are only responsible for mild respiratory tract infections in a wide range of animals including humans, pigs, cows, mice, cats, and birds [10, 19] . In this report, we described the isolation of a new SARS-CoV strain (WHU) from a patient in Hubei Province, China during the late period of SARS outbreak. Comparative study of genetic characterization and nucleotide variation of all known SARS-CoV offers insights into understanding functions of the viral genes and revealing the evolution trends of the virus. doi = 10.1007/s11262-004-4586-9 id = cord-307504-cogk5kig author = Zhu, Yuanmei title = Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date = 2020-03-28 keywords = HR1; SARS summary = title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. Taken together, these results suggested that 128 SARS-CoV-2 might evolve an increased interaction between the HR1 and HR2 domains in 129 the S2 fusion protein thus critically determining its high fusogenic activity. Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: 354 implications for virus fusogenic mechanism and identification of fusion inhibitors Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition 368 using spike protein heptad repeat-derived peptides Heptad repeat-derived peptides block protease-mediated direct entry from the cell surface of 371 severe acute respiratory syndrome coronavirus but not entry via the endosomal pathway doi = 10.1101/2020.03.26.009233 id = cord-327808-k3jec87p author = Zhu, Yunkai title = The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date = 2020-08-25 keywords = SARS; Sdel summary = We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. The sequence at the S1/S2 boundary contains a cleavage site for the furin protease, 61 which could preactivate the S protein for membrane fusion and potentially reduce the 62 dependence of SARS-CoV-2 on plasma membrane proteases, such as transmembrane 63 serine protease 2 (TMPRSS2), to enable efficient cell entry (Shang et al., 2020) . Intriguingly, 188 these genes edited also significantly inhibited the infection by pseudovirus bearing the 189 spike protein of MERS-CoV in A549-ACE2-DPP4 cells ( Figure 3D ). Although no infectious virus was detected by focus-forming 299 assay (data not shown), viral RNA levels were higher in fecal samples for Sfull (20 and 300 40-fold) than Sdel at days 2 and 4, respectively ( Figure 5B ). doi = 10.1101/2020.08.25.266775 id = cord-311123-swiewewq author = Zhuang, Shu-Fan title = Low-grade fever during COVID-19 convalescence: A report of 3 cases date = 2020-06-26 keywords = February; SARS summary = Reports of such cases are rare, and the mechanism and outcome of low-grade fever during COVID-19 convalescence are not completely clear. The patient''s condition did not improve, and COVID-19 was confirmed on February 7 by positive SARS-CoV-2 oropharyngeal swab test at our local Center for Disease Control (CDC). From disease onset on 4 February 2020, the patient had a fever with a maximum axillary temperature of 38.1°C, accompanied by a cough (details shown in Table 1 ) and multiple lesions on CT ( Figure 1 ). The patient''s condition did not improve, and COVID-19 was confirmed on February 5 by positive SARS-CoV-2 oropharyngeal swab test at our local CDC. During convalescence, the patient''s cough was completely relieved, and CT lesions resolved ( Figure 1 ), but her SARS-CoV-2 test remained positive. During the course of low-grade fever, the 3 patients had no other discomfort or comorbidities, and their temperature returned to normal without any treatment. doi = 10.12998/wjcc.v8.i12.2655 id = cord-346138-ip42zcld author = Zhurakivska, Khrystyna title = An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date = 2020-08-20 keywords = PCR; RNA; SARS summary = The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. Several authors therefore suppose an infection of the gastrointestinal tract by the virus (11, 24) , with its continuous elimination with the feces which has been reported to last from 1 to 12 days (24) and in some cases, viral RNA were detected in feces or anal swabs even after the respiratory tests became negative (11, 22, 24) . The reference method for testing positivity to SARS-CoV-2 infection is represented by the pharyngeal swab that is taken from the patient''s nasopharynx or oropharynx and, through an RT-PCR analyzed for the presence of viral RNA (8) . doi = 10.3389/fpubh.2020.00487 id = cord-274231-2s7ki6g7 author = Ziebuhr, John title = SARS – Unprecedented global response to a newly emerging disease date = 2003-12-31 keywords = SARS; coronavirus summary = 293, 229 ± 231 (2003) ¹ Urban & Fischer Verlag http://www.urbanfischer.de/journals/ijmm Editorial SARS ± Unprecedented global response to a newly emerging disease Severe acute respiratory syndrome (SARS) is a life-threatening form of pneumonia that is characterized by fever, chills, myalgia, dry cough, and progressing lung infiltrates (Nicholls et al., 2003; Peiris et al., 2003a) . Only few weeks after the outbreak, the concerted global efforts have resulted in the identification of first coronavirus enzyme inhibitors (Anand et al., 2003; Xiong et al., 2003) that are hoped to be useful for the development of anti-SARS drugs. SARS Working Group: A novel coronavirus associated with severe acute respiratory syndrome SARS study group: Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome doi = 10.1078/1438-4221-00270 id = cord-349417-vn7q8wc4 author = Ziebuhr, John title = The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date = 2006 keywords = RNA; SARS; coronavirus summary = Activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce 16 (in IBV: 15) mature products called nonstructural proteins (nsp) 1 to 16 (reviewed in Refs. The N-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups I, II, and III, are cleaved at two (in IBV) or three sites (in all other coronaviruses) by one (IBV and SARS-CoV) or two zinc-finger-containing papain-like cysteine proteases called PL1 pro and PL2 pro . The observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified RNA-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, NendoU, playing a central role. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication doi = 10.1007/978-0-387-33012-9_1 id = cord-264916-c4n0kyog author = Zimmerman, Keith title = Natural protection of ocular surface from viral infections – a hypothesis date = 2020-07-09 keywords = SARS; infection; ocular; virus summary = A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. doi = 10.1016/j.mehy.2020.110082 id = cord-322102-4fi0y96f author = Zimmermann, Matthias title = Approaches to the management of patients in oral and maxillofacial surgery during COVID-19 pandemic date = 2020-04-04 keywords = COVID-19; SARS; patient summary = During the SARS-CoV-2 pandemic, the specialty must organize patient treatment in such a way that infection transmission is reduced to a minimum, while all relevant treatment options are at hand to provide adequate patient care. The search items used were "coronavirus disease 19, COVID-19, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, transmission, pandemic, oral surgical procedures, oral and maxillofacial surgery, dental, personal protective equipment, infection prevention and control." The last search was run on 29 March 2020. Healthcare workers who have been infected with SARS-CoV-2 and have recovered from COVID-19 should continue to follow infection control precautions, including use of the recommended personal protective equipment. Depending on the number of infected patients, there might come a time of risk of a scarcity of medical staff, ventilators, negative pressure rooms, and personal protective equipment. doi = 10.1016/j.jcms.2020.03.011 id = cord-318478-fn0gcxbb author = Ziv, Omer title = The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date = 2020-10-07 keywords = RNA; SARS; figure summary = Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. doi = 10.1101/2020.07.19.211110 id = cord-353812-4oxbczqe author = Zoghi, Anahita title = A case of possible atypical demyelinating event of the central nervous system following COVID-19 date = 2020-06-24 keywords = CNS; SARS summary = Some COVID-19 patients, especially those suffering from a severe disease, are highly likely to have central nervous system (CNS) manifestations. It has been shown that severe infection with SARS-CoV-2 is associated with neurological manifestations such as headache, epilepsy, cerebrovascular events, and encephalitis (Bohmwald et al. Studies on SARS-CoV-1 revealed a delayed self-reactive T-cell suppression due to viral replication, which leads to neuroinflammation, demyelination or axonal damage of the CNS (Savarin et al., 2017 . Recent studies have shown that the novel coronavirus appears to cross the blood-brain barrier and cause acute or delayed CNS demyelination or axonal damage (Desforges et al., 2020) . Moreover, a recent report revealed that CNS delayed demyelinating events following COVID-19 . Severe COVID-19 may affect the CNS and have various acute or delayed neurological complications. During the COVID-19 pandemic, it is important to consider SARS-CoV-2 infection when seeing patients with neurological manifestations, especially those needing immune-modulator therapy, since the established recommendations are insufficient at this time. doi = 10.1016/j.msard.2020.102324 id = cord-271978-j5enftje author = Zoltán, Köntös title = In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date = 2020-11-10 keywords = EID; SARS; iodine summary = Conclusion Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients. Enthused by promising findings from a recent study by Pelletier and colleagues (12) , the present study was interested in Essential Iodine Drops (EID) for oral/nasal decontaminant in known or suspected cases of COVID-19 as a potentially better alternative to PVP-I. Briefly, the three dilutions of Essential Iodine Drops (EID) containing SARS-CoV-2 virus solution (1:1; 2:1 and 3:1) were tested in triplicates for virucidal activity as described by Pelletier and colleagues (12) . In vitro virucidal assay in the present study has indeed demonstrated that 75% and 50% of Essential Iodine Drops (EID) solution reduced SARS-CoV-2 virus titre after 60 seconds and 90 seconds of incubation by an LRV of 2.0 (99%). doi = 10.1101/2020.11.07.370726 id = cord-314933-wq1xo0z0 author = Zores, Florian title = COVID and the Renin-Angiotensin System: Are Hypertension or Its Treatments Deleterious? date = 2020-04-23 keywords = ACE2; ANGII; SARS summary = In this paper, we hypothesize that the reductions in Angiotensin-Converting Enzyme 2 (ACE-2) observed in hypertension and obesity can explain many abnormalities observed in SARS-CoV-2 and question the role of treatments interfering with ACE2. Like SARS-CoV, SARS-CoV-2 fuses with human cells after the receptor-binding domain of its S (Spike) protein binds with Angiotensin-Converting Enzyme 2 (ACE-2), an enzyme located on membrane of lung alveolar epithelial cells, renal tubular epithelial cells, enterocytes of the small intestine, and arterial and venous endothelial cells of the kidney (5-10). ACE2, Angiotensin Converting Enzyme 2; ACEi, Angiotensin Converting Enzyme Inhibitor; ang-(1-7), Angiotensin-(1-7); ANGII, angiotensin II; ANGIV, angiotensin IV; ARB, Angiotensin Receptor Blocker; ARDS, Acute Respiratory Distress Syndrome; AT1R, Angiotensin II Type 1 Receptor; AT4R, Angiotensin II Type 4 Receptor; SARS-CoV-2, Severe Acute Respiratory Syndrome CoronaVirus 2. Thus, decreased ACE2 expression promotes increased lung injury and ARB prevents it by limiting ANGII binding to AT1R (7, 8, 24, 25) (Figure 1C) . doi = 10.3389/fcvm.2020.00071 id = cord-283861-kcv1bmyx author = Zou, J. title = Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents date = 2020-05-06 keywords = Atlanta; SARS summary = We quantitated anti-SARS/CoV-2 IgG and IgM by ELISA in self-collected blood samples (n=142) in arbitrarily-selected metro Atlanta residents, primarily acquaintances of the authors'' lab members from 4/17-4/27, 2020. While we do not claim this small immune survey is 49 broadly representative of metro Atlanta, and we have greater confidence in the IgG results, 50 which had only 2.4% positivity, it nonetheless demonstrates that persons with antibodies to 51 SARS/CoV-2, who''ve not suspected they''d been exposed to this virus, can readily be found in 52 various Atlanta area neighborhoods (9 positives were in 8 zip codes). Nonetheless, our quantitative approaches enabled seemingly readily and 74 reliable discernment that about 3 and 6 of 127 arbitrarily subjected Atlanta area residents 75 displayed SARs/CoV-2-specific IgG and IgM, respectively, which likely reflects that they have 76 been exposed to this virus. doi = 10.1101/2020.05.01.20087478 id = cord-313627-g1iqhsdk author = Zou, Xiaojing title = Characteristics of liver function in patients with SARS-CoV-2 and chronic HBV co-infection date = 2020-06-15 keywords = HBV; SARS summary = Conclusion Liver injury in patients with SARS-CoV-2 and chronic HBV co-infection was associated with severity and poor prognosis of disease. In this study, we aimed to describe the characteristics of liver function and its 3 relation with severity and prognosis in patients with SARS-CoV-2 and chronic HBV 4 co-infection, in order to provide evidence for the clinical treatment of these specific 5 patients and contribute to improving their prognosis. In the present study, we found that liver test abnormalities were relatively common 1 in patients with SARS-CoV-2 and chronic HBV co-infection, and the values of ALT, 2 AST, TBIL, ALP and γ-GT increased substantially during hospitalization. 6 The present study reported evidence of liver injury in patients with SARS-CoV-2 7 and chronic HBV co-infection. These findings 9 indicate that liver injury in patients with SARS-CoV-2 and chronic HBV co-infection 10 was associated with disease severity and worse prognosis. doi = 10.1016/j.cgh.2020.06.017 id = cord-319704-xzhoa03d author = Zuercher, S. J. title = Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence date = 2020-05-22 keywords = MHP; SARS; health summary = Results: Most original studies on MHP were conducted in China in the context of SARS-CoV-1, and reported on anxiety, depression, post-traumatic stress symptoms/disorder, general psychiatric morbidity, and psychological symptoms. While considerable efforts rely on protective and treatment measures such as virus transmission pathways, clinical presentations, and the development of vaccinations, attention is only recently given to short or long-term mental health problems (MHP, hereafter defined as psychiatric/psychological symptoms and mental illness/disorders) (Rajkumar, 2020) that may arise due to the different surrounding consequences of an epidemic in the general public, health care workers (HCW), and survivors of infectious diseases (survivors). In this rapid review of 74 original articles we found a wide range of MHP including anxiety, depression, PTSD and stress related symptoms or disorders, psychiatric morbidity, and many further MHP like paranoid ideation, hallucinations, and insomnia that may occur in the general public, HCW or survivors during and after epidemic outbreaks. doi = 10.1101/2020.05.19.20103788 id = cord-269001-m4mpcoab author = Zullo, Fabrizio title = COVID-19 Antibody Testing in Pregnancy date = 2020-05-18 keywords = SARS summary = 1, 2 Almost all patients with COVID-19 infection test positive for 23 antiviral immunoglobulin-G (IgG) within about 10-20 days after symptom onset (Figure 1 ), but the 24 clinical value of antibody testing has not yet been completely elucidated, either in non-pregnant or 25 even more pregnant patients. Testing pregnant women for antibody response to COVID-19 may have different advantages, 33 including identifying: 1. Women still at risk for COVID-19 infection (e.g. IgM and IgG negative). Those tested positive to either IgM 69 or IgG at the rapid combined antibody test, have NP swab offered, and the outpatient appointment is 70 postponed, as shown in Figure 2B . In summary, we recommend testing for antibody response to SARS-CoV-2 for pregnant women Development and Clinical Application of A Rapid IgM-IgG Combined Antibody 111 Test for SARS-CoV-2 Infection Diagnosis doi = 10.1016/j.ajogmf.2020.100142 id = cord-275404-hv3y4x4g author = Zumla, Alimuddin title = Infection control and MERS-CoV in health-care workers date = 2014-05-20 keywords = MERS; SARS summary = 1 The WHO Emergency Committee concluded that the increase in cases reported among health-care workers from hospitals in Jeddah was amplifi ed due to overcrowding and inadequate infection control measures. 11 On the basis of analysis of data in a case-control study that involved 124 medical wards in 26 hospitals in Guangzhou, China, and Hong Kong, the risk factors for super-spreading events of SARS-CoV in the hospital setting were: close separation between beds of less than 1 m; performance of resuscitation; staff working while experiencing symptoms; and patients requiring oxygen or non-invasive ventilation therapy. A systematic review of fi ve case-control and fi ve retrospective cohort studies identifi ed tracheal intubation, tracheotomy, and manual ventilation before intubation as procedures associated with risk of transmission of SARS-CoV to health-care workers. Interim infection prevention and control recommendations for hospitalized patients with Middle East respiratory syndrome coronavirus (MERS-CoV) doi = 10.1016/s0140-6736(14)60852-7 id = cord-292988-q1yz9y8k author = Zumla, Alimuddin title = Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date = 2020-05-17 keywords = MSC; SARS; cell; covid-19 summary = title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . doi = 10.1016/j.ijid.2020.05.040 id = cord-320646-xk77u4g0 author = Zumla, Alimuddin title = The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security date = 2020-04-09 keywords = China; SARS; covid-19 summary = The emergence of new pathogens that cause lethal human respiratory illnesses with pandemic potential [2, 3] pose major challenges and rapidly focus the attention of global public health authorities and HCWs. Two zoonotic coronaviruses which cause lethal respiratory tract infections in humans feature on the WHO Blueprint list of priority pathogens for research and development [4] because of their pandemic potential. The World Health Organization International Health Regulations Emergency Committee declared COVID-19 outbreak a Global emergency [11] because SARS-CoV has spread rapidly within and outside China at an alarming pace and has caused considerable consternation and panic among the national, regional, and international public and political communities compounded by news media and social media hype [12] . Although the world awaits the development and evaluation of new vaccines, anti-SARS-CoV-2 specific drugs, antibody, and/or other host-directed interventions [32, 33] , public health infection control measures remain of prime importance in limiting human-to-human transmission, especially among close contacts and HCWs, and minimizing risk of international spread by identifying and isolating patients early. doi = 10.1097/mcp.0000000000000676 id = cord-329129-t84pu00z author = Zuo, J title = Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date = 2020-11-02 keywords = CD4; SARS summary = We analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. In conclusion, our data are reassuring that functional SARS-CoV-2-specific T-cell responses are retained at six months following infection although the magnitude of this response is related to the clinical features of primary infection. In this study we characterised SARS-CoV-2-specific T cell immune responses in a cohort of 100 donors at 6-months post-infection. Peptide pools from a range of viral proteins, including spike, nucleoprotein and membrane protein, were used to stimulate fresh PBMC and the magnitude of the global SARS-CoV-2-specific T-cell response was determined. Here we undertook, to our knowledge, the first assessment of the SARS-CoV-2-specific T cell immune response at six months following primary infection in a unique cohort of healthy adults with asymptomatic or mild-to-moderate COVID-19. doi = 10.1101/2020.11.01.362319 id = cord-023867-ti4b03lh author = Zuo, Wei title = SARS Coronavirus and Lung Fibrosis date = 2009-07-22 keywords = SARS; TGF summary = The mechanisms by which SARS-CoV infection causes lung fibrosis are not fully understood, but transforming growth factor-β (TGF-β) and angiotensin-converting enzyme 2 (ACE2)-mediated lung fibrosis are among the most documented ones. Therefore, SARS-CoV infection may lead to lung fibrosis through multiple signaling pathways and TGF-β activation is one of the major contributors. ACE2 proteins are expressed by alveolar epithelial cells, the primary targets of SARS-CoV in lung. Altogether, infection with SARS-CoV results in ACE2 downregulation through the binding of SARS-CoV spike protein to ACE2, and this spike protein-mediated ACE2 downregulation is responsible for the pathogenesis of lung fibrosis by upregulating ANG-II and activating TGF-b signaling. Both the TGF-b/Smad and the ACE2/ANG-II/CTGF pathways contribute to myofibroblast activation and ECM accumulation, collectively leading to the final lung fibrosis Role of extracellular signal-regulated kinase, p38 kinase, and activator protein-1 in transforming growth factor-beta 1-induced alpha smooth muscle actin expression in human fetal lung fibroblasts in vitro Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling doi = 10.1007/978-3-642-03683-5_15 id = cord-307942-t8165mdx author = Zwald, Marissa L. title = Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 date = 2020-04-10 keywords = SARS summary = On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19). During the investigation period, 226 patients seen at one of the four urgent care centers met the inclusion criteria (i.e., Santa Clara County resident, respiratory symptoms, no recent travel, and no known close contact with a patient with confirmed COVID-19) and were tested for evidence of influenza virus infection; among those, 53 (23%) had positive test results for influenza. doi = 10.15585/mmwr.mm6914e3 id = cord-337372-y43prnko author = bin‐Reza, Faisal title = The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence date = 2011-12-21 keywords = SARS; mask; respirator summary = A limited effort was made to identify additional studies: reference lists of review articles were examined; the European Centre for Disease Prevention and Control''s (ECDC) Antimicrobial Resistance and Health Care Associated Infection Programme was consulted; and MEC''s and AN''s hardcopy literature files were hand-searched. [7] [8] [9] [10] [11] Two of these studies compared N95 respirators (designed to seal tightly to the wearer''s face and filter out very small particles or aerosols that may contain viruses) and surgical masks (used to block large droplets from coming into contact with the wearer''s mouth or nose) amongst healthcare workers; one trial found a lower rate of clinical respiratory illness associated with the use of non-fit-tested N95 respirators compared with medical masks, 6 whilst a non-inferiority trial found that masks and respirators offered similar protection to nurses against laboratory-confirmed influenza infection. doi = 10.1111/j.1750-2659.2011.00307.x id = cord-306017-4wf4yhyz author = d''Aloja, Ernesto title = COVID-19 and medical liability: Italy denies the shield to its heroes date = 2020-07-24 keywords = SARS; italian summary = As well known, Italy is one of the Countries in a worldwide context more severely affected by the SARS-CoV-2 pandemic and some of the northern regions paid the highest price in terms of deaths among health care workers (HCWs).The ''Istituto Nazionale Assicurazione Infortuni sul Lavoro'' (INAIL), the Italian public insurance body that protects workers in the event of accidents and occupational diseases, reported that 40% of the 236 filedfatal cases involved HCWs [1] . From a negligent pandemic point of view, this may mean that if the hospital À even a no-COVID one -does not provide for all these measures, and one or more cases of SARS-COV-2 positive patients are detected in the healthcare facility, a presumption of liability may be enough to pursuing a negligent pandemic crime (article 452, Italian penal code). doi = 10.1016/j.eclinm.2020.100470 id = cord-278923-u4gv2e7w author = da Silva, Joyce Kelly R. title = Essential Oils as Antiviral Agents, Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation date = 2020-05-12 keywords = SARS; essential; oil summary = A molecular docking analysis was carried out using 171 essential oil components with SARS-CoV-2 main protease (SARS-CoV-2 M(pro)), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP-ribose-1″-phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). One study evaluated the in vitro antiviral effect against influenza type A (H1N1) of commercial essential oils that included cinnamon (Cinnamomum zeylanicum), bergamot (Citrus bergamia), lemongrass (Cymbopogon flexuosus), thyme (Thymus vulgaris), and lavender (Lavandula angustifolia). In this work, we carried out a molecular docking analysis of the major components of essential oils that exhibit antiviral activity (Tables 1 and 2 ) with known SARS-CoV-2 protein targets. Docking scores, normalized for molecular weight (DS norm , kJ/mol), of essential oil components with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular targets. doi = 10.3390/ijms21103426 id = cord-347613-tjeo62dv author = da Silva, Priscilla Gomes title = Corrigendum to “Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2”[Sci. Total Environ. 750 (2021) 141483] date = 2020-09-10 keywords = SARS summary = In this study, HeLa cells that expressed or did not express ACE2 proteins from humans, Chinese horseshoe bats, civets, pigs and mice were used, and it was found that SARS-CoV-2 is able to use all ACE2 proteins (except for mouse ACE2) as an entry receptor to enter ACE2-expressing cells, but it could not enter cells that did not express ACE2, indicating that ACE2 is probably the cell receptor through which SARS-CoV-2 enters cells (Zhou et al., 2020) . This and other bat-coronaviruses share 88-92% nucleotide sequence homology with SARS-CoV-1 (Ye et al., 2020) , leading scientists to believe that SARS-CoV was transmitted directly to humans from wet market civets, with bats as the main reservoir hosts (Cui et al., 2019; Hu et al., 2017) ". Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus doi = 10.1016/j.scitotenv.2020.142123 id = cord-350925-1h6pbfwp author = da Silva, Priscilla Gomes title = Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date = 2020-10-08 keywords = MERS; SARS; virus summary = Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . doi = 10.1016/j.scitotenv.2020.142802 id = cord-268561-vq1uhj5i author = da Silva, Severino Jefferson Ribeiro title = Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19 date = 2020-08-04 keywords = COVID-19; China; CoV-2; Coronavirus; Disease; SARS; patient summary = 11 The causative agent was identified as a novel CoV, eventually named SARS-CoV-2, and the respiratory syndrome associated with the infection was designated as coronavirus disease-2019 (COVID-19) by the World Health Organization (WHO). In direct tests, the clinical sample is examined directly for the presence of particles, virus antigens, or viral nucleic acids, whereas indirect methods detect the serological response against the infection (Figure 2 ). 11 Culture-based methods for SARS-CoV-2 detection have been used in research and public health laboratories in different parts of the world, but virus isolation is not recommended as a routine diagnostic procedure because it has low sensitivity, it is time-consuming, and it requires BSL-3 containment. 11 In addition to unequivocally confirming the diagnosis of a SARS-CoV-2 infection, regular sequencing of a percentage of patient samples from clinical cases can be used to monitor changes in the viral genome over time and trace transmission patterns. doi = 10.1021/acsinfecdis.0c00274 id = cord-307229-wjx90xki author = da Silveira, Matheus Pelinski title = Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date = 2020-07-29 keywords = COVID-19; SARS; exercise; immune; physical; response summary = Additionally, elevations of IL-1β, IFN-γ, IP10 and MCP1 in infections by the novel coronavirus were associated with the Th1 response; however, an increase in interleukins of the T helper type 2 (Th2) profile, such as IL-4, IL-5, IL10, which suppress the inflammation, was also associated with a greater severity of COVID-19, which may demonstrate an imbalance in immune regulation and an attempt to minimize tissue inflammatory damage [35, 40] . In addition, obesity is an important factor for the development of T2DM-especially when associated with low levels of physical activity and poor physical conditioning-and as mentioned, both diseases are related to higher expression of ACE2, increasing the risk of advanced infection by SARS-CoV-2 [43] . Similarly, regular exercise practices at moderate levels favor the function of the human body''s immune surveillance against pathogens, as they stimulate an exchange of white blood cells between the circulatory system and tissues, a fact that reduces morbidity and mortality from acute respiratory disease and infections viral. doi = 10.1007/s10238-020-00650-3 id = cord-035067-ic843wr9 author = de Almeida, Joana Ferro Machado title = COVID-19 and the gastrointestinal tract: what do we already know? date = 2020-11-05 keywords = COVID-19; RNA; SARS; patient summary = Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. Information on country of origin, mean age, different comorbidities, typical symptoms (fever, cough, and dyspnea, among others), gastrointestinal symptoms (diarrhea, nausea, vomiting, and abdominal pain), and the presence of viral RNA in feces, when cited, were included in this study for analysis. (19) According to the descriptive, cross-sectional, multicenter study (three hospitals in Hubei, China) by Pan et al., with 204 patients, in which 107 were male, mean age of 52.91±15.98 years, 103 (50.5%) reported some gastrointestinal symptom, such as lack of appetite (81; 78.6%), diarrhea (35; 34.0%), vomiting (4; 3.9%), and abdominal pain (2; 1.9%). (26) Cipriano et al., conducted a systematic review with six studies of patients from China, which points to the possibility of SARS-CoV-2 infection in the gastrointestinal tract and fecal-oral transmission. doi = 10.31744/einstein_journal/2020rw5909 id = cord-321049-9ozn6il7 author = de Almeida, Paula Rodrigues title = SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date = 2020-05-01 keywords = SARS summary = title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. Here, we present a fast, accurate and simple method of viral titration using QuantStudio 3D® microchip based RT-dPCR to titrate SARS-CoV2 genomic copies from controls to be used in RT-qPCR assays for diagnosis and research purposes. A dilution that results in approximately 200 to 2000 target copies in the final reaction usually presents better precision values. Results with precision values below 5% were selected to estimate quantity of SARS-CoV2 genomic copies based on RT-dPCR. RT-dPCR results of 10-fold serial dilution of SARS-CoV2 control using assays for three targets in the Nucleocapsid gene. These results indicate that these primer-probe assays are suitable for SARS-CoV2 quantification through RT-dPCR. doi = 10.1101/2020.05.01.072728 id = cord-275569-i5y23mmz author = de Bernardis, E. title = A putative role for the tobacco mosaic virus in smokers’ resistance to COVID-19 date = 2020-07-31 keywords = SARS; TMV summary = Though it is intuitively tempting, on the basis of physiopathological common knowledge, to predict a greater risk of contracting the SARS-CoV-2 infection in tobacco smokers, an analysis of studies from various countries shows that hospitalized COVID-19 patients have a lower, and apparently inversely proportional, rate of current tobacco smoking, in comparison with the respective general population, although once the disease has developed meta-analyses suggest that smoking is associated with a worse prognosis [1] . Incidentally, this behavior reminds the proposed effects of tobacco smoking, protective against initial SARS-CoV-2 infection and deleterious in the florid phase of the COVID-19 disease. Taken together, all these elements suggest that the oral use of tobacco, continuously exposing to non-pathogenic but immunogenic TMV particles, and chronically stimulating a natural antiviral response, may induce a state of resistance to the initial SARS-CoV-2 infection. doi = 10.1016/j.mehy.2020.110153 id = cord-354510-jlg5je0s author = de Carvalho, A. F. title = THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date = 2020-06-20 keywords = RNA; SARS summary = Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. 13 Here we describe the use of a simple, virus-inactivating and denaturing solution as part of a swab collection kit, aiming to decrease the infectious potential of the clinical sample and, at the same time, to preserve highly frail RNA molecules during transportation and short-term storage before testing. In order to increase personnel safety, to avoid losing collaborators due to infections by SARS-CoV-2, and at the same time to increase preservation of the RNA contained in clinical samples, we introduced the use of the guanidinecontaining solution as collection and transport media instead of commonly used viral transport media (VTM). doi = 10.1101/2020.06.18.20134304 id = cord-308597-ieju8gd8 author = de Carvalho, Renata Cristina title = The interference of COVID-19 in the male reproductive system: Important questions and the future of assisted reproduction techniques date = 2020-08-21 keywords = COVID-19; SARS summary = If the presence of SARS-Cov-2 in semen is confirmed, the methods of assisted human reproduction conduct should be modified, ensuring the timely safety of couples; however, current information about the virus raises other issues, such as: if seminal transmission exists, should a couple avoid sexual intercourse or use a barrier method if the male partner is known to be positive for the coronavirus disease 2019 (COVID-19)? If there is SARS-Cov-2 in an infected male''s semen, is double sperm washing effective in isolating the virus as it is for HIV and hepatitis C? In addition, even with the absence of the virus in the seminal sample, a study has reported the presence of orchialgia in men diagnosed with COVID-19 (16) , which is indicative of testicular damage. Absence of 2019 novel coronavirus in semen and testes of COVID-19 patients Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease doi = 10.6061/clinics/2020/e2183 id = cord-340015-x9frt0jh author = de Carvalho, Werther Brunow title = Expert recommendations for the care of newborns of mothers with COVID-19 date = 2020-05-11 keywords = COVID-19; SARS; newborn summary = Despite the lack of scientific evidence regarding the potential for viral transmission to their fetus in pregnant mothers diagnosed with or suspected of COVID-19, it is important to elaborate the lines of care by specialists from hospitals caring for suspected and confirmed COVID-19 cases to guide multidisciplinary teams and families diagnosed with the disease or involved in the care of pregnant women and newborns in this context. (10) proposed the presence of at least one of following clinical signs or symptoms as criteria for the neonatal diagnosis of COVID-2: thermal instability, hypoactivity, feeding difficulty, respiratory distress, chest X-ray with changes (including single or bilateral ground-glass patterns), COVID-19 diagnosis in family or caregiver of the newborn, intimate contact with people with suspected or confirmed COVID-19, or patients with unclear pneumonia. Despite the lack of scientific evidence regarding the potential viral transmission to their fetus by pregnant women with suspected or positive for COVID-19, multidisciplinary teams must be attentive to the disease signs and symptoms for guided and assertive decision making in the management of both mothers and newborns in the hospital environment and discharge. doi = 10.6061/clinics/2020/e1932 id = cord-290428-zrlqzbss author = de Faria Coelho-Ravagnani, Christianne title = Dietary recommendations during the COVID-19 pandemic date = 2020-07-12 keywords = SARS; covid-19; dietary; food; vitamin summary = Since to date there is no vaccine or evidence-based treatment for COVID-19, the optimization of nutrient intake through well-balanced meals and the use of good hygiene practices in food selection, preparation, and conservation is probably the most effective approach for managing the continuous risk of viral infection. There is no evidence that COVID-19 is spread through eating or touching raw fruits or vegetables; Prior to consumption, fresh fruits and vegetables should be washed or scrubbed under cold, running, potable tap water; While there are no special precautions for storing food, handwashing after putting away purchased food and before preparing food is recommended; Hands should be washed before and after food containers are washed EUFIC (2020) 19 Appropriate intakes of copper, folate, iron, selenium, zinc, and vitamins A, B 6 , B 12 , C, and D play an important role in the immune system; In general, these nutrients should be obtained through foods Supplements can be used to add nutrients to the diet in individuals who have specific challenges in meeting dietary requirements doi = 10.1093/nutrit/nuaa067 id = cord-321770-g5xcfhnh author = de Farias, Emmerson Carlos Franco title = MULTISYSTEM INFLAMMATORY SYNDROME IN A CHILD ASSOCIATED WITH CORONAVIRUS DISEASE 19 IN THE BRAZILIAN AMAZON: FATAL OUTCOME IN AN INFANT date = 2020-08-26 keywords = COVID-19; SARS summary = CASE DESCRIPTION: A seven-month-old infant, with SARS-CoV-2 infection and a history of extreme preterm birth and very low weight at birth, with an initial course of mild respiratory symptoms and abrupt progression to vasoplegic shock, myocarditis and hyperinflammation syndrome, shown by high levels of troponin I, ferritin, CRP, D-dimer and hypoalbuminemia. The diagnosis of MIS-C should be considered among children and adolescents aged from zero to 19 years, with characteristics of typical or atypical Kawasaki disease or shock syndrome, according to the case definition proposed by the World Health Organization (WHO) 8 , described in Chart 1. In this study, we describe a case of MIS-C in an infant infected with SARS-CoV-2, after parental authorization, which had a fatal outcome despite the support received in pediatric intensive care. This case report emphasizes the fatal clinical course of an infant admitted with infection by SARS-CoV-2, associated with significant comorbidity, presenting with hyperinflammatory and multiple organ dysfunction syndromes. doi = 10.1590/1984-0462/2020/38/2020165 id = cord-283705-ia65pade author = de Gabory, Ludovic title = Le virus influenza, le SARS-CoV2 et les voies aériennes : mise au point pour l’Otorhinolaryngologiste date = 2020-06-05 keywords = SARS summary = L''objectif de cet article est de faire une mise au point sur les mécanismes de production et de pénétration des gouttelettes de sécrétions, émises lors de tous les phénomènes expiratoires, susceptibles de transporter ces virus et venir au contact de la muqueuse respiratoire. Si ces ARNs sont détectables autour des patients, sur les surfaces et dans l''air ambiant à des distances variables selon les études (de 0,5 m jusqu''au-delà de la chambre du patient) cela ne préjuge pas du caractère infectieux (viabilité) du virus et de la dose minimale infectieuse. L''objectif de cette mise au point était d''analyser les données objectives de contagiosité des patients lors du transport des virus par le produit des sécrétions et leur possibilité de pénétration dans les voies aériennes. En pratique le pourcentage de VI infectieux dans les gouttelettes produites lors de la toux ou de l''expiration variaient de 5 à 42 % pour des particules de 0,3 à 8 µm de diamètres lorsque les patients ont les signes cliniques depuis 2 jours [47, 49, 54, 55] . doi = 10.1016/j.aforl.2020.05.010 id = cord-315465-u3zq9k5j author = de Jesus, Myrela Conceição Santos title = Family COVID-19 cluster analysis of an infant without respiratory symptoms date = 2020-08-26 keywords = COVID-19; SARS summary = Here, we report the case of a child with COVID-19 who attended an outpatient clinic in Aracaju, Northeast-Brazil, with gastrointestinal symptoms and no respiratory problems and the subsequent screening of his close family members. A 45-year-old asymptomatic uncle, who was unable to maintain social isolation due to work commitments had a positive nasopharyngeal/oropharyngeal RT-PCR assay result on 15th May 2020, but his IgM and IgG tests performed on the same day yielded negative results. This is a case report comprising a child with a chief complaint of diarrhea and the clinical history of his six contact family members during the 20 days prior to the onset of his symptoms. We also describe the clinical findings, molecular and serological assay results of the family members with whom he had been in contact up to 20 days before symptom onset. doi = 10.1590/0037-8682-0494-2020 id = cord-260729-b12v3c8c author = de Lang, Anna title = Functional Genomics Highlights Differential Induction of Antiviral Pathways in the Lungs of SARS-CoV–Infected Macaques date = 2007-08-10 keywords = CoV; IFN; SARS; lung; stat1 summary = As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs) and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. In order to elucidate early host responses during the acute phase of SARS-CoV infection, we infected cynomolgus macaques with SARS-CoV and used macaque-specific microarrays and real-time (RT)-PCR techniques to study host gene expression profiles. In this study, we simultaneously examined virus replication and host-response gene expression profiles in macaque lungs during the acute phase of SARS to gain more insight into the early events that take place after SARS-CoV infection. In order to visualize the host response in the lungs of SARS-CoV-infected macaques, IFN-b production and translocation of phosphorylated STAT1 was studied using immunohistochemistry. The expression of IFN-b, which strongly correlated to the amount of virus present, continued throughout day 4 and was confirmed using immunohistochemistry; IFN-b-positive cells could be detected in the lungs of the SARS-CoV-infected macaques. doi = 10.1371/journal.ppat.0030112 id = cord-274252-h4occy7h author = de Lima Menezes, Gabriela title = Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) date = 2020-07-13 keywords = SARS; figure summary = After main pocket validation using two control drugs and the main conformations of nsp1, molecular docking based on virtual screening were performed to identify novel potential inhibitors from DrugBank database. Three of them was ranked as the best compounds among them and showed better energy score than control molecules that have in vitro activity against nsp1 from SARS-CoV-2. Due to lack of active site information a blind docking using two cyclophilin inhibitors described as potential CoV suppressors (Carbajo-Lozoya et al., 2014; Kamitani et al., 2009; Pfefferle et al., 2011) were performed by AutoDock Vina (Morris et al., 2009 ) with nsp1 conformations in order to define the best pocket for virtual screening. After that, based on AutoDock Vina energy scores, it was possible to identify the main residues/regions involved in the interactions and thus define the target pockets to be used in the virtual screening simulations with DrugBank database. doi = 10.1080/07391102.2020.1792992 id = cord-307406-59yh48tt author = de Loyola, Mariana Braccialli title = Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19 date = 2020-08-26 keywords = A1AT; ACE2; SARS; TMPRSS2; covid-19 summary = 2, 3 A1AT is an inhibitor of SARS-CoV-2 infection and two of the most important proteases in the pathophysiology of Covid-19: the transmembrane serine protease 2 (TMPRSS2) and the disintegrin and metalloproteinase 17 (ADAM17), as was well as an inhibitor of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. [4] [5] [6] Moreover, recent data indicate that lower IL-6:A1AT levels are related to worse prognosis in This review addresses the interplay between A1AT, TMPRSS2, ADAM17, and inflammatory molecules during SARS-CoV-2 infection with the aim of identifying new avenues for effective treatments against Covid-19. In order to achieve a more comprehensive understanding of A1AT in Covid-19, is important to address the following concerns: The evidence presented in this review highlights the relevance of the A1AT as a host protective factor, which can inhibit the TMPRSS2-mediated SARS-CoV-2 infection, modulate the deleterious effect of ADAM17 activation and the activity of inflammatory molecules, such as IL-8, TNF-α, and neutrophil elastase. doi = 10.1002/rmv.2157 id = cord-353217-gmc3qrci author = de Miranda Santos, Isabel Kinney Ferreira title = Impact of Hydroxychloroquine on Antibody Responses to the SARS-CoV-2 Coronavirus date = 2020-08-04 keywords = SARS summary = Recent large observational studies indicate that hydroxychloroquine (HY) does not affect outcomes of patients hospitalized with COVID-19 (1, 2) and may even be harmful (3) . In view of this situation and of the importance of correct interpretation of antibody profiles for planning preventive measures for COVID-19, we would like to bring the attention of readers to studies that raise concerns about the possible impact of HY upon antibody responses to SARS-CoV-2. To the best of our knowledge, there are no new facts in the scientific and medical literature that indicate that the same mechanism could not operate in HY-treated patients suffering from COVID-19 and negatively impact their SARS-CoV-2-specific antibody responses. As more needs to be learned about the role of antibodies in recovery from and protection against infection with SARS-CoV-2, the impact of HY and other treatment regimens on antibody responses requires systematic evaluation. doi = 10.3389/fimmu.2020.01739 id = cord-346248-6wkyar57 author = de Moura, Diogo Turiani Hourneaux title = Diagnostic Characteristics of Serological-Based COVID-19 Testing: A Systematic Review and Meta-Analysis date = 2020-08-06 keywords = COVID-19; SARS; testing summary = The aim of this study was to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based COVID-19 testing. This meta-analysis demonstrates suboptimal sensitivity and specificity of serologic-based diagnostic testing for SARS-CoV-2 and suggests that antibody testing alone, in its current form, is unlikely to be an adequate solution to the difficulties posed by COVID-19 and in guiding future policy decisions regarding social distancing and reopening of the economy worldwide. While this test is still the most effective method to date for the diagnosis of active COVID-19, serologic-based antibody testing to assist with known exposure to SARS-CoV-2 remains pivotal to accurately assessing the burden of disease. Therefore, we aim to perform a structured systematic review and meta-analysis to evaluate the diagnostic characteristics of serological-based testing (IgG and IgM) for COVID-19. doi = 10.6061/clinics/2020/e2212 id = cord-306308-zjq6cscm author = de Moura, Ronald Rodrigues title = Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date = 2020-08-05 keywords = HLA; MHC; SARS summary = Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. doi = 10.1136/jclinpath-2020-206946 id = cord-323440-u3iz79kk author = de Niet, Annikki title = The role of children in the transmission of mild SARS‐CoV‐2 infection date = 2020-05-04 keywords = SARS summary = We thank Dr Ludvigsson 1 on his effort to improve knowledge on SARS-CoV-2 infection in children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. In trying to understand the spread of the disease, one of the most notable features is that only a small number of severe SARS-CoV-2 infections have involved children. 4 Furthermore, SARS-CoV-2 infection in children differs from adults in that they have a lower prevalence of increased C-reactive protein, signifying a milder immunological response and less immune damage. 1 The viral load in patients with mild disease showed to be lower compared with those having severe SARS-CoV-2 infection. 2 Reports from severe disease in infected healthcare workers further hint towards an association between higher viral load in critically ill patients and transmission of more severe SARS-CoV-2 infection. doi = 10.1111/apa.15310 id = cord-323824-74xvvwrw author = de Oliveira, Osmair Vital title = Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening date = 2020-06-02 keywords = SARS; Smith summary = Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below –8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. Our approach adopted here differs from those studies in the following way: the isolated S-protein receptor for docking calculations will be obtained from molecular dynamics (MD) simulation, and not directly from crystal structure or S-protein@ACE2 complex. (Muralidharan et al., 2020) obtained from docking calculations a binding energy of -4.1 kcal/mol using the SARS-CoV-2 protease and lopinavir drug, respectively, as receptor and ligand. In this way, our calculations indicate that the ivermectin drug may bind in the RBD region, inhibiting the coupling of the SARS-CoV-2 S-protein with the human ACE2 receptor. Therefore, herein we used molecular dynamics (MD) simulation and docking calculations to study the SARS-CoV-2 S-protein with the main goal to obtain possible drugs candidates for repurposing them against to COVID-19. doi = 10.1080/07391102.2020.1772885 id = cord-103945-q3ry13vp author = de Oliveira, P. M. title = Evolution of spray and aerosol from respiratory releases: theoretical estimates for insight on viral transmission date = 2020-07-24 keywords = Fig; SARS; droplet summary = By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. By modelling the evaporation and settling of droplets emitted during respiratory releases and using previous measurements of droplet size distributions and SARS-CoV-2 viral load, estimates of the evolution of the liquid mass and the number of viral copies suspended were performed as a function of time from the release. The Lagrangian framework, given in Sec. 2(a), is considered in one (vertical) dimension and droplet clouds for two exhalation modes, speaking and coughing, are released at the height of the emitter''s mouth (1.5 m) and then let settle by gravity while evaporating in ambient air. doi = 10.1101/2020.07.23.20160648 id = cord-352911-9wbq9qo2 author = de Oliveira, Pedro Gonçalves title = Diacerein: a potential multi-target therapeutic drug for COVID-19 date = 2020-06-01 keywords = COVID-19; SARS; cell summary = The mortality related to severe acute respiratory distress syndrome (ARDS) and multi-organ failure in COVID-19 patients has been suggested to be connected with cytokine storm syndrome (CSS), an excessive immune response that severely damages healthy lung tissue. Total extracts from monolayer cell cultures infected with SARS-CoV-2 and treated with rhein under the conditions described above will be analysed using commercially available protein arrays to determine the levels and activation state of proteins involved in the TLR-, Akt-, MAPK-, and NF-B-regulated signalling pathways. The mechanisms of action involved include the control of hyperinflammatory conditions by multi-faceted cytokine inhibition of IL-1, IL-2, IL-6, IL-8, IL-12, IL-18 and TNF-α; anti-platelet aggregation activity; and potential effects on viral infection and replication. Rhein suppresses lung inflammatory injury induced by human respiratory syncytial virus through inhibiting NLRP3 inflammasome activation via NF-κB pathway in mice doi = 10.1016/j.mehy.2020.109920 id = cord-344829-adlp2rjy author = de Rivero Vaccari, Juan Carlos title = The Inflammasome in Times of COVID-19 date = 2020-10-08 keywords = ARDS; COVID-19; NLRP3; SARS; activation; inflammasome summary = Here we review the literature regarding the mechanism of inflammasome activation by CoV infection, the role of the inflammasome in ARDS, ventilator-induced lung injury (VILI), and Disseminated Intravascular Coagulation (DIC) as well as the potential mechanism by which the inflammasome may contribute to the damaging effects of inflammation in the cardiac, renal, digestive, and nervous systems in COVID-19 patients. Here we review the literature on the role of the inflammasome in CoV infections, which includes how CoVs activate inflammasomes upon infection, the role of the inflammasome in acute respiratory distress syndrome (ARDS), how ventilator-induced lung injury (VILI) activates the inflammasome, how the inflammasome plays a role in the systemic complications associated with COVID-19, and how the inflammasome is involved in the process of Disseminated Intravascular Coagulation (DIC). doi = 10.3389/fimmu.2020.583373 id = cord-291729-4l4v9jxd author = de Salazar, Adolfo title = Sample pooling for SARS-COV-2 RT-PCR screening date = 2020-09-10 keywords = PCR; SARS summary = CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. Our objective in this study has been to evaluate the efficacy of sample pooling in a multicentre way compared to the individual analysis for the detection of COVID-19 by using different commercial platforms available for genomic extraction and amplification by RT -PCR in real time. Here we report on the high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. In summary, we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. doi = 10.1016/j.cmi.2020.09.008 id = cord-322087-gj5mfzxz author = de Sanctis, Vincenzo title = Coronavirus Disease 2019 (COVID-19) in adolescents: An update on current clinical and diagnostic characteristics date = 2020-05-11 keywords = COVID-19; China; Disease; SARS summary = This paper summarises the current findings (April 3,2020) from a systematic literature review on the current knowledge of COVID-19 in adolescents (10-19 years according to the WHO definition) and reports the preliminary epidemiological data stated by the Italian National Institute of Health. SARS-CoV-2 RNA was also detected in stool specimens but according to WHO-China report, fecal-oral transmission did not appear to be a significant factor in the spread of infection (Report of the WHO-China Joint Mission on Coronavirus Disease 2019,COVID-2019. Detailed epidemiological information based on a larger sample of COVID-19 patients is needed to determine the infectious period of SARS-CoV-2, as well as whether transmission can occur from asymptomatic individuals during the incubation period ("pre-symptomatic" period). In a small number of case reports and studies, a familial cluster of infection associated with SARS-CoV-2 has been reported, indicating possible personto-person transmission during the incubation period (18, 19) . doi = 10.23750/abm.v91i2.9543 id = cord-349124-nhnl7zgi author = de Sandes‐Freitas, Tainá Veras title = Lessons from SARS‐CoV‐2 screening in a Brazilian organ transplant unit date = 2020-07-13 keywords = COVID-19; SARS summary = Evidence suggests that asymptomatic carriers might transmit the SARS‐CoV‐2, challenging the implementation of transmission preventive strategies. We report a single‐center experience using universal SARS‐CoV‐2 screening for all inpatients and newly admitted patients to an Organ Transplant Unit located in a region with significantly high community‐based transmission. We will describe the experience of a single center of screening all inpatients and newly admitted patients to the Organ Transplant Unit. On March 31, 2020, a 43-year-old man with alcoholic liver cirrhosis, hospitalized since March 23rd presented acute dyspnea and fever and was tested positive for SARS-CoV-2 (patient 1). We reported the COVID-19 screening strategy adopted by our center in a attempt to prevent nosocomial transmission and keep "clean" the Transplant Unit. Alert for non-respiratory symptoms of coronavirus disease 2019 (COVID-19) patients in epidemic period: a case report of familial cluster with three asymptomatic COVID-19 patients Lessons from SARS-CoV-2 screening in a Brazilian organ transplant unit doi = 10.1111/tid.13376 id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 keywords = HLA; MHC; SARS summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. doi = 10.1016/j.ijid.2020.07.016 id = cord-299544-r3cqvf0c author = de Souza, T. H. title = Clinical Manifestations of Children with COVID-19: a Systematic Review date = 2020-04-03 keywords = COVID-19; SARS summary = Study Selection: Inclusion criteria were: (1) studied patients younger than 18 years old; (2) presented original data from cases of COVID-19 confirmed by reverse-transcription polymerase chain reaction; and (3) contained descriptions of clinical manifestations, laboratory tests or radiological examinations. https://doi.org/10.1101/2020.04.01.20049833 doi: medRxiv preprint children infected with SARS-CoV-2 may not meet all the criteria required in the suspected case definition. The following data were extracted, when available, from each elected article: first author, publication year, study design, number of cases, gender, age, clinical manifestations, laboratory tests, radiological examinations and outcomes (discharged, still hospitalized or death). In our study, we described the main clinical, laboratorial and radiological characteristics of children infected with SARS-CoV-2 reported in the literature. A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study doi = 10.1101/2020.04.01.20049833 id = cord-310333-70ldbw3r author = de Souza, Wanderley title = COVID-19 and parasitology date = 2020-05-30 keywords = SARS summary = Emerging and reemerging diseases are a challenge for public health worldwide and particularly for Brazil, where the existence of the Amazon region provides a constant source of new pathogens that are transmitted from wild animals to man. Infectious diseases, such as severe acute respiratory syndrome (SARS), represent a major threat to public health. At present, the available data indicate the presence of 2.6 million infected people and 178 thousand dead (April 22), demonstrating the severity of COVID-19 due to the rapid spread of the virus and its high pathogenicity, which mainly, but not exclusively, affects the pulmonary system. Therefore, members of the parasitology community, especially those working with parasite-host cell interaction processes, can and shall contribute at this time. Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease Epidemiology and cause of severe acute respiratory syndrome (SARS) in 304 Guangdong, People''s Republic of China doi = 10.1007/s00436-020-06719-y id = cord-332992-8rmqg4rf author = de Vries, A. A. F. title = SARS-CoV-2/COVID-19: a primer for cardiologists date = 2020-07-15 keywords = COVID-19; CoV-2; RNA; SARS; cell; patient; virus summary = Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . doi = 10.1007/s12471-020-01475-1 id = cord-321598-ae241pmd author = de Vries, A.P.J. title = Immediate impact of COVID-19 on transplant activity in the Netherlands date = 2020-05-01 keywords = COVID-19; SARS; transplant summary = Worldwide, the delivery of transplant care is severely challenged by matters concerning but not limited to organ procurement, risk of SARS-CoV-2 transmission, screening strategies of donors and recipients, decisions to postpone or proceed with transplantation, the attributable risk of immunosuppression for COVID-19 and entrenched health care resources and capacity. In less than 60 days, despite increasingly stringent measures of the Dutch government to halt the spread of the infection, 28, 153 individuals have tested positive for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), 9,127 patients have been admitted to hospitals across the country (of which 2,508 in the Intensive Care Units (ICU) [4] ) and 3,134 have died, according to RIVM (National Institute for Public health and the Environment, April 15, 2020). To facilitate extra time needed for recipient test results to become available, allocation for liver, heart and lung transplantation is initiated before donor SARS-CoV-2 screening is known (Table 1A) . doi = 10.1016/j.trim.2020.101304 id = cord-286703-ipoj13va author = de Wilde, Adriaan H. title = Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date = 2017-01-15 keywords = ALV; MERS; SARS summary = Data from cell culture infection models (Chan et al., 2013a (Chan et al., , 2013b de Wilde et al., 2013b; Falzarano et al., 2013a; Kindler et al., 2013; Zielecki et al., 2013) and experiments in rhesus macaques (Falzarano et al., 2013b) and marmosets (Chan et al., 2015) suggested that interferons (IFNs) are potent inhibitors of MERS-CoV replication. As ribavirin has previously been reported to inhibit MERS-CoV replication (Falzarano et al., 2013a) and ALV and ribavirin have been used together during clinical trials for hepatitis C treatment (Pawlotsky et al., 2015) , this combination was tested in LLC-MK2 cells. (e, f) SARS-CoV-infected (e) Vero or (f) VeroE6 cells (MOI 0.01) were treated with various concentrations of ALV from 1 h p.i. onwards, and virus titers in the culture medium at 32 h p.i. were determined by plaque assay. doi = 10.1016/j.virusres.2016.11.011 id = cord-319877-izn315hb author = de Wit, Emmie title = SARS and MERS: recent insights into emerging coronaviruses date = 2016-06-27 keywords = CoV; East; MERS; Middle; SARS; respiratory summary = Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters). doi = 10.1038/nrmicro.2016.81 id = cord-350104-b99y6n43 author = de Zwart, Onno title = Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey date = 2009-01-06 keywords = Asia; Europe; SARS summary = title: Perceived Threat, Risk Perception, and Efficacy Beliefs Related to SARS and Other (Emerging) Infectious Diseases: Results of an International Survey PURPOSE: To study the levels of perceived threat, perceived severity, perceived vulnerability, response efficacy, and self-efficacy for severe acute respiratory syndrome (SARS) and eight other diseases in five European and three Asian countries. To explore if country differences were specific for SARS, perceived threat, risk perception, and efficacy beliefs related to avian influenza and other (infectious) diseases were also investigated. -To study levels of perceived threat, vulnerability (or risk perception), severity and comparative vulnerability for SARS in Denmark, The Netherlands, Poland, Spain, the UK, China, Hong Kong, and Singapore; -To compare perceived severity, vulnerability, and threat of SARS with other diseases and conditions, i.e., avian influenza, common cold, diabetes, HIV, high blood pressure, tuberculosis, food poisoning, and a heart attack; -To study differences and associations between these factors across the eight countries and between Europe and Asia. doi = 10.1007/s12529-008-9008-2 id = cord-332457-gan10za0 author = de Ángel Solá, David E. title = Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date = 2020-04-10 keywords = Caribbean; SARS; virus summary = On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . doi = 10.1002/jmv.25864 id = cord-321380-e5zq15hz author = del Campo, P. Lázaro title = No transmission of SARS-CoV-2 in a patient undergoing allogeneic Hematopoietic Cell Transplantation from a matched-related donor with unknown COVID-19 date = 2020-08-24 keywords = COVID-19; SARS summary = In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. In our knowledge this is the first case report of an adult hematopoietic cell donor with COVID-19 in the J o u r n a l P r e -p r o o f incubation period where the transplant is successfully completed with no transmission of SARS-CoV-2. Lastly, applied to our case, the low concentration of viral RNA in plasma of asymptomatic patients with COVID-19 [5] , and a theoretical inefficacy of SARS-CoV-2 J o u r n a l P r e -p r o o f to replicate inside lymphocytes could support the safety of blood products, including peripheral blood hematopoietic cells. doi = 10.1016/j.transci.2020.102921 id = cord-329392-fufattj8 author = den Hartog, Gerco title = SARS-CoV-2–Specific Antibody Detection for Seroepidemiology: A Multiplex Analysis Approach Accounting for Accurate Seroprevalence date = 2020-08-08 keywords = RBD; SARS summary = Serum samples were obtained from the following cohorts: (1) a random selection of individuals (n = 224) from a national (Dutch) cohort representing all age groups and obtained 3 years prior to SARS-CoV-2 emergence (Pienter3 study, Netherlands trial register number NL5467); (2) individuals (Supplementary Table 2 ) with proven non-SARS-CoV-2 ILI caused by human coronaviruses (n = 110, HCoV ILI) or other viruses (n = 74, non-HCoV ILI) obtained from the National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands (trial register number NL4666) [18] , and from Erasmus Medical Center, Rotterdam, collected prior to the SARS-CoV-2 outbreak and at least 2 weeks after polymerase chain reaction (PCR) detection of the virus; and (3) The steps in assay validation were similar to recently developed bead-based multiplex immunoassays for CMV, EBV, and RSV, with minor modifications as described below [16, 17] . doi = 10.1093/infdis/jiaa479 id = cord-296579-oa67njov author = d’Ettorre, Gabriella title = Analysis of type I IFN response and T cell activation in severe COVID-19/HIV-1 coinfection: A case report date = 2020-09-04 keywords = COVID-19; SARS summary = Hence, this study aims to compare type I IFN response and T cell activation levels between a SARS-CoV-2/HIV-1-coinfected female patient and age-matched HIV-1-positive or uninfected women. LESSONS: These results indicate that SARS-CoV-2 infection in HIV-1-positive female patient was associated with increased levels of IFNα/β-mRNAs and T cell activation compared to healthy individuals. [1] Despite high number of people living with human immunodeficiency virus (HIV)-1 globally (about 37 million) and higher severity impact for certain viral infections in this category, [2] severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)/HIV-1 coinfection has been described in few cases. This study reports a severe case of SARS-CoV-2 in a black female patient co-infected by HIV-1 under protease inhibitors (PI) regimen, who was treated with hydroxychloroquine. Because of the key role of chronic immune activation and persistent IFN-I response in driving HIV-1 disease, [8, 9] we evaluated IFNa and IFNb gene expression and T cell activation levels in patient with SARS-CoV-2/HIV-1 coinfection. doi = 10.1097/md.0000000000021803 id = cord-102807-cxtzf5oe author = fiore, j. r. title = FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy date = 2020-06-19 keywords = SARS summary = title: FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint ABSTRACT 27 28 Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors 29 from a low incidence COVID-19 area (Apulia region, South Eastern Italy). . https://doi.org/10.1101/2020.06.17.20133678 doi: medRxiv preprint Studies on blood donor cohorts are useful to evaluate the prevalence, incidence and natural course 63 of infectious diseases in the general population and may thus help to assess both the viral 64 circulation and the evolution of the COVID-19 outbreak. We therefore studied a group of healthy blood donors from Foggia province for the presence of IgM 66 and IgG to antibodies to SARS-CoV-2 to examine the circulation of the virus in the general 67 population three months after the local start of the epidemic. doi = 10.1101/2020.06.17.20133678 id = cord-290598-wquwtovs author = li, s. title = Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients date = 2020-09-23 keywords = SARS summary = Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases. In this study, we assay the IgG and IgM antibodies in ocular disease patients undiagnosed COVID-19 (people have no symptom of COVID-19 and negative result for viral RNA testing) to estimate the seropositivity rate in different type of ocular disease. We enrolled 1331 individuals with different ocular diseases but negative to SARS-CoV-2 RNA testing in Eye and ENT Hospital of Fudan University from February 2020 to May 2020. We conducted a serological survey testing the IgG and IgM antibodies against SARS-CoV-2 antigens in each participant of different ocular disease. Our study evaluated the seroprevalence in patients with different ocular diseases, including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others. doi = 10.1101/2020.09.22.20198465 id = cord-015009-3o90pzw7 author = nan title = How and who does SARS kill? date = 2003-06-10 keywords = SARS summary = Analysis of the complete genome sequence of the SARS virus, published in May 11 , suggests that it is not closely related to any of the three previously identified coronavirus subfamilies, nor does it seem to have arisen through a chance genetic recombination between known coronaviruses12. "Its unique sequence suggests that it has evolved independently from the other members of the family, in some animal host, for a long time," says Malik Peiris, a virologist at the University of Hong Kong. Recent investigations by researchers at the China Agricultural University in Beijing, for instance, have failed to find SARS-like coronaviruses in 732 animals from 54 wild and 11 domestic species in southern China, including palm civets. "The animals walk in and out of their houses," says Kenneth Shortridge, who led the University of Hong Kong''s efforts to monitor avian viruses in southern China until his retirement last year. doi = 10.1038/nature.2003.2 id = cord-015516-hx7ktq8j author = nan title = In the Literature date = 2005-10-15 keywords = SARS summary = Experimental pulmonary infection with SARS coronavirus infection in mice reduced the expression of ACE2 in the lungs and, as also occurs in humans, caused diffuse lung injury. On the basis of these findings, the investigators proposed that the severe pulmonary alveolar injury seen in patients with SARS is the consequence of SARS coronavirus spike surface protein-associated down-regulation of ACE2. The authors suggest that recombinant ACE2 protein could be a potential therapeutic agent in this and related pulmonary infections and diffuse alveolar injuries. In patients with chronic infections involving the exit site or tunnel portion of peritoneal dialysis catheters, treatment with antibiotics and local care is often unsuccessful. This procedure was used by Crabtree and Burchette in 13 consecutive patients with chronic peritoneal dialysis catheter infections that had been present for a mean duration of 3.2 months, with successful results for all 13. Three patients subsequently had their catheters removed because of peritonitis without exit-site or tunnel infection at months 8-11. doi = 10.1086/497097 id = cord-015619-msicix98 author = nan title = Virus Structure & Assembly date = 2009-02-24 keywords = SARS; dna; structure; virus summary = The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. doi = 10.1016/s0006-3495(08)79065-9 id = cord-015701-0m17unfx author = nan title = Neuartiges Coronavirus (SARS-CoV-2) date = 2020-02-24 keywords = SARS summary = key: cord-015701-0m17unfx authors: nan title: Neuartiges Coronavirus (SARS-CoV-2) date: 2020-02-24 journal: Dtsch Med Wochenschr DOI: 10.1055/a-1113-3096 sha: doc_id: 15701 cord_uid: 0m17unfx nan . Von der Gabe von Kortikosteroiden wird eher abgeraten. An einem Impfstoff gegen SARS-CoV-2 wird fieberhaft gearbeitet. Auch im Idealfall dürften entsprechende Zulassungsstudien aber nicht vor Ende 2020 zu erwarten sein. china World Health Organization. Novel Coronavirus (SARS-CoV-2) situation reports First Case of 2019 Novel Coronavirus in the United States doi = 10.1055/a-1113-3096 id = cord-025794-ckrclrwz author = nan title = Mitteilungen der ÖGKJ date = 2020-06-02 keywords = SARS; die summary = Vom Roten Kreuz werden zusätzlich auch Kontaktpersonen von gesicherten SARS-CoV2 Fällen getestet, sodass diese gezielte Testung von Kindern als Kontaktpersonen die wahrscheinlichste Erklärung für die höheren Positivitätsraten in den behördlichen Angaben -verglichen mit den Daten allein aus den Kinderabteilungen -ist. Wenn eine Infektion ausgeschlossen werden kann, bedeutet dies für Mutter, Kind und auch das betreuende Personal eine enorme Erleichterung der Situation. Wenn die Mutter so krank ist, dass sie sich nicht selbst um das Kind kümmern kann, sollte das Neugeborene, nach Abwägung der individuellen Situation und den vorhandenen Optionen vor Ort, temporär von ihr getrennt und als Kontaktperson eines COVID-19-Falls eingestuft werden. Wenn eine Mutter (unabhängig von einem möglichen Verdacht auf SARS-CoV2-Infektion) sich entschieden hat, nicht zu stillen, ist es immer wünschenswert, dass das Neugeborene auf alle Fälle Kolostrum erhalten sollte. bei Einstufung als Verdachtsfall werden Mutter und Kind gemeinsam isoliert und wie jeder Isolationsfall den Richtlinien der Klinik entsprechend durch die Pflege betreut. doi = 10.1007/s00112-020-00930-y id = cord-029332-yn603pvb author = nan title = Full Issue PDF date = 2020-07-15 keywords = Brugada; COVID-19; China; SARS; acute; clinical; disease; figure; patient summary = Included are cases of Brugada type I pattern positivization (1) in the context of fever, one of the most common presenting symptoms of the disease (2); electrical ventricular storm (3); transient atrioventricular block in the absence of myocarditis (4); sinus node dysfunction requiring pacemaker implantation (5) ; and finally a provocative report on the use of amiodarone as a possible treatment for COVID-19 (6) . In addition to cases of direct myocardial injury, some with pathological evidence, we also present 2 cases of takotsubo cardiomyopathy (16, 17) Two cases highlight the special circumstances faced by patients with left ventricular assist devices (18, 19) , which include the inability to tolerate prone positioning to augment respiratory support because of the mechanical equipment and the hypothesis that mechanical circulatory support may provide a type of protection against the most serious hemodynamic consequences of severe acute respiratory syndrome coronavirus-2 infection. doi = 10.1016/s2666-0849(20)30838-x id = cord-252550-yaosufpm author = nan title = Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission date = 2020-09-09 keywords = SARS summary = authors: nan title: Correction: Unpuzzling COVID-19: tissue-related signaling pathways associated with SARS-CoV-2 infection and transmission SARS-CoV-2 infection down-regulates ACE2 expression and leads to the production of pro-inflammatory mediators, such as IL-6 [1] . As they lose ACE2-mediated protection, Ang-II signaling contributes to the pathological findings observed in COVID-19 patients, such as disseminated coagulopathy and acute tissue damage [4] . Toll-like receptors (TLRs) 3 and TLR 7/8 recognize SARS-CoV-2 RNA and initiate the inflammatory cascade via type I and type II IFN gene expression and NF-κB nuclear translocation [5, 6] . IL-6, an important player in COVID-19, binds IL-6R and gp130 receptors to activate JAK/STAT-3 pathway and then contribute to the CRS observed in COVID-19 patients [13] . Severe respiratory SARS-CoV2 infection: Does ACE2 receptor matter? Toll-like receptor 3 signaling via TRIF contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection doi = 10.1042/cs-20200904_cor id = cord-281754-auqh3vtr author = nan title = EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date = 2017-09-12 keywords = Coronavirus; H7N9; SARS; respiratory summary = As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] . doi = 10.1016/j.disamonth.2017.03.019 id = cord-324357-ys4tqy5x author = nan title = Hygiene at home: A bulwark against COVID-19 to be protect from SARS-CoV-2 date = 2020-05-15 keywords = SARS summary = • by droplets emitted from the nose and mouth (splutering) when coughing, sneezing, but also when speaking, singing and screaming, • by direct contact between people: shaking hands, hugging, kissing, • secondarily through indirect contact: objects contaminated by an infected person. The National Academy of Medicine wishes to recall the fundamental rules of hygiene at home which it is essential to observe in the current epidemic context, especially in families with children. The respiratory hygiene rules are: • cover your mouth and nose if you cough or sneeze, preferably with a disposable tissue, throw away the tissue immediately and wash your hands immediately before touching anything. • avoid touching your face, nose, eyes and mouth, which can spread respiratory viruses through contaminated hands; • ventilate the housing by opening the windows for at least 20 min in the morning and evening and during houseworking. Hydro-alcoholic solutions disinfect but do not clean: so they cannot replace washing with soap and water when hands are dirty. doi = 10.1016/j.banm.2020.05.020 id = cord-332245-yfj1kkj7 author = nan title = SARS-CoV-2 Infektion bei Kindern und Jugendlichen: Ein Literaturüberblick der AG Infektiologie der ÖGKJ1 date = 2020-06-10 keywords = COVID-19; China; Kindern; SARS summary = aktuell Infektiologie SARS-CoV-2 Infektion bei Kindern und Jugendlichen Ein Literaturüberblick der AG Infektiologie der ÖGKJ 1 F Im Dezember 2019 kam es in der chinesischen Region Hubei zum gehäuften Auftreten von Pneumoniefällen unbekannter Ätiologie [1] . Allerdings waren in dieser Altersgruppe knapp 80 % der Fälle lediglich Verdachtsfälle (ohne SARS-CoV-2-Laborbestätigung), sodass die Autoren davon ausgehen, dass ein nicht unbeträchtlicher Teil dieser schweren Verläufe durch andere Viren (v. Jedoch zeigten sich in einer diesen Kohorten vermehrte fetale Komplikationen wie Frühgeburtlichkeit oder respiratorischer Stress, wobei der direkte Zusammenhang mit SARS-CoV-2 nicht geklärt ist. So muss natürlich auf neonatalen Intensivstationen damit gerechnet werden, dass aufgrund einer SARS-CoV-2-Erkrankung der Mutter eine prämature Entbindung indiziert wird und die Frühgeborenen behandelt werden müssen. Bei den wenigen detaillierten Berichten über spezifische Symptome bei Kindern mit COVID-19 wird Fieber in 40-100 % und Husten in 40-100 % der symptomatischen Fälle beschrieben [7, 8, [15] [16] [17] [18] [19] . Bisher gibt es keine zugelassenen Medikamente zur Therapie von COVID-19 bei Erwachsenen und Kindern [32] . doi = 10.1007/s00608-020-00794-1 id = cord-335597-anrzcsrt author = nan title = 44. Jahrestagung der Österreichischen Gesellschaft für Pneumologie date = 2020-10-26 keywords = COPD; FEV1; SARS; covid-19; lung; patient; pulmonary; result; vat summary = Conclusions: In this study assessing the prognostic relevance of pulmonary exercise hemodynamics in patients with systemic sclerosis, PVR and TPR at peak exercise as well as mPAP/CO-slope and TPG/CO-slope turned out as age-independent predictors of all-cause mortality. Later-line treatment with lorlatinib in ALKand ROS1-rearrangement-positive NSCLC: a retrospective, multicenter analysis Background: Anti-fibrotic medication is effective in progressive fibrosing interstitial lung diseases (ILD), but a subgroup of fibrotic ILD patients also benefits from immunomodulatory therapies. Methods: HRCT of 127 subsequent single-center ILDboard patients (mean age 65 (standard deviation 14) years, 65 % male), were evaluated for radiological findings considered noninflammatory (reticulation including honeycombing (RET), traction bronchiectasis (TBR), emphysema (EMP)) or active inflammatory (consolidations (CON), ground glass opacities (GGO), noduli (NDL), mosaic attenuation (MOS)) in 6 distinct lung regions. doi = 10.1007/s00508-020-01745-3 id = cord-337462-9mvk86q6 author = nan title = Humanity tested date = 2020-04-08 keywords = SARS; test summary = The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus'' RNA in selected populations. Singapore, Hong Kong and Taiwan have shown the world that, to contain the propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments need to quickly implement aggressive testing (by detecting the viral RNA through polymerase chain reaction (PCR)), the isolation of those infected and the tracing and quarantining of their contacts, while educating their citizens about the need for physical distancing and basic public health measures (in particular, frequent hand-washing and staying at home if feeling unwell). Medical-device companies and government and research laboratories around the world have rushed to adapt and scale up nucleic acid tests (mostly employing PCR, but also CRISPR-based detection and loop-mediated isothermal amplification) to detect the virus'' RNA, and government agencies are scrambling to assess them via emergency routes (such as the Emergency Use Authorization program 3 by the United States Food and Drug Administration (FDA)). doi = 10.1038/s41551-020-0553-6 id = cord-337646-gkcm6ds0 author = nan title = The Federation’s Pages: WFPHA: World Federation of Public Health Associations www.wfpha.org Bettina Borisch and Marta Lomazzi, Federation’s Pages Editors date = 2020-09-17 keywords = COVID-19; SARS; human summary = The next coronavirus to generate a global public health crisis was the Middle East Respiratory Syndrome (MERS-CoV) that emerged in Saudi Arabia in 2012 among people working closely with camels. During the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV), held on 30 January 2020, the COVID-19 pandemic was underway. The association between Emerging Infectious Diseases (EIDs) and environmental destruction is widely recognized: deforestation destroys natural habitats, increases the density of remaining wild animal populations, increases their movements to look for food accompanied by the probability of human contact-all induce stress that impairs immune systems and increases viral shedding [16] . Environment preservation is urgent for many reasons: conservation of biodiversity, the fight against climate change, reduction of air, water and food pollution, and improvement of human health and quality of life [18] . doi = 10.1057/s41271-020-00240-3 id = cord-338123-4pshh5ov author = nan title = SARS Alert Applicability date = 2004-08-17 keywords = SARS; case summary = If the illness is included in the list of notifiable infectious diseases, the case must be reported to the local public health authority so infection control measures can be implemented. To determine how the sickness certification system in other European Union countries operates and assesses the feasibility of the WHO alert surveillance, we interviewed specialists in infectious diseases or public health in France (seven imported cases of SARS, two in healthcare workers), Spain (one case), and Denmark (no cases) (2) by electronic mail. All hospitals that treated patients with suspected SARS either had their own committee to classify patients according to World Health Organization guidelines or followed the protocol for classification or reclassification of reported cases by the team members (3). From the first day that suspected cases were reported to the Taiwan Center for Disease Control, the patients were placed in negative-pressure isolation rooms when available. doi = 10.3201/eid1008.040221 id = cord-344454-hs3tthzi author = nan title = Les animaux contaminés par le SARS-CoV-2 représentent-ils un risque pour l’Homme ? date = 2020-09-15 keywords = SARS summary = Bien que l''origine zoonotique de la COVID-19 soit bien établie (chauves-souris du genre Rhinolophus, hôtes intermédiaires possibles, dont le Pangolin asiatique), un seul cas de contamination animal-Homme par le SARS-CoV-2 ayant été documenté avec des visons d''élevage aux Pays-Bas, rien ne prouve à l''heure actuelle que les animaux participent à la propagation de la pandémie dans la population humaine. Bien que ces infections animales ne jouent pas de rôle dans l''évolution de la pandémie de COVID-19, l''Académie nationale de médecine et l''Académie vétérinaire de France recommandent, dans le cadre d''une stratégie globale « une seule santé » : • de mettre en oeuvre les mesures de biosécurité les plus strictes dans les élevages de visons encore indemnes afin d''éviter les contaminations humaines et tout risque de propagation ultérieure, voire la constitution d''un réservoir animal ; • d''éviter tout contact entre les personnes infectées par le SARS-CoV-2 ou suspectes de l''être, avec leurs animaux de compagnie, notamment s''il s''agit de furet ou de chat, et d''observer les mêmes mesures barrière que pour prévenir la contamination de leur entourage (lavage des mains, masques. doi = 10.1016/j.banm.2020.09.010 id = cord-353293-vjdwh19x author = nan title = Post-COVID-19 global health strategies: the need for an interdisciplinary approach date = 2020-06-11 keywords = COVID-19; CoV-2; SARS; patient summary = Gemelli IRCSS (Rome, Italy) has set up a multidisciplinary healthcare service called "Post-COVID-19 Day Hospital." The specialist assessments offered to patients are outlined in the following sections. Furthermore, the important role of geriatrician acting as a care manager of patients who suffered COVID-19 disease is described. A respiratory follow-up is of pivotal importance to evaluate lung function, alveolar-arterial gas exchange, and exercise tolerance in recovered non-infective COVID-19 patients [5] . In this Post-COVID-19 Day Hospital, internal medicine and geriatric specialists are integrated with infectious disease physicians, pneumologists, immuno-rheumatologists, and other specialists into the management of the SARS-CoV-2 infection. As a whole, the post-acute care service at the Fondazione Policlinico Gemelli aims at expanding the knowledge of COVID-19 and its impact on health status and care needs as well as at promoting healthcare strategies to treat and prevent the clinical consequence of SARS-CoV-2 infection across different organs and systems. doi = 10.1007/s40520-020-01616-x id = cord-329221-miztel9l author = rudolf, f. title = Clinical Characterisation of Lateral Flow Assays for Detection of COVID-19 Antibodies in a population date = 2020-08-21 keywords = August; SARS; preprint summary = Conclusions and Relevance: This study emphasizes the need for large and diverse negative cohorts when determining specificities, and for diverse and representative positive samples when determining sensitivities of lateral flow assays for SARS-CoV-2 infections. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint On the other hand, the sensitivity needs to be assayed using a sufficiently large and representative sample of the antibody response in a population for time post infection, (but especially also in disease severity) i don''t know what you mean. To accurately calculate the specificity, we used the plasma of a blood donor cohort comWe characterised eleven different commercially available lateral flow assays (LFA) for detection of SARS-CoV-2 specific IgM and IgG with serum samples from the three cohorts (Table 1 ). doi = 10.1101/2020.08.18.20177204 id = cord-339709-49q2xxkw author = sermet, i. title = Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children date = 2020-06-30 keywords = HOS; MIS; SARS summary = Despite a low frequency of respiratory symptoms, cases of Multisystem Inflammatory 108 Syndrome (MIS) have been reported in children that were infected by SARS-CoV-2 or were in contact 109 with COVID-19 patients 14, 15 . We also analysed SARS-CoV-2 and seasonal HCoVs humoral responses of patients with MIS 122 regarding antibody targets and functional neutralizing activity. Our study is the first to analyse in depth 123 the typology of humoral responses to SARS-CoV-2 in children, and provides evidence that prior 124 infections by seasonal coronaviruses has no significant impact on SARS-CoV-2 infection or related MIS 125 disease in children. We compared the prevalence of anti-N and -S antibodies against the four seasonal HCoVs in a 220 subpopulation of children among the HOS-P (n=54), MIS-P (n=15) and CTL (n=118) groups (Figure 1) . doi = 10.1101/2020.06.29.20142596 id = cord-271701-tx0lqgff author = te Velthuis, Aartjan J.W. title = The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date = 2011-10-29 keywords = RNA; SARS; figure summary = Commonly, its core subunit is a single RNA-dependent RNA polymerase (RdRp) that drives the production of template strands for replication, new genome molecules, and-in many RNA virus groupsalso subgenomic (sg) mRNAs. This canonical RdRp is structurally conserved among RNA viruses and widely accepted to drive catalysis of phosphodiester bond formation via a well-established reaction mechanism involving two metal ions that are coordinated by aspartate residues in its motifs A and C (3) (4) (5) . Interestingly, both nsp8 and nsp(7+8) are able to extend the RNA primers beyond template length in the presence of heparin ( Figure 4D and Supplementary Figure S2B ), suggesting that these extensions result from terminal transferase activity and not from template switching, as was previously observed for poliovirus 3D pol (20) . Subsequent alanine substitution of the N-terminal D/ ExD/E motif, composed of D50 and D52 in SARS-CoV, greatly affected primer extension activity on the CU 10 template as shown in Figure 5C . doi = 10.1093/nar/gkr893 id = cord-270994-1mmqfp7g author = ul Qamar, Muhammad Tahir title = Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants date = 2020-03-26 keywords = 3CL; SARS summary = title: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants Therefore, herein, we analysed the 3CL(pro) sequence, constructed its 3D homology model, and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds. On January 21, the first article related to 2019-nCoV was 27 published, which revealed that 2019-nCoV belongs to the beta-coronavirus group, sharing 28 ancestry with bat coronavirus HKU9-1, similar to SARS-coronaviruses, and despite sequence 29 diversity its spike protein interacts strongly with the human ACE2 receptor [1] . Structure-based activity analyses and high-57 throughput studies have identified potential inhibitors for SARS-CoV and MERS-CoV 3CL pro 58 Our analyses identified nine novel non-toxic, 171 druggable natural compounds that are predicted to bind with the receptor binding site and 172 catalytic dyad (Cys-145 and His-41) of SARS-CoV-2 3CL pro ( Table 2 ; Fig. S5 ). doi = 10.1016/j.jpha.2020.03.009 id = cord-295742-d11ty5ed author = van Dam, Peter A. title = High mortality of cancer patients in times of SARS-Cov-2: do not generalize! date = 2020-08-10 keywords = SARS summary = This is an important issue as in times limited of resources, the label "cancer with COVID-19" can compromise the access of intensive care (ICU) and outcome of patients dramatically in overwhelmed health care systems due to the outbreak of the SARS-CoV-2 pandemic. 4 The OpenSAFELY study, looking at factors associated with 5683 COVID-19-related hospital deaths in the linked electronic health records of 17 million adult NHS patients clearly showed that male gender (HR 1.99; 95% CI 1.80-2.10), age (with a very strong gradient), ethnicity (adjusted HR 1.71; 95% CI 1.44-2.02), uncontrolled diabetes (HR 2.26 95% CI: 2.18-2.56), obesity (with a very strong gradient) and various other medical conditions often had a higher impact on the probability to die of SARS-CoV-2 then cancer. High Mortality Rate in Cancer Patients With Symptoms of COVID-19 With or Without Detectable SARS-COV-2 on RT-PCR doi = 10.1016/j.ejca.2020.07.021 id = cord-310507-5h6egve4 author = van Doorn, Amarylle S. title = Systematic review with meta‐analysis: SARS‐CoV‐2 stool testing and the potential for faecal‐oral transmission date = 2020-08-27 keywords = COVID-19; CoV-2; SARS summary = Since December 2019, the world has been dealing with the outbreak of the novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) leading to Corona Virus Disease 2019 (COVID-19) that emerged in Wuhan, China. However, there is a growing body of studies in which SARS-CoV-2 RNA was detected in stool samples (including anal swabs) from COVID-19 patients. 11, 15, 16 This study aims to (1) critically assess the clinical relevance of testing stool samples and anal swabs and (2) provide a critical overview of the available literature regarding the faecal-oral transmission of SARS-CoV-2. We collected the following data from the eligible original articles: study design, geographic location, study period, number of patients, age, types of tested specimens, number of tested specimens, methods of the performed tests, duration and prevalence of positive test results in different specimens, disease severity, gastrointestinal symptoms, endoscopic results, specific evidence supporting faecal-oral transmission and remarkable patient/population characteristics. doi = 10.1111/apt.16036 id = cord-265329-bsypo08l author = van Dorp, Lucy title = Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 date = 2020-05-05 keywords = CoV-2; SARS; figure; genome summary = Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1 ) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk). In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. The genomic diversity of the global SARS-CoV-2 population being recapitulated in multiple countries points to extensive worldwide transmission of COVID-19, likely from extremely early on in the pandemic. doi = 10.1016/j.meegid.2020.104351 id = cord-024786-f33eb1nf author = van Rensburg, V title = Current evidence for directed and supportive investigational therapies against COVID-19 date = 2020-04-24 keywords = COVID-19; HCQ; SARS summary = Multiple trials across the globe are currently underway to assess the efficacy of CQ for the treatment and prevention of COVID-19, but no published, peer-reviewed results are available at the time of writing. [33] The rationale for the use of lopinavir/ritonavir (LPV/r) in COVID-19 stems from its in vitro activity against SARS-CoV-1, [34] as well as from a retrospective, multicentre cohort study evaluating LPV/r as early treatment in SARS-CoV-1, which demonstrated decreased mortality and intubation rates. [50] At the time of writing, there were no published peer-reviewed trials or case studies evaluating favipiravir in COVID-19, and its use is not currently recommended outside of clinical trials. A systematic review of treatment options in SARS-CoV-1 infection included corticosteroids'' effects on mortality, in vitro inhibition of SARS viral replication and acute respiratory distress syndrome. Drugs that purportedly inhibit SARS-CoV-2 replication (such as the investigational antivirals) or viral entry and replication (CQ and HCQ) may therefore be more effective when given earlier in the COVID-19 disease course. doi = 10.7196/ajtccm.2020.v26i2.072 id = cord-323327-08p122lw author = van de Veerdonk, Frank L. title = Blocking IL-1 to prevent respiratory failure in COVID-19 date = 2020-07-18 keywords = COVID-19; MAS; SARS summary = These findings open new avenues for host-directed therapies in patients with symptomatic SARS-CoV-2 infection and might in addition to antiviral treatment be enough to curb the currently unacceptably high morbidity and mortality associated with COVID-19. Although ICU patients have been treated with glucocorticoids, some experts have even argued, based on studies in Middle-Eastern respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome (SARS), influenza, and respiratory syncytial virus (RSV), that they are likely to do more harm than good [1, 2] . The autoinflammatory loop can exacerbate from increase innate immune response into uncontrolled MAS a spectrum that associates with increasing ferritin levels van de Veerdonk and Netea Critical Care (2020) 24:445 patients in the early phase and reports that high dose intravenous anakinra started in patients outside of the ICU was safe and resulted in clinical benefit in 72% of patients [56] . doi = 10.1186/s13054-020-03166-0 id = cord-309043-dlmx12vt author = von Brunn, Albrecht title = Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date = 2007-05-23 keywords = RNA; SARS; interaction; protein; y2h summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. doi = 10.1371/journal.pone.0000459 id = cord-297326-n0fpu8s3 author = ÁLVAREZ, E. title = New coronavirus outbreak. Lessons learned from the severe acute respiratory syndrome epidemic date = 2015-01-16 keywords = Hong; Kong; SARS summary = Here, we develop a model that explains the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic that occurred in Hong Kong in 2003. These equations involve three stocks (SUSCEPTIBLE, LATENT, INFECTED), three auxiliary variables (prevalence, contagion rate, recovery rate) and three parameters (incubation period, case fatality, disease duration). The simulation output for the variable ''sick per day'' fit the data reported by the Hong Kong authorities (Fig. 4a) , suggesting that the model was able to reproduce the epidemic curve. These results are consistent with a previous report showing the basic reproductive numbers for different SARS epidemic curves, which supports the notion that our model is able to largely replicate the disease outbreak in Hong Kong [31] . Under these conditions, the model output fits the epidemic curve observed in the Hong Kong SARS-CoV outbreak (Fig. 4) . doi = 10.1017/s095026881400377x id = cord-295792-hajvtzj9 author = Álvez, Fernando title = SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date = 2020-07-03 keywords = ACE2; SARS; child; virus summary = In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice doi = 10.1016/j.aller.2020.05.003