Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 242 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 2584 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 51 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 80 SARS 40 COVID-19 21 covid-19 20 patient 17 PCR 8 HIV 6 respiratory 5 influenza 5 case 5 United 5 RSV 5 MERS 5 CoV-2 4 virus 4 test 4 disease 4 Wuhan 3 treatment 3 therapy 3 laboratory 3 infection 3 clinical 3 cap 3 bal 3 States 3 RNA 3 H1N1 3 China 2 vaccine 2 saliva 2 household 2 figure 2 contact 2 cold 2 antibody 2 antibiotic 2 Sciences 2 PWH 2 PLWH 2 New 2 NL63 2 LRTI 2 ICU 2 HSCT 2 HCQ 2 Ebola 2 East 2 COVID 2 CFR 2 Africa Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 4874 patient 3812 % 3302 infection 2930 study 2402 case 2152 virus 1996 c 1886 p 1874 disease 1432 day 1419 influenza 1336 t 1237 treatment 1235 risk 1211 symptom 1168 e 1132 test 1096 time 1076 result 1058 pneumonia 1048 datum 1012 coronavirus 985 sample 967 group 925 analysis 909 antibody 883 testing 876 cell 848 child 843 r 815 transmission 812 therapy 794 year 770 control 768 rate 749 use 741 hospital 736 outbreak 734 population 716 outcome 715 age 704 adult 701 laboratory 683 contact 682 specimen 677 health 668 vaccine 653 community 633 care 614 response Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2820 SARS 1738 CoV-2 1691 COVID-19 934 M 844 u 821 PCR 799 s 688 a 627 d 530 China 451 RT 450 HIV 413 CoV 355 RSV 349 Health 345 Coronavirus 338 United 330 States 330 RNA 327 Wuhan 320 t 313 MERS 297 Disease 293 c 264 A 246 March 240 Clin 235 sha 212 S. 210 al 201 Table 199 CI 191 CT 189 Dis 186 ICU 184 e 173 M. 169 April 168 CAP 166 HCoV 165 NP 163 H1N1 162 US 162 CDC 160 et 152 Hospital 149 Control 145 C 142 New 134 T Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1831 we 941 it 425 they 399 i 94 them 64 he 58 us 51 she 36 itself 29 themselves 26 one 8 me 7 you 4 ours 4 her 3 him 2 mg 2 himself 2 em 1 yourself 1 u 1 seniors(n=353 1 seasons[7 1 ourselves 1 mrnas 1 icd-9-cm 1 herself 1 hap_023 1 covid-19 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 19205 be 4209 have 1702 use 1223 include 1067 report 931 associate 752 do 673 infect 664 base 655 show 652 increase 619 compare 594 identify 573 test 559 perform 553 find 546 confirm 527 require 513 provide 513 detect 508 suggest 474 receive 466 hospitalize 465 follow 425 develop 406 acquire 401 occur 395 consider 388 cause 387 reduce 377 obtain 375 collect 371 treat 325 define 323 determine 318 give 307 describe 296 need 276 remain 276 assess 266 indicate 265 evaluate 264 relate 264 make 261 observe 255 present 255 lead 250 result 250 know 244 demonstrate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2161 not 2111 respiratory 1720 clinical 1309 viral 1302 high 1132 severe 1067 other 1036 acute 966 also 930 positive 906 more 869 - 826 low 737 however 694 covid-19 680 human 678 first 634 such 587 most 583 only 519 negative 511 early 485 asymptomatic 475 well 469 available 463 specific 462 potential 411 significant 395 different 387 important 379 new 378 medical 376 likely 361 infectious 353 large 346 diagnostic 344 public 332 non 329 similar 326 old 321 novel 317 common 296 as 296 antibiotic 294 current 289 bacterial 287 chronic 286 rapid 282 possible 281 immune Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 214 most 152 least 97 high 76 Most 66 good 44 large 44 great 28 low 14 early 8 late 7 close 6 bad 5 strong 4 old 3 near 2 young 2 tough 2 safe 2 long 1 themost 1 slow 1 simple 1 sick 1 short 1 secondholi 1 poor 1 new 1 http%3a%2f%2fwww.acc.org%2flat 1 holy 1 furth 1 full 1 fine 1 fast 1 deep 1 cord-292546-un0blb3w 1 common 1 clear 1 bright 1 HbA1 1 89%-97.2 1 -Viral 1 -California 1 -8 1 -3.44 Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 373 most 66 least 8 well 5 hard 1 ® 1 worst 1 highest 1 fast 1 farthest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 4 www.who.int 2 www.idsociety.org 2 www.cdc.gov 2 www 2 cid.oxfordjournals.org 1 www.yomecorono.com 1 www.surgeongeneral.gov 1 www.pandemicflu.gov 1 www.nottingham.ac.uk 1 www.niid.go.jp 1 www.nhc.gov.cn 1 www.mbio.ncsu.edu 1 www.gatesfoundation.org 1 www.faben 1 www.covid19-druginteractions.org 1 www.change4health.gov.hk 1 www.cebm.brown.edu 1 www.bloddonor.dk 1 www.accessdata.fda.gov 1 www.r-project.org 1 qianxi.baidu.com 1 huttenhower.sph.harvard.edu 1 github.com 1 cran.r-project.org 1 coronavirus.jhu.edu 1 clinicaltrials.gov 1 bigd 1 awoko.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www 2 http://cid.oxfordjournals.org 1 http://www.yomecorono.com/ 1 http://www.who.int/substance_abuse/activities/gsrah/en/ 1 http://www.who.int/csr/sars/diagnostic 1 http://www.who.int/csr/sars/casedefinition/ 1 http://www.who.int 1 http://www.surgeongeneral.gov/tobacco 1 http://www.pandemicflu.gov 1 http://www.nottingham.ac.uk/research/groups/healthprotection/projects/pride.aspx 1 http://www.niid.go.jp/niid/images/epi/corona/2019-nCoVmanual20200217-en.pdf 1 http://www.nhc.gov.cn/ 1 http://www.mbio.ncsu.edu/BioEdit/ 1 http://www.idsociety.org/covid19guidelines 1 http://www.idsociety.org 1 http://www.gatesfoundation.org/Media-Center/Press-Releases/ 1 http://www.faben 1 http://www.covid19-druginteractions.org/ 1 http://www.change4health.gov.hk/ 1 http://www.cebm.brown.edu/openmeta/ 1 http://www.cdc.gov/ 1 http://www.cdc.gov 1 http://www.bloddonor.dk/antisarscov2 1 http://www.accessdata.fda.gov/scripts/cdrh/ 1 http://www.R-project.org 1 http://qianxi.baidu.com 1 http://huttenhower.sph.harvard.edu/galaxy/ 1 http://github.com/linwangidd/covid19_transmissionPairs_China 1 http://cran.r-project.org 1 http://coronavirus.jhu.edu/map.html 1 http://clinicaltrials.gov/ 1 http://bigd 1 http://awoko.org/2014/12/09/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 cedric.annweiler@chu-angers.fr Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 13 patients receiving presatovir 12 study did not 12 study has several 11 data are available 10 a confirmed case 8 data were available 8 patients were more 7 pneumonia requiring hospitalization 6 patients did not 6 patients were randomly 6 results were positive 5 % were male 5 cov-2 infected patients 5 data do not 5 groups were similar 5 patients were not 5 study does not 4 infections were not 4 results are consistent 4 results were negative 4 samples were available 4 studies did not 4 tests are not 3 % confirmed cases 3 % were female 3 case report form 3 cases were due 3 cov-2 are not 3 covid-19 was significantly 3 infection is not 3 infection was not 3 infection was significantly 3 patients do not 3 patients receiving treatment 3 patients requiring hospitalization 3 patients were eligible 3 patients were male 3 patients were younger 3 results did not 3 results were similar 3 sample was negative 3 samples had negative 3 studies have not 3 symptoms was significantly 3 treatment did not 3 virus was first 3 virus was not 2 % had abnormal 2 % had at 2 % had ever Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 cases reported no symptoms 2 data were not available 2 study had no role 2 treatment did not significantly 1 % had no comorbidities 1 cases caused no transmission 1 cases have not yet 1 cases is not clear 1 cases was not significantly 1 cov-2 are not surprising 1 cov-2 are not yet 1 cov-2 is not capable 1 cov-2 showed no activity 1 cov-2 test no more 1 cov-2 was not consistently 1 data are not available 1 data do not fully 1 disease are not clear 1 disease is not well 1 disease were not yet 1 diseases are not well 1 groups showed no significant 1 groups was not possible 1 infection are not well 1 infection is not congenital 1 infection was not clear 1 infection was not more 1 infections are not uncommon 1 patient had no travel 1 patients do not necessarily 1 patients has not yet 1 patients is not unexpected 1 patients receiving no antibiotic 1 patients showed no positive 1 patients were not available 1 patients were not immunodeficient 1 patients were not more 1 result is not surprising 1 result was not surprising 1 results are not generalizable 1 results do not directly 1 results have not clearly 1 results showed no infected 1 results showing no activity 1 results were not immediately 1 samples are not routinely 1 samples showed no growth 1 samples showed no increase 1 samples were not evenly 1 sars are not infectious A rudimentary bibliography -------------------------- id = cord-307497-wtfvoifb author = Abu-Raya, Bahaa title = Predictors of refractory Coronavirus disease (COVID-19) pneumonia date = 2020-04-09 keywords = COVID-19 summary = In addition, refractory COVID-19 patients were more likely to receive oxygen, mechanical ventilation, expectorant, adjunctive treatment including corticosteroids, antiviral drugs and immune enhancers when compared to general COVID-19 patients. The authors have further attempted to explore predictive factors for refractory COVID-19 using a multivariate analysis showing that male sex, anorexia on admission and being afebrile are independent risk factors for the development of a refractory disease. Furthermore, out of this analysis the authors have found that patients with refractory COVID-19 were more likely to receive oxygen, expectorant, corticosteroids, lopinavir/ritonavir and immune enhancer. In their paper, the authors compared categorical and continuous variables between the two groups of patients and these variables that differed significantly between the two groups were included in the multivariate regression analysis. In their paper, the authors included the treatment introduced at the time of patient admission and/or hospitalization in the multivariate analysis aiming to identify independent risk factors for refractory COVID-19. doi = 10.1093/cid/ciaa409 id = cord-280954-wd89nka9 author = Ackerson, Bradley title = Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults date = 2019-07-15 keywords = RSV summary = doi = 10.1093/cid/ciy991 id = cord-323125-qtlevnbt author = Al Hosani, Farida Ismail title = Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date = 2019-02-01 keywords = East; MERS; Middle summary = BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review. doi = 10.1093/cid/ciy503 id = cord-254458-bbcef8xt author = Ali, Farhana title = Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is? date = 2020-04-30 keywords = COVID-19 summary = The tragedy that is the US aircraft carrier Theodore Roosevelt, in which 60 percent of the 600 sailors who tested positive for SARS-CoV-2 infection were asymptomatic, further highlights the need for accurate laboratory diagnostics for COVID-19 disease [2] . make the case that testing of throat wash samples may be more sensitive than testing of NP swabs for COVID-19 disease. Interestingly, there is biologic plausibility that a sample collected via the oral cavity (such as a throat wash) may yield higher results than a NP swab test based on a study by Xu et al. Finally, the authors'' detection of virus late in the patients'' clinical course emphasizes the uncertainty faced by policy makers as they try to determine the optimal length of isolation for an individual recovering from COVID-19 disease. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs doi = 10.1093/cid/ciaa511 id = cord-260457-m1jbpo5l author = Allander, Tobias title = Human Bocavirus and Acute Wheezing in Children date = 2007-04-01 keywords = HBoV; PCR; respiratory summary = We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study. doi = 10.1086/512196 id = cord-303240-tv1ta3z5 author = Althoff, Keri N title = Contact tracing: Essential to the public health response and our understanding of the epidemiology of COVID-19 date = 2020-06-11 keywords = COVID-19 summary = M a n u s c r i p t As the pandemic in the US continues to evolve, data from contact tracing can continue to inform our understanding about SARS-CoV-2 transmission and guide the public health response. Contact tracing that includes home-based molecular and/or serologic specimen collection to trigger isolation and quarantine may be especially critical when both testing and physical distancing are necessary to achieve the public health goals of epidemic control and mitigation of community transmission. "re-opening"), and test and trace strategies will again be deployed to facilitate epidemic control and interruption of SARS-CoV-2 transmission via isolation and quarantine. Test and trace initiatives will yield equally important information in the current phase of the epidemic as communities begins to "re-open." The contact tracers who will continue to log endless hours to protect the health of the population against COVID-19, and subsequently the stability of our healthcare systems, should be supported and commended. doi = 10.1093/cid/ciaa757 id = cord-287676-qh7zeyyx author = Angoulvant, François title = COVID-19 pandemic: Impact caused by school closure and national lockdown on pediatric visits and admissions for viral and non-viral infections, a time series analysis date = 2020-06-03 keywords = COVID-19; lockdown summary = doi = 10.1093/cid/ciaa710 id = cord-261270-jkm9c5yv author = Annweiler, Cédric title = National French survey of COVID-19 symptoms in people aged 70 and over date = 2020-06-18 keywords = covid-19 summary = The following symptoms observed within the first 72 hours of SARS-CoV-2 infection (i.e., 72h from suspicion, possibly before diagnostic confirmation by RT-PCR test) were collected for each patient using yes/no questions: general signs (sudden deterioration of general condition, temperature, blood pressure), respiratory signs (cough, polypnea), ear nose and throat (ENT) signs (rhinorrhea, odynophagia, otalgia, conjunctivitis, dysgeusia or ageusia, anosmia), gastrointestinal signs (diarrhea, nausea or vomiting) and geriatric syndromes (falls, hypo or overactive delirium, altered consciousness). This national French survey shows that older adults with COVID-19 exhibit a paucisymptomatic clinical picture with less than 3 signs during the first 72h of the infection, generally combining general and respiratory signs (e.g. hyperthermia and cough) with peculiarities that should alert the clinician (e.g. sudden deterioration of general condition, diarrhea, lymphopenia, and/or geriatric syndromes including falls and delirium). doi = 10.1093/cid/ciaa792 id = cord-355734-pz64534w author = Antonio-Villa, Neftali Eduardo title = Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date = 2020-09-28 keywords = Mexico; SARS; covid-19 summary = Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. doi = 10.1093/cid/ciaa1487 id = cord-331731-c2r0kfaz author = Anugwom, Chimaobi M title = Inverse association between chronic hepatitis B infection and COVID-19: immune-exhaustion or coincidence? date = 2020-06-05 keywords = HBV summary = M a n u s c r i p t Dear Editor, We read with great interest the report by Zhao et al, regarding a case of delayed immune response to SARS-CoV-2 in a patient with HIV and HCV co-infection [1] . It is unclear whether this is a simple epidemiological "misconnection" or if being chronically infected with HBV impacts the chances of clinically significant infection with SARS-CoV-2 leading to less hospital admissions, in a similar fashion as that reported by Zhao et al to HIV and HCV. Early virus clearance and delayed antibody response in a case of COVID-19 with a history of co-infection with HIV-1 and HCV Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1093/cid/ciaa592 id = cord-287923-ev93r09i author = Apisarnthanarak, Anucha title = Infection Prevention and Control in Asia: Current Evidence and Future Milestones date = 2017-05-15 keywords = Asia; Pacific summary = This issue of Clinical Infectious Diseases focuses on 3 key themes of infection prevention and control in healthcare settings across the Asia-Pacific regions: (1) epidemiology and evidence to support prevention and control interventions, (2) enhancements to infection prevention and control in healthcare settings, and (3) practices associated with the containment of emerging infectious diseases and outbreaks. We thank the Infectious Diseases Association of Thailand for its partial sponsorship of this issue and share our hope that the collective experience from the study contributors reporting work in this issue will serve as a 2017 platform for improvement in the science and practice of infection prevention in the Asia-Pacific region and in other resource-limited settings. This article appears as part of the supplement "Infection Prevention in Asia Pacific, " sponsored by the Infectious Diseases Association of Thailand (IDAT) with additional author sponsorship. doi = 10.1093/cid/cix071 id = cord-346502-x2b0ao3q author = Arabi, Yaseen M title = Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study date = 2019-06-25 keywords = MERS; RBV summary = BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). The objective of this study was to examine the effect of RBV/ rIFN therapy in a large cohort of critically ill patients with MERS on the 90-day mortality and MERS-CoV RNA clearance by accounting for baseline and time-varying confounders. doi = 10.1093/cid/ciz544 id = cord-325455-e464idc0 author = Atchison, Christina title = Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date = 2020-08-12 keywords = LFIA2; test summary = BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible. doi = 10.1093/cid/ciaa1178 id = cord-258304-86gqxajw author = Bahl, Prateek title = Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs date = 2020-09-18 keywords = covid-19; droplet summary = title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs The results of detailed particle tracking (in supplementary video) reveals that the maximum velocity of droplets expelled, specifically for certain syllables such as ''do'', ''fa'' and ''ti'', is approx. Figure 2c shows the velocity distribution of droplets that are visible while the subject was singing syllable ''sol'' & ''la'' and the direction in which these droplets are moving. Nevertheless, the droplets observed do not appear to be settling down rapidly and without adequate ventilation, these droplets can potentially saturate the indoor environment which can likely explain the very high attack rates of COVID-19 seen in choirs in the US and Europe (almost 87% in Skagit County, Washington) [1] . We note the present study only provides visual evidence of the droplets and aerosols expelled during singing and compare the associated velocities and directions with speaking and coughing. doi = 10.1093/cid/ciaa1241 id = cord-351231-aoz5jbf1 author = Bartlett, John G. title = Why Infectious Diseases date = 2014-09-15 keywords = States; United; antibiotic; disease; infectious summary = The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. The point is that epidemics are the domain of infectious diseases and public health, with the expectation for management or prevention of outbreaks with requirements for detection, reporting, isolation, and case management. This began with a patient transferred from a New York City hospital with a KPC infection and became the source of an institutional outbreak that required extraordinary efforts to control, including a wall constructed to isolate cases, removal of plumbing (as a possible source), use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) molecular diagnostics to detect cases and carriers, hydrogen peroxide room aerosols, and "whole house" surveillance cultures. The new healthcare system should value infectious disease expertise based on its important role in addressing resistance and costs associated with nosocomial infections. doi = 10.1093/cid/ciu441 id = cord-354011-v9t2b2ca author = Benkouiten, Samir title = Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage date = 2013-10-01 keywords = HRV; Hajj; KSA summary = We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims'' home countries upon their return. This study, including sample collection and laboratory methods, was conducted among a cohort of pilgrims departing from Marseille, France, to Mecca in the KSA for the 2012 Hajj season. Each sample was tested for the following viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR): influenza A (FLUA) [11] , influenza B (FLUB) [11] , influenza C (FLUC), and A/2009/H1N1 [12] viruses; human respiratory syncytial virus A and B (RSVB) [13] ; human metapneumovirus (HMPV) [14] ; human rhinovirus (HRV) [15] ; MS2 bacteriophage; human adenovirus (HAdV) [16] ; and human enterovirus (HEV) [17] . doi = 10.1093/cid/cit446 id = cord-353116-7t1prfkr author = Bhargava, Ashish title = Predictors for Severe COVID-19 Infection date = 2020-05-30 keywords = CRP; SARS; covid-19 summary = BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. doi = 10.1093/cid/ciaa674 id = cord-336563-hwemigk7 author = Bhimraj, Adarsh title = Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date = 2020-04-27 keywords = COVID-19; SARS; clinical; patient; treatment summary = Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . doi = 10.1093/cid/ciaa478 id = cord-268809-plgip4h6 author = Bielecki, Michel title = Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date = 2020-06-29 keywords = COVID-19; SARS summary = doi = 10.1093/cid/ciaa889 id = cord-001800-644lf8vn author = Biggerstaff, Matthew title = Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States date = 2015-05-01 keywords = States; United summary = For the second scenario, we clinical attack rate of the influenza pandemic is 20% and the overall case fatality ratio is 0.53% (high-severity scenario); 10 million doses (left) or 30 million doses (right) of vaccine are administered each week; the vaccination program begins 16 weeks after, 8 weeks after, the same week as, 8 weeks before, and 16 weeks before the first cases of a novel influenza virus occur in the United States; and the efficacy is "H1N1pmd09 monovalent vaccine-like." 2009 H1N1-like vaccine effectiveness: 2 doses of vaccine administered 3 weeks apart required to be fully effective (62% for persons aged <60 years and 43% for persons ≥60 years) in protecting against subclinical and clinical cases, hospitalizations, and deaths. For an influenza pandemic with a 30% overall cumulative attack rate and high-severity scenario, we estimated that a vaccination program beginning the same week as the pandemic started in the United States that administered 10 million doses of vaccine with the moderate VE per week could avert 260 000 hospitalizations and 32 000 deaths (6% reduction) (Tables 2 and 3 ; Figures 2 and 3) . doi = 10.1093/cid/ciu1175 id = cord-350686-q2bu7o4i author = Bilder, Christopher R title = Pool size selection when testing for SARS-CoV-2 date = 2020-06-16 keywords = SARS summary = title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people doi = 10.1093/cid/ciaa774 id = cord-273839-oasgagpc author = Bisno, Alan L. title = Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline date = 1997-09-17 keywords = culture; group; pharyngitis; streptococcal summary = Except under special circumstances, neither repeated bacteri-Evidence ologic testing (culture or RADT) of patients who have success-We reviewed a large number of clinical trials of diagnostic fully completed a course of antimicrobial therapy nor routine and treatment strategies for group A streptococcal pharyngitis. ple, studies of treatment were evaluated for randomization, A small percentage of patients will have recurrences of acute blinding, use of streptococcal typing to differentiate treatment pharyngitis that are associated with throat cultures (or RADTs) failures from new infections, duration and timing of follow-up positive for group A streptococci within a short period following examinations, and statistical power [1, 2] . Such tests are appropriate for streptococci in the upper respiratory tract and for the confirmation of the clinical diagnosis of acute streptococcal pharyngitis use by microbiology laboratory personnel, but most physicians who perform throat cultures would find it difficult to justify [12] (category A, grade II). doi = 10.1086/513768 id = cord-299274-gnbp7so5 author = Bodkin, Claire title = Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings date = 2020-06-08 keywords = Hamilton; covid-19 summary = title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. The objective of this report is to describe our experience with shelter facility restructuring, daily symptom screening and rapid testing to mitigate the risk of COVID-19 in the homeless shelter setting in Hamilton, Ontario, Canada. Between March 17 and April 30, 2020, COVID-19 testing was performed on all shelter residents and staff who failed daily screening for potential COVID-19 related symptoms as well as staff and residents identified as close contacts of positive cases. We have thus far been successful in preventing large outbreaks in the shelter setting despite identifying positive cases in both staff and residents. doi = 10.1093/cid/ciaa743 id = cord-340956-1t3o24u5 author = Borkenhagen, Laura K title = High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date = 2019-09-01 keywords = H1N1; H3N2 summary = Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China. doi = 10.1093/cid/ciz865 id = cord-279828-es498qul author = Boulle, Andrew title = Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date = 2020-08-29 keywords = Cape; HIV; PLWH; art; covid-19 summary = We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector "active patients" (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We conducted a cohort study using de-identified data from the Western Cape Provincial Health Data Centre (WCPHDC) of public sector patients aged ≥20 years with documented sex and not known to have died before March 1, 2020 (before the first diagnosed COVID-19 case in South Africa, and several weeks before the first documented COVID-19 death) and included all follow up through June 9, 2020. We used Cox-proportional hazards models adjusted for age, sex and other comorbidities to examine the association between HIV, tuberculosis and COVID-19 death among (i) all public sector patients with ≥1 health visit in the 3 years before March 1, 2020 (considered "active patients"), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. doi = 10.1093/cid/ciaa1198 id = cord-300013-6m1f4q5r author = Brahier, Thomas title = Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study date = 2020-09-17 keywords = COVID-19; LUS summary = This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs Despite the potential of LUS as a cheap, portable and accessible point-of-care triage tool in acute respiratory disease (especially in low resource settings), a multinational consensus recently stated that the lack of studies limited specific recommendations for the management of COVID-19 patients (27) . doi = 10.1093/cid/ciaa1408 id = cord-351314-atsuh8e2 author = Bryson-Cahn, Chloe title = A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date = 2020-03-12 keywords = SARS; hat summary = Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. doi = 10.1093/cid/ciaa256 id = cord-277611-3iynrfzq author = Buetti, Niccolò title = Risk factors for SARS-CoV-2 detection in blood of critically ill patients date = 2020-09-02 keywords = SARS summary = In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms'' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . doi = 10.1093/cid/ciaa1315 id = cord-331465-humpwwk2 author = Canaday, David H title = On setting expectations for a SARS-CoV-2 Vaccine date = 2020-06-04 keywords = SARS summary = Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials doi = 10.1093/cid/ciaa726 id = cord-010570-ytv7dwr0 author = Casadevall, Arturo title = Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date = 1995-07-17 keywords = antibody; human; infection; serum; therapy; treatment summary = In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. We briefly review the use of antibody-based therapy in the early 20th century and make the case for reintroducing passive antibody administration for the treatment ofinfectious diseases. Given the diminishing efficacy of existing antimicrobials because of widespread resistance and the difficulties of treating infections in immunosuppressed individuals, the reintroduction of antibody-based therapies is an option that should be given serious consideration. Thus, antibody therapy is still widely used in medicine, but its role in the treatment of infections is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. In the past, serum therapy was effective against various pathogens despite the fact that immune sera contained only small amounts of specific antibody. Antibody-based therapies have traditionally been most effective in infections where viral and toxin neutralization modifies the course of the disease. doi = 10.1093/clinids/21.1.150 id = cord-282539-skzosh6u author = Casadevall, Arturo title = Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date = 2020-08-17 keywords = SARS; Wang summary = doi = 10.1093/cid/ciaa1213 id = cord-312928-ef8hqs4s author = Chavanet, Pascal title = Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children date = 2008-03-15 keywords = respiratory summary = title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children [1] conducted a large, longitudinal observational study of children with upper respiratory infection and examined for otitis complicationeither acute otitis media or otitis media with effusion. Indeed, in this study, the rate of respiratory syncitial virus infection was found to be low, probably as a result of the method used (conventional assays, type of molecular technique, RT-PCR vs. In this study, children aged !1 year and those who attended day care centers had a greater risk of acquiring upper respiratory tract infection and otitis media, compared with older children and those who were cared for at home. This article is important, especially because the rate of complications of otitis in upper respiratory tract infection was longitudinally studied. Viral upper respiratory tract infection and otitis media complication in young children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children doi = 10.1086/528686 id = cord-291726-8670s4st author = Che, Xiao-yan title = A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date = 2006-07-01 keywords = SARS; case summary = Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. doi = 10.1086/504943 id = cord-007064-nepgttxf author = Chemaly, Roy F title = A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients date = 2019-12-03 keywords = Inc.; RSV; Sciences; day summary = title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients This is the largest randomized, double blind, placebo-controlled clinical trial to date for the treatment of allogeneic and autologous HCT recipients with RSV URTIs. Presatovir treatment did not meet the coprimary endpoints of a greater time-weighted average change in the RSV viral load from Day 1 to 9 and the reduced development of LRTCs through Day 28, but was well tolerated, with a comparable safety profile relative to the placebo. In a post hoc analysis of patients with lymphopenia, the proportion who developed an LRTC through Day 28 was 51% lower following treatment with presatovir, as compared to the placebo; other post hoc analyses also indicated trends toward a treatment effect on LRTCs. The results suggest lessons for the design of future clinical trials of drugs for RSV or other respiratory viruses in transplant recipients or other immunocompromised patients. doi = 10.1093/cid/ciz1166 id = cord-288558-rthnj6wd author = Cheng, V. C. C. title = Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date = 2004-02-15 keywords = SARS; diarrhea; patient summary = doi = 10.1086/382681 id = cord-301066-62qe4fb0 author = Chiu, Susan S. title = Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date = 2005-06-15 keywords = NL63; OC43; PCR summary = In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] . doi = 10.1086/430301 id = cord-278259-pbnnp9i1 author = Choi, Eun Hwa title = The Association of Newly Identified Respiratory Viruses with Lower Respiratory Tract Infections in Korean Children, 2000–2005 date = 2006-09-01 keywords = NL63; RSV summary = doi = 10.1086/506350 id = cord-007321-7gi6xrci author = Chow, Anthony W. title = Evaluation of New Anti-Infective Drugs for the Treatment of Respiratory Tract Infections date = 1992-11-17 keywords = AOM; MEE; acute; clinical; patient; study; therapy summary = These guidelines for the evaluation of drugs for the treatment of respiratory tract infections include acute streptococcal pharyngitis and tonsillitis, acute otitis media, acute and chronic sinusitis, acute exacerbations of chronic bronchitis, and acute infectious pneumonia (table 1). This is often the case in otitis media, sinusitis, and pneumonia, when the use of invasive procedures such as tympanocentesis, sinus puncture, or transtracheal aspiration to confirm microbial eradication in the patient who is improving clinically generally is considered unjustified. Patients eligible for study entrance are children or adults with symptomatic pharyngitis or tonsillitis of acute onset clinically consistent with infection with group A I3-hemolytic streptococci and from whom group A (3-hemolytic streptococci have been isolated in cultures of throat -swab specimen or for whom a rapid screening test has indicated the presence of streptococci. doi = 10.1093/clind/15.supplement_1.s62 id = cord-275454-an8xvow3 author = Clark, Andrew E title = Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date = 2020-09-28 keywords = CoV-2; SARS summary = doi = 10.1093/cid/ciaa1145 id = cord-307342-3gkiukh4 author = Clark, Eva title = Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S date = 2020-08-06 keywords = U.S.; contact; covid-19 summary = By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe "re-opening" of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future. Partly for this reason, our nation rushed to espouse the idea of targeted, case-based COVID-19 management [3] [4] [5] [6] , focusing on expanded testing and contact tracing, while disregarding several major obstacles that set us apart from countries that succeeded in mounting a timely, targeted response. doi = 10.1093/cid/ciaa1155 id = cord-353342-2n6kqyeo author = Corman, Victor M. title = Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date = 2016-02-15 keywords = MERS; RNA; SARS summary = title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays doi = 10.1093/cid/civ951 id = cord-264660-tfktgy57 author = Creech, C Buddy title = It’s True Even in a Pandemic: Children are Not Merely Little Adults date = 2020-05-30 keywords = disease summary = In this issue of CID, Mehta et al (CID PAPER) provide a systematic review of pediatric COVID-19, evaluating the available literature to date to glean characteristics of disease and transmission. The authors report that children represent only 5% or less of diagnosed COVID cases and the data available at the time of review suggest that children are less likely to develop either severe pneumonia or the laboratory alterations commonly associated with severe disease, such as lymphopenia and elevated inflammatory markers. The authors also report that intrauterine transmission appears to be extremely uncommon and that newborns born to infected mothers are likely to experience either asymptomatic disease or mild disease. Taken together, it would appear that children experience a very different response to SARS-CoV-2 infection than adults and raises the hypothesis that dysregulated host responses may be the primary driver of disease severity. doi = 10.1093/cid/ciaa680 id = cord-265242-y8t37p0b author = Cui, Wei title = Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date = 2003-09-15 keywords = SARS summary = doi = 10.1086/378587 id = cord-292546-un0blb3w author = Dandachi, Dima title = Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date = 2020-09-09 keywords = COVID-19; HIV; PWH summary = BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival. doi = 10.1093/cid/ciaa1339 id = cord-341435-b36h69r1 author = Dawson, Patrick title = Loss of Taste and Smell as Distinguishing Symptoms of COVID-19 date = 2020-06-21 keywords = COVID-19; taste summary = In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. This investigation provided an opportunity to identify household COVID-19 cases and describe their symptom profiles, including loss of taste and smell, prior to diagnosis. Among the 64 household members of COVID-19 index cases, loss of taste and/or smell was reported by 12 individuals, of whom 10 were positive for SARS-CoV-2. The positive predictive value (PPV) of any loss of taste and/or smell (83%, 95% CI: 55-95%) was higher than for fever (subjective or measured) and cough, two of the three classic symptoms, and equal to the third, shortness of breath (83%, 95% CI: 44-97%) ( Table 1 ). In the absence of confirmatory laboratory testing, CSTE criteria for a probable COVID-19 case now include loss of taste and/or smell in conjunction with other non-classic symptoms (3). doi = 10.1093/cid/ciaa799 id = cord-291286-diwigcy9 author = De Schutter, Iris title = Microbiology of Bronchoalveolar Lavage Fluid in Children With Acute Nonresponding or Recurrent Community-Acquired Pneumonia: Identification of Nontypeable Haemophilus influenzae as a Major Pathogen date = 2011-06-15 keywords = Rec; bal; cap summary = doi = 10.1093/cid/cir235 id = cord-280958-36ytqapi author = Decker, Summer J title = 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date = 2020-09-10 keywords = FLNP; SARS summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. doi = 10.1093/cid/ciaa1366 id = cord-015493-vf4et613 author = Deresinski, Stan title = In the Literature date = 2007-10-15 keywords = MRSA summary = Tetracyclines as an oral treatment option for patients with community-onset methicillin-resistant Staphylococcus aureus skin and soft-tissue infections. Subgroup analysis that included only the 225 episodes in which incision and drainage were performed at presentation confirmed that blactam antibiotic therapy was significantly associated with treatment failure. These results are consistent with those of several other recent studies that have found that administration of an antibiotic that inhibits the growth of MRSA improves outcomes, even in patients who have undergone incision and drainage. For example, in a similar retrospective study of 531 episodes of community-acquired MRSA SSTI, most of which were treated with incision and drainage, Ruhe et al. Although Ruhe and colleagues provide evidence of the benefit of doxycyline for the treatment of SSTI due to antibioticsusceptible MRSA, alternative antibiotic choices may be considered. Prospective randomized trial of empiric therapy with trimethoprim-sulfamethoxazole or doxycycline for outpatient skin and soft tissue infections in an area of high prevalence of methicillin-resistant Staphylococcus aureus doi = 10.1086/522526 id = cord-340317-gwqy6u9x author = Dora, Amy V title = Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date = 2020-08-28 keywords = PCR summary = title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility Despite numerous outbreaks, the performance of serologic testing for SARS-CoV-2 in residents of skilled nursing facilities (SNF) is not well described; its utility in epidemiologic sero-surveillance studies and outbreak reporting is under evaluation. As our objective was to identify potentially missed cases of COVID-19 during serial surveillance testing, samples from residents with historically negative SARS-CoV-2 RT-PCR tests with DiaSorin IgG-positive results were re-tested on a second serologic testing platform (Abbott SARS-CoV-2 IgG Immunoassay) for IgG antibody specific to SARS-CoV-2 nucleocapsid. In a cohort of 150 nursing home residents tested for SARS-CoV-2 infection by RT-PCR, including 26 previously diagnosed with COVID-19, the sensitivity of the DiaSorin assay was 92% (24/26) and the specificity was 98% (122/124). doi = 10.1093/cid/ciaa1286 id = cord-327069-vjlisnui author = Driscoll, Amanda J. title = Standardization of Laboratory Methods for the PERCH Study date = 2017-06-15 keywords = PCR; laboratory; perch; site summary = To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] . doi = 10.1093/cid/cix081 id = cord-340579-cvze15cj author = Dudley, Joseph P title = Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date = 2020-03-31 keywords = China; SARS summary = There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 doi = 10.1093/cid/ciaa354 id = cord-271014-xzpvupms author = Erikstrup, Christian title = Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date = 2020-06-25 keywords = IFR; SARS summary = title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. doi = 10.1093/cid/ciaa849 id = cord-318204-t024w7h6 author = Fang, Ferric C title = The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date = 2020-06-08 keywords = COVID-19; CoV-2; SARS summary = As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection doi = 10.1093/cid/ciaa742 id = cord-269455-pkjov371 author = Faust, Jeremy Samuel title = Towards a better case fatality estimate for SARS-CoV-2 during the early phase of the United States outbreak date = 2020-05-30 keywords = CFR summary = doi = 10.1093/cid/ciaa639 id = cord-280915-yk872yaz author = Flaherman, Valerie J title = Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date = 2020-09-18 keywords = SARS; mother summary = In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. doi = 10.1093/cid/ciaa1411 id = cord-322650-q8inhgtr author = Fung, Yin-Wan Wendy title = Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date = 2004-08-15 keywords = ERT; SARS summary = title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests doi = 10.1086/422887 id = cord-322448-s04e6po9 author = Gadsby, Naomi J. title = Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date = 2016-04-01 keywords = CAP; PCR; patient summary = Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. The development of multiplex real-time polymerase-chain reaction (PCR) assays currently enables a respiratory specimen to be rapidly screened for a wide range of viral and atypical bacterial pathogens in a small number of reactions [10] [11] [12] [13] [14] [15] . As our study focused on testing sputum by molecular methods, our high level of pathogen detection for typical bacteria may not be directly comparable to results from other recent studies in hospitalized adult CAP. doi = 10.1093/cid/civ1214 id = cord-354265-udt2spoe author = Gersh, Felice title = Menopause status and COVID-19 date = 2020-09-23 keywords = COVID-19 summary = A c c e p t e d M a n u s c r i p t Dear Editor, We greatly appreciate the publication of this important research article, for its exploration of the connection of estradiol levels and menopausal status with outcomes from infections with SARS-CoV-2 in women. We advocate for the use of physiologically dosed human-identical transdermal estradiol as hormone replacement, combined with human-identical cyclic progesterone, in appropriate recently menopausal women. (8) Given the potential for serious negative effects ensuing from a state of estradiol deficiency, heightened by the COVID-19 pandemic, not only should appropriate postmenopausal women be considered for hormone replacement therapy, but women being treated with aromatase inhibitors and estrogen receptor antagonists should be counseled on the risks and benefits of those drugs, personalized in each case, in light of the findings of this study. Potential influence of menstrual status and sex hormones on female SARS-CoV-2 infection: A cross-sectional study from Multicentre in Wuhan doi = 10.1093/cid/ciaa1447 id = cord-341838-lkz8ro90 author = Gervasoni, Cristina title = Clinical features and outcomes of HIV patients with coronavirus disease 2019 date = 2020-05-14 keywords = HIV; SARS summary = The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. doi = 10.1093/cid/ciaa579 id = cord-280571-ntgt5hy9 author = Ginocchio, Christine C. title = Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date = 2011-05-01 keywords = FDA; Mycobacterium; RSV; test summary = doi = 10.1093/cid/cir046 id = cord-272956-0yumc7em author = Gnavi, Roberto title = Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-05-22 keywords = SARS; case summary = Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. doi = 10.1093/cid/ciaa634 id = cord-271269-0gimxteg author = Gourtsoyannis, John title = COVID-19: Possible reasons for the increased prevalence of Olfactory and Gustatory dysfunction observed in European studies date = 2020-05-31 keywords = european summary = doi = 10.1093/cid/ciaa685 id = cord-351348-lzo0dz7z author = Gu, Silan title = Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza date = 2020-06-04 keywords = COVID-19; H1N1 summary = METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. Previous studies indicated that the intestinal flora was closely related to respiratory virus infection and could affect the occurrence and development of diseases through the gut-lung axis [13] . The analysis of group similarities indicated that differences in richness, diversity, A c c e p t e d M a n u s c r i p t and structure of the gut microbiota were not significantly different between general and severe COVID-19 patients (ANOSIM, p=0.426; Supplementary Figure S1 ), indicating that the experimental design was adequate. The gut microbiota signature of COVID-19 and H1N1 patients was analyzed to assess correlations between disease characteristics and the microbiome. doi = 10.1093/cid/ciaa709 id = cord-277307-wabruzfs author = Gu, Wei title = Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date = 2020-05-21 keywords = New; SARS summary = In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region doi = 10.1093/cid/ciaa599 id = cord-299499-66qh3r75 author = Guilamo-Ramos, Vincent title = Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date = 2020-09-07 keywords = AYA; SARS; covid-19 summary = In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. doi = 10.1093/cid/ciaa1348 id = cord-354943-wxhbwcfr author = Guo, Li title = Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date = 2020-03-21 keywords = COVID-19; PCR; SARS summary = METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. doi = 10.1093/cid/ciaa310 id = cord-279167-fj36mzm5 author = Gwaltney, Jack M. title = Acute Community-Acquired Sinusitis date = 1996-12-17 keywords = ACABS; VRS; nasal; sinus; sinusitis summary = doi = 10.1093/clinids/23.6.1209 id = cord-306495-o0ah1gj9 author = Haidar, Ghady title = COVID-19, organ transplantation, and the nuances of immunomodulation: lessons learned and what comes next date = 2020-08-11 keywords = COVID-19; SOT summary = Thus, while morbidity and mortality related to COVID-19 in SOT recipients are substantial, A c c e p t e d M a n u s c r i p t 3 they appear to be driven by age and underlying medical conditions and unaffected by immunosuppression, corroborating the results of other studies in the general population. The study included only 30 lung transplant recipients was therefore unable to assess whether mortality in these patients is greatest (as is the case with sepsis [3] ), or whether COVID-19 precipitates acute or chronic lung allograft rejection. Furthermore, since all laboratory testing was done as standard of care, the study could not evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viremia or the duration of SARS-CoV-2 PCR positivity, which may be longer than that of non-transplant patients. doi = 10.1093/cid/ciaa1193 id = cord-312797-hohzjx74 author = Hamelin, Marie-Ève title = Human Metapneumovirus: A New Player among Respiratory Viruses date = 2004-04-01 keywords = hmpv; infection; respiratory summary = Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups doi = 10.1086/382536 id = cord-344038-20n74z3o author = Han, Mi Seon title = Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date = 2020-04-16 keywords = SARS summary = In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate''s clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother''s respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . doi = 10.1093/cid/ciaa447 id = cord-310390-7pkbd3kg author = Han, Xiaoyu title = Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery date = 2020-03-30 keywords = COVID-19; week summary = title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. Hence, this study aimed to analyze the serial thin-section CT changes of 17 discharged patients with COVID-19, and to compare the progression trend of imaging pattern and clinical parameters. The standard for survive and discharge of patients was according to the guideline of Diagnosis and Treatment of Pneumonia Caused by SARS-COV-2 (trial sixth version) published by the China Ministry of Health [22] , which include: temperature returning to normal for more than 3 days, both the clinical and chest imaging showing significant improvement, and two consecutive respiratory pathogen nucleic acid tests turning negative (the interval at least 24 hours). doi = 10.1093/cid/ciaa271 id = cord-296588-q2716lda author = Hanson, Kimberly E title = Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date = 2020-06-16 keywords = COVID-19; SARS; patient; test summary = OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. doi = 10.1093/cid/ciaa760 id = cord-326297-0r9pex1o author = Hartmann, Stacy title = Coronavirus 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February - May 2020 date = 2020-08-17 keywords = DPH; LAC summary = The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. All LAC residents who test positive for COVID-19 are interviewed by LAC DPH using a standardized form that identifies if the case-patient worked in a high-risk environment, such as a healthcare setting. From case-patient interviews and/or emailed reports, LAC DPH recorded occupational setting, occupational role, date of symptom onset, date last worked, known exposure, and if hospitalized for each HCW. At the end of April, HCWs represented 12.8% of all LAC cases, whereas only 9.6% at the end of May. When asked if they had a known exposure to COVID-19, (Table 3) , healthcare exposures within their facility accounted for nearly 44%, including contact with either a positive patient, co-worker, or both. doi = 10.1093/cid/ciaa1200 id = cord-010599-nwp2if8d author = Hayden, Frederick G. title = Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials date = 2003-06-15 keywords = cold; pleconaril summary = More recently, retrospective analysis of 2 phase II randomized, double-blind, placebo-controlled studies found that pleconaril treatment provided clinical benefit for colds due to picornaviruses in previously healthy adults [10] . Calculations indicated that enrollment of 1000 subjects in each study was required to detect a 25% relative difference between treatment groups in the proportion of picornavirus-infected subjects reaching the primary end point (or an estimated 2-day difference in median time) with 90% power (2-sided test at the 5% level of significance [20] ). Among the picornavirus-infected (ITT-I) population, the time to reach the primary end point of illness alleviation was significantly shorter among pleconaril-treated subjects than among placebo recipients in each study (figure 1). severity score was reduced by 19% over the duration of the study for pleconaril recipients (table 4) , who also experienced significant reductions from baseline in symptom severity scores by day 2 of treatment, compared with placebo recipients (figure 2). doi = 10.1086/375069 id = cord-352837-a29d5dkv author = Hirsch, Hans H title = Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date = 2019-04-01 keywords = respiratory; sari summary = Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future. doi = 10.1093/cid/ciy663 id = cord-315180-itvc86cv author = Hollingsworth, T Déirdre title = Counting Down the 2020 Goals for 9 Neglected Tropical Diseases: What Have We Learned From Quantitative Analysis and Transmission Modeling? date = 2018-06-15 keywords = MDA; disease; figure summary = In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. This article acts as an introduction for a special issue that aims to increase the accessibility of the results so far by summarizing insights from NTD models and identifying key themes for the control of these diseases. The modeling summarized in this issue highlights the value of vector control in reducing the infectiousness of all infected individuals, as well as the value of increasing diagnosis rates (Table 1) . doi = 10.1093/cid/ciy284 id = cord-001381-b0tlco4t author = Howie, Stephen R. C. title = Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples date = 2014-09-01 keywords = Gambia summary = title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. influenzae), 16S rRNA PCR, multilocus sequence typing (MLST), molecular serotyping, and multiplex fast-track 33 PCR, all using standard methods (Supplementary Appendix 2) [2, [6] [7] [8] [9] [10] [11] [12] [13] , were performed at the MRC Unit in The Gambia, and multiplex MassTag PCR [14] was performed at Columbia University. This study also confirms that molecular methods are able to detect potential pathogens far more readily than culture and have a role in defining the etiology of pneumonia. doi = 10.1093/cid/ciu384 id = cord-335038-q32ghvsv author = Huang, Jiao title = Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study date = 2020-08-17 keywords = PLWH; covid-19 summary = title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. Previous studies have found that PLWH with low CD4 cell count, high HIV viral load and not taking antiretroviral treatment have an increased risk of other respiratory infections [9] . This indicates that COVID-19 cases in PLWH may have delayed viral clearance for SARS-CoV-2 because of immunosuppression, although clinical improvement of COVID-19 in PLWH was not worse than that of individuals without HIV infection as described in the present study and other published studies [25, 32] . CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE doi = 10.1093/cid/ciaa1186 id = cord-284782-51mbq7qb author = Huang, Jing title = Care for the psychological status of frontline medical staff fighting against COVID-19 date = 2020-04-03 keywords = COVID-19 summary = key: cord-284782-51mbq7qb authors: Huang, Jing; Liu, Fangkun; Teng, Ziwei; Chen, Jindong; Zhao, Jingping; Wang, Xiaoping; Wu, Renrong title: Care for the psychological status of frontline medical staff fighting against COVID-19 cord_uid: 51mbq7qb Besides, a total of 6, 097 medical workers from different provinces in China were in Hubei province to assist in the COVID-19 by Jan 30, 2020 2 . For example, the emergency medical team from the Second Xiangya Hospital is able to set up field hospitals and ambulances to help and serve the With the increasing spreading of the virus worldwide, COVID-19 outbreak is now becoming a pandemic. None of the authors has any potential conflicts of interest to disclose. Timely mental health care for the 2019 novel coronavirus outbreak is urgently needed The immediate psychological and occupational impact of the 2003 SARS outbreak in a teaching hospital Protecting Health Care Workers during the COVID-19 Coronavirus Outbreak -Lessons from Taiwan''s SARS response doi = 10.1093/cid/ciaa385 id = cord-335691-lsuwsm43 author = Jackson, Michael L. title = The Burden of Community-Acquired Pneumonia in Seniors: Results of a Population-Based Study date = 2004-12-01 keywords = United; cap summary = To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. In multivariate analysis, age, male sex, current smoking, diabetes mellitus, congestive heart failure, lung cancer, serious nonlung cancer, COPD, asthma without COPD, dementia, stroke, receipt of prednisone, use of home oxygen services, greater number of outpatient visits, and hospitalization for pneumonia in the year prior to the study start date were independently associated with risk of all CAP (table 3) . A population-based study involving 4175 elderly persons in Finland found that crude CAP rates did not differ between men and women and that male sex was not significantly associated with CAP after accounting for age and certain chronic medical conditions and risk factors, including asthma, receipt of immunosuppressive therapy, and heart disease [21] . doi = 10.1086/425615 id = cord-333943-9d93na7s author = Jeong, Han Eol title = Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study date = 2020-07-27 keywords = COVID-19; Health summary = title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. [1, 2] Concerns exist that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 by upregulating angiotensin-converting enzyme 2 (ACE2) expressions, [3, 4] the enzyme which SARS-CoV-2 binds to enter cells. This cohort study therefore aimed to examine the association between NSAIDs use, compared to non-use, and worsened clinical outcomes among adults hospitalized with A c c e p t e d M a n u s c r i p t page | 5 COVID-19 using South Korea''s nationwide healthcare database containing all COVID-19 patients. To our knowledge, this is the first population-based study conducted using all hospitalized patients with COVID-19 to assess the association between NSAID use and COVID-19 related outcomes. doi = 10.1093/cid/ciaa1056 id = cord-349070-bqv03u2e author = Jiang, Shih Sheng title = Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date = 2004-01-15 keywords = PCR; SARS summary = title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. doi = 10.1086/380841 id = cord-318458-jadk2qbm author = Jung, Chan-Young title = Association between Body Mass Index and Risk of COVID-19: A Nationwide Case-Control Study in South Korea date = 2020-08-25 keywords = BMI; Korea; covid-19 summary = METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively. doi = 10.1093/cid/ciaa1257 id = cord-324307-2zbm4iwn author = Kam, Kai-qian title = A Well Infant With Coronavirus Disease 2019 With High Viral Load date = 2020-02-28 keywords = COVID-19; SARS summary = A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. doi = 10.1093/cid/ciaa201 id = cord-314489-e5r5s5ee author = Katsidzira, Leolin title = The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date = 2020-05-11 keywords = Africa; SARS summary = The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . doi = 10.1093/cid/ciaa552 id = cord-329290-vqvujry3 author = Kempker, Russell R title = Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date = 2020-06-28 keywords = HCP; SARS summary = HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. doi = 10.1093/cid/ciaa877 id = cord-316970-n2dly3oa author = Kerbaj, Jad title = COVID-19: The New Caledonia experience date = 2020-05-16 keywords = SARS summary = Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island''s hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. doi = 10.1093/cid/ciaa600 id = cord-322204-kc7dy2za author = Khalil, Asma title = SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date = 2020-08-08 keywords = SARS summary = title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of doi = 10.1093/cid/ciaa893 id = cord-299720-f0ny4ur5 author = Kim, Seung Woo title = Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea date = 2017-03-01 keywords = East; MERS; transmission summary = title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Transmission heterogeneity was a significant characteristic of the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection [1] . Epidemiological reports from the outbreak were evaluated to collect data regarding basic demographic characteristics, medical history, MERS-CoV exposure, symptoms and their onset date(s), sampling date(s), contact history, and post-exposure infection control. In the univariate analyses, transmission was associated with underlying respiratory disease, Ct value, interval from symptom onset to diagnosis, number of contacts, and pre-isolation hospitalization or ER visits. It appears that both host infectivity and the number of contacts influenced MERS-CoV transmission, whereas super-spreading events were mostly associated with a greater likelihood of encountering other people under diverse environmental conditions. doi = 10.1093/cid/ciw768 id = cord-329323-1cquorhs author = Ko, Jean Y title = Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System date = 2020-09-18 keywords = COVID; hispanic; net summary = Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. BRFSS data were used to calculate weighted population estimates of community-dwelling adults with and without individual underlying medical conditions by age, sex, and race/ethnicity strata for the COVID-NET catchment area and served as the analytic A c c e p t e d M a n u s c r i p t 7 denominators. doi = 10.1093/cid/ciaa1419 id = cord-257553-479x7av6 author = Kortepeter, Mark G. title = Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date = 2010-12-01 keywords = HIV; MDR; tuberculosis; virus summary = title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] . doi = 10.1086/657115 id = cord-007325-g8ke9rfg author = Koskiniemi, Marjaleena title = CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review date = 1993-08-17 keywords = mycoplasma summary = title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. Besides encephalitis, adult patients had meningitis, myelitis, and polyradiculitis, two cases of each (figure 2). Central nervous system disease associated with Mycoplasma pneumoniae infection: report of five cases and review of the literature Central nervous system manifestations associated with serologically verified Mycoplasma pneumoniae infection Two fatal cases of meningoencephalitis associated with Mycoplasma pneumoniae infection Central nervous system disease associated with Mycoplasma pneumoniae infection Neurological manifestations and Mycoplasma pneumoniae infection A brainstem syndrome associated with Mycoplasma pneumoniae infection-a report of two cases Antibodies to brain and other tissues in cases of Mycoplasma pneumoniae infection doi = 10.1093/clinids/17.supplement_1.s52 id = cord-265006-m1dmgcd1 author = Kow, Chia Siang title = Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19? date = 2020-08-08 keywords = COVID-19 summary = In fact, we are aware of the publication of few systematic reviews and metaanalyses [2] [3] [4] [5] [6] [7] [8] which included these observational studies with questionable quality to determine the association between renin-angiotensin system (RAS) inhibitors use, including angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), and mortality/severity of COVID-19. A systematic review and meta-analysis to evaluate the clinical outcomes in COVID-19 patients on angiotensin-converting enzyme inhibitors or angiotensin receptor blockers ACEI/ARB use and risk of infection or severity or mortality of COVID-19: A systematic review and meta-analysis Outcomes of renin-angiotensin-aldosterone system blockers in patients with COVID-19: a systematic review and meta-analysis The use of renin angiotensin system inhibitor on mortality in patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-analysis doi = 10.1093/cid/ciaa1167 id = cord-314025-h9gj814e author = Lai, Mary Y. Y. title = Survival of Severe Acute Respiratory Syndrome Coronavirus date = 2005-10-01 keywords = SARS; TCID summary = SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. doi = 10.1086/433186 id = cord-338899-qt17jhg0 author = Lakshmi, Vemu title = Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date = 2008-05-01 keywords = CHIK; LAMP; PCR summary = Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries. doi = 10.1086/529444 id = cord-309091-te15ahvw author = Larson, Derek title = A Case of Early Re-infection with SARS-CoV-2 date = 2020-09-19 keywords = SARS summary = A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus doi = 10.1093/cid/ciaa1436 id = cord-341359-c34gyuv6 author = Larson, Derek T title = Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care date = 2020-05-30 keywords = COVID-19; patient summary = This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies. Following widespread use of therapeutic agents with limited data to support their use, calls were made to focus on the evidence-based care that has been the foundation of modern medical therapy for most acute respiratory viral infections [7, 8] . Our study is the first report of COVID-19 outcomes when institutional standards of care consist solely of known evidence-based practices of supportive care. Of those diagnosed with COVID-19, 21 (15.6%) had severe enough disease to necessitate hospitalization and 6 (4.4%) required care in the ICU. Our study demonstrates favorable outcomes for patients with mild to moderately severe COVID-19 disease when evidence-based supportive care is considered the institutional standard. doi = 10.1093/cid/ciaa678 id = cord-275349-b35pt3mo author = Lenz, Heinz-Josef title = The Emergence of Baricitinib: A Story of Tortoises Versus Hares date = 2020-07-06 keywords = COVID-19; patient summary = The artificial intelligence algorithms predicted that baricitinib would inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of cells [2] , (an effect later confirmed in human liver spheroids) [3] , combined with its better-known anti-inflammatory properties. Consequently, the combined potential antiviral and anti-inflammatory effects of this dually acting drug could be ideal for halting the progression of the disease in hospitalized patients, when taken for a limited duration. This new paper in the journal extends the previous published reports of baricitinib treatment in mild-tomoderate COVID19 patients and provides further evidence that baricitinib could be a potential treatment for unwell hospitalized patients with this disease, independent of severity. One would be advised to remain vigilant of such signals reflecting thromboembolic or infection risk in randomized controlled trials testing a variety of immunomodulatory therapies in COVID-19 patients, either alone or in combination, especially in view of associations between clots and SARS-CoV-2 infection [10] . doi = 10.1093/cid/ciaa940 id = cord-252005-3ld5e7f5 author = Lewis, Nathaniel M title = Household Transmission of SARS-CoV-2 in the United States date = 2020-08-16 keywords = SARS; household summary = doi = 10.1093/cid/ciaa1166 id = cord-312905-8xlt92pl author = Li, Guanjian title = Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease date = 2020-04-09 keywords = COVID-19 summary = At the time of writing this paper, the authors claimed that "evidence regarding transmission from individuals with asymptomatic infection or mild illness is limited", but that the current evidence may need an update. Recently, two epidemiological studies on COVID-19 have reported that typically asymptomatic carriers transmit the virus to close contacts, resulting in aggregated infection of symptomatic COVID-19 diseases [2, 3] . This study used a prospective design to follow up the viral load and clinical manifestations of 2147 close contacts of symptomatic and asymptomatic COVID-19 cases. The authors suggested that the transmission ability of asymptomatic individuals should not be ignored. First Mildly Ill, Non-Hospitalized Case of Coronavirus Disease 2019 (COVID-19) Without Viral Transmission in the United States Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing The epidemiological characteristics of infection in close contacts of COVID-19 in Ningbo city doi = 10.1093/cid/ciaa418 id = cord-348178-6bjimde4 author = Li, Ling title = Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date = 2005-09-15 keywords = BSL-3; SARS; area summary = title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) doi = 10.1086/432720 id = cord-353862-7xe3fvd5 author = Li, Na title = Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date = 2020-03-30 keywords = SARS; Wuhan; covid-19 summary = METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. doi = 10.1093/cid/ciaa352 id = cord-332469-zegawla5 author = Li, Wei title = The characteristics of household transmission of COVID-19 date = 2020-04-17 keywords = SARS; household summary = Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. doi = 10.1093/cid/ciaa450 id = cord-288432-n2y9cunc author = Liu, Kun title = Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020 date = 2020-04-17 keywords = China; Wuhan summary = BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. Thus, we conducted this study with the following objectives: 1) to evaluate the impacts of the population movement on the spatial transmission of the 2019-nCoV cases at the provincial and city levels in China; 2) to estimate the potential outbreak risk at areas with the population outflowed from Wuhan; 3) to evaluate the effectiveness of the city closure measures on the epidemic control. doi = 10.1093/cid/ciaa422 id = cord-328267-tk0zc8il author = Liu, Qiao title = Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China date = 2020-08-28 keywords = China; covid-19 summary = title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China We compared tuberculosis case notifications, tuberculosis treatment outcomes, and diagnostic screening for multidrug resistance (MDR) among tuberculosis patients from 2015-2020 before and after the Covid-19 pandemic began in China. We A c c e p t e d M a n u s c r i p t Discussion This is the first data from China reporting the potential indirect impact on tuberculosis control of the Covid-19 pandemic. In addition, reductions in treatment completion and MDR screening during this time period suggest that both deterred health care seeking and community disease management are likely drivers of these trends. Our analysis suggests that collateral effects of the Covid-19 pandemic on tuberculosis control are substantial, with a reduction of 36%-52% in tuberculosis notifications in 2020 compared to 2015-2019. doi = 10.1093/cid/ciaa1289 id = cord-348144-t0chpsuh author = Lucas, Alexander H. title = Carbohydrate Moieties as Vaccine Candidates date = 2005-09-01 keywords = cell; vaccine summary = We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans. It has long been known that bactericidal and/or opsonic antibodies directed against capsular polysaccharide (PS) glycotopes protect against invasive diseases caused by encapsulated bacteria, and, accordingly, vaccine development has focused on the elicitation of these antibody specificities. Purified microbial PS vaccines have been in use for 140 years, but they have proven to be variably immunogenic and variably efficacious in protecting susceptible populations against invasive meningococcal, pneumococcal, and Haemophilus influenzae type b (Hib) diseases [1, 2] . Significant variation in serotype-specific immunogenicity of the sevenvalent Streptococcus pneumoniae capsular polysaccharide-CRM197 conjugate vaccine occurs despite vigorous T cell help induced by the carrier protein doi = 10.1086/432582 id = cord-300550-l28tadhn author = Luers, Jan C title = Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19) date = 2020-05-01 keywords = COVID-19; symptom summary = In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics. First of all, patients were asked for the onset of fever, cough, sore throat, rhinitis, muscle aches, headache, diarrhea, reduced olfaction, and a reduced sense of taste during COVID-19. To investigate factors related to reduced olfaction as well as to a reduced sense of taste two general linear models were used with explanatory variables of age, gender, TNSS, fever, cough, sore throat, rhinitis, and headache, respectively. In addition, fever, cough, sore throat, rhinitis, headache, and TNSS were also not associated with reduced olfaction or reduced sense of taste (p ≥ 0.05, respectively). Our study shows for the first time that both olfactory and gustatory dysfunction is very common in COVID-19 patients, with olfactory dysfunction even leveling the symptom ''cough'' at > 70%. doi = 10.1093/cid/ciaa525 id = cord-327862-zcg3baym author = Luo, Yiqi Ruben title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-09-14 keywords = SARS summary = The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity doi = 10.1093/cid/ciaa1389 id = cord-303330-zh8wzza5 author = Magleby, Reed title = Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date = 2020-06-30 keywords = COVID-19; SARS; viral summary = In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. doi = 10.1093/cid/ciaa851 id = cord-260630-vvpzp73r author = Mandell, Lionel A. title = Etiologies of Acute Respiratory Tract Infections date = 2005-08-15 keywords = patient; respiratory summary = In this issue of Clinical Infectious Diseases, there are 2 articles that provide us with some insight into the various etiologic agents that can cause acute respiratory tract infection (ARTI) in general practice patients in The Netherlands [1] and into the significance of the human metapneumovirus (hMPV) in patients with community-acquired pneumonia (CAP) and exacerbations of chronic obstructive pulmonary disease (COPD) in Quebec, Canada [2] . The objectives of the Dutch study were to estimate the incidence of influenza-like illnesses (ILIs) and of other ARTIs in patients visiting their general practitioners (to determine the etiologic agents) and to test the hypothesis that asymptomatic persons with subclinical infection may act as sources of transmission [1] . Nose and throat swab specimens were obtained from case patients and control subjects, and viral cultures and PCR tests were performed for detection of adenovirus, coronavirus, enterovirus, hMPV, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus (RSV), as well as for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Chlamydophila psittaci. doi = 10.1086/432019 id = cord-292094-vmsdhccp author = Mandell, Lionel A. title = Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults date = 2007-03-01 keywords = ICU; Legionella; PSI; antibiotic; cap; community; patient; pneumonia; risk; therapy summary = Severity-of-illness scores, such as the CURB-65 criteria (confusion, uremia, respiratory rate, low blood pressure, age 65 years or greater), or prognostic models, such as the Pneumonia Severity Index (PSI), can be used to identify patients with CAP who may be candidates for outpatient treatment. A respiratory fluoroquinolone should be used for penicillin-allergic patients.) Increasing resistance rates have suggested that empirical therapy with a macrolide alone can be used only for the treat-ment of carefully selected hospitalized patients with nonsevere disease and without risk factors for infection with drug-resistant pathogens. Advantages include the high specificity, the ability of some assays to distinguish between influenza A and B, the rapidity with which the results can be obtained, the possibly reduced use of antibacterial agents, and the utility of establishing this diagnosis for epidemiologic purposes, especially in hospitalized patients who may require infection control precautions. doi = 10.1086/511159 id = cord-313427-6y4zvrmn author = Mani, Nandita S title = Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date = 2020-06-16 keywords = COVID-19; SARS summary = Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. doi = 10.1093/cid/ciaa761 id = cord-252761-ro5tj0tx author = Marriott, Deborah title = Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date = 2020-08-25 keywords = SARS summary = doi = 10.1093/cid/ciaa1256 id = cord-348350-pac9ha4q author = Martin-Blondel, G title = Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics date = 2020-05-11 keywords = covid-19 summary = Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations. Because of the severity of COVID-19 and the pharmacokinetics of hydroxychloroquine in SLE patients [5] , a loading dose was rapidly included in the new hospital regimens to optimize drug distribution in tissues and more precisely in the lungs. For each regimen applied at the Toulouse University Hospital, an example of the expected kinetic profiles for a body weight of 80 kg (the median weight in our population) are presented in Figure 1 with the corresponding serum concentration for each patient. doi = 10.1093/cid/ciaa558 id = cord-278084-km04sz2s author = Martino, Rodrigo title = Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study date = 2003-01-01 keywords = LRTI; URTI summary = On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. We performed a prospective 2-year study to assess the role of respiratory virus infections in the pathogenesis of URTI and LRTI and risk factors for severe LRTI in an adult clinical hematology department. All adult patients with a hematologic malignancy (including HSCT recipients) who had signs and symptoms of a URTI or LRTI in the inpatient and outpatient settings underwent a detailed clinical evaluation, and samples from the upper and/or lower respiratory tracts were screened for the presence of respiratory viruses. A first episode of infection was defined as the period during which the patient had symptoms of URTI and/ or LRTI, regardless of whether a respiratory virus was isolated. doi = 10.1086/344899 id = cord-007075-sl45z4i0 author = Marty, Francisco M title = A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date = 2019-12-03 keywords = Gilead; LRTI; RSV; Sciences summary = doi = 10.1093/cid/ciz1167 id = cord-303603-4mi64bgm author = Martínez-Urbistondo, Diego title = Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) date = 2020-07-04 keywords = COVID summary = title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) In our experience, the early administration of corticosteroids associated to tocilizumab, according to the previously published recommendations by the Spanish Ministry of Health [6] , may solve this high failure rate. In the HM Sanchinarro Hospital, a 200 bed teaching institution, we consecutively and ambispectively collected the outcome of 136 patients who received tocilizumab plus corticosteroids to treat severe COVID, defined as a SpO2/FiO2 <325 with bilateral pneumonia and a clinical diagnosis of infection by SARS-CoV-2. Generalized linear and Cox regression models, adjusted by age, sex, interaction between age and sex, CCI, time from onset to admission, dose of corticosteroids and tocilizumab and C-reactive protein and D-dimer levels at anti-inflammatory therapy administration, showed benefit in the use of ET in COVID patients (Relative Risk, 0.18, P = .01, and Hazard Ratio, 0.13, P = .01, respectively). doi = 10.1093/cid/ciaa910 id = cord-010578-uib9h1lb author = Mawle, Alison C. title = Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study date = 1995-12-17 keywords = CFS; ELISA; antibody summary = We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We conducted serological tests for a large number of infectious agents as part of a case-control study assessing risk factors for CFS. Antibodies against human T-lymphotrophic virus types I and II were detected with an ELISA, and confirmatory testing was performed by western blotting [5] . All other agents tested were detected in ;;:::25% of CFS cases, and antibody levels were compared between cases and controls. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illness: elevated anti-early antigen antibodies doi = 10.1093/clinids/21.6.1386 id = cord-331978-y4uo7o8g author = Maxwell, Daniel N title = “The Art of War” in the Era of Coronavirus Disease 2019 (COVID-19) date = 2020-03-04 keywords = COVID-19; PPE summary = With rapidly increasing cases and local community transmission in multiple countries outside of China, including the United States, the outbreak has entered a new phase, which requires a shift in primary battle strategy from a focus on containment in China to international mitigation. As cases of COVID-19 explode internationally, a strategic shift is required away from primarily containment, keeping the virus "out there", to home-based mitigation and public health responses. Now, the task is bearing the burden of identifying, isolating, triaging and managing the rising number of cases, necessitating total engagement of the medical community, public health sector, governments and society as a whole. As Sun Tzu noted, "If in training soldiers'' commands are habitually enforced, the army will be well-disciplined." 1 The authors also highlight improvements in infection prevention and control (IPC) infrastructure, administrative controls, and public health coordination compared to their 2003 SARS experience. doi = 10.1093/cid/ciaa229 id = cord-355618-7kfxc2w1 author = McAteer, John title = The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19 date = 2020-04-13 keywords = hesitancy; vaccine summary = In his statement of support 7 , the WHO Director-General Dr. Tedros Ghebreyesus asserted that "These online efforts must be matched by tangible steps by governments and the health sector to promote trust in vaccination and respond to the needs and concerns of parents." In order to adequately respond to these needs and concerns, which differ depending on the cultural, societal, and personal beliefs of a particular region, the WHO recommends that each country take steps to develop an understanding of vaccine hesitancy at a local level on an ongoing basis 8 . In recognition of these missed opportunities and in response to declining immunization rates and increasing national skepticism on the safety of vaccines, Congress has introduced bipartisan legislation to expand research into vaccine hesitancy. The bipartisan VACCINES Act is an important step in supporting evidence-based research into vaccine hesitancy. Association between vaccine refusal and vaccine-preventable diseases in the United States: a review of measles and pertussis doi = 10.1093/cid/ciaa433 id = cord-007049-02p8ug67 author = McGeer, Allison title = Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date = 2004-07-15 keywords = SARS; hospital summary = In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants doi = 10.1086/421784 id = cord-324007-hapzf0fl author = McGeer, Allison J. title = Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza: What to Do? date = 2009-01-01 keywords = influenza; patient summary = In a retrospective study of adult patients with influenza who were admitted to the Prince of Wales Hospital in Hong Kong during the 2004-2005 influenza season with fever and respiratory and systemic symptoms, a clinically and statistically significant reduction in length of hospital stay was associated with treatment with oseltamivir [14] . The accumulating evidence suggests that, for patients with acute cardiorespiratory illness requiring hospital admission during influenza season, consideration should be given to either prompt laboratory diagnostic testing and treatment for influenza virus-infected patients or empirical antiviral therapy for influenza. The best choice is made on a case-by-case basis and depends on the severity of illness in the patient being admitted (since earlier therapy for pneumonia is more effective), the probability of influenza virus infection in the individual patient, and the sensitivity of the rapid diagnostic tests available. doi = 10.1086/591852 id = cord-012511-fl5llkoj author = Meltzer, Martin I. title = Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date = 2015-05-01 keywords = figure; number summary = We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years). doi = 10.1093/cid/civ088 id = cord-324707-9ld73wv1 author = Mitjà, Oriol title = Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date = 2020-07-16 keywords = HCQ; Jordi; SARS; covid-19 summary = Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . doi = 10.1093/cid/ciaa1009 id = cord-322082-80ym2rsq author = Monto, Arnold S title = Lessons From Influenza Pandemics of the Last 100 Years date = 2020-03-01 keywords = influenza; pandemic; virus summary = Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] . doi = 10.1093/cid/ciz803 id = cord-007068-vcfs41eb author = Moradi, Tony title = Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date = 2019-10-22 keywords = BPA; PCR; PCT summary = We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics. doi = 10.1093/cid/ciz1042 id = cord-348392-e35cd9sg author = Moraleda, Cinta title = Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date = 2020-07-25 keywords = SARS summary = Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. doi = 10.1093/cid/ciaa1042 id = cord-007296-q9rn75qb author = Muether, Philipp S. title = Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold date = 2001-11-01 keywords = antihistamine; cold; generation summary = Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla. Also, treatment with first-generation antihistamines is highly effective in reducing sneezing in subjects with experimental and natural colds [3] [4] [5] . Therefore, it would be desirable to confirm the results of the natural cold studies by testing a second-generation antihistamine in the rhinovirus challenge model, which provides more precision in the measurement of sneezing. Although the study was originally designed to determine whether loratadine by down-regulating expression of intercellular adhesion molecule-1 (ICAM-1) on nasal epithelial cells reduces rhinovirus infection rates, it provides heretoforemissing information on the results of testing a second-generation antihistamine in the virus challenge mode. doi = 10.1086/322518 id = cord-268233-ibxufjrv author = Nagappa, Bharathnag title = Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date = 2020-05-30 keywords = PCR summary = We read the recent article by Zhao J et al which studied the antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 [1] . However in results, the authors have mentioned that only 112 out of 173 participants tested positive for RNA over complete duration of the study, which contradicts the methodology. Third, Antibody tests in this study population should be interpreted cautiously since 1) there is plausibility to have cross reaction to antibodies related to other corona virus strains and 2) also diseases caused by other corona virus present with similar symptoms as COVID-19, and symptomatic patients might have antibodies which may lead to increased false positivity rate. Therefore present study should carefully interpret the serological tests and sensitivity should be calculated only in participants tested positive for RNA. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 doi = 10.1093/cid/ciaa676 id = cord-266808-wyuodzyt author = Nagler, Arielle R title = Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City date = 2020-06-28 keywords = COVID-19; NYULH summary = title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City Over the following eight weeks three groups were tested: 1) symptomatic staff with fever or respiratory illness; 2) asymptomatic employees with self-reported exposure to COVID-19 which included any degree or duration of contact with an individual who had a documented COVID-19 infection in the work place or in the community; and 3) all employees who were returning to work in services that had been suspended during the epidemic''s peak. Positivity rates amongst all groups of employees being tested including symptomatic employees, asymptomatic employees with self-reported exposure to COVID-19, and employees being screened for returning work declined over time ( Figure 1 ). Thus during this testing program, most NYULH employees had continued exposure to COVID patients, yet A c c e p t e d M a n u s c r i p t employees still demonstrated sharp declines in COVID infection rates. doi = 10.1093/cid/ciaa867 id = cord-318358-glbr8kxh author = Naik, George O A title = COVID-19 and the RAAS date = 2020-06-20 keywords = Ang summary = Further to Thomas Hanff et al [1] timely call for epidemiological and clinical investigations of COVID-19 infectious disease, measurements of the renin angiotensin aldosterone system (RAAS) components, as sub-studies would be insightful of this pandemic. Angiotensin-converting enzyme 2 (ACE 2) participates in the coronavirus (SARS-CoV-2) cell entry. Drugs that block RAAS also affect ACE 2 expression: it is down regulated by renin inhibition (RI) and up regulated by angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs) (1) and mineralocorticoid receptor antagonists (MRAs) [2] . Such perturbations would also indirectly influence other RAAS components, and the coordination between circulating and local tissue expressions, as shown in Figure 1 ACE 2 is distributed throughout the body and is abundantly expressed in the lung, small intestine, and in blood vessels of many organs including the brain, heart, kidney and testis [4] . Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients doi = 10.1093/cid/ciaa818 id = cord-277788-6ls21tkr author = Nelson, Brian C title = Clinical Outcomes Associated with Methylprednisolone in Mechanically Ventilated Patients with COVID-19 date = 2020-08-09 keywords = ARDS; COVID-19 summary = doi = 10.1093/cid/ciaa1163 id = cord-294853-8b0s5w4u author = Nolen, Leisha D title = Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska date = 2020-09-05 keywords = Alaska summary = title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. People in the remote Yukon-Kuskokwim Delta (YKD) region of Alaska have a high burden of respiratory illnesses, with up to ten times the rate of infant hospitalization for pneumonia compared to the general US population [4] and the highest reported rates of infant RSV hospitalization in the United States, reaching 259 per 1,000 We compared the total, ARI, and RSV hospitalization rate in YKD children <3 years in the first 5 months of 2020 to the previous ten respiratory illness seasons. One limitation of our study is the inability to distinguish what proportion of the decline in ARI hospitalizations in YKD children is due to avoidance of care versus a decrease in circulation of respiratory pathogens secondary to the health mandates. doi = 10.1093/cid/ciaa1328 id = cord-297612-swc2pitd author = Nosyk, Bohdan title = Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date = 2020-04-27 keywords = HIV; contact summary = title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. M a n u s c r i p t Massive SARS-CoV2 testing and contact tracing at a scale and speed never before seen have been proposed as critical components of a COVID-19 public health strategy that could, in theory, safely allow us to relax social distancing measures and begin to bring back the world we left behind before a cure or effective vaccine is delivered. Aside from the potentially profound health benefits of a combination implementation approach, pairing COVID-19 contact tracing with testing for HIV may serve to offset the immense costs of such an approach. doi = 10.1093/cid/ciaa501 id = cord-259471-lsdodl0a author = Pagliano, Pasquale title = Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date = 2020-03-24 keywords = SARS summary = doi = 10.1093/cid/ciaa320 id = cord-339859-anatn295 author = Paret, Michal title = SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date = 2020-04-17 keywords = CoV-2; SARS summary = title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient''s NP sample. doi = 10.1093/cid/ciaa452 id = cord-348478-ho89o8mj author = Pawlotsky, Jean-Michel title = SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date = 2020-05-15 keywords = SARS summary = This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) doi = 10.1093/cid/ciaa587 id = cord-325068-j1lfq60o author = Pene, Frédéric title = Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date = 2003-10-01 keywords = PCR; bal summary = The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] . doi = 10.1086/377612 id = cord-303968-ikr6eeov author = Perinel, Sophie title = Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients date = 2020-04-07 keywords = HCQ summary = Apart from the ongoing clinical evaluation of the efficacy of HCQ, little information is available concerning the modalities of administration of this drug for Intensive Care Unit (ICU) patients, especially in the context of COVID-19. M a n u s c r i p t Treatment Patients received 200 mg of oral HCQ, three times daily, as suggested by a recent study [9] . To more clearly understand HCQ PK and the effect of the dosing regimen, a simulation based on a PK population study in patients with rheumatoid arthritis was performed [2] . In this study, we demonstrated that the 200 mg three times daily dosing regimen is inappropriate to reach a supposed target blood level of 1 -2 mg/L in this population. This regimen could constitute an appropriate option, although the results of our study suggest that 800 mg once daily on the first day can more rapidly reach therapeutic levels in ICU patients. doi = 10.1093/cid/ciaa394 id = cord-325136-oyizfh2z author = Pham, Quang Thai title = The first 100 days of SARS-CoV-2 control in Vietnam date = 2020-08-01 keywords = SARS; Vietnam summary = METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). doi = 10.1093/cid/ciaa1130 id = cord-280763-4bnv2t3f author = Piñana, José Luis title = Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study date = 2019-06-01 keywords = HSCT; RVI summary = METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). The influenza virus has a significant impact on morbidity and mortality in allogeneic hematopoietic stem cell transplantation patients (allo-HSCT), leading to complications ranging from self-limited upper-respiratory tract infections to life-threatening or fatal pneumonias [1] [2] [3] [4] . We conducted a prospective, cross-sectional, observational epidemiological study of community-acquired respiratory virus (CARV) respiratory tract disease (RTD) in allo-HSCT recipients who developed upper RTD (URTD) and/or lower RTD (LRTD) symptoms after transplant. In this study, we report the prevalence of influenza RTD according to the vaccination status over 5 consecutive influenza seasons in a consecutive series of allo-HSCT recipients with virologically-documented respiratory virus infections (RVIs). doi = 10.1093/cid/ciy792 id = cord-279932-bilr71ay author = Plotkin, Stanley A title = The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date = 2020-07-16 keywords = SARS summary = A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development doi = 10.1093/cid/ciaa1013 id = cord-330951-k54e3lbu author = Pollett, S title = Social media and the new world of scientific communication during the COVID19 pandemic date = 2020-05-12 keywords = COVID19 summary = The human and social toll of the COVID19 pandemic has already spurred several major public health ''lessons learned'', and the theme of effective and responsible scientific communication is among them. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitterfeed. The expansion of the outbreak has demanded a rapid response from public health authorities; fundamental epidemiological and scientific evidence has been acquired at break-neck speed to support those decisions. We propose that Twitter has played a fundamental -but often precarious -role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter-feed. doi = 10.1093/cid/ciaa553 id = cord-329311-p68kr4ga author = Prebensen, Christian title = SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date = 2020-09-05 keywords = RNA; SARS summary = title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . doi = 10.1093/cid/ciaa1338 id = cord-330742-m5xx8861 author = Qian, Jie title = Age-dependent gender differences of COVID-19 in mainland China: comparative study date = 2020-05-30 keywords = CFR; PSCC summary = METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. In this study, we used the surveillance data containing all confirmed cases in mainland China as of April 28, 2020 to evaluated gender-specific differences in attack rate, proportion of severe and critical cases, and case fatality in relation to age, affected province and onset-to-diagnosis interval, in order to provide evidence-based guidance for more effective and equitable interventions and treatments. doi = 10.1093/cid/ciaa683 id = cord-343827-jo61t3m0 author = Qian, Qun title = Direct evidence of active SARS-CoV-2 replication in the intestine date = 2020-07-08 keywords = CoV-2; SARS summary = We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. doi = 10.1093/cid/ciaa925 id = cord-252423-ojmt4k2w author = Qu, Bing title = Monologue of a physician who tested persistently positive for COVID-19 date = 2020-05-11 keywords = COVID-19 summary = The COVID-19, as other new infectious diseases, has presented us unprecedented challenges and put us into huge dilemma. As a physician on clinical frontline, I had been treating patients actively and wishing them an early recovery, but never expecting that I would be infected. As in the early stage we knew little about COVID-19 and the possibility that someone with COVID-19 can transmit the virus even if they are not showing symptoms, many healthcare professionals were infected. According to a Press Conference of the WHO-China Joint Mission on COVID-19 on February 24, 3387 medical staff have been reported to be infected, among which over 90% were from Hubei province. Exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (COVID-19) in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China doi = 10.1093/cid/ciaa551 id = cord-356084-621qzpqd author = Qu, Jiuxin title = Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-04-27 keywords = SARS; patient summary = title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus doi = 10.1093/cid/ciaa489 id = cord-335767-omm04fg5 author = Raabe, Vanessa N title = Importance of Pediatric Inclusion in COVID-19 Therapeutic Trials date = 2020-05-27 keywords = COVID-19 summary = Not only do children and the medical community lose out on opportunities to gain the highest level of clinical evidence for efficacy in a vulnerable population, but due to the lack of availability of pediatric trials, many children hospitalized for COVID-19 are receiving off-label use of therapeutic agents with unproven benefit against COVID-19. In addition to offering enhanced safety monitoring, enrollment of children in clinical trials ensures that parents and older children are fully informed of the potential risks and benefits associated with use of the therapeutic agent, a conversation often omitted when medications are prescribed off-label. Inclusion of children in these clinical trials is feasible under current regulations, provides direct benefit to pediatric trial participants from a safety perspective compared to off-label prescribing, and provides systematic collection of the highest quality of evidence for COVID-19 therapeutics in a vulnerable population where SARS-CoV-2 infection behaves differently from adults. doi = 10.1093/cid/ciaa656 id = cord-321603-lbbsnriv author = Rao, Mohan title = Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date = 2020-08-06 keywords = SARS; saliva summary = The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. doi = 10.1093/cid/ciaa1156 id = cord-307770-1igydu3y author = Rawson, Timothy M title = Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date = 2020-05-02 keywords = SARS summary = title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. doi = 10.1093/cid/ciaa530 id = cord-007047-7ty9mxa9 author = Reller, L. Barth title = Implications of New Technology for Infectious Diseases Practice date = 2006-11-15 keywords = PCR; dna; laboratory; test summary = Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N. doi = 10.1086/508536 id = cord-007170-svsfu7fj author = Richt, J. A. title = Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date = 1992-06-17 keywords = BDV; Borna; CNS; disease; virus summary = Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease. doi = 10.1093/clinids/14.6.1240 id = cord-266820-exl36jt3 author = Rivera, Frida title = Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date = 2020-08-19 keywords = SARS summary = title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. doi = 10.1093/cid/ciaa1225 id = cord-324607-rpwccvqi author = Rojek, Amanda M title = Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases date = 2020-02-15 keywords = clinical; trial summary = Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research. Table 1 identifies some key domains that could contribute to a core minimal dataset that informs clinical trial design for each priority pathogen. While these data have their most important benefits in improving patient management (through better recognition of disease complications and informing supportive care) and public health control, patient-based data are also used to determine key parameters for clinical trials, such as the inclusion criteria, the nature and rate of clinically relevant outcomes, and potential confounders. A systematic review and meta-analysis of patient data from the west Africa (2013-16) Ebola virus disease epidemic doi = 10.1093/cid/ciz760 id = cord-349556-k312qkvh author = Roldán-Santiago, Ernesto title = SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date = 2020-09-18 keywords = SARS summary = title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient''s cervical LN. doi = 10.1093/cid/ciaa1422 id = cord-298539-yncda1us author = Ruan, Linhui title = New measures for COVID-19 response: a lesson from the Wenzhou experience date = 2020-04-03 keywords = Wenzhou summary = This is the result of the more than 90,000 people who return to Wenzhou from Wuhan during On January 17 when the first case of COVID-19 was confirmed, the Wenzhou New Coronavirus Pneumonia Prevention and Control Committee launched emergency epidemic prevention and control measures, which in general consisted of two phases. The main measures included (1) centralizing the confirmed and suspected patients in designated hospitals for treatment, (2) identifying and investigating all returnees from Wuhan using a big data network and persuading them to undergo 14-day home quarantine, and (3) centralizing and medically observing individuals who had been exposed to a confirmed COVID-19 patient. However, the numbers of new cases in these cities were meaningfully reduced after implementation of most aggressive social distancing and quarantining measures, which was similar to Wenzhou second-phase measures on February 10 ( Figure 1A) . doi = 10.1093/cid/ciaa386 id = cord-295940-siy32dj7 author = Saito, Makoto title = Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan date = 2020-04-02 keywords = gargle summary = title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan Moreover, the sensitivity for virus detection is low with these swabs; viral load is reportedly higher in sputum samples. 3 Here we report a case in which gargle lavage samples yielded a positive PCR result. Additional gargle lavage samples and oropharyngeal swabs were collected and tested on Days 8 and 9 and found to be positive, with a slightly higher amount of viral genome in the gargle lavage sample (Supplement Figure 3) . For other respiratory pathogens, gargle lavage samples have been reported to be more sensitive than throat swabs. 1 Gargle lavage thus offers a safer and possibly more sensitive alternative or additional option for diagnosing COVID-19. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens doi = 10.1093/cid/ciaa377 id = cord-277410-lt19mijb author = Salvatore, Phillip P title = Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date = 2020-09-28 keywords = SARS summary = doi = 10.1093/cid/ciaa1469 id = cord-291363-re45w37d author = Sanville, Bradley title = A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date = 2020-03-30 keywords = SARS; case summary = title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . doi = 10.1093/cid/ciaa347 id = cord-328667-r5w09lb6 author = Schwartz, David A title = The Effects of Pregnancy on Women with COVID-19: Maternal and Infant Outcomes date = 2020-05-11 keywords = COVID-19; woman summary = In contrast, some pregnant women might be asymptomatic or have only mild or nonspecific symptoms from an infectious disease, resulting in their escaping detection as having infection even when the embryo or fetus is severely affected. [9] evaluated for the first time the effects of being pregnant on COVID-19 disease and pneumonia using a case-control experimental design conducted at the Maternal and Child Health Hospital of Hubei Province, a 1900-bed tertiary medical center in Wuhan, China. To accomplish this, the authors enrolled two cohorts of pregnant women with COVID-19 and pneumonia -one consisting of 16 pregnant women with pneumonia and rt-PCR confirmed SARS-CoV-2 infection, and the other with 18 pregnant women with pneumonia who were clinically and radiologically suspected of having COVID-19 but had negative rt-PCR test results. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study doi = 10.1093/cid/ciaa559 id = cord-313617-hh7lccet author = Sigel, Keith title = Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date = 2020-06-28 keywords = HIV; PWH summary = We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status. doi = 10.1093/cid/ciaa880 id = cord-350972-0n4dumgg author = Sing, Chor-Wing title = Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date = 2020-07-16 keywords = SARS; VHD summary = title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. doi = 10.1093/cid/ciaa992 id = cord-317092-5qba9jiq author = Singh, Tulika title = Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date = 2020-05-08 keywords = SARS; child; covid-19 summary = The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children''s immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. doi = 10.1093/cid/ciaa547 id = cord-340678-2e2s1gof author = Skowronski, Danuta M title = Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17 date = 2020-05-22 keywords = NIRV; influenza summary = Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Here, we use historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) to assess the association between influenza vaccine and NIRV risk, notably seasonal coronaviruses. Conversely, influenza vaccine had no effect on non-influenza causes of ILI, with the likelihood of vaccination among NIRV cases relative to test-negative controls approaching unity. In combined NIRV analysis, relative to pan-negative controls, Wolff adjusted for age and excluded specimens that tested influenza-positive. We illustrate the impact of this bias in Supplementary_Material_3, where we have re-analyzed Wolff''s data as well as our own, comparing influenza vaccine effect against NIRV when influenza testpositive specimens are properly excluded (as per TND prerequisite) or improperly included (as per Wolff [4] ) within the control group. doi = 10.1093/cid/ciaa626 id = cord-281418-mvgp6qfv author = Soccal, P. M. title = Upper and Lower Respiratory Tract Viral Infections and Acute Graft Rejection in Lung Transplant Recipients date = 2010-07-15 keywords = bal; rejection; respiratory summary = doi = 10.1086/653529 id = cord-260274-c3586tp6 author = Somers, Emily C title = Tocilizumab for treatment of mechanically ventilated patients with COVID-19 date = 2020-07-11 keywords = COVID-19; IL-6; patient; tocilizumab summary = CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence. At our institution, IL-6 blockade with tocilizumab is considered for patients with severe COVID-19 and suspected hyperinflammation based on rapidly worsening respiratory status and elevated inflammatory markers, with the majority of usage occurring in patients requiring mechanical ventilation. Using our COVID-19 Rapid Response Registry infrastructure, we performed an observational study of outcomes in patients with COVID-19 requiring mechanical ventilation, comparing those treated with tocilizumab with those who were not. In this observational, controlled study of patients with severe COVID-19 necessitating mechanical ventilation, receipt of tocilizumab was independently associated with improved survival. To date, the risk of superinfection in mechanically ventilated patients with severe COVID-19 remains poorly described and the incremental risk associated with a single dose of tocilizumab is not well characterized. doi = 10.1093/cid/ciaa954 id = cord-313499-8ijbesl8 author = Stowell, Sean title = Role of serology in the COVID-19 pandemic date = 2020-05-01 keywords = NAT summary = In this issue of Clinical Infections Diseases, F Xiang et al present a serologic study of 85 nucleic acid test (NAT) SARS-CoV-2 positive patients and 24 NAT negative patients who had symptoms suspicious for COVID-19 1 . Serological testing consisted of an enzyme linked immunosorbent assay designed to detect IgM and IgG antibodies against the N protein of SARS-CoV-2. In patients with suspected COVID-19 who tested NAT negative, IgM antibodies were detected in 87.5% and IgG was present in 70.8%. In the case of COVID-19, while serological analysis may be helpful in examining exposure, such approaches can be more challenging to interpret in patients with acute infection. Despite these considerations, the results of this manuscript suggest repeat serological testing may be informative in the acute setting, especially in patients who continue to follow a COVID-19-like disease course despite NAT negativity. Additional testing, such as NAT testing, may be warranted in serological positive individuals to determine potential risk for infecting others. doi = 10.1093/cid/ciaa510 id = cord-299359-s8j78naz author = Sundaram, Maria E. title = Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness date = 2013-09-15 keywords = control; influenza summary = We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. This could theoretically contribute to overestimation of true VE (ie, bias away from the null); therefore, a key assumption of the test-negative control design of influenza vaccine effectiveness studies is that the proportion of noninfluenza viral illness does not differ by influenza vaccination status [9] . The goals of this study were to determine if influenza vaccination is associated with detection of noninfluenza respiratory viruses and to determine if vaccine effectiveness estimates differ when different control groups are used in the analysis. For participants in these age groups, multiplex reverse transcription polymerase chain reaction (RT-PCR) testing was subsequently performed to detect other respiratory viruses, providing an opportunity to investigate the relationship between influenza vaccination and infection with other viral pathogens. doi = 10.1093/cid/cit379 id = cord-294718-n3gx862b author = Tam, Patrick C K title = Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date = 2020-05-30 keywords = RNA; SARS summary = title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. doi = 10.1093/cid/ciaa673 id = cord-011745-dbdtpojs author = Thompson, Mark G. title = Effectiveness of Nonadjuvanted Monovalent Influenza A(H1N1)pdm09 Vaccines for Preventing Reverse Transcription Polymerase Chain Reaction–Confirmed Pandemic Influenza Hospitalizations: Case-Control Study of Children and Adults at 10 US Influenza Surveillance Network Sites date = 2013-12-01 keywords = case summary = doi = 10.1093/cid/cit551 id = cord-251945-v077hhgk author = Titanji, Boghuma K title = Response to Correspondence: Baricitinib as Treatment of COVID-19 Friend or Foe of the Pancreas? Cerda-Contreras et.al date = 2020-08-14 keywords = COVID-19 summary = doi = 10.1093/cid/ciaa1212 id = cord-295270-6ptaxg74 author = Titanji, Boghuma K title = Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al. date = 2020-08-14 keywords = COVID-19 summary = authors: Titanji, Boghuma K; Farley, Monica M; Schinazi, Raymond F; Marconi, Vincent C Baricitinib through its immunomodulatory effects as highlighted by Jorgensen et.al may in fact be beneficial in terms of reducing coagulopathy in patients with COVID-19, which is thought to be primarily mediated by hyper-inflammation and endothelial damage. All of the cohort studies of baricitinib for COVID-19 treatment led to significant decline in inflammatory M a n u s c r i p t markers for patients who received the drug 2,3,8 . Regarding baricitinib, ACTT2 should provide clarity on the VTE issue in the near future and its role in the treatment of COVID-19 in moderate to severe patients. Ruxolitinib in treatment of severe coronavirus disease 2019 (COVID-19): A multicenter, single-blind, randomized controlled trial Use of Baricitinib in patients with moderate and severe COVID-19 Vincent Marconi and Raymond F Schinazi are partially funded by -Emory University Center for AIDS Research (AI050409). doi = 10.1093/cid/ciaa1210 id = cord-307660-onz6vfre author = Titanji, Boghuma K title = Use of Baricitinib in Patients with Moderate and Severe COVID-19 date = 2020-06-29 keywords = COVID-19; patient summary = Coronavirus Infectious Disease-19 (COVID-19), caused by Severe Acute Respiratory Virus Syndrome Coronavirus-2 (SARS-CoV-2) has led to over 8 million confirmed infections worldwide with an estimated global mortality of 5.6% as of June 17 th 2020 1 . Patients had laboratory confirmed COVID-19, diagnosed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) testing of oropharyngeal, nasopharyngeal or tracheal aspirate samples and were treated at the discretion of the medical team with a combination of hydroxychloroquine and baricitinib if they fulfilled at least one of the following criteria: 1) evidence of pneumonia on lung imaging and requiring supplemental oxygen on admission or development of a new oxygen requirement during the course of their hospitalization 2) moderate disease requiring hospitalization (e.g., severe diarrhea requiring volume resuscitation, encephalopathy, evidence of end-A c c e p t e d M a n u s c r i p t organ damage); 3) elevated or rising inflammatory markers during hospitalization. doi = 10.1093/cid/ciaa879 id = cord-269973-sntnmqqd author = To, Kelvin Kai-Wang title = Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date = 2020-08-05 keywords = Kong; SARS summary = However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. doi = 10.1093/cid/ciaa1119 id = cord-295525-emrwcx0m author = To, Kelvin Kai-Wang title = Consistent Detection of 2019 Novel Coronavirus in Saliva date = 2020-02-12 keywords = SARS; saliva summary = The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. doi = 10.1093/cid/ciaa149 id = cord-266150-wox7pnkr author = Torres, Juan Pablo title = SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date = 2020-07-10 keywords = PCR; SARS; covid-19 summary = Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. doi = 10.1093/cid/ciaa955 id = cord-331930-w2055c42 author = Tso, Eugene Y. K. title = Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date = 2004-05-01 keywords = SARS summary = title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. doi = 10.1086/383580 id = cord-273840-jjm7y07m author = Vabret, Astrid title = Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date = 2006-03-01 keywords = HKU1; PCR summary = doi = 10.1086/500136 id = cord-352899-bt2xg0ha author = Van Kerkhove, Maria D. title = Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus date = 2016-10-15 keywords = MERS summary = authors: Van Kerkhove, Maria D.; Peiris, Malik J. Researchers in Korea have recently published studies [4, 5] evaluating environmental and/or air contamination by MERS-CoV and should be commended for their efforts to evaluate the hospital outbreaks in their country. To fully understand the possible role of environmental contamination, including the possible detection of MERS-CoV in the air, additional studies must be conducted to see whether these results can be replicatedfor example, in hospitals in the Middle East where patients with MERS-CoV are treated, to evaluate virus persistence in hospital environments. A more complete understanding of the results of environmental and air contamination studies will have important implications for the application of infection prevention and control measures [8] currently used in hospitals treating patients with MERS-CoV, possibly leading to more detailed recommendations. Environmental contamination and viral shedding in MERS patients during MERS-CoV outbreak in South Korea Middle East respiratory syndrome coronavirus (MERS-CoV) doi = 10.1093/cid/ciw478 id = cord-354877-n5du3bqt author = Vasoo, Shawn title = Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1 date = 2009-10-01 keywords = H1N1; Influenza summary = During the period from 1 May 2009 through 2 June 2009, a convenience sample of 84 positive, nonduplicate nasopharyngeal specimens were tested using 3 different rapid antigen test kits: BD Directigen EZ Flu A+B test (Becton Dickinson), BinaxNOW Influenza A&B (Inverness Medical), and QuickVue Influenza A+B Test (Quidel). Patient charts were reviewed, if available, for potential factors that may have been associated with rapid antigen test result; these included patient age, duration of symptoms before presentation, inpatient or emergency department versus outpatient status, and the median number of RT-PCR fluorescence intensity (MFI) units. Because of the widespread interest regarding the clinical performance of rapid antigen tests for detection of pandemic influenza A/H1N1 virus, we used a convenience sample of positive specimens to allow for a quick yet relatively accurate assessment of these tests. doi = 10.1086/644743 id = cord-002514-pp06m5xk author = Venkatesan, Sudhir title = Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis date = 2017-05-15 keywords = NAI; patient; treatment summary = title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. In patients with laboratory-confirmed or clinically diagnosed A(H1N1)pdm09 influenza, after adjustment for community-based antibiotic treatment and propensity score, the likelihood of hospital admission in patients with outpatient or community-based NAI treatment was 0.24 (95% CI, 0.20-0.30) when compared to no NAI treatment in the community (Table 2) . Our main findings ( Table 2) suggest that NAI treatment in the community for patients with severe pandemic influenza substantially reduced the likelihood of hospital admission due to influenza A(H1N1)pdm09. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data doi = 10.1093/cid/cix127 id = cord-305394-wwabxlgr author = Venter, W D Francois title = COVID-19: First data from Africa date = 2020-08-31 keywords = Africa; HIV summary = This data is from an ongoing surveillance cohort that has previously generated rich data on disease patterns in the Western Cape, and currently continues to provide near real-time updates on the impact of PCR-confirmed SARS-CoV-2 on factors ranging from death to oxygen consumption within hospitals. Key strengths of the paper include a dataset covering over 3 million healthcare users in the Western Cape Province, and the use of both hospitalized and nonhospitalized cases and deaths Davies'' data shows similar mortality risk factors, including age, sex, diabetes (especially uncontrolled diabetes), hypertension and renal disease to other cohorts from richer countries. For South Africa, a sigh of relief at a relatively small increase in mortality in HIV and TB should be quickly tempered; diabetes was the second commonest cause of death in the country pre-COVID-19, and most patients in the country have poor glucose control, a major risk factor from Davies'' data (7) . doi = 10.1093/cid/ciaa1293 id = cord-254183-98o0dssj author = Waggoner, Jesse J. title = Rare and Emerging Viral Infections in Transplant Recipients date = 2013-10-15 keywords = HSCT; recipient; transplant summary = In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections. In a multicenter review of 85 cases of acute HEV infection, 65.9% of the solid organ transplant (SOT) recipients developed chronic hepatitis of whom 14.3% developed cirrhosis. Cases of lymphocytic choriomeningitis virus (LCMV) transmitted through organ transplantation (4 clusters, including 14 cases and 11 deaths) document the ability of this pathogen to cause severe disease in the immunocompromised host [10, [49] [50] [51] . Human T-cell leukemia virus type I-associated myelopathy following living-donor liver transplantation doi = 10.1093/cid/cit456 id = cord-007073-soov8q3q author = Wang, Claire Y T title = Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study date = 2019-08-13 keywords = Supplementary; pev summary = doi = 10.1093/cid/ciz761 id = cord-279550-7u2hksxm author = Wang, Kai title = Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date = 2020-08-03 keywords = SARS; covid-19; patient summary = doi = 10.1093/cid/ciaa1143 id = cord-350338-lcsa06gm author = Wang, Kun title = Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China date = 2020-05-03 keywords = COVID-19; Wuhan; patient summary = title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. We developed a clinical model and laboratory model for predicting the in-hospital mortality of COVID-19 patients, the AUCs (95% CI) were 0.88 (0.80, 0.95) and 0.98 (0.92, 0.99) in training cohort, and 0.83 (0.68, 0.93) and 0.88 (0.77, 0.95) in validation cohort, respectively. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China doi = 10.1093/cid/ciaa538 id = cord-280005-i9fp5rys author = Wang, Mengmei title = Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial date = 2020-09-21 keywords = COVID-19; IFN; patient summary = title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -a Single-Center, Randomized, Controlled Clinical Trial CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone. Based on that background, we conducted a prospective randomized, controlled, open-label trial, to evaluate the efficacy and safety of oral leflunomide to treat hospitalized COVID-19 patients with prolonged post-symptomatic viral shedding. Fifty eligible patients were randomly assigned to a combination treatment group that received leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once a day for 8 days; a total course of 10 days) plus nebulized IFN -2a (3 million IU each time, adding 2 ml of sterilized water, atomization inhalation twice daily for 10 days), or to a control group that received nebulized IFN -2a This was an open-label, prospective randomized, controlled trial, which was conducted at East Campus, Renmin Hospital of Wuhan University. doi = 10.1093/cid/ciaa1417 id = cord-294558-cqa58db8 author = Wang, Yubo title = Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date = 2020-05-22 keywords = SARS summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. doi = 10.1093/cid/ciaa629 id = cord-354009-1ek4s8oe author = Wang, Yun title = Spatiotemporal Characteristics of COVID-19 Epidemic in the United States date = 2020-07-08 keywords = COVID-19; States; United summary = We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. The results would enhance our understanding of small area-based spatiotemporal dynamics of COVID-19 outbreak, thus help inform multilevel strategies to control the spread of coronavirus and appropriate allocations of public health and healthcare resources in the United States. To identify the characteristics of counties with a high burden of COVID-19, we examined county-level geographic and sociodemographic factors, including rural-urban context, distance to the nearest core airport, population density, percentage of non-white minority population, percentage of population 65 years or older, and percentage of population below the federal poverty line. doi = 10.1093/cid/ciaa934 id = cord-326138-16kpn9db author = Weinstein, Robert A. title = Laboratory-Acquired Infections date = 2009-07-01 keywords = United; infection; laboratory summary = Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Surveys of diagnostic laboratory workers in the United Kingdom conducted since 1971 have reported that tuberculosis and enteric infections (especially shigellosis) were the most common laboratory-acquired infections [7, 8] . Similar results were obtained from a survey of clinical microbiology laboratories in Utah from the period 1978-1992, with shigellosis reported to be the most common laboratory-acquired infection [10] . Although no controlled studies have been performed to assess the benefit of postexposure prophylaxis (PEP), it should be considered for laboratory workers who have high-risk exposure to Brucella species (e.g., because of direct manipulation of Brucella cultures outside of laminar-flow BSCs). Viral agents transmitted through blood and bodily fluids cause most of the laboratory-acquired infections in diagnostic laboratories and among health care workers [1] . doi = 10.1086/599104 id = cord-290133-4ou7ubb4 author = Weiss, Martin M. title = Rethinking Smallpox date = 2004-12-01 keywords = case; smallpox; vaccination; virus summary = doi = 10.1086/425745 id = cord-304487-ycvu5l5f author = Wertheim, Joel O title = A glimpse into the origins of genetic diversity in SARS-CoV-2 date = 2020-03-04 keywords = SARS summary = Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. doi = 10.1093/cid/ciaa213 id = cord-276995-b003vcdc author = Wiese, Andrew D title = Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date = 2020-06-20 keywords = SARS summary = And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. doi = 10.1093/cid/ciaa834 id = cord-327324-4c4a4bfz author = Wilkinson, Robert J title = Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date = 2020-06-13 keywords = HIV summary = title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis doi = 10.1093/cid/ciaa747 id = cord-313693-qmkrn7pr author = Wong, Bonnie C. K. title = Possible Role of Aerosol Transmission in a Hospital Outbreak of Influenza date = 2010-11-15 keywords = influenza; outbreak; patient summary = Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. A major nosocomial outbreak of severe acute respiratory syndrome (SARS) occurred at PWH in 2003 [15, 23] ; since then, all patients hospitalized with acute febrile respiratory illnesses are put on droplet precautions; if influenza is confirmed, the patients will be isolated or cohorted in designated wards [21, 22] . Dispersion of the hypothetical virus-laden aerosols, originated from the index patient''s bed through the entire ward, was analyzed by computational fluid dynamics (CFD) method. In clinical studies, virus-laden particles less than 5-6 mm (ie, within the respirable aerosol fraction) have been detected in exhaled breaths of patients with influenza and in the air sampled from an acute healthcare setting during seasonal peak [19, 35, 36] . In conclusion, our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. doi = 10.1086/656743 id = cord-317948-svgguadm author = Xiao, Ai Tang title = Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date = 2020-04-19 keywords = PCR summary = title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients To date, an outbreak of infectious diseases--coronavirus disease 2019 (COVID-19) associated with Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) continues in Wuhan, China and threatens countries such as Korea, Italy, Iraq and Japan, etc. Currently no study reported the viral dynamics of SARS-CoV-2 infection in a long observation period. Therefore, we collected clinical specimens from 56 COVID-19 patients and reported the results of SARS-CoV-2 detection during the disease course. If two consecutive negative results were achieved, the period between symptoms onset and the date of first negative RT-PCR test result was defined as viral nucleic acid conversion time. In first 3 weeks after symptoms onset, majority results of RT-PCR for SARS-CoV-2 were positive. [14] [15] [16] This preliminary study has found evidence of the dynamic profile of SARS-CoV-2 in non-ICU COVID-19 patients during disease course. doi = 10.1093/cid/ciaa460 id = cord-266775-4npowkkz author = Xu, Jun title = Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date = 2005-10-15 keywords = Mig; SARS; patient summary = In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . doi = 10.1086/444461 id = cord-007050-ibmr5bev author = Xu, Wei title = Serological Investigation of Subclinical Influenza A(H7H9) Infection Among Healthcare and Non–Healthcare Workers in Zhejiang Province, China date = 2013-09-15 keywords = A(H7N9 summary = doi = 10.1093/cid/cit396 id = cord-267152-m9m0aunk author = Yang, Philip title = Investigating the sex differences in COVID-19: Another step forward, but many unanswered questions date = 2020-06-28 keywords = COVID-19 summary = doi = 10.1093/cid/ciaa776 id = cord-353103-sdij1d90 author = Yao, Xueting title = In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-09 keywords = PBPK; SARS; chloroquine summary = title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug''s safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. doi = 10.1093/cid/ciaa237 id = cord-317823-ztawznod author = Yehya, Nadir title = Statewide Interventions and Covid-19 Mortality in the United States: An Observational Study date = 2020-07-08 keywords = New; covid-19 summary = Historical analysis of the 1918-1919 influenza pandemic during the second wave of infections that examined 43 cities in the United States demonstrated an association between earlier school closures and bans on public gatherings with lower mortality [5] . Therefore, we assessed the association between the timing of emergency declarations and school closures, two specific statewide distancing measures, and subsequent Covid-19 mortality. Second, because deaths per million is a common method to compare localities, we provide an analysis testing the association between deaths per million at the state level after multivariable adjustment relative to timing of emergency declarations or statewide school closures. States implementing emergency declarations or school closures later in the course of the pandemic experienced higher Covid-19 mortality, with each day of delay increasing mortality risk 5 to 6%. doi = 10.1093/cid/ciaa923 id = cord-256583-z3pd339v author = Yen, Muh-Yong title = Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date = 2015-03-01 keywords = Ebola summary = doi = 10.1093/cid/ciu978 id = cord-310476-mhm7r3qc author = Yi, Huiguang title = 2019 novel coronavirus is undergoing active recombination date = 2020-03-04 keywords = haplotype summary = The single origin of 2019-nCov indicates a persistent animal to human transmission is unlikely, otherwise, multiple nodes with above characteristics should be observed. To quantify the significance of recombination over recurring sequencing error/mutations, Phi [6] and Max Chi-squared tests [7] in the software PhiPack [8] were performed. It showed p-values of 0.03 and 0.005 for Phi and Max Chi-squared, respectively, indicating the presence of recombinants in 2019-nCoV population. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event doi = 10.1093/cid/ciaa219 id = cord-278045-hr3r17mz author = Yokota, Isao title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-09-25 keywords = NPS; SARS summary = doi = 10.1093/cid/ciaa1388 id = cord-289598-t8upoq9a author = Yoon, Jane C title = COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date = 2020-09-08 keywords = CoV-2; PEH; SARS summary = doi = 10.1093/cid/ciaa1340 id = cord-258724-1qhen1bj author = Young, Barnaby E title = Viral dynamics and immune correlates of COVID-19 disease severity date = 2020-08-28 keywords = PCR; SARS summary = doi = 10.1093/cid/ciaa1280 id = cord-294335-qnu19ru5 author = Yousaf, Anna R title = A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date = 2020-07-28 keywords = PCR; SARS summary = We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . doi = 10.1093/cid/ciaa1072 id = cord-281726-s1o5l7ns author = Yu, Ignatius T. S. title = Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date = 2005-05-01 keywords = March; SARS summary = doi = 10.1086/428735 id = cord-339004-49dkucxd author = Yu, Ignatius Tak-Sun title = Severe Acute Respiratory Syndrome Beyond Amoy Gardens: Completing the Incomplete Legacy date = 2014-03-01 keywords = Amoy; Gardens summary = The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The temporal and spatial distributions of the 2003 severe acute respiratorysyndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. In 2004, we analyzed the temporal and spatial distributions of the initial 187 cases in 7 blocks (A-G) of Amoy Gardens, a residential building complex with 19 buildings, where the largest community outbreak of SARS took place. Considering that cases in Telford Gardens and Tak Bo Garden with symptom onset during 24-29 March were most likely resulting from the common source originating in block E of Amoy Gardens, the distance of airborne transmission in that outbreak could be >200 m. In conclusion, the airborne spread in the largest community outbreak of SARS in 2003 actually extended beyond the Amoy Gardens and affected residential buildings >200 m from the source. doi = 10.1093/cid/cit797 id = cord-345045-nlui9d6e author = Zahn, Matthew title = Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date = 2019-07-15 keywords = health; physician summary = Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities. doi = 10.1093/cid/ciy888 id = cord-283780-h4lwzpl9 author = Zhang, John J Y title = Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis date = 2020-05-14 keywords = ARDS; ICU summary = title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. To address this gap in the literature, we conducted a systematic review, meta-analysis and meta-regression to 1) investigate the predictive value of laboratory investigations for severe disease and adverse outcomes, and 2) evaluate the efficacy of antivirals and corticosteroids for COVID-19. Among the patients with antiviral use reported in our meta-analysis, overall rates of mortality, ICU admission and ARDS were 5.7%, 11.8% and 20.2%, respectively. Our meta-analysis suggested that the use of corticosteroids is associated with disease severity (ICU admission) and higher ARDS rates. To the best of our knowledge, this is the first systematic review and meta-analysis of COVID-19 to describe specific laboratory predictors of severe disease and adverse outcomes. doi = 10.1093/cid/ciaa576 id = cord-285403-h8ahn8fw author = Zhang, Liangsheng title = Origin and Evolution of the 2019 Novel Coronavirus date = 2020-02-03 keywords = Wuhan summary = To the Editor-The 2019 novel coronavirus disease (2019-nCoV or COVID-19) recently reported from Wuhan (China), which has cases in Thailand, Japan, South Korea, and the United States, has been confirmed as a new coronavirus [1] . Based on our phylogenomic analysis of the recently released genomic data of 2019-nCoV, we showed that the 2019-nCoV is most closely related to 2 severe acute respiratory syndrome (SARS)-like CoV sequences that were isolated in bats during 2015 to 2017 [2] , suggesting that the bats'' CoV and the human 2019-nCoV share a recent common ancestor ( Figure 1A) . This market also sells wild animals or mammals, which were likely intermediate hosts of 2019-nCoV, which originated from bat hosts ( Figure 1B ). The 2019-nCoVs have long branches (0.09) for the 2 isolated in the phylogenomic tree ( Figure 1A) , indicating that the 2019-nCoVs likely share bat hosts. There were 3 genotypes present in samples from Guangdong province, indicating that the 6 strains were infected from different places in Wuhan. doi = 10.1093/cid/ciaa112 id = cord-330214-28ah3nig author = Zhao, Jiao title = Relationship between the ABO Blood Group and the COVID-19 Susceptibility date = 2020-08-04 keywords = ABO summary = To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk. Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China. These results showed associations between ABO blood groups and COVID-19 susceptibility. The COVID-19 risk significantly increased for blood group A ( Figure 1 shows the estimates of ORs of the risk of ABO blood groups for COVID-19 on the pooled data from the three hospitals by random effects models. In this study, we found that ABO blood groups displayed different association risks for the infection with SARS-CoV-2 resulting in COVID-19. In the 285 patients from Shenzhen, we also found that blood group AB had an increased risk of infection. doi = 10.1093/cid/ciaa1150 id = cord-321873-9l9zp6gm author = Zhou, Bo title = The duration of viral shedding of discharged patients with severe COVID-19 date = 2020-04-17 keywords = covid-19 summary = title: The duration of viral shedding of discharged patients with severe COVID-19 However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding. The RT-PCR tests were performed on throat swabs following a previously described method 3 Moreover, another study displayed that four patients with COVID-19 who met the criteria for hospital discharge in China had positive RT-PCR test results 5 to 13 days later 6 , suggesting that recovered patients might still be virus carriers. Based on the results, we did not observe shortening of viral shedding time in the above groups, so it implied that all patients with severe COVID-19 should complete adequate course of treatment, regardless of sex and age. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study doi = 10.1093/cid/ciaa451 id = cord-266696-w9sb038q author = Zhou, Yi-Hua title = Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date = 2004-03-15 keywords = SARS summary = [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China doi = 10.1086/382081 id = cord-349566-zx9kt144 author = de Alencar, Julio Cesar Garcia title = Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 date = 2020-09-23 keywords = NAC; covid-19; patient summary = title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 There is still no robust experimental confirmation for this fact; however, increased serum AngII levels have been reported in patients with severe Covid-19 cases [7] and enhanced expression of ACE2 in adults, compared to children, has been advocated to cause the difference of disease prevalence in these age ranges [8] . Therefore, we designed a double-blind, placebo-controlled, randomized clinical trial to determine whether NAC (in doses used to treat acute liver failure), is able to protect alveolar cells and avoid respiratory failure in patients with severe acute respiratory syndrome caused by (confirmed or suspect) Covid-19. This is a double-blind, randomized, placebo-controlled trial to assess the effectiveness and safety of intravenous NAC to prevent respiratory failure in patients with confirmed or suspect severe Covid-19. doi = 10.1093/cid/ciaa1443 id = cord-292372-kn27ghlv author = de Chaisemartin, Clément title = BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden date = 2020-08-23 keywords = BCG; covid-19 summary = Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG''s effect without the biases associated with cross-country comparisons. found that countries with universal Bacillus Calmette-Guérin (BCG) childhood vaccination policies tend to be less affected by the COVID-19 pandemic, in terms of their number of cases and deaths [7] . In this study, we took advantage of a change in vaccination policy in Sweden to investigate the link between BCG vaccination in infancy and Covid-19 cases, hospitalizations and deaths, using a regression discontinuity approach. For instance, this study estimates the effect of universal BCG vaccination for individuals born around April 1st 1975, who are in their mid-forties during the COVID-19 pandemic, and cannot be generalized to the entire population. doi = 10.1093/cid/ciaa1223 id = cord-015516-hx7ktq8j author = nan title = In the Literature date = 2005-10-15 keywords = SARS summary = doi = 10.1086/497097 id = cord-260779-riw5xs3j author = van Griensven, Johan title = The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field date = 2016-01-01 keywords = EVD; Ebola summary = The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. The World Health Organization (WHO) guidelines recommend both convalescent whole blood (CWB) and CP for use against Ebola virus disease (EVD) [12] . Blood transfusion is routinely done in all 3 high-transmission countries involved in the current EVD outbreak; however, plasma has numerous advantages in these settings. Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an empirical treatment during outbreaks. Treatment of Ebola hemorrhagic fever with blood transfusions from convalescent patients. Clinical trial to evaluate the efficacy and safety of convalescent plasma for Ebola treatment (EVD001). Acute respiratory distress syndrome after convalescent plasma use: treatment of a patient with Ebola virus disease Large-scale convalescent blood and plasma transfusion therapy for Ebola virus disease doi = 10.1093/cid/civ680 id = cord-259243-1lkzcslx author = Álvarez-Aragón, Luis Miguel title = Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality date = 2020-04-08 keywords = RAS summary = title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality We have read with great interest the elegant manuscript by Hanff et al [1] proposing a very interesting association between the classical renin-angiotensin system (RAS) and angiotensinconverting enzyme 2 (ACE2) dysregulation present in cardiovascular disease (CVD) and the high mortality index in patients with CVD and coronavirus disease 2019 (COVID-19). On the one hand, it will decrease the proinflammatory effect of Angiotensin II with its subsequent benefit on decreasing the risk of acute respiratory distress syndrome (ARDS) observed in these patients, and on the other hand, it will increase ACE2 expression and therefore the virulence of SARS-Cov2. In addition, in vitro studies in human renal cells treated with SLGT2 inhibitors have shown an increment in Angiotensin(1-7) due to the independent activation of the non-classical RES, leading to important anti-inflammatory and anti-M a n u s c r i p t fibrotic effects [6, 7] . doi = 10.1093/cid/ciaa402