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?' ---------------------------------------------------------- 1203 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 7232 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 45 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 1186 virus 243 RNA 140 infection 123 cell 116 SARS 75 respiratory 73 viral 73 dna 72 influenza 65 PCR 63 protein 63 Fig 60 disease 58 vaccine 58 human 52 RSV 45 HIV 44 figure 42 IFN 42 H5N1 39 Ebola 35 HIV-1 34 COVID-19 31 host 31 HCV 30 H1N1 25 bat 21 antiviral 18 detection 18 Zika 18 CNS 17 antibody 17 Virus 16 mouse 16 IAV 15 patient 15 MERS 15 China 14 sequence 14 genome 14 gene 14 animal 14 HBV 13 drug 13 IBV 12 pandemic 12 membrane 12 child 12 Nipah 11 cause Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 142197 virus 46853 infection 46266 cell 31004 protein 27159 influenza 23876 disease 18670 study 18432 vaccine 17632 host 17017 % 13200 antibody 13054 response 12955 mouse 12897 gene 11590 replication 11485 type 11058 patient 10839 sequence 10781 genome 10609 animal 10210 case 9741 strain 8713 activity 8473 effect 8414 transmission 8262 system 8237 receptor 7957 membrane 7856 time 7816 analysis 7600 human 7493 sample 7440 factor 7439 acid 7296 role 7285 treatment 7278 group 7136 detection 7107 model 7019 particle 6948 day 6897 result 6698 number 6616 level 6600 expression 6567 mechanism 6502 pathogen 6370 child 6270 year 6192 outbreak Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 30587 al 25711 et 23717 . 17223 RNA 7207 SARS 5105 C 5082 PCR 4641 Fig 4189 RSV 3891 A 3746 H1N1 3659 IFN 3653 HIV 3557 Ebola 3474 H5N1 3391 HA 3206 HCV 2888 HIV-1 2881 de 2791 B 2770 Influenza 2733 T 2687 CoV 2450 Virus 2427 ⁄ 2381 CoV-2 1997 RT 1986 China 1823 der 1802 Table 1782 United 1750 West 1710 II 1688 M 1680 DNA 1677 Zika 1644 Health 1624 States 1591 la 1590 COVID-19 1551 IAV 1508 NA 1503 MERS 1444 Africa 1406 USA 1361 Nile 1331 S 1271 F 1201 N 1154 Human Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 20272 it 10992 we 8072 they 4640 i 2222 them 740 he 716 us 658 itself 472 one 356 themselves 265 you 189 she 50 em 42 me 41 him 33 himself 32 mrnas 23 ourselves 20 her 15 ifitm3 9 yourself 9 ns3/4a 7 p~ 7 pdcs 7 ours 7 nsp15 7 nsp10 7 herself 6 s 6 mg 6 isgf3 5 oneself 5 myself 5 igg1 5 e4narrow 4 nsp7 4 irfibv32 4 gh625 4 clustalx 4 's 3 ⍬ 3 theirs 3 nsps 3 nr-818 3 jcpyv 3 isg15-/-bmdm 3 imagej 3 his 2 virusdb 2 tecpr2 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 264753 be 52821 have 23599 use 13475 show 11718 infect 11537 include 10087 associate 10011 cause 9033 induce 8322 base 8092 do 7553 find 7103 bind 7028 detect 6902 develop 6875 increase 6858 occur 6667 identify 6336 contain 6328 report 6189 suggest 5885 follow 5736 require 5663 provide 5262 result 5182 know 5051 describe 5024 lead 4960 isolate 4908 produce 4900 involve 4744 observe 4610 mediate 4600 reduce 4471 inhibit 4187 see 4127 indicate 4094 make 4080 determine 4076 emerge 4010 express 3935 demonstrate 3824 compare 3761 relate 3751 target 3504 affect 3494 consider 3480 remain 3469 give 3305 allow Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 35745 viral 23401 not 21380 human 18482 also 17278 respiratory 15435 other 14691 - 12499 high 12056 such 11522 more 9461 however 9454 immune 9352 clinical 9305 most 9229 different 8920 specific 8757 antiviral 8413 only 8006 new 7957 well 7435 low 6673 infectious 6507 first 6136 many 6129 severe 6048 acute 6003 several 5923 important 5512 as 5467 cellular 5402 large 5091 genetic 5088 infected 5081 early 4877 small 4855 molecular 4761 non 4722 avian 4623 similar 4568 single 4532 common 4508 like 4416 positive 4382 highly 4376 thus 4294 novel 4238 further 4076 long 3757 anti 3742 same Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 2973 most 1195 least 995 Most 765 high 608 good 412 large 275 great 214 low 142 late 116 close 105 early 97 small 72 simple 69 bad 56 long 55 strong 49 common 41 big 36 short 33 old 32 vRNA 30 near 30 fast 23 deadly 22 young 19 fit 18 broad 16 new 15 ⁄ 15 easy 14 poor 11 flat 10 AuNPs 8 wide 7 weak 7 safe 7 -I 6 slight 6 preS1 6 deep 6 clear 5 rich 5 ClustalW 5 -which 4 vRNPs 4 rare 4 mild 4 heavy 4 fine 4 cheap Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 6332 most 928 least 328 well 8 long 8 hard 7 highest 6 worst 4 lowest 3 vrna 3 smallest 3 near 2 α2-ar 2 oldest 2 furthest 2 fast 2 farthest 2 early 2 close 2 aunps 2 -i 1 ® 1 youngest 1 slowest 1 rrna 1 prints201910.0144.v46 1 latest 1 gelpest 1 fewest 1 clustalw 1 3-o 1 -tag 1 -just Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 46 doi.org 27 www.who.int 25 www.ncbi.nlm.nih.gov 18 www 17 www.cdc.gov 17 creativecommons.org 15 orcid.org 15 dx.doi.org 12 github.com 8 www.ebi.ac.uk 8 clinicaltrials.gov 6 www.mdpi.com 6 www.gisaid.org 6 www.frontiersin.org 6 www.drugbank.ca 5 www.genego.com 5 talk.ictvonline.org 5 blast.ncbi.nlm.nih.gov 4 www.virologyj.com 4 www.thermofisher.com 4 www.oie.int 4 www.megasoftware.net 4 dx 4 crdd.osdd.net 4 arbidol.org 3 www.ncbi.nlm.nih 3 www.mgc.ac.cn 3 www.geneious.com 3 www.fludb.org 3 www.ecevr.org 3 www.bioinformatics.babraham.ac.uk 3 tree.bio.ed.ac.uk 3 prodata.swmed.edu 3 drugvirus.info 2 zinc15.docking.org 2 www.viprbrc.org 2 www.uniprot.org 2 www.sternadi.com 2 www.sanger.ac.uk 2 www.rivm.nl 2 www.r-project.org 2 www.nlm.nih.gov 2 www.ncbi.nlm 2 www.ncbi 2 www.multiplex-eu.org 2 www.microbialrosettastone.com 2 www.mgc.ac 2 www.labonsite.com 2 www.iucnredlist.org 2 www.isar-icar.com Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 18 http://www 11 http://creativecommons.org/licenses/by/4.0/ 9 http://doi.org/10.1101/2020.04.03.20047175 6 http://www.ncbi.nlm.nih.gov/ 5 http://www.gisaid.org 5 http://blast.ncbi.nlm.nih.gov/Blast.cgi 4 http://www.who.int/ 4 http://www.thermofisher.com 4 http://dx 4 http://creativecommons.org/ 3 http://www.ncbi.nlm.nih 3 http://www.genego.com/pdf/MC_legend 3 http://www.fludb.org 3 http://www.ecevr.org/ 3 http://www.drugbank.ca/ 3 http://github.com/ 3 http://drugvirus.info/ 3 http://doi.org/10.7774/cevr.2017.6.2.72 2 http://www.who.int/mediacentre/news/new/2006/nw02/en 2 http://www.who.int/hiv/data/en/ 2 http://www.who.int/emergencies/mers-cov/en/ 2 http://www.who.int 2 http://www.virologyj.com/content/7/1/312 2 http://www.virologyj.com/content/2/1/70 2 http://www.uniprot.org/ 2 http://www.sternadi.com/phyvirus 2 http://www.r-project.org/ 2 http://www.ncbi.nlm.nih.gov/orffinder/ 2 http://www.ncbi.nlm.nih.gov/genomes/ 2 http://www.ncbi.nlm.nih.gov/genome/ 2 http://www.ncbi.nlm.nih.gov/genbank 2 http://www.ncbi.nlm 2 http://www.ncbi 2 http://www.multiplex-eu.org/ 2 http://www.microbialrosettastone.com/ 2 http://www.mgc.ac.cn/DRodVir/ 2 http://www.mgc.ac 2 http://www.megasoftware.net 2 http://www.labonsite.com/ 2 http://www.gvn.org 2 http://www.geneious.com/ 2 http://www.eurosurveillance.org 2 http://www.ebi.ac.uk/asd-srv/wb.cgi?method=7 2 http://www.cdc.gov/ncidod/sars 2 http://www.cdc.gov/flu/ 2 http://talk.ictvonline.org/ 2 http://sysbio.cvm.msstate.edu/IPMiner 2 http://prodata.swmed.edu/ross-mann_fold/viruses/ 2 http://prodata 2 http://mbio.asm.org Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 2 journals.permissions@oup.com 1 weixiaofeng@cngb.org 1 thosaka@pd6.so-net.ne.jp 1 sunillal@icgeb.res.in 1 shohei@mbk.nifty.com 1 sfelena@ibmcp.upv.es 1 sandrine.wiramus@ap-hm.fr 1 robert.snoeck@rega.kuleuven.be 1 regavir@rega.kuleuven.be 1 pp.pastoret@oie.int 1 pk5@sanger.ac.uk 1 philip.efron@surgery.ufl.edu 1 oliver.pybus@zoo.ox.ac.uk 1 ncbi-help@ncbi.nlm.nih.gov 1 morikawa@iph.pref.osaka.jp 1 mkleines@ukaachen.de 1 mjackwoo@uga.edu 1 liujun@ivdc.chinacdc.cn 1 liud@im.ac.cn 1 lieve.naesens@kuleuven.be 1 kwatkin4@gmail.com 1 kubyshkin_av@mail.ru 1 kohdera@nakano-kodomo.or.jp 1 kasetetsuo@iph.pref.osaka.jp 1 jean-louis.romette@univmed.fr 1 irv.eo@wiley.com 1 info@isaricar.com 1 info@cbs.knaw.nl 1 ilane.hernandezm@gmail.com 1 hiroi@iph.pref.osaka.jp 1 grippe@pasteur.fr 1 graciela.andrei@rega.kule 1 g.reina@ibmc-cnrs.unistra.fr 1 doljav@science.oregonstate.edu 1 darwin@rvrcmn.com 1 battery203@163.com 1 antivirals-etn@uu.nl 1 amy.patick@pfizer.com 1 akulas@ecu.edu 1 a.bianco@ibmc-cnrs.unistra.fr 1 dan.li@ugent.be 1 cheryl_bletchly@health.qld.gov.au 1 abrass@partners.org 1 1396320174@qq.com 1 .ishii@gmail.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 97 viruses do not 89 virus is not 79 virus was not 75 virus does not 72 virus was first 72 viruses are not 65 vaccines are available 53 virus infected cells 49 virus was also 47 infection is not 46 virus did not 43 viruses have also 41 studies have also 40 cells were then 40 viruses are also 38 vaccines are not 37 viruses are more 36 disease is not 35 vaccine is available 35 virus has not 35 viruses is not 33 vaccine is not 33 virus is highly 33 viruses were also 32 cells are not 32 infection does not 32 viruses are able 31 infection is usually 31 virus is present 29 viruses are responsible 29 viruses have not 28 protein is not 28 proteins are also 27 infections are asymptomatic 27 virus is also 27 viruses did not 26 cells do not 25 infections are common 25 protein is also 25 virus is able 24 virus has also 24 viruses are highly 24 viruses were more 23 protein does not 23 studies have not 22 response is not 22 vaccines are currently 22 virus was present 22 viruses are capable 22 viruses were not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 9 vaccines are not available 8 vaccine is not available 8 virus has not yet 5 mice are not susceptible 5 vaccines are not yet 5 vaccines have not yet 4 study had no role 4 vaccine is not currently 4 vaccine is not yet 4 vaccines are not currently 4 virus is no longer 4 virus is not easily 4 virus was not detectable 4 viruses is not always 3 antibodies are not available 3 disease is not yet 3 genes are not essential 3 replication is not well 3 studies showed no significant 3 vaccine has not yet 3 vaccine is not contraindicated 3 virus has no nonhuman 3 virus is not necessarily 3 virus is not only 3 virus is not sufficient 3 virus is not yet 3 virus was not present 3 viruses do not readily 3 viruses have not yet 3 viruses is not clear 3 viruses is not well 2 activity is not only 2 activity is not yet 2 animals is not yet 2 antibodies are not present 2 antibodies was not significant 2 cases are not due 2 cells are not permissive 2 cells do not normally 2 cells had no effect 2 disease are not readily 2 disease are not synonymous 2 disease are not yet 2 disease is not always 2 disease is not completely 2 disease is not perfectly 2 disease is not readily 2 diseases are not necessarily 2 infection are not fully 2 infection are not readily A rudimentary bibliography -------------------------- id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 keywords = HMPV; HRV; PCR; RNA; RSV; SARS; child; infection; respiratory; virus summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. doi = 10.1016/b978-0-443-06668-9.50064-8 id = cord-341050-hnuogpqn author = Acharya, Dhiraj title = An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date = 2016-05-18 keywords = NS2B; Nile; RNA; WNV; West; ns3; virus summary = Among these structural proteins, E protein mediates crucial roles in binding to cellular receptors, membrane fusion, and entry of WNV into host cells, making it a key target for the development of vaccines, neutralizing antibodies, and entry inhibitors . In addition, a recent successful clinical trial of a hepatitis C virus NS5A inhibitor suggests that targeting non-structural proteins may be an ideal strategy to develop therapeutics against other fl aviviruses, including WNV [ 71 ] . In addition, better understanding of the pathogenesis of WNV and other fl aviviruses has offered new opportunities for designing many different classes of promising antiviral therapeutics by targeting both viral replication and the host cell metabolism. Several natural and synthetic compounds, antiviral peptides and siRNAs have been identifi ed to target both structural and nonstructural proteins of WNV and evaluated for their potential therapeutic roles. A VLP-based vaccine targeting domain III of the West Nile virus E protein protects from lethal infection in mice doi = 10.1007/978-1-4939-3670-0_19 id = cord-312461-5qzpo6l1 author = Adalja, Amesh A. title = Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date = 2019-08-30 keywords = RNA; disease; human; influenza; pandemic; virus summary = A substantial proportion of pandemic and biological threat preparedness activities have focused on list-based approaches that were in part based on pandemic influenzas of the past, historical biological weapon development programs, or recent outbreaks of emerging infectious diseases (e.g., SARS, MERS, Ebola) (Centers for Disease Control and Prevention 2017; Casadevall and Relman 2010) . Cultivating and maintaining expertise in the epidemiology, surveillance, and pathogenicity of all classes of microbes, with explicit incorporation of a One Health approach-which incorporates and integrates information from infectious diseases of plants, amphibians, and reptiles-will help foster the broad capacities needed for emerging pandemic and global catastrophic biological risks. Pathogen-based lists, both USA and global, based on influenza precedents, historical biological weapon programs, and emerging infectious diseases were responsible for galvanizing early activities in the field of pandemic preparedness and have helped drive many important contributions. doi = 10.1007/82_2019_176 id = cord-293472-d3iwlpsr author = Afilalo, Marc title = Evaluation and Management of Seasonal Influenza in the Emergency Department date = 2012-04-06 keywords = influenza; patient; symptom; virus summary = During influenza season (testing should be done in the following persons if the result will influence clinical management) Outpatient immunocompetent persons of any age at high risk of developing influenza complications (eg, hospitalization or death) presenting with acute febrile respiratory symptoms 5 days or less after illness onset (when virus is usually being shed) Outpatient immunocompromised persons of any age presenting with febrile respiratory symptoms, irrespective of time since illness onset (because immunocompromised persons can shed influenza viruses for weeks to months) Hospitalized persons of any age (immunocompetent or immunocompromised) with fever and respiratory symptoms, including those with a diagnosis of community-acquired pneumonia, irrespective of time since illness onset Elderly persons and infants presenting with suspected sepsis or fever of unknown origin, irrespective of time since illness onset Children with fever and respiratory symptoms presenting for medical evaluation, irrespective of time since illness onset Persons of any age who develop fever and respiratory symptoms after hospital admission, irrespective of time since illness onset Immunocompetent persons with acute febrile respiratory symptoms who are not at high risk of developing complications secondary to influenza infection may be tested for purposes of obtaining local surveillance data doi = 10.1016/j.emc.2011.10.011 id = cord-297203-f3f31h4r author = Afrough, B. title = Emerging viruses and current strategies for vaccine intervention date = 2019-04-16 keywords = Ebola; dna; pathogen; vaccine; virus summary = While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Modified vaccinia virus Ankara (MVA) is licensed as a third-generation vaccinia type vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against a range of infectious diseases, including those caused by emerging pathogens. Additionally, MVA elicits a strong immunological response against a range of other orthopoxviruses (OPXVs) (including Variola), and vaccines based on this platform can be considered as providing added value, as human immunity to OPXVs is low (after the cessation of the smallpox vaccination campaign) opening a gap for OPXV emergence, as evidenced by the recent occurrence of monkeypox virus in West Africa and onward cross boarder transmissions [39, 40] . doi = 10.1111/cei.13295 id = cord-016808-gy8d8285 author = Agol, Vadim I. title = The Origin and Evolution of Viruses date = 2008 keywords = RNA; dna; virus summary = Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain doi = 10.1007/978-1-4020-8761-5_7 id = cord-325230-3kg4oe4g author = Agol, Vadim I. title = Viral security proteins: counteracting host defences date = 2010-11-09 keywords = RNA; protein; viral; virus summary = These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. doi = 10.1038/nrmicro2452 id = cord-017167-8cdbcrh7 author = Ahola, Tero title = Functions of Chikungunya Virus Nonstructural Proteins date = 2016-12-03 keywords = CHIKV; RNA; virus summary = The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. However, recent studies of SFV P1234 processing reveal that a second mechanism, the presentation of cleavage sequences via long-range interactions between different domains of the polyprotein, Processing of CHIKV ns polyprotein P1234 and RNA synthesis. The main interaction appears to be mediated by a membrane-binding peptide located in the central part of the protein (approximately residues 244-263 in CHIKV nsP1; Fig. 2 ), which forms an amphipathic alpha helix, as characterized for the corresponding peptide from SFV (Ahola et al. However, the effects of mutations introduced into the NTPase/helicase active site were different for these viruses: in SINV such a mutation strongly reduced the nsP2-dependent degradation of Rpb1 whereas CHIKV nsP2 mostly retained its ability to block host gene expression. doi = 10.1007/978-3-319-42958-8_6 id = cord-280391-5kiu2pb6 author = Akinloye, Oluwabukola M. title = Specific Viruses Detected in Nigerian Children in Association with Acute Respiratory Disease date = 2011-10-11 keywords = HRV; virus summary = Adenoviruses, coronaviruses, human enteroviruses (HEV), human rhinoviruses (HRV), influenza viruses, parainfluenza viruses (PIV), and respiratory syncytial viruses (RSV) are well-known causes of acute respiratory tract infections (ARTI) in both industrialized and developing countries. Moreover, different viruses, including influenza viruses and RSV, are also frequently detected in samples obtained from patients with lower respiratory tract infection (LRTI), either alone or together with pathogenic bacteria. While the overall proportion of virus-positive specimens was similar in children aged under or over two years, as well as in the group with unrecorded age, all adenovirus, influenza virus A, RSV, and all but one HBoV and "true HEV" detections were in the youngest age group (Table 1) . This study revealed that all major respiratory virus groups tested for can be detected in Nigerian children with respiratory tract infection. Rhinoviruses and parainfluenza viruses were the most prevalent virus groups while influenza A and B viruses, as well RSV were rarely detected, possibly due to low season of these viruses during the time of sample collection. doi = 10.1155/2011/690286 id = cord-278876-il7g78w1 author = Akkina, Ramesh title = 2016 International meeting of the Global Virus Network date = 2017-03-16 keywords = Ebola; GVN; HIV; Institute; University; cell; virus summary = This report highlights the accomplishments of GVN researchers in many priority areas of medical virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C, and chikungunya viruses, and the development of improved diagnostics and new vaccines. This meeting report highlights accomplishments of GVN researchers in many priority areas of human virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C and chikungunya viruses, and the development of improved diagnostics and new vaccines. The main objectives of the meeting were to present and discuss current findings in medical virology, including advances in research on HIV vaccines and other important retroviruses; provide a framework to encourage collaborations among world experts; and address the GVN''s annual strategy for continued development. Hideki Hasegawa, a GVN center director at the National Institute of Infectious Diseases in Tokyo, explained that secretory IgA antibodies on mucosal surfaces play an important role in protection against influenza virus infection. doi = 10.1016/j.antiviral.2017.03.005 id = cord-267733-fuz8r3vj author = Al Ali, Sally title = Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date = 2016-05-21 keywords = VACV; dna; gene; recombinant; virus summary = This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost in comparison to other production systems [21, 24] . This reporter gene system has been widely used in transgenic plants, and it has also been successfully used in mammalian cells for VACV recombinant virus selection [54] . Reporter-gene assays have helped the pox virologists in basic research, for example for the study of the location, structure and function of many VACV proteins during the infection cycle and their interaction with proteins of the host cell [44, 70] . The main limitation of using VACV as a vector is the short-term gene expression, since it is a lytic virus killing the infected cells. Insertion sites for recombinant vaccinia virus construction: Effects on expression of a foreign protein doi = 10.3390/v8050134 id = cord-255339-oudj079q author = Al-Tayib, Omar A. title = An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia date = 2019-02-22 keywords = Arabia; Hajj; Jeddah; MERS; Rift; Saudi; Valley; virus summary = The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] . doi = 10.3390/pathogens8010025 id = cord-294125-v2dr4hm0 author = Albert, Manuel title = ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis date = 2018-11-13 keywords = IFN; cell; isg15; mitochondrial; protein; virus summary = Finally, based on our recent observations, we discuss the essential functions of mitochondria in the antiviral response and examine the role of ISG15 in the regulation of mitochondrial processes, specifically OXPHOS and mitophagy. Binding to IFNARs leads to the activation of the Janus kinase-signal transducer and activator of transcription proteins (JAK-STAT) signaling pathway and the formation of the interferon-stimulated gene factor 3 (ISGF3) complex, with the subsequent expression of IFN-stimulated genes [3] that establish an antiviral state and play important roles in determining the host innate and adaptive immune responses [4] . In the following sections, we discuss the antiviral mechanisms mediated by ISGylation of both viral and cellular proteins, with a focus on mitochondrial proteins, as we recently showed that ISG15 modulates essential mitochondrial metabolic processes such as respiration and mitophagy in macrophages, with important implications for innate immune responses [29] . doi = 10.3390/v10110629 id = cord-349225-504kr50e author = Alcami, Antonio title = Viral mechanisms of immune evasion date = 2000-09-01 keywords = MHC; immune; virus summary = Viruses such as HIV, human cytomegalovirus (HCMV) and vaccinia virus (VV) utilize a clever strategy, ''borrowing'' host cellular factors, including CD59, which normally protects cells from complement lysis, and incorporating them into the viral envelope. Additionally, several viruses inhibit the activity of IFN-␥, a key activator of cellular immunity, by blocking the synthesis or activity of factors required for its production, such as interleukin (IL)-18 or IL-12 (Table 4 ): CPV cytokine response modifier (Crm A) inhibits caspase-1, which processes the mature forms of IL-1␤ and IL-18 (Refs 2,6); various poxviruses encode soluble IL-18binding proteins (IL-18BPs) [8] [9] [10] ; measles virus (MeV) binds CD46 in macrophages and inhibits IL-12 production 1 ; and herpesviruses and poxviruses express IL-10 homologs that diminish the Th1 response by downregulating the production of IL-12 (Refs 1,11,12). doi = 10.1016/s1357-4310(00)01775-5 id = cord-313598-2t40ss6h author = Ali, Mohsin title = Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis date = 2015-10-29 keywords = swab; virus summary = Our objective was to determine whether sampling with a throat swab provides incremental benefit—when used in conjunction with a nasal swab—to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting. FINDINGS: Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Our primary objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among adults with acute pharyngitis. In addition, previous research among adults has shown that flocked nasal mid-turbinate swabs are as sensitive for respiratory virus testing as flocked nasopharyngeal swabs, and since nasal mid-turbinate swabs are more comfortable and acceptable for patients, these swabs are preferred for sample collection in outpatient studies [5] . doi = 10.1186/s12985-015-0408-z id = cord-010343-tqqt0hj7 author = Alidjinou, Enagnon Kazali title = Resistance of Enteric Viruses on Fomites date = 2017-06-15 keywords = MNV; surface; virus summary = The survival of main enteric viruses on fomites and its implication for virus transmission will be analyzed, and the major disinfection procedures and their impact will be described. Available data suggest that the majority of viruses persist longer on nonporous surfaces [7] ; however, results are sometimes conflicting, and the effect of fomite properties might also depend on the viral type. Therefore, survival and inactivation studies are commonly conducted using cultivable surrogates such as feline calicivirus (FCV) or murine norovirus (MNV) [40] . In another study conducted at room temperature, the authors demonstrated that MNV could survive for up to 28 days on 6 different surfaces and the rank order of infectivity reduction from highest to lowest was stainless steel, plastic, rubber, glass, ceramic, and wood [44] . Disinfectants are commonly used for virus inactivation, especially in the health care settings and the food industry, to prevent outbreaks due to enteric viruses. doi = 10.1159/000448807 id = cord-278913-u6vihq3u author = Allam, Zaheer title = The Rise of Machine Intelligence in the COVID-19 Pandemic and Its Impact on Health Policy date = 2020-07-24 keywords = datum; outbreak; virus summary = For instance, despite the challenges raised earlier, some startup companies were able to use the available data from social media, airline ticketing, and medical institutions to identify that the world is experiencing a new virus outbreak days before those in medical fraternity had made similar findings (Gaille, 2019) . According to Niiler (2020) , BlueDot, whose profile is shared in the following, was able to employ the services of AIdriven algorithms, to analyze data gathered from sources such as new reports, air ticketing, and animal disease outbreaks to predict that the world is facing a new type of virus outbreak. In the recent case of COVID-19, Metabiota was in the forefront to analyze the outbreak, and during the analysis of the data, some even sourced from social media, the company was able to predict which neighboring countries were at high risk of being the next target of the virus spread, more so because the panic in Wuhan had stated to trigger some fear, forcing people to flee. doi = 10.1016/b978-0-12-824313-8.00006-1 id = cord-285462-9i61rsei author = Almomani, Hesham title = L''ampleur de la réaction des gens aux rumeurs et aux fausses nouvelles à la lumière de la crise du virus Corona date = 2020-06-25 keywords = Corona; information; rumor; virus summary = In addition to the concerns that the World Health Organization fears about the Corona virus epidemic, the combination of false information and rumors also contributes to exaggerating the epidemiological situation and the difficulty of combating it, because most users and pioneers of social media are at their best in tracking fake sources and competing to spread misinformation [24, 25] . As the situation worsens and the number of concerns increases, the state of suspicion will increase among the general public, thus spreading false information and rumors greatly [17] , in addition to the presence of free times due to curfews, spacing, and social closures, which will make the situation more anxious and thus persistent and pervasive misinformation [38] , especially with the ease of finding fake news and information about the Corona virus [14] . doi = 10.1016/j.amp.2020.06.011 id = cord-018816-v3ylisbt author = Alroy, Joseph title = Viral Pulmonary Disorders in Animals: Neoplastic and Nonneoplastic date = 2013-08-26 keywords = Fig; cell; virus summary = Gross fi ndings in the lung of a nonneurological EHV-1 infection may include severe edema ( Fig. 24 .6 ) and hydrothorax. The lungs with the diffuse pattern of disease seen in monkeys (Baskin 1987 ) and sheep (Hoover and Thacker 1979 ) are heavy, wet, and consolidated. The alveolar spaces contain proteinaceous exudate with macrophages, neutrophils, and multinucleated giant cells with intranuclear basophilic inclusion bodies (Figs. In some species, such as marmosets and colobus monkeys, measles infection is more severe resulting in primary giant cell pneumonia followed by secondary bacterial bronchopneumonia (Jones et al. The presence of multinucleated giant cells containing intranuclear and intracytoplasmic eosinophilic inclusion bodies is a characteristic fi nding (Fig. 24.18 Histological findings are varied, including mild to moderate interstitial edema, mild infiltration by mononuclear cells (Fig. 24.28 ) , presence of alveolar macrophages, hemorrhagic foci, and capillary thrombosis as well as the presence of syncytial cells and eosinophilic inclusion bodies. doi = 10.1007/978-3-642-40605-8_24 id = cord-292828-29jbf9ik author = Alsaleh, Asma N title = Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date = 2014-01-09 keywords = ERV3; PCR; respiratory; virus summary = title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. doi = 10.1186/1471-2334-14-15 id = cord-287554-2lqy2ix9 author = Amarelle, Luciano title = Tratamiento antigripal: fármacos actualmente utilizados y nuevos agentes en desarrollo date = 2017-01-31 keywords = ARN; del; influenza; virus summary = El tratamiento disponible con fármacos antivirales, de ser administrado de forma precoz, puede reducir el riesgo de complicaciones severas; sin embargo, muchos tipos de virus desarrollan resistencia a fármacos, reduciendo su efectividad, por lo que ha habido un gran interés en los últimos años en el desarrollo de nuevas opciones terapéuticas para combatir la enfermedad. La estructura del virus influenza A consta de una envoltura lipídica que proviene de la célula huésped y lleva ancladas las glucoproteínas hemaglutinina (HA) y neuraminidasa (NA), antígenos de superficie usados para clasificar a los virus (por ejemplo, H1N1, H3N2, H5N1). Se ha demostrado que posee actividad antiviral en diferentes tiempos del ciclo del virus: en fases tempranas inhibe la transcripción de ARN viral y la síntesis proteica, y en fases tardías bloquea el tráfico citoplasmático de las nuevas ribonucleoproteínas 71 . Por ejemplo, se ha demostrado que los inhibidores de la Na,K-ATPasa poseen actividad antiviral frente a distintos tipos de virus ADN y ARN. doi = 10.1016/j.arbres.2016.07.004 id = cord-338737-phv12m1q author = Amor, A. title = Infecciones víricas. Clasificación. Infecciones por virus herpes date = 2006-06-30 keywords = virus summary = Los virus son microorganismos de pequeño tamaño (generalmente de 20-400 nm de diámetro) formados por una molécula de ácido nucleico, ADN o ARN, que puede ser de cadena sencilla (ss) o doble (ds) y una cápside proteica de simetría icosaédrica o helicoidal. Así, la transmisión y reactivación de los virus herpes constituye un problema clínico de primer orden en pacientes infectados por el virus de la inmunodeficiencia humana (VIH) o inmunodeprimidos debido a tratamientos quimioterápicos, corticoideos o tras trasplantes de órganos. La frecuencia de las reactivaciones varía con la localización anatómica, el subtipo vírico y el estado inmunológico del paciente, de tal forma que los sujetos inmunocomprometidos pueden tener mayor número de reactivaciones, cuadros más graves y extensos, y un riesgo elevado de diseminación. doi = 10.1016/s0211-3449(06)74333-8 id = cord-335948-qkfxfmxb author = Ampofo, William K. title = Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010 date = 2011-08-08 keywords = GISRS; HAI; Influenza; Programme; vaccine; virus summary = • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • The selection process is highly coordinated and involves continual year-round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). The continuing threat posed by avian H5N1, the aftermath of the 2009 H1N1 pandemic, the increased knowledge of influenza, and the development and availability of new technologies provide a timely opportunity to review the complex processes and issues involved in influenza vaccine virus selection and to identify potential areas for improvement. doi = 10.1111/j.1750-2659.2011.00277.x id = cord-321741-aq76s37x author = Andersen, Petter I. title = Discovery and development of safe-in-man broad-spectrum antiviral agents date = 2020-04-30 keywords = Zika; cell; drug; virus summary = Although the concept of BSAAs has been around for almost 50 years, the field received a new impetus with recent outbreaks of Ebola, Zika, Dengue, influenza and other viral infections, the discovery of novel host-directed agents, as well as development of drug repositioning methodology. The discovery of novel activities of BSAAs starts with exposing cells to the candidate antiviral agent at different concentrations and infecting the cells with a virus or mock. Given that emetine also inhibits ZIKV, EBOV, RABV, CMV, HCoV-OC43 and HIV-1 infections (Chaves Valadao et al., 2015; MacGibeny et al., 2018; Mukhopadhyay et al., 2016; Shen et al., 2019; Yang et al., 2018) , and that it is an FDA-approved anti-protozoal drug, it may represent a promising safe-in-man BSAA candidate. Thereby, novel antiviral activities of BSAAs should be further validated in primary human cells using different viral strains (including wild-type viruses), different viral loads, different times of compound addition, different endpoint measurements and compound concentration range. doi = 10.1016/j.ijid.2020.02.018 id = cord-004672-0lf5j8lo author = Anderson, Kevin title = Structural and physiological properties of mengovirus: Avirulent, hemagglutination-defective mutants express altered alpha (1 D) proteins and are adsorption-defective date = 1987 keywords = mutant; protein; virus summary = doi = 10.1007/bf01313891 id = cord-299786-wuve0tjz author = Anderson, Robert title = Manipulation of cell surface macromolecules by flaviviruses date = 2004-02-27 keywords = Halstead; MHC; cell; dengue; infection; virus summary = Dengue virus infection of immature myeloid dendritic cells has been shown to induce their maturation accompanied by the expression of major histocompatibility complex (MHC) class I and II antigens; the costimulatory molecules CD40, CD80, and CD86; and the dendritic cell marker CD83 (Libraty et al., 2001) . Flaviviruses, including dengue and West Nile (Shen et al., 1997) viruses, activate endothelial cell adhesion molecule expression by either direct (virus-mediated) or indirect (cytokine-mediated) mechanisms (see Section V,C). A major candidate event in such a route is the activation of endothelial cell adhesion molecules by a factor(s) (particularly TNF-) produced by dengue virus-infected blood monocytes . Thus the roles of prior immunity, antibody-enhanced virus infection, and immune-mediated pathologic effects on the vascular system are key points in understanding the pathogenesis of dengue hemorrhagic disease. Activation of endothelial cells via antibody-enhanced dengue virus infection of peripheral blood monocytes doi = 10.1016/s0065-3527(03)59007-8 id = cord-002338-ri7v2ka3 author = Anderson, Tavis K. title = A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses date = 2016-12-14 keywords = H1N1; virus summary = A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. Similarly, IAV in Asia reflects the regional introduction and subsequent evolution and cocirculation of multiple genetic clades of classical-swine H1N1, avian-like H1N1, and human seasonal-like H1N1 and H1N2 viruses (6, 27, 28) . Three major first-order H1 lineages continued to circulate in pigs ( Fig. 1 ; also see Fig. S1 in the supplemental material): the 1A classical lineage, viruses related to the 1918 human influenza pandemic; the 1B human seasonal lineage, the result of multiple human-to-swine transmission episodes of human seasonal H1 strains over decades; and the 1C Eurasian avian lineage, arising from an introduction from wild birds into pigs in the 1970s. doi = 10.1128/msphere.00275-16 id = cord-009820-fi54s0x7 author = Andries, K. title = Pathogenicity of Hemagglutinating Encephalomyelitis (Vomiting and Wasting Disease) Virus of Pigs, using Different Routes of Inoculation date = 2010-05-13 keywords = disease; pig; virus summary = SUMMARY: Forty‐eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. The present studies were primarily designed to determine whether a virus isolate, obtained from pigs with the vomiting and wasting syndrome only, could produce clinical signs after inoculation by different routes. When sick, pigs were killed at time intervals varying from one to five days after the appearance of clinical signs and different tissues were collected for virus isolation. From the pigs killed at different time intervals after inoculation, the following tissues were collected for virus isolation : nasal mucosa, tonsils, lungs (apical and cardiac lobes), pyloric region of the stomach, pons and medulla combined, cerebrum, cerebellum and blood clot. Forty-eight pigs were inoculated by different routes with the VW 572 isolate of the hemagglutinating encephalomyelitis (vomiting and wasting disease) virus. doi = 10.1111/j.1439-0450.1978.tb00754.x id = cord-273708-2q64at3z author = Annunziata, Giuseppe title = May Polyphenols Have a Role Against Coronavirus Infection? An Overview of in vitro Evidence date = 2020-05-15 keywords = RSV; polyphenol; virus summary = In this context, a great interest has been focused on resveratrol (RSV), whose antiviral mechanisms of actions are mainly attributable to its ability to inhibit the viral replication via (i) inhibition of immediate-early virus protein expression (i.e., ICP-4 and−27), (ii) inhibition of the NFκB signaling pathway, and (iii) activation of the AMPK/Sirt1 axis in the host cell (14) . The present mini-review aimed to report the few promising evidence regarding the potential anti-coronavirus activity of polyphenols, which may serve to drive the research toward the development of novel strategies to counteract the SARS-CoV2 pandemic. Studies available in the literature agree in establishing that the reduction of virus titer and the inhibition of nucleocapsid protein expression are their main general mechanisms of action at the base of this promising effect of polyphenols. doi = 10.3389/fmed.2020.00240 id = cord-271709-5frm3dnb author = Arden, Katherine E. title = Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001 date = 2019-11-04 keywords = IFAV; virus summary = We aimed to estimate the spectrum of RV genotypes, species seasonality and RV involvement in co-detections in Queensland using a convenience collection of airway sample extracts from patients with suspected respiratory infections, collected during 2001 and tested using molecular tools expected to account for all RV species. Extracts had been previously tested by PQ using direct or culture-amplified direct fluorescent assay to detect respiratory syncytial virus (RSV), adenoviruses (AdV), parainfluenza viruses (PIVs) and influenza viruses A and B (IFAV, IFBV) [9] . Positive correlations included RV with RSV; EV with RSV; AdV with PIVs; HMPV with IFAV, HCoV-OC43, HCoV-NL63 and PIV RVs were detected in all seasons, but a bimodal distribution was evident with peaks in spring (36.5 % of all picornaviruses) and autumn (35.8%) and a trough in winter (13.2 %; summer extract numbers were low, so prevalence was difficult to determine; Fig. 2 ). doi = 10.1099/acmi.0.000075 id = cord-002601-d8908t93 author = Arellano-Llamas, Rocío title = Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date = 2017-07-10 keywords = Mexico; PB2; virus summary = Substitutions that have been previously reported are involved in host specificity shift, viral oligomerization interfaces (VOI), binding small ligands (BSL), Ab''s recognition, binding host proteins (BHP), binding nucleic acids (BNA) and antigenic drift. In this study we sequenced the entire genome of pandemic A/H1N1 strains isolated from patients in a reference Hospital in Mexico City (INER) in different years and we compared these sequences with consensus sequences in order to detect mutations that might be associated with viral evolution or might influence the antigenicity of the virus. This might also be a reflection of differences in selective pressure once the virus is in the infected host; regarding the rest of the viral genome segments, all the Mexican isolates from season 2013-2014 clustered with sequences from New York and Helsinki. In HA we observe changes that could affect immunogenicity of the influenza virus; sequences from 2015 to 2016 had additional mutations (S162N) in antigenic site (Sa) and together with the substitution I276T are defining a new clade 6B.1 [21, 22] . doi = 10.1371/journal.pone.0180419 id = cord-265445-bazcczdj author = Arias-Bravo, Guisselle title = Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study date = 2020-02-18 keywords = RSV; child; respiratory; virus summary = title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. However, the empirical evidence needed to estimate the impact of overnutrition (including overweight and obese conditions) on the severity of viral respiratory infections in children is still lacking (10) . Hence, the objective of this study was to estimate the relationship of overnutrition on severity of illness in infants (aged between 0 and 5 months) and children (aged between 6 and 24 months) hospitalized with ALRIs. Moreover, frequency of viral coinfection, RSV viral load and levels of leptin according to nutritional status were evaluated. doi = 10.3389/fped.2020.00044 id = cord-003861-qeao4ghg author = Aris-Brosou, Stéphane title = Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation date = 2019-07-24 keywords = evolution; figure; virus summary = To understand how these two processes affect the long-term evolution of viruses infecting humans, we comprehensively analyzed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus types and which functions show evidence for episodic diversifying selection and correlated evolution. To better understand the role of correlated evolution and positive selection in the evolutionary dynamics of viruses infecting humans, we constructed a nearly exhaustive viral data set spanning all dsDNA, dsRNA, ssRNA, and ssDNA viruses deposited in GenBank (as of August 2017), and conducted an extensive survey of correlated evolution and diversifying selection in these viruses, asking more specifically about the prevalence of these two processes in each viral type, independently or jointly, with the specific hypothesis that the genes affected by both processes encode functions that are most critical to each viral life cycle. doi = 10.3390/v11080677 id = cord-004998-wuixnqy5 author = Arnold, W. title = Identic viral infections in four cases of malignant lymphoepithelioma date = 1978 keywords = virus summary = The viral particles found in this study are not yet described in human lymphoepithelioma; they are very similar to those found in tissue culture lines derived from Burkitt''s lymphoma (Epstein, 1962) and from nasopharyngeal carcinoma (De The et al., 1969) . The demonstration of herpes virus like nucleocapsids in malignant lymphoepithelioma might be of great interest because many of those patients show a changing level of EB-virus antibody titer during therapy or recurrence of the disease (Lynn et al., 1977) . This fact points at the possible role of a specific viral infection although it has to be mentioned that elevated EB-virus antibody titer is also present in mononucleosis or recurrent tonsillitis (Veltri et al., 1975) . Lymphoblastoid transformation and presence of herpes-type viral particles in a Chinese nasopharyngeal tumor cultured in vitro Prognosis of nasopharyngeal carcinoma by Epstein-Barr virus antibody titer doi = 10.1007/bf00455364 id = cord-347509-2ysw9a0a author = Aronen, Matti title = Virus Etiology of Airway Illness in Elderly Adults date = 2016-06-20 keywords = respiratory; virus summary = 1, 2 Susceptibility to respiratory viral infections may be important especially in older age, but the viral etiology and clinical significance of respiratory illnesses in elderly adults is poorly documented. [2] [3] [4] The aims of this study were to investigate the presence of viruses in elderly adults and to assess the association between viral infection and respiratory illness and between viral infection and chronic illness in individuals with an illness that requires hospitalization. 10 The current study shows that there is an association between respiratory virus detection and weight in elderly adults. 3, 4 The objective of the current study was to assess what older adults with cancer know about their diagnosis and treatment and to identify factors associated with the completeness of this information. doi = 10.1111/jgs.14175 id = cord-356176-1nwjjgul author = Atherton, J. G. title = The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus date = 1978 keywords = virus summary = Chick embryo tracheal organ cultures showed increased resistance to infection by a coronavirus after exposure to ascorbate, while chick respiratory epithelium and allantois-on-shell preparations showed no increase in resistance to infection by an influenza virus or a paramyxovirus. Titrations of avian infectious bronchitis virus were performed by inoculating 4 replicate chick-embryo tracheal organ culture tubes previously selected for ciliat activity, with dilutions of virus made in half-log steps, then continuing to incubate the preparations on a roller drum at 15 rev/hour at 37 ° C. However resistance of CETO cultures to IB virus infection rose with increasing ascorbic acid content (Table t and Fig. 1 ). Our results show t h a t aseorbic acid exerted no direct effect on the infectivity of a n y of the three viruses tested, nor did it affect the resistance of cells to infection by the 0 r t h o m y x o v i r u s (influenza) or the P a r a m y x o v i r u s (NDV). doi = 10.1007/bf01317848 id = cord-311908-sgdq6j6x author = Atkins, G. J. title = Transient virus infection and multiple sclerosis date = 2000-09-28 keywords = CNS; infection; virus summary = Multiple sclerosis (MS) is a chronic, demyelinating disease of the CNS in which autoimmunity to myelin plays a role in pathogenesis. These include subacute sclerosing panencephalitis (SSPE), caused by a persistent measles virus infection, and human T cell lymphotropic virus-I (HTLV-I)associated myelopathy, which is a slowly progressive neurological disease characterised by in¯ammatory in®ltrates and demyelination in the CNS, and is caused by an exogenous retrovirus. Another study that does not involve virus infection, but may nonetheless provide information concerning the possible viral aetiology of MS, concerns the exacerbation of brain damage following EAE induction. With regard to the activity of known human viruses in the induction of myelin damage, there is evidence that virus infections associated with CNS demyelination can cause damage to oligodendrocytes. It is possible that virus infection could induce secretion of pro-in¯ammatory cytokines that could penetrate the CNS parenchyma from the blood and lead to the recrudescence of anti-myelin autoimmunity by reactivation of previously primed T-cells. doi = 10.1002/1099-1654(200009/10)10:5<291::aid-rmv278>3.0.co;2-u id = cord-010235-hu6o1ggc author = Atmar, Robert L. title = Nonculturable agents of viral gastroenteritis date = 1997-12-01 keywords = Norwalk; PCR; virus summary = (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. This article describes the structure and genome organization of the human caliciviruses that cause gastroenteritis, the clinical and epidemiologic features of these viruses, and new methods for the laboratory diagnosis of infection with these viruses. The inability to cultivate the HuCVs and establish neutralization assays has prevented the definition of specific serotypes; however, at least five different serotypes are thought to exist based on early human cross-challenge studies and comparisons of the IEM and enzyme-linked immunosorbent assay (ELISA) reactivities of several prototype virus strains. doi = 10.1016/s0196-4399(00)89189-8 id = cord-006106-u5npu6ng author = Attoui, H. title = Genus Coltivirus (family Reoviridae): genomic and morphologic characterization of Old World and New World viruses date = 2002 keywords = Colorado; EYA; Reoviridae; ctf; virus summary = We report a genomic and morphologic study of the European Eyach (EYA) virus (genus Coltivirus, family Reoviridae) and a comparative analysis with the American Colorado tick fever (CTF) virus (the type species of the genus). These findings, together with the comparative analysis to genomes of south-east Asian isolates, support the recent classification of arboviruses with 12 segments of dsRNA within two distinct genera (genus Coltivirus and genus Seadornavirus) and raise interesting questions about the evolutionary origins of coltiviruses. Analyses of VP5 showed the presence of a potential phosphamide linkage site (amino acid 342-347 of CTF virus: LNYDKY and for EYA virus: LNYIKH) comparable to that found in the protein encoded by segment 2 of members of the genus Orthoreovirus (position 1166-1171: ANPDKF, 40). Sequence determination and analysis of the full-length genome of Colorado tick fever virus, the type species of genus Coltivirus (family Reoviridae) doi = 10.1007/s007050200005 id = cord-344006-0iq9s94n author = Atzrodt, Cassandra L. title = A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date = 2020-05-23 keywords = COVID-19; CRISPR; RNA; SARS; vaccine; virus summary = All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . doi = 10.1111/febs.15375 id = cord-016995-5izyl234 author = Auewarakul, Prasert title = The Past and Present Threat of Avian Influenza in Thailand date = 2008 keywords = H5N1; Thailand; influenza; virus summary = The plan aims at effective control of avian influenza spread in animals as well as in humans for a three-year period and at efficient pandemic preparedness within one year. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. When this result was reported to the Ministry of Public Health, the government announced that there was a highly pathogenic avian influenza (AI) outbreak in Thailand. Although several clusters of H5N1 infections have been observed in Thailand, Vietnam, and Indonesia, it is difficult to prove human-to-human transmission, as most of these patients had exposure to poultry and it is not possible to prove whether they contracted the disease from animals or humans. The genome sequence analysis of H5N1 avian influenza A virus isolated from the outbreak among poultry populations in Thailand doi = 10.1007/978-0-387-75722-3_2 id = cord-295191-xu26mvc3 author = Avirutnan, Panisadee title = Complement and its role in protection and pathogenesis of flavivirus infections date = 2008-12-30 keywords = DENV; WNV; complement; virus summary = Complement evasion mechanisms include: (a) use of complement receptors to enhance viral entry or suppress adaptive immune response (e.g., HIV, West Nile virus (WNV), measles virus, adenoviruses, herpesviruses, enteroviruses, hepatitis B and C viruses ); (b) expression of viral proteins that directly inhibit complement (e.g., herpesviruses, coronaviruses, and astroviruses [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] ); (c) modulation of expression of complement regulators on host cells to prevent complement-dependent lysis (e.g., herpesviruses [137] [138] [139] ); (d) incorporation of human regulators on the surface of virions to protect from complement-mediated virolysis (e.g. HIV, HTLV, cytomegalovirus, and vaccinia virus [140] [141] [142] [143] [144] [145] [146] ); (e) recruitment of soluble complement regulatory proteins to the virion or infected cell surface (e.g., WNV and HIV [147] [148] [149] [150] [151] ); (f) expression of viral decoy proteins that structurally or functionally mimic complement regulatory proteins (e.g., poxviruses and herpesviruses [152] [153] [154] [155] [156] [157] [158] [159] . doi = 10.1016/j.vaccine.2008.11.061 id = cord-311410-lgqup9ug author = Ayers, M. title = A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date = 2006-05-02 keywords = Nile; PCR; virus summary = In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. For specificity studies, several viral samples were used, including clinical samples found to contain CMV and EBV DNA by PCR testing, as described (Johnson et al., 2000) ; a clinical isolate of influenza virus from the 2004-2005 season, typed as H3 by sequencing of the hemagglutinin gene; echovirus 11 from the laboratory collection at the Hospital for Sick Children; hepatitis C virus RNA was obtained by in vitro transcription of the infectious clone pCV-H77C (Yanagi et al., 1997) (the clone was kindly provided by Dr. J. Coupled with sequencing, it could detect with great sensitivity and identify several mosquito-borne flaviviruses including WNV, Kunjin, SLE, YFV and dengue fever viruses. doi = 10.1016/j.jviromet.2006.03.009 id = cord-006954-ec9x8thb author = Aznar, María title = Viral nanomechanics with a virtual atomic force microscope date = 2018-07-04 keywords = AFM; capsid; shell; virus summary = Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid''s structural units. Instead of placing the focus on the finest structural details of the nanoindentation of a specific virus, the aim is to provide a highly coarse-grained description, allowing to simulate large viruses at realistic timescales and with the advantage of being able to link the mechanical behavior to the essential physical ingredients of the interaction between capsid''s structural units. Next, we will show how the elastic response of viruses depends on different physical parameters of their effective interactions, including the bending rigidity of the shell, the adsorption to the substrate, the radius of the AFM tip or the capsid shape. doi = 10.1088/1361-648x/aac57a id = cord-022453-xe5v7947 author = BABIUK, L.A. title = Viral Gastroenteritis in Ruminants date = 2013-11-17 keywords = infection; virus summary = Rotavirus infection is generally limited to the small intestine in calves, pigs and humans (Middleton et al., 1974; Mebus and Newman, 1977; McAdaragh et al., 1980) , but antigen can be found in the colon of lambs (Snodgrass et al., 1977) , pigs (Theil et al., 1978) and mice (Little and Shadduck, 1982) . Bovine Coronavirus diarrhea, like rotavirus diarrhea, occurs within 15-24 h p.i. Early in infection the villous epithelial cells appear morphological normal but they contain large amounts of antigen. Since diarrhea occurs before denudation and loss of enterocytes it is postulated that it is a direct result of infection of the cell and the ensuing redirection of cellular functions from absorption to virus replication. Because of the replication in lymphoid tissue this disease can be more severe, especially in small animals, than other viral infections, because of interference with immune responses and damage to the crypts. doi = 10.1016/b978-0-444-87312-5.50076-x id = cord-307899-427a7i3h author = BITTLE, JAMES L. title = Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date = 1989-12-31 keywords = States; United; cause; disease; infection; vaccine; virus summary = Adenoviruses cause significant disease in dogs, foxes, and man, but have also been isolated from cattle, swine, goats, sheep, horses, turkeys, and chickens, where they produce mild infections, mainly associated with the respiratory and intestinal tracts. The latter modified the virus by serial passage in porcine and canine tissue cultures; the resulting vaccine immunized dogs and did not produce clinical signs of infection except for occasional corneal opacity similar to that caused by natural infection. The immunity produced by the attenuated live-virus CAV-1 vaccines is long lasting and has drastically reduced the incidence of the canine disease. The exception is human hepatitis A virus, which causes a serious disease and has one serotype; the development of both inactivated virus and attenuated live-virus vaccines is in progress (Hilleman et al., 1982; Provost et al., 1983) . An attenuated live-virus yellow fever vaccine was developed by passage of the virulent Asibi strain in mouse brain and cell culture until it had lost its pathogenicity for monkeys and man (Theiler, 1951) . doi = 10.1016/b978-0-12-039233-9.50005-6 id = cord-000760-4yfohp9w author = Babapoor, Sankhiros title = A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection date = 2012-01-12 keywords = LPAI; M2e; Tetra; influenza; virus summary = Using peptide nanoparticle technology, we have designed two novel vaccine constructs representing M2e in monomeric (Mono-M2e) and tetrameric (Tetra-M2e) forms. A multiple antigenic peptide construct containing M2e (M2e-MAP) induced strong M2especific antibody titers in the serum of mice and resulted in significant protection against influenza virus challenge [13] . Chickens after each inoculation developed high levels of antibody against the injected construct and anamnestic response clearly was seen when the plates were coated with Mono-M2e and Tetra-M2e nanoparticles and M2e-GCN4 (tetrameric M2e), respectively (Table 1, Figures 7 and 8) . In the present study, protection efficiency of two different nanoparticle constructs harboring M2e was studied as possible vaccine candidates for low-pathogenicity avian influenza infection. Vaccination of chickens with recombinant Salmonella expressing M2e and CD154 epitopes increases protection and decreases viral shedding after low pathogenic avian influenza challenge doi = 10.1155/2011/126794 id = cord-339382-ii4xurmr author = Bachofen, Claudia title = Selected Viruses Detected on and in our Food date = 2018-03-21 keywords = HEV; foodborne; human; virus summary = Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. RECENT FINDINGS: Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. Furthermore, some plant viruses are known to infect and persist in insect-vectors and one of them, Tomato spotted wilt virus, a member of the genus Tospovirus of the Bunyaviridae family, was even shown to replicate in human cell lines [71] . HEV-3 and 4 strains infect humans, but the reservoir is thought to be in several animal species, whereof the pig plays the most important role for foodborne transmission. While foodborne HEV and TBEV clearly represent a threat for human public health, the role of several other viruses of animal origin detected in food still needs to be assessed. doi = 10.1007/s40588-018-0087-9 id = cord-271313-h9v0nmx5 author = Bagust, T. J. title = A REVIEW OF VIRAL INFECTIONS OF HORSES date = 2008-03-10 keywords = Australia; horse; virus summary = In Australia, extensive investigation of respiratory diseases seen in horses in Victoria and Queensland have shown that equine herpesvirus type 1 (rhinopneumonitis) is the most common aetiological agent (Duxbury and Oxer 1968; Bagust and Pascoe 1968, 1970) . These clinical signs may be produced by any of several groups of viruses (Studdert 1967) , including equine herpesvirus type 1 (previously called equine influenza virus, then *This is the third article in a series of reviews on viral diseases of animals. Virus diseases of the skin of horses in Australia have not been investigated in detail, but there is ample clinical evidence for the occurrence of equine cutaneous papillomatosis (warts), caused by a host-specific papovavirus and appearing approximately 2 -3 months after infection. Equine viral arteritis has not been detected in Australian horses, but the disease is important in that clinical signs of acute infection (fever, depression, ocular and nasal discharges, oedema of the eyelids, limbs and abdomen, coughing and difficulty in breathing, colic, enteritis, jaundice, abortion) could be confused with infection by several viruses previously discussed. doi = 10.1111/j.1751-0813.1972.tb02314.x id = cord-321835-qn33sx8x author = Bailey, Emily S. title = A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date = 2018-04-09 keywords = human; infection; virus summary = In particular, respiratory infections are problematic; in early 2003, World Health Organization issued a worldwide alert for a previously unrecognized illness that was subsequently found to be caused by a novel coronavirus [severe acute respiratory syndrome (SARS) virus]. Influenza A virus H3N2 subtypes are frequently reported in swine, avian, and canine hosts that are responsible for highly infectious respiratory diseases in pigs and have been examined as a potential cause of influenza in humans. In a recent review of the risks of potential outbreaks associated with zoonotic Ad (48) , it was noted that intense human-animal interaction is likely to increase the probability of emergent cross-species Ad infection. This suggests that strategies for novel virus detection should incorporate global surveillance at the human-animal interface to detect potentially emerging zoonotic viruses. Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome doi = 10.3389/fpubh.2018.00104 id = cord-346096-aml84iv1 author = Bailey, Emily S. title = Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date = 2018-09-17 keywords = PCR; respiratory; virus summary = These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. In this pilot study, we studied bioaerosol samples collected in Raleigh Durham International Airport for molecular evidence of respiratory viruses. Although not the focus of our study, we did not detect viable viruses using culture analysis associated with positive aerosol samples at RDU airport. In this pilot aerosol study, we conducted surveillance for human and zoonotic respiratory viruses in an airport setting over a period of nine weeks from January to March 2018. Despite these limitations, the results of this study suggest that aerosol sampling is a useful technique for respiratory virus surveillance in high traffic and crowded areas such as airports. doi = 10.1186/s40794-018-0071-7 id = cord-302277-c66xm2n4 author = Bakaletz, Lauren O. title = Developing animal models for polymicrobial diseases date = 2004 keywords = Candida; disease; infection; model; virus summary = Briefly, viral infection compromises the protective functions of the Eustachian tube, alters respiratory-tract secretions, damages the mucosal epithelial lining, interferes with antibiotic efficacy, modulates the immune response and enhances bacterial adherence 77 and colonization 78 to predispose the host to bacterial OM. In otitis media, which is a middle ear infection, a synergistic interaction that results in disease owing to co-infection with an upper respiratory tract virus and three bacterial species -Streptococcus pneumoniae, nontypeable Haemophilus influenzae (NTHI) and Moraxella catarrhalis -is well documented. It seems likely that the transient suppression of RDC migration and the delayed development of an effective adaptive immune response to a second infection might be another mechanism by which influenza virus predisposes the host to bacterial co-infection. Using this criterion, a mouse model of polymicrobial-induced osteoclastogenesis, bacterial penetration, leukocyte recruitment and softtissue necrosis has been developed to clarify the role of cytokines in periodontal disease. doi = 10.1038/nrmicro928 id = cord-298489-uqrzzh0e author = Bale, James F. title = Emerging Viral Infections date = 2012-08-11 keywords = Nile; Nipah; West; virus summary = The viruses and disorders discussed herein include West Nile virus, an arboviral infection that swept across the United States in the early years of the 21st century; Nipah encephalitis, a paramyxovirus-induced disorder endemic to India, Bangladesh, and South Asia; chikungunya, a mosquito-borne viral disorder that affects persons in Africa, India, and Southeast Asia; dengue virus, an arthropod-borne Flavivirus that infects more than 100 million persons annually; and parechovirus, a picornavirus that can cause severe disease in neonates and permanent neurodevelopmental disability in surviving infants. 6 Infection control measures, including the slaughter and disposal of Ͼ1 million pigs, contained the disease; during this outbreak, human-to-human transmission of Nipah virus was not observed. The virus, first associated with human disease in Tanzania in the early 1950s, reemerged in 2005-2006 when Ͼ200,000 persons living in the Reunion Islands contracted chikungunya disease 29 ; nearly 1000 deaths among children and adults were reported. doi = 10.1016/j.spen.2012.02.001 id = cord-319754-5isw53wl author = Balgoma, David title = Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update date = 2020-08-31 keywords = HCV; SARS; cell; fusion; lipid; membrane; protein; virus summary = Some viruses may use different entry mechanisms, this feature being likely dependent upon the membrane lipid composition of the host cell they infect as well as the particular cell surface factor attachment used. The question regarding whether the lipid-raft domains may serve as platforms to concentrate the proteins required for viral entry and, even though some evidence exists, to activate signaling pathways inside the host cell still remains unsolved. More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . More recently, a Ca 2+ -dependent pathway of infection by the Rubella virus (RuV, Rubivirus family, Togaviridae) was demonstrated to proceed through direct binding of the fusion loop in the viral E1 protein to SM/cholesterol-enriched membranes [49] . doi = 10.3390/metabo10090356 id = cord-333228-ejkgune0 author = Ball, Andrew S title = Chapter 1 Introduction into nanotechnology and microbiology date = 2019-12-31 keywords = Nanotechnology; application; detection; food; nanoparticle; virus summary = Abstract The current chapter summaries the world of Microbiology and boom of Nanotechnology and how both the exciting fields come together to help men kind with various new applications in water, food, medical biology and immunology. It is now possible to build materials atom by atom and impose desired characteristics for numerous applications in almost every area, such as composite materials development, electronics, nano-electro-mechanical systems (NEMS), biomedical technologies, renewable energy solutions and environmental remediation (Navya & Daima, 2016 Nanomaterials are classified into nine major groups based on their shape, size, composition, surface charge, aggregation and chemical nature. However, due to instances where the frequent use of drugs has led to antibiotic/multidrug resistance in microorganisms, and the delivery of metal nanoparticles is impacting the food chain, it is now necessary to develop interdisciplinary approaches combining Microbiology and Nanotechnology to combat secondary human health, and environmental and ecological damage. doi = 10.1016/bs.mim.2019.04.003 id = cord-342936-43u7afl3 author = Balzarini, Jan title = Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date = 2007 keywords = CBA; HIV; HIV-1; SIGN; virus summary = Perhaps more importantly, such carbohydrate-binding agents (CBAs) may force the virus to delete at least part of its glycan shield to escape drug pressure 5 ; this might result in the initiation of an immune response against uncovered immunogenic envelope epitopes. Although such a mechanism may be efficient for a first-line inactivation of HIV, CBA-exposed HIV strains may decrease the efficiency of LCs to eliminate HIV, but at the same time may compromise the ability of the virus to be efficiently transmitted by DCs. The interactions of several CBAs have been extensively investigated, including: the prokaryotic CV-N and actinohivin; a variety of plant lectins, including Hippeastrum hybrid agglutinin (HHA) and UDA; the non-peptidic low-molecular-weight antibiotic PRM-A; and the monoclonal antibody 2G12 with the HIV-envelope gp120 and/or several glycan structures. doi = 10.1038/nrmicro1707 id = cord-284880-xsh3wkqy author = Bandaly, Victor title = The Fate of Mengovirus on Fiberglass Filter of Air Handling Units date = 2017-06-28 keywords = air; filter; study; virus summary = The aim of this work is to study the characterization of viral bioaerosols in indoor environments and to understand the fate of mengovirus eukaryote RNA virus on glass fiber filter F7 used in AHU. Regarding the virus infectivity on the filter under a constant air flow, mengovirus was remained infectious during 10 h after aerosolization. From an average of 4.43 9 10 8 PFU L -1 of initial solution of virus aerosolized, 3.43 9 10 2 PFU cm -2 of infectious mengovirus was detected after 25 min of air flow. With a continuous air flow in the system, the persistence of mengovirus was assessed at different times and showed infectivity on the filter up to 10 h after aerosolization (Fig. 7) . Thus, time has an effect on the infectivity of the virus; this study showed that, with a continuous air flow in the doi = 10.1007/s12560-017-9310-8 id = cord-295433-olmein3q author = Banerjee, Arinjay title = Bats and Coronaviruses date = 2019-01-09 keywords = MERS; SARS; bat; virus summary = Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] . doi = 10.3390/v11010041 id = cord-334010-gxu0refq author = Banerjee, Nilotpal title = Viral glycoproteins: biological role and application in diagnosis date = 2016-01-18 keywords = Ebola; HIV; glycoprotein; viral; virus summary = The sema-domain is the [18, 43] Fusion with host cell membrane Sialic Acid and attachment [43] 3-5 million cases Worldwide [78, 105] SARS-CoV Spike(S) glycoprotein [25, 115] Membrane fusion [115] 8422 within the duration of 1st November 2002 to 7th August 2003 occurring worldwide [113, 114] Hepatitis C virus E1 and E2 [55, 98] Binding to Host receptor and Conformational change necessary for membrane fusion [98] 130 to 150 million people globally [103, 106] Human immunodeficiency virus 1 gp120, gp160, gp41 [16] Intracellular transport [16] 35 million globally up to 2013 [83, 104, 108, 112] Zaire Ebola virus Spike Protein Gp1-Gp2 [64] Primary Host cell activation [64] up to 28th June 2015 total 27,550 cases [107, 110, 111] Dengue virus E (dimer) [64] Host cell fusion and attachment [64] WHO reported recently that there are 390 million dengue infections per year globally [109] . doi = 10.1007/s13337-015-0293-5 id = cord-346904-aa88gtzr author = Bao, Y. title = Virus Classification by Pairwise Sequence Comparison (PASC) date = 2008-07-30 keywords = PASC; virus summary = Pairwise sequence comparison (PASC) is a molecular classification tool for viruses. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine demarcations at different taxonomic levels such as strain, species, genus, and subfamily levels. In the PASC system, pairwise global alignment is performed on complete genomes or particular protein sequences for each viral family, and their percentage of identity is calculated. For those virus families that are suitable for PASC analyses, demarcations can be easily determined and new viruses can be clearly placed into the correct taxonomy. PASC is a molecular classification tool for many virus families. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine the demarcations at strains, species, genera, and subfamilies level. doi = 10.1016/b978-012374410-4.00710-x id = cord-011880-qlutgfu2 author = Barberis, Abdelheq title = Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria date = 2020-07-17 keywords = AIV; H5N1; H9N2; algerian; virus summary = In addition, different studies, showed that circulating H9N2 strains have acquired affinity to mammalian like-receptors and gained high virulence and pathogenicity through substitutions in their viral proteins [13, 14] ; the most known substitutions are in the HA protein that promotes virus binding to cellular receptors. While the substitution 627 K that confers high pathogenicity, virulence and increased replication in mice [63] , was not detected in our Algerian viruses, three substitutions 318R, 590S and 661 T, associated with mammalian adaptation, were observed [71, 72] . The PB1 substitutions N105S, K577E/M and 578Q, known to be associated with increased polymerase activity, H9N2 pathogenicity in mice as well as adaptation to mammalians [61, 64, 78] , were not observed in the currently circulating Algerian strains, which however shared 105 N, 577 K and 578 K. Amino acids analysis showed that the Algerians H9N2 strains carried out different molecular markers associated with affinity to human-like receptors and increased virulence. doi = 10.1186/s12985-020-01377-z id = cord-254200-9bpdfxrt author = Barin, F. title = La sécurité virale des médicaments d’origine biologique date = 2008-06-30 keywords = des; les; virus summary = Résumé Les crises sanitaires survenues dans les années 1980 ont dramatiquement contribué à la prise de conscience des risques iatrogènes liés aux médicaments d''origine biologique et, ainsi, au développement du concept de sécurité virale de ces médicaments, qu''ils soient d''origine humaine, avec notamment les médicaments dérivés du sang (MDS), animale ou issus des biotechnologies (produits par des cellules eucaryotes). La sécurité virale des médicaments repose sur trois éléments : la qualité de la matière première, le procédé de fabrication qui inclue des étapes aptes à éliminer ou à inactiver les virus et, éventuellement, les contrôles des produits intermédiaires ou finis. L''objectif des études de validation virale est de fournir des éléments tangibles, concrets, démontrant que telle ou telle étape permet effectivement d''éliminer ou d''inactiver tel ou tel type de virus, susceptible de contaminer spécifiquement la matière première (par exemple, VIH, VHC ou parvovirus B19 pour le plasma) ou représentatif de familles non encore impliquées dans des contaminations liées aux produits sanguins. doi = 10.1016/j.pharma.2008.05.004 id = cord-257255-n5o368ih author = Barker, J. title = Spread and prevention of some common viral infections in community facilities and domestic homes date = 2001-12-21 keywords = infection; surface; virus summary = Amongst health care professionals there is growing awareness that improved standards of hand, surface and air hygiene in community settings could do much to prevent the spread of viral infections within these environments. In a preschool daycare centre, respiratory and gastrointestinal infections decreased following implementation of measures which included reinforcing existing handwashing procedures and education of staff and families on issues of infection control including environmental surface cleaning and disinfection and disinfection of toys (Krilov et al. Nevertheless, overall, there is convincing circumstantial evidence to suggest that improved standards of hygiene can have a signi®cant impact in reducing the rates of respiratory, intestinal and other viral infections in childcare facilities, domestic homes, hospitals and adult care centres and the circulation of infections between these communities. Potential role of hands in the spread of respiratory viral infections Ð studies with human parain¯uenza virus 3 and rhinovirus 14 doi = 10.1046/j.1365-2672.2001.01364.x id = cord-293975-np9xdag5 author = Barnett, E. M. title = Two neurotropic viruses, herpes simplex virus type 1 and mouse hepatitis virus, spread along different neural pathways from the main olfactory bulb date = 1993-12-31 keywords = Fig; JHM; MHV; hsv-1; virus summary = The data also demonstrate that two viruses can enter the brain via the olfactory system and localize to different structures, suggesting that neurological diseases involving disparate regions of the brain could be caused by different viruses, even if entry occurred at a common A number of viruses have been shown to spread transneuronally into and throughout the rodent CNS following intranasal inoculation, including herpes simplex virus type 1 (HSV-I)," vesicular stomatitis virus,43 Borna disease virus," mouse hepatitis virus (MHV),-pseudorabies viru? Abbreviafions: HSV-1, hernes simplex virus, type 1; LC, locus coeruleus; MHV''-JHM, -mouse hepatitis virus, strain JHM; MOB, main olfactorv bulb; PFU, plaque forming unit; p.i. post-inoculation; TH, tyrosine hydroxylase; TH + , tyrosine hydroxylase immunoreactive; TH -, tyrosine hydroxylase immunonegative; VTA, ventral tegmental area; WGA-HRP, wheatgerm agglutinin-horseradish peroxidase. doi = 10.1016/0306-4522(93)90045-h id = cord-340423-f8ab7413 author = Barr, J.N. title = Genetic Instability of RNA Viruses date = 2016-09-09 keywords = RNA; genome; mutation; viral; virus summary = We then discuss evidence that at least some RNA viruses have a replication fidelity that is poised to maximize genome sequence space without incurring catastrophic lethal mutations and describe how this can be exploited to control viral infections. The error-prone nature of polymerase activity, coupled with the absence of a proofreading mechanism, is the key reason why RNA virus genomes acquire mutations and exist as a swarm of genetic variants. The mutation rate of the viral polymerase, coupled with the replication mode that the virus employs (and extrinsic factors, described in the following text) will determine the extent of genetic variability of viruses released from an infected cell. Thus, it is possible that the high mutation rates of RNA viruses are simply a consequence of polymerases that are under selective pressure to replicate genomes very rapidly to ensure efficient viral infection [79] [80] [81] . doi = 10.1016/b978-0-12-803309-8.00002-1 id = cord-022324-tcltmhi7 author = Barthold, Stephen W. title = MOUSE HEPATITIS VIRUS BIOLOGY AND EPIZOOTIOLOGY date = 2012-12-02 keywords = JHM; MHV; mouse; virus summary = Interest in MHV has evolved from a number of different perspectives, including emphasis on MHV as a model of viral hepatitis, viral encephalitis and demyelinating disease, genetic mechanisms of host resistance to viral infection, and the molecular biology of coronaviruses, using MHV as a prototype. Virus strain, passage history, dose, route of inoculation, host genotype, age, immune function and co-infection with other agents all interact to determine the ultimate expression of MHV disease. Mice of the semisusceptible C3H genotype that survive intraperitoneal inoculation of virulent MHV-3 can have persistent infections, in which virus can be recovered in low titer from liver, brain and lymphoid organs for up to 42 days (68). Therefore, when MHV initially infects a naive mouse population, neonatal mice suffer high mortality, particularly with enterotropic MHV strains (13,14). Persistent infection with mouse hepatitis virus of low virulence in nude mice Enterotropic mouse hepatitis virus infection in nude mice doi = 10.1016/b978-0-12-095785-9.50032-9 id = cord-340537-pdvpmydk author = Bañon-Gonzalez, Rafael title = Autopsies of suspected SARS-CoV-2 cases date = 2020-07-15 keywords = COVID-19; SARS; virus summary = Abstract Forensic physicians should consider the possibility that people who have died from violent or unknown causes may be infected by the virus SARS-CoV-2, or that the diagnosis of the disease has legal implications, which requires adequate knowledge of the epidemiology of the disease, protective measures, adequate sampling and the pathological characteristics. This article reviews the aspects of the pathophysiology of the disease that have an impact on the infectivity of the body''s tissues and fluids, measures for preventing biological risk, taking samples and pathological findings, both macroscopic and microscopic, associated with death caused by infection with the SARS-CoV-2 virus. 13 Nevertheless, infection by SARS-CoV-2 is associated with a high rate of mortality, and many carriers are known to exist who have no symptoms or only mild ones, so that it is possible that some of the corpses that will be subjected to a medical-legal autopsy are infected by this virus. doi = 10.1016/j.remle.2020.05.002 id = cord-348669-mizygp4j author = Beall, Anne title = Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date = 2016-01-05 keywords = ORF3-RFP; PEDV; RNA; pc22a; virus summary = title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines. doi = 10.1128/mbio.01451-15 id = cord-289093-si8btsab author = Beard, Philippa M. title = A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date = 2014-06-05 keywords = RNA; VACV; figure; viral; virus summary = To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. doi = 10.1371/journal.pone.0098431 id = cord-018265-twp33bb6 author = Becker, Pablo D. title = Community-acquired pneumonia: paving the way towards new vaccination concepts date = 2007 keywords = RSV; SARS; dna; protein; response; vaccine; virus summary = A live vaccine based on a master virus strain developed at the Institute of Applied Microbiology (Austria) by growing wild influenza virus in Vero cells at 25°C was also demonstrated to be safe, well-tolerated and immunogenic after intranasal immunization in young adults [18]. Candidate vaccines should be able to replicate and induce a protective immune response in young infants, even in the presence of maternally acquired antibodies. This demonstrates that antibodies play a major role in protection against this disease, whereas T-cell immunity targeted to internal viral proteins appears to contribute to clearance. The second generation of PS-based conjugate vaccines stimulates stronger antibody responses, even in infants, young children and immune deficient individuals, as well as immunological memory. The resulting proteins are then used to perform immunological and/or functional studies to select the most promising candidates (e.g., able to induce the production of microbicidal or neutralizing antibodies, capacity to confer protective immunity). doi = 10.1007/978-3-7643-7563-8_10 id = cord-022349-z8w1wkm8 author = Beeler, Judy A. title = Human and Animal Viruses date = 2007-09-02 keywords = freeze; vaccine; viral; virus summary = However, freeze-drying provided a way to maintain virally infected material over long periods of time with relative ease when compared to serial passage in a susceptible animal host. The first experiment to demonstrate that this method could provide long-term stability was reported for a bovine virus that had been freeze-dried in 1916 and was shown to be viable after being maintained at room temperature for 30 years (Fasquelle and Barbier, 1950) . In general, most viruses may be "snap frozen" in a dry ice/ethanol bath prior to storage at temperatures _<-70~ It may be preferable to freeze some viruses, such as cytomegalovirus or varicella-zoster virus, as viable infected cells. Calcium lactobionate and human serum albumin were cryoprotective for measles virus during freeze-drying (Greiff and Rightsel, 1967) , whereas cell culture medium alone was less protective. doi = 10.1016/b978-012361946-4/50010-7 id = cord-332088-5c77h0of author = Beena, V. title = Emerging horizon for bat borne viral zoonoses date = 2019-10-26 keywords = China; India; bat; virus summary = In Asia and Pacific regions, bats were demonstrated as natural reservoirs for a large number of this types of emerging as well as re-emerging pathogens such as SARS, Ebola, Marburg, Nipha, Hendra, Tioman, Menangle, Australian bat lyssa virus, Rabies and many encephalitis causing viruses in humans and animals [2] . From bats the pathogen get transmitted to humans via intermediate hosts like horses(hendra) and pigs(nipah) and different species of animals get infected by consumption of partially eaten fruits of bats and the chewed out materials of bats after extracting the juice. The first report of a transmission of a viral disease from bats to humans was a rabies virus (RABV) belonging to the Lyssa virus genus [5] . Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China doi = 10.1007/s13337-019-00548-z id = cord-325326-2bbqz4o7 author = Beitzel, Brett F. title = High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date = 2010-10-14 keywords = RNA; Sindbis; VEEV; insertion; virus summary = We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. Toward this goal, we used transposon mutagenesis, reverse genetics, and fragment analysis by capillary electrophoresis to identify regions of the nsP3 gene that are important for replication and that result in temperature sensitive (ts) mutations. We used transposon mutagenesis to construct a cDNA library with small DNA fragments randomly inserted throughout the VEEV genome and then produced replication-competent virus through reverse genetics. Comparing transposon insertion sites in the resultant viruses to those in the starting library, we were able to produce a functional map of the entire genome of VEEV, and to identify several hundred potential ts mutations, including those we originally identified with the capillary electrophoresis method. doi = 10.1371/journal.ppat.1001146 id = cord-255026-fdp6mies author = Belák, Sándor title = Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date = 2007-07-26 keywords = OIE; PCR; assay; virus summary = The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. doi = 10.1016/j.vaccine.2006.11.068 id = cord-291156-zxg3dsm3 author = Bernasconi, Anna title = Empowering Virus Sequences Research through Conceptual Modeling date = 2020-05-01 keywords = SARS; VCM; sequence; virus summary = We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). -We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6] ; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM. Some interesting portals have become interfaces to GISAID data with particular focuses: NextStrain [18] overviews emergent viral outbreaks based on the visualization of sequence data integrated with geographic information, serology, and host species; CoV-GLUE, 9 part of the GLUE suite [38] , contains a database of replacements, insertions and deletions observed in sequences sampled from the pandemic. doi = 10.1101/2020.04.29.067637 id = cord-323358-05bk91lm author = Bhaskar, Sathyamoorthy title = Engineering protein nanocages as carriers for biomedical applications date = 2017-04-07 keywords = cell; nanocage; protein; virus summary = We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity. 1, 3 Examples of naturederived nanocarriers include protein nanocages such as viruses, ferritin and many others that are formed by the self-assembly of protein subunits, resulting in a cage-like structure. 8 In this review, we focus on natural and synthetic protein scaffolds engineered with specific functional groups to impart non-native functions, including aiding the delivery of active molecules through targeting of malignant cells and overcoming cellular barriers. 3 In addition to cell targeting ability and gene delivery efficiency, these protein-based multifaceted systems have highly ordered spatial configurations, and the stability and functionality of these materials have already been established through intensive research with advances in understanding virus infection, replication and assembly pathways. doi = 10.1038/am.2016.128 id = cord-016928-yigz9qiz author = Bhattacharyya, Sankar title = Inflammation During Virus Infection: Swings and Roundabouts date = 2019-11-05 keywords = Nile; West; virus summary = The tissue damage is caused from a combination of either direct neuronal infection which activates intrinsic apoptosis or a hyperactive inflammatory response mediated by PICs or CD8+ cytotoxic T cells (CTLs) (Wang et al. Spread through aerosols, SARS-CoV primarily infect lung cells triggering an often fatal inflammatory response clinically called acute respiratory distress syndrome (ARDS) that starts with severe hypoxia, pulmonary edema progressing to systemic inflammation, and failure of multiple organs, culminating in high rate of mortality (Peiris et al. Although evidence suggests that SARS-CoV can infect multiple cell types, lung type-II pneumocytes and ciliated epithelial cells constitute primary sites of virus replication, consequent to which these cells undergo apoptotic and/or necrotic death attracting innate immune cells and activating them to secrete PICs (Sims et al. Pro-inflammatory cytokines derived from West Nile virus (WNV)-infected SK-N-SH cells mediate neuroinflammatory markers and neuronal death doi = 10.1007/978-981-15-1045-8_3 id = cord-271171-tohbzenc author = Bhola, J. title = Corona Epidemic in Indian context: Predictive Mathematical Modelling date = 2020-04-07 keywords = India; preprint; virus summary = Scientists also believe that peri-domestic mammals may also serve as For long, human viruses have not been considered severe pathogens as infected people develop flu like symptoms and then get cured on their own as innate immune system triggers antibody formation that provides resistance against the diseases (Chiu, 2013; Kistler et al., 2007; Wrammert et al., 2008) . https://doi.org/10.1101/2020.04.03.20047175 doi: medRxiv preprint Figure 2 From what is known about corona viruses, it is evident that the per capita rate of increase in the number of infectives is directly proportional to the number of susceptible in the vicinity of an infective and hence, the total intake in the first compartment looks like (kS)I ; where k signifies the rate of transmission indicated by the average number of people who will catch the virus from one infected person. doi = 10.1101/2020.04.03.20047175 id = cord-002072-qbh728ec author = Bi, Yuhai title = A new reassortment of influenza A (H7N9) virus causing human infection in Beijing, 2014 date = 2016-05-27 keywords = BJ02; H7N9; virus summary = Genetic and phylogenetic analyses revealed that the virus belonged to a novel genotype, which probably emerged and further reassorted with other H9 or H7 viruses in poultry before transmitting to humans. The IFN-induced transmembrane protein-3 (IFITM3) C/C genotype was reported to be associated with severe clinical outcomes, as reflected by a higher viral load, more rapid progression to ARDS, higher cytokine/chemokine levels, and an increased mortality rate after H7N9 infection 22 . Although this was a severe H7N9-infected case with cytokine storm-like appearances and multiple organ failure, the patient was eventually cured after combination therapy with antivirals, mechanical ventilation, supportive nutrition and symptomatic treatment. Clinical, virological and immunological features from patients infected with re-emergent avian-origin human H7N9 influenza disease of varying severity in Guangdong province Cytokine and chemokine levels in patients infected with the novel avian influenza A (H7N9) virus in China doi = 10.1038/srep26624 id = cord-347577-p0a2rboi author = Bibby, Kyle title = Persistence of Ebola Virus in Sterilized Wastewater date = 2015-08-17 keywords = Ebola; virus; wastewater summary = The subsequent viral titer decrease was less rapid, and infectious Ebola virus particles persisted for all 8 days of the test. 17, 18 In response to the EVD epidemic, both the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention advised direct disposal of Ebola-contaminated liquid waste into sewage systems (wastewater collection and treatment systems) and latrines without disinfection. A current Ebola virus outbreak strain from Guinea (Makona-WPGC07) was spiked to two end concentrations (10 2 and 10 6 TCID 50 mL −1 ) into a domestic wastewater (untreated sewage) sample. Microbial activity within wastewater matrices would be expected to contribute to more rapid inactivation of infectious viral particles; 36, 42 however, the true effect of microbial activity on Ebola virus persistence is unknown. 34 Further assessment is necessary to determine Ebola inactivation and dilution within this period and potential human exposure routes, including workers within the sewer system and Ebola virus persistence within wastewater sludges. doi = 10.1021/acs.estlett.5b00193 id = cord-007362-pjpkz6wv author = Bielefeldt-Ohmann, Helle title = The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date = 2016-01-06 keywords = BVDV; Fig; bovine; cell; infection; virus summary = Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necrotic-erosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. 3, 22, 29 In PI calves, BVDV can be isolated from lung tissue, and virus antigen is widespread in bronchiolar and alveolar epithelial cells, however, without accompanying histopathologic changes (see section on persistent infection without overt clinical disease and Fig. 5 ).17 Conversely, a proportion (the size varying with study) of cattle succumbing to BRD are positive for BVDV, by virus isolation from or antigen detection in lung tissue, but the ensuing pathologic changes cannot be distinguished from those of other viral pathogens in the BRD complex (perhaps with the exception of BHV-P5), and usually are dominated by the pathology caused by the secondary bacterial agent. doi = 10.1016/s0749-0720(15)30461-8 id = cord-000012-p56v8wi1 author = Bigot, Yves title = Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date = 2008-09-18 keywords = dna; gene; genome; protein; virus summary = CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. With respect to both species number and mechanisms that lead to successful parasitism, endoparasitic wasps are known to inject secretions at oviposition, but only a few lineages use viruses or virus-like particles (VLPs) to evade or to suppress host defences. Extending our investigations to proteins encoded by open reading frames of certain ascoviruses and bracoviruses, hosts and bacteria, in the light of recent analyses about the involvement of the replication machinery of virus groups related to ascoviruses in lateral gene transfer [29] , we discuss the robustness and the limits of the molecular evidence supporting an ascovirus origin for ichnovirus lineages. doi = 10.1186/1471-2148-8-253 id = cord-349606-lup6tm2s author = Biill Primo, Osvaldo Vinícius title = Detection of Respiratory Viruses in Nasopharyngeal Swab and Adenoid Tissue from Children Submitted to Adenoidectomy: Pre- and Postoperative Analysis date = 2014-02-17 keywords = respiratory; virus summary = Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using real-time polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using realtime polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Several respiratory viruses (influenza A and B; parainfluenza 1, 2, 3, and 4; rhinovirus; respiratory syncytial virus; human bocavirus; coronaviruses; and metapneumovirus) were investigated by quantitative real-time polymerase chain reaction (q-PCR) in adenoid tissue removed surgically and nasal swab specimens collected preoperatively and at 1 month postoperative follow-up visit. doi = 10.1055/s-0034-1368135 id = cord-310371-pylrg91h author = Bishop, R.F. title = Enteric Viruses date = 2008-07-30 keywords = RNA; human; infection; virus summary = The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. doi = 10.1016/b978-012374410-4.00386-1 id = cord-008149-kdlcaium author = Blacklaws, B.A. title = Emerging viruses of zoonotic and veterinary importance date = 2017-12-30 keywords = virus summary = Emerging viruses of zoonotic and veterinary importance To enable discussion of all aspects of emerging virus infections, an Emerging Viruses meeting was held at the University of Nottingham, UK, on 27-29 July 2015. Given the success of this meeting, a second meeting was organised, now called ''Emerging Viruses of Zoonotic and Veterinary Importance'', at Churchill College, Cambridge, UK, on 24-26 July 2017 to encourage discussion of emerging virus infections from a One Health perspective. This is formulated in the One Health approach to infectious disease, where the possibility of infectious agent movement between species, including human beings, is key. Whilst a major driver of emerging virus disease research is public health concern over zoonotic infections, there are also veterinary drivers for emerging viral diseases. With the accelerating changes in our world, emerging viral infections will continue to be an important issue for human and veterinary health. doi = 10.1016/j.tvjl.2017.12.022 id = cord-253825-d9borky8 author = Blaising, Julie title = Arbidol as a broad-spectrum antiviral: An update date = 2014-04-24 keywords = ARB; HCV; antiviral; virus summary = ARB has been shown to display antiviral in vitro and/or in vivo activity against a number of enveloped or non-enveloped RNA or DNA viruses, including influenza viruses A, B and C , respiratory syncytial virus, SARS-CoV, adenovirus, parainfluenza type 5, poliovirus 1, rhinovirus 14, coxsackievirus B5, hantaan virus, Chikungunya virus, HBV and HCV [reviewed in Boriskin et al. Shi and coworkers showed a greater inhibitory effect on influenza A H1N1 when ARB was added before infection or when it was pre-incubated with the virus (Shi et al., 2007) , suggesting that membrane impregnation and/or metabolites could underlie ARB antiviral activity (see Section 6.). Recently, Tannock and coworkers reported a potent antiviral activity of ARB on several virus families responsible of respiratory infections in animals and humans, in particular on influenza A H3N2 (IC50 12 lM), and the non-enveloped Picornaviridae poliovirus 1 and rhinovirus 14 (Brooks et al., 2012 ; see also Brooks et al., 2004) . doi = 10.1016/j.antiviral.2014.04.006 id = cord-318172-bdotp9ko author = Blanco, Jorge C. G. title = PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date = 2014-01-01 keywords = HRV16; cotton; infection; rat; virus summary = In this work we show that, without requiring any genetic modification of either the host or the virus, intranasal infection of cotton rats with HRV16 resulted in measurable lower respiratory tract pathology, mucus production, and expression of interferon-activated genes. Over the years, the cotton rat (Sigmodon hispidus) has been shown to support replication of a broad spectrum of human viruses including respiratory syncytial virus (RSV) [25] , nonadapted strains of human influenza [26, 27] , and measles [28, 29] , among others [30] , providing modeling capabilities for the corresponding infections. The results of the described experimental work show that HRV16 infection in the cotton rat reproduces aspects of HRVassociated human disease in the respiratory tract, causing detectable inflammation in the lower airways and lung parenchyma and mucus production, and inducing a transient expression of interferon-stimulated genes that merits further investigation. In addition we demonstrated that passive transfer of antibodies generated in vaccinated cotton rats can protect naïve animals from Infectious virus titers in the lung were determined by plaque assay at the indicated times p.i. doi = 10.1016/j.trivac.2014.02.003 id = cord-005281-wy0zk9p8 author = Blinov, V. M. title = Viral component of the human genome date = 2017-05-09 keywords = RNA; dna; genome; host; virus summary = In the human genome, this capacity is determined by the portion of chromosomal DNA, which does not contain species-specific protein-encoding sequences and, thus, can basically make a place for novel information that will be modified to reach a new balance. In fact, the scope of the described phenomena is not limited to retroviruses as such, since the ubiquity of retroviral elements in animal genomes, their activity in germline cells [31] , along with the fact that viral replication depends significantly on RNA expression, allow retroviruses to contribute in different ways to the insertion of nonretroviral genes into animal germline cells. Finally, the ability to incorporate parts of the viral genome into the chromosomal DNA of host germline cells can vary strongly among different taxonomic groups of viruses, i.e., orders, families, genera, and even species If insertions of viral sequences remain functionally active in the host cell genome, they can give rise to either proteins that function in a new environment or untranslated RNAs of different sizes. doi = 10.1134/s0026893317020066 id = cord-310942-191m0e65 author = Boga, Jose Antonio title = Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date = 2012-04-18 keywords = IFN; TNF; cell; infection; melatonin; virus summary = The potential protective mechanisms include melatonin acting as a free radical scavenger, an antioxidant enzyme inducer, a positive regulator of immune functions and an inhibitor of inflammation, as well as a regulator of programmed cell death (PCD) [ Table 2 ]. Melatonin treatment also caused a rise in protein expression of the nuclear factor erythroid 2 (Nrf2), a transcription factor that plays a critical role by binding to the antioxidant response element in the promoter region of a number of genes encoding for antioxidant and detoxifying enzymes in several types of cells and tissues [109] . Respiratory syncytial virus infection of human respiratory epithelial cells enhances inducible nitric oxide synthase gene expression Melatonin decreases nitric oxide production and lipid peroxidation and increases interleukin-1 beta in the brain of mice infected by the Venezuelan equine encephalomyelitis virus doi = 10.1002/rmv.1714 id = cord-318551-c1qr27lg author = Boguszewska‐Chachulska, Anna M. title = Rna Viruses Redirect Host Factors to Better Amplify Their Genome date = 2005-12-29 keywords = RNA; protein; replication; virus summary = (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3'' end of (À) RNA; Leader RNA (þ), 5'' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. doi = 10.1016/s0065-3527(05)65002-6 id = cord-329527-0rlotyz3 author = Bohmwald, Karen title = Neurologic Alterations Due to Respiratory Virus Infections date = 2018-10-26 keywords = CNS; CSF; RNA; virus summary = In addition to this, a fatal case attributed to the H1N1 pandemic infection was reported, and the clinical finding showed that the cause of death was an intracerebral thrombosis and hemorrhage with presence of the virus in the brain, but not in lungs or CSF (Simon et al., 2013 ; Figure 2) . In another approximation to understand the etiologic agent causing myelopathy post-influenza-like syndrome, CSF obtained from a patient with this disease was inoculated in several cell lines, previously reported to be permissive for the growth FIGURE 2 | Influenza virus (IV) spreads from the lungs to the CNS through the vagus nerve promoting an inflammatory state. As described so far, CoVs are respiratory viruses that exhibit neurotropic capacities that not only allows them to achieve latency and avoid the immune response of the host, but also have neurological implications that can complicate the disease associated to its infection. Although there are extensive case reports that indicate neurological manifestations associated to hMPV-infection in humans, further studies are required in mice models to characterize this disease. doi = 10.3389/fncel.2018.00386 id = cord-338083-77re4l0w author = Bolin, Steven R. title = Origination and consequences of bovine viral diarrhea virus diversity date = 2005-03-04 keywords = BVDV; RNA; viral; virus summary = The genetic diversity that occurs among isolates of BVDV is characteristic of RNA viruses that exist in nature as quasispecies (a swarm of viral mutants). However, altered base sequence in this region of the viral genome has been identified after passage of the virus in cell culture, and has been detected in viral RNA that was extracted from tissues of an infected animal [20, 21] . The selection of the antigenic variants likely occurred during the acute infection of the dams of those PI cattle and resulted in transplacental transmission of slightly different BVDV to a group of fetuses. Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium Pathogenesis of primary respiratory disease induced by isolates from a new genetic cluster of bovine viral diarrhea virus type I Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus doi = 10.1016/j.cvfa.2003.11.009 id = cord-017537-ztdz4a2s author = Bologna, Mauro title = Biological Agents and Bioterrorism date = 2014-09-18 keywords = human; infection; specie; virus summary = For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] . doi = 10.1007/978-94-017-9238-7_1 id = cord-323404-3mw4q7m3 author = Bomsel, Morgane title = Entry of viruses through the epithelial barrier: pathogenic trickery date = 2003 keywords = cell; epithelial; receptor; viral; virus summary = In polarized monostratified epithelium -where the plasma membrane is divided into two domains that have a different lipid and protein composition and different membrane dynamics -viruses usually attach and penetrate the cell cytosol preferentially at the restricted pole of the by epithelial cells and cross the epithelial barrier using TRANSCYTOSIS (BOX 1), as has been described recently for the human immunodeficiency virus (HIV) 3, 4 . Similarly, human JC virus 49 and Sendai 50 virus, as well as sialyloligosaccharide-dependent strains of rotavirus 20 and reovirus, also attach themselves to epithelial cells to block or abuse normal cell processes and, as with bacteria 43 , the surface proteins of enveloped or naked viruses bind to host-cell molecules that have receptor functions. As the cell attachment receptors for numerous enveloped and naked viruses, the glycosyl epitopes of the epithelial-cell-surface proteoglycans mediate virus adhesion, in turn initiating signal transduction as described for the GLYCOSYNAPSE 54 . doi = 10.1038/nrm1005 id = cord-001065-j4hvyyoi author = Boncristiani, Humberto F. title = In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date = 2013-09-05 keywords = IAPV; PBS; bee; honey; virus summary = title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. Little is known about the specific biology of the viruses in these families that infect honey bees, although they contain important bee pathogens, such as Deformed Wing Virus (DWV) and Israeli Acute Paralysis Virus (IAPV). Post-hoc tests of main treatment effects showed significantly higher gene expression in the IAPV-inoculated bees compared to the two control groups for Actin, 28S rRNA, and mGST1. The observed gene expression patterns could be due to viral manipulation of the cells to increase virus replication or present cell compensatory responses to IAPV infection. doi = 10.1371/journal.pone.0073429 id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 keywords = SARS; bat; figure; human; virus summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . doi = 10.1016/j.ijid.2020.08.050 id = cord-265681-ab8j4o1u author = Boroomand, Zahra title = Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date = 2012-04-01 keywords = IBV; virus summary = title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay ( Table 1) . In this study, the pathogenesis of the infectious bronchitis virus isolate IRFIBV32 which was recently isolated in Iran [12] , tissue tropism, and dissemination of the virus throughout the body were evaluated following intranasal (IN) inoculation of commercial broiler chickens by RT-PCR. Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos doi = 10.1100/2012/402537 id = cord-009836-7o6htufh author = Borrow, Persephone title = Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date = 2006-04-28 keywords = CTL; HLA; response; virus summary = Epitope mapping performed using the Gpl 60 sequence of the patient''s autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. doi = 10.1111/j.1600-065x.1998.tb01206.x id = cord-018166-savdgy0u author = Bosch, Albert title = Survival and Transport of Enteric Viruses in the Environment date = 2006 keywords = enteric; soil; survival; virus; water summary = Environmental virology may be defined as the study of viruses that can be transmitted through various environments (water, sewage, soil, air, or surfaces) or food and persist enough in these vehicles to represent a health threat. Since that time, other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection in the environment, although the near eradication of poliomyelitis from the globe calls for exhaustive studies on the occurrence of wild-type and vaccinal-type polioviruses in environmental samples. The possibility nowadays to detect the presence of human enteric viruses in different types of water samples and foodstuff, in particular shellfish samples, should be a valuable tool in the prevention of waterborne and food-borne diseases. These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright, 1954) , due to the influence of these factors on virus persistence. doi = 10.1007/0-387-29251-9_6 id = cord-309179-5hlatbqe author = Bosch, Albert title = New tools for the study and direct surveillance of viral pathogens in water date = 2008-05-26 keywords = detection; virus; water summary = Main difficulties to overcome for virus detection and characterisation in water samples encompass viral diversity, occurrence of low particle numbers, particularly in drinking water, and the technical challenges of virus assays. Nucleic acid amplification techniques are currently the most widely used methods for detection of viruses in 298 Environmental Biotechnology water, which also enable to gather information of the virus genotypes occurring in the environment, thus providing most relevant epidemiological information, particularly important for the implementation and follow-up of vaccination programmes [2, 3, 4 ] . Nevertheless, as stated above, no alternative to molecular detection analysis exists for highly health significant waterborne viruses such as human norovirus and hepatitis A virus. Development, evaluation, and standardization of a real-time TaqMan reverse transcription-PCR assay for quantification of hepatitis A virus in clinical and shellfish samples doi = 10.1016/j.copbio.2008.04.006 id = cord-338331-27ic5zen author = Boulagnon, Camille title = Influenza A/H1N1 (2009) Infection as a Cause of Unexpected Out‐of‐Hospital Death in the Young date = 2012-05-14 keywords = H1N1; virus summary = In conclusion, this case report shows that influenza A/H1N1 (2009) virus can be a cause of sudden cardiac death in the young and demonstrates the importance of quantitative virological analyses for the diagnosis of myocarditis. We have reported on an unexpected sudden out-of-hospital death caused by influenza A ⁄ H1N1 (2009) infection involving a young immunocompetent and previously healthy male. In our case, virological investigations were performed, including molecular analyses of common pulmonary and cardiotropic viruses in frozen cardiac samples, as well as genetic analysis of the influenza A ⁄ H1N1 (2009) virus for both hemagglutinin and neuraminidase genes. In our case, determination of viral loads in the absence of any inflammatory infiltrate in the myocardium has shown that influenza A ⁄ H1N1 (2009) virus can be a cause of out-of-hospital unexpected death in the young. Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses doi = 10.1111/j.1556-4029.2012.02180.x id = cord-305165-3twlnkac author = Bourgueil, E. title = Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion date = 1992-04-30 keywords = PRCV; virus summary = title: Experimental infection of pigs with the porcine respiratory coronavirus (PRCV): measure of viral excretion Common causes of the disease includes pseudorabies virus (PRV), influenza viruses and the porcine respiratory coronavirus (PRCV), the latter being first detected in different European countries in 1983-1984 (Brown et al., 1986; Duret et al., 1988; Pensaert et al., 1986) . Until now, great attention has been given to clinical disorders induced by PRCV in the field (Jestin et al., 1987; Brown and Cartwright, 1986) and under experimental conditions (Vannier, 1990; Pensaert et al., 1986; O''Toole et al., 1989) , but nothing is known about excretion and airborne transmission of the virus. A high correlation rate (r= 0.83 ) was found between viral titres obtained from air samples collected with that medium and the amount of virus in nasal swabs (see tables 1 and doi = 10.1016/0378-1135(92)90136-h id = cord-048466-fj9l8che author = Bragstad, Karoline title = The evolution of human influenza A viruses from 1999 to 2006: A complete genome study date = 2008-03-07 keywords = H3N2; virus summary = BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. The influenza virus evades host immunity by accumulation of point mutations (drift) in the major surface glycoproteins, haemagglutinin (HA) and neuraminidase (NA) or by reassortment of segments from different viruses co-infecting the same cell leading to a new stain with a HA (and NA) not seen in the population before (shift). The A/Fujian/411/02(H3N2)-like clinical Danish viruses had several substitutions in HA at sites that might influence the virus'' capability for egg growth [10, 37] . Substitutions at antigenic site B and the predicted N-glycosylation at position 144 in HA antigenic site A together with a stronger NA might have contributed to the increased infectivity of the reassorted Fujian-like viruses of the 2003-2004 season, causing an epidemic in Denmark. Positive selection on the H3 hemagglutinin gene of human influenza virus A doi = 10.1186/1743-422x-5-40 id = cord-016796-g4kqqpy1 author = Bramhachari, Pallaval Veera title = Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date = 2019-11-05 keywords = PCR; RNA; ZIKV; detection; virus summary = As a part of modern research on immunotechniques, a diagnostic approach for chronic hepatitis C infection (CHC), detects specific antibody to HCV (anti-HCV) (indirect tests) and assays that can detect, quantify, or characterize components of HCV viral particles, viz. Nonetheless, recent studies on respiratory syncytial virus (RSV) developed Luciferase Immunoprecipitation Systems (LIPS) assay to detect IgG Antibodies against Human RSV G-Glycoprotein. Sensitive and specific detection of Crimean-Congo hemorrhagic fever virus (CCHFV) was developed employing specific IgM and IgG antibodies in human sera using recombinant CCHFV nucleoprotein as antigen in μ-capture and IgG immune complex (IC) ELISA tests (Emmerich et al. A rapid diagnostic platform for colorimetric differential detection of DENV and CHIKV viral infections was recently developed with a possibility to alter clinical diagnosis of acute febrile illnesses in resource-limited settings. This novel antibody demonstrates noteworthy specificity to identify H7N9 virus compared to homemade target-captured ELISA, qRT-PCR, and rapid influenza diagnostic test (RIDT) with high sensitivity (Chang et al. doi = 10.1007/978-981-15-1045-8_17 id = cord-310795-n78s0sg2 author = Brand, H. Kim title = Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis date = 2011-09-07 keywords = RSV; virus summary = This study evaluated the association between the detection of multiple viruses by RT‐PCR and disease severity in children with bronchiolitis. In RSV infected children younger than 3 months, disease severity was not associated with the number of detected viruses. Therefore, we prospectively studied the association between the detection of multiple viral pathogens by RT-PCR and disease severity in young children with bronchiolitis included during three consecutive winter seasons. As the differences in age between the groups may have influenced our results, we also evaluated the association between disease severity and the detection of multiple viruses in children diagnosed with RSV bronchiolitis younger and older than 3 months (Fig. 2) . In the present study, we evaluated the viral etiology in young children with bronchiolitis during three consecutive winter seasons and examined the association between the detection of two or more viruses by RT-PCR and disease severity. doi = 10.1002/ppul.21552 id = cord-000804-0hlj6r10 author = Brauburger, Kristina title = Forty-Five Years of Marburg Virus Research date = 2012-10-01 keywords = EBOV; Ebola; MARV; Marburg; RNA; VP40; virus summary = doi = 10.3390/v4101878 id = cord-003817-k3m72uxw author = Braun, Elisabeth title = Furin‐mediated protein processing in infectious diseases and cancer date = 2019-08-05 keywords = Env; cell; cleavage; furin; protein; virus summary = For example, avirulent Newcastle disease virus (NDV) strains harbour a monobasic cleavage site in their Fusion (F) protein and result only in local infections (mainly in the respiratory tract) since expression of the respective host proteases is limited to a few cell types. Notably, proteolytic processing of Env depends on correct N-linked glycosylation as aberrant carbohydrate side chains may result in subcellular mistrafficking or sequestration of Env. 49 Most likely, HIV-1 takes advantage of the redundancy of several proprotein convertases recognising the polybasic cleavage motif in Env. Furin, PCSK5, PCSK6 and PCSK7 have all been shown to cleave gp160 in cells, albeit with different efficiencies. 59, 60 Notably, a subset of H9N2 lowly pathogenic avian influenza A virus strains also harbour R-S-K-R↓ or R-S-R-R↓ sites that are not only cleaved by trypsin-like proteases, such as TMPRSS2 or HAT, but also by PCSKs. 61 However, their cleavage is only efficient in the presence of very high amounts of furin or upon mutation of a glycosylation site in HA. doi = 10.1002/cti2.1073 id = cord-021499-up5vftj4 author = Brayton, Cory title = Viral Infections date = 2007-09-02 keywords = Barthold; Council; MHV; MPV; National; Research; infection; mouse; virus summary = Depending on inoculation route, dose, strain, and age of mice, experimental infections may result in inflammation or cytomegaly with inclusion bodies in a variety of tissues, pneumonitis, myocarditis, meningoencephalitis, or splenic necrosis in susceptible strains (National Research Council, 1991; Osborn, 1982; Percy and Barthold, 2001) . Both strains are apathogenic for adult mice, but the immunosuppressive variant is more pathogenic for neonatal mice than is MMVp. Serological surveys show that the mouse is the primary natural host (Parker et al., 1970; Smith et al., 1993b; Singleton et al., 2000) , but the virus is also infective for rats, hamsters (Garant et al., 1980; Ward and Tattersall, 1982) , and Mastomys (Haag et al., 2000) during foetal development or after parenteral inoculation. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS, and intestine. doi = 10.1016/b978-012336425-8/50076-5 id = cord-296635-8r3tm966 author = Breed, Andrew C. title = Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date = 2011-12-14 keywords = Hendra; Pteropus; infection; virus summary = title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. doi = 10.1371/journal.pone.0028816 id = cord-014541-2i0jga5v author = Breedlove, Byron title = The Exploding Aliveness of the World date = 2017-04-17 keywords = virus summary = "The exploding aliveness of the world" that fuels artistic creativity also finds full expression in dynamic microscopic realms teeming with unfathomable numbers of viruses, bacteria, fungi, prions, and protozoa that lead to an incredible variety of pathologic consequences when infecting their hosts. Those influential reports-which represent the insights of Joshua Lederberg, Robert Shope, and their colleagues-from the Institute of Medicine (now National Academy of Medicine) Committee on Emerging Microbial Threats offered far-reaching recommendations and galvanized support for research and public health action to address the challenges posed by new, emerging, and reemerging infectious diseases. The time and attention given to tending to our backyard gardens, our larger communities, our public health infrastructure, and our approach to addressing emerging infections will be apparent and on display when that inevitable exploding aliveness occurs. Emerging infections: microbial threats to health in the United States doi = 10.3201/eid2304.ac2304 id = cord-027752-xcpv9k22 author = Bresalier, Michael title = Uses of a Pandemic: Forging the Identities of Influenza and Virus Research in Interwar Britain date = 2011-12-15 keywords = Fletcher; Influenza; Laidlaw; MRC; NIMR; Research; virus summary = In May 1922, Walter Morley Fletcher, Secretary of the Medical Research Council (MRC), organized a secret meeting of pathologists at the War Office to outline a new scheme of research on ''diseases probably caused by filter-passing organisms.'' 1 Created in 1913, the MRC had used the war to apply laboratory science to military medicine. The pandemic had ignited interest in the nature of filterable viruses, however, the way forward was unclear, as Fletcher observed: ''The chief problem which the investigator of [filterable viruses] meets is the difficulty of proceeding by sound experimental methods.'' 3 The purported influenza agent was one of a group of pathogens that could not be seen with light microscopes or studied by the culture methods that had been so successful with bacteria. 11 Especially important were military pathology investigations, supported by the War Office and MRC, into the bacteriology of the pandemic and, in due course, into the role of a ''filterable virus''. doi = 10.1093/shm/hkr162 id = cord-254592-wa5il5go author = Brierley, Liam title = Tissue tropism and transmission ecology predict virulence of human RNA viruses date = 2019-11-26 keywords = RNA; human; virulence; virus summary = To quantify the effects of the most informative risk factors, averaged partial dependence was extracted from the random forests, describing the marginal predicted probabilities of severe virulence associated with each virus trait (Fig 4, S2 Table) . Predicted probability of classifying virulence as ''severe'' for each of the most informative risk factors in random forest models applied to all known human RNA viruses and zoonotic viruses only (primary tissue tropism, any known neural tropism, any known renal tropism, level of human-to-human transmissibility, primary transmission route, and any known vector-borne transmission). In both classification tree and random forest models, viruses were more likely to be predicted to cause severe disease if they caused systemic infections, had neural or renal tropism, transmitted via direct contact or respiratory routes, or had limited capability to transmit between humans (0 < R 0 � 1). doi = 10.1371/journal.pbio.3000206 id = cord-315339-dcui85lw author = Broadbent, Andrew J. title = Respiratory Virus Vaccines date = 2015-03-13 keywords = CD8; RSV; SARS; cell; influenza; respiratory; vaccine; virus summary = Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . doi = 10.1016/b978-0-12-415847-4.00059-8 id = cord-022163-7klzsrpu author = Broder, Christopher C. title = Henipaviruses date = 2016-09-09 keywords = CNS; Hendra; Nipah; infection; virus summary = Central pathological features of both HeV and NiV infection in humans and several susceptible animal species is a severe systemic and often fatal neurologic and/or respiratory disease (Abdullah and Tan 2014 ; Wong and Ong 2011 ; Playford et al. A new paramyxovirus was isolated and identifi ed in 1994 in an outbreak of fatal cases of respiratory disease in horses and humans in the Brisbane suburb of Hendra, Australia, and was shown to be distantly related to measles virus and other morbilliviruses (Murray et al. HeV in nature appears less transmissible and naturally acquired infections have been observed only in bats, horses, dogs and humans; however, experimentally, HeV can infect and cause disease in guinea pigs, cats, hamsters, ferrets, mice and African green monkeys (reviewed in Geisbert et al. More recently, several viral vector-based henipavirus vaccines have also been examined in animal challenge studies; these have included immunizations using the vesicular stomatitis virus based platform (VSV) expressing either the NiV G or F glycoprotein in the hamster model (DeBuysscher et al. doi = 10.1007/978-3-319-33133-1_3 id = cord-019982-hyxrgamj author = Brookfield, D.S.K. title = Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles date = 2005-04-14 keywords = Salaam; virus summary = authors: Brookfield, D.S.K.; Cosgrove, B.P.; Bell, E.J.; Madeley, C.R. title: Viruses demonstrated in children in Tanzania: Studies in diarrhoea and measles Causes of diarrhoea with particular reference to viral agents were investigated in 123 infants and young children in Dar es Salaam, Tanzania. The pattern of virus infection causing infantile diarrhoea was similar in Dar es Salaam to other parts of the world. The present study attempted to investigate the viruses associated with diarrhoea in Dares Salaam and, since electron microscopy was considered essential, the study was limited to the number of stools that could be sent in one consignment by air to Scotland. Examination of stools from 26 cases of measles failed to implicate any particular virus as a likely cause of the associated diarrhoea. However the diarrhoea associated with measles in Tanzanian children does not appear to be caused by any of the electron microscopically detectable viruses. doi = 10.1016/s0163-4453(79)91285-4 id = cord-002410-2zi5iv2t author = Bruening, Janina title = The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy date = 2017-02-01 keywords = HCV; IFNL; hepatitis; virus summary = Among the three classes of IFNs, type III IFNs, also called IFN lambdas (IFNLs), are an essential component of the innate immune response to hepatitis C virus (HCV). Here, we will review our current knowledge on IFNL gene expression, protein properties, signaling, ISG induction, and its implications on HCV infection and treatment. Type III IFNs and ISGs are similarly inducted upon HCV infection of primary human fetal liver cells [98, 99] . In summary, expression of specific IFNL subtypes is induced in PHH and some hepatoma cell lines upon infection with HCV, resulting in limiting virus production. Viral infection and toll-like receptor agonists induce a differential expression of type I and interferons in humans plasmacytoid and monocyte-derived dendritic cells HepG2 cells mount an effective antiviral interferon-lambda based innate immune response to hepatitis C virus infection HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons doi = 10.1155/2017/7232361 id = cord-023584-yaxawqhj author = Bucknall, R.A. title = The Continuing Search for Antiviral Drugs date = 2008-04-10 keywords = antiviral; compound; disease; test; virus summary = Of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (Bauer and Sadler, 1960) and possibly adenoviruses (Bauer and Apostolov, 1966) ; l-aminoadamantane is active only against influenza A1 and As and not against other myxo-or paramyxoviruses (Davies et al., 1964) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (RNA) viruses (Eggers and Tamm, 1961) . In summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. doi = 10.1016/s1054-3589(08)60460-3 id = cord-171099-d0qr84xg author = Buehler, Markus J. title = Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date = 2020-03-30 keywords = protein; sound; structure; virus summary = Presenting musical encoding in two versions one in the amino-acid scale and one based on equal temperament tuning the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across lengthand time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodiesforming counterpoint music -reflecting the complex hierarchical intersecting geometry of the protein. doi = nan id = cord-337361-salby0fu author = Bujarski, Jozef J. title = Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date = 2013-03-26 keywords = BMV; RNA; recombination; viral; virus summary = In some viruses, the frequency of homologous crossing-over is very high and practically every replicated viral RNA molecule can be considered as chimerical in nature, as we have demonstrated for brome mosaic virus (BMV) RNAs (Urbanowicz et al., 2005) . The generally accepted mechanism of RNA recombination is currently explained by a copy-choice model where the viral RNA polymerase (RdRp) complex in mRNA viruses [reverse transcriptase (RT) in retroviruses] changes templates during synthesis of the nascent strand (Galetto et al., 2006) . Among the factors known to promote replicase to switch are sequence homologies between recombination substrates along with secondary structures at the crossover sites, as demonstrated with the BMV and other systems (Figlerowicz and Bujarski, 1998; Nagy et al., 1999b) . Comparison among three plant RNA virus replication systems (TBSV, BMV, and dianthoviruses) reveals general patterns within the stepwise process of viral replicase complex assembly which requires concerted involvement of protein-protein, RNA-protein, and protein-lipid interactions (Mine and Okuno, 2012) . doi = 10.3389/fpls.2013.00068 id = cord-016309-6mw8okmt author = Bule, Mohammed title = Antivirals: Past, Present and Future date = 2019-06-06 keywords = RNA; antiviral; dna; drug; feline; virus summary = Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives'' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al. doi = 10.1007/978-981-13-9073-9_22 id = cord-262776-6k7tcgfs author = Burnouf, Thierry title = Assessment of the viral safety of antivenoms fractionated from equine plasma date = 2004-09-30 keywords = RNA; antivenom; horse; plasma; viral; virus summary = Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. Among those, caprylic acid and low pH treatments, both of which are commonly used also for the purification of antivenom IgG, have been shown to contribute to the viral safety of human plasma IgG products as described below. It should be kept in mind that treatment of whole plasma or crude fractions, as is the case for equine antivenoms production, may lead to lower rate and kinetics of viral inactivation, due to the high endogenous lipid content, as found in a study that evaluated the virucidal effect of sodium oleate [85] . However, a comparison with validated manufacturing processes used for human IgG clearly indicates that at least two widely used antivenom production steps, caprylic acid treatment and low-pH incubation, are likely to contribute in a robust manner to viral safety, at least against enveloped viruses. doi = 10.1016/j.biologicals.2004.07.001 id = cord-355913-fhvt1ht1 author = Burrell, Christopher J. title = Virus Replication date = 2016-11-11 keywords = RNA; cell; dna; protein; viral; virus summary = Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. doi = 10.1016/b978-0-12-375156-0.00004-7 id = cord-257220-fe2sacjj author = Butler, J. E. title = Porcine reproductive and respiratory syndrome (PRRS): an immune dysregulatory pandemic date = 2014-07-01 keywords = IFN; PRRSV; cell; porcine; respiratory; virus summary = LDV elevates IgG levels in mice with little production of virus-specific antibodies [11, 21] , which is almost identical to what is seen in isolator piglets infected with PRRSV [22] (''''The effect of age, rearing, complement and the role of mucosal immunity'''' section). Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-induced pigs The presence of alpha interferon at the time of infection alters the innate and adaptive immune responses to porcine reproductive and respiratory syndrome virus Interferon type I response in porcine reproductive and respiratory syndrome virus-infected MARC-145 cells Antigen-specific B cell responses to porcine reproductive and respiratory syndrome virus infection Antibody production and blastogenesis response in pigs experimentally infected with porcine reproductive and respiratory syndrome virus Neutralizing antibody responses of pigs infected with natural GP5 N-glycan mutants of porcine reproductive and respiratory syndrome virus doi = 10.1007/s12026-014-8549-5 id = cord-323683-9h9mld6x author = Butler, M. title = Virus Removal by Disinfection of Effluents date = 2013-11-17 keywords = chlorine; effluent; treatment; virus; water summary = The removal of viruses from sludges has only relatively recently attracted serious attention (Cliver, 1975; Berg, 1978; Osborn and Hattingh, 1978) but for effluents, various procedures have been adopted for some time, particularly disinfection with chlorine, a treatment now under critical review. Although many different enteric viruses are likely to be present in wastewater, the risks of transmission of infection via contaminated water in developed countries by various routes (Fig. 1 ) is thought to be slight although probably increasing, but elsewhere the risks may be very great indeed (WHO, 1976) . 4. The methods available for the inactivation of viruses in effluent differ little in principle from those applied to potable water, but are distinct from the disinfection of viruses contaminating, laboratory or medical equipment, where highly toxic chemicals like detergents, phenols, formaldehyde or permanganate may be used (Spalding et al 1977) . doi = 10.1016/b978-0-08-026401-1.50025-7 id = cord-297960-4x1j0iqg author = Bösl, Korbinian title = Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date = 2019-10-04 keywords = figure; host; protein; viral; virus summary = Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Global systems-level approaches including functional RNAi screens, interactome mapping technologies such as affinity-purification mass spectrometry (AP-MS), quantitative proteomics, and CRISPR/Cas9-based screens have provided unparalleled details and insights into the dynamics of host proteome in immune cells (21) (22) (23) (24) , host-virus interactome (15-17, 25, 26) , and also identified important host dependency factors of various viruses (25, 27, 28) . We hypothesized that combining a meta-analysis of host-virus protein-protein interactions of multiple viruses and functional RNAi screens would provide novel insights for developing broadspectrum antiviral strategies. High-Definition analysis of host protein stability during human cytomegalovirus infection reveals antiviral factors and viral evasion mechanisms doi = 10.3389/fimmu.2019.02186 id = cord-003993-3bozjfv7 author = Cagliani, Rachele title = Mode and tempo of human hepatitis virus evolution date = 2019-10-25 keywords = Fig; HBV; HCV; hepatitis; virus summary = Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. This finding, as well as the increasing availability of the genome sequences of human-infecting viruses sampled across different geographic areas, has largely expanded our knowledge about the genetic diversity and evolutionary origin of these human pathogens. Studies that did not account for the TDRP provided estimates of the time to the most recent common ancestor (TMRCA) of HCV genotypes in a range between $200 and 1000 years ago [63, 64, 76, 87, 88] ; the origin of the horse virus was dated around 1800 CE [85] . Although several human hepatitis E cases have a zoonotic origin and orthohepeviruses A are found in diverse mammals, recent data indicated that one or more reverse zoonoses led to the emergence and radiation of HEV genotypes [121] . doi = 10.1016/j.csbj.2019.09.007 id = cord-290539-8ak2tths author = Cagno, Valeria title = Novel broad spectrum virucidal molecules against enveloped viruses date = 2018-12-07 keywords = Fig; HSV-2; cell; compound; virus summary = To further elucidate the mechanism of action we performed a virucidal assay in which 9d was incubated with the virus at 10 μM 5μM or 1μM concentration for different times (Fig 6A) or for 1h with serial dilutions of compound ( Fig 6B) ; subsequently, the mixture was titrated on cells and the viral titer was evaluated at dilutions at which the compound concentration was known not to be active in plaquing efficiency assays. The irreversibility of the mechanism was also tested with an assay in which the compound was incubated with the virus for 1h and subsequently the mixture has been diluted in drug free medium for additional 1, 2, 3 or 4 hours before the addition on cells (S2 Fig) . doi = 10.1371/journal.pone.0208333 id = cord-286219-qcx5ehnh author = Calistri, Arianna title = The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date = 2014-05-06 keywords = HIV-1; Vpr; Vpu; protein; viral; virus summary = In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. Furthermore, small DNA viruses with known oncogenic activity, such as the human papillomavirus (HPV), adenoviruses and polyomaviruses, take control of the cell cycle by usurping specific cellular Ub ligase complexes to target crucial cell cycle regulators such as p53 and the protein of the retinoblastoma (pRB) for degradation [58] . In addition to this important function, which is likely required for proper trafficking and maturation of the viral envelope glycoproteins, Vpu has been more recently characterized for yet another crucial role, connected with the ability of the virus to evade a specific IFN-1 induced antiviral factor: the B cell stromal factor 2 (BST-2) or tetherin. doi = 10.3390/cells3020386 id = cord-344889-1y4ieamp author = Cameron, Robert J. title = Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date = 2006-05-24 keywords = COPD; PCR; respiratory; virus summary = OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients. doi = 10.1007/s00134-006-0202-x id = cord-023724-5at0rhqk author = Cann, Alan J. title = Infection date = 2015-07-24 keywords = IFN; MHC; RNA; cell; dna; infection; virus summary = The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. doi = 10.1016/b978-0-12-801946-7.00006-7 id = cord-277392-s0bldxg9 author = Cann, Alan J. title = Replication date = 2012-02-29 keywords = cell; chapter; figure; replication; virus summary = This simple step is the key to the entire experiment, because it effectively synchronizes the infection of the cells and allows the subsequent phases of replication in a population of individual cells and virus particles to be viewed as if they were a single interaction (in much the same way that molecular cloning of nucleic acids allows analysis of populations of nucleic acid molecules as single species). (At the time, it was generally believed that proteins, which consist of a much more complex mixture of more than 20 different amino acids, were the carriers of the genes and that DNA was probably a structural component of cells and viruses.) Together, these two experiments illustrate the essential processes of virus replication. n Fusion of the virus envelope (so this is only applicable to enveloped viruses) with the cell membrane, either directly at the cell surface or following endocytosis in a cytoplasmic vesicle (Figure 4.12) , which requires the presence of a specific fusion protein in the virus envelopedfor example, influenza hemagglutinin or retrovirus transmembrane (TM) glycoproteins. doi = 10.1016/b978-0-12-384939-7.10004-3 id = cord-203232-1nnqx1g9 author = Canturk, Semih title = Machine-Learning Driven Drug Repurposing for COVID-19 date = 2020-06-25 keywords = SARS; drug; sequence; virus summary = Using the National Center for Biotechnology Information virus protein database and the DrugVirus database, which provides a comprehensive report of broad-spectrum antiviral agents (BSAAs) and viruses they inhibit, we trained ANN models with virus protein sequences as inputs and antiviral agents deemed safe-in-humans as outputs. Using sequences for SARS-CoV-2 (the coronavirus that causes COVID-19) as inputs to the trained models produces outputs of tentative safe-in-human antiviral candidates for treating COVID-19. For Experiment II, we split the data on virus species, meaning the models were forced to predict drugs for a species that it was not trained on, and have to detect peptide substructures in the amino-acid sequences to suggest drugs. In post-processing, we applied a threshold to the sigmoid function outputs of the neural network, where we assigned each drug a probability of being a potential antiviral for a given amino acid sequence. doi = nan id = cord-002728-6oyw5sqv author = Carding, S. R. title = Review article: the human intestinal virome in health and disease date = 2017-09-04 keywords = human; phage; virome; virus summary = 2 With the advent of new, sequence-based technologies that do not rely on the ability to isolate viruses for their identification, it is now possible to define and characterise viruses in different environmental samples in greater detail than ever before, which has resulted in an increased interest in the role the viral assemblage of the human gut microbiota plays in health and disease. The genetic content of VLPs comprising bacteriophages (phages) that infect bacteria and archaea and, to a much lesser extent, human-, plant-, amoebae-and animal-infecting viruses found along the GI tract constitute the human intestinal virome (Figure 1 ). Analyses of metagenomic sequence data provide detailed information on phage-host and phage-phage competition within the human faecal microbiome, implying CRISPR spacers are actively and continuously acquired by prokaryotes in response to the presence of phages in the GI tract. doi = 10.1111/apt.14280 id = cord-342277-v6310fjh author = Carducci, A. title = Environmental survey to assess viral contamination of air and surfaces in hospital settings date = 2011-01-31 keywords = PCR; TTV; virus summary = The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. Moreover, viral agents transmitted via the faecaleoral route, such as rotavirus, human adenovirus 40 and 41 and norovirus, are frequently associated with healthcare setting infections spread by air, hand and surface contamination. The nucleic acids extracted from samples were analysed according to published protocols of nested (RT)ePCR to detect and distinguish the target viruses: the primers, virus genome regions and reaction conditions are reported in Table I . Although this is particularly true for viruses, where detection on surfaces and in air is very difficult, the low reliability of bacterial counts as indicators of viral contamination, suggests studying alternative parameters for assessing virological safety. doi = 10.1016/j.jhin.2010.10.010 id = cord-287770-oxfnt2n4 author = Caricati, C. P. title = Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date = 2013-06-27 keywords = SAI; inactivation; viral; virus summary = title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. The main steps are cited in sequential order (a) ammonium sulfate precipitation of immunoglobulins, (b) pepsin digestion to obtain F(ab'')2 fragments, (c) caprylic acid precipitation of nonimmunoglobulin proteins, (d) heat treatment, (e) ammonium sulfate precipitation of F(ab'')2 fragments, (f) tangential filtration, (g) ion-exchange chromatography, (h) tangential filtration, and (i) phenol addition. 34 We found no reports using both viruses as models for viral inactivation concerning the described purification steps. 52, 55 Phenol inactivated both viruses, which indicates that it might also be an effective preservative for human-derived immunoglobulins, when it comes to viral safety. doi = 10.1002/btpr.1758 id = cord-267194-i6vetquk author = Carman, William F. title = The pathogens date = 2007-10-31 keywords = NL63; RSV; virus summary = In a number of occasions, patients can have a severe lower respiratory tract infection, with no bacteriological cause and the only pathogen found is rhinovirus. hMPV causes both upper and lower tract infections and the signs and symptoms are very similar to those caused by RSV ranging from mild rhinorrhea associated with common colds to severe cough, wheezing, bronchiolitis and pneumonia (Konig et al., 2004; Van den Hoogen et al., 2001) . Although the main clinical symptoms are those of severe respiratory tract disease, the virus also infected other organs. NL63 is predominantly a common cold virus like OC43 and 229E that can cause lower respiratory tract disease in young children, the elderly and immunocompromised patients. HBoV has been associated with both upper and lower tract infections with prevalences ranging from 1% to 19%, with most reports indicating prevalences in the range of 3−6% in hospitalized children <5 years with ARI. doi = 10.1016/s1386-6532(07)70003-3 id = cord-004848-2cfphi88 author = Carter, M. J. title = Transcription of feline calicivirus RNA date = 1990 keywords = FCV; RNA; virus summary = In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3'' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3'' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3'' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules. doi = 10.1007/bf01310744 id = cord-023293-te0n2vvp author = Carter, M. J. title = Caliciviruses date = 2005-10-18 keywords = SRSV; non; virus summary = Antibodies to SMSV were also found in some land animals including potential scavengers such as foxes, and the virus was also obtained from a fish preyed on by sealions thus raising the possibility that SMSV could be transmitted through food.'' SMSV is serologically distinct from vesicular exanthema of swine virus (VESV), but the viruses are clearly related by RNA homology, and are also similar in terms of the cells in which the virus can replicate in culture. These include the small round structured viruses (SRSV) which are also associated with diarrhoea, and the virus causing enterically transmitted non-A, non-B hepatitis now termed hepatitis E virus (HEV). Most of the increases in serum titre took place between the ages of 14-36 months.23 Broadly similar results were obtained in studies performed in Ecuador and the phi lip pine^.^^^^^ Volunteers infected with Norwalk virus commonly develop vomiting and diarrhoea, often associated with headache and abdominal discomfort.26 Illness generally lasts 24-48 hours. doi = 10.1002/rmv.1980010307 id = cord-309489-ubf55eux author = Carvalho, John J. title = OUR COMMON ENEMY: COMBATTING THE WORLD''S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date = 2009-02-19 keywords = AIDS; HIV; dengue; virus summary = Of the emerging viruses, five have particular importance for what scientists and world leaders can learn concerning their impact on geopolitical stability, human rights, and equity health care for the underprivileged in both developed and developing nations. For example, in Latin America, population growth and uncontrolled migration from the countryside to the cities have resulted in poor housing conditions, inappropriate disposal of waste, and lack of adequate food, clean water and health care-all of which are concurrent with an increase in infected mosquitoes carrying different versions of dengue virus (Torres and Castro 2007) . Continuing with these themes, it is clear that the geographical expansion of three viruses (HIV, dengue, and rotavirus), the increase in frequency of the infectious diseases they cause, and the relationship between these viruses and geopolitical stability, human rights, and equity health care for developing nations are problems of great concern promoted not only by biological and technological factors but also by social, religious, and cultural ones. doi = 10.1111/j.1467-9744.2009.00985.x id = cord-245161-xbw72k4m author = Castano, Nicolas title = Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date = 2020-05-23 keywords = PCR; SARS; disinfectant; disinfection; fomite; surface; transmission; virus summary = Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface. doi = nan id = cord-298214-ivu4erpq author = Castrignano, Silvana Beres title = The metagenomic approach and causality in virology date = 2015-04-01 keywords = Koch; virus summary = 9, 13, 16 Among these recent propositions, both the criteria of Mokili et al, 16 based on the comparison of metagenomic characteristics among infected and healthy individuals, and the criteria of Lipkin, 13 who grouped laboratory, clinical and epidemiological data into three certainty levels to establish an association between pathogens and diseases, considered the inoculation of the infectious agent in a healthy individual as INTRODUCTION a criterion for the confirmation of causality (this criterion was inherited from Koch''s postulates). This virus was identified in human Merkel cell carcinoma (MCC) samples, 8 and the investigation of the causal association between MCV and the disease began with the investigation of 10 MCC samples from different patients; of these, the viral genome was detected in eight samples. doi = 10.1590/s0034-8910.2015049005475 id = cord-003044-9uqa39j9 author = Cervera, Héctor title = Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date = 2018-03-19 keywords = RNA; TEV; fitness; gene; virus summary = doi = 10.1093/molbev/msy038 id = cord-290385-0smnl70i author = Chan, Jasper F.W. title = Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date = 2016-03-03 keywords = Aedes; Brazil; DENV; ZIKV; Zika; infection; virus summary = Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected "congenital Zika syndrome", while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. ZIKV RNA could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 Perinatal transmission of other arboviruses, including DENV, CHIKV, WNV, and YFV, has also been reported. 115,120 74/ 8750 (0.8%) patients with suspected ZIKV infection in the French Polynesia outbreak developed neurological syndromes after presenting with a Zika fever-like illness. Zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital ZIKV infection. doi = 10.1016/j.jinf.2016.02.011 id = cord-283964-k3hy2ewx author = Chan, Jasper Fuk-Woo title = Cross-species transmission and emergence of novel viruses from birds date = 2015-01-31 keywords = avian; novel; virus summary = Birds may act as a vehicle for vector dissemination, an amplifying host in bird-vector-bird cycles, or the gene source of emerging viruses in cross-species virus transmission ( Figure 1) Sixteen of 18 hemagglutinin (HA) subtypes and nine of 11 neuraminidase (NA) subtypes of influenza viruses can be found in birds, especially waterfowl and shorebirds [2 ] . A study using influenza viruses generated with gene segments originating from circulating avian influenza viruses and the 1918 pandemic A(H1N1) virus showed that substitutions in the HA, PB2 and PA are important for virulence and efficient transmission in ferrets [35] . Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds doi = 10.1016/j.coviro.2015.01.006 id = cord-329857-pcsuu597 author = Chan, Kuan Rong title = Fc receptors and their influence on efficacy of therapeutic antibodies for treatment of viral diseases date = 2015-11-02 keywords = ADCC; antibody; virus summary = The binding affinity of antibodies to viruses can directly impact the efficacy of mAbs [4] , suggesting that target-specific mechanisms likely account for much of the efficacy of therapeutic mAbs. However, many studies have also highlighted the contribution of Fc-mediated immune effector functions in modulating the efficacy of these mAbs [5] . FcgRs have been shown to be important in modulating the efficacy of therapeutic mAbs [5] due to their involvement in FcgRmediated phagocytosis, cytokine production, ADCC and complement-dependent cytotoxicity (CDC) that aids in virus neutralization (FIGURE 1). Given the importance of FcgRs in mediating virus neutralization and Fc effector functions, a better understanding of how therapeutic antibodies neutralize virus infections in FcgRbearing cells will impact implementation of dosing regiments and allow development of improved therapeutic antibodies against infectious diseases. Given the importance of Fc-FcgR interaction in antibodymediated effector functions, Fc modification could lead to the development of therapeutic antibodies with improved interaction to activating FcgRs. This could enhance FcgR-mediated uptake, cytokine production, antigen presentation, ADCC and CDC. doi = 10.1586/14787210.2015.1079127 id = cord-336225-ijodhrwf author = Chang, Mee Soo title = Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease date = 2013-06-03 keywords = SFTS; virus summary = title: Severe Fever with Thrombocytopenia Syndrome: Tick-Mediated Viral Disease A small tick Haemaphysalis longicornis called ''Sochamjindeugi'' in Korean has bitten a week before, and an onset is characterized by fever, lymph node swelling, diarrhea, thrombocytopenia, leucocytopenia, multiorgan dysfunction, altered consciousness, and occasionally to death in extreme cases (1, 2) . This emerging febrile disease, severe fever with thrombocytopenia syndrome (SFTS), was reported in 2007 by the New England Journal of Medicine (3) and Clinical Infectious Diseases (4) (5) (6) . The vaccine development to combat the SFTS virus is not easy due to its characteristics. Also any treatment by killing the virus is able to give human damage. Severe Fever with Thrombocytopenia Syndrome confirmed cases and follow-up measure Document for physicians about Severe Fever with Thrombocytopenia Syndrome (SFTS) Epidemiologic features of severe Fever with thrombocytopenia syndrome in China Person-to-person transmission of severe fever with thrombocytopenia syndrome bunyavirus through blood contact doi = 10.3346/jkms.2013.28.6.795 id = cord-297131-3a9vjpvn author = Charlton Hume, Hayley K. title = Synthetic biology for bioengineering virus‐like particle vaccines date = 2018-12-31 keywords = VLP; like; vaccine; virus summary = Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. Seconded by a multitude of tools, such as omics technologies, structural biology, system immunology, and bioinformatics and computational biology, one can now screen for pathogen-specific antigens with high immunogenic potential and apply that information to rationally design modern VLP vaccines ( Figure 1 ). Virus-like particles as a highly efficient vaccine platform: Diversity of targets and production systems and advances in clinical development Synthetic biology design to display an 18 kDa rotavirus large antigen on a modular virus-like particle Integrated molecular and bioprocess engineering for bacterially produced immunogenic modular virus-like particle vaccine displaying 18 kDa rotavirus antigen A novel virus-like particle based vaccine platform displaying the placental malaria antigen VAR2CSA doi = 10.1002/bit.26890 id = cord-310255-aixq5mhf author = Charlton, Frank W. title = Ion Channels as Therapeutic Targets for Viral Infections: Further Discoveries and Future Perspectives date = 2020-08-03 keywords = CFTR; channel; virus summary = More recent evidence highlights how viruses can regulate and/or depend on the ion channels expressed by host cells, highlighting them as new host targets for therapeutic intervention (reviewed by Hover et al., 2017) [14] . We then discuss how intracellular ion channels contribute to the Two-pore channels 1 and 2 (TPC1/2) Gunaratne et al., 2018 [34] Severe fever with thrombocytopenia syndrome virus (SFTSV) Unknown channel Li et al., 2019 [35] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Two-pore channel 2 (TPC2) Ou et al., 2020 [36] Bunyamwera orthobunyavirus (BUNV) Two-pore domain K + (K 2P ) Hover et al., 2016/18 [28, 37] Hazara orthonairovirus (HAZV) Unknown K + channel Punch et al., 2017 [38] Charlton et al., 2019 [39] Human immunodeficiency virus (HIV) G-Protein coupled inwardly rectifying K + (GIRK) ATP-sensitive K + K ATP Dubey et al., 2019 [40] Merkel cell polyomavirus (MCPyV) doi = 10.3390/v12080844 id = cord-274306-cxvnv8dy author = Chastel, C. title = Émergence de virus nouveaux en Asie : les changements climatiques sont-ils en cause ? date = 2004-11-30 keywords = H5N1; Hong; Kong; virus summary = L''Asie, en particulier la Chine et le Sud-est asiatique, a également connu l''émergence de viroses humaines graves, telles que la dengue hémorragique (les Philippines, 1954) ou plusieurs pandémies grippales, la grippe asiatique (N2H2) en 1957, la grippe de Hong-Kong (H3N2) en 1968, et la grippe russe (H1N1) en 1977. Mais, c''est surtout au cours des dix dernières années que les émergences virales s''y sont multipliées avec l''apparition de la fièvre hémorragique à virus Alkhurma en Arabie Saoudite (1995), de la grippe aviaire H5N1 à Hong-Kong, en 1997, de l''encéphalite à virus Nipah en Malaisie, en 1998, et surtout du SRAS, en Chine du sud en 2002. Depuis l''extermination des porcs infectés, on a plus signalé de cas d''encéphalite à virus Nipah, mais il convient de rester vigilant car les roussettes et les porcs sont très nombreux dans tout le Sud-est asiatique. doi = 10.1016/j.medmal.2004.07.027 id = cord-340042-intxyu46 author = Chaudhry, Sundas Nasir title = New insight on possible vaccine development against SARS-CoV-2 date = 2020-09-11 keywords = COVID-19; CoV-2; SARS; vaccine; virus summary = In December 2019, a novel virus, namely COVID-19, caused by SARS-CoV-2, developed from Wuhan, Hubei territory of China, which used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Different subunits of spike proteins like the S1 and S2 subunits, and the receptor-binding domain (RBD) are the critical elements for the formation of a vaccine against the newly emerged virus that helped in producing T cell responses and protective immunity against SARS-CoV-2 [29] . The recombinant protein is known as one of the emerging fields for the development of a vaccine against viruses due to several properties including tight binding to specific ACE-2 receptor, provoke immune protection against viral infections, increase antibody-dependent viral entry, and promote antigenicity against virus like SARS-CoV [52] . doi = 10.1016/j.lfs.2020.118421 id = cord-314825-fzba05wn author = Chauhan, Ravendra P. title = A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide date = 2020-05-08 keywords = H1N1; H1N2; H3N2; IAV; IDV; swine; virus summary = doi = 10.3390/pathogens9050355 id = cord-018319-tylkbh4h author = Chemaly, Roy F. title = Respiratory Viruses date = 2011-01-04 keywords = HSCT; RSV; infection; respiratory; virus summary = Historically, the most common causes of respiratory infections in cancer patients were thought to be opportunistic bacteria and fungi, but newer diagnostic methods have revealed that respiratory viruses can cause serious morbidity and mortality in such patients, including leukemia patients and hematopoietic stem cell transplant (HSCT) recipients. Many viruses are known to cause respiratory tract infections, but the most common in hospitalized cancer patients are influenza viruses, respiratory syncytial virus (RSV), and parainfluenza viruses (PIV) [1, 2] . Although the combination of ribavirin and intravenous immunoglobulin (IVIG) or palivizumab has not been evaluated in a randomized trial, it is sometimes used in severely ill patients with RSV pneumonia, especially HSCT recipients, given that they have high mortality rates from this infection [3, 11, 14] . However, because other viruses can produce the same syndrome and influenza infection can produce other respiratory syndromes, a confirmatory test detecting the virus or viral antigens in nasal washes, throat swabs, respiratory tract secretions, or bronchoalveolar lavage specimens is needed in sporadic cases and in immunocompromised patients. doi = 10.1007/978-1-60761-644-3_32 id = cord-257321-l1swyr6g author = Chen, Lihong title = DRodVir: A resource for exploring the virome diversity in rodents date = 2017-05-20 keywords = bat; rodent; virus summary = The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases. To facilitate online data analysis, two visualization tools are integrated into the result table: i) a statistical pie chart is available with a single click on the column title of virus family, rodent species/family, sample type and sampling country (Fig. 2B) ; ii) a global map with indicative markers is provided for the column of sampling country to better illustrate the geographic distribution of the rodent-associated viruses (http://www.mgc.ac. doi = 10.1016/j.jgg.2017.04.004 id = cord-282343-cko4curf author = Cheng, Han title = A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus date = 2015-11-24 keywords = AIV; MARV; virus summary = RESULTS: The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. This strategy was used for an RNAi screen to identify host proteins specific for the entry process of Marburg virus (MARV) or avian influenza virus H5N1 (AIV), demonstrating the utility of this approach. The key feature of the protocol is that AIV and siRNA showing low signals in assay plates of both viruses is regarded as a "shared" hit by the two viruses MARV pseudovirions were used in parallel in the RNAi screen which allowed us to reduce the number of false positives and to quickly identify Marburg-specific and flu-specific host factors (which will be further discussed below). doi = 10.1186/s12985-015-0420-3 id = cord-255697-trig04hd author = Cheng, Vincent Chi-Chung title = Viral Infections, an Overview with a Focus on Prevention of Transmission date = 2016-10-24 keywords = HBV; HIV; SARS; virus summary = Hand hygiene is always the core component of infection control measures in both community and hospitals to prevent the transmission of influenza A virus. Wearing face masks by either the index case as source control or the health-care workers as contacts has shown to be equally effective in the control of nosocomial transmission of pandemic influenza A H1N1 (Cheng et al., 2010) . Timely implementation of infection control measures by single room isolation of index case with strict contact precautions significantly reduced the incidence of hospital-acquired norovirus infection from 131 (baseline) to 16 cases per 1000 potentially infectious patient-days (P < 0.001) (Cheng et al., 2011) . When there is no highly effective antiviral for the treatment of a severe viral illness, especially in patients at the extremes of age or with medical comorbidities, and infection control measures are difficult to implement or comply with, vaccination is the final option to prevent massive outbreaks. doi = 10.1016/b978-0-12-803678-5.00514-2 id = cord-016451-k8m2xz0e author = Chertow, Daniel S. title = Influenza, Measles, SARS, MERS, and Smallpox date = 2020-01-03 keywords = East; MERS; Middle; SARS; respiratory; virus summary = Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection doi = 10.1007/978-3-030-33803-9_5 id = cord-308066-lrbi5198 author = Childs, James E. title = Pre-spillover Prevention of Emerging Zoonotic Diseases: What Are the Targets and What Are the Tools? date = 2007 keywords = Disease; H5N1; SARS; States; United; surveillance; virus summary = The uneven standards of surveillance, humanor animal-based, for zoonotic diseases or pathogens maintained and transmitted by wildlife H R s, or even domestic species, is a global problem, readily apparent even within the United States, where investment in public health, including surveillance systems, has a long and enviable history. Following an outbreak of human monkeypox in several US states (Centers for Disease Control and Prevention 2003a; see the chapter by Regnery, this volume), local populations of indigenous North American rodents were captured and examined for infection from areas around animal-holding facilities housing African rodents imported for the pet-trade and implicated as the source of monkeypox virus (Cunha 2004; Check 2004) . National institutions charged with strategic planning for emerging diseases or intentional releases of zoonotic agents have emphasized improving diagnostic capabilities for detecting human infections, modifying the immune status of human or domestic animals through vaccines, producing better antiviral or antibacterial drugs, and enhancing human-based surveillance as an early warning system (Fauchi 2002 ; Centers for Disease Control and Prevention 1998). doi = 10.1007/978-3-540-70962-6_16 id = cord-320015-lbr2q4qh author = Chinchar, V. Gregory title = The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date = 2011-10-20 keywords = FV3; dna; protein; viral; virus summary = Additional IE and DE proteins include proteins that may play roles in blocking host immune responses such as a virus-encoded, CARD (caspase activation and recruitment domain) motif-containing protein (vCARD), β-hydroxysteroid dehydrogenase (βHSD), and a RNAse III-like protein, catalytic proteins involved in nucleic acid synthesis (Proliferating Cell Nuclear Antigen [PCNA], DNA methyltransferase [DMTase], the large and small subunits of the viral homolog of cellular RNA polymerase II [vPOL-IIα and -IIβ], transcription factor IIS), catalytic proteins that may act to increase dTTP pool sizes and influence host range (deoxyuridine triphosphatase [dUTPase], deoxynucleotide kinase, the large and small subunits of ribonucleotide reductase), and proteins non-essential for replication in vitro, but needed for growth in vivo (the 18K protein) [22] . Lastly, Sample and co-workers observed that KD of the 18K IE protein had no observable effect on viral gene expression or replication in vitro suggesting that, at least in fathead minnow cells, 18K was not required for the production of infectious virions. doi = 10.3390/v3101959 id = cord-343784-zgvxl4h3 author = Cho, Chi Hyun title = Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date = 2014-05-31 keywords = PCR; RV15; virus summary = Several studies have demonstrated the advantages of multiplex PCR assays such as xTAG RVP, RVP fast (Luminex Molecular Diagnostics, Toronto, ON, Canada), Resplex II (Qiagen, Mississauga, ON, Canada), FilmArray® Respiratory panel (Idaho Technology Inc., Salt Lake City, UT, USA), and Seeplex RV assays (Seegene, Seoul, Korea), which are used routinely for the detection of respiratory viral infection (Bibby et al., 2011; Couturier et al., 2013; Gharabaghi et al., 2011; Kim et al., 2013; Zhang et al., 2012) . In the previous study evaluating Seeplex RV12 detection kit (Seegene, Rockville, MD, USA), viral culture, RV12, and real-time PCR detected 8, 6, and 11 of 11 influenza B-positive specimens, respectively (Bruijnesteijn van Coppenraet et al., 2010) . Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens doi = 10.1016/j.diagmicrobio.2014.01.016 id = cord-306083-juysx6yo author = Choe, Young June title = Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date = 2020-09-10 keywords = RSV; virus summary = OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] . doi = 10.1016/j.cmi.2020.09.006 id = cord-305488-vk59ghjm author = Choi, Kang-Seuk title = Newcastle disease virus vectored vaccines as bivalent or antigen delivery vaccines date = 2017-07-26 keywords = NDV; Newcastle; vaccine; virus summary = They also induced a marked and efficient cellular and protective immune response in mice after challenge with vaccinia viruses expressing HIV-1 Env and Gag. These results suggest that vaccination with a single NDV vector coexpressing Env and Gag is a promising strategy that increases vaccine immunogenicity and subsequent protective efficacy against HIV. Immunization of cattle with recombinant Newcastle disease virus expressing bovine herpesvirus-1 (BHV-1) glycoprotein D induces mucosal and serum antibody responses and provides partial protection against BHV-1 Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus Newcastle disease virus-based live attenuated vaccine completely protects chickens and mice from lethal challenge of homologous and heterologous H5N1 avian influenza viruses Immunization of chickens with Newcastle disease virus expressing H5 hemagglutinin protects against highly pathogenic H5N1 avian influenza viruses doi = 10.7774/cevr.2017.6.2.72 id = cord-270243-moxleyjg author = Cholleti, Harindranath title = Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date = 2018-05-28 keywords = RNA; Rhipicephalus; tick; virus summary = Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Different studies have shown that viral pathogens, such as Thogoto viruses, Wad Medani virus, Nairobi sheep disease virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus and Tick-borne encephalitis virus [1, [6] [7] [8] , can be found in Rhipicephalus ticks. Numerous studies have used metagenomics to explore viral communities in different arthropod species and have in these identified viruses associated with a broad range of animals, plants and insects. However, the identified ORFs exhibit high genetic diversity to known quaranjavirus genomes, with an amino acid identity of only 32-55%, indicating that these represent novel viral sequences belonging to the Quaranjavirus genus. The parvovirus sequences identified in the current study had closest similarity to non-structural protein 1 of different densoviruses, which were shown previously to integrate into tick genomes such as in Ixodes, Amblyomma and Rhipicephalus genera [28, 29] . doi = 10.1080/20008686.2018.1478585 id = cord-324696-htx0ul4o author = Chothe, Shubhada K. title = Avian and human influenza virus compatible sialic acid receptors in little brown bats date = 2017-04-06 keywords = IAV; virus summary = This first ever study of IAV receptors in a bat species suggest that LBBs, a widely-distributed bat species in North America, could potentially be co-infected with avian and human IAVs, facilitating the emergence of zoonotic strains. To resolve this enigma, we investigated for the first time the distribution of SA receptors in little brown bats (LBBs) (Myotis lucifugus), a widely-distributed bat species in North America and their compatibility to support avian and human IAV binding. H5N2 virus binding pattern was in accordance with the relative abundance of SA α2,3-Gal receptors in tissues such that greater virus binding to the tracheal ( In addition to the virus binding assay using antibody-based detection, we also visualized virus binding using scanning electron microscopy (SEM) which also confirmed abundant binding of avian H5N2 virus (Fig. 5A ) and human H1N1 virus (Fig. 5B ) to LBB trachea (Fig. 5) . time, this study demonstrated that little brown bats (LBBs), a widely-distributed bat species in North America, co-express both avian and human type influenza receptors in their respiratory and gastrointestinal systems. doi = 10.1038/s41598-017-00793-6 id = cord-286708-igu984oc author = Chua, Kaw Bing title = Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date = 2008-11-25 keywords = Kampar; NBV; bat; virus summary = Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity. doi = 10.1371/journal.pone.0003803 id = cord-351197-xv6ymc4l author = Cibulski, Samuel title = A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date = 2020-09-28 keywords = dna; virus summary = From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes doi = 10.1016/j.virol.2020.09.005 id = cord-317277-rr9zue4l author = Cifuentes-Munoz, Nicolas title = Viral cell-to-cell spread: Conventional and non-conventional ways date = 2020-09-29 keywords = HIV-1; cell; spread; viral; virus summary = Cell-free viral particles can be released into the extracellular space through different mechanisms, such as: (a) cell lysis induced by viral proteins, as is the case for many non-enveloped viruses such as reoviruses, rotaviruses, adenoviruses and picornaviruses (Giorda and Hebert, 2013; Hu et al., 2012; Nieva et al., 2012) ; (b) by budding directly from the plasma membrane, where virions acquire their envelope, as is the case of human immunodeficiency virus (HIV-1), influenza, paramyxoviruses, and pneumoviruses (Lorizate and Krausslich, 2011; Votteler and Sundquist, 2013; Weissenhorn et al., 2013) ; (c) by exocytosis of intracellularly assembled viral particles, as is the case for bunyaviruses, flaviviruses and coronaviruses (Cifuentes-Munoz et al., 2014; Lorizate and Krausslich, 2011) . An interesting observation made for alphaviruses is that the filopodia-like extensions are not able to transfer cytosolic or plasma membrane components, suggesting they are not openended connections like TNTs. Instead, viral particles are hypothesized to bud into a protected space at the filopodial tip and then rapidly enter the target cell, preventing access of neutralizing antibodies. doi = 10.1016/bs.aivir.2020.09.002 id = cord-275821-yu39aw54 author = Ciminski, Kevin title = Novel insights into bat influenza A viruses date = 2017-09-14 keywords = IAV; virus summary = Although there is a certain degree of functional compatibility between bat and conventional influenza A virus proteins, there are striking differences, including receptor usage, polarity of infection and reassortment potential. In addition, as the bat IAV non-structural protein 1 (NS1) was previously shown to share the dsRNA-binding property and IFN-suppression characteristics of conventional IAV NS1s [38] , an infectious recombinant PR8 virus encoding the NS1 but not NEP gene of HL17NL10 could be generated [39] . The vRNA packaging signals and the NP proteins of The exchange of genomic segments is known to take place in cells co-infected with different conventional IAV subtypes. Likewise, based on experiments with chimeric bat influenza viruses, genomic reassortment is believed to occur in cells co-infected with the known bat IAV subtypes. doi = 10.1099/jgv.0.000927 id = cord-350467-18bvwxci author = Clark, K.J title = In vitro studies on the use of clay, clay minerals and charcoal to adsorb bovine rotavirus and bovine coronavirus date = 1998-10-01 keywords = HSCAS; rotavirus; virus summary = Experiments were designed to test the ability of various adsorbent materials to tightly bind bovine rotavirus and coronavirus. The suspended samples of clay bound virus or clay/virus complex retained from the adsorption and desorption experiments were used for infectivity testing. Charcoal, sodium bentonite, attapulgite, kaolinite, and HSCAS III were found to adsorb greater than 99.0% of bovine rotavirus while the other materials assayed ranged in their adsorptive capabilities from less than 99% to greater than 78% (Table 1) . As both bovine rotavirus and coronavirus bound to various adsorbent materials, including HSCAS I and II, with high affinity, both were tested for infectivity when in the bound state. They may have a distinct advantage in prevention of infection and/or disease because most agents that cause gastroenteritis, including rotavirus and coronavirus, are generally contracted orally, usually via contaminated food and water. doi = 10.1016/s0378-1135(98)00241-7 id = cord-302486-z36hcvrx author = Cobo, Fernando title = Diagnostic approaches for viruses and prions in stem cell banks date = 2006-03-30 keywords = PCR; cell; detection; dna; virus summary = Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. doi = 10.1016/j.virol.2005.11.026 id = cord-270091-sqrh8ylt author = Cohen, Pascal title = Vascularites associées aux infections virales date = 2004-11-30 keywords = B19; infection; vasculitis; virus summary = Résumé Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. Cryoglobulinemia related to the hepatitis C virus (HCV) The clinical manifestations are those of systemic vasculitis with particular tropism for the skin (involvement generally inaugural and almost constant), peripheral nerves and the glomerula. Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. L''infection à HTLV1 est rarement compliquée de vascularite ;cette dernière a un tropisme neurologique central 181 192, 193 qui fut le premier à décrire la responsabilité liée à l''hépatite B au cours de la périartérite noueuse 194 , nous décidâmes d''inclure dans un protocole prospectif tous les patients atteints de PAN HBV+ et de traiter les patients par une combinaison d''antiviraux et d''échanges plasmatiques 195 . doi = 10.1016/s0755-4982(04)98936-1 id = cord-004501-guiy89x8 author = Cojocaru, Florina-Daniela title = Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date = 2020-02-18 keywords = ACV; BBB; HIV; HSV; antiviral; cell; dna; drug; nanoparticle; viral; virus summary = doi = 10.3390/pharmaceutics12020171 id = cord-004280-c470nlie author = Coleman, Kristen K. title = Airborne Influenza A Virus Exposure in an Elementary School date = 2020-02-05 keywords = IAV; RNA; influenza; virus summary = In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Significantly different (p = 0.049) airborne IAV densities were detected between all three indoor locations (i.e., gymnasium, classroom, and corridor) and all positive samples were collected during the last two weeks of 66 , and a 20-30% relative humidity level; Descriptive of an average elementary school student in the USA weighing ~23-32 kg with an assumed tidal volume (V T ) of 7 mL per kg of body mass. Given the high airborne IAV densities detected in the school corridor, along with elevated student contact rates, it is plausible to conclude that the school corridor is a "hotspot" for influenza virus transmission. doi = 10.1038/s41598-020-58588-1 id = cord-339973-kj56zi59 author = Coleman, Kristen K. title = Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date = 2018-11-30 keywords = MRT; PCR; Singapore; virus summary = Although baseline metagenomic maps created from these studies are said to be useful for mitigating bioterrorism and infectious disease outbreaks, most of them focus largely on mapping surface-borne bacterial DNA 17 and neglect to address the threat of weaponized or global catastrophic biological risk-level (GCBR-level) agents, both of which would likely be aerosolized or respiratory-borne RNA viruses 19 . Bioaerosol sampling in the field provides a noninvasive way to monitor and characterize the community of aerosolized respiratory viruses that regularly infect the public, as well as potentially detect or discover novel pathogens with pandemic potential, such as the influenza A(H7N9) virus. Although the air pump flow rate and sample collection times used in our study have been demonstrated to efficiently capture aerosolized influenza virus and RSV RNA [33] [34] [35] , it is possible that these parameters are not optimal for capturing the other respiratory virus DNA/RNA targeted in our study. doi = 10.1038/s41598-018-35896-1 id = cord-355872-z6vsjmxn author = Colón-López, Daisy D. title = Emerging viral infections date = 2019-08-15 keywords = Ebola; infection; viral; virus summary = Characterization of bacterial and viral relationships in mosquito arthropods demonstrated a symbiotic relationship between the bacterium and host, limiting dengue virus infection and potentially revealing new antiviral strategies [39, 40] . The Ebola virus outbreak in West Africa resulted in 26,648 cases and 11,017 documented deaths, and genomic sequencing was applied in near real-time to provide information to aid in containing the outbreak [44, 45] . During the Ebola virus outbreak, sequence analysis of the viral genome over time demonstrated changes which could make the pathogen resistant to therapeutics such as siRNAs, phosphorodiamidate morpholino oligomers (PMOs), and antibodies [56] . This agnostic method is appropriate for identifying changes in the human transcriptome as a result of an emerging viral infection to show specific mechanisms of immune response evasion and other effects in the host''s biology at the transcriptomic level. doi = 10.1016/b978-0-12-801496-7.00010-1 id = cord-289017-vwye3pk9 author = Comach, Guillermo title = Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date = 2012-09-11 keywords = ILI; PCR; Venezuela; virus summary = CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . doi = 10.1371/journal.pone.0044511 id = cord-020714-h1fevqcw author = Compans, Richard W. title = Membrane Glycoproteins of Enveloped Viruses date = 2008-05-30 keywords = Compans; Sindbis; VSV; glycoprotein; membrane; virus summary = Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) . doi = 10.1016/s0070-2161(08)60750-9 id = cord-280564-kgoczioe author = Conceição-Neto, Nádia title = Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs date = 2017-09-08 keywords = Fig; PEDV; Porcine; virus summary = title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs In the sample, we observed the presence of a small Torovirus contig of 256 bp, which was included in the phylogenetic tree (Fig. 1A , Torovirus/BEL/2015), showing very low similarity with the gene insertion found in the recombinant virus. The enterovirus genome region before the torovirus insertion (VP1-VP4, 2 A, 2B, and 2 C) showed its highest similarity on the amino-acid level (94.5%) with EVG/Porcine/USA/Texas1/ 2014 (Fig. 1C) . In addition to confirming the presence of the enterovirus-torovirus recombinant using Sanger sequencing, we used proteomics to infer whether the protein of the insertion could be found in the sample. Taking the metagenomics data, the Sanger sequence confirmation and the proteomics results all together we can conclude that this recombinant virus is present in the sample and that the inserted protein is being expressed. doi = 10.1093/ve/vex024 id = cord-212761-4bwatc2r author = Contoyiannis, Y. title = On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 date = 2020-04-01 keywords = critical; virus summary = title: On the effectiveness of imposing restrictive measures in a graded Self-Organized Criticality epidemic spread model The case of COVID-19 However, it is revealed that very close to the critical point, the critical slowing-down (CSD) phenomenon, introduced by the theory of critical phenomena, emerges, leading to a tremendous increase of both the percentage of active carriers and the duration of the epidemic. As expected from the theory of critical phenomena, in the case of initial virus densities ρ below the critical value, time durations of the epidemic spread become significantly small. As already discussed, the proposed self-organized model seems to demonstrate a noteworthy behavior for a virus density equal to its critical value ρc, due to the CSD phenomenon, further leading to spectacularly increased relaxation times (high durations of the epidemic). doi = nan id = cord-022378-ovxmy1as author = Cook, Jane K.A. title = Coronaviridae date = 2009-05-15 keywords = IBV; virus summary = IBV also aff ects egg-laying performance, and renal damage associated with infectious bronchitis has become increasingly important, particularly in broilers. Economically, the most important aspects are the eff ects on egg production and quality in laying hens and production performance in broilers, where the initial respiratory infection is frequently exacerbated by secondary infections. In turkeys, coronaviruses (TCoV, also called Bluecomb disease virus and Turkey enteric coronavirus) are known to be associated with enteric disease, mortality and underperformance and to aff ect egg-laying performance in older birds. Th is is a new area of investigation and, while the coronaviruses detected in some gallinaceous and nongallinaceous birds have not so far been associated with disease, these species are potential carriers of IBV and other coronaviruses and could therefore play a role in global transmission of infection. In IBV infection of commercial layers or broiler breeders, respiratory signs may or may not be observed and the most common manifestation is the eff ect on egg production and egg quality. doi = 10.1016/b978-0-7020-2862-5.50033-7 id = cord-276506-dj7dyo0x author = Coria, M. F. title = Protective effect of an inactivated avian coronavirus vaccine administered by aerosol date = 1973 keywords = AIB; virus summary = Chickens administered 2 doses of the inactivated Connecticut strain (IBV-46) vaccine by aerosol at 3-week intervals had significant levels of virus-neutralizing antibodies and were resistant to infection by the Massachusetts strain (IBV-41) as determined by virus isolation attempts. Immunity to avian infectious bronchitis (AIB), a highly contagious viral infection of the respiratory tract of chickens has been studied using live and inactivated virus vaccirres (6) . However, more recent evidence shows that a BPL-inactivated AIB virus vaccine administered by an aerosol and concurrent subcutaneous inoculation induced significant levels of VN antibodies and afforded a good degree of protection against infection (4) . Immunization of the human respiratory tract with inactivated influenza A2 I-IongKong virus (13) and rhinovirus type 13 (ii), administered by an aerosol, indicates that a significant protective effect was observed when compared to individuals vaccinated by subcutaneous or intra-muscular routes. The immune response to BPL-inactivated AIB virus vaccines administered by an aerosol, as determined by PI~-NI''s, virus isolation (VI) and respiratory signs are shm~a~ in Table 1 . doi = 10.1007/bf01249930 id = cord-302425-aaxvlktp author = Cortey, Martí title = High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date = 2019-12-05 keywords = RNA; RVA; RVC; virus summary = In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. doi = 10.1186/s12917-019-2204-2 id = cord-316273-vo6j8zb0 author = Cosset, François-Loic title = Cell Entry of Enveloped Viruses date = 2011-02-08 keywords = Ebola; HIV; HIV-1; cell; fusion; protein; receptor; virus summary = On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. doi = 10.1016/b978-0-12-380860-8.00004-5 id = cord-281844-c0uhcatg author = Costa, Lusmaia D.C. title = Exacerbation of asthma and airway infection: is the virus the villain? date = 2014-12-31 keywords = PCR; asthma; child; viral; virus summary = Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Studies using reverse transcriptase polymerase chain reaction (RT-PCR) as the detection technique, isolated or combined with traditional methods, observed positivity for respiratory viruses in up to 92.2% of episodes of acute asthma exacerbation in children. Several authors have performed studies aiming to detect viruses in respiratory secretions of exacerbated asthma patients, showing a prevalence of viral identification that varies with several factors, such as patient age, time of the year, method of sample collection, and method of viral detection. The use of viral detection techniques with high sensitivity and specificity has increased the identification of some respiratory viruses in children with asthma exacerbation. doi = 10.1016/j.jped.2014.07.001 id = cord-277327-il8uaavn author = Couch, MD, Robert B. title = Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date = 1997-03-17 keywords = infection; respiratory; virus summary = At the M.D. Anderson Cancer Center (MDACC), infection surveillance of mostly hospitalized adults with leukemia or a recent bone marrow transplant yielded a respiratory virus from 181 of 668 (27.1%) respiratory illness episodes. The frequencies of pneumonia and death associated with a documented infection among immunocompromised adult leukemia and bone marrow transplant patients hospitalized at MDACC are shown in Table VII . Although overall frequencies of pneumonia and death appear similar for each virus, analysis of patterns of occurrences suggested a greater severity for RSV infection after bone marrow transplantation or chemotherapy than for the other viruses. Thus, the immune deficiencies described for immunocompromised persons can account for a high frequency of viral respiratory infections as well as an increased severity of illness and a significant risk of death. Combination therapy with aerosolized ribavirin and intravenous immunoglobulin for respiratory syncytial virus disease in adult bone marrow transplant recipients doi = 10.1016/s0002-9343(97)00003-x id = cord-296935-y77c4ro4 author = Couch, Robert B. title = Prior Infections With Seasonal Influenza A/H1N1 Virus Reduced the Illness Severity and Epidemic Intensity of Pandemic H1N1 Influenza in Healthy Adults date = 2011-11-10 keywords = H1N1; influenza; virus summary = Serum antibody to the pH1N1 and seasonal A/H1N1 viruses was measured in 579 healthy adults at enrollment (fall 2009) and after surveillance for illness (spring 2010). Preexisting antibody to pH1N1 virus, responses to a single vaccine dose, a low infection-to-illness ratio, and a short duration of illness and virus shedding among those with influenza indicated presence of considerable preexisting immunity to pH1N1 in the population. To assess the clinical and epidemiological impact of pH1N1 infections and to identify immunologic factors correlating with infections and illnesses, we conducted a prospective study of influenza in a young adult population. Occurrences of pH1N1 influenza infections and illnesses in relation to serum HAI antibody titer at enrollment are shown in Table 2 . When the retrospectively identified moderate to severe ARIs with a significant antibody response were included, the inverse correlation between baseline titer and frequency of pH1N1 infection and illness was significant (v 2 for trend, P 5 .01). doi = 10.1093/cid/cir809 id = cord-287466-ag5y781z author = Cowley, J.A. title = Nidoviruses of Fish and Crustaceans date = 2016-09-09 keywords = Cowley; GAV; PCR; Penaeus; RNA; YHV; virus summary = As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . doi = 10.1016/b978-0-12-801573-5.00032-2 id = cord-284372-v95fzp8n author = Coyle, Peter V title = A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date = 2004-10-25 keywords = PCR; respiratory; specimen; virus summary = title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. doi = 10.1186/1471-2180-4-41 id = cord-021588-ec7udsmw author = Craighead, John E. title = Enteric Viral Disease date = 2007-05-09 keywords = infection; virus summary = This virus and its soon-to-be-discovered close relatives (the so-called Norwalk-like viruses [NLVs]) proved to be important causes of explosive outbreaks of diarrhea in both children and adults. But, this painstaking approach has now yielded evidence to indicate that viruses of at least six families may contribute to enteric illness in children and in adult citizens whose immunity has waned (Figure 32.1, Table 32 .1). The etiological role of these viruses as a cause of intestinal disease was established by demonstrating a temporal association of naturally occurring infections (as demonstrated by stool examination using electron microscopy) with illness and by experimental induction of disease in both human volunteers and experimental animals (Hall et al, 1984) . Volunteer studies have yielded important histological and ultrastructural documentation of the profound but relatively transient changes that occur in the mucosa of the small intestine during the course of infections with NLVs (Agus ei al, 1973; Schreiber ei al, 1973 Schreiber ei al, , 1974 Dolin ei al, 1975) . doi = 10.1016/b978-012195160-3/50033-9 id = cord-001142-puj74k7y author = Crescenzo-Chaigne, Bernadette title = The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date = 2013-11-21 keywords = virus summary = To investigate whether, or not, and how the complete NC regions of a given segment are involved in type specificity, we attempted to rescue, by reverse genetics, type A and C influenza viruses with chimeric non-coding sequences. The sole difference between 5''A/3''C(C5U) and wild-type 5''A/3''A viruses being the 3'' distal extremity of the NS segment suggested that the level of NS encoded proteins (i.e. NS1 or/and NS2/NEP) was affected at early stages of infection for this virus (5''A/3''C(C5U)). The major role of the proximal panhandle in type specificity that we identified and the hypothesized involvement of the distal panhandle in transcription need to be tested on the other (2 PFU/cell), viral vRNA and mRNA levels for each segment were evaluated by specific two-step RT-qPCRs previously described [23] . doi = 10.1371/journal.pone.0081550 id = cord-001420-b4zcvd04 author = Crescenzo-Chaigne, Bernadette title = Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date = 2014-09-30 keywords = virus summary = Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. The sequence of both ends of each segment of each rescued virus was verified as described [9] , and no Influenza NP Non Coding Region Role in Translation PLOS ONE | www.plosone.org genetics, type A and type C viruses with one or both heterotypic ends. These data based on type A influenza virus NP segment showed that it is possible to obtain virus by reverse genetics when a homotypic proximal panhandle and a homotypic strength of the initial distal panhandle are maintained, and that the length of the 59 end plays an important role in the efficiency of rescue. doi = 10.1371/journal.pone.0109046 id = cord-324775-3x5os79m author = Crowe, J.E. title = Human Respiratory Viruses date = 2008-07-30 keywords = RSV; disease; infection; respiratory; virus summary = Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenoviruses, and influenza viruses were identified initially as the most common causes of serious lower respiratory tract disease in infants and children. These patients also suffer more frequent and more severe disease including mortality with common respiratory viruses, including RSV, hMPV, PIV, influenza viruses, rhinoviruses, and adenoviruses. Enterovirus infections occur most commonly in the summer months in temperate areas, which differs from the season of many of the other most common respiratory viruses such as paramyxoviruses and influenza virus. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. doi = 10.1016/b978-012374410-4.00488-x id = cord-017364-d9zmdm23 author = Crowe, James E. title = Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date = 2014-02-27 keywords = MPV; RSV; human; infection; metapneumovirus; respiratory; syncytial; virus summary = A virus causing a similar cytopathic effect in cultured cells was recovered from infants with respiratory illness shortly after, and studies of human antibodies in the serum of infants and children indicated that infection was common early in life [ 1 , 2 ] . Higher titers of virus in respiratory secretions usually are associated with increased severity of disease, in prospective studies of natural infection [ 114 ] or of clinical vaccine trials [ 115 ] . Most epidemiologic studies of MPV in children show that the virus is the second leading cause of lower respiratory infection after RSV. Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: a 2-year study The impact of infection with human metapneumovirus and other respiratory viruses in young infants and children at high risk for severe pulmonary disease Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children doi = 10.1007/978-1-4899-7448-8_26 id = cord-316245-n6tmn4ph author = Cui, Binglin title = Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China date = 2015-03-13 keywords = HRV; PIV3; virus summary = METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV) by multiplex real-time PCR. Multiplex real-time PCR was performed using Roche, Lightcycler 480 II (Roche Diagnostics, Penzberg, Germany) to identify the following 14 respiratory viruses: influenza A (FluA), influenza B (FluB), respiratory syncytial viruses A and B (RSV), human coronaviruses 229E, OC43, HKU1 and NL63 (hCoV), human metapneumoviruses A and B (hMPV), human parainfluenza virus types 1, 2 , 3, and 4 (PIV1, PIV2, PIV3, and PIV4), human rhinoviruses A, B, and C (HRV), human enteroviruses (EV), human adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV). doi = 10.1186/s12879-015-0863-6 id = cord-291113-iizj932l author = Cumbo, Enzo title = Alternative Methods of Sterilization in Dental Practices Against COVID-19 date = 2020-08-08 keywords = SARS; air; virus summary = It is time to consider a dental practice quite similar to a hospital surgery room, where particular attention should be paid to problems related to the spread of infections caused by air and surface contaminations, especially a time when viruses such as SARS-CoV-2 have emerged as an important public health problem due to their ability to spread through close person-to-person contact. Ultraviolet light has proven effective against corona viruses and, therefore, could be used against COVID-19 both in the case of bioaerosols and in the sterilization of contaminated environmental surfaces in which this microorganism is present-in particular, on products of unstable composition that cannot be treated by conventional means [62, 63] . Now that the risk of spreading COVID-19 is very high, it is necessary to pay particular attention to all the sterilization procedures that should be reviewed, improved, and perhaps used in combinations to obtain a final result that aims to complete the sterilization of all structures present in the operating room, including air, which for some dangerous diseases, such as SARS-CoV-2, is the transmission route. doi = 10.3390/ijerph17165736 id = cord-315346-ebfjba4y author = Cummings, Kristin J. title = Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? date = 2014-03-04 keywords = virus summary = title: Exposure to Influenza Virus Aerosols in the Hospital Setting: Is Routine Patient Care an Aerosol Generating Procedure? As the authors note, current World Health Organization and Centers for Disease Control and Prevention guidelines for protection of healthcare professionals from influenza virus infection rely on the supposition that, under routine conditions, most transmission occurs via large droplets, rather than via smallparticle aerosols [2, 3] . On each day, influenza virus RNA was detected in particles of respirable size, but a relationship to what we considered to be potential AGPs (mechanical ventilation, suctioning, extubation, and use of an incentive spirometer) was not evident. Indeed, potential respiratory exposures to healthcare professionals in the room appeared highest on hospital day 4, when the patient was breathing on his own and care was routine. This observation corroborates previous work [5] [6] [7] and raises the possibility that aerosol transmission of influenza virus may occur during routine patient care [8] . doi = 10.1093/infdis/jiu127 id = cord-344408-4ko557n1 author = Cunningham, Andrew A. title = One Health, emerging infectious diseases and wildlife: two decades of progress? date = 2017-07-19 keywords = Health; disease; emergence; virus; wildlife summary = Around this time, emerging diseases were identified in a series of well-reported die-offs in wildlife, including canine distemper in African lions (Panthera leo) in the Serengeti, chytridiomycosis in amphibians globally, pilchard herpesvirus disease in Australasia and West Nile virus in corvids and other birds in New York [10 -13] . There are likely to be multiple causes of novel disease emergence, but the human-mediated transport of pathogens (often in infected hosts) or vectors across geographical or ecological boundaries, a process termed ''pathogen pollution'', has been identified as a major driver of this in wildlife [64] and also in plants [65] . salamandrivorans as a novel lethal fungus infecting and killing captive and wild salamanders in Europe [67, 85, 86] Challenges remain to understanding the wildlife origins of zoonotic EIDs. It is often difficult, time-consuming, logistically challenging and very expensive to identify the origins of newly emerged pathogens of humans. doi = 10.1098/rstb.2016.0167 id = cord-021894-lq8yr710 author = Cunningham, Steve title = Bronchiolitis date = 2018-03-13 keywords = RSV; bronchiolitis; respiratory; virus summary = Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis doi = 10.1016/b978-0-323-44887-1.00024-9 id = cord-004830-vmka378d author = Cursiefen, Dagmar title = In vitro cultivation of cells from the chorioallantoic membrane of chick embryos date = 1975 keywords = cam; cell; virus summary = By treatment of chorioallantoic membranes from embryonated eggs with collagenase and hyaluronidase before the conventional application of trypsin cells could be grown in culture which supported growth of a large variety of myxoviruses, herpesviruses, avian reoviruses and the infectious bronchitis virus of chickens. In an attempt to plaque-purify and to quantitatc some strains of influenza viruses and of avian reoviruses we succeeded to cultivate cells from the chorioallantoic membrane of chick embryos. The following strains were tested for their ability to grow, induce a cytopathie effect and form plaques in chorioallantoic cells of the chick embryo (CAM-cells). After an incubation period of 8 to 16hrs the media were assayed for hemagglutinating activity and for infectivity by plaque tests on the same cell type used for growing the viruses, i.e. CAM cells or chick embryo fibroblasts. doi = 10.1007/bf02120764 id = cord-022439-8wy7rpqv author = DENMAN, A.M. title = Viral Etiology of Polymyositis/Dermatomyositis date = 2013-11-17 keywords = antibody; cell; viral; virus summary = Thus, theories based on a viral etiology must invoke a highly un usual host response to ubiquitous agents, the existence of uncommon viruses with the abil ity to provoke the disorder, or the possibility that virus infections operate synergistically with other factors. Attempted isolation Electron-microscopic studies Viral probes Antiviral antibody titers Establishing clones from infiltrating T lymphocytes and screening their antigen specificities Exploring the antigen specificities of associated autoantibodies In vitro models of virus-infected muscle cells In vivo models of experimental polymyositis ceptually. In clinical studies, EBV transformed blood lymphocytes from both normal individuals and patients with autoimmune diseases pro duced monoclonal autoantibodies reactive with antigens in multiple organs [93] . Myocarditis and PM induced by coxsackievirus infection is mediated by immunopathologic mechanisms that may continue to dam age muscle fibers long after infectious virus and even viral antigens have been eliminated. doi = 10.1016/b978-0-409-95191-2.50010-0 id = cord-279849-zzkliu76 author = DaPalma, T. title = A systematic approach to virus–virus interactions date = 2010-01-20 keywords = HIV; VVI; infection; virus summary = Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection doi = 10.1016/j.virusres.2010.01.002 id = cord-330131-yfhrmbvx author = Danchin, Antoine title = Cytosine drives evolution of SARS‐CoV‐2 date = 2020-04-27 keywords = CTP; RNA; SARS; virus summary = In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. doi = 10.1111/1462-2920.15025 id = cord-006819-sxz1s6kz author = Daniel Givens, M. title = Infectious causes of embryonic and fetal mortality date = 2008-05-27 keywords = abortion; cause; disease; infection; virus summary = The clinical presentations of disease due to reproductive pathogens are emphasized, with a focus on assisting development of complete lists of causes that result in abortion and infertility in these species. Fetal maceration results when abortion or parturition fails to occur following fetal death and CL regression (occasionally in bovine www.theriojournal.com Available online at www.sciencedirect.com Theriogenology 70 (2008) 270-285 Table 1 Infectious causes of infertility and abortion in domestic animals Infected animals can experience signs of infertility due to early embryonic death and abortion between 4 and 7 months of gestation. Transmission occurs via contact with materials contaminated by infected respiratory or vaginal discharges; the bacteria then spread hematogenously to the fetus. Affected animals might have no clinical signs of disease, but serve as a source of infection, or they can abort late in gestation and have stillbirths. doi = 10.1016/j.theriogenology.2008.04.018 id = cord-276616-odmnvv7m author = Darcel, C. title = Reflections on scrapie and related disorders, with consideration of the possibility of a viral aetiology date = 1995 keywords = BSE; agent; disease; encephalopathy; scrapie; spongiform; virus summary = Conclusions drawn from the vaccination trials and transmission experiments were that ~crapie, given by subcutaneous inoculation, had a latent period of 2 years and longer; that the infective agent was resistant to 0.35% formalin; that the disease appeared more quickly and in a higher percentage of recipients following intracerebral than following~subcutaneous injection; and that the causative agent was probably a filtrable virus. There are many difficulties in studying either the natural or experimentally induced diseases: the animals involved, the incubation period required for the emergence of the disease, the innate resistance of a proportion of the population seen as an expression of genetic influences, the differing behaviour of strains of agents isolated from a given species, the symptomatology, the pathology, the uncertain nature of the agent and its means of transmission, the perceived ''lack'' of an immunological response or changes in the immune system, and the biological hazards involved in conducting experiments. doi = 10.1007/bf01839302 id = cord-302111-kg0dmgq0 author = Darden, Dijoia B. title = The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date = 2020-04-29 keywords = SARS; pneumonia; respiratory; viral; virus summary = Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. doi = 10.1097/cce.0000000000000109 id = cord-292657-gq3965se author = Das, Piyanki title = Decoding the global outbreak of COVID-19: the nature is behind the scene date = 2020-06-22 keywords = SARS; host; virus summary = The rapid evolving nature by changing host body environment and extreme environmental stability, collectively makes SARS-CoV-2 into an extremely virulent genetic variant. Thus both the host body or internal environment and the external environment performs equally as a source, responsible for shaping the genetic evolution of the SARS-CoV-2 towards theCOVID-19 disease fitness in nature in a pandemic form. The probable line of development for such pandemic outcomes happened by continuous evolutionary procedure within different species or host environment exposure, by mutation during replication or genetic recombination between two different viral species and ultimate adaptation to a susceptible host by natural selection of the new version of the viable pathogen resulting infection [7, 8] . Then genetically close different subtypes of SARS-CoV-2 develops unique spike protein receptor binding domain with high degree of receptor binding property to human cells and adapt itself to fit the character inside the host body. doi = 10.1007/s13337-020-00605-y id = cord-102862-oq54sfx6 author = Dastjerdi, Akbar M. title = Characterisation of the bovine enteric calici-like virus, Newbury agent 1 date = 2000-11-01 keywords = SPIEM; na1; virus summary = A single capsid protein of 49.4 kDa was detected by Western blotting in purified NA1 preparations prepared from post-infection but not pre-infection faecal samples and with postbut not pre-infection sera. Calici-like virus particles were identi¢ed in faecal samples by electron microscopy but no other viruses were seen. Western blotting analysis of NA1 virions puri¢ed from faeces by CsCl density gradient centrifugation demonstrated the presence of a single protein band in each of ¢ve separate preparations from the day 2 p.i. faecal sample from calf 1424 (Fig. 4a, track 2) . The speci¢city of the protein band was con¢rmed by examination of day 0 versus day 2 p.i. faecal samples, staining with pre-and postinoculation antisera and association with the presence of virus particles in CsCl gradients. Capsid diversity in small round-structured viruses : molecular characterization of an antigenically distinct human enteric calicivirus doi = 10.1016/s0378-1097(00)00422-5 id = cord-258626-p469ysi8 author = Davis-Wurzler, Gina M. title = 2013 Update on Current Vaccination Strategies in Puppies and Kittens date = 2014-02-26 keywords = CAV; cat; disease; vaccination; vaccine; virus summary = Criteria for assigning vaccines into these categories, and a third category, "generally not recommended," are based on: (1) morbidity and mortality associated with the specific disease (does the organism cause serious illness or does it cause a mild, transient disease that may pose only minimal risk to the individual or population?); (2) the prevalence and/or incidence rate of the disease (although a specific disease may not commonly be seen, the organism is ubiquitous in the environment and therefore poses risk to the individual or population); (3) the risk of the individual for exposure to the disease (indoor-only animal vs free-roaming individual, regional variations of occurrence); (4) the efficacy of the vaccine (does the vaccine prevent infection or simply ameliorate some signs or length of disease?); (5) the risks associated with administering the vaccine (are the risks associated with that vaccine greater than the risk of the disease?); (6) the potential for zoonotic disease; (7) the route of infection or transmissibility. 9, 13 The current recommendation is to use the CAV-II modified live virus product, as it stimulates the immune system to protect against both CAV-I and CAV-II, without the associated adverse reaction caused by the type I vaccine. doi = 10.1016/j.cvsm.2013.11.006 id = cord-275538-c44gmu22 author = Davis-Wurzler, Gina M. title = Current Vaccination Strategies in Puppies and Kittens date = 2006-03-24 keywords = CAV; MLV; disease; vaccination; vaccine; virus summary = The current recommendation is to use the CAV-II MLV because it stimulates the immune system to protect against CAV-I and CAV-II without the associated adverse reaction caused by the type I vaccine [4, 14, 20] . There is a killed vaccine available; however, vaccination against this agent is typically not recommended, because most animals are not at risk to contract the parasite, the vaccine does not prevent infection (it may ameliorate clinical signs and decrease cyst shedding), and the disease is readily amenable to therapy (fenbendazole, albendazole, and metronidazole are off-label uses but commonly accepted as standard of care). Because the vaccine does not fully prevent infection and carries an association with adverse events that may be greater than the actual disease, routine vaccination of household pets with this product is generally not recommended. doi = 10.1016/j.cvsm.2005.12.003 id = cord-346063-7u1a198p author = De Clercq, Erik title = Avian influenza A (H5N1) infection: targets and strategies for chemotherapeutic intervention date = 2007-05-04 keywords = H5N1; influenza; virus summary = We have recently reviewed the antiviral agents that are active against influenza viruses and that could be used, either therapeutically and/or prophylactically, in an influenza virus pandemic, whether it be human, avian, equine, porcine or other [1] . Even if based only on the currently available drugs, there are several double-, tripleand quadruple-drug combinations that could be envisaged for the prevention and treatment of avian H5N1 (Figure 3 ) -including the combination of oseltamivir and zanamivir (because their resistance profiles overlap only partially), the combination of these neuraminidase inhibitors with M2 ion channel blockers, and further extension of these combinations to include pegylated interferon and ribavirin. In addition to viral RNA polymerase and/or endonuclease, mentioned earlier as potential targets for new anti-influenza-virus agents, there are some other clues regarding the virulence of H5N1 viruses in humans [41] that could be considered as points of attack for chemotherapeutic intervention. doi = 10.1016/j.tips.2007.04.005 id = cord-299379-ch7a39d6 author = De Conto, Flora title = Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date = 2019-01-17 keywords = HADV; HRSV; respiratory; virus summary = title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. doi = 10.1016/j.diagmicrobio.2019.01.008 id = cord-004724-llex3yed author = Dea, S. A. title = Isolation of encephalomyocarditis virus among stillborn and post-weaning pigs in Quebec date = 1991 keywords = EMC; Quebec; virus summary = Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Serological evidence of EMC virus infection was reported in Canadian swine herds and associated with sudden death in young piglets and reproductive problems [20, 21] . This report describes the isolation of EMC virus from the tissues of aborted fetuses and post-weaning piglets obtained from three different farms. Necropsied fetuses did not show typical gross and microscopic heart lesions previously reported from experimental and natural infection of newborn piglets with EMC virus [12] [13] [14] . An association between encephalomyocarditis virus infection and reproductive failure in pigs doi = 10.1007/bf01310497 id = cord-265461-hj2b1wc4 author = Decroly, Etienne title = Biochemical principles and inhibitors to interfere with viral capping pathways date = 2017-05-18 keywords = GMP; RNA; cap; virus summary = Some virus families code for two different MTase domains carrying a cap-binding site (e.g., poxviruses [11] , coronaviruses [ Structure of inhibitors targeting enzymes involved in viral RNA capping pathways. Cap analogues exemplified here with m7 GTP, and several inhibitors of cap-binding protein have been identified through X-ray structure analysis of the influenza virus PB2-CBD in complex with the corresponding ligands. The X-ray structure of influenza A or B virus PB2 in complex with m7 GTP [49, 50] reveals a conserved cap-recognition mechanism in which the methylated guanosine is stacked between two aromatic residues similar to its binding mode with the eukaryotic initiation factor (eIF4E). However, the past research decade has a contrario unveiled that RNA capping is essential for virus replication, and is in fact a most interesting target for the design of potent antivirals due to two main reasons: (i) incomplete/inhibited RNA capping triggers a potent host immune response adding up to direct inhibition of viral gene expression, and (ii) structural and functional studies of viral capping enzymes have revealed a profound uniqueness of the viral enzymes involved, which shows promises to achieve high drug selectivity. doi = 10.1016/j.coviro.2017.04.003 id = cord-332181-k90i33gp author = Degeling, Chris title = Hendra in the news: Public policy meets public morality in times of zoonotic uncertainty date = 2012-12-29 keywords = Hendra; fox; medium; risk; virus summary = Because flying foxes are a highly visible, widespread and relatively novel source of infectious risk for humans, the emergence of Hendra virus presents an opportunity to track and compare media representations of disease ''events'', health policy goals, political discourses and public opinions in ways that are difficult for noncommunicable diseases. Articles then were coded for: mention of horses, flying foxes/fruit bats or Hendra virus mention of debates about flying fox control report of distal ecological causes (loss of natural habitat) for the emergence of Hendra virus or the possibility of viral mutation mention of ignorance about Hendra virus amongst scientists, healthcare providers or members of the public reference to government inaction as a factor contributing to the Hendra problem reference to people''s health and welfare not being high enough on the political agenda. doi = 10.1016/j.socscimed.2012.12.024 id = cord-021555-rrverrsj author = Delano, Margaret L. title = Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date = 2007-09-02 keywords = Smith; States; United; animal; bovine; cattle; cause; clinical; day; diagnosis; differential; disease; etiology; goat; infection; lesion; necropsy; organism; ruminant; sheep; sign; treatment; virus summary = These references also provide information regarding vaccination products licensed for use in ruminants and typical herd and flock vaccination parasite control schedules ("Current Veterinary Therapy," 1986 , 1999 "Council report," 1994; "Large Animal Internal Medicine," 1996; Smith and Sherman, 1994) When designing a vaccination program during qualification of a source or at the research facility, it is important to evaluate the local disease incidence and the potential for exposure. Clinical signs in chronic cases in older animals, such as adult goats, include soft stools, weight loss, anorexia, depression, and severe diarrhea, sometimes with mucus and blood. This pathogen does present a complication due to the carrier status of some animals, the likelihood of herd outbreaks, the severity of disease in younger animals, and the morbidity, possible progression to uveitis, and time and treatment costs associated with infections. doi = 10.1016/b978-012263951-7/50017-x id = cord-301362-f3lp10lm author = Delgui, Laura R. title = A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses'' Replicases date = 2017-01-20 keywords = RNA; replication; rig; virus summary = Recognition of viral double-strand RNA (dsRNA) molecules by intracellular Toll-like receptors (TLRs) or retinoic acid inducible gene I-like receptors (RLRs) is a central event which entails the early steps of the immune response elicited during viral infections. Despite several differences among host range, viral structure, genome organization or membrane-donor organelles from the cell, these analyses revealed that +sRNA viruses are able to induce two types of membranous modifications as replicative niches: invaginated vesicles or spherules or a double membrane vesicle type. Endogenous RNAs forming secondary double-stranded structures that are released after necrosis and tissue damage after viral infection represent another source of dsRNA molecules reaching the endosomes, inducing host-derived dsRNA-mediated inflammatory responses through TLR-3 recognition (Kawai and Akira, 2010) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication. doi = 10.3389/fcimb.2017.00005 id = cord-327777-pg98zc6o author = Delogu, Mauro title = Eco-Virological Preliminary Study of Potentially Emerging Pathogens in Hedgehogs (Erinaceus europaeus) Recovered at a Wildlife Treatment and Rehabilitation Center in Northern Italy date = 2020-03-01 keywords = Erinaceus; Italy; virus summary = However, the high mutation rates characterizing members of the Coronaviridae family and their potential successful interspecies host jumps—as that likely occurred in the Novel coronavirus (2019-nCoV) emergence—should be considered in the management of hedgehogs admitted to multi-species wildlife rehabilitation centers, recommending their return back to the original recovery areas. Western European hedgehogs'' ecological and feeding habits, along with their high population densities, notable synanthropic attitudes, frequent contacts with sympatric wild and domestic species, including humans, implicate the possible involvement of E. The wild bird Influenza A virus (IAV) gene pool poses significant risks for both animal and human health because of its ability to colonize a wide variety of animal species (included in the Mammalia, Aves and Reptilia classes) in which IAV can cause variable outcomes of infection, with possible high morbidity and fatality rates [20] . doi = 10.3390/ani10030407 id = cord-304498-ty41xob0 author = Denison, Mark R title = Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date = 2011-03-01 keywords = ExoN; RNA; SARS; genome; virus summary = Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. doi = 10.4161/rna.8.2.15013 id = cord-345654-vyz6f3he author = Dennehy, John J. title = Evolutionary ecology of virus emergence date = 2016-12-30 keywords = RNA; emergence; evolution; host; mutation; recombination; virus summary = Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Virus quasispecies may facilitate host range expansion Viruses are among the smallest nucleic acid-based replicating entities and possess characteristics associated with exceptionally fast evolutionary change: small genomes, short generation times, high mutation rates, large population sizes, high levels of genetic diversity, and strong selection pressures. doi = 10.1111/nyas.13304 id = cord-341138-mxjsp3cm author = Denner, Joachim title = Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) date = 2016-12-20 keywords = retrovirus; virus summary = title: Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV) The gibbon ape leukaemia virus (GaLV) and koala retrovirus (KoRV), two gammaretroviruses, are also the result of a transspecies transmission, however from a still unknown host. The transspecies transmission of the gibbon ape leukaemia virus (GaLV) and the koala retrovirus (KoRV) is a prime example of a transmission that is still not yet fully understood. Searching for the precursor virus, retroviruses related to KoRV and GaLV have been described in rodents such as South East Asian mice (e.g., Mus caroli [9, 10] and Mus dunni [11] ), as well as in two subspecies of Melomys burtoni in Australia and Indonesia [12, 13] . The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to gibbon ape leukemia virus doi = 10.3390/v8120336 id = cord-294812-nnlzwaf1 author = Desforges, Marc title = Neuroinvasive and Neurotropic Human Respiratory Coronaviruses: Potential Neurovirulent Agents in Humans date = 2014-03-12 keywords = CNS; OC43; SARS; human; virus summary = However, in some circumstances, viruses can avoid the immune response and cause more severe respiratory diseases [1] or even spread to other tissues, including the central nervous system (CNS), where they could induce other types of pathologies [7] . Coronaviruses, a family of enveloped positive-stranded RNA viruses with a characteristic crown-shaped appearance, are widespread in nature and can infect several different species [44] , in which they cause mainly respiratory and enteric pathologies, with neurotropic and neuroinvasive properties in various hosts including humans, cats, pigs, rodents, and fowl [45] [46] [47] [48] . Furthermore, we have shown that these viruses are able to establish a persistent infection in human cells representative of the CNS [64, 65] and that HCoV-OC43 RNA could be detected for at least a year in the CNS of infected mice that survived the virus-induced acute encephalitis [71] . doi = 10.1007/978-81-322-1777-0_6 id = cord-308201-lavcsqov author = Desforges, Marc title = Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date = 2019-12-20 keywords = CNS; OC43; acute; human; infection; respiratory; virus summary = Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Even though no clear cause and effect link has ever been made with the onset of human neurological diseases, their neuropathogenicity is being increasingly recognized in humans, as several recent reports associated cases of encephalitis [244] , acute flaccid paralysis [271] and other neurological symptoms, including possible complications of HCoV infection such as Guillain-Barré syndrome or ADEM [249, [272] [273] [274] [275] [276] [277] [278] [279] . Like for several other respiratory viruses, accumulating evidence now indicate that HCoV are neuroinvasive in humans and we hypothesize that these recognized respiratory pathogens are potentially neurovirulent as well, as they could participate in short-and long-term neurological disorders either as a result of inadequate host immune responses and/or viral propagation in the CNS, which directly induces damage to resident cells. doi = 10.3390/v12010014 id = cord-004827-bnf3mvaf author = Desselberger, U. title = Report on an ICTV-sponsored symposium on Virus Evolution date = 2005-01-13 keywords = HIV; RNA; virus summary = Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a ''swarm'' of closely related mutants. ''To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome''. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution doi = 10.1007/s00705-004-0466-9 id = cord-010168-aiqbqnaa author = Desselberger, Ulrich title = Classical and molecular techniques for the diagnosis of viral gastroenteritis() date = 1999-03-11 keywords = Norwalk; virus summary = The vaccine response is widened by applying a cocktail of viruses, e.g. containing a native rhesus rotavirus (RRV) of G3 type and reassortants carrying the VP7 genes of human serotypes G1, G2 and G4 in the RRV genetic background (Rennels et al., 1996) . These have been used as antigens in ELISA, and it was shown that NV or related viruses infect children worldwide in large numbers, and 60 80% of young adults have NV-reactive antibody (Gray et al., 1993) . Norwalk-like viruses are transmitted by the faeco-oral route and were found to be causative agents of various outbreaks of viral gastroenteritis occurring in recreational camps, schools and nursing homes, on cruise ships, around contaminated swimming pools, or in the community (Greenberg et al., 1981) . Sequence and genome organization of a human small, round-structured (Norwalk-like) virus doi = 10.1016/0928-0197(96)00211-5 id = cord-266199-smlq11y9 author = Dhakal, Santosh title = Nanoparticle-based vaccine development and evaluation against viral infections in pigs date = 2019-11-06 keywords = PLGA; PRRSV; pig; porcine; vaccine; virus summary = The economic burden caused by virus infections such as Porcine Reproductive and Respiratory Syndrome Virus, Swine influenza virus, Porcine Epidemic Diarrhea Virus, Porcine Circovirus 2, Foot and Mouth Disease Virus and many others are associated with severe morbidity, mortality, loss of production, trade restrictions and investments in control and prevention practices. Likewise, DCs targeted chitosan NPs loading plasmid DNA encoding nucleocapsid protein of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) induced better nucleocapsid protein-specific mucosal IgA antibody response compared to soluble unentrapped antigens after nasal immunization in mice [57] . In this review, only studies conducted in pigs related to the development and evaluation of NPs-based vaccine candidates by using virus-like particles (VLPs), biodegradable polymers, polysaccharides and liposomes against porcine viral infections are included (Table 3) . Chitosan-based NPs are used in pigs to deliver adjuvants such as bee venom and plasmid encoding porcine IL-2 and IL-4/IL-6 genes, which improved induction of better virus-specific immune responses of respective vaccines against PRRSV and PCV2 [103, 104] . doi = 10.1186/s13567-019-0712-5 id = cord-331289-02411gfv author = Di Minno, Giovanni title = Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date = 2015-07-20 keywords = B19; HBV; HIV; NAT; blood; virus summary = In general, clinicians assess the level of risk associated with the use of blood/ plasma-derived products by evaluating factors such as patient characteristics (e.g. age, immune status, geographical location, lifestyle) and the nature of the pathogen (e.g. physical characteristics, level of virulence, chronicity of infection, prevalence). Current donor selection and screening practices have improved our ability to detect or reduce the presence of pathogens in blood/plasma-derived products; for example, the residual risk of transfusion-transmitted infection (TTI) with HIV/HBV/HCV has fallen to near or less than 1 per million transfused units [14, 15] . Since TTV is often detected in healthy individuals and is not associated with any particular disease, routine screening for this virus is not considered to be necessary; even a test with excellent sensitivity/specificity would not contribute to increase the level of safety of blood/plasma-derived products with regard to TTV. doi = 10.1016/j.blre.2015.07.004 id = cord-011129-btaxvmsr author = Di Paola, Nicholas title = Viral genomics in Ebola virus research date = 2020-05-04 keywords = Congo; EBOV; EVD; Ebola; Republic; outbreak; virus summary = Here, we review how recent advances in genomic technologies have shaped past and current responses to outbreaks of Ebola virus disease (EVD), including insights into filovirus diversity and evolution. After this identification, considerations other than sequencing speed (for example, sequencing accuracy and processivity) become paramount in determining virus transmission networks and in detecting changes in the viral genome (between cases in the current outbreak and between the current and previous outbreaks) that could subvert MCMs. However, whereas unbiased sequencing approaches using high fidelity platforms can lead to the discovery of co-infections and reveal important clinical considerations during the treatment of patients near the point of need, targeted methods of pathogen characterization using the portable sequencing platforms iSeq 100 and MiSeq (which use bait-enrichment techniques) and MinION (which uses amplicon sequencing) can still provide useful genomic data albeit with a lower sequencing output (that is, a lower number of reads) than unbiased sequencing. doi = 10.1038/s41579-020-0354-7 id = cord-007733-zh8e76w7 author = DiMenna, Lauren J. title = Pandemic Influenza Vaccines date = 2009-06-15 keywords = CD8; H5N1; influenza; vaccine; virus summary = The efficacy of seasonal vaccines is linked to their ability to induce virus-neutralizing antibodies, which provide subtype-specific protection against influenza A viruses. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. Alternatively, the scientific community could step up efforts to generate a universal vaccine against influenza A viruses that provides broadly cross-reactive protection through the induction of antibodies or T cells to conserved regions of the virus. WHO recommends three measures to lessen the impact of the next influenza virus pandemic: (1) increased surveillance to allow for the earliest possible warning that a human pandemic has started; (2) early intervention to stall global spread and prevent further adaptations; and (3) development of an effective pandemic vaccine. doi = 10.1007/978-3-540-92165-3_15 id = cord-288372-48wao8a0 author = Dia, Ndongo title = Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date = 2014-04-08 keywords = ILI; Senegal; virus summary = The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. Viral aetiology, prevalence and diversity data in people with influenza like illness (ILI) and/or acute respiratory illness (ARI) in Africa, (especially in West Africa), are scarce and often limited to the influenza viruses'' infection. For example in the United States alone, up to 40% of non-pneumonic lower respiratory illnesses in the elderly have been associated with respiratory viral infection [10] , and an estimated 54,000 deaths annually have been attributed to the influenza and respiratory syncytial viruses (RSV) [11] . The present study is the first description of the etiology of respiratory viruses associated with patients with ILI in a cohort of elderly people in the West African context. doi = 10.1186/1471-2334-14-189 id = cord-333463-u7je0d1o author = Diaz-Salazar, Carlos title = Natural killer cell responses to emerging viruses of zoonotic origin date = 2020-08-09 keywords = Ebola; IFN; cell; virus summary = Nearly all emerging viruses, including Ebola, Dengue, Nipah, West Nile, Zika, and coronaviruses (including SARS-Cov2, the causative agent of the current COVID-19 pandemic), have zoonotic origins, indicating that animal-to-human transmission constitutes a primary mode of acquisition of novel infectious diseases. Natural killer (NK) cells are innate lymphocytes that play a critical role in the early antiviral response, secreting effector cytokines and clearing infected cells. This review describes the role of Natural killer (NK) cells, a critical component of early antiviral immunity, in the establishment of tolerance to viral infections in natural hosts, as well as their role in the development of disease in nonnatural hosts. Altogether, it is believed that quick control of viral infections and reduced induction of pro-inflammatory cytokines have allowed bat viruses to rapidly co-evolve with their host without provoking major immuneThe careful study of the immune system in reservoirs of zoonotic diseases will certainly offer insights into how these animals carry high viral loads while remaining asymptomatic. doi = 10.1016/j.coviro.2020.07.003 id = cord-312332-rwmuucsp author = Dicker, Kate title = The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date = 2020-09-10 keywords = ESCRT; HIV-1; RNA; protein; viral; virus summary = title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the ''knowns'' and ''unknowns'' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . doi = 10.1016/j.semcdb.2020.08.002 id = cord-017070-05vlz5dn author = Dimitrov, Dimiter S. title = Human Monoclonal Antibodies Against HIV and Emerging Viruses date = 2008 keywords = HIV; SARS; antibody; virus summary = These antibodies also protected uninfected animals from SARS-CoV infection, e.g., passive transfer of immune serum to naive mice prevented virus replication in the lower respiratory tract following intranasal challenge (61) . Recently, an improved method for Epstein-Barr virus transformation of human B cells has been developed based on CpG oligonucleotide (CpG 2006) that increases the B cell immortalization efficiency from 1-2% to 30-100%, and used for selection of hmAbs specific for SARS-CoV proteins (68) . We have recently identified a novel cross-reactive potent SARS-CoV-neutralizing hmAb, m396, by using a fragment containing residues 317 through 518 as a selecting antigen for panning of a large human antibody library constructed from the B lymphocytes of healthy volunteers (75) . These antibodies specific for SARS-CoV, HeV, and NiV have potential for further development into a clinically useful product for prophylaxis and perhaps treatment of the diseases caused by these infections. Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association doi = 10.1007/978-1-59745-569-5_34 id = cord-260956-w6wxsg4p author = Dimitrov, Kiril M. title = Newcastle disease vaccines—A solved problem or a continuous challenge? date = 2017-07-31 keywords = NDV; Newcastle; vaccine; virus summary = When administered correctly to healthy birds, ND vaccines formulated with NDV of low virulence or viral-vectored vaccines that express the NDV fusion protein are able to prevent clinical disease and mortality in chickens upon infection with virulent NDV. Characterization of live LaSota vaccine strain-induced protection in chickens upon early challenge with a virulent Newcastle disease virus of heterologous genotype Protection from clinical disease against three highly virulent strains of Newcastle disease virus after in ovo application of an antibody-antigen complex vaccine in maternal antibodypositive chickens Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge Level of protection of chickens against highly pathogenic H5 avian influenza virus with Newcastle disease virus based live attenuated vector vaccine depends on homology of H5 sequence between vaccine and challenge virus doi = 10.1016/j.vetmic.2016.12.019 id = cord-286559-y8z0pwgn author = Ding, Nai-Zheng title = A permanent host shift of rabies virus from Chiroptera to Carnivora associated with recombination date = 2017-03-21 keywords = Fig; rabv; virus summary = Bat virus host shifts have resulted in the emergence of several serious diseases in humans and animals, such as SARS 1 , Ebola 2 , and rabies 3 viruses. Interestingly, although evolutionary analyses have demonstrated that bat-to-carnivore host-shifting viruses accumulate few adaptive mutations 4, 6, 11 , in none of these examples did bat RABV establish permanent transmission cycles in the new host species 7 . The second permanent host shift appears to have occurred in North America, producing a lineage including two variants, raccoon rabies virus (RRV) and south-central skunk variant (SCSKV). Since bat RABVs are potentially able to infect carnivore species 6, 11, 14, 45 , we also propose that recombination may function as the third and fourth stages of establishment of a permanent host shift by significantly enhancing the adaptability of a bat virus in terrestrial mammals. doi = 10.1038/s41598-017-00395-2 id = cord-291816-d4j8samu author = Diniz Beduschi Travassos Alves, Christian title = Mamastrovirus 5 detected in a crab-eating fox (Cerdocyon thous): Expanding wildlife host range of astroviruses date = 2018-08-15 keywords = CDV; bra; canine; crab; virus summary = Herein, we describe the genomic characterization of a MAstV5 (strain crab-eating fox/2016/BRA) identified in a wild canid (Cerdocyon thous) diagnosed with canine distemper virus (CDV) as causa mortis. The present report is the first evidence of MAstV5 infection in an animal species other than the dog and highlights a possible natural astrovirus spillover between domestic and wild canids. The data presented herein shows two important findings: (i) it is the crab-eating fox/BRA/2016 strain was likely derived from the canine host, and (ii) the extra intestinal MAstV5 presence. The sequence for the ribosomal frameshift site between ORF1a and ORF1b, which is conserved in the Astrovirudae family members [38] , is present in the crab-eating fox/2016/BRA nearly full genome (Fig. 2) . The crab-eating fox/2016/BRA nearly full genome, as expected, grouped in the MAstV5 cluster with all other characterized canine astroviruses. doi = 10.1016/j.cimid.2018.08.002 id = cord-282742-eyukbot7 author = Diosa-Toro, Mayra title = Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date = 2013-02-20 keywords = DENV; RNA; WNV; virus summary = Geiss, Pierson, and Diamond (2005) observed that siRNAs targeting the C gene had no effect on virus replication when transfected into cells 10 h after WNV infection using lipid-based reagents. In addition, no significant reduction in viral protein or RNA levels was seen in WNV replicon-expressing cells transfected with siRNAs targeting the NS3 gene using lipid-based reagents. Also, a recent report showed that siRNA toward the TNF-a gene reduced cytokine response in DENV-infected DCs, highlighting the potential of targeted RNAi-based approaches to simultaneously decrease viral replication and the detrimental host immune response (Subramanya et al., 2010) . In addition, it has been shown that WNV (Chotkowski et al., 2008) and DENV (Mukherjee & Hanley, 2010) infection (Mukherjee & Hanley, 2010) of Drosophila cell lines induce functional virus-specific siRNAs that promote a protective RNAi response. So far we have described the antiviral effect of the RNAi mechanism induced by exogenous delivery of siRNA or precursors, and how cellular miRNA can target sequences artificially introduced within the genome of flaviviruses. doi = 10.1016/b978-0-12-408116-1.00004-5 id = cord-104286-5yw4zwo4 author = Doane, F. W. title = Virus morphology as an aid for rapid diagnosis. date = 1980 keywords = virus summary = A specimen is inoculated into a host system (tissue culture, eggs, animals), and subsequent detection and identification of an isolated virus depends on indicators such as cytopathic effect, hemagglutinin, complement fixation, etc. The following brief review will examine some of the ways in which virus morphology can serve as an important aid for rapid virus diagnosis, some of the limitations of this approach, and current and future developments in electron microscopy relating to diagnostic virology. The same results can be obtained within one hour if one uses immunoelectron microscopy (IEM), by which the virusantiserum mixtures are negatively stained and examined on an EM specimen grid. A major advantage of using electron microscopy for rapid virus diagnosis is that one can actually see the virus and identify it by its morphology. Hepatitis A: detection by immune electron microscopy of a virus-like antigen associated with acute illness doi = nan id = cord-309488-8guapzke author = Dodd, R. title = Other emerging viral pathogens date = 2006-08-15 keywords = USA; infection; virus summary = Attention was refocused on viral infections as a result of the outbreak of West Nile virus (WNV) disease in the USA along with the recognition that it was transmissible by transfusion [1] . In 1997, Blackbourn and colleagues [17] reported on the detection of HHV-8 DNA in the blood of a seropositive blood donor; based on evidence of in vitro passage of the virus to allogeneic cells, the authors expressed concern about the potential for transmission by transfusion. This concern is based upon the historical fact that there have been periodic pandemics associated with the circulation of new strains of the virus in humans and the current outbreak of the H5N1 strain of avian influenza, which causes high mortality when it does infect humans [27] . Seroprevalence of human herpes virus 8 antibody in populations at high or low risk of transfusion, graft, or sexual transmission of viruses Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent doi = 10.1111/j.1751-2824.2006.00043.x id = cord-016538-4og05fuo author = Dolja, V. V. title = Biotechnology Applications of Grapevine Viruses date = 2017-03-30 keywords = RNA; virus summary = Although in theory any of the grapevine-infecting viruses can be engineered into transient gene expression or VIGS vector, in practice, only one of them, the filamentous Grapevine leafroll-associated virus-2 (GLRaV-2) from the genus Closterovirus (family Closteroviridae), was demonstrated to fulfill these roles (Dolja and Koonin 2013; Kurth et al. Among these viruses, only GLRaV-2, a closterovirus, has been so far engineered into a vector capable of systemic infection of grapevine that either produces recombinant protein or elicits VIGS response (Kurth et al. The more recently developed CTV-based gene expression vectors were shown to be not only capable of systemic infection in the natural citrus hosts but also exhibited remark-able genetic stability in regard to retention of the inserted recombinant gene, as well as VIGS capability (Dawson et al. Another candidate to be developed as a vector for protein expression and VIGS is GRSPaV, which is the only grapevine-infecting member of the genus Foveavirus that was recently characterized (Meng et al. doi = 10.1007/978-3-319-57706-7_31 id = cord-290481-i2ppvsh5 author = Dolja, Valerian V. title = Comparative and functional genomics of closteroviruses date = 2006-03-09 keywords = BYV; Fig; RNA; virus summary = It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . doi = 10.1016/j.virusres.2006.02.002 id = cord-270670-cubh9jxc author = Domingo, E. title = Viruses as Quasispecies: Biological Implications date = 2006 keywords = RNA; mutant; viral; virus summary = a Upon infection with an RNA virus (even with a single particle, as depicted here, enlarged about 10 6 times), viral replication leads to a mutant spectrum of related genomes, termed viral quasispecies. As further discussed in the text, in real infections multiple mutant spectra that can amount to a large number of replicating (or potentially replicating) genomes (up to 10 9 or even 10 12 per infected individual) provide highly dynamic mutant repertoire viral yields in cell culture, have been immensely powerful in characterizing the population dynamics of RNA viruses (see references in the reviews by Domingo and Holland 1997; Quiñones-Mateu and Arts 2002; Novella 2003; and the chapters by Quiñones-Mateu and Arts and Escarmís et al., this volume) . Despite these limitations, determination of nucleotide sequence heterogeneities in virus populations using correct reagents and adequate controls has consistently documented that most RNA viruses (and also some DNA viruses) consist of complex mutant spectra, with an average number of 1-100 mutations per genome (Sect. doi = 10.1007/3-540-26397-7_3 id = cord-022128-r8el8nqm author = Domingo, Esteban title = Molecular basis of genetic variation of viruses: error-prone replication date = 2019-11-08 keywords = HIV-1; RNA; chapter; dna; genome; mutation; recombination; virus summary = In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity. doi = 10.1016/b978-0-12-816331-3.00002-7 id = cord-280048-b4dz1lnn author = Domingo, Esteban title = Viral quasispecies date = 2019-10-17 keywords = RNA; mutant; population; viral; virus summary = Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ). doi = 10.1371/journal.pgen.1008271 id = cord-298033-kzdp9edn author = Domingo, Esteban title = Quasispecies dynamics in disease prevention and control date = 2019-11-08 keywords = HCV; HIV-1; chapter; drug; mutant; resistance; section; viral; virus summary = Quasispecies dynamics in disease prevention and control following statement will be obvious to the reader: "If a single mutation is able to confer resistance to an antiviral agent, and the mutation does not cause a significant selective disadvantage to the virus (fitness decrease) in the considered environment, a drug-resistant virus mutant will be present in most, if not all, virus populations" (Domingo, 1989) . The phenotypic barrier to drug resistance is equivalent to the fitness cost inflicted upon the virus by the mutations and corresponding amino acid substitution(s) required for resistance [Fitness cost is treated in Chapter 4 (Section 4.6) and in Chapter 7 (Section 7.4.2) in connection with the frequency of monoclonal antibody-or cytotoxic T-cell-escape mutants in viral populations]. For viruses that replicate in cell culture, it is possible to estimate the minimal viral population size needed to select a drug-resistant mutant which is generally positively correlated with the genetic barrier ( Fig. 8.5 ). doi = 10.1016/b978-0-12-816331-3.00008-8 id = cord-303265-v6ci69n0 author = Domingo, Esteban title = Introduction to virus origins and their role in biological evolution date = 2019-11-08 keywords = Earth; Eigen; RNA; cell; chapter; dna; life; origin; virus summary = Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). doi = 10.1016/b978-0-12-816331-3.00001-5 id = cord-252147-bvtchcbt author = Domingo-Espín, Joan title = Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date = 2011-11-15 keywords = VLP; cell; delivery; dna; drug; gene; like; particle; peptide; protein; virus summary = Modular protein engineering, virus-like particles (VLPs), and other self-assembling entities are envisioned as modulatable novel protein nanoparticles able to include many desirable properties in the correct delivery of drugs and nucleic acids. 120 Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA or drugs present an attractive approach for the development of self-assembling vectors for targeted gene or drug delivery. 215, 216 Although VLP-based vaccines have been primarily developed for their use against the corresponding virus, in the last decades genetic engineering or chemical modifications have been applied in order to generate chimeric VLPs. Thus, on the one hand, commonly short heterologous peptide epitopes or full proteins that are unable to form VLPs or that are unsafe for vaccination have been presented on surface-exposed loops or fused to N-or C-exposed termini of structural viral capsid proteins on VLPs. 154, 161, 210 Different HPV, 217-219 HBV, 220,221 parvovirus, 222, 223 and chimeric polyoma VLPs have been engineered 170, 175 and tested for different applications including vaccination against viral or bacterial diseases, against virus-induced tumors, and more recently, for immunotherapy of nonviral cancer. doi = 10.1016/b978-0-12-416020-0.00006-1 id = cord-006892-n2ncamqh author = Donaldson, Braeden title = Virus-like particle vaccines: immunology and formulation for clinical translation date = 2018-09-19 keywords = VLP; like; particle; vaccine; virus summary = For example, chemical conjugation of mannoside-based saccharides on the surface of Rabbit hemorrhagic disease virus (RHDV) VLP selectively targets the mannose receptor expressed on the surface of APCs, inducing increased uptake and alteration of antigen cross-presentation in murine dendritic cells [57] . While the induction of a potent humoral immune response and the subsequent production of anti-VLP antibodies is the primary desired outcome of most commercial VLP vaccines, these is increasing appreciation for the role of vaccine-induced cell-mediated immunity [123] [124] [125] . Novel Epstein-Barr virus-like particles incorporating gH/gL-EBNA1 or gB-LMP2 induce high neutralizing antibody titers and EBV-specific T-cell responses in immunized mice Induction of immune memory following administration of a prophylactic quadrivalent human papillomavirus (HPV) types 6/11/16/18 L1 virus-like particle (VLP) vaccine. Antigen incorporated in virus-like particles is delivered to specific dendritic cell subsets that induce an effective antitumor immune response in vivo doi = 10.1080/14760584.2018.1516552 id = cord-318725-09a32vyg author = Dong, Rui title = Virus Database and Online Inquiry System Based on Natural Vectors date = 2017-12-17 keywords = Baltimore; natural; virus summary = The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Using the natural vector representation, if a viral genome consists of a single-nucleotide sequence, known as single-segmented, then the virus will be represented by a 12-dimensional numerical vector in the database. As natural vector can reflect core information stored in sequences and genomes, we use it to construct the virus classification system introduced in this article. doi = 10.1177/1176934317746667 id = cord-003122-a3f4l6iu author = Dou, Dan title = Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date = 2018-07-20 keywords = RNA; figure; influenza; virus summary = The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments ( Figure 1A ) (3, 4) , which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins ( Figure 1B) . In contrast to the early steps in IAV entry, vRNP trafficking to the nucleus following the fusion event is highly dependent on the host cell machinery and transport pathways [reviewed in Ref. doi = 10.3389/fimmu.2018.01581 id = cord-312964-vsrqmmv7 author = Doyle, William J. title = Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date = 2003 keywords = AOM; infection; virus; vuri summary = Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Active synergy between certain upper respiratory viruses and nasopharyngeal pathogens was demonstrated for OM pathogenesis in chinchillas and humans [27] [28] [29] , and pre-existing or concurrent vURI in infants and children with acute, bacterial OM is frequently observed [24, 25] . In one double-blind clinical study, intranasal steroid (fluticasone propionate) was administered for 7 days immediately after onset of vURI symptoms in an attempt to decrease nasopharyngeal inflammation (and possible eustachian-tube obstruction), but was not efficacious in preventing AOM and might have increased OM incidence during rhinovirus infection [69] . doi = 10.1007/s11882-003-0093-7 id = cord-293540-45awgabp author = Drancourt, Michel title = Point-of-care testing for community-acquired pneumonia date = 2013-07-23 keywords = POC; virus summary = The rate and timing of pandemic A H1N1 virus infections might have revealed the diff erences in H7N9 disease outcome, by contrast with historical infections with seasonal infl uenza A H3N2 viruses. To avoid this delay, we introduced point-of-care (POC) microbiology laboratories near emergency departments where patients with community-acquired pneumonia are seen fi rst. However, it should be noted that not all pathogens that can cause community-acquired pneumonia can be detected by POC tests, and molecular tests for Staphylococus aureus have not been approved by the US Food and Drug Administration (FDA) or the European Conformity (CE). 9 This new capacity of POC tests increases the number of diagnoses 11 and underscores that community-acquired pneumonia can result from co-infection with several pathogens, 10 which will challenge common notions about causation and management. Furthermore, detection by POC testing of an abnormal increase in group A streptococci might suggest co-infection with infl uenza. doi = 10.1016/s1473-3099(13)70165-8 id = cord-286719-1xjmlwqr author = Draz, Mohamed Shehata title = Applications of gold nanoparticles in virus detection date = 2018-02-15 keywords = AuNPs; Fig; HBV; HCV; HIV; RNA; assay; detection; dna; virus summary = The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . doi = 10.7150/thno.23856 id = cord-279557-hk77e3pp author = Drosten, Christian title = Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection date = 2013-06-17 keywords = Germany; MERS; patient; virus summary = BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. [4] [5] [6] Here, we provide a full description of a fatal case of MERS-CoV infection imported to Munich, Germany, from Abu Dhabi, including a chronological profi le of virus concentrations in diverse body compartments. We subjected all available MERS-CoV genome sequences to phylogenetic analysis, including a correlation and regression analysis of known dates of virus isolation versus tree branch lengths (fi gure 3). Without quantitative laboratory data from well documented cases of MERS-CoV infection, most considerations had been made on the basis of an assumed analogy to severe acute respiratory syndrome (SARS). The recorded viral load profi le, with highest RNA concentrations in bronchoalveolar lavage and tracheobronchial aspirates, confi rms suggestions made in another report about the preferential use of lower-respiratory-tract samples for virus diagnostic tests. doi = 10.1016/s1473-3099(13)70154-3 id = cord-304850-9xetsc2c author = Drosten, Christian title = Virus ecology: a gap between detection and prediction date = 2013-05-22 keywords = bat; virus summary = 7, 8 These and other recent findings remind us of an important issue in viral reservoir ecology: non-persisting viruses are maintained on a social level, requiring large, dense and interconnected host groups for their perpetual transmission. 13 There are prominent examples of bat-borne viruses that can be passed between humans, including Ebola virus, Marburg virus, Nipah virus and the severe acute respiratory syndrome agent. However, there remains a large gap between the many studies describing novel reservoir-borne viruses and our capabilities to use this knowledge to predict or prevent future human disease outbreaks. 13 As we dig deeper into viral reservoir ecology, including its man-made modifications, we may find that changes in host populations affect the transmission and maintenance of viruses with possible consequences for their potential to infect humans (Figure 1 ). Habitat fragmentation Resource abundance Change of social structure Risk Virus replication / transmission Duration of excretion / infectivity Figure 1 Modification of viral maintenance optimum. doi = 10.1038/emi.2013.25 id = cord-260690-h5pjv2dw author = Druce, Julian title = Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date = 2004-11-12 keywords = PCR; influenza; virus summary = A total of 333 additional respiratory specimens, including 20 from asymptomatic laboratory staff was used to validate the PCR assays for influenza A virus (H1 and H3 subtypes), influenza B virus, RSV, parainfluenza viruses (at least one of types 1-3), picornaviruses (a mixture of enteroviruses and rhinoviruses), and adenoviruses (each of different serotype) (Table III) . The process included the design and evaluation of primers; optimization of nucleic acid extraction conditions; establishment of optimum PCR amplification conditions; evaluation of applicable specimen types; determination of assay sensitivity compared to conventional assays; specificity testing using clinical material likely to be negative (including asymptomatic staff volunteers); or material previously shown to be positive for respiratory viruses by conventional assays or by sequencing of an amplified product where no other confirmatory method was available. doi = 10.1002/jmv.20246 id = cord-294108-uvnh0s9r author = Dube, Taru title = Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date = 2020-10-25 keywords = COVID-19; CoV-2; FDA; Phase; RNA; SARS; patient; vaccine; virus summary = [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. doi = 10.1002/adtp.202000172 id = cord-313301-7mkadtp9 author = Duffy, Siobain title = EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date = 2007-08-23 keywords = RNA; host; virus summary = In particular, the high pernucleotide mutation rates of RNA viruses (Drake 1993) provide extensive genetic variation that fuels evolution by natural selection, making the study of reproductive isolation and speciation especially feasible (Holmes 2004) . We tested the plausibility of the no-gene mechanism of speciation by examining the consequences of adaptation to a novel host in laboratory populations of the RNA phage 6, which infects a number of Pseudomonas species. The same microevolutionary processes of mutation and natural selection, which led to the adaptation of 6 populations to a novel host also resulted in a macroevolutionary event: the evolution of a new virus species that is reproductively isolated from the ancestral phage 6 wt . Beyond uniquely demonstrating the evolution of reproductive isolation in the laboratory, our study extends the literature describing the evolutionary genetics of narrowed host range when viruses adapt to a single host. doi = 10.1111/j.1558-5646.2007.00226.x id = cord-269975-1ebmq7t8 author = Duplantier, Allen J. title = Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date = 2020-05-27 keywords = Burkholderia; Ebola; FDA; RNA; host; infection; treatment; virus summary = None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. doi = 10.1016/b978-0-12-818480-6.00007-2 id = cord-323987-gh1m05gi author = Dziąbowska, Karolina title = Detection Methods of Human and Animal Influenza Virus—Current Trends date = 2018-10-18 keywords = Influenza; PCR; RNA; Rapid; detection; virus summary = RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional ''gold star'' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. doi = 10.3390/bios8040094 id = cord-022393-s26d54ew author = E. Newcomer, Christian title = Zoonoses and Other Human Health Hazards date = 2007-09-02 keywords = LCMV; Mus; animal; disease; human; infection; laboratory; mouse; virus summary = Wild caught mice that are maintained in naturalistic housing environments in the laboratory, laboratory mice that have contact with wild or feral mice, and mice kept as pets in the home environment are examples of animal management conditions that would be conducive to the expression and transmission of zoonotic diseases and other mouse-associated implications in the New World serocomplex group are present among the wild rodents endemic to the United States such as Neotoma spp. Many published reports of human LCM infection are associated with laboratory animal and pet contact, particularly mice and hamsters, and these studies now span many decades (Armstrong and Lillie 1934; Bowen et al. The apparent ease with which LCMV is transmitted to humans also occurs in a variety of other laboratory animal species; hamsters, guinea pigs, swine, dogs, and nonhuman primates, especially callitrichids, which readily sustain natural infections. akari infections depend on the prevention of wild mice and the mite vector from entering laboratory animal facilities and human dwellings. doi = 10.1016/b978-012369454-6/50054-6 id = cord-255217-l2ak5ygj author = Eccles, Ronald title = Why is temperature sensitivity important for the success of common respiratory viruses? date = 2020-08-10 keywords = sensitivity; temperature; virus summary = 34 It has been known for some time that human influenza viruses vary in their temperature sensitivity with those adapted to the cooler human airway causing mild disease and those adapted to higher temperatures causing more serious lower respiratory tract infections. 44, 45 The common cold syndrome is a mild disease because the respiratory viruses have a permissive temperature sensitivity close to that found in the human upper airways 30 C-34 C and a restrictive temperature sensitivity that conThe acquisition of temperature sensitivity is key to the success of a respiratory virus and this is well illustrated with emerging avian influenza H5N1. The temperature sensitivity of respiratory viruses should be considered as an important factor in determining their success as parasites of the human airway. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology doi = 10.1002/rmv.2153 id = cord-342412-azkamnpa author = Ecker, David J title = The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date = 2005-04-25 keywords = Additional; File; RNA; United; disease; figure; virus summary = This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. For example, the Centers for Disease Control and Prevention (CDC) maintains an ever-changing list of notifiable diseases, the National Institute of Allergy and Infectious Disease (NIAID) lists agents with potential for use in bioterrorist attacks, and the Department of Health and Human Services (HHS) maintains a list of critical human pathogens. This article focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. It provides a compilation of lists, taken from the database, of important and/or regulated biological agents from a number of agencies including HHS, the United States Department of Agriculture (USDA), the CDC, the World Health Organization (WHO), the NIAID, and other sources. doi = 10.1186/1471-2180-5-19 id = cord-289406-54vyzxjf author = Edwards, Suzanne title = An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date = 1992-01-17 keywords = heart; infection; virus summary = In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. Both Coxsackie Band encephalomyocarditis virus infections in mice may progress to myocarditis and congestive heart failure, and some survi-vors may progress to a dilated cardiomyopathy later in life [5, [14] [15] [16] . Rabbits that died on days 10-12 had pleural effusion, pulmonary edema, ascites, enlarged hearts, dilated right and left ventricular cavities, and congestion in the lungs and liver. It seems likely that pleural effusion disease virus infection also results in a significant percentage of animals dying from heart failure, since degeneration and necrosis of myocytes, pulmonary edema, pleural effusion, dilated ventricles, and congestion of the lungs, liver, and spleen are common [18, 26] . doi = 10.1093/infdis/165.1.134 id = cord-318686-we6pveus author = Ehlen, Lukas title = Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses date = 2016-05-04 keywords = VSV; cell; virus summary = CONCLUSION: In the current study, we showed that newly established cell lines from the cotton rat can serve as host-specific in vitro models for viral infection experiments. The cotton rat (Sigmodon hispidus) is a unique example of a rodent species that is a well-established animal model to study viral pathogenesis and is also associated with a large range of zoonotic viruses in the wild [20] [21] [22] . To evaluate whether the broad viral susceptibility seen in both animalmodel and wild cotton rats was also reflected in in vitro cell culture models, we generated continuous cell lines from the respiratory and renal tracts of a cotton rat, and assessed their use for virus replication studies of known and potentially novel zoonotic viruses. In the work presented herein, we generated epithelial cell lines from the respiratory and renal tracts of a cotton rat due to its susceptibility to a broad range of human viruses, as well as the association of multiple important and emerging zoonotic viruses with this species. doi = 10.1186/s12985-016-0531-5 id = cord-337914-1hwnxkdd author = Ehlkes, L. title = Epidemiologie des Ebolafiebers und anderer, in Deutschland seltener hochkontagiöser, lebensbedrohlicher Erkrankungen date = 2015-05-22 keywords = Congo; Ebola; Ebolavirus; Lassa; Organisation; Virus summary = Hochsicherheitsbetten für die Versorgung von Patienten mit Ebolafieber gibt es -anders als in industrialisierten Ländern -in den Ausbruchsgebieten in der Regel nicht. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Subsequent human-to-human transmission can lead to epidemics, such as the current outbreak of Ebola virus disease in West Africa. Ebola virus disease · Highly contagious · Outbreak · Epidemic · Viral hemorrhagic fever laufen derzeit z. Die Epidemiologie von Lassa-Fieber ist eng geknüpft an das zeitliche und räumliche Auftreten des wichtigsten Reservoirtiers, der Vielzitzenmaus (Mastomys natalensis), in der Nähe des Menschen. Neben intensivmedizinischen Maßnahmen wird Ribavirin zur antiviralen Therapie gegen das Lassa-Virus eingesetzt [42] , das bei Behandlung in den ersten sechs Tagen nach Beginn der Symptomatik die Letalität bei Lassa-Fieber von 60-80 % auf 10 % senken kann [43] . Die Falldetektion mit anschließender Isolierung ist auch bei SARS das Rückgrat der Ausbruchs-Kontrolle. doi = 10.1007/s00103-015-2165-y id = cord-302529-43pd2qsp author = El Moussi, Awatef title = Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date = 2013-09-19 keywords = Influenza; Tunisia; virus summary = METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses'' infection during three seasons in Tunisia. A subset of sentinel primary care physicians participating in virological surveillance schemes in the community submits respiratory samples for virological testing from patients presenting in primary health care with an ILI, as well as all regional emergency centres and hospitals that take on surveillance of influenza from community, hospitalized and fatal cases. Phylogenetic analysis of the HA1 nucleotid sequence of 23 influenza A(H1N1)pdm09 viruses from mild, severe (patients hospitalized with severe pneumonia and severe acute respiratory syndrome) and fatal cases, shows that all viruses characterised in Tunisia during season 2009-2010 were outside the seven genetic groups described in the European Centre for Disease Prevention and Control (ECDC) report [19] . doi = 10.1371/journal.pone.0074064 id = cord-003598-m2fsrwvw author = Elbahesh, Husni title = Response Modifiers: Tweaking the Immune Response Against Influenza A Virus date = 2019-04-12 keywords = IAV; infection; influenza; virus summary = doi = 10.3389/fimmu.2019.00809 id = cord-007784-fq2urilg author = Elderfield, Ruth title = Influenza Pandemics date = 2011-09-22 keywords = H1N1; H3N2; PB1-F2; influenza; pandemic; virus summary = H5N1 virus has been responsible for over 500 cases of human infection and 300 deaths (as of 31st August 2010 according to the World Health Organisation avian influenza surveillance system) but thankfully has not yet reassorted with a human-adapted influenza virus, nor given rise to a pandemic outbreak [45] . For avian influenza viruses to adapt to and transmit between humans, it is now apparent that in addition to the reassortment events that occur during antigenic shift, their HA proteins must also undergo modifications that alter their fine receptor binding specificity. However, the human seasonal virus had changed so dramatically that it shared only 79% amino acids with the 1918 HA protein, and this did not allow for any antigenic cross protection for humans who had been infected with seasonal H1 in recent years against the novel 2009 pandemic strain. doi = 10.1007/978-1-4614-0204-6_8 id = cord-317851-lj07947c author = Elena, S F title = Experimental evolution of plant RNA viruses date = 2008-02-06 keywords = RNA; evolution; virus summary = In this review, we will focus on recent studies that used plant viruses to address evolutionary questions of general interest, such as the rate and fitness effects of deleterious mutations and the role of neutrality as a source of mutational robustness, the evolution of generalist viruses, or the effect of vertical versus horizontal transmission on virulence. Despite mutation rate is still high compared to that of DNA-based microorganisms, a classic field observation is that natural plant virus populations generally exhibit limited genetic variation (García-Arenal et al., 2001) , which may imply either that purifying selection may be strong or that genome replication occurs mainly by Luria''s stamping machine model (Luria, 1951) rather than exponentially (French and Stenger, 2003) , the two hypotheses being nonexclusive. doi = 10.1038/sj.hdy.6801088 id = cord-301064-ex6qb6zj author = Elena, Santiago F. title = Editorial: A home for virology, ecology, epidemiology, and evolutionary biology date = 2015-03-26 keywords = evolution; virus summary = Although genetic diversity is an essential part of virus biology, classical approaches to virus control often ignore evolutionary processes and focus on understanding in great detail the molecular bases of pathogenesis, virus-host interaction, and drug-virus interference. Although many studies appear in evolutionary biology journals, particularly those on viral experimental evolution, mathematical modeling, molecular evolution, and phylogenetics, a large proportion are submitted to journals that focus on virology and pathogenesis. We have established the journal Virus Evolution with this aim in mind, and we hope that it will grow into a successful and dynamic inter-disciplinary community of researchers interested in understanding why and how viruses have and continue to evolve. The Board has expertise in animal, plant, and bacterial viruses and in a wide range of techniques, including experimental evolutionary biology, molecular epidemiology, metagenomics, structural biology, population genetics, ecology, and molecular virology. doi = 10.1093/ve/vev001 id = cord-336510-qzm9wgde author = Ellermann-Eriksen, Svend title = Macrophages and cytokines in the early defence against herpes simplex virus date = 2005-08-03 keywords = HSV; IFN; IL-12; IL-4; TNF; cell; infection; virus summary = In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. Generally the type I IFNs exhibit a huge range of biological effects, such as antiviral and antiproliferative effects, stimulation of immune cells such as T cells, natural killer (NK) cells, monocytes, macrophages, and dendritic cells, increased expression of MHC-I, activation of pro-apoptotic genes and inhibition of anti-apoptotic mechanisms, modulation of cellular differentiation, and inhibition of angiogenesis [171] . Effect of IL-4 and IL-13 on IFN-gamma-induced production of nitric oxide in mouse macrophages infected with herpes simplex virus type 2 Herpes Simplex virus type 1-induced interferon production and activation of natural killer cells in mice NF-kappaB activation is responsible for the synergistic effect of herpes simplex virus type 2 infection on interferon-gamma-induced nitric oxide production in macrophages doi = 10.1186/1743-422x-2-59 id = cord-022947-ruizhgwh author = Elliot, Elisa L title = Indicator organisms for estuarine and marine waters date = 2006-03-27 keywords = bacteria; coliform; fecal; indicator; virus; water summary = These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . doi = 10.1111/j.1574-6968.1985.tb01183.x id = cord-320055-6ycp8m89 author = Elliot, Elisa L title = Indicator organisms for estuarine and marine waters date = 1985-07-31 keywords = bacteria; coliform; fecal; indicator; virus; water summary = These bacteria and other coliforms were used in the past as indicators of water-borne pathogens, that is, the presence of fecal contamination being correlated with the occurrence of pathogens, for which direct detection methods were not available. Total coliforms are the most universally used indicator group, but include bacteria, in addition to Escherichia coil, that are not specifically associated with fecal pollution, i.e., Klebsiella spp., Citrobacter spp., and Enterobacter spp. Finding an appropriate indicator for the presence of enteric viruses, i.e., poliovirus, coxsackievirus A, coxsackievirus B, and echovirus [50, 147] , in sea water, is a vexing problem, especially for those responsible for regulating the use of sewage-contamined sites, including fresh, estuarine, and marine water and sediment, and shellfish harvested from these waters. Correlations between the number of fecal bacterial pathogens and indicator bacteria and their respective bacteriophages in fresh and marine water have been reported [185] . doi = 10.1016/0378-1097(85)90057-6 id = cord-298862-8bijio30 author = Eltom, Kamal H. title = Buffalopox Virus: An Emerging Virus in Livestock and Humans date = 2020-08-20 keywords = BPXV; India; VACV; virus summary = Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à-vis the vaccine strains. Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India doi = 10.3390/pathogens9090676 id = cord-326719-p1ma4akz author = Enjuanes, Luis title = Virus-based vectors for gene expression in mammalian cells: Coronavirus date = 2003-12-31 keywords = RNA; TGEV; gene; virus summary = Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. doi = 10.1016/s0167-7306(03)38010-x id = cord-021805-2j07zw6q author = Epstein, Jonathan H. title = Emerging Diseases in Bats date = 2018-09-28 keywords = Ebola; SARS; bat; virus summary = 6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts. doi = 10.1016/b978-0-323-55228-8.00040-0 id = cord-338400-30vl2hks author = Epstein, Jonathan H. title = Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date = 2010-07-01 keywords = GBV; bat; virus summary = Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades. GBV-A viruses have been described in New World primates and are not known to infect humans [17] [18] [19] , while GBV-C (also known as Hepatitis G virus (HGV)) have frequently been isolated from humans in many regions of the World, including India and Bangladesh [19] [20] [21] [22] [23] , and from wild chimpanzees (Pan troglodytes) in Africa [24, 25] . Our findings provide new insight into the range of known hosts for GB-like viruses and demonstrate the power of unbiased sequencing to characterize the diversity of potentially zoonotic pathogens carried by bats and other reservoirs. Molecular analyses of sera from Pteropus giganteus bats from Faridpur, Bangladesh led to the identification of a 9,633 nt sequence consistent in genomic organization with known GBV and other species within the family Flaviviridae [16] . doi = 10.1371/journal.ppat.1000972 id = cord-001616-9sc2xmqr author = Erdem, Hakan title = New global viral threats date = 2015 keywords = Ebola; H7N9; virus summary = In March 2014, the Ministry of Health of Guinea reported a disease outbreak characterized by fever, severe diarrhea, vomiting, and a high case-fatality rate. 31 One avian influenza case was detected in Taiwan due to H6N1 subtype, whereas 2 of 3 H10N8 human infections observed in China were lethal. In late March 2013, novel human infections due to avian influenza A H7N9 virus were reported from China. Frequently Asked Questions on human infection caused by the avian influenza A(H7N9) virus Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a populationbased study of laboratory-confirmed cases Human infections with avian influenza A(H7N9) virus Human infection with avian influenza A(H7N9) virus -update Human infection with a novel avian-origin influenza A (H7N9) virus Epidemiology of human infections with avian influenza A(H7N9) virus in China doi = 10.15537/smj.2015.4.10089 id = cord-015871-1tuf4zxi author = Ergonul, Onder title = Treatment of Crimean-Congo Hemorrhagic Fever date = 2007 keywords = CCHF; Congo; Crimean; RNA; ribavirin; virus summary = In contrast, a dose of ribavirin at least nine times greater was required to induce a comparable inhibitory effect on the yields of Rift Valley fever virus, for which the drug has been shown to inhibit replication in monkeys and rodents [104] . However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. In recent times, several groups have studied the antiviral activities of interferons against hemorrhagic fever viruses. Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus Type I interferon inhibits Crimean-Congo hemorrhagic fever virus in human target cells Genotoxic effect of ribavirin in patients with Crimean-Congo hemorrhagic fever Ribavirin efficacy in an in vivo model of Crimean-Congo hemorrhagic fever virus (CCHF) infection Inhibition of Crimean-Congo hemorrhagic fever viral infectivity yields in vitro by ribavirin doi = 10.1007/978-1-4020-6106-6_19 id = cord-334941-6uattdti author = Espmark, Åke title = Other viruses date = 2014-06-27 keywords = Lassa; fever; virus summary = Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. Of the orbiviruses, the Colorado tick fever virus is the only one known to cause disease in man. It has recently been demonstrated that its aetiological agent probably is a bunyavirus which is antigenically related to haemorrhagic fever virus, and is endemic in the Soviet Union and large parts of Asia {Korean haemorrhagic fevery see also Chapter 34). In non-endemic areas units for the hospital care of imported cases of Lassa fever are needed as are the high-risk units of the national virological laboratories permitting work with highly contagious viruses like that of the Lassa fever. In 1967 a number of cases of a haemorrhagic disease with a considerable mortality rate was reported from laboratories at Marburg in the Federal Republic of Germany. Rabies virus causes an acute CNS disease which is lethal for man. doi = 10.1016/b978-0-407-00253-1.50038-4 id = cord-288348-b10e023s author = Estes, Mary Kolb title = Epidemic viral gastroenteritis date = 1979-06-30 keywords = Norwalk; agent; gastroenteritis; virus summary = Of the many viruses identified in stools, only two groups have met the criteria as definite etiologic agents of epidemic gastroenteritis in human subjects: rotaviruses and the small 27 nm agents [Norwalk-like agents) ( of investigations which began with an epidemic of gastroenteritis occurring in the newborn in the Baltimore-Washington area in the fall of 1941. Rotaviruses have been established as enteritis viruses by isolation and purification from stools of subjects suffering from gastroenteritis, and by induction of disease and seroconversion in both animals and volunteer subjects with purified preparations, Epidemiologic studies on the prevalence of rotavirus infections have shown these ubiquitous agents to be a major cause of gastroenteritis in children. Local immune factors, such as secretory immunoglobulin A or interferon, may therefore be important in protection against rotavirus infection, Alternatively, reinfection in the presence of circulating antibody could reflect the presence of multiple serotypes of virus [37] ; at least four agents in human subjects have been characterized to date [38-411. doi = 10.1016/0002-9343(79)90457-1 id = cord-291946-kq0rsuxj author = Etienne, Lucie title = The Mongoose, the Pheasant, the Pox, and the Retrovirus date = 2013-08-27 keywords = REV; host; virus summary = The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20 th century. doi = 10.1371/journal.pbio.1001641 id = cord-008686-9ybxuy00 author = Everett, Tom title = Poor transmission of seasonal cold viruses in a British Antarctic Survey base date = 2019-03-14 keywords = China; H1N1; H7N9; SHBV; case; virus summary = However, in the acute infection stage respiratory viruses are generally present in relatively high copy numbers, with median values of mostly 4-8 log 10 (i.e. 10,0 0 0-10 0,0 0 0,0 0 0 copies/ml) for adeno-, corona-, hMPV, influenza, PIV and RSV, as reported in one comprehensive paediatric study. 2 A 26-year-old male ( index case of the outbreak report 2 ) from Kerala''s Perambra town died undiagnosed with fever, en-cephalitis and respiratory distress in Government Medical College Kozhikode(GMCK), after being transferred from Taluk Hospital, Perambra(THP). 6 Along with the wound cleansing and post-exposure rabies immunoglobulin (RIG) and vaccination, any risk of SHBV requires that high dose acyclovir (preferably valaciclovir 1 g TDS PO; or acyclovir 800 mg 5 times daily PO, for adults) PEP for at least 14 days should be considered. After the first dengue-fever epidemic in China, which occurred in May 1978 in Foshan, Guangdong Province, there have been regional outbreaks of dengue every year and the number of cases has increased. doi = 10.1016/j.jinf.2019.03.007 id = cord-001120-fxd533b4 author = Everitt, Aaron R. title = Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date = 2013-11-21 keywords = Ifitm3; RSV; figure; infection; virus summary = We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). doi = 10.1371/journal.pone.0080723 id = cord-345848-s84lxe6l author = Everitt, Aaron R. title = IFITM3 restricts the morbidity and mortality associated with influenza date = 2012-03-25 keywords = Fig; Ifitm3; Supp; influenza; virus summary = We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. We find that a statistically significant number of hospitalised subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Given the higher viral load in Ifitm3 −/− mice and increased replication of influenza A virus in Ifitm3 deleted cells in vitro (Fig. 1d) , we examined both viral nucleic acid and protein distribution in the lung. Analysis of cell populations resident in the lung tissue on day 6 post-infection showed that Ifitm3 −/− mice displayed significantly reduced proportions of CD4+ (p=0.004) and CD8+ Tcells (p=0.02) and natural killer (NK) cells (p=0.0001) but an elevated proportion of neutrophils (p=0.007) (Fig. 3a) . doi = 10.1038/nature10921 id = cord-325827-492xi3ee author = Evermann, J. F. title = Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah date = 1988 keywords = FIPV; cheetah; feline; virus summary = Subsequent observations based upon seroepidemiological surveys and electron microscopy of fecal material verified that cheetahs were indeed capable of being infected by coronaviruses, which were antigenically related to coronaviruses affecting domestic cats, i.e. feline infectious peritonitis virus/feline enteric coronavirus. The purpose of this review is to present desciptions of the various forms of coronaviral infections in the cheetah relying upon studies of both natural infections, as well as experimental infections in other species with coronaviruses, such as mouse hepatitis virus (MHV), canine coronavirus (CCV), transmissible gastroenteritis virus (TGEV) of swine, and bovine coronavirus (BCV) of neonatal calves [28, 36, 39, 49, 57, 60, 61, 75, 79, 92] . The occurrence of coronaviral infections of the cheetah have now been documented based on serology, electron microscopy of fecal contents, and the occurrence of fatal forms of infectious peritonitis compatible with the clinicopathologic signs observed in domestic cats with FIP [7, 10, 26, 29, 38, 43, 56, 72] . doi = 10.1007/bf01310822 id = cord-048368-wm4c7rk6 author = Evseenko, Vasily A title = Experimental infection of H5N1 HPAI in BALB/c mice date = 2007-07-27 keywords = H5N1; HPAI; virus summary = Serological analysis showed wide cross-reactivity of this virus with sera produced to H5N1 HPAI viruses isolated earlier in South-East Asia. Earlier HPAI viruses were investigated in mice [4, 5] and murine models were successively used for reverse genetics made influenza vaccines [6] . Sequence comparison of the NA protein of A/duck/Tuva/01/06 aligned with the NA of N2 subtype of A/Wuhan/359/95 (H3N2) influenza virus showed phenotype potentially sensitive to neuraminidase inhibitors. Despite powerful anti-influenza virus effects of TNF-α in lung tissue, as it was described previously [28] , we consider that elevated production of the cytokines seems to be crucial in the pathogenesis of HPAI infection. Summing up, in our study BALB/c mice infected with HPAI, strain A/duck/Tuva/01/06, appeared to be able to produce the innate immune response, which culminated to the development of shock and subsequent multiple organ failure. doi = 10.1186/1743-422x-4-77 id = cord-022196-1tionxun author = FENNER, FRANK title = The Nature and Classification of Animal Viruses date = 2013-11-17 keywords = RNA; acid; dna; nucleic; viral; virus summary = With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized. doi = 10.1016/b978-0-12-253040-1.50006-3 id = cord-023705-3q9yr6np author = FENNER, FRANK title = Viral Replication date = 2014-06-27 keywords = Fig; RNA; dna; viral; virus summary = Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis. doi = 10.1016/b978-0-12-253055-5.50008-6 id = cord-023731-jqgervt7 author = FENNER, FRANK title = Laboratory Diagnosis of Viral Diseases date = 2014-06-27 keywords = animal; antibody; diagnosis; viral; virus summary = Having allocated it to a particular family (e.g., Adenoviridae), one can then go on to determine the species or serotype (e.g., canine Immunodiffusion Antibody neutralizes infectivity of virion; inhibits cytopathology, reduces plaques, or protects animals Antibody inhibits viral hemagglutination Antigen-antibody complex binds complement, which is thereafter unavailable for the lysis of hemolysissensitized sheep red blood cells Antibody-aggregated virions are visible by electron microscopy Antibody labeled with fluorochrome binds to intracellular antigen; fluoresces by UV microscopy Peroxidase-labeled antibody binds to intracellular antigen; colored precipitate forms on adding substrate Enzyme-labeled antibody (or antigen) binds to antigen (or antibody); substrate changes color Radiolabeled antibody (or antigen) binds to antigen (or antibody), e.g., attached to solid phase Antibodies and soluble antigens produce visible lines of precipitate in a gel adenovirus 1) by more discriminating serological procedures. doi = 10.1016/b978-0-12-253055-5.50017-7 id = cord-354109-mli0c97c author = Faezi, Nasim Asadi title = Viral infections in patients with acute respiratory infection in Northwest of Iran date = 2017-01-22 keywords = H1N1; RSV; virus summary = The aim of this study was to determine the frequency, mortality and association with clinical entities of influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI. Aim of the present study was to determine the frequency and mortality of the viral respiratory infections including influenza virus type A, influenza virus type B, respiratory syncytial virus (RSV), coronavirus, and adenoviruses in patients with ARI that referred to central Hospital in Northwest of Iran during September 2014 till May 2015. In another study that conducted in a Tehran hospital on children with acute respiratory infection, influenza A virus, RSV, and adenovirus were detected in 4.4, 5.7, and 6.3%, respectively [15] . Diagnosis of the adenovirus, RSV, and influenza virus by rapid detection test (immunochromatography) in children with acute respiratory infection, Iran doi = 10.3103/s0891416816030046 id = cord-334027-xhfmio7k author = Fagre, Anna C. title = Can Bats Serve as Reservoirs for Arboviruses? date = 2019-03-03 keywords = Artibeus; Uganda; bat; egyptian; infection; japanese; virus summary = No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . doi = 10.3390/v11030215 id = cord-023200-3caevjvh author = Falanga, Annarita title = Membranotropic peptides mediating viral entry date = 2018-02-13 keywords = fusion; membrane; peptide; virus summary = The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes. doi = 10.1002/pep2.24040 id = cord-014796-6rw2wk1q author = Fayyadh, Thaer Kadhim title = Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes date = 2017-05-06 keywords = Fig; H1N1; virus summary = title: Simultaneous detection of multiple viruses in their co-infected cells using multicolour imaging with self-assembled quantum dot probes The authors introduce a method for simultaneous imaging, detection and quantitative evaluation of multiple viruses in single cells by using multicolor quantum dot (QD) probes and in a single staining cycle. In this study, by using the multicolour QD-probes and a single staining procedure cycle, we have realized the simultaneous detection and quantitative evaluation of multiple viruses in their infected cells. As shown in Fig. 2a , there is obvious QD fluorescent signal in the cells infected with H1N1 virus incubated with fully assembly QD625-SpA-MAb as a Bone-step procedure^. As shown in Fig. 5 , by using the one-step staining procedure with a cocktail of QD625-SpA-MAb, QD525-SpA-MAb and QD705-SpA-MAb probes, the three influenza A virus subtypes H1N1, H3N2 and H9N2 were detected in the same co-infected MDCK cells with three types of corresponding QD signals (Fig. 5a) . doi = 10.1007/s00604-017-2300-6 id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 keywords = COVID-19; SARS; virus summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). doi = 10.3389/fmicb.2020.01821 id = cord-003302-vxk7uqlc author = Fedson, David S title = Influenza, evolution, and the next pandemic date = 2018-10-03 keywords = H1N1; influenza; pandemic; virus summary = These studies help explain the lower mortality in children compared with adults seen in the 1918 influenza pandemic and in many other types of acute illness. They agree with Worobey et al that early life antigenic imprinting might have led to a dysregulated T-cell response that increased the risk of death following infection in 1918 with a new and antigenically dissimilar influenza virus. In trying to understand the ''mystery'' of greater mortality among young adults during the 1918 pandemic, scientists have studied influenza viruses and the human response to previous infection. Considered with evidence from endotoxemic mice [28] and other studies [4] [5] [6] [7] [8] [9] , their findings suggest that the mortality impact of pandemic and seasonal influenza and other forms of acute critical illness might be reduced by treating the host response. doi = 10.1093/emph/eoy027 id = cord-287851-9p0dr7rl author = Fedson, David S title = Confronting an influenza pandemic with inexpensive generic agents: can it be done? date = 2008-09-30 keywords = H5N1; infl; uenza; virus summary = The investigators commented that because of the functional redundancy of many cytokines and chemokines, deleting more than one of these genes might have had a greater (presumably more adverse) eff ect on the course of disease, and concluded that mice are suitable for evaluating agents that "modulate the infl ammatory response induced by H5N1 viruses, either alone or in combination with antiviral therapy". 18 More recently, a study of acute infl uenza pneumonia showed that compared with normal mice, Toll-like receptor (TLR) 3 knockout mice had reduced levels of several proinfl ammatory cytokines and chemokines and high pulmonary virus titres, yet mortality was unexpectedly low. For reasons of global public health it is crucially important for investigators to undertake experimental studies to determine whether these or other generic agents (or several of them in combination) could be eff ective in treating H5N1 and other potentially pandemic infl uenza virus infections. doi = 10.1016/s1473-3099(08)70070-7 id = cord-006640-25ykas09 author = Fedson, David S. title = What treating Ebola means for pandemic influenza date = 2018-07-16 keywords = Ebola; Leone; Sierra; virus summary = Physicians should be prepared to undertake clinical trials of widely available generic drugs to determine whether they improve survival in patients with seasonal influenza, other emerging virus diseases, and other forms of acute critical illness. An experience during the recent Ebola outbreak in Sierra Leone (2014-2016) suggests that inexpensive generic drugs might be used to treat patients with pandemic influenza and other emerging virus diseases. Several new investigational treatments targeting the Ebola virus were tested in clinical trials in West Africa (Guinea, Liberia, Sierra Leone): antiviral agents, convalescent plasma, and monoclonal antibody preparations [3, 4] . The Ebola treatment experience in Sierra Leone suggests that generic drugs targeting the host response might be used to treat patients who develop severe illness due to pandemic influenza, other emerging virus diseases, and everyday diseases like seasonal influenza, bacterial sepsis, and community-acquired pneumonia [11] . doi = 10.1057/s41271-018-0138-8 id = cord-326960-9phlylce author = Felberbaum, Rachael S. title = The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors date = 2015-03-20 keywords = BEVS; cell; influenza; vaccine; virus summary = This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. expresSF+ cells are used to manufacture three licensed products: Flublok ® influenza vaccine (Protein Sciences Corporation), Glybera ® gene therapy for the treatment of familial lipoprotein lipase deficiency (uniQure), and Ingelvac CircoFLEX ® veterinary vaccine to protect against porcine circovirus type 2 (Boehringer Ingelheim Vetmedica). Recombinant AAV-based gene therapies have been in development and shown promise for some time; however, a major limitation to their implementation had been the inability to scale up the manufacturing process to produce sufficient quantities of rAAVs. The original rAAV vectors were produced in mammalian tissue culture using adherent cells such as HEK293 cells, which required about 5000 175-cm 2 flasks to produce enough material for a large animal study or human clinical trial (~10 15 rAAV particles) [55] . doi = 10.1002/biot.201400438 id = cord-017249-la5sum39 author = Feldblyum, Tamara V. title = Seasonal and Pandemic Influenza Surveillance and Disease Severity date = 2015-05-12 keywords = H1N1; disease; infl; pandemic; uenza; virus summary = With the growing focus of the US health care system on the meaningful use of electronic medical records, one of the practical applications is expanding biosurveillance and preparedness capabilities, such as surveillance of infl uenza severity and associated risk factors during seasonal epidemics and pandemics [ 18 , 22 ] . EHR-based surveillance systems such as Electronic Medical Record Support for Public Health (ESP) implemented in Ohio and Massachusetts and BioSense were successfully used for analyzing ICD-9 diagnosis codes, reporting notifi able disease cases, surveillance of ILI, identifi cation of infl uenza or upper respiratory infection risk factors among hospitalized patients, and for monitoring diabetes prevalence, risk factors, and disease severity [ 13 , 19 ] . Pregnancy has been reported as a risk factor for seasonal and pandemic infl uenza infections and severe disease outcomes using historical and current data. doi = 10.1007/978-1-4939-2410-3_29 id = cord-339744-xrit0w5i author = Feng, Bo title = Investigation of antiviral state mediated by interferon-inducible transmembrane protein 1 induced by H9N2 virus and inactivated viral particle in human endothelial cells date = 2017-11-03 keywords = H9N2; ifitm1; virus summary = Our previous microarray analysis showed that H9N2 virus infection and inactivated viral particle inoculation increased the expression of interferon-inducible transmembrane protein 1 (IFITM1) in human umbilical vein endothelial cells (HUVECs). In present study, we deeply investigated the expression patterns of IFITM1 and IFITM1-mediated antiviral response induced by H9N2 virus infection and inactivated viral particle inoculation in HUVECs. Epithelial cells that are considered target cells of the influenza virus were selected as a reference control. The results indicated that the cellular interaction between intracellular molecules and viral particles might be involved in the induction of IFITM1 expression in HUVECs. To determine the antiviral activity of IFITM1 protein induced by H9N2 virus infection, HUVECs or BEAS-2Bs were infected with H9N2 virus at MOI of 5 and incubated for 1 h, then cells were transfected with IFITM1 specific siRNA or control siRNA for 36 h. doi = 10.1186/s12985-017-0875-5 id = cord-294568-12eyo13f author = Fernandes-Matano, Larissa title = Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date = 2017-05-03 keywords = HRSV; infection; respiratory; virus summary = Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. doi = 10.1371/journal.pone.0176298 id = cord-305807-n3fs7533 author = Ferreira, T B title = Use of adenoviral vectors as veterinary vaccines date = 2005-10-18 keywords = adenovirus; pfu; vaccine; vector; virus summary = 11 Then recognition that purified replication-defective Ads could be propagated on 293 cells without helper viruses paved the way toward intentional production of genetically modified Ads. 12 The popularity of Ad as a recombinant viral vector is largely due to the successful and safe immunization of millions of US military recruits in 1971 with enterically coated Ad4 and Ad7 as a prevention against acute respiratory disease (ARD) outbreaks. Gonin et al, 37 10 years ago, constructed a replicationdefective HAd5, containing the envelope protein ENV gene of FIV; however, despite the fact that an antibody response to pseudorabies virus in cats showed the potential of rHAd5 vectors to be used in this species, cats injected with 10 10.8 -10 11.8 of 50% tissue culture infectious dose (TCID 50 ) adjuvanted with montanide ISA 708 (water in nonmineral oil) or with montanide ISA 206 (double water/mineral oil/water) of this rAd did not develop detectable antibody response against ENV. doi = 10.1038/sj.gt.3302618 id = cord-008454-8brxpotx author = Field, Anne M. title = Diagnostic Virology Using Electron Microscopic Techniques date = 2008-04-09 keywords = IEM; electron; negative; particle; section; stain; thin; virus summary = The morphology of negatively stained virus particles is sufficient for grouping purposes but it is necessary to use immune electron microscopy (IEM) to differentiate morphologically identical but antigenically distinct viruses. Virus particles are sometimes present in such large numbers in clinical specimens that they can be detected directly by electron microscopy and negative staining methods in particular can be used to provide a rapid diagnosis. Immune electron microscopy on sectioned material presents considerable technical difficulties and viral content of tissue homogenates may be too low for negative stain IEM so a virus seen in the tissue cannot always be sufficiently well identified for diagnostic purposes. Similarly, thin section studies on livers of marmosets infected with hepatitis A virus showed cytoplasmic picornavirus-like particles which could be extracted for use as antigen to detect antibodies by negative stain IEM (Provost et al., 197513) and by complement fixation (Provost et al., 1975a) . doi = 10.1016/s0065-3527(08)60432-7 id = cord-298745-3rrlap70 author = Field, H. E. title = Henipaviruses: Emerging Paramyxoviruses Associated with Fruit Bats date = 2007 keywords = Australia; Hendra; Malaysia; Nipah; virus summary = The apparent temporally clustered emergence of Hendra virus and Nipah virus in Australia and Malaysia, respectively, and the identification of species of fruit bats ( Pteropus spp., commonly known as flying foxes) as likely reservoir hosts, poses a number of important questions on the ecology of henipaviruses. Hendra virus was first described in 1994 in Australia when it caused an outbreak of severe acute respiratory disease with high mortality in thoroughbred horses in a training stable in the city of Brisbane (Murray et al. The negative surveillance findings (based on a highly sensitive serum neutralisation test) provided a high level of confidence that Hendra virus was not being sustained by in-contact domestic animal transmission, was not established in the Queensland horse population, and that the outbreak was unlikely to have originated from domestic species. giganteus , Nipah virus infection dynamics in the species, potential modes of transmission to humans, and identification of factors precipitating emergence. doi = 10.1007/978-3-540-70962-6_7 id = cord-018393-5jlqn7wq author = Finke, Ernst-Jürgen title = Bioterrorismus, infektiologische Aspekte date = 2011-12-14 keywords = Antikörper; Blut; CMV; Ektoparasiten; Erkrankung; Erreger; Fieber; GBV; Hepatitis; Infektion; Menschen; Nachweis; Patienten; Regel; Tage; Therapie; Virus; auf; bei; der; des; die; durch; eine; ist; mit; nicht; oder; sind; und; von; werden summary = Wenn sie sich jedoch verstärkt, kann man sie leicht erkennen, aber nur schwer heilen." (Nicolo Macchiavelli, 1449 -1527 Es ist wenig wahrscheinlich, dass biologische Anschläge rechtzeitig als solche erkannt werden, sofern kein automatisches Monitoring mit einem zuverlässigen Echtzeit-Nachweis von B-Agenzien existiert. B. Enzephalitiden viraler Genese sowie die Frühstadien von nvCJD und möglicherweise auch die Frühsymptomatik der Alzheimer-Krankheit; außerdem die Borreliose-Infektion (Neuroborreliose), bei der ein heterogenes Symptomenbild angenommen wird, das sich wenig mit der Ausprägung einer (BDV-spezifischen) Dysfunktion im limbischen System deckt. Unklar ist jedoch, wie häufig sich aus initial milden Infektionen der oberen Luftwege eine Bronchitis oder eine Pneumonie entwickelt und was die auslösenden Faktoren dafür sind. Beim Nachweis hoch positiver (häufig mit anderen Chlamydienspezies kreuzreagierender) Antikörper ist bei entsprechender klinischer Symptomatik die gezielte Erhebung der Anamnese hinsichtlich einer möglichen Exposition des Patienten gegenüber den natürlichen Wirten diagnostisch wegweisend. Aus Patientenseren wurden Cyclospora-spezifische Antikörper isoliert, jedoch sind die Vorgänge der Immunantwort auf Cyclospora noch nicht vollständig geklärt und ob sich eine Immunität entwickelt, ist fraglich. doi = 10.1007/978-3-642-17158-1_3 id = cord-313356-ninzeazy author = Fiorillo, Luca title = COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings date = 2020-04-30 keywords = COVID-19; SARS; surface; virus summary = title: COVID-19 Surface Persistence: A Recent Data Summary and Its Importance for Medical and Dental Settings Recently, due to the coronavirus pandemic, many guidelines and anti-contagion strategies continue to report unclear information about the persistence of coronavirus disease 2019 (COVID-19) in the environment. The purpose of this article is to highlight all the sources currently present in the literature concerning the persistence of the different coronaviruses in the environment as well as in medical and dental settings. The aim of this article is to evaluate, through the analysis of the current literature, how long this virus can remain active on different surfaces. On average, the different coronaviruses persist in an infectious state on surfaces for several days, even up to nine. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention doi = 10.3390/ijerph17093132 id = cord-316682-4360s2yu author = Fischer, William A. title = Personal Protective Equipment: Protecting Health Care Providers in an Ebola Outbreak date = 2015-11-01 keywords = Ebola; HCP; PPE; virus summary = Given that the Ebola virus is primarily transmitted through direct contact of mucous membranes and cuts in the skin with infected patients and/or their bodily fluids, it is necessary to cover these potential portals of infection with PPE as part of a structured and instructed donning and doffing procedure. Personal protective equipment (PPE) plays a critical role in mitigating the risk of health care personnel (HCP) exposure to contaminated body fluids in the care of patients with communicable infectious diseases, including EVD. 5 In the PAPR PPE set HCP wore a Tyvek (DuPont, Wilmington, Delaware) suit, shoe covers, a surgical gown, and a large hood, whereas the enhanced respiratory and contact precautions system included only a surgical gown, indicating that a second covering significantly reduced exposure to contaminated body fluids and provided evidence for the use of aprons on top of gowns or coveralls in the care of Ebola-infected patients. doi = 10.1016/j.clinthera.2015.07.007 id = cord-330852-n7j0c4ne author = Fischer, Wolfgang B. title = Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date = 2012-02-23 keywords = HIV-1; NMR; TMD; Vpu; channel; protein; virus summary = By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 doi = 10.1016/b978-0-12-394305-7.00006-9 id = cord-290509-56pfww0l author = Fleet, Graham H title = Foodborne viral illness - status in Australia date = 2000-07-25 keywords = Anonymous; Australia; Norwalk; virus summary = Norwalk-like virus contamination of oysters and orange juice, and hepatitis A virus contamination of oysters have been responsible for large outbreaks of foodborne viral disease in Australia. However, 1973, and were found in the faeces and duodenal genuine interest in food or waterborne viral diseases mucosal epithelial cells of children who had been did not develop in Australia until 1978 when oysters hospitalised with acute, non-bacterial gastroenteritis were found to be responsible for a very large (Bishop et al., 1974) . Oysters harvested Victoria, by examining for the virus in faecal specifrom an estuary in northern NSW and supposedly mens that had been submitted for suspected viral depurated were suspected of causing an outbreak of gastroenteritis over the period 1980-1996. A recent report has suggested that Norwalk virus was not detected in the juice but the outbreak and Norwalk-like viruses probably account for the terminated when the juice was withdrawn from the greatest incidence of foodborne disease in Australia market. doi = 10.1016/s0168-1605(00)00249-x id = cord-103135-nly9vojr author = Fletcher, Nicola F. title = A novel antiviral formulation inhibits a range of enveloped viruses date = 2020-03-30 keywords = ViroSAL; cell; figure; virus summary = ViroSAL had no effect on the infectivity of a non-enveloped virus, norovirus, which is in agreement with previous studies demonstrating that free fatty acids are ineffective against nonenveloped viruses (Thormar et al., 1987 , Kohn et al., 1980 . In this study, ViroSAL at the indicated concentrations was mixed with an equal volume of viral inoculum (MeV:original TCID50 = 4.48 7 /mL, HSV-1: 100 PFU/mL, EBV: MOI=10, Zika: MOI=10, Orf: 4 PFU/mL) or pseudoviruses bearing VSV, Ebola, Lassa or SARS-CoV-1 envelope glycoproteins, and incubated at room temperature for 2 minutes. Virus/ViroSAL or control treated virus was inoculated onto appropriate target cells and incubated for 48h at 37°C, then fixed and infection enumerated, or, for pseudovirus assays, lysed and luciferase activity quantified as previously described (Fletcher et al., 2015) . Milk-based free fatty acids, as well as fatty acid emulsions, have been shown to inhibit infection of Vero cells with VSV and HSV-1, with no antiviral effect on poliovirus, a non-enveloped virus (Thormar et al., 1987) . doi = 10.1101/2020.03.29.009464 id = cord-314190-fvdock94 author = Florin, Todd A title = Viral bronchiolitis date = 2017-01-01 keywords = bronchiolitis; child; infant; respiratory; virus summary = The evidence and guideline recommendations consistently support a clinical diagnosis with the limited role for diagnostic testing for children presenting with the typical clinical syndrome of viral upper respiratory infection progressing to the lower respiratory tract. 24, 25, 27, 29, 30 Studies have investigated whether severity of illness, as measured by need for hospital admission, length of hospital stay, intensive care unit admission, repeated emergency department visits, and apnoea, is associated with specifi c viral infections or co-infections, but the evidence is confl icting. Recent studies suggest that higher respiratory syncytial virus genomic load, measured using quantitative PCR, might be associated with increased length of stay, use of respiratory support, and need for intensive care, in addition to recurrent wheezing, compared with lower viral loads. Systematic literature review assessing tobacco smoke exposure as a risk factor for serious respiratory syncytial virus disease among infants and young children doi = 10.1016/s0140-6736(16)30951-5 id = cord-017758-zfudssm9 author = Fong, I. W. title = Emergence of New Tickborne Infections date = 2017-02-08 keywords = China; SFTSV; fever; severe; tick; virus summary = These include new phleboviruses of the Bunyaviridae family, exemplified by severe fever with thrombocytopenia syndrome virus [SFTSV] recognized in China in 2010, and the Heartland virus, a closely related but distinct virus, presenting with similar clinical features and discovered in Missouri in 2012. Other newly recognized tickborne infections include a novel spirochete of the relapsing fever group, Borrelia miyamotoi, first reported to cause human infection in Russia in 2011 and subsequently discovered to cause clinical disease in the Netherlands, Japan, and the United States, with transmission by the black-legged deer tick Ixodes scapularis. Transmission of SFTSV is considered mainly from tick bites, but there is also evidence from multiple reports that the virus can be transmitted from human to human by direct contact with blood of infected patients [67] [68] [69] [70] [71] . Severe fever with thrombocytopenia syndrome virus in ticks collected from humans, South Korea doi = 10.1007/978-3-319-50890-0_5 id = cord-000113-d0eur1hq author = Fooks, Anthony R. title = Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date = 2009-09-29 keywords = PCR; RNA; rabies; virus summary = The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. doi = 10.1371/journal.pntd.0000530 id = cord-252974-pwx27kdi author = Fornek, Jamie L. title = Use of Functional Genomics to Understand Influenza–Host Interactions date = 2007-08-31 keywords = influenza; virus summary = We will explore increasingly complex models for studying influenza-host interactions using functional genomics, including cell culture systems, murine models of infection, and nonhuman primates (Fig. 1) . These studies, led by John Kash, revealed that genes related to various immune cells, notably NK cells, neutrophils, macrophages, and T helper 1 (Th1) cells, were upregulated in mice infected with the fully reconstructed 1918 virus as early as 1 day postinfection. To expand upon the above study, we have also employed functional genomics to assess the effect of influenza infection on the early innate immune response in the lungs of pigtailed macaques, how genes related to this response were regulated over time, and whether gene expression signatures of infection could also be detected in the blood. Global host immune response: Pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus doi = 10.1016/s0065-3527(07)70003-9 id = cord-001528-33f94doo author = Fouchier, Ron A. M. title = Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited date = 2015-01-23 keywords = H5N1; LAI; virus summary = Initial calculations of the potential risks associated with research on influenza virus transmission via respiratory droplets or aerosols between ferrets (1-4) used reports on select agent theft, loss, and release collected by the U.S. Centers for Disease Control and Prevention (CDC) from 2004 to 2010 (7) to calculate the probability of occurrence of LAIs. Although these reports have limitations (1, 4, 7) , they provide the most recent account of LAIs in the United States and probably reflect the current state of the art in biosafety and biosecurity practices better than older studies on laboratory incidents (8, 9) , e.g., as a consequence of the implementation of the U.S. select agent program and best practices developed in biosafety and biosecurity in general over the last decades. doi = 10.1128/mbio.02560-14 id = cord-291294-w5ecsht4 author = Foulongne, V. title = Le bocavirus humain (HBoV) date = 2008-03-17 keywords = les; virus summary = Dans le domaine des infections respiratoires, le recourt extensif à la biologie moléculaire a également apporté des progrès très significatifs, avec les découvertes respectives depuis 2001 du metapneumovirus humain (HMPV) [3] , du SARS-Co [4, 5] , des nouveaux coronavirus humains HCoV-NL63 et HCoV-HKU1 [6] [7] [8] et du bocavirus humain (HBoV) [9] . Des observations récentes en microscopie électronique, conduites sur des prélèvements respiratoires dans lesquels l''ADN du virus avait pu être détecté, ont confirmé que le bocavirus humain présentait toutes les caractéristiques structurales des Parvoviridae. Cette prévalence place le HBoV selon les études et les régions au deuxième ou troisième rang des agents viraux détectés dans ces prélèvements, derrière le virus respiratoire syncytial mais à une fréquence comparable avec les rhinovirus ou le HMPV. Enfin, certaines études décrivent une phase virémique chez quelques patients, notamment en phase aiguë de l''infection, [35] suggérant que le HBoV puisse induire des infection systémiques comme cela est d''ailleurs observé avec les autres parvovirus [35, 36] . doi = 10.1016/j.patbio.2008.01.001 id = cord-355685-wgad0eoh author = Francesconi, Valeria title = Synthesis and Biological Evaluation of Novel (thio)semicarbazone-Based Benzimidazoles as Antiviral Agents against Human Respiratory Viruses date = 2020-03-25 keywords = RSV; figure; virus summary = Compounds 6, 8, 16 and 17, bearing the 5-(thio)semicarbazone and 5-hydrazone functionalities in combination with the 2-benzyl ring on the benzimidazole core structure, acted as dual inhibitors of influenza A virus and human coronavirus. For respiratory syncytial virus (RSV), activity is limited to the 5-thiosemicarbazone (25) and 5-hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold. The herein-investigated benzimidazole-based derivatives may represent valuable hit compounds, deserving subsequent structural improvements towards more efficient antiviral agents for the treatment of pathologies caused by these human respiratory viruses. For RSV, activity is restricted to the 5-(thio)semicarbazone (25) and hydrazone (22) compounds carrying the 2-[(benzotriazol-1/2-yl)methyl]benzimidazole scaffold, in line with the previously synthesized analogues (see above), which show comparable potency in the low micromolar range. In summary, this study reports the synthesis of a series of (thio)semicarbazone-and hydrazone-containing benzimidazoles for the development of novel antiviral agents which have shown the ability to inhibit the replication of three human respiratory viruses. doi = 10.3390/molecules25071487 id = cord-300189-gsp1dozg author = Franci, Gianluigi title = Infectivity inhibition by overlapping synthetic peptides derived from the gH/gL heterodimer of herpes simplex virus type 1 date = 2017-02-14 keywords = HSV; cell; peptide; simplex; virus summary = To date, few peptide molecules outside the well-known inhibitory regions of Class 1 viral fusion proteins, the heptad repeats, should be as fusion; therefore, a brute force approach to the identification of peptide entry inhibitors may help in the dissection of HSV-1 glycoproteins domains. Previous works using a physico-chemical algorithm, the Wimley-White Interfacial Hydrophobicity Scale (WWIHS), in combination with other structural data allowed us to predict regions in gH potentially involved in membrane interactions during the entry and fusion process, and some of them were found to possess HSV antiviral activity in dose-dependent inhibition assays [66] . [76] used a phage display methodology to identify a peptide (named P1) to inhibit West Nile virus (WNV) infectivity, possibly by binding to the envelope glycoprotein (E protein) necessary for membrane fusion. Substitution of herpes simplex virus 1 entry glycoproteins with those of saimiriine herpesvirus 1 reveals a gD-gH/gL functional interaction and a region within the gD profusion domain that is critical for fusion doi = 10.1002/psc.2979 id = cord-266136-81sx505i author = Freymuth, F. title = Les virus des bronchiolites aiguës date = 2010-06-16 keywords = les; virus summary = In Normandy (France), human respiratory syncytial virus (hRSV) was detected in 64.1% of acute bronchiolitis in hospitalized children, rhinovirus in 26.8%, human metapneumovirus (hMPV) in 7.6%, and parainfluenza virus (PIV) in 3.4%. Une étude américaine a estimé à 18 % la fréquence des infections à hRSV chez les enfants de moins de 5 ans atteints d''une infection respiratoire aiguë ; 20 % de ces infections conduisant à une hospitalisation, 18 % à une consultation dans un service d''urgence pédiatrique et 15 % à la visite d''un médecin [7] . Une étude caennaise a été menée entre septembre 1998 et octobre 2000 chez 211 enfants hospitalisés pour une infection respiratoire aiguë dans laquelle seul un rhinovirus était détecté dans les voies respiratoires, alors que la recherche des virus influenza, PIV, hRSV, adénovirus était négative [31] . doi = 10.1016/j.arcped.2010.05.006 id = cord-354068-4qlk6y7h author = Friedrich, Brian M. title = Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date = 2012-09-21 keywords = EBOV; MARV; ebola; infection; vaccine; virus summary = Due to the difficulties in evaluating wild-type filovirus infection in small animals and the generally high level of immune protection correlates derived from non-human primate (NHP) models of infection, therapeutics and vaccines are ultimately evaluated in NHP species for efficacy against filovirus. In their study, a heterologous prime/boost strategy with recombinant adenovirus serotypes 26 and 35 carrying GP (Z) and GP (S/G) demonstrated complete protection among NHPs. Each of these vectors was capable of stimulating humoral and cell-mediated immune responses in the context of NHPs pre-vaccinated with rAd5 as evidenced by antibody titers reaching an order of magnitude above those achieved in rAd5 vaccinated subjects (1:32,000 compared to 1:6,800), and CD8 + intracellular cytokine staining was 4.7-fold greater among heterologous prime/boosted subjects (0.41% compared to 0.09%) [59] . This GP-Fc fusion protein induced both cell-mediated and humoral immune responses, and mice vaccinated with ZEBOVGP-Fc demonstrated 90% protection against a lethal EBOV challenge. doi = 10.3390/v4091619 id = cord-353869-l53ms3q8 author = Friesen, Robert H. E. title = New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date = 2010-02-08 keywords = CR6261; H5N1; influenza; virus summary = METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the prophylactic and therapeutic efficacy of the human monoclonal antibody CR6261 against lethal challenge with the highly pathogenic avian H5N1 virus in ferrets, the optimal model of human influenza infection. CONCLUSIONS/SIGNIFICANCE: These data demonstrate the prophylactic and therapeutic efficacy of this new class of human monoclonal antibodies in a highly stringent and clinically relevant animal model of influenza and justify clinical development of this approach as intervention for both seasonal and pandemic influenza. Mean decline in body weight at the end of the experiment was 6.2% in the group of ferrets that received CR6261 4 hours after challenge ( Figure 2B) , which was significantly less (p = 0.025) than the 10.1% observed in control animals. These findings were in accordance with the observation that the mean lung weights of ferrets treated with CR6261 at 4 hours post challenge were lower compared to the control group (5.7 g versus 14.9 g, p,0.001; Figure 2F ). doi = 10.1371/journal.pone.0009106 id = cord-001974-wjf3c7a7 author = Friis-Nielsen, Jens title = Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers date = 2016-02-19 keywords = Sequencing; Table; cluster; sequence; virus summary = Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. The datasets went through a sequential pipeline with modules (in order) of preprocessing, computational subtraction of host sequences, low-complexity sequence removal, sequence assembly, clustering, association to metadata features, and taxonomical annotation. Associations from the shortest mode tended to have higher dispersion in the range of ORs. Furthermore, one block of clustering results using global alignment mode, alignment length based on the shortest contig, and a minimum sequence identity of 90% (c09ˆaSyG1), had an overall high range of ORs as well as the highest minimum values. The clusters are significantly associated with lowest p-values to biological features and the species annotations are described by HMP. doi = 10.3390/v8020053 id = cord-003523-byxuruk1 author = Fritsch, Annemarie title = Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date = 2019-03-07 keywords = influenza; sample; virus summary = title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. In Germany, no surveillance data and no sequence information on circulating influenza C viruses have ever been reported. We furthermore sequenced the haemagglutinin esterase (HE) gene from influenza C-positive samples to phylogenetically characterise the detected viruses. To extend the basis for the co-infection data, all influenza C-positive samples were additionally tested for human parainfluenza viruses types 1-4 and coronaviruses OC43, NL63, HKU1 and 229E. Thereby, the low detection rates in the general population were confirmed, but a higher clinical impact for paediatric patients was indicated, as influenza C was described to also cause lower respiratory tract disease [6] [7] [8] [9] [10] . doi = 10.2807/1560-7917.es.2019.24.10.1800174 id = cord-004761-cgby8bhz author = Fuchs, N. title = Virus isolation and titration at 33‡ and 37‡ C date = 1975 keywords = virus summary = Various prototype viruses and original specimens were comparatively titrated in cell cultures at 33‡ and 37‡ C. g. Lennette and Schmidt, 1969) recommend an incubation temperature of 33 ~ rather than 37~ for the isolation of viruses from the human respiratory tract. Original specimens (stool suspensions, throat and conjunetival swabs, vesicular fluid) containing the following virus types were inoculated: adenovirus I, 2, 3, 5, 7, 8, herpesvirus hominis, poliovirus 1 and 3, coxsackievirus A9 and B5, eehovirus types 6, 9, 11, 18 and 30. To our knowledge influenza viruses are the only ones of the viruses occurring in the human respiratory tract, in which a comparative testing of original specimens (in embryonated eggs) has demonstrated the superiority of the lower temperature (Stern and Tippett, 1963) . Both temperatures appear satisfactory for vaccinia virus, herpesvirus, enteroviruses and parainfluenza viruses. doi = 10.1007/bf02121753 id = cord-271091-ffn59sgf author = Galao, Rui P title = Saccharomyces cerevisiae: a versatile eukaryotic system in virology date = 2007-10-10 keywords = HCV; RNA; protein; virus; yeast summary = These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. doi = 10.1186/1475-2859-6-32 id = cord-254194-962vynwk author = Galdiero, Stefania title = Silver Nanoparticles as Potential Antiviral Agents date = 2011-10-24 keywords = HIV-1; cell; nanoparticle; silver; viral; virus summary = Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. Theoretically, any metal could be analysed for antiviral activity, however, little effort has been done to determine the interactions of metal nanoparticles with viruses, and only recently some studies have emerged showing that metal nanoparticles can be effective antiviral agents against HIV-1 [37] [38] [39] [40] , hepatitis B virus [41] , respiratory syncytial virus [42] , herpes simplex virus type 1 [43, 44] , monkeypox virus [45] , influenza virus [46] and Tacaribe virus [47] . doi = 10.3390/molecules16108894 id = cord-298019-gf2asni1 author = Galdiero, Stefania title = gH625: A milestone in understanding the many roles of membranotropic peptides date = 2014-10-12 keywords = fusion; membrane; peptide; viral; virus summary = While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery doi = 10.1016/j.bbamem.2014.10.006 id = cord-266985-9qwttt2y author = Gale, P. title = Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date = 2014-11-04 keywords = RNA; infection; virus summary = At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. The binding of NoV capsid protein to its HBGA receptor Table 1 Breakdown of the initial infection process into four steps for building a mechanistic dose-response relationship for RNA viruses through the oral route: information needs Host glycans play a central role in the pathogen infection process including binding of virus to specific receptors in steps 1 and 2 and also in the immune system. doi = 10.1111/jam.12656 id = cord-012582-k1mjik27 author = Gallego, Iván title = Stronger Together: Multivalent Phage Capsids Inhibit Virus Entry date = 2020-08-27 keywords = multivalent; virus summary = This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. This report highlights a phage capsid scaffold strategy that can be used to precisely position sialic acid moieties to inhibit influenza A virus replication. In this work, the authors have selected the icosahedral capsid of the bacteriophage Qβ as the rigid scaffold for the attachment of the sialic acid to achieve a structurally defined presentation of the ligands that matches the binding sites of the trimeric hemagglutinin. All these findings demonstrate that these phage capsid nanoparticles can be employed as efficient inhibitors of influenza A virus and may be the first step towards the development of a new group of antivirals based on protein scaffolds for the treatment of influenza. This new approach from the Hackenberger group represents a promising example of how controlled protein assemblies can be used as precise multivalent scaffolds in the development of innovative antiviral therapeutics. doi = 10.1002/cbic.202000536 id = cord-312431-de7zhswl author = Ganesh, Atheesha title = Detecting Virus‐Like Particles from the Umgeni River, South Africa date = 2013-08-30 keywords = Fig; RNA; River; Umgeni; Water; virus summary = These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. It is well recognised that monitoring the presence of enteric viruses could be challenging due to the relatively low level of infectious viral particles towards the respective host species and small viral particle size existing in environmental waters, thus making it essential to start with a large water sample volume and concentrate it to several orders of magnitude [27] [28] [29] [30] [31] . The present study was conducted to optimise procedures to extract and enumerate indigenous virus-like particles (VLPs) and to determine the community structures and infectivity of these viruses from river water. Canonical correspondence analysis (CCA) was used to reveal the association amongst the bacteriophages, VLPs and the physical and chemical water quality variables, which were measured from the same sites and seasons in concurrent studies performed in this laboratory [46] , with a view to defining the significant variables accountable for the observed spatial and temporal distribution of the communities. doi = 10.1002/clen.201200564 id = cord-000265-llilwq1u author = Gao, Rongbao title = A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date = 2010-10-12 keywords = H5N1; PCR; RNA; virus summary = Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. doi = 10.1371/journal.pone.0013315 id = cord-281429-6lv3di4x author = García-Nicolás, Obdulio title = Targeting of the Nasal Mucosa by Japanese Encephalitis Virus for Non-Vector-Borne Transmission date = 2018-11-27 keywords = Fig; JEV; Laos; NEC; japanese; virus summary = Using nasal mucosal tissue explants and primary porcine nasal epithelial cells (NEC) at the air-liquid interface (ALI) and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could represent the route of entry and exit for JEV in pigs. Porcine NEC at the ALI exposed to with JEV resulted in apical and basolateral virus shedding and release of monocyte recruiting chemokines, indicating infection and replication in macrophages. Using nasal mucosa tissue explants and three-dimensional porcine nasal epithelial cells cultures and macrophages as ex vivo and in vitro models, we determined that the nasal epithelium could be a route of entry as well as exit for the virus. In fact, our data demonstrate that JEV has the ability of infecting apically, resulting in both apical and basolateral virus shedding in swine nasal epithelial cells and indicating that the porcine nasal mucosa could represent a gateway for JEV entry and exit in pigs. doi = 10.1128/jvi.01091-18 id = cord-284479-75zgljet author = García-Serradilla, Moisés title = Drug repurposing for new, efficient, broad spectrum antivirals date = 2019-04-15 keywords = antiviral; drug; virus summary = Thus, the antiviral activity of cyclosporine A (CsA) and some of its nonimmunosuppressive analogs against these viruses has been shown to be related to its ability to bind cellular cyclophilins and inhibiting the interaction with the viral proteins (Bienkowska-Haba et al., 2009; Bose et al., 2003; Damaso and Moussatche, 1998; Franke et al., 1994; Kaul et al., 2009; Nakagawa et al., 2004; Thali et al., 1994; Wainberg et al., 1988; Yang et al., 2008) . CsA has also been reported to inhibit the propagation of several strains of influenza A virus in cell cultures blocking a late step of the replication cycle by mechanisms that might implicate CypA-dependent and -independent pathways (Hamamoto et al., 2013; Liu et al., 2012a; Ma et al., 2016) . Therefore, further studies are needed to better understand the mode of action of AgNPs, their cell specificity and toxicological issues in order to generate new and more effective compounds as well as the use in combination with other drugs in the treatment of different viral diseases. doi = 10.1016/j.virusres.2019.02.011 id = cord-016798-tv2ntug6 author = Gautam, Ablesh title = Bioinformatics Applications in Advancing Animal Virus Research date = 2019-06-06 keywords = genome; sequence; tool; viral; virus summary = The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. This chapter will introduce virologists to some of the common as well virus-specific bioinformatics tools that the researches can use to analyse viral sequence data to elucidate the viral dynamics, evolution and preventive therapeutics. Novel virus types comprise of new CDSs that are different than previously known CDSs. There are multiple databases and tools available for analysis of human viruses; however, there are still only a limited number of resources designed specifically for veterinary viruses. VIRsiRNAdb is an online curated repository that stores experimentally validated research data of siRNA and short hairpin RNA (shRNA) targeting diverse genes of 42 important human viruses, including influenza virus (Tyagi et al. doi = 10.1007/978-981-13-9073-9_23 id = cord-014397-7b88ycv8 author = Gavora, JS title = Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date = 1996-12-15 keywords = RNA; cell; dna; host; resistance; viral; virus summary = Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential ''biological cost'' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection. doi = 10.1186/1297-9686-28-5-385 id = cord-304747-ojyxs3cp author = Gaynor, Anne M title = Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections date = 2007-05-04 keywords = SV40; virus summary = Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The virus was detected in the respiratory secretions from an additional 43 patients in two continents, and the complete genomes of multiple isolates were sequenced. In the early region, an unspliced open reading frame of 194 amino acids was detected that possibly encodes for the STAg. As the paradigm in other polyomaviruses is that STAg is expressed from a spliced message, analysis of potential splice sites revealed the presence of a putative splice donor sequence just one nucleotide 59 of the initially predicted The initial screen used primers targeting the VP2 region, which possessed less than 20% amino acid homology to JC and BK virus to minimize the possibility of cross reactivity with the known human polyomaviruses. doi = 10.1371/journal.ppat.0030064 id = cord-002423-1u44tdrj author = Geoghegan, Jemma L. title = Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date = 2017-02-08 keywords = Fig; RNA; host; virus summary = While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species. Across the data set as a whole we found that all virus families displayed relatively large tree topological distances with nPH85 values of !0.6, suggesting that cross-species transmission is widespread, at least at the family-level (Fig 2; S3 Table) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). doi = 10.1371/journal.ppat.1006215 id = cord-277417-f71jwdzj author = Geoghegan, Jemma L. title = The phylogenomics of evolving virus virulence date = 2018-10-10 keywords = HIV; MYXV; evolution; host; virulence; virus summary = Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. Such a phylogenomic approach to studying virulence evolution is timely because of the rapidity with which virus genome sequence data are now being generated, including during ongoing disease outbreaks of emerging viruses [19] [20] [21] , and because of the development of new phylogeny-based methods for studying and visualizing genomic data [22] [23] [24] . For example, the repeated evolution of the same amino acid changes following the cross-species transmission of avian influenza virus to humans strongly suggests that they directly affect host range 66 , and a similar approach has been used to elucidate the nature of the evolutionary arms race between viruses and their hosts 67, 68 . doi = 10.1038/s41576-018-0055-5 id = cord-017748-xy26tk0t author = Georgiev, Vassil St. title = Influenza date = 2009 keywords = H5N1; H9N2; NIAID; influenza; virus summary = This, coupled with the difficulty to predict which subtype of avian influenza virus will cause the next human pandemic means that an ideal vaccine would elicit an immune response that protects the host from infection with a broad range of influenza viruses from the same or different subtypes (14) . Therefore, if a virus with a new HA and/or NA glycoprotein emerges in the human population, cell-mediated immunity directed against the highly conserved internal proteins could have a role in protection at the time of a pandemic (14) . Although most influenza vaccines are designed to induce HA-specific antibody responses to protect the host from infection, the biology of avian influenza viruses presents several unique challenges compared with human influenza viruses. DNA vaccines encoding the HA and NA glycoproteins of avian influenza viruses or conserved internal virus proteins, such as matrix proteins and nucleoproteins, induced protective immunity in mice and chickens (90) (91) (92) (93) . doi = 10.1007/978-1-60327-297-1_13 id = cord-025995-nxeg03xj author = Gerba, Charles P. title = Pathogen Removal from Wastewater during Groundwater Recharge date = 2013-11-17 keywords = Survival; Wastewater; Water; sewage; soil; type; virus summary = Studies indicate that bacteria and viruses are not removed effectively from wastewaters during primary treatment [19] ; removal of viruses during secondary treatment (active sludge) is dependent largely on virus adsorption to solids. [40] with cores of sandy forest soil receiving poliovirus in sewage effluent at various pH levels between 5.5 and 9.0, virus retention was best at pH 5.5, and the release and migration of retained viruses by subsequent distilled water applications was lower from the cores that re ceived sewage effluent having lower pH values. [57] on virus survival and movement in a rapid-infiltration system for wastewater, the rate of inactivation of indigenous viruses was greater in the fall than in the winter, possibly due in part to the effects of higher temperatures in the former season. doi = 10.1016/b978-0-250-40549-7.50015-1 id = cord-290851-1e5e033r author = Gerlier, Denis title = Emerging zoonotic viruses: new lessons on receptor and entry mechanisms date = 2011-06-12 keywords = ACE2; SARS; virus summary = Here I review the receptors and mode of entry of three emerging zoonotic viruses, responsible for rare but deadly diseases, whose natural reservoir is the bat: severe acute respiratory syndrome coronavirus (SARS-CoV), Hendra (HeV), Nipah (NiV), Ebola (EboV), and Marburg (MarV) viruses. S mediates binding to the cellular receptor Angiotensin Converting Enzyme 2 (ACE2) [4 ] , and ensures the viral-cell membrane fusion that allows virus entry. The EboV (and MarV) entry process lasts for about 1 h [94, 95] and can be schematized as follows ( Figure 3) : Firstly, (i) EboV attaches to the cells via the GP1/GP2 interaction with DC-SIGN/R and/or LECStin and is (ii) immediately internalized by constitutive and/or virus-contact-induced macropinocytosis. Cell adhesion promotes ebola virus envelope glycoprotein-mediated binding and infection doi = 10.1016/j.coviro.2011.05.014 id = cord-298736-9bvyp21d author = Gerold, Gisa title = Decoding protein networks during virus entry by quantitative proteomics date = 2016-06-15 keywords = HCV; SILAC; cell; protein; virus summary = In the past decade mass spectrometry based proteomics methods have reached sensitivities and high throughput compatibilities of genomics methods and now allow the reliable quantitation of proteins in complex samples from limited material. Since then technological developments like antibody based affinity purification (AP), mass spectrometry (MS) of proteins, DNA mediated transformation and molecular cloning led to the discovery of dozens of receptors for human pathogenic viruses (Fig. 1) . While transcriptomics can reveal long-term alterations of the cellular state, virus entry usually occurs within minutes and typically relies on rapid changes of protein conformation, localization, interactions and post-translational modifications (PTM). Of note, high resolution proteomics can not only reveal transient interactions of VAP with enzymes, but also has the potential to identify proteolytic cleavage sites and redox modifications in VAPs. It is conceivable that virus induced protein interactions during entry not only serve to promote the virus uptake pathway, but can also help cloak viruses and lead to immune evasion. doi = 10.1016/j.virusres.2015.09.006 id = cord-321053-lgae22f8 author = Gerold, Gisa title = Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date = 2013-10-04 keywords = HCV; NS5A; RNA; hepatitis; virus summary = Numerous in vitro studies in combination with a growing number of HCV sequencing data from patients undergoing DAA treatment underline that the virus can develop drug-resistance and fitness restoring compensatory mutations [11] . An emerging third group of antivirals, so called hosttargeting antivirals (HTA), may be part of such future combination therapies, in particular as HTAs hold the promise of overcoming some of the caveats of DAAs. HTAs are antibodies, RNAs or small molecules, which interfere with host factors needed for HCV propagation. On the one hand, this demonstrates that HCV can in theory evade HTA therapy by mutating the viral binding partner of the targeted host factor and in fact suggests a low genetic barrier to resistance. Targeting HCV RNA Replication: Phosphatidylinositol 4-kinase III alpha (PI4KIIIα) Genome wide RNA interference screens and in depth cell culture replication assays with HCV replicons and full length infectious virus have revealed numerous additional host dependency factors, that could in principle serve as antiviral targets [99] [100] [101] [102] [103] [104] [105] [106] [107] . doi = 10.1007/s11901-013-0187-1 id = cord-292075-t9z7zqz4 author = Gessain, Antoine title = Mécanismes d’émergence virale et transmission interespèces : l’exemple des rétrovirus Foamy simiens chezl’Homme en Afrique Centrale date = 2013-12-31 keywords = human; simian; virus summary = After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy retroviruses, we will report the results of our study. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simian foamy virus. After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy INTRODUCTION L''espèce humaine est en contact permanent avec l''environnement qui contient une multitude d''agents infectieux (virus, bactéries, parasites, champignons). Cross-species transmission of simian retroviruses, how and why they could lead to the emergence of new diseases in the human population Two distinct variants of simian foamy virus in naturally infected mandrills (Mandrillus sphinx) and cross-species transmission to humans doi = 10.1016/s0001-4079(19)31387-1 id = cord-305302-go87uu06 author = Gessain, Antoine title = Editorial overview: Emerging viruses: interspecies transmission date = 2015-02-28 keywords = emergence; human; virus summary = Furthermore, some of these diseases, associated with emerging viruses, had recent major public health impact, as exemplified in humans by the AIDS [1] , hepatitis C pandemics [2] , or the current Ebola disease epidemic, or in crops by cassava mosaic disease, which seriously compromises food security in East Africa [3] . The emergence of a new viral associated disease or of a new virus is indeed the result of a sequence of successive steps, sometimes complex, and is often related to the entanglement of several factors: socioeconomic or particular cultural activities, increased mobility of human, animal and plant mobility (''the world is a global village''), human exploitation of the environment as deforestation or increase of agricultural or otherwise human managed land, resulting in loss of biodiversity or ecosystem simplification, disruption of human, animal and plant health systems in armed conflict, urbanization with development of huge slums of great poverty and basic hygiene, decreased interest in the surveillance and control of infectious diseases, use of unsterile medical equipment as part of therapeutic and/or mass vaccination and, finally, the ability of certain viruses to adapt quickly to a changing environment. doi = 10.1016/j.coviro.2015.02.001 id = cord-276583-j8bf0eme author = Ghalyanchi Langeroudi, Arash title = Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998–2007 date = 2012-01-21 keywords = H9N2; Iran; virus summary = The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Amino acid sequences at the cleavage site of the HA of the isolates possessed -P-A-R-S-S-R-G-L-motif, except for two isolated: TH85 (A to T) and Fig. 1 Phylogenetic relationships of HA genes of representative influenza A viruses isolated in Iran, Middle Eastern, Eurasian countries, and USA. In the present study, seven from nine H9N2 Iranian isolates possessed amino acid 226-L (numbered according to H3) at the receptor binding site, indicating its potential to infect humans. Sequence and phylogenetic analysis of the haemagglutinin genes of H9N2 avian influenza viruses isolated from commercial chickens in Iran Sequence analysis and phylogenetic study of hemagglutinin Gene of H9N2 subtype of avian influenza virus isolated during 1998-2002 in Iran doi = 10.1007/s00580-012-1405-x id = cord-317198-mean7sj9 author = Giamberardin, Heloisa I.G. title = Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date = 2016-02-09 keywords = HRV; infection; virus summary = title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil This study reports the results of a systematic screening for respiratory viruses in pediatric outpatients from an emergency department (ED) in southern Brazil during two consecutive influenza seasons. © 2016 Wiley Periodicals, Inc. Viral acute respiratory infections (ARIs) in pediatric outpatients represent a significant burden on emergency departments (EDs) and the patients'' families, mainly during influenza seasons, being associated with around 20% of all deaths in pre-school children worldwide, with 90% of these deaths due to pneumonia. This study reports, the results of a laboratory-based surveillance for respiratory viruses in preschool children who were treated in the ED of a pediatric referral hospital during two consecutive influenza seasons. doi = 10.1002/jmv.24477 id = cord-268999-6748c617 author = Gibson, Kristen E title = Viral pathogens in water: occurrence, public health impact, and available control strategies date = 2014-01-14 keywords = virus; water summary = Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. Although there have been advances in both drinking water treatment technologies and source water protection strategies, waterborne disease outbreaks (WBDOs) due to viral pathogens still occur each year worldwide. The current review ( Figure 1 ) focuses on (1) the occurrence of viral pathogens of primary concern in various water sources; (2) virus-related WBDOS by water type reported worldwide over the past decade (from approximately 2000 to 2012); and (3) DW treatment options for the inactivation or removal of viruses. This paucity of available data for viruses in DW can most likely be attributed to the need for very large volumes (>100 to 6000 L) of water to be concentrated followed by subsequent recovery and detection of virus targets -a process that is challenging often Viral pathogens in water Gibson 51 Treatment options specific to removal/inactivation of viruses: -Many options available though implementation varies worldwide due to availability of technology. doi = 10.1016/j.coviro.2013.12.005 id = cord-346916-jj4l9ydl author = Girardi, Erika title = Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date = 2020-08-23 keywords = Fig; PKR; RNA; protein; rig; translation; viral; virus summary = Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . doi = 10.1016/j.semcdb.2020.08.006 id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 keywords = RNA; cell; infection; protein; viral; virus summary = Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host''s fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . doi = 10.1016/j.micinf.2018.06.002 id = cord-350747-5t5xthk6 author = Gmyl, A. P. title = Diverse Mechanisms of RNA Recombination date = 2005 keywords = RNA; fragment; genome; recombination; virus summary = It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. An illustrative example of deletions is provided by defective interfering (DI) genomes, which accumulate in a virus population upon high-multiplicity infections and lack a fragment of the sequence coding for viral proteins [5] [6] [7] . A special role in the variation of RNA viruses is played by recombination, the generation of new genomes from two or more parental RNAs. Recombination between viral RNA molecules was observed for the first time as early as in the 1960s in the poliovirus [14, 15] . In other words, it is possible to assume that some of the mechanisms of nonreplicative RNA recombination play an important role in the evolution of not only viral, but also cell genomes [51, 90] . doi = 10.1007/s11008-005-0069-x id = cord-308857-otsrexqu author = Goel, Saurav title = Resilient and Agile Engineering Solutions to Address Societal Challenges such as Coronavirus Pandemic date = 2020-05-28 keywords = COVID-19; CoV-2; SARS; coronavirus; figure; human; mask; surface; virus summary = This newly identified disease is caused by a new strain of the virus being referred to as Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS CoV-2; formerly called 2019-nCoV). We review the current medical and manufacturing response to COVID-19, including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. However, the coronavirus isolated from pangolins is 99% similar in a specific region of the Spike protein, which corresponds to the 74 amino acids involved in the Angiotensin-Converting Enzyme 2 (ACE 2) receptor binding domain, which allows the virus to enter human cells to infect them as shown in Figure 2 (b). (figures reprinted with permission) Our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme 2 (ACE2), which are favourable sites for the SARS CoV-2 to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. doi = 10.1016/j.mtchem.2020.100300 id = cord-310171-1fmsxx2s author = Goffard, Anne title = Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date = 2014-02-25 keywords = HRV; virus summary = Since the sensitive molecular methods for detection of viruses are more and more common, several recent studies highlight the clinical importance of respiratory viruses especially during exacerbation of asthma, chronic obstructive pulmonary disease (COPD) or CF [3] [4] [5] [6] [7] [8] [9] . In the present study, we reported detection of respiratory viruses from adult patients with CF during either routine visit or acute pulmonary exacerbation. To conclude, we have reported a relatively high frequency of respiratory viruses in a cohort of CF adult patients from France, and demonstrated for the first time that rhinovirus detection including newly identified HRV-Ca variants are the most frequent and significantly associated with respiratory exacerbations. Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings Association of respiratory viral infections with pulmonary deterioration in patients with cystic fibrosis doi = 10.1016/j.jcv.2014.02.005 id = cord-323700-5awng7h1 author = Goggin, Rachel K. title = Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date = 2018-09-19 keywords = PCR; virus summary = The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients doi = 10.3389/fcimb.2018.00334 id = cord-315167-ph15z424 author = Goka, E. A. title = Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date = 2014-12-05 keywords = PCR; virus summary = title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. This study did not find a significant association between seasonal influenza A viruses co-infection with hCoV and hBoV and severe disease. doi = 10.1007/s15010-014-0710-5 id = cord-305742-wf6qxplf author = Gomez, Santiago A. title = Binding of SARS–CoV–2 to cell receptors: a tale of molecular evolution date = 2020-09-28 keywords = SARS; rbd(s; virus summary = In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus· · · cell interacting residues yields significant shifts of ∆λ max = 47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively. In this work, we are interested in two crucial aspects of the initial virus· · · cell interaction problem: to pinpoint the specific residue to residue binding sites between the structurally known spike proteins of the virus [6] and the structurally known ACE2 receptor in cell membranes, [5] and to understand, from a fundamental, quantum perspective, the molecular factors driving the virus· · · cell binding. Therefore, we characterize the virus· · · cell binding as due to a large number of non-covalent contacts between the two proteins, enhanced by the water molecules, acting in conjunction with the specific residue to residue hydrogen bonds. doi = 10.1002/cbic.202000618 id = cord-305327-hayhbs5u author = Gonzalez, Jean-Paul title = Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics date = 2017-09-19 keywords = Africa; Ebola; disease; epidemic; host; pandemic; risk; virus summary = Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Emergence from a sporadic case to an outbreak, to an epidemic, and ultimately to a pandemic depends upon effective transmission among nonimmune hosts, host availability (density), characteristics of the vector (natural or human made) that would enable it to circumvent distances, and the pathogen infectiousness. Although MARV expansion appears to be limited to a few countries in Africa, the recent emergence (estimated at a few decades ago) of a second human pathogenic marburgvirus known as Ravn virus, and the widely distributed Old World rousette fruit bats (Rousettus spp.) serving as reservoir for both viruses [45] , are two factors that favor pandemic risk. doi = 10.1007/978-1-4939-6981-4_1 id = cord-009577-29u7pdpk author = Gonzalez‐Scarano, F. title = Molecular pathogenesis of neurotropic viral infections date = 2004-10-08 keywords = CNS; cell; infection; viral; virus summary = To cause systemic illness, a virus must first enter the host animal, undergo primary replication at a site near its portal of entry, and then ultimately spread to distant target tissues, such as the central nervous system (CNS). An infecting animal virus faces two main blocks to penetration of the CNS or any other specific target organ: (1) a variety of barriers prevent the free access of viruses to target cells, and (2) even when these barriers are ineffective, only certain cell types will support the internalization and replication of a particular virus. Monoclonal antibody variants have been used to map the antigenic sites of the influenza hemagglutinin 122, 76, 771 and have been used successfully to define important regions of the cellular binding proteins of rabies virus, reovirus, coronaviruses, and the California serogroup-all CNS pathogens. Viruses bind to the plasma membrane of susceptible target cells through specific receptors which may be proteins (HIV), lipids (vesicular stomatitis virus), or contain sialic acid (reovirus, influenza) [21, 641. doi = 10.1002/ana.410220502 id = cord-278684-txlvla0j author = Gonzalez–Dunia, Daniel title = Borna Disease Virus and the Brain date = 1998-01-30 keywords = BDV; Borna; CNS; PTI; RNA; disease; virus summary = The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Evidence provided by epidemiological and clinical data, together with virological studies, have led to the hypothesis that chronic viral infections of the CNS contribute to human mental disorders of unknown etiology. Therefore, neuronal damage seen in BD appears to be mediated by the cytotoxic activity of CD8 ϩ T-cells present in the brain parenchyma of BDV-infected rats. Studies on PTI-NB rats may provide valuable information regarding the contribution of CNS resident cells to disturbances in cytokine gene expression caused by BDV. Borna disease virus replicates in astrocytes, Schwann cells and ependymal cells in persistently infected rats: Location of viral genomic and messenger RNAs by in situ hybridization Expression of tissue factor is increased in astrocytes within the central nervous system during persistent infection with Borna disease virus doi = 10.1016/s0361-9230(97)00276-1 id = cord-334365-idjvbcy4 author = Gooding, J. Justin title = Virus Detection: What Were We Doing before COVID-19 Changed the World? date = 2020-05-29 keywords = Detection; Virus summary = The papers in this virtual issue are by some of the researchers that have been developing tests to detect viruses. It is clear that a rapid, portable test that could detect the virus directly, with high sensitivity and specificity, would be a brilliant advance. In this virtual issue we concentrate on the development of molecular tests for viruses, a focus not surprising for two chemistry journals dealing with analytical measurement. The issue leads with a review on detection of biothreats (Mother Nature is an accomplished bioterrorist!), and then covers a range of innovative technologies 1 that focus on assays for point of care testing, 2−4 faster diagnostic testing, 5−8 more sensitive diagnostic testing, 9−17 characterizing the response to the virus, 18−21 and highly sensitive methods for biologically tracking and characterizing the virus. Development of an Electrochemical Paper-Based Analytical Device for Trace Detection of Virus Particles doi = 10.1021/acssensors.0c01029 id = cord-343918-5yk1j4ms author = Gorbalenya, A.E. title = Phylogeny of Viruses date = 2008-07-30 keywords = RNA; phylogeny; virus summary = For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. With the latter virus, poor sampling of the coronavirus diversity in the SARS-CoV lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. doi = 10.1016/b978-012374410-4.00712-3 id = cord-338081-ggw5l1qm author = Gorbalenya, Alexander E. title = Phylogeny of Viruses date = 2017-06-26 keywords = Fig; tree; virus summary = For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Bayesian methods have the highest computational cost due to their sampling approach and thus show the lowest speed, while realization of the similarly advanced ML algorithm may be largely comparable in speed to distance methods, allowing for the phylogenetic analysis of very large data sets like genome-wide tree reconstructions of cellular organisms or thousands of viruses. In the case of SARS-CoV, poor sampling of the coronavirus diversity in the lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. doi = 10.1016/b978-0-12-801238-3.95723-4 id = cord-307893-mvl0wrsj author = Goulter-Thorsen, R.M. title = Disciplines Associated with Food Safety: Food Virology date = 2014-01-13 keywords = HAV; RNA; food; virus summary = Poliovirus was the first enteric virus to be widely recognized, causing foodborne disease outbreaks in the early 1900s associated with the consumption of contaminated raw milk. This method, as well as cultivation methods for the vaccine strain of poliovirus, eventually allowed for the quantification of infective virus plaque forming units and facilitated studies on detection and control of enteric viruses in water and foods, with a particular focus on molluscan shellfish. Although promising, the utility of these molecular amplification methods for virus detection in food and environmental samples was limited by low levels of contamination; high levels of matrix-associated inhibitory substances that interfered with nucleic acid amplification; and the lack of broadly reactive primers and probes for HuNoV. Recent epidemiological data continue to support the fact that viruses, particularly HuNoV, are the most common cause of foodborne disease of known etiology in USA. HEV is a positive-sense single-stranded RNA virus that is transmitted via the fecal-oral route, generally through the consumption of water and sometimes food that has become contaminated with human feces. doi = 10.1016/b978-0-12-378612-8.00024-x id = cord-007710-0u5ot5h4 author = Graham, Barney S. title = Challenges and Opportunities for Respiratory Syncytial Virus Vaccines date = 2013-05-24 keywords = RSV; vaccine; virus summary = Several technological and conceptual advances have recently occurred that make RSV vaccine development more feasible, and this collected knowledge is intended to help inform and organize the future contributions of funding agencies, scientists, regulatory agencies, and policy makers that will be needed to achieve the goal of a safe, effective, and accessible vaccine to prevent RSV-associated disease. Barik, this volume), and suggest that vaccines that elicit responses that block or avoid the immunomodulation associated with wild-type RSV infection without enhancing disease could provide more potent and durable immunity than natural infection. These include the need for improved animal models, better understanding of mucosal immunity, more definitive clinical endpoints to use in efficacy trials, alternate vaccination strategies to protect the young infant (e.g., vaccinating pregnant women) and other high risk populations for whom vaccination may have limited effectiveness, and remedies for liability concerns. doi = 10.1007/978-3-642-38919-1_20 id = cord-349011-kxhpdvri author = Grandvaux, Nathalie title = CSV2018: The 2nd Symposium of the Canadian Society for Virology date = 2019-01-18 keywords = CRISPR; Cas; Dalhousie; Dr.; RNA; University; virus summary = Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O''Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. The "Viral Subversion of Host Cell Processes" session also included presentations from the following trainees: Nichole McMullen (Dalhousie University) who reported the unconventional egress mechanisms of non-enveloped reoviruses, Justine Sitz (Université Laval) who described interactions between a human papillomavirus protein and a host DNA repair-specific E3 ubiquitin ligase, and Quentin Osseman (Université de Montréal) who described interactions between respiratory syncytial virus (RSV) and the host autophagy pathway. doi = 10.3390/v11010079 id = cord-000501-qz68gtd4 author = Greatorex, Jane S. title = Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date = 2011-11-22 keywords = PR8; surface; virus summary = METHODOLOGY AND PRINCIPAL FINDINGS: Influenza A/PuertoRico/8/34 (PR8) or A/Cambridge/AHO4/2009 (pandemic H1N1) viruses were inoculated onto a wide range of surfaces used in home and work environments, then sampled at set times following incubation at stabilised temperature and humidity. The potential for transmission of influenza by indirect contact (i.e. via fomites) is linked to the ability of virus to survive in transmissible titres on commonly touched surfaces; however few data exist on this subject. We evaluate the survival of influenza A (H1N1) viruses deliberately applied to a range of commonly touched household and workplace surfaces, using RT-PCR for genome detection and culture methods to determine viability. Our data are consistent with recent findings from a study of environmental deposition of pandemic H1N1 virus in the homes of infected patients, involving our laboratory, when almost 10% of tested surfaces yielded viable virus [15] . doi = 10.1371/journal.pone.0027932 id = cord-287286-4l963z2q author = Green, Victoria A. title = Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date = 2010-07-28 keywords = Gag; HIV-1; cell; dna; hpv; virus summary = The main themes of discussion at the summer school were: 1) why viral infection can lead to cancer; 2) how a greater understanding of the mechanisms underpinning human immunodeficiency virus (HIV) propagation can inform new antiviral strategies; 3) the abilities of viruses to evade the immune system and the obstacles to the development of effective vaccines; and, 4) the potential afforded by viruses as research tools. The import of the host, including an ability to regulate viral gene expression in different tissues and to mount an effective immune response, is becoming increasingly apparent in determining the molecular basis of HPV-associated tumor progression. Advantages CoVs possess over other viruses as expression vectors include: 1) the possibility of spike protein manipulation, to engineer virus tropism (88, 89) ; 2) the replication of the RNA genome in the cytoplasm, side-stepping potential problems associated with integration (90); 3) the existence of nonpathogenic strains that infect a wide range of species of health and economic importance; 4) the ability to carry large genomes (27-30 kb) , which could favor the introduction of extensive foreign genes (91); and 5) the availability of cDNA clones derived from infectious strains (92, 93) . doi = 10.1002/iub.364 id = cord-337577-dqikrmk7 author = Greenberg, Harry B. title = Vaccination against Viruses date = 2016-05-09 keywords = cell; vaccine; virus summary = In the elderly, measures of cell-mediated immunity, such as granzyme B levels in virus-stimulated peripheral blood mononuclear cells, may correlate better than serum antibody titers with vaccine-elicited protection (McElhaney et al., 2009 ). Whether cell-mediated effector mechanisms, mucosal antibody, or some other factor is primarily responsible for protection by live attenuated influenza vaccines or natural infection remains controversial despite several decades of study. A key finding has been that, among the neutralizing antibodies elicited in response to influenza virus, HIV, or RSV infection or immunization, some have remarkably broad specificity (Burton and Mascola 2015; Corti et al., 2013 Corti et al., , 2011 . The elucidation of Toll-like receptors as key sentry molecules that detect potential pathogens and recruit antigen-presenting cells for a subsequent antigen-specific response has enabled the rational design of a new generation of potential vaccine adjuvants (Wu et al., 2014) . doi = 10.1016/b978-0-12-374279-7.14016-0 id = cord-304424-048xo7jn author = Greninger, Alexander L. title = A decade of RNA virus metagenomics is (not) enough date = 2018-01-15 keywords = Greninger; RNA; dna; metagenomic; novel; viral; virus summary = That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. doi = 10.1016/j.virusres.2017.10.014 id = cord-325825-0lyt8gfq author = Griffiths, Samantha J. title = A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication date = 2013-08-08 keywords = IFN; Med23; Mediator; cell; figure; hsv-1; protein; virus summary = Host factors (HFs) which positively or negatively regulate HSV-1 replication were identified by screening a druggable genome siRNA library (4 siRNAs per gene) targeting 7,237 human genes against a HSV-1 reporter virus expressing the enhanced green fluorescent protein (eGFP; HSV-1 strain C12) in the epithelial Hela cell line, due to their ease of transfection and susceptibility to HSV-1 infection [34] . Combined bioinformatic analyses of protein interaction and siRNA depletion screens found a significant functional enrichment for proteins involved in transcription, and identified multi-protein complexes enriched for pro-viral HFs which strongly inhibited HSV-1 upon depletion, including the RNA-polymerase II, eIF3 and Mediator complexes ( Figure 3a) . Furthermore, qPCR analysis found depletion of Med23 inhibited the induction of IFN-l expression following HSV-1 infection of A549 cells in comparison to cells transfected with the RSCF siRNA control ( Figure 4e ). doi = 10.1371/journal.ppat.1003514 id = cord-022262-ck2lhojz author = Gromeier, Matthias title = Genetics, Pathogenesis and Evolution of Picornaviruses date = 2007-09-02 keywords = IRES; RNA; Wimmer; figure; genome; poliovirus; protein; virus summary = The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . doi = 10.1016/b978-012220360-2/50013-1 id = cord-006252-cbelsymu author = Gross, Peter A. title = Current Recommendations for the Prevention and Treatment of Influenza in the Older Population date = 2012-11-18 keywords = influenza; vaccine; virus summary = Other groups merit consideration (Recommendations of the Immunization Practices Advisory Committee 1990): (a) in the general population, anyone who wishes to reduce the chance of acquiring influenza infection; (b) anyone who provides essential community services and persons living or working in an institutional setting; (c) persons infected with HIV should be vaccinated, although they may not respond as well if their disease is far advanced; and (d) foreign travellers should be immunised when travelling to the trop-Prevention and Treatment of Influenza implication here is that B cell epitopes are intact external molecules such as haemagglutinins, while T cell epitopes appear to be linear sequences exposed by enzymatic breakdown of the original molecule. doi = 10.2165/00002512-199101060-00003 id = cord-260147-w19hl2vs author = Gröner, Albrecht title = Effective inactivation of a wide range of viruses by pasteurization date = 2017-11-16 keywords = inactivation; product; virus summary = STUDY DESIGN AND METHODS: The virus inactivation kinetics of pasteurization for a broad range of viruses were evaluated in the relevant intermediates from more than 15 different plasma manufacturing processes. The first reliable virus inactivation method, pasteurization (heat treatment in aqueous solution at 608C for 10 hr), to effectively inactivate HBV and HCV (at that time called non-A/non-B hepatitis virus) in coagulation factor concentrates was studied and implemented at Behringwerke (a predecessor company of CSL Behring) in the late 1970s and early 1980s by employing suitable stabilizers and conditions to permit pasteurization without modifying the product, for example, formation of neoantigens or activated factors. 11, 12 Virus validation guidelines were ultimately developed and issued by the European authorities, requiring manufacturers to carry out studies to demonstrate the capacity, reliability, and effectiveness of the manufacturing processes to inactivate and/or remove viruses potentially present in the starting material (plasma pool for fractionation). doi = 10.1111/trf.14390 id = cord-260168-rb7j94dh author = Gu, Jiang title = H5N1 infection of the respiratory tract and beyond: a molecular pathology study date = 2007-09-27 keywords = H5N1; PCR; RNA; virus summary = Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. doi = 10.1016/s0140-6736(07)61515-3 id = cord-267326-355q6k6k author = Gu, Xiaoqiong title = Geospatial distribution of viromes in tropical freshwater ecosystems date = 2018-06-15 keywords = RNA; Singapore; site; viral; virus summary = This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. doi = 10.1016/j.watres.2018.03.017 id = cord-290231-4m9lj0uq author = Guirakhoo, Farshad title = The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein date = 1992-12-31 keywords = E-8; MVE; virus summary = Abstract To study the role of the precursor to the membrane protein (prM) in flavivirus maturation, we inhibited the proteolytic processing of the Murray Valley encephalitis (MVE) virus prM to membrane protein in infected cells by adding the acidotropic agent ammonium chloride late in the virus replication cycle. By using monoclonal antibodies (MAbs) and protease maps, we previously demonstrated that the E glycoprotein of tick-borne encephalitis (TBE) virus undergoes an irreversible conformational change, predominantly in the epitopes of domain A, at mildly acidic pH . To understand the role of prM protein in virus maturation and its interaction with the E glycoprotein, we investigated the effect that ammonium chloride had on MVE viruses grown in C6/36 mosquito cells. The reactivities of MAbs defining nine distinct epitopes on the MVE E glycoprotein were compared on M-and prMcontaining viruses using supernatants of ammonium chloride-treated or untreated virus-infected C6/36 cells. doi = 10.1016/0042-6822(92)90267-s id = cord-271692-60nlid3c author = Guo, Wen-Ping title = Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents date = 2013-02-07 keywords = China; figure; virus summary = Notably, the phylogenetic histories of the viruses are not always congruent with those of their hosts, suggesting that cross-species transmission has played a major role during hantavirus evolution and at all taxonomic levels, although we also noted some evidence for virus-host co-divergence. Our phylogenetic analysis also suggests that hantaviruses might have first appeared in Chiroptera (bats) or Soricomorpha (moles and shrews), before emerging in rodent species. An evolutionary analysis of all known hantaviruses including the novel viruses described here reveals the existence of four distinct phylogenetic groups of viruses that infect a range of mammalian hosts, and which have sometimes exchanged genes through segment reassortment. Irrespective of this history of reassortment it is clear that there have been multiple cross-species transmission events in the evolutionary history of the hantaviruses with, for example, those viruses sampled Soricomorpha forming a paraphyletic group, as do those from bats shown in the L tree. doi = 10.1371/journal.ppat.1003159 id = cord-276908-9jthjf24 author = Gupta, Akanksha title = COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date = 2020-07-06 keywords = COVID-19; RNA; SARS; viral; virus summary = In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. doi = 10.1002/slct.202001709 id = cord-291534-c6cjxq07 author = Gwyer Findlay, Emily title = Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date = 2013-05-07 keywords = HIV-1; HNP1; IAV; LL-37; peptide; virus summary = In addition, various a-defensins are described as having additional, non-microbicidal properties, including chemotaxis for effector cells of the innate and adaptive immune systems [24, 25] , inhibition of macrophage pro-inflammatory cytokines [26] , modulation of the intestinal microbiome [27] and the formation of protective peptide nanonets [28] . In particular, it demonstrated direct antiviral activity of HNP1 against HSV-1 in a temperature-and pH-dependent manner, inhibited by serum, but interestingly less sensitive to the inhibitory effects of cations than the more broadly studied antibacterial properties. Thus, although b-defensins can inhibit influenza virus infectivity (albeit less potently than the a-defensins or LL-37) [89] , immunomodulatory properties, perhaps also including up-regulation of IAV uptake by neutrophils [84] , may prove to be key to their protective function against this virus in vivo and future therapeutic developments. Both rhesus h-defensins and retrocyclins (including RTD3, RC1 and RC2) have been found to inhibit HSV-1 and HSV-2 infection of human cervical epithelial cell lines following pre-incubation of virus and peptide [66] . doi = 10.1007/s40259-013-0039-0 id = cord-007898-nky7bo6u author = HUGHES, C.S. title = Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds date = 2018-09-04 keywords = bird; virus summary = authors: HUGHES, C.S.; GASKELL, R.M.; JONES, R.C.; BRADBURY, J.M.; JORDAN, F.T.W. title: Effects of certain stress factors on the re-excretion of infectious laryngotracheitis virus from latently infected carrier birds Experiments were set up to assess the effects of ''natural'' and ''artificial'' stresses on the re-excretion of infectious laryngotracheitis (ilt) virus in latently infected chickens recovered from the acute phase of the disease. Experiments were set up to assess the effects of ''natural'' and ''artificial'' stresses on the re-excretion of infectious laryngotracheitis (In) virus in latently infected chickens recovered from the acute phase of the disease. It appears from these studies that the ''nat ural'' stress of rehousing and, or, the addition of a contact bird, and also the onset of lay may increase the shedding rate in the ILT virus carrier. Nine of the 10 birds shed virus after onset of lay compared with only two in the three-and-a-half weeks before, and there was a highly significant increase in the overall number of virus isolations during this period. doi = 10.1016/s0034-5288(18)31158-5 id = cord-022354-aqtceqqo author = HUNTER, ERIC title = Membrane Insertion and Transport of Viral Glycoproteins: A Mutational Analysis date = 2012-12-02 keywords = Golgi; RSV; membrane; protein; virus summary = second apolar region in gp 37 consists of a 27 amino acid long stretch of hydrophobic residues near the carboxy terminus that functions during translation to stop the movement of the protein into the lumen of the rough endoplasmic reticulum (RER) and to anchor the complex in the membrane. In order to examine the role of the signal peptide in RSV glycoprotein biosynthesis we constructed a series of deletion mutations within the 5'' coding region of the env gene using the double-stranded exonuclease BaBl. Oligonucleotide linkers of the sequence CATCGATG were ligated to the ends of the truncated molecules to introduce a unique restriction endonuclease cleavage site and to replace the deleted in-frame AUG. We found that replacement of the nonconserved region of the cytoplasmic domain with a longer unrelated sequence of amino acids from SV40 vector sequences (mutant Cl) did not alter the rate of transport to the Golgi apparatus nor the appearance of the glycoprotein on the cell surface. doi = 10.1016/b978-0-12-203460-2.50007-x id = cord-021552-6jbm869r author = HURST, CHRISTON J. title = Relationship Between Humans and Their Viruses date = 2007-05-09 keywords = host; human; infection; virus summary = Viral replication ~ at the individual host level, the primary tissue and organ tropisms are toward the cervix, conjunctiva, pharynx, small intestine, and urethra; the secondary tissue and organ tropisms are toward the brain, kidney, lungs, and lymph nodes; at the host population level, these viruses generally are endemic and initially acquired at a very early age, with the infections very often asymptomatic in young children. ~ral replication ~ at the individual host level, primary tissue and organ tropisms are toward the small intestine; secondary tissue and organ tropisms are toward the liver; at the host population level, these tend to be epidemic within human populations; for the hepatitis E virus it seems that acquisition occurs from swine, with the result being epidemics (often very widespread) of human disease; some acquisition from animals may come from eating infected animals; subsequent transmission of all caliciviruses within human populations is by fecally contaminated waste and thus can be very widespread. Alternate hosts: One species of viral family Hepadnaviridae (hepatitis B virus) is known to infect humans, and it seems naturally limited to humans. doi = 10.1016/b978-012362675-2/50015-x id = cord-288231-vg8bwed9 author = Haagmans, Bart L. title = The Application of Genomics to Emerging Zoonotic Viral Diseases date = 2009-10-26 keywords = SARS; host; virus summary = Other viruses, such as influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), may need multiple genetic changes to adapt successfully to humans as a new host species; these changes might include differential receptor usage, enhanced replication, evasion of innate and adaptive host immune defenses, and/or increased efficiency of transmission. New molecular techniques such as high-throughput sequencing, mRNA expression profiling, and array-based single nucleotide polymorphism (SNP) analysis provide ways to rapidly identify emerging pathogens (Nipah virus and SARS-CoV, for example) and to analyze the diversity of their genomes as well as the host responses against them. After introduction of a new influenza A virus from an avian or porcine reservoir into the human species, viral genomics studies are essential to identify critical mutations that enable the circulating virus to spread efficiently, interact with different receptors, and cause disease in the new host. doi = 10.1371/journal.ppat.1000557 id = cord-256917-6h1ip37z author = Habibi-Yangjeh, Aziz title = Review on heterogeneous photocatalytic disinfection of waterborne, airborne, and foodborne viruses: Can we win against pathogenic viruses? date = 2020-07-15 keywords = disinfection; photocatalytic; virus summary = suggested three mechanisms for viral disinfection in photocatalytic processes, which include physical damage of viruses, metal ion toxicity obtained from metal-including photocatalysts, and chemical oxidation by ROS generated over the photocatalysts [5] . Therefore, by considering the actual state of the review, this study focuses on a survey of the photocatalytic inactivation of waterborne, airborne, and foodborne viruses using semiconductor-assisted photocatalysis and the perspective of this important research field to tackle issues related to the spread of different viruses worldwide. In a research conducted by Kim and Jang [18] , the photocatalytic processes were investigated by V-UV with short illumination times to simultaneously disinfect MS2 as an airborne virus (nearly 90% disinfection efficiency at a VUV illumination time of 0.009 s) and remove the produced ozone toward an air inactivation system. After designing and fabricating more efficient photocatalysts, these photoactive materials could be used for inactivation of waterborne viruses in water decontamination plants and fabrication of more effective filters to disinfect airborne viruses. doi = 10.1016/j.jcis.2020.07.047 id = cord-310920-itqwhi6a author = Haddad, Christina title = Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date = 2020-07-02 keywords = RNA; SARS; viral; virus summary = Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. doi = 10.1016/j.ymeth.2020.06.013 id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 keywords = Coronavirus; Protein; RNA; Replication; SARS; Virus summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). doi = 10.3390/v4113245 id = cord-291561-sxvgue36 author = Haixu, Liang title = Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016–2018 date = 2019-11-25 keywords = ASF; ASFV; China; Fig; GETV; SARS; virus summary = A full genome phylogenetic analysis of this 2019-nCoV indicates that it is closely related to bat SARS-like CoV ( Fig. 1 ) , compatible with a zoonotic origin for this virus, similar to SARS-CoV and MERS-CoV. 3 5 This study aim to assess the genetic diversity and potential role of genetic recombination in the evolutionary dynamics of FRCoVs. Genetic analyses were conducted with five complete genomes and 160 gene sequences of FRCoVs downloaded from the NIAID Virus Pathogen Database and Analysis Resource. 3 Ten years after the SARS, MERS emerged in 2012, have caused 2494 human infections with 858 deaths (as of November 2019) and remains a disease of global, and particularly Middle Eastern, public health concern. Relatively low detection rates have even been reported in studies conducted in other geographical areas, such as Gansu Province in China, 6 The discrepancies in the influenza detection rates among patients with ILI from different areas highlighted the geographical differences in virus burdens. doi = 10.1016/j.jinf.2019.11.014 id = cord-343347-guciupc8 author = Hajj Hussein, Inaya title = Vaccines Through Centuries: Major Cornerstones of Global Health date = 2015-11-26 keywords = Jenner; Pasteur; U.S.; disease; vaccination; vaccine; virus summary = Consequently, this work tried to put together the major achievements through history stressing the importance, continuous vital role, and the need for immunization for health prevention and protection as well as its impact on human experience. A few years later, word of his success circulated among the public, and Jenner wrote "An Inquiry into the Causes and Effects of the Variolae Vaccinae, a Disease Discovered in some of the Western Counties of England, particularly Gloucestershire and Known by the Name of CowPox, " after adding several cases to his initial achievement with the boy Phipps. Takahashi was able to make this remarkable advance at a time when very few viruses had been attenuated to produce efficacious live-virus vaccines including yellow fever, polio, measles, mumps, and rubella as previously mentioned. As a result of these successful trials, the live varicella virus vaccine (Varivax) was licensed in 1995 for the active immunization of persons 12 months of age and older (51) . doi = 10.3389/fpubh.2015.00269 id = cord-292643-n6xp5mlz author = Hall, Richard J. title = Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date = 2013-09-13 keywords = RNA; USA; dna; virus summary = The relative abundance of a virus (or viral nucleic acid) in a sample, compared to that of other organisms such as bacteria or host cells (or their genomes), is a critical factor for the discovery of viruses when using metagenomics. A study on human liver tissue compared enrichment techniques of freeze-thaw, centrifugation and nuclease-treatment for the detection of Hepatitis C Virus using both Roche 454 and Illumina high-throughput sequencing platforms (Daly et al., 2011) . After an initial 10 min reverse transcription step at 45 • C and 10 min denaturation Table 1 Virus enrichment process prior to sequencing in metagenomic studies on human and animal samples. This artificial sample represents a starting point to evaluate simple and rapid viral enrichment methods for use in virus metagenomics studies that seek to detect a virus that is causing disease in humans or animals. doi = 10.1016/j.jviromet.2013.08.035 id = cord-315131-4yb2b70g author = Hammerschmidt, Sven title = Threat of infection: Microbes of high pathogenic potential – strategies for detection, control and eradication date = 2005-06-28 keywords = Shiga; disease; vaccine; virus summary = This report highlights some of the lectures that were presented during the international symposium ''Threat of infection: Microbes of high potential -strategies for detection, control and eradication'' in July 2004 in Wu¨rzburg (Germany). E. Kaufmann (Max-Planck-Institute for Infection Biology (MPI), Berlin) suggested that the following vaccination strategies against intracellular bacteria deserve consideration: (i) attenuated viable strains, (ii) naked DNA encoding protective antigens and (iii) protective antigens expressed by recombinant viable vectors (bacteria or viruses). Based on the initial finding that several live-attenuated PrV vaccine strains lack a major surface antigen (glycoprotein E, gE) which is invariably present in all field strains (Mettenleiter et al., 1985) , a simple ELISA system has been developed that is able to specifically detect the presence or absence of anti-gE antibodies in the animal (van Oirschot et al., 1986) . doi = 10.1016/j.ijmm.2005.03.004 id = cord-292575-vsswxwdi author = Hammou, Rahma Ait title = Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date = 2020-12-31 keywords = PCR; detection; disease; miRNA; virus summary = It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. The availability of nucleic acidÀbased technology, such as real-time PCR, along with conventional staining and culture methods and immunoassays, can provide laboratories of many sizes with a comprehensive and responsible approach for the detection of both commonly encountered and emerging or reemerging pathogens. As is the case for SARS, agents of bioterrorism, and the other pathogens, rapid diagnostic methods, such as real-time PCR, and microarray will likely play a major role in the early and sensitive detection of emerging and reemerging infectious diseases encountered in the future. doi = 10.1016/b978-0-12-814966-9.00007-x id = cord-306948-wkisfz1m author = Han, Mingyuan title = Engineering the PRRS virus genome: Updates and perspectives date = 2014-12-05 keywords = PRRSV; RNA; virus summary = Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region Recovery of viable porcine reproductive and respiratory syndrome virus from an infectious clone containing a partial deletion within the Nsp2-encoding region Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion doi = 10.1016/j.vetmic.2014.10.007 id = cord-354536-c9v9kbw8 author = Han, Yan-Jie title = Advances and challenges in the prevention and treatment of COVID-19 date = 2020-07-09 keywords = Coronavirus; MERS; RNA; SARS; virus summary = This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. doi = 10.7150/ijms.47836 id = cord-257569-36qx1sy9 author = Hanada, Kousuke title = A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date = 2004-06-17 keywords = RNA; virus summary = title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. First, we estimated the rates of synonymous substitution for 46 different species of RNA viruses except Puumala virus, human T-lymphotropic virus 1 (HTLV-1) and GB virus C/hepatitis G virus (HGV), using the time-serial sample data. This indicated that the transmission mode affected the replication frequency and that differences in the replication frequencies contributed to the variation of the rate of synonymous substitution for RNA viruses. Moreover, in the present study, we proved that the variation in the synonymous substitution rates among RNA viruses was caused by variation of the replication frequency, and that differences in the infection and transmission modes affected the variation of replication frequencies. doi = 10.1093/molbev/msh109 id = cord-007417-az8xd66p author = Hansbro, Nicole G. title = Understanding the mechanisms of viral induced asthma: New therapeutic directions date = 2008-01-29 keywords = AHR; CD8; IFN; RSV; infection; respiratory; th2; virus summary = Whether an infection induces disease depends on viral (type (E.g. RSV, RV)), host (genetic susceptibility, age, immune responses) and environmental (allergen exposure, season) factors. With respect to allergy RSV infection might only trigger defective immunity in genetically susceptible individuals or that allergic inflammatory and immune responses may promote the influx of virus-specific cells into the airways increasing inflammation and AHR (Schwarze et al., 1999c) . Nevertheless most studies suggest that Th1 responses may result in viral clearance and mild symptoms whereas an aberrant bias towards a Th2 phenotype may lead to more intense RSV-induced disease and promote the development of asthma . Animal models have been used to determine if RSV can induce the development of asthma by triggering pro-asthmatic immune responses that lead to variable airflow obstruction and airway inflammation. Further studies are required to elucidate the links between infection, immune responses and susceptibility to chronic respiratory diseases and why some individuals but not others develop persistent wheeze and asthma. doi = 10.1016/j.pharmthera.2007.11.002 id = cord-273777-qb0vp9gr author = Happel, Anna-Ursula title = The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date = 2020-07-30 keywords = FGT; HIV; bacterial; vaginal; virus summary = A range of vaginal DNA viruses infecting eukaryote cells have been identified by shotgun metagenomics of vaginal samples from generally healthy, asymptomatic women of reproductive age participating in the Human Microbiome Project (HMP) [9] , including double-stranded (ds) DNA (families Adenoviridae, Herpesviridae, Papillomaviridae and Polyomaviridae) and single-stranded (ss) DNA viruses (families Anelloviridae) ( Table 1 and Figure 1 ). Although prokaryotic-infecting viruses, from now on referred to as bacteriophages, are estimated to be amongst the most abundant living entities on Earth [24] and are thought to play an important role in shaping the bacterial microbiota and associated health outcomes in the human gut [5, [25] [26] [27] , oral cavity [28, 29] , skin [30, 31] and lungs [32] , their role in the lower reproductive tract is understudied. Observational studies have shown that the acquisition and transmission of viral sexually transmitted infections (STIs), including HSV-2, HPV and HIV, are more common in women with high diversity, nonoptimal vaginal bacterial microbiota [42] [43] [44] . doi = 10.3390/v12080832 id = cord-262514-1e2bc0bi author = Harrison, Alyne K title = Visceral target organs in systemic St. Louis encephalitis virus infection of hamsters date = 1982-12-31 keywords = SLE; cell; virus summary = SLE virus causes a widespread infection in suckling mice and hamsters when it is inoculated by a peripheral route and involves numerous organs and tissues in addition to the CNS, the principal target when the virus is injected intracerebrally. Light microscopic observations were of little help in identifying major extraneural target organs and tissues in the clinically ill and moribund hamsters, but frozen-section immunofluorescence of all organ systems indicated significant virus growth in the pancreas, adrenal gland, small intestine, heart, skeletal muscle, and kidney. Immunofluorescence studies of mice experimentally infected with tick-borne encephalitis virus indicated that, in addition to the CNS, the peripheral nervous system, the special sensory nerve cells of the retina and olfactory mucosa, the secretory glands, the tubular epithelium of the kidney, and both striated and smooth muscle tissue were affected (Albrecht, 1960) . doi = 10.1016/0014-4800(82)90043-0 id = cord-008013-blf57r7u author = Hartmann, K. title = Feline immunodeficiency virus infection: an overview date = 2005-03-02 keywords = FIV; Hartmann; Yamamoto; cat; feline; virus summary = Acquired immune dysfunction in cats with experimentally induced feline immunodeficiency virus infection: comparison of short-term and long-term infections Programmed cell death (apoptosis) as a mechanism of cell death in peripheral blood mononuclear cells from cats infected with feline immunodeficiency virus (FIV) Journal ¢![ the American VeteHna U Medical Association hnmunization-induced decrease of the CD4+ CD8+ ratio in cats experimentally infected ~,4th feline immunodeficiency virus, l/etm4na O, Immunolo~, and hnm u nopathoh~© Effects of incidental infections and immnne activation on disease progression in experimentally feline immunodeficiency virus-infected cats Characterization of mo''rphologic changes and lymphocyte subset distribution in lymph nodes from cats with naturally acquired feline immunodeficiency virus infection Gag-and em,-specific antibodies in cats after natural and experimental infection with feline immunodeficiency virus. Effect of 3''-acido-2'',3''-dideoxythymidine (AZT) on experimental feline immunodeficiency virus infection in domestic cats Progressive immune dysfunction in cats experimentally infected with feline immunodeficiency virus Pathogenesis of experimentally induced feline immunodeficiency virus infection in cats doi = 10.1016/s1090-0233(98)80008-7 id = cord-272052-8vvpm4tx author = Hartmann, Katrin title = Clinical aspects of feline immunodeficiency and feline leukemia virus infection date = 2011-10-15 keywords = FIV; cat; feline; infection; virus summary = In a survey study of 826 naturally FIV-infected cats examined at North American Veterinary Teaching Hospitals, the most common disease syndromes were stomatitis, neoplasia (especially lymphoma and cutaneous squamous cell carcinoma), ocular inflammation (uveitis and chorioretinitis), anemia and leukopenia, opportunistic infections, renal insufficiency, lower urinary tract disease, and endocrinopathies such as hyperthyroidism and diabetes mellitus (Levy, 2000a) . Causes of CD4 + cell loss include decreased production secondary to bone marrow or thymic infection, lysis of infected cells induced by FIV itself (cytopathic effects), destruction of virus-infected cells by the immune system, or death by apoptosis (cell death that follows receipt of a membrane signal initiating a series of programmed intracellular events) (Bishop et al., 1993; Ohno et al., 1993 Ohno et al., , 1994 Johnson et al., 1996; Guiot et al., 1997a,b; Mizuno et al., 1997; Mortola et al., 1998a,b; Piedimonte et al., 1999; Mizuno et al., 2001 Mizuno et al., , 2003b Tompkins et al., 2002) . doi = 10.1016/j.vetimm.2011.06.003 id = cord-343690-rafvxgx1 author = Hartmann, Katrin title = Clinical Aspects of Feline Retroviruses: A Review date = 2012-10-31 keywords = FeLV; cat; feline; fiv; infection; virus summary = Although FIV can cause an acquired immunodeficiency syndrome in cats ("feline AIDS") comparable to human immunodeficiency virus (HIV) infection in humans, with increased risk for opportunistic infections, neurologic diseases, and tumors, in most naturally infected cats, FIV does not cause a severe clinical syndrome. Experimental FIV infection also progresses through several stages, similar to HIV infection in people, including an acute phase, a clinically asymptomatic phase of variable duration, and a terminal phase sometimes called "feline acquired immunodeficiency syndrome" ("AIDS") [18, 19] . Of 8642 FeLV-infected cats presented to North American Veterinary Teaching Hospitals, various co-infections (including FIV infection, feline infectious peritonitis (FIP), upper respiratory infection, hemotropic mycoplasmosis, and stomatitis) were the most frequent findings (15%), followed by anemia (11%), lymphoma (6%), leukopenia or thrombocytopenia (5%), and leukemia or myeloproliferative diseases (4%) [20] . An early defect in primary and secondary t cell responses in asymptomatic cats during acute feline immunodeficiency virus (fiv) infection doi = 10.3390/v4112684 id = cord-261417-4pf5nsw2 author = Harwig, Alex title = The Battle of RNA Synthesis: Virus versus Host date = 2017-10-21 keywords = RNA; RNAPII; dna; figure; virus summary = Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells. doi = 10.3390/v9100309 id = cord-341101-5yvjbr5q author = Hashem, Anwar M. title = Therapeutic use of chloroquine and hydroxychloroquine in COVID-19 and other viral infections: A narrative review date = 2020-05-06 keywords = Chloroquine; HCQ; SARS; virus summary = While approved specific antiviral drugs against SARS-CoV-2 are still lacking, a large number of existing drugs are being explored as a possible treatment for COVID-19 infected patients. In general, studies showed no significant effect of CQ on CoVs including SARS-CoV and feline infectious peritonitis virus (FIPV) replication or clinical scores in mice and cats, respectively [105, 110] . There are very limited published clinical trials that studied the possible antiviral effect of CQ or HCQ in CoV and non-CoV infected patients (Table 5 ). Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model 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) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro doi = 10.1016/j.tmaid.2020.101735 id = cord-348427-worgd0xu author = Hatcher, Eneida L. title = Virus Variation Resource – improved response to emergent viral outbreaks date = 2017-01-04 keywords = Resource; Variation; Virus; sequence summary = The resource now includes expanded data processing pipelines and analysis tools, and supports selection and retrieval of nucleotide and protein sequences from four new viral groups: Ebolaviruses, MERS coronavirus, rotavirus, and Zika virus ( Table 2 ). New processes have been added to parse source descriptor terms from Gen-Bank records and map these to controlled vocabulary, and the resource now supports retrieval of sequences based on standardized isolation source and host terms in addition to standardized gene and protein names. The resource includes data processing pipelines that retrieve sequences from GenBank, provide standardized gene and protein an-notation, and map sequence source descriptors (i.e. metadata) to uniform vocabularies. To resolve this issue, the Virus Variation database loading pipeline parses Gen-Bank records, identifies important metadata terms, such as sample isolation host, date, country and source, and maps these to a standardized vocabulary using a hierarchical approach. doi = 10.1093/nar/gkw1065 id = cord-342915-r9kv67we author = Hayden, Frederick G. title = Advances in antivirals for non‐influenza respiratory virus infections date = 2013-11-01 keywords = RSV; SARS; infection; respiratory; virus summary = Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. doi = 10.1111/irv.12173 id = cord-337712-ylqgraos author = Heinz, Franz X. title = Profile of SARS-CoV-2 date = 2020-10-30 keywords = ACE2; CoV-2; Fig; SARS; virus summary = Despite these similarities, distinguishing features were identified that are likely to contribute to the biological differences observed between the two viruses, including the significantly higher rate of subclinical and mild infections caused by SARS-CoV-2, which makes control of virus spread currently so difficult. If expectations were too optimistic and results obtained with some of the front runners are disappointing, windows of opportunity will open for an arsenal of alternative developments in progress [54, 59] (https:// www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines, accessed 2 October 2020) These include subunit vaccines with S proteins stabilized in their prefusion conformation in combination with potent adjuvants, use of the RBD only as an immunogen instead of the whole S protein [67, 68] , other rationally designed immunogens [69] , other (non-Adeno) vector vaccines including replication-competent vectors [55, 70] , self-amplifying RNA vaccines [71] , live-attenuated vaccines [55] , DNA vaccines [72] , and intranasally applied vaccines with the potential to induce local immunity at the site of virus entry [73] . doi = 10.1007/s00508-020-01763-1 id = cord-338804-nreqluol author = Heise, M.T. title = Viral Pathogenesis date = 2014-11-28 keywords = HIV; host; viral; virus summary = Viral interactions with these receptors can have a significant impact upon several aspects of viral pathogenesis, including determining the cell or tissue tropism of a virus or even whether a virus can efficiently infect and cause disease in a specific host species. Therefore, viruses that are defective in their ability to antagonize the host type I interferon system are often unable to replicate and spread efficiently within the host, illustrating the importance of viral immune evasion strategies in determining whether a virus will be pathogenic ( Figure 2) . (b) If the virus effectively interferes with the type I interferon response, interferon will be prevented from inducing a robust antiviral state within the host, and the virus is able to replicate to higher levels, will spread more efficiently, and may cause more severe disease. Therefore, like other aspects of viral pathogenesis, a complex series of virus-host interactions determines whether infection with cancer associated viruses ultimately results in disease development. doi = 10.1016/b978-0-12-801238-3.00079-9 id = cord-254890-4ynsgu6c author = Heldens, J.G.M. title = Veterinary vaccine development from an industrial perspective date = 2008-03-03 keywords = EEC; GMP; development; vaccine; virus summary = Live vaccine: Low passage lot for safety (GLP) on target species including pregnant animals in case indication is required High passage lot for efficacy: Onset of immunity and duration of immunity Inactivated vaccine: High passage lot for safety (GLP) and efficacy Licensing batches (10% commercial scale, GMP) -Consistency of production, process validation -Transfer of production process and control tests to manufacturing departments and quality control departments -Stability studies on antigen and final product in final container Field studies (GCP) -Safety -Efficacy derived from treated animals from which food is derived, and the consumer. The likely approach to develop vaccines would be, first, the cloning and site directed mutagenesis to turn the HA-gene into a non-pathogenic form, and, second, the production of so-called high growth re-assortants producing considerable amounts of the new HA protein, which is, among others, the protective antigen in influenza virus. doi = 10.1016/j.tvjl.2007.11.009 id = cord-005885-r3qtoqu1 author = Hellmich, Luisa title = Exantheme nach Auslandsreisen date = 2019-10-09 keywords = Dengue; Fieber; Infektion; Virus; Zika; der summary = Auch wenn die jährlich übermittelten Zika-Virus-Infektionen insgesamt zurückgehen (2016: 222 Fälle, 2017: 69 Fälle, 2018: 18 Fälle), ist aufgrund der häufig symptomlosen Infektion von einer beträchtlichen Dunkelziffer auszugehen (RKI [Robert Koch-Institut]) [8] . Typisch für eine Zika-Virus-Infektion ist eine meist gleichzeitig mit dem Exanthem auftretende Konjunktivitis, die im Schnitt etwas länger als das Exanthem anhält (Median 4 bis 6 Tage) [9] . Bei der Erstinfektion mit einer der 4 DENV-Typen kann sich nach einer Inkubationszeit von 4 bis 7, maximal 14 Tagen ein klassisches Dengue-Fieber mit plötzlichem (häufig biphasischem) Fieber (>38°C), einem hämmernden Retrobulbärschmerz, starken muskuloskelettalen Schmerzen ("break-bone-fever") und Konjunktivitis entwickeln. Bei der Infektion mit dem zu den Togaviridae gehörenden RNA-Virus kommt es nach einer Inkubationszeit von 3 bis 12 Tagen zu einem plötzlichen Fieberanstieg, starken Kopfschmerzen und sehr heftigen bilateralen Arthralgien (v. doi = 10.1007/s00105-019-04489-y id = cord-286298-pn9nwl64 author = Helmy, Yosra A. title = The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date = 2020-04-24 keywords = COVID-19; China; CoV-2; MERS; RNA; SARS; virus summary = Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. doi = 10.3390/jcm9041225 id = cord-006129-5rog0s98 author = Hemida, Maged Gomaa title = Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date = 2012-08-16 keywords = HCV; RNA; infection; viral; virus summary = [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. doi = 10.1007/bf03256383 id = cord-252456-971d0sir author = Hemida, Maged Gomaa title = The SARS-CoV-2 outbreak from a one health perspective date = 2020-03-16 keywords = CoV; MERS; SARS; virus summary = The SARS-CoV-2 is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. Currently, the case fatality rate is relatively low (⁓3.6%) compared to infections with severe acute respiratory syndrome coronavirus (SARS-CoV, (10%) and MERS-CoV (32%) [11] . Based on the previous emergence history of SARS-CoV, the presence of a large number of mammals and birds overcrowded in one place may give a chance for pathogens, particularly those with RNA genomes such as coronaviruses and influenza viruses, to emerge. Based on the previous experience from the other emerging diseases, particularly SARS-CoV and influenza viruses, avoiding the mixing of various species of animals, birds, and mammals, is highly suggested [51, 65, 66] . The process of decontamination of the virus-contaminated surfaces by the appropriate disinfectants or virucidal agents was successful in case of other respiratory viruses such as SARS-CoV and avian influenza [59] . doi = 10.1016/j.onehlt.2020.100127 id = cord-325875-93krp81r author = Henao-Diaz, Alexandra title = Guidelines for oral fluid-based surveillance of viral pathogens in swine date = 2020-10-19 keywords = PRRSV; detection; fluid; oral; virus summary = (2020) showed that the probability of detecting porcine reproductive and respiratory syndrome virus (PRRSV) ribonucleic acid (RNA) in serum by reverse transcription polymerase chain reaction (RT-PCR) at 98 days post infection (DPI) was~2% versus~30% in lymphoid tissues (tonsil) by bioassay [16] . Similarly, differences in detection rates have been reported for pen-based oral fluids versus individual Table 1 provides examples of the detection of virus-specific nucleic acids and/or antibody in swine oral fluids, i.e., is not comprehensive b Acronyms defined in the list of abbreviations and terms pig buccal or nasal swabs for animals inoculated with FMDV, IAV, Senecavirus A (SVA), and swine vesicular disease virus (SVDV) [45, 62, 63, 68] . Diagnosis of the Lelystad strain of porcine reproductive and respiratory syndrome virus infection in individually housed pigs: comparison between serum and oral fluid samples for viral nucleic acid and antibody detection doi = 10.1186/s40813-020-00168-w id = cord-267003-k7eo2c26 author = Hendaus, Mohamed A title = Virus-induced secondary bacterial infection: a concise review date = 2015-08-24 keywords = infection; respiratory; virus summary = 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells doi = 10.2147/tcrm.s87789 id = cord-017527-ylng1us2 author = Herman, Philippe title = Biosafety Recommendations on the Handling of Animal Cell Cultures date = 2014-11-05 keywords = cell; culture; human; risk; virus summary = While biosafety recommendations (as outlined hereafter) are principally aimed at providing maximal protection of human health (including laboratory workers) and the environment, it is recognised that many of the precautionary measures will also directly benefit the quality of research activities involving animal cell cultures. The methodology of biological risk assessment of contained use activities involving pathogenic and/or genetically modified organisms (GMO) identifies and takes into account the probability of occurrence and the severity of a potential negative effect on public health (including the exposed workers) and/or the environment. The risk assessment applied to animal cell cultures relies on a thorough evaluation of both the intrinsic properties of the cell culture -including subsequent properties acquired as a result of genetic modification(s) -and the possibility that the cell culture may inadvertently be contaminated or deliberately infected with pathogenic micro-organisms. doi = 10.1007/978-3-319-10320-4_22 id = cord-326027-58whwspe author = Hernaez, Bruno title = Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera date = 2006-06-20 keywords = ASFV; B54GFP-2; african; cell; virus summary = title: Visualization of the African swine fever virus infection in living cells by incorporation into the virus particle of green fluorescent protein-p54 membrane protein chimera To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). To determine that protein p54, a major component of the external envelope of ASFV, fused to EGFP protein remains incorporated to the viral particle, BA71V and B54GFP-2 virions were Percoll purified and analyzed by SDS-PAGE and Western blotting using specific antibodies (Fig. 2a) . This new role for p54 in morphogenesis supports the selection of p54 as viral fusion protein and suggests that studies about p54-EGFP trafficking during infection in live cells would be helpful to analyze the acquisition of ASFV envelopes from ER during virus assembly. doi = 10.1016/j.virol.2006.01.021 id = cord-304807-j2k1oel2 author = Herrera-Rodriguez, José title = Inactivated or damaged? Comparing the effect of inactivation methods on influenza virions to optimize vaccine production date = 2019-03-14 keywords = BPL; TLR7; virus summary = The properties of the viral formulation, such as successful inactivation, preservation of hemagglutinin (HA) binding ability, fusion capacity and the potential to stimulate a Toll-like receptor 7 (TLR7) reporter cell line were then assessed and compared to the properties of the untreated virus. Hemagglutination and fusion ability were highly affected by those treatments that conferred higher inactivation, with BPL-treated virus binding and fusing at a lower degree compared to FA-inactivated samples. Our aim was to compare the effects of these procedures on the key properties, namely residual infectivity, receptor binding, fusion, and Toll-like receptor 7 (TLR7) mediated activation of innate immune mechanisms, and to determine whether these effects are similar for different virus strains. Previous studies show that BPL is capable of complete inactivation of influenza virus; however, the effectivity might vary depending on the incubation time and temperature. doi = 10.1016/j.vaccine.2019.01.086 id = cord-348141-eskefcwk author = Herrington, CS title = Viruses and disease: emerging concepts for prevention, diagnosis and treatment date = 2014-12-11 keywords = disease; virus summary = Articles on emerging diseases caused by Ebola virus, Marburg virus, coronaviruses such as SARS and MERS, Nipah virus and noroviruses are followed by reviews of enteroviruses, HIV infection, measles, mumps, human respiratory syncytial virus (RSV), influenza, cytomegalovirus (CMV) and varicella zoster virus (VZV). The issue concludes with a series of articles reviewing the relationship between viruses and cancer, including the role played by Epstein–Barr virus (EBV) in the pathogenesis of lymphoma and carcinoma; how human papillomaviruses (HPVs) are involved in the development of skin cancer; the involvement of hepatitis B virus infection in hepatocellular carcinoma; and the mechanisms by which Kaposi''s sarcoma‐associated herpesvirus (KSHV) leads to Kaposi''s sarcoma. Nevertheless, in this new era, pathology will continue to be a vital component of identifying the true relationships between viruses and human disease, and we hope that this Annual Review Issue will serve as a blueprint for future studies in the diagnosis, treatment and prevention of virus-related conditions through an improved understanding of the processes involved. doi = 10.1002/path.4476 id = cord-023678-9q68ftr9 author = Hierholzer, J.C. title = Virus isolation and quantitation date = 2007-09-02 keywords = CPE; Hierholzer; Lennette; virus summary = The method conserves the virus and viral antigens, because the supernatant fluid is decanted from the cell culture into a sterile tube at the end of the incubation period (7-10 days); the monolayer is washed twice with 2-3 ml of plain Hanks Balanced Salt Solution (HBSS) at room temperature; 1 ml of fresh HBSS followed by 0.2 ml of 0.4% mammalian erythrocyte suspension from the appropriate species is added to the monolayer; the tube is incubated stationary with the fluid covering the monolayer; and the test is read 3 times at 20-min intervals by agitating the tube in a sideways motion and then observing the monolayer at 40-100x magnification to see if the erythrocytes are firmly attached to the cultured cells or are floating free in the fluid (see Fig. 15 .4). doi = 10.1016/b978-012465330-6/50003-8 id = cord-269519-8hr8wyrr author = Hirotsu, Yosuke title = Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date = 2020-07-07 keywords = SARS; virus summary = Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. This epidemiologic study shows the infectability of each virus after implementing social preventive measures against SARS-CoV-2. The respiratory panel detected that 17% of the cohort (32/191 patients) were infected with causative viruses. At the start of the coronavirus epidemic, the infectivity of SARS-CoV-2 was unknown compared to that of influenza viruses. This study evaluated the differences in infectivity between SARS-CoV-2 and influenza viruses. The This study showed that taking stringent measures may prevent influenza viruses, which have more strongly affected human life for a longer time. doi = 10.1016/j.jcv.2020.104543 id = cord-269426-82g5eiyg author = Holman, David H. title = Viral Vectors date = 2009-01-30 keywords = AAV; dna; vector; virus summary = Abstract Traditional vaccine development platforms such as live-attenuated virus, killed virus, or recombinant subunit-based vaccines are often effective in eliciting long-term immunity to a number of infectious human pathogens. Finally, it is suggested that vaccination by alternate routes of administration (such as oral or intranasal) rather than injection can overcome pre-existing vector immunity ( Appaiahgari et al., 2006 ; Xiang et al., 2003 ) , which is supported by data from a human clinical trial ( Van Kampen et al., 2005 Lusky et al., 1998 ; Moorhead et al., 1999 ) or the E4 region ( Dedieu et al., 1997 ; Gao et al., 1996 ) of the Ad genome, which reduced or eliminated the expression of E2 or E4 proteins. High-level primary CD8( ϩ ) T-cell response to human immunodeficiency virus type 1 gag and env generated by vaccination with recombinant vesicular stomatitis viruses doi = 10.1016/b978-0-12-369408-9.00007-x id = cord-346853-0c1qdjb5 author = Holmes, E. C. title = The Evolutionary Genetics of Viral Emergence date = 2007 keywords = RNA; dna; virus summary = Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. For example, one model of viral emergence posits that adaptation to a new host species during the early period of an epidemic is of fundamental importance, because this raises the basic reproductive rate of the virus, R 0 , to greater than 1, so that sustained transmission networks can be established (Anita et al. doi = 10.1007/978-3-540-70962-6_3 id = cord-286137-4cbh3u3z author = Honce, Rebekah title = They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date = 2020-08-13 keywords = viral; virus summary = In mineral-and vitamin-deficient mice, genetic mutations arise in coxsackie B and influenza virus populations that promote virulence even in well-nourished hosts [36] [37] [38] [39] [40] . Experimental evolution of CA/09 virus through two models of murine obesity resulted in a viral population displaying increased virulence upon inoculation of a wild-type host. Interestingly, arbovirus-infected obese or protein-deficient mice showed higher morbidity but lower viral diversity, and both malnourished models transmitted virus less efficiently, highlighting that the effects of nutrition may vary based on the natural life cycles of viral families [42] . In our studies with influenza virus, we linked the emergence of a more diverse and virulent viral population with blunted interferon responses in obese hosts. Interferon treatment of obese mice restricted the emergence of a diverse quasispecies and attenuated the virulence of the resulting viral population, strengthening the claim that a robust innate immune response restricts subsequent infection severity, possibly through reduced viral replication and acquisition of a genetically diverse viral population [8, 20, 41] . doi = 10.1371/journal.ppat.1008711 id = cord-022399-66mzbynu author = Hopkins, Graham title = Basic microbiology date = 2009-05-15 keywords = bacteria; cause; cell; eye; infection; organism; virus summary = Bacteria are important because of their ubiquity -that is, their ability to infect and multiply in varied environments -and the ability of many types of bacteria to cause disease -their pathogenicity. To reduce problems caused by bacteria, it is important to understand something of their structure, growth, environmental and metabolic requirements, classification, relationship with disease and the particular problems they can cause to the eye. The result is that the cells tend to grow and divide at a slower rate but are more resistant to antibacterial chemicals, viruses (bacteriophages), phagocytes and other adverse agents. As causative organisms of disease, fungi are less important than bacteria and viruses. • Sterilization: the killing or removal of all viable organisms (including bacterial spores) from an object or pharmaceutical product by the use of chemical or physical agents. Developments have led to the introduction of agents that are more effective against the infecting organism and less toxic to the host. doi = 10.1016/b978-0-7506-8864-2.50005-2 id = cord-298905-c2uuvfm5 author = Horzinek, M. C. title = Molecular pathogenesis of virus infections date = 1987 keywords = RNA; cell; infection; virus summary = Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as ''nonself''. doi = 10.1007/bf01945522 id = cord-023092-unjv71qv author = Horzinek, Prof. Dr Marian C. title = Feline leukaemia prophylaxis date = 2008-04-10 keywords = feline; virus summary = The humoral immune response against FeLV is directed mainly against the viral surface structure gp70/85 and against the so-called ''feline oncornavirus-associated membrane antigen'' (FOCMA). The numerous experiments to develop an efficient vaccine against FeLV infection have recently shown their first success: in the U.S.A. a preparation is presently being marketed for use by the small animal practitioner. (1) cells (virus-producing, live or inactivated) (2) virus (live or inactivated) (3) split products (viral or cellular surface structures; gp7O/gp85, FOCMA) (4) synthetic antigens ( 5 ) products obtained by genetic engineering (antigens from pro-or eukaryotic Each of the above-mentioned strategies has been followed with varying success, cells after cloning of the respective viral genes) and the hope for the future is directed towards development of synthetic and genetically engineered vaccines. Vaccination against feline leukaemia virus using a cell membrane antigen system Feline leukemia virus envelope glycoprotein vaccine: preparation and evaluation of immunizing potency in guinea pig and cat doi = 10.1111/j.1748-5827.1986.tb02146.x id = cord-296309-i1mpov7k author = Houldcroft, Charlotte J. title = Clinical and biological insights from viral genome sequencing date = 2017-01-16 keywords = HIV; PCR; RNA; WGS; Zika; virus summary = We will also explore two areas in which viral WGS has recently proven its clinical utility: metagenomic sequencing to identify viruses that cause encephalitis (BOX 1) ; and the role of WGS in molecular epidemiology and public health management of the Pan-American Zika virus outbreak (BOX 2) . However, the increasing number of resistance genes that are located across viral genomes, together with decreasing costs of sequencing and the use of sequence data for transmission studies, are driving a reappraisal of the need for WGS. The numerous phylogenetically informative variant sites that can be obtained from full-length or near full-length genomes removes the need for high-quality sequences, which enabled the robust linking of cases of Ebola virus infection and public health interventions in real time during the 2015 epidemic 39 . There are several methods that are available to achieve WGS of viruses from clinical samples; amplicon sequencing, target enrichment or metagenomics. doi = 10.1038/nrmicro.2016.182 id = cord-320693-de1lmzl1 author = Hu, Han title = Antiviral activity of Piscidin 1 against pseudorabies virus both in vitro and in vivo date = 2019-07-31 keywords = PRV; activity; peptide; virus summary = METHODS: In this study, we evaluated the activities of five broad-spectrum antimicrobial peptides (AMPs) against several important swine-origin pathogenic viruses by TCID(50) assay. The pathogenic viruses isolated from pigs including pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and rotavirus (RV) are commonly observed in China. In this study, we investigated the activity of five AMPs including piscidin, caerin, maculatin, lactoferricin B, and indolicidin against several porcine-origin viruses. The antiviral effects of the peptides (maculatin, caerin, piscidin, lactoferricin B, indolicidin) were investigated in vitro against several viral pathogens that severely threaten the porcine industry. Three peptides (caerin, piscidin, maculatin) exhibited inhibitory activity against PRV, PEDV, TGEV, PRRSV, and rotavirus. Our plaque reduction assay result indicated that piscidin, caerin, and maculatin could inhibit PRV by directly interacting with the virus. doi = 10.1186/s12985-019-1199-4 id = cord-016576-1yqwci0y author = Hu, Xiaohua title = Mining Candidate Viruses as Potential Bio-terrorism Weapons from Biomedical Literature date = 2005 keywords = search; virus summary = In this paper we present a semantic-based data mining approach to identify candidate viruses as potential bio-terrorism weapons from biomedical literature. If a virus is found in the different document sets obtained by several search keywords, the virus should be considered as suspicious and treated as candidate viruses for bio-terrorism. We propose an automated, semantic-based data mining system to identify viruses that can be used as potential weapons in bio-terrorism. Following the criteria established by Geissler and the similar ideas used by Swanson [10] , in the mining procedure, we consider many important properties of the virus such as the genetic aspects of virulence; airbone transmission of viral disease; and stability of viruses in air or aerosol mixtures etc.. We introduce an automated semantic-based search system, called Combinational Search based Virus Seeker (CSbVS), to identify viruses that can be used as potential weapons in bio-terrorism. doi = 10.1007/11427995_6 id = cord-002937-7xauocti author = Huang, Chung-Guei title = A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date = 2018-02-20 keywords = H7N9; IFN; IL-8; RNA; virus summary = We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host''s response to infection. In this scenario, primary cultures of human respiratory tract epithelial cells would be invaluable to understand H7N9 virus tissue tropism and pathogenesis, as well as to evaluate how patient-related characteristics can modulate the host''s response to infection. With regard to virus tropism, viral RNA quantities were significantly higher in epithelial cells obtained from the upper anatomical locations than from the lower anatomical locations, without adjustment (P = 0.030); however, the difference lost significance after adjustment for age, sex, medical comorbidities, and obesity (P = 0.490; Figure 2B ). doi = 10.18632/oncotarget.24537 id = cord-259627-8stewshp author = Huang, Qing title = Inactivation of dengue virus by methylene blue/narrow bandwidth light system date = 2004-12-02 keywords = virus summary = Because photodynamic virus inactivation with methylene blue (MB)/light system has proven effective in blood banking, MB was selected as a photosensitizing agent, dengue virus as a model virus for enveloped RNA viruses, and an in-house fabricated narrow bandwidth light system overlapping the absorption spectrum of MB as the light source. Results showed that the concentration of MB working solution, illumination intensity of light source, illumination distance and time were four key factors affecting efficiency of virus inactivation using the MB/narrow bandwidth light system. The results indicate that MB concentration, illumination time and distance are three key factors affecting efficiency of virus inactivation when the illumination intensity of the light source was held constant. MB working concentration and illumination intensity, time and distance are the four key factors affecting the inactivation efficiency of the MB/narrow bandwidth light system. doi = 10.1016/j.jphotobiol.2004.08.005 id = cord-336493-ggo9wsrm author = Huang, Stephen S. H. title = Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure date = 2013-04-23 keywords = H1N1; influenza; virus summary = In our present study, we investigated the clinical characteristics and immune cross-reactivity of significant H1N1 influenza strains in the past 100 years in ferrets to determine the immunogenicity of important H1N1 viruses. Ferrets show respiratory illness similar to humans and clinical features of disease are easily observed where fevers can persist days following infection of viruses such as 2009 H1N1pdm influenza 21, 23, 30 . As well as fever, nasal discharge and sneezing can also be observed in animals infected with influenza viruses 21 These influenza A viruses were chosen due to their emergence and influence in H1N1 genetic history (Fig. 1 , strains used in this study are marked with an asterisks) as covered in the introduction. The immunogenic findings showed antisera produced from ferret infection with Taiwan/86 was not able to inhibit hemagglutination with the other viruses on our virus panel, which compliments the literature describing the 1986 strain. doi = 10.1038/srep01698 id = cord-017429-3evwlfac author = Hubálek, Zdenek title = Vertebrates as Hosts and Reservoirs of Zoonotic Microbial Agents date = 2010-11-10 keywords = BACTERIA; Yersinia; american; virus summary = VIRUSES: Lyssavirus s.s. Colonial species distributed in southern USA; roosts in caves, also mine tunnels, hollow trees, buildings, and migrates up to 70 km. Noctule Bat (Nyctalus noctula: Photo 7.12) A large Eurasian species, living in deciduous and mixed forests, and roosting in tree hollows (e.g., woodpecker holes), feeds on large insects. Extensive home range (usually up to 15 km, occasionally 160 km recorded North-American, medium-sized (about that of a small dog) species living near wooded areas, closely to streams and lakes, rock cliffs, but also in urban areas. Comparatively large (25-40 cm long plus tail 7-12 cm; weight about 1 kg) rodent, living in steppe habitat (dry upland prairies) of central and southern areas of USA, and forming extensive colonies ("towns") with deep burrows. BACTERIA: Leptospira grippotyphosa, Francisella tularensis, Borrelia burgdorferi s.s. North-Eurasian species of flying nocturnal squirrel. doi = 10.1007/978-90-481-9657-9_7 id = cord-332205-ydijp66b author = Hufsky, Franziska title = Virologists—Heroes need weapons date = 2018-02-08 keywords = virologist; virus summary = Nowadays, nearly everyone in the life sciences has used BLAST [8] at least once, or made an alignment, or asked a bioinformatician to analyze high-throughput sequencing data. Bioinformaticians routinely have to develop tailored, study-specific algorithms and tools used by a wide variety of scientists, including biochemists, biologists, geneticists, and molecular life scientists; but we rarely find virus-specific tools used by virologists. But astonishingly, we now know that the human genome consists of 8%-60% virus-derived sequences (depending on how this is measured: 8% can be directly traced back to viruses, whereas a figure of 60% includes LINEs and SINEs that are thought to be of viral origin [12] ). The EVBC aims to develop bioinformatical tools for nearly all areas: (1) for detection of viruses, e.g., from high-throughput sequencing data; (2) virus assembly; (3) quasispecies reconstruction; (4) intraviral interactions; (5) virus entry, i.e., protein-protein interaction; (6) virus -host interactions; (7) phylogeny/cophylogeny; and (8) therapy. doi = 10.1371/journal.ppat.1006771 id = cord-295531-zojb3cew author = Huggett, Kathryn D. title = Influenza A date = 2008-01-10 keywords = influenza; virus summary = Subtypes of influenza A viruses that are prominent in one species may on occasion infect and cause disease in another. Influenza A is a single-stranded RNA virus that causes an acute and highly contagious upper respiratory disease. It was approved in 1966 for chemoprophylaxis and in 1976 for treatment and chemoprophylaxis of influenza type A virus in both adults and children 1 year of age. It was approved in 1993 for the treatment and chemoprophylaxis of influenza A infections in adults and prophylaxis in children. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. It was approved in 1999 for the treatment of uncomplicated influenza infections in patients aged 1 year. Basic information on the diagnosis, clinical findings, complications, prevention and treatment of influenza, including vaccine safety recommendations, can be found at: http://www3.accessmedicine.com/content.aspx?aID=17572#17572 Information on the common cold and flu can be located at: http://familydoctor.org/517. doi = 10.1016/b978-008055232-3.60922-5 id = cord-334560-1j9zmuub author = Hunt, Catherine L. title = Filovirus Entry: A Novelty in the Viral Fusion World date = 2012-02-07 keywords = EBOV; NPC1; virus summary = Details of the molecular events following cathepsin-dependent trimming of GP(1) are currently incomplete; however, the processed GP(1) specifically interacts with endosomal/lysosomal membranes that contain the Niemann Pick C1 (NPC1) protein and expression of NPC1 is required for productive infection, suggesting that GP/NPC1 interactions may be an important late step in the entry process. However, for reasons that are not entirely clear, this type of study has not been successful in identifying cell surface proteins that directly interact with EBOV GP to mediate virus entry [41, 42] . However, as both of these regions can be deleted from EBOV GP 1 without loss of viral transduction efficiency [16, [50] [51] [52] , it is likely that C-type lectins increase filovirus attachment to cells rather than serving as cellular receptors that mediate internalization of the virus into endosomes [53] . doi = 10.3390/v4020258 id = cord-022674-90g0461f author = Hurst, Christon J. title = Detecting Viruses in Water date = 1989-09-01 keywords = Concentration; Viruses; Water; filter; virus summary = Subsequent recovery of the adsorbed viruses can occur either by dissolving the filter material, if it is composed of alginate,"" or by exposing the adsorbent to a volume of eluant that is smaller than the original water sample and facilitates a reversal of the virus adsorption process. Of the many different types and configurations of virus adsorbents, those now preferred for use in recovering viruses from large volumes of water are wound cartridge filters*'' and pleated cartridge filter@ based on either glass fiber or nylon, including types that are positively charged, and columns of glass powder.26 Also of interest is the use of sheet filter material that has been modified in situ either by a precipitation of metal hydroxides within the filter ma-trix2" or by coating the filter with cationic 74 RESEARCHANDTECHNOLOGY Cultures of mammalian cells were prepared using a laminar-flow filtered air hood. doi = 10.1002/j.1551-8833.1989.tb03273.x id = cord-348163-9q1rt8i7 author = Hussein, Hosni A. M. title = Beyond RGD: virus interactions with integrins date = 2015-09-01 keywords = RGD; cell; integrin; receptor; virus summary = Integrins are a family of receptor molecules that serve as entry receptors for a variety of different viruses, including foot-and-mouth disease virus (FMDV) [97] , Kaposi''s sarcoma-associated herpesvirus (KSHV) [5], herpes simplex virus-2 (HSV-2) [31], adenovirus [168] , human papillomavirus-16 (HPV-16) [3] , reovirus [40] , and others. On the other hand, interactions of viruses with cellular integrins induce conformational changes in the viral surface proteins, helping to expose the essential domains required for virus entry into a host cell [107] . Similarly, several human herpesviruses, including HSV [147] , KSHV [4], and CMV [93] , make their initial contact with cells by binding to cellsurface HSPGs. In general, binding of viruses to carbohydrate moieties on the surface of cells is the key step that induces conformational changes in the viral structure that are critical for interactions with entry-promoting receptors such as integrins. doi = 10.1007/s00705-015-2579-8 id = cord-292353-z86rjwle author = Hussein, Islam T.M. title = Recent Advances in Hantavirus Molecular Biology and Disease date = 2011-04-01 keywords = Hantaan; Hantavirus; RNA; virus summary = Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The sequences at both the 3 0 and 5 0 termini of each RNA segment are complementary forming ''''panhandle'''' structures that are specifically recognized by the N protein and were shown to be important for viral transcription and replication. Further studies revealed that cellular 5 0capped mRNA oligoribonucleotides are rescued by N in virus-infected cells and stored in P-bodies for the later use as primers by the viral RdRp during transcription initiation . The UTRs are encapsidated by nucleocapsid protein and associate with RdRp both in the host cells and in the virion, and only these nucleocapsids are believed to be functional templates for mRNA synthesis and RNA replication by the viral RdRp. c. doi = 10.1016/b978-0-12-387022-3.00006-9 id = cord-322206-roxa3ix6 author = I. Sardi, Silvia title = High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date = 2020-07-21 keywords = RNA; Zika; figure; virus summary = Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Here, we applied RNA-based metatranscriptomics associated with Ion Torrent deep sequencing and a newly developed Bioinformatics approach to the high-quality reconstitution of viral genomes. doi = 10.3390/v12070782 id = cord-272099-26nhza2s author = IKEDA, KEIKO title = Survival of influenza A virus on contaminated student clothing date = 2015-02-09 keywords = cloth; virus summary = The amount of infectious virus recovered from the nine types of clothing decreased with time and was shown to differ widely between clothing samples, when the contaminated clothing samples were maintained in uncovered glass Petri dishes in a safety cabinet under air blowing. At the indicated time points after virus deposition, one piece of the contaminated cloth was transferred into a glass test tube, immediately followed by the addition of 1,000 µl ice-cold Dulbecco''s phosphate-buffered saline (PBS) without Ca 2+ and Mg 2+ , but containing 0.1% BSA. After leaving for 20 min in air, the cloths were transferred to glass test tubes, the contaminated virus was extracted with PBS containing 0.1% BSA by vigorous mixing with a Vortex mixer, and the amount of infectious virus recovered in the extract was measured. These observations support the importance of water in the deposit for the maintenance of the infectivity and transmissibility of influenza virus on contaminated clothes. doi = 10.3892/etm.2015.2278 id = cord-292830-gcfx1095 author = Ianevski, Aleksandr title = Novel activities of safe-in-human broad-spectrum antiviral agents date = 2018-04-23 keywords = HIV-1; ZIKV; cell; virus summary = Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. Here, we hypothesised that some of the identified safe-in-human BSAs could possess novel antiviral activities and, therefore, could be used for treatment of many different viral infections. Fig. 1 shows BSAs and other approved antiviral drugs linked to viral and host targets through viruses they inhibit. Thus, we tested several known BSA agents against (−)ssRNA, (+) ssRNA, ssRNA-RT and dsDNA viruses and identified novel activities for dalbavancin against EV1, ezetimibe against ZIKV and HIV-1, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against RVFV. We identified novel antiviral activities for dalbavancin (against EV1), ezetimibe (against HIV-1 and ZIKV), azacitidine, cyclosporine, minocycline, oritavancin and ritonavir (against RVFV) (Fig. 4) . doi = 10.1016/j.antiviral.2018.04.016 id = cord-259260-qcfgigga author = Ibrahim, Ibrahim M. title = GRP78: A cell''s response to stress date = 2019-06-01 keywords = GRP78; cancer; cell; protein; virus summary = GRP78 expression is increased in cases of ER stressors like when the cell is abridged from sugar, treated with reagents that inhibit the process of protein glycosylation or disturb the intercellular calcium storage [5] . In the standard conditions of balance in the cell (homeostasis) GRP78 is bounded in an inactive form to Activating transcription factor 6 (ATF6), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and Inositol-requiring enzyme 1 (IRE1) which are UPR transmembrane stress sensors. According to the ligand or the peptide that bind to CS-GRP78, it will be activated in a defined signaling pathway that affects Besides, if the cell is cancerous, CS GRP78 will induce resistance to chemotherapy. Glucose regulated protein 78 (GRP78) inhibits apoptosis and attentinutes chemosensitivity of gemcitabine in breast cancer cell via AKT/mitochondrial apoptotic pathway De-regulation of GRP stress protein expression in human breast cancer cell lines Kringle 5 of human plasminogen induces apoptosis of endothelial and tumor cells through surface-expressed glucose-regulated protein 78 doi = 10.1016/j.lfs.2019.04.022 id = cord-035163-tqh5wv12 author = Ijaz, M. Khalid title = Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses date = 2020-09-08 keywords = Health; SARS; virus summary = In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses. These therefore included coronaviruses, Lassa virus, SFTSV, Hantaan virus, MERS-CoV, SARS-CoV, SARS-CoV-2, Ebola virus, influenza H5N1, Nipah virus, EV-D68, particle size, reservoir species, tissue tropism, mode of transmission, transmissibility, virus shedding, minimal infectious dose, infectious dose 50 , mortality, survival on surfaces, persistence on surfaces, stability on surfaces, survival in aerosols, persistence in aerosols, stability in aerosols, microbicidal efficacy, virucidal efficacy, disinfectant efficacy, antiseptic efficacy, emerging/re-emerging enveloped viruses, UVC susceptibility, zoonoses, and personal hygiene for SARS-CoV-2. As mentioned in Table 2 , the most common modes of transmission for the emerging/ re-emerging viruses discussed in this review are contact with infected bodily secretions/ excretions and contaminated fomites, especially high-touch environmental surfaces (HITES), and inhalation of respiratory droplets/aerosols containing infectious virus (Fig. 1) . doi = 10.7717/peerj.9914 id = cord-337285-t6qr41wc author = Ikeda, Masanori title = Modulation of host metabolism as a target of new antivirals() date = 2007-10-10 keywords = HCV; IFN; RNA; replication; virus summary = Using cell culture systems, several cellular proteins have been identified as effective molecules for HCV RNA replication (Table 1) . [66] reported that lovastatin (LOV), one of the HMG-CoA reductase inhibitors, inhibited HCV RNA replication in HCV replicon-harboring cells. Depletion of the GGPP by statins may inhibit the geranylgeranylation of cellular proteins such as FBL2 and cause the anti-HCV effect in the cells. During the development of IFN therapy for patients with CH-C, the lack of a robust method of HCV RNA replication in cell culture has hampered research into the HCV life cycle and the discovery of potent new anti-HCV reagents. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells doi = 10.1016/j.addr.2007.03.021 id = cord-346836-6jyv0q5e author = Ikegami, Tetsuro title = The Pathogenesis of Rift Valley Fever date = 2011-05-06 keywords = IFN; RVFV; Rift; day; fever; infection; valley; virus summary = RVFV infection in humans usually causes a self-limiting, acute and febrile illness; however, a small number of cases progress to neurological disorders, partial or complete blindness, hemorrhagic fever, or thrombosis. This review describes the pathology of RVF in human patients and several animal models, and summarizes the role of viral virulence factors and host factors that affect RVFV pathogenesis. RVFV infection in humans primarily causes a self-limiting febrile illness; however, some patients develop hemorrhagic fever, neurological disorders, or blindness after the febrile period [5, 7, 8] . Inbred rat strains mimic the disparate human response to rift valley fever virus infection Clinical, virological and serological response of the west african dwarf sheep to experimental infection with different strains of rift valley fever virus doi = 10.3390/v3050493 id = cord-003092-3owcqt3d author = Iketani, Sho title = Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation date = 2018-07-03 keywords = HPIV-3; culture; virus summary = These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates. doi = 10.1128/mbio.00898-18 id = cord-338727-1kodz527 author = Ilinskaya, O. N. title = Ribonucleases as antiviral agents date = 2014-10-11 keywords = RNA; activity; antiviral; virus summary = Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. Therefore, the formation of RNA fragments enhanced by RNase L, followed by their interaction with RIG I and MDA5, activates transcription factor NF κB and triggers transcription of interferon β gene, which prevents virus replication and stimulates the growth of immune system cells [9] . Previously, onconase, an RNases from oocytes of the leopard frog Rana pipiens, efficiently suppresses the replication of HIV 1 due to the selective degrada tion of viral RNA, which exhibits no pronounced cytotoxic effect on infected human cells [22] . At the first stage, when binase meets the virus outside cell, its catalytic activity is not inhibited by the natural RNase and it may destroy viral RNA (Fig. 3, C) . Ribonucleases in HIV type 1 inhibition: Effect of recombinant RNases on infection of primary T cells and immune activation induced RNase gene and protein expression doi = 10.1134/s0026893314040050 id = cord-018040-k0h5ejjt author = Ilyinskii, P. title = Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date = 2009 keywords = HIV; immune; vaccine; virus summary = Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. The size of these vectors is generally within 10-1000 nm and it is a specific mechanism by which our immune system recognizes such particles that underlies their adjuvant potencies (in addition, many carriers protect proteins/NA from rapid degradation in vivo and release them into the organism during prolonged periods of time, which also results in higher immunogenicity). Several VLPbased vaccines have been licensed for general use, many of them against HBV, which are composed of HBV surface antigen (HBsAg), which is a main component of currently used protein-based, alum adjuvant-potentiated vaccine. doi = 10.1007/978-90-481-2523-4_26 id = cord-289360-h6wvx7gw author = Imperiale, Michael J. title = The Importance of Virology at a Time of Great Need and Great Jeopardy date = 2015-03-10 keywords = vaccine; virus summary = journal: mBio Viruses account for up to 20% of all human cancers, and although a large percentage of new human papillomavirus (HPV) and HBV infections can now be prevented by vaccination, many are already infected, and the vaccines are not being used to their full potential. The tremendous reduction in mortality from such diseases as variola, measles, and rubella came about only because the causative viruses were identified, cultivated, attenuated, and made into effective vaccines by biomedical research. While we scientists cannot directly control funding or regulations, we can take charge of some aspects of the research enterprise in a way to ensure that it continues to benefit society. This requires engaging our elected officials both directly and indirectly by continuing to educate them and the public at large about the importance of fundamental research in infectious diseases. doi = 10.1128/mbio.00236-15 id = cord-298036-2zurc60t author = Imre, Gergely title = Cell death signalling in virus infection date = 2020-09-12 keywords = IRF-3; RNA; SARS; cell; death; virus summary = Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . doi = 10.1016/j.cellsig.2020.109772 id = cord-271105-eyigl0wz author = Ionidis, Georgios title = Development and virucidal activity of a novel alcohol-based hand disinfectant supplemented with urea and citric acid date = 2016-02-11 keywords = DVV; Guideline; RKI; virus summary = Under the Guideline of Deutsche Vereinigung zur Bekämpfung der Viruskrankeiten e.V. and the Robert Koch-Institute (DVV/RKI Guideline) [22] , disinfectants achieving at least 4 log 10 titer reduction factor (RF of 4) against vaccinia virus and bovine viral diarrhea virus (BVDV) are active against all enveloped viruses (limited spectrum virucidal) [23, 24] . The different formulations of the new hand rub based on ethanol, citric acid and urea were screened undiluted (80.0 % due to the addition of test virus suspension and interfering substance) against PV, AdV and polyomavirus SV40 as non-enveloped test viruses of the Guideline of DVV/RKI in the presence of FCS with a fixed exposure time of 60 s. Consequently, the formulation with the sufficient virucidal activity containing 69.39 % w/w ethanol, 3.69 % w/w 2-propanol, 2.0 % urea and 2.0 % citric acid was tested against several non-enveloped (MNV, AdV, PV, polyomavirus SV40) and enveloped viruses (BVDV, vaccinia virus strain Elstree) in the presence or absence of FCS according to Guideline of DVV/RK or in clean conditions according to EN 14476. doi = 10.1186/s12879-016-1410-9 id = cord-288703-wdh1jiry author = Ishtiaq, Farah title = A Call to Introduce Structured Zika Surveillance in India date = 2017-11-15 keywords = India; Zika; virus summary = India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. Farah Ishtiaq 1, * India has the climatic conditions conducive to year-round transmission of Zika virus, and a structured disease surveillance program should be implemented to prevent an outbreak. In fact, India is an ideal place to explore the coevolutionary dynamics of this host-parasite system because of several factors: (i) the high volume of human movements [5] , (ii) the apparent immunity to Zika from circulating strains of the virus [1] , and (iii) the possibility of transmission in less immunocompetent hosts, such as pregnant women and the elderly viii , and (iv) adults with a prior history of malaria or dengue infections, which may help facilitate transmission and pathogenesis of Zika, potentially resulting in a positive feedback loop [12] . doi = 10.1016/j.pt.2017.10.008 id = cord-016754-6fv8mjld author = Iturriza-Gómara, Miren title = Gastroenteric Viruses date = 2007 keywords = Norwalk; detection; virus summary = Enzyme immunosorbent assays (EIA) and passive particle agglutination tests (PPAT), some of which are available commercially, provide sensitivity comparable to, or better than, EM for the detection of RVs, NVs, ASVs, and ADVs. More recently, molecular methods, reverse-transcription polymerase chain reaction (RT-PCR), PCR, or nucleic acid-based sequence amplification (NASBA) assays have been developed for the detection of enteric viruses. Testing for the presence of viruses in food, water, or environmental samples has only been possible since the development of very sensitive molecular methods, which include virus elution from the foodstuff, followed by concentration (36) efficient nucleic acid extraction methods for the removal of inhibitors of amplification. Multiple enteric viruses, SVs, ADVs, NVs, and RVs were detected in symptomatic patients suggesting the ingestion of fecally contaminated food or water (unpublished data). Polymerase chain reaction detection of small round-structured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers The development of polymerase chain reaction assays for detection of small round structured and other human enteric viruses in molluscan shellfish doi = 10.1007/978-1-59745-501-5_8 id = cord-301592-n5ns3m34 author = Ivaska, Lauri title = Aetiology of febrile pharyngitis in children: Potential of myxovirus resistance protein A (MxA) as a biomarker of viral infection date = 2017-01-07 keywords = gas; patient; pharyngitis; virus summary = We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. Methods: In this prospective observational study, throat swabs and blood samples were collected from children (age 1e16 years) presenting to the emergency department with febrile pharyngitis. 23e25 The aim of this study was to document the microbial causes of acute pharyngitis in children and adolescents in an outpatient setting and to evaluate the causative role of viruses by determining myxovirus resistance protein A (MxA) and other biomarker levels. doi = 10.1016/j.jinf.2017.01.002 id = cord-018017-c8myq6bi author = Iversen, Patrick L. title = The Threat from Viruses date = 2018-09-30 keywords = EBV; Ebola; HIV; RNA; disease; human; infection; virus summary = Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. doi = 10.1007/978-3-319-98164-2_3 id = cord-276009-p98wjtjb author = Iyer, Arun V. title = Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 date = 2009-02-05 keywords = Nile; VSV; WNV; West; virus summary = title: Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01 These results suggest that VSV-vectored vaccines administered intranasally can efficiently induce protective humoral and cellular immune responses against WNV infections. The salient features of this vaccine study are: (1) A prime-boost intranasal vaccination approach with recombinant VSVs expressing the WNV E glycoprotein produced robust CD8 + IFN␥ + T cell responses; (2) This vaccine approach produced strong neutralizing titers against the WNV; (3) Vaccinated mice were protected against lethal challenge and they were free of neuronal necrosis, while unvaccinated mice There was no statistically significant difference observed between these two groups. These results suggest that a prime-boost VSV-vectored intranasal vaccine approach induces strong humoral and cellular immune responses that protect mice against WNV-induced neuronal necrosis. doi = 10.1016/j.vaccine.2008.11.087 id = cord-341968-uc8i9h0m author = Izaguirre, Gonzalo title = The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases date = 2019-09-09 keywords = cleavage; furin; site; virus summary = A wide variety of viruses exploit furin and other proprotein convertases (PCs) of the constitutive protein secretion pathway in order to regulate their cell entry mechanism and infectivity. Like other enveloped viruses that rely on surface glycoproteins for binding and fusion, coronaviruses have the Spike (S) protein, which is cleaved by proteases during virion biosynthesis, as well as during entry into target cells [53] . The location of furin and related PCs in the vesicles of the constitutive protein secretion pathway, where viruses are assembled during morphogenesis or disassembled during cell entry, explains why a diversity of virus types have evolutionarily converged to depend on PCs. Viruses also use other types of proteases for the proteolytic regulation of the binding and fusion functions; however, proteases are restricted to specific cell types, which limits the range of the viral infection, so when some viruses mutate and acquire PC reactivity, they may expand their cell tropism and become more pathogenic. doi = 10.3390/v11090837 id = cord-003792-v48xeqdz author = Izquierdo-Suzán, Mónica title = Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date = 2019-08-17 keywords = Aedes; RNA; Zika; virus summary = We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Several studies carried out under laboratory conditions have demonstrated that Zika virus can infect many different Aedes mosquito species (3) ; still, the key species for the transmission of Zika virus to humans are Ae. aegypti and Ae. albopictus (4) (5) (6) . In this study, we sought to demonstrate natural vertical transmission in Ae. aegypti mosquitoes by detecting viral RNA and isolating infectious Zika virus from larvae hatched from field-collected eggs. In this work, we were also able to demonstrate the natural vertical transmission of Zika virus in Ae. aegypti mosquitoes by the successful isolation of infectious Zika virus (31N) from larvae raised from field-collected eggs. doi = 10.3201/eid2508.181533 id = cord-007176-61e9obb3 author = Jackson, George Gee title = Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date = 1973-11-17 keywords = infection; respiratory; virus summary = RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture doi = 10.1093/infdis/128.5.674 id = cord-271568-qgpi2kcs author = Jackwood, M.W. title = Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date = 2010-01-21 keywords = IBV; bird; challenge; virus summary = Genomic diversity and the Abbreviations: CPE, cytopathic effects; EID50, 50% embryo infectious dose; ELISA, enzyme linked immunosorbent assay; HMA, hexamethylene amiloride; IBV, infectious bronchitis virus; MHV, mouse hepatitis virus; PBS, phosphate buffered saline; RFLP, restriction fragment length polymorphism; RT-PCR, reverse transcriptasepolymerase chain reaction; SARS-CoV, Severe Acute Respiratory Syndrome virus; SPF, specific pathogen free; TCID50, 50% tissue culture infectious dose. Clinical signs were observed in all of the Mass41 virus challenged groups of birds regardless of treatment but in the intranasal and spray treated groups, fewer birds had signs and the signs were milder, as reflected by lower average scores (Table 1) . Virus was detected in 1 of 5 vaccinated birds in the treated group at 7 days post-vaccination Table 3 Experiment 4: clinical signs a in broiler chickens challenged with IBV at various times after treatment with QR448(a) at 1 day of age. doi = 10.1016/j.virusres.2010.01.006 id = cord-009144-3slh1nbk author = Jacobs, J.W. title = RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date = 1971-05-01 keywords = infant; infection; virus summary = Diagnosis by virus isolation and serology was attempted in 377 cases of respiratory-tract infection in infants under one year of age admitted to hospital during two winters. THERE have been few intensive studies of respiratoryvirus infections of infants.1-5 To prevent these infections, it is necessary to know which viruses cause the most severe illness and whether maternal antibody plays any part in their prevention. We report here the results of a survey of respiratory-virus infections in infants under one year of age in hospital. In this survey, as in others, R.s. virus was the commonest cause of respiratory illness requiring admission at this age (40°0), and the illnesses were more severe than those associated with other viruses (table iv). 23 Effect of Maternal Antibody The few parainfluenza virus infections observed in this survey occurred only in infants more than four months of age. doi = 10.1016/s0140-6736(71)92440-8 id = cord-022305-uvor9rts author = Jacoby, Robert O. title = Viral Diseases date = 2013-11-17 keywords = Fig; HAI; RCV; SDAV; Sendai; infection; rat; virus summary = The number of viruses known to be naturally infectious for laboratory rats is small, and most cause inapparent infections which usually are detected by serological monitoring (Table I) . Significance: Latent, vertically-transmissible agent isolated from submaxillary gland; no signs or lesions; induces HAI antibody; unre lated antigenically to rat coronaviruses or cytomegalovirus; must dif ferentiate isolates from coronaviruses, cytomegaloviruses C. Infected rats excrete virus from the respiratory tract for about 7 days, at which time anti-SDAV antibody is first detectable in serum by either NT or CF tests ( Fig. 30 and Table V) (61) . Infections of SDAV or RCV can be diagnosed on the basis of clinical signs, lesions, and serological profiles of NT and CF antibody and confirmed by isolation of the causative virus. The pathogenesis and lesions of natural and experimental Sendai virus infection have been well described for mice (2, 132, 160) , but only limited information on rats is available. doi = 10.1016/b978-0-12-074901-0.50018-6 id = cord-295041-5vpawtef author = Jakhmola, Shweta title = SARS-CoV-2, an Underestimated Pathogen of the Nervous System date = 2020-09-28 keywords = ACE-2; CNS; COVID-19; SARS; virus summary = Numerous clinical studies have reported neurological symptoms in COVID-19 patients since the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), apart from the atypical signs of pneumonia. Angiotensin-converting enzyme-2 (ACE-2), a potential receptor for SARS-CoV-2 entry, is expressed on various brain cells and cerebral parts, i.e., subfornical organ, paraventricular nucleus, nucleus of the tractus solitarius, and rostral ventrolateral medulla, as well as in non-cardiovascular areas such as the motor cortex and raphe. The resident CNS cells like astrocytes and microglia also express ACE-2, thus highlighting the vulnerability of the nervous system to SARS-CoV-2 infection. Furthermore, the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) of COVID-19 patients is confirmed through genome sequencing [4] ; however, experimental evidence is needed to validate virusmediated neurological damage. Furthermore, the interaction of SARS-CoV-2 and ACE-2-expressing neuronal/glial cells may facilitate virus entry into the nervous system through different routes. doi = 10.1007/s42399-020-00522-7 id = cord-002274-6rddtogo author = James, Joe title = Influenza A virus PB1-F2 protein prolongs viral shedding in chickens lengthening the transmission window date = 2016-10-13 keywords = PB1-F2; virus summary = Here we report that the presence of a full-length PB1-F2 protein, from a low pathogenicity H9N2 avian influenza virus, prolongs infectious virus shedding from directly inoculated chickens, thereby enhancing transmission of the virus by lengthening the transmission window to contact birds. Spillover of these viruses into domesticated poultry populations has resulted in the evolution of highly pathogenic avian influenza (HPAI) subtypes such as the Asian-lineage H5N1 which has been circulating continuously in birds since 2003 and has caused upwards of 700 human infections . To ascertain if the presence of a full-length PB1-F2 protein effected in vivo virus replication in chickens, we determined the level of infectious virus shed from both the buccal and cloacal cavities of birds inoculated with both high and low doses for 10 days following infection. We assessed viral infectivity, pathogenicity and transmissibility between chickens of isogenic viruses differing only by the presence of a full-length PB1-F2 protein. doi = 10.1099/jgv.0.000584 id = cord-256370-cz88t29n author = Jansen van Vuren, Petrus title = Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date = 2016-02-29 keywords = MAHLV; RNA; Vero; bat; virus summary = This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF''s) of all the virus'' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) . doi = 10.3390/v8030065 id = cord-276006-mjjnkqv6 author = Jarach, Natanel title = Polymers in the Medical Antiviral Front-Line date = 2020-07-31 keywords = HIV-1; RNA; antiviral; effect; polymer; virus summary = Those anions show antiviral properties by affecting Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. doi = 10.3390/polym12081727 id = cord-010159-uo47oab1 author = Jartti, Tuomas title = Respiratory viruses and acute asthma in children date = 2007-04-02 keywords = virus summary = title: Respiratory viruses and acute asthma in children We read with great interest the article by Khetsuriani et al 1 on the prevalence of respiratory tract viruses in children with asthma. The results of PCR analysis of combined nasopharyngeal and throat swabs for 13 different viruses were positive in 63% of patients with asthma exacerbation in the 1-year study. We disagree with the low virus detection rate reported by Khetsuriani et al 1 because many studies in wheezing children have shown virus detection rates of close to 90%. 1 Interestingly, 2 or more viruses were detected in 43% of the children compared with 7% in the study by Khetsuriani et al. Our findings suggest that nearly all exacerbations of asthma in children necessitating hospitalization are associated with viral infection. Prevalence of viral respiratory tract infections in children with asthma Human bocavirus and acute wheezing in children doi = 10.1016/j.jaci.2007.02.025 id = cord-004211-58x3nnsc author = Javelle, Emilie title = The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal date = 2020-01-22 keywords = Fever; RVF; RVFV; Rift; Valley; case; virus summary = title: The challenging management of Rift Valley Fever in humans: literature review of the clinical disease and algorithm proposal Clinicians need to consider RVF in the differential diagnosis for febrile illnesses in a suitable context, however manifestations of RVFV in humans are varied and unspecific including hepatitis, encephalitis, hemorrhagic disease, and retinitis with potential dramatic consequences. during the major outbreak in Egypt in 1977, it is considered that less than 5% of symptomatic cases will present complications including ocular, neurologic and hemorrhagic symptoms, while favorable outcome will occur within 1 week for the others [17] . Epidemic Rift Valley fever in Saudi Arabia: a clinical study of severe illness in humans Pathologic studies on suspect animal and human cases of Rift Valley fever from an outbreak in Eastern Africa Severe human illness caused by Rift Valley Fever Virus in Mauritania doi = 10.1186/s12941-020-0346-5 id = cord-307744-wbr84taq author = Jayadevan, Rajeev title = Does a younger host make the virus weaker? Presenting a new hypothesis date = 2020-09-13 keywords = virus summary = RESULTS: Virus become more virulent as it passes through weaker hosts and vice versa. CONCLUSIONS: Viruses become more virulent when it passes through weaker and older hosts. While compiling the data about doctors'' deaths in India during the COVID-19 pandemic, the case of a 50-year-old doctor who contracted the infection while taking care of his mother at home was observed. Did the son get a more virulent selection of virus after it passed through his mother, who was an older and weaker host? Coxsackie virus CVB3 is known to become more virulent as it passes through weaker and older mice hosts [4] . In the study of 108 COVID-related deaths among doctors in India, nearly half were general practitioners, who saw older patients [5]. It will be worth analysing the transmission chain of COVID-19 from this perspective, specifically to see if the age and frailty of the donor of the virus made a difference in the outcome in the host. doi = 10.1016/j.dsx.2020.09.011 id = cord-269126-d81z6t0a author = Jayaseelan, Vijayashree Priyadharsini title = Repurposing calcium channel blockers as antiviral drugs date = 2020-08-19 keywords = calcium; virus summary = As convincing reports on calcium channel blockers mediated increase in ACE2 expression has not been documented so far, these drugs can be a safe alternative for treating CoVID patients with hypertension. Host cells are found to modulate calcium signalling in response to viral infection and the viruses in-turn harness this environment for their own survival and propagation. Interestingly, in an attempt made to identify genetic variants associated with susceptibility to neuro-invasive disease caused by West Nile virus, CASNA1H (Calcium Voltage-Gated Channel Subunit Alpha1 H) achieved a genome-wide significance implying the fact that ionchannels could be as important as other immuno-modulatory proteins controlling host response to viral infections (Long et al. Extensive research on existing calcium channel blockers intended for use as anti-hypertensives might as well aid in repurposing these drugs into the anti-viral regimen. Host calcium channels and pumps in viral infections Calcium ions directly interact with the Ebola virus fusion peptide to promote structure-function changes that enhance infection doi = 10.1007/s12079-020-00579-y id = cord-295189-bz3gi15h author = Jennings, Lance C. title = Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study date = 2015-03-14 keywords = respiratory; virus summary = STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. In a 2008 study, we sought to assess the prevalence of influenza infection in symptomatic and asymptomatic arriving international airline travellers and whether using a symptom-screening questionnaire and temperature measurement could reliably predict seasonal influenza infection [16] . The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptoms to influenza, has important implications for any screening strategy for the prediction of influenza in airline travellers. doi = 10.1016/j.jcv.2015.03.011 id = cord-324984-ojrpsdt9 author = Ji, Xingyue title = Medicinal chemistry strategies toward host targeting antiviral agents date = 2020-02-14 keywords = CCR5; HBV; HCV; HIV-1; RNA; antiviral; inhibitor; virus summary = In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. 3 Altogether, targeting host factors is a very promising strategy with possibility to address the critical challenges faced with the DAAs. In this review, we summarize the recent advances made in HTAs from a medicinal chemistry standpoint, and the host targets are generally classified into three different categories based on the development stage of their corresponding inhibitors/modulators, namely the ones which reached Food and Drug Administration (FDA) approval, that have entered clinical trials and those in preclinical studies. doi = 10.1002/med.21664 id = cord-252397-qlu7dilh author = Johnson, Reed F. title = Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease date = 2015-11-01 keywords = EMC; JOR; MERS; virus summary = Results from a natural history study of MERS-CoV-infected rhesus monkeys indicated that intratracheal inoculation induced a non-lethal disease with limited pathology observed in recovering animals at 28 days post-inoculation and infectious virus could be recovered from lung but not other tissues assayed (Yao et al., 2014) . One subject in the MERS-EMC inoculated group appeared to develop a secondary infection observed by CT that increased to study end, day 25 post-exposure. With the use of CT, we observed that IT inoculation of common marmosets with MERS-JOR or MERS-EMC isolates resulted in a non-lethal disease characterized by limited clinical signs and moderate consolidative lung pathology that did not completely resolve by study end. In this experiment, we sought to determine if there were virus specific differences in disease progression following intratracheal inoculation of common marmosets with Middle Eastern Respiratory Syndrome Coronavirus, commonly known as MERS-CoV, with two common laboratory viral isolates (MERS-EMC and MERS-Jordan). doi = 10.1016/j.virol.2015.07.013 id = cord-009561-pg4jmvw4 author = Johnson, Richard T. title = The virology of demyelinating diseases date = 2004-10-08 keywords = AIDS; multiple; virus summary = The possible role of a virus or viruses is supported by data that (1) a childhood exposure is involved and "viral" infections may precipitate exacerbations of disease, (2) experimental infections in animals and natural infections in humans can cause diseases with long incubation periods, remitting and relapsing courses, and demyelination, and (3) patients with multiple sclerosis have abnormal immune responses to viruses. Thud, studies of patients with multiple sclerosis consistently have shown higher levels of antibody against measles virus in serum and cerebrospinal fluid (CSF) than in controls and in some studies antibodies have been elevated to other viral agents as well (Table 2) . In studies of CSF we found no intrathecal synthesis of antibody in posuneasles encephalomyelitis to suggest antigenic stimulation Subsequently, a variety of diseases of the central and peripheral nervous system and muscle have been described as complications of HIV infection [58, 591. doi = 10.1002/ana.410360715 id = cord-285367-jxlt0gby author = Johnson, Richard T. title = Emerging Issues in Neurovirology: New Viruses, Diagnostic Tools, and Therapeutics date = 2008-08-31 keywords = Nile; West; new; virus summary = In the current era of escalating globalization with rapid transport, changing climate, and an ever growing human population with associated changes in lifestyle, poverty, and war, the emergence of new neurologic infections is accelerated. In the 1960s and 1970s, this emergence was foreshadowed by the appearance of new recombinant (duck-human) influenza viruses, legionnaires'' disease, toxic shock syndrome, Lyme disease, and the neurovirulent La Crosse strains of California encephalitis virus. Some have been due to the evolution of more virulent agents (eg, enterovirus 71, chikunqunya virus, and drug-resistant microbes), some to geographic relocation of agents (eg, Dengue type 3 in Sri Lanka and West Nile virus in North America), and some to contact with animals and crossing of species barriers (eg, bovine spongiform encephalopathy, variant Creutzfeldt-Jakob disease, Nipah virus, and the severe acute respiratory syndrome [SARS] virus). doi = 10.1016/j.ncl.2008.04.003 id = cord-015023-ishxfinx author = Jones, David title = Hard water date = 1995 keywords = virus summary = divert the search for environmental clues away from specific uncommon viruses to a broader category of events occurring early in life which are applicable to regional populations"; this comment is presumably aimed at Kurtzke and those sharing his view 3 that existing epidemiological data point to a specific infectious (presumably viral) agent as a direct cause of MS. Aircraft and rockets, for example, have to be very light but stiff structures; they also depend on liquid fuels pumped at high velocities. Many aircraft already store their fuel in compartments in their wings, and little modification should be needed to pump it to the engines through the hollow spars of the wing structure. More cunning still, its stiffness and damping could even be altered in flight by redistributing the fuel flow between different spars of the structure. doi = 10.1038/377106a0 id = cord-304876-txaoz7oh author = Jordan, Paul C title = Nucleosides for the treatment of respiratory RNA virus infections date = 2018-03-21 keywords = RNA; RSV; polymerase; respiratory; t-705; virus summary = 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein doi = 10.1177/2040206618764483 id = cord-254527-zddwajzg author = Junter, Guy-Alain title = Polysaccharide-based chromatographic adsorbents for virus purification and viral clearance date = 2020-01-13 keywords = AEC; AFC; SEC; Sart; Seph; dna; purification; virus summary = Table 2 gathers a variety of packed-bed column chromatography procedures applied to viral particle purification in which the stationary phase consists of AG -essentially Sepharose® ("Separation-Pharmacia-AG"; GE Healthcare, Chicago, Ill.) (Seph) -or CELe.g., Cellufine™ (JNC Corporation, Tokyo, Japan) -gel beads, modified to fulfill varying separation modes, i.e., ion exchange, size exclusion and affinity (Table 3 [77] [78] [79] [80] [81] ). For instance, the purification process for Nuwiq®, a recombinant coagulation factor VIII (a blood-clotting protein whose deficiency is associated with hemophilia A) patented by Octapharma AG (Lachen, Switzerland) [195] , includes solvent/detergent (S/D) treatment, Planova NF, and five chromatography steps using PS-based stationary phases, i.e., MMC (Capto MMC), CEC (SP Seph FF), AFC (VIIISelect, a Capto matrix with factor VIIIselective ligand), AEC (Q Seph FF) and SEC (Superdex 200). doi = 10.1016/j.jpha.2020.01.002 id = cord-287711-gw8mgg4m author = Junter, Guy-Alain title = Cellulose-based virus-retentive filters: a review date = 2017-06-01 keywords = Table; filter; filtration; viral; virus; water summary = Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption-elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. doi = 10.1007/s11157-017-9434-1 id = cord-319210-yqimufdh author = KENNEDY, P.G.E. title = On the possible viral aetiology of multiple sclerosis date = 1994-09-17 keywords = virus summary = 1 The presence of inflammatory histological changes in the MS lesions such as perivenular lymphocytic infiltration, and the raised cerebrospinal fluid (CSF) immunoglobulins in an oligoclonal pattern detected in most MS patients are very suggestive of an immune basis for the disease, 23 one that may possibly be related to some kind of viral infection. Although by their very nature animal models of virus-induced demyelination only produce a form of indirect evidence for the viral aetiology of MS, nevertheless they can reveal important insights into the possible mechanisms by which a virus can initiate a pathogenetic cascade leading to CNS myelin destruction. 36 In the brains, only a small percentage of the oligodendrocytes are infected with the virus, so the main mechanism of demyelination is almost certainly indirect, presumably via the generation of Class II antigen-induced T cell responses and release of cytokines and/or toxic viral proteins. doi = 10.1093/oxfordjournals.qjmed.a068963 id = cord-010001-u0d5jkp1 author = KOTWAL, GIRISH J. title = Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date = 2006-01-22 keywords = HIV; Secomet; virus summary = With a well-established infrastructure and the methodology to cultivate and to titer viruses accurately 6 to evaluate antiviral effects, it was possible to show that indeed a small volume of the plant extract termed Secomet-V was able to inactivate approximately 1 million virus particles of the attenuated recombinant vaccinia virus vGK5 7 in 1 minute consistently and reproducibly. Secomet-V, an extract of an African plant also found elsewhere in Asia, has been found to have potent antiviral activity against a poxvirus (vaccinia virus), rendering about 1 million particles noninfectious in 1 min with a 50th of a milliliter in in vitro assays (FIG. HIV-infected cells treated with plant extract showed no significant effect on the viral levels (TABLE 1) . There was no difference in the effectiveness of the plant extract in rendering vaccinia virus noninfectious whether it was autoclaved or not, suggesting that the bioactive agent is most likely but not necessarily a heat-stable compound and not a small peptide. doi = 10.1196/annals.1352.014 id = cord-026641-eemp6b5j author = Kabiljo, Julijan title = From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date = 2020-06-11 keywords = RNA; cell; influenza; ns1; virus summary = In the absence of NS1 apoptosis appears to be induced through the viral-RNA-mediated induction of retinoic acidinducible gene I (RIG-I) and interferon (IFN) signaling including protein kinase R (PKR) and eukaryotic initiation factor 2 alpha (eIF2α) activation and subsequent block of translation [39] [40] [41] . Another study screened a variety of wild-type influenza A viruses for their infectivity in pancreatic carcinoma cell lines and showed oncolytic effectiveness in a mouse model of human pancreatic cancer 67 . expressed a recombinant humanized cytotoxic T-lymphocyte-associated protein 4 (CTLA4) immune checkpoint inhibiting antibody from two different RNA fragments of the influenza A virus genome in order to enhance its anti-cancer effectiveness in a murine B16 melanoma model 96 . Further effects of oncolytic influenza A viruses on the cancer-immune microenvironment shown in murine models include activation of NK-cells and macrophage polarization towards immuno-stimulatory M1 phenotypes 66, 114 . doi = 10.1038/s41420-020-0284-1 id = cord-323311-xl2fv0qx author = Kahn, R. E. title = 6th International Conference on Emerging Zoonoses date = 2012-09-07 keywords = BSE; H1N1; H5N1; Health; Professor; States; United; University; disease; human; infection; virus summary = The three key characteristics of this integrated approach to so many infectious diseases are as follows: (i) to use cell culture, primary cells, nonhuman primate and human clinical models to study viral infection; (ii) to combine traditional histopathological, virological and biochemical approaches with functional genomics, proteomics and computational biology (Haagmans et al., 2009); and (iii) to obtain signatures of virulence and insights into mechanisms of host defense response, viral evasion and pathogenesis (Casadevaill et al., 2011) . The unity of human, animal and ecosystem health outlined by Professor Aguirre, as well as the interactions among multiple tick-borne pathogens in a natural reservoir host set out by Professor Fish and his research team, both summarized in Topic 1 above, highlight the necessity of cross-disciplinary collaboration in studying zoonotic bacterial diseases (Daszak et al., 2007, pp. doi = 10.1111/j.1863-2378.2012.01539.x id = cord-311748-yr2ep7uf author = Kahyaoglu, L. N. title = 11 New approaches in microbial pathogen detection date = 2013-12-31 keywords = PCR; detection; virus summary = In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. In recent years, qRT-PCR has been widely used in food virology as the most promising nucleic acid detection method, since it offers several advantages over conventional RT-PCR, including high sensitivity, the possibility of simultaneous amplifi cation, detection and quantifi cation of the target nucleic acids in a single step, and with minimum risk of carry-over contamination through the use of a closed system (Mackay et al. The challenges associated with the detection of foodborne viruses, such as PCR inhibitors and low virus concentrations in foods, affect the effi ciency of realtime assay adversely, therefore, for process control (PC) an internal amplifi cation control (IAC), which is extracted and amplifi ed with the target sequence, is crucial in the evaluation of PCR and to prevent false negatives (Di Pasquale et al. doi = 10.1533/9780857098740.3.202 id = cord-270940-acwkh6ed author = Kallio-Kokko, Hannimari title = Viral zoonoses in Europe date = 2005-06-29 keywords = Congo; Crimean; Europe; Fig; RNA; fever; human; infection; table; virus summary = Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. doi = 10.1016/j.femsre.2005.04.012 id = cord-274643-vjb2yt93 author = Kang, G. title = Viral Diarrhea date = 2008-08-26 keywords = child; diarrhea; gastroenteritis; infection; virus summary = Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for more than 72 hours in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections do not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. doi = 10.1016/b978-012373960-5.00571-2 id = cord-314390-q36ye9ff author = Kang, Gagandeep title = Viral Diarrhea date = 2016-10-24 keywords = child; diarrhea; gastroenteritis; infection; virus summary = Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for >72 h in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections may not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. doi = 10.1016/b978-0-12-803678-5.00486-0 id = cord-277970-sb1wjd3b author = Kang, Qianli title = Screening for Anti-Influenza Actives of Prefractionated Traditional Chinese Medicines date = 2020-10-14 keywords = TCM; influenza; virus summary = It''s therefore of great value to discover novel antivirals from TCMs. In this paper, One hundred medicinal plants which have been included in TCM prescriptions for antiviral treatment were selected and prefractionated into 5 fractions each by sequentially using cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water. As a result, ten TCM fractions were identified to have antiviral potency against IAV, deserving further analysis for novel anti-influenza lead drugs. To this end, 100 medicinal plants which have been recorded as antiviral formula compositions were fractionated with cyclohexane, dichloromethane, ethyl acetate, n-butanol, and water sequentially, generating a library consisting of 500 prefractionated TCM extracts (Figure 1, Table S1 ). By using a HTS approach based on recombinant reporter influenza PR8-PB2-Gluc virus, the antiviral activity of each fraction against IAV was evaluated, and 10 simplified extracts were identified as anti-influenza actives ( Figure 3 ). doi = 10.1155/2020/4979850 id = cord-267831-uu883ofc author = Kang, Yuan-Lin title = Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date = 2020-06-15 keywords = SARS; virus summary = We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. 143 All of these viruses require low pH to trigger viral membrane fusion with the endosomal 144 membranes, and as expected, infection was fully blocked by Bafilomycin A1, which 145 inhibits the vacuolar type H + -ATPase (V-ATPase) acidification activity (Fig. 1C) . Mammalian cell morphology and 671 endocytic membrane homeostasis require enzymatically active phosphoinositide 672 5-kinase PIKfyve The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry doi = 10.1101/2020.04.21.053058 id = cord-351377-xorj8tnz author = Kao, Chi-Fei title = The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date = 2018-10-04 keywords = P96; PEDVPT; RNA; Vero; virus summary = Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. While one piglet in the PEDVPT-P96 group showed intermittent loose diarrhea (score = 1) and viral shedding at 6 to 11 days post-inoculation (DPI) with the peak viral titer of 1.45 ± 3.24 log 10 RNA copies/mL at 8 DPI (Figure 4) , no evidence of PEDV-associated clinical signs and fecal viral shedding were demonstrated in both iPEDVPT-P96 and mock groups. doi = 10.3390/v10100543 id = cord-258783-ev0h95b9 author = Kapil, Sanjay title = Canine Distemper Spillover in Domestic Dogs from Urban Wildlife date = 2011-11-30 keywords = CDV; United; canine; distemper; dog; virus summary = Canine distemper virus (CDV) causes a major disease of domestic dogs that develops as a serious systemic infection in unvaccinated or improperly vaccinated dogs. 68 In addition to domestic dogs, urban wildlife in the United States such as raccoons, foxes, and skunks may play a role in direct transmission of distemper to large felids and other carnivores in zoos, wildlife parks, circuses, and captive breeding facilities. Canine distemper is a highly contagious disease of domestic dogs that also infects multiple wildlife hosts, some that serve as secondary or amplifying reservoirs of the virus. Because canine distemper is an RNA virus, a potential for emergence of antigenic variants exists, particularly in situations where wildlife that are infected with a strain of CDV that has adapted to that host spills back to domestic dogs. Introduction of novel canine distemper viruses in improperly vaccinated dog populations with insufficient immunity can cause new outbreaks of CDV. doi = 10.1016/j.cvsm.2011.08.005 id = cord-294478-3ickafd3 author = Kapil, Sanjay title = Diagnostic Investigation of Emerging Viruses of Companion Animals date = 2008-05-22 keywords = ELISA; animal; diagnostic; disease; viral; virus summary = Variants of a known virus that has gained enhanced virulence or that is able to infect completely vaccinated animals A known virus that has reappeared in the population after a decline in incidence Novel or previously unidentified viral agents detected for the first time because of improved diagnostic capabilities ''''Mystery diseases'''' with large numbers of naive animals involved that are caused by previously uncharacterized viruses Spread of an emerging virus among small companion animals is multifactorial and includes animal health and sanitation practices; migration of a pathogen from a wild reservoir to domestic animals because of changes in populations, trade, climate, land use, and the introduction of invasive species (eg, plant, animal, insect); and, finally, globalization, as was the case with West Nile virus (WNV). Detecting emerging viral diseases of companion animals requires interaction and discussion among clinicians, pathologists, and virologists, and practicing small animal veterinarians must stay engaged in communication with these specialists through their state diagnostic laboratories or nearby colleges of veterinary medicine. doi = 10.1016/j.cvsm.2008.02.009 id = cord-297494-6yxmaihl author = Katsurada, Naoko title = The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study date = 2017-12-06 keywords = patient; pneumonia; virus summary = However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). We conducted this prospective multicentre study to determine the distribution of viruses associated with pneumonia in adults and to establish their virus-specific effects on pneumonia mortality stratified by age group and comorbidity status. To the best of our knowledge, this study is the first to systematically investigate virus-specific effects on pneumonia mortality by age group and comorbidity status among adults. In our study, multiple viruses were identified in 5.1% of virus-associated pneumonia and were associated with higher mortality than single viral infection in patients with chronic respiratory disease and other comorbidities. Systematic reviews have shown that multiple viral infections in patients with respiratory disease are not associated with disease severity [27, 28] ; however, the majority of previous studies included young children but not adults. doi = 10.1186/s12879-017-2858-y id = cord-300435-vs0ntcsb author = Katz, Al title = Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability date = 2018-10-01 keywords = particle; sediment; virus summary = Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. A study of heteroaggregation of the non-enveloped cowpea mosaic virus with colloidal hematite revealed that at pH 6, at which hematite carries a positive surface charge and the virus a negative charge, the aggregates accumulated four times as many viruses as hematite particles Vilker et al. In this work, we employ turbidity measurements to investigate the heteroaggregation of a model envelope virus, the bacteriophage φ6, with colloidal goethite and three clay minerals: illite, kaolinite and montmorillonite. Although imprecise knowledge of doublet shape complicates calculations of heteroaggregation rates, analysis of the turbidity slope coupled with particle concentrations allows one to determine relative aggregation rates between φ6 and the four sediment types, elucidating the nature of the interaction. doi = 10.1016/j.scitotenv.2018.04.425 id = cord-311823-85wj08gr author = Katze, Michael G. title = Innate immune modulation by RNA viruses: emerging insights from functional genomics date = 2008 keywords = HCV; IFN; response; rig; virus summary = In this section, we review recent studies in which genomic approaches have been used to provide new information on how viruses trigger and regulate innate immune pathways, and to evaluate the use of type I IFN-based therapy as a means to enhance the innate immune response to HCV. In RIg-I-deficient cells, influenza virus fails to elicit the expression of IFNβ and of many ISgs, including key antiviral mediators such as IRF3, STAT1 (signal transducer and activator of transcription 1), IFIT1 (IFN-induced protein with tetratricopeptide repeats 1; also known as ISg56) and ISg54 (also known as IFIT2). Although these studies have provided considerable information regarding the genes activated downstream of TlR activation, it will be advantageous to extend genomic analyses in the context of viral infection using cells lacking the expression of specific TlRs. The ability of a virus to establish an infection depends, at least to some extent, on its ability to block the host innate immune response or to modulate the activity of antiviral effector proteins. doi = 10.1038/nri2377 id = cord-301285-p83ondy8 author = Kautz, Tiffany F title = Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date = 2018-03-06 keywords = Fig; RNA; TC-83; virus summary = To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. doi = 10.1093/ve/vey004 id = cord-344749-omzhhr0k author = Kaya, Sariye Irem title = Electrochemical virus detections with nanobiosensors date = 2020-02-14 keywords = PCR; RNA; detection; dna; electrochemical; virus summary = Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen doi = 10.1016/b978-0-12-819870-4.00017-7 id = cord-264350-4zxp3uae author = Kelley, James L. title = Chapter 12. Antiviral Agents date = 1984-12-31 keywords = agent; antiviral; virus summary = The focus of this year''s chapter is on agents with activity A brief update of this year''s advances More comprehensive reviews dealing VIRAL RESPIRATORY DISEASE RNA viruses are the major causative factors of the various forms of acute respiratory disease .8 respiratory tract are probably the most common cause of symptomatic human infections. Ribavirin (l-~-~-ribofuranosyl-1,2,~-triazole-3-carboxamide) -This nucleoside has activity against a broad range of DNA and RNA viruses in An tissue culture and in animal model systems.2 analysis of the status of ribavirin 3) as an is still unresolved but may involve guanosine nucleotides and inhibition of inosine monophosphate dehydrogenase.Z6 In a clinical trial against influenza A, oral ribavirin failed to alter clinical signs and symptoms of the disease.2 However, it OR OR has recently been reported to have a therapeutic effect against both influenza A and influenza B virus infections when administered to patients by inhalation of small-particle aerosol through a face m a s k . doi = 10.1016/s0065-7743(08)60688-0 id = cord-331739-y1d0leic author = Kempf, Christoph title = Pathogen inactivation and removal procedures used in the production of intravenous immunoglobulins date = 2007-03-31 keywords = IVIG; inactivation; non; virus summary = Since plasma pools from 250 to 2000 blood donations were being used to produce albumin, efforts were initiated to inactivate hepatitis virus in human serum albumin solutions [6] . The emergence of human immunodeficiency virus (HIV) and reports of non-A, non-B hepatitis transmission by some IVIG products [11, 12] but not others caused manufacturers and regulatory agencies to examine existing IVIG manufacturing processes for their capacity to eliminate viruses [13e22]. Studies of IVIG manufacturing procedures suggested that cold ethanol fractionation removes viruses by two mechanisms: 1) inactivation and 2) partitioning. Efficient elimination of TSE infectivity from IgG solutions by Table 3 Log 10 reduction factors of model viruses observed during laboratory experiments of IVIG production (Carimune NF Ò ) Process (step in Fig. 1 [53] . To date IVIG therapeutics have reached a high safety standard due to consequent blood and plasma testing and the introduction of virus elimination steps in the manufacturing process. doi = 10.1016/j.biologicals.2006.01.002 id = cord-309067-aemjbkfj author = Kennedy, Melissa title = Methodology in diagnostic virology date = 2005-03-01 keywords = Fig; antibody; assay; virus summary = Detection of the virus that causes an infection uses one of several methods: The virus may be propagated in the laboratory and characterized; the virus may be visualized by electron microscopy; the viral proteins may be detected using specific antibody; the viral nucleic acid may be detected; or an activity of the virus, such as red blood cell agglutination, may be assayed. Antigen detection assays involve the use of virus-specific antibody to detect or bind to the viral protein or antigen in the sample. The assays vary in the sample substrate, how the binding of antibody to antigen is visualized, sensitivity, and specificity. Most use pathogen-specific antibody for capture and detection as for IFA assays (Fig. 4B) . Variations on this protocol may be found with different assays, but the underlying technique of pathogen-specific antibody binding the virus in the sample is similar in all (Fig. 4) [1, 3, 4] . doi = 10.1016/j.cvex.2004.09.009 id = cord-316951-1swlhdz5 author = Kennedy, Melissa title = General concepts of virology date = 2005-03-01 keywords = cell; virus summary = Virus pathogenesis is defined as the mechanism by which a virus replicates in the cell, and in doing so, injures a cell and produces disease. The virus must first attach to a cell by way of a surface receptor, followed by entry or penetration into the cell The virus uncoats within the cell and releases its nucleic acid For most viruses, the next step is viral transcription to produce mRNA. Genetic characteristics of the host include species, breed, organ, tissue susceptibility, and function at the cellular level (eg, cell receptor types and intracellular hospitality to the virus). It is defined as the specific cells and tissue in the host in which the virus replicates in a natural infection. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. A basic understanding of viruses and how they replicate and produce disease can aid in the management of virus infections. doi = 10.1016/j.cvex.2004.09.010 id = cord-288238-36hiiw91 author = Keshavarz, Mohsen title = Metabolic host response and therapeutic approaches to influenza infection date = 2020-03-05 keywords = ATP; IFN; ROS; infection; influenza; virus summary = It is also reported that influenza infection significantly increases ROS production by inducing Nox4, and the proliferation of this virus in lung epithelial cells is dependent on redox-sensitive pathways activated by Nox4-derived ROS [16] . IFN can also exert its function on metabolic changes by producing several mediators including indoleamine-2,3-dioxygenase (IDO) and nitric oxide (NO), both of which appear to have either an inducible or an inhibitory role in viral replication [33] . In addition, increased temperature of cells during infection (which could be the result of virus replication and fever) causes heat stress which in turn can considerably downregulate carnitine palmitoyltransferase II (CPT II) activity and reduce the β-oxidation and ATP levels in fibroblasts of influenza-associated encephalopathy patients and healthy volunteers [110] . Through enhancing the activity of the mTORC1 complex, the influenza virus strengthens several metabolic pathways, including glycolysis, glutaminolysis, pentose phosphate, and fatty acid synthesis, to provide more ATP and structural materials for viral replication. doi = 10.1186/s11658-020-00211-2 id = cord-294544-iutcduix author = Kesson, Alison M. title = Respiratory virus infections date = 2007-09-06 keywords = RSV; respiratory; virus summary = 1 This has enabled the identification of many viruses, including those commonly causing respiratory infections -influenza, RSV, PIV 1-4, adenoviruses, measles, enteroviruses, rhinoviruses, VZV, CMV and HSV. 3 After 24-72 h of culture, using pooled or single fluorescein isothiocyanate (FITC)-labelled monoclonal antibodies directed against influenza A and B, RSV, parainfluenza 1-3 and adenoviruses, rapid identification of a respiratory virus infection can be established. Diagnosis of rhinovirus infection rarely requires laboratory testing but virus isolation, detection of viral RNA by RT-PCR, antigen detection by DIF in cells from respiratory secretions or detection of a fourfold rise in antibody titres by neutralization test or EIA can be performed if required. Diagnosis of the specific cause of an acute pneumonia due to a particular viral agent is complicated by difficulty in obtaining appropriate lower respiratory tract samples for culture and in isolating or detecting certain pathogens, and additionally by the frequent asymptomatic shedding of some viruses, e.g. herpes simplex virus or adenoviruses. doi = 10.1016/j.prrv.2007.07.003 id = cord-349358-leicos9j author = Ketzinel‐Gilad, Mali title = RNA interference for antiviral therapy date = 2006-06-16 keywords = HCV; HIV; HIV-1; RNA; siRNA; viral; virus summary = During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. doi = 10.1002/jgm.929 id = cord-252725-e3pazjdi author = Khalil, Ayman title = The upshot of Polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: An appraisal date = 2020-10-15 keywords = COVID-19; Fig; SARS; TNF; anti; virus summary = In fact, several studies and clinical trials increasingly proved the role of polyphenols in controlling numerous human pathogens including SARS and MERS, which are quite similar to COVID-19 through the enhancement of host immune response against viral infections by different biological mechanisms. Actually, data indicated that activation of the nuclear factor (NF)-κB transcription factor (NF-κB) signaling pathway represents a major contribution to the inflammation induced post SARS-CoV infection and that NF-κB inhibitors are promising antiviral drugs against infections caused by the virus and potentially other pathogenic human coronaviruses [8] . Moreover, it was found to reduce the reactive oxygenated species (ROS) produced during viral infection and subsequently decrease pro-inflammatory markers such as IL-8, TNF-α, IL-1β and IL-6 [25] and increases anti-inflammatory cytokines such as IL-10 [35] , indicating that it has clear antiviral effects on several respiratory and common cold viruses through its ability to reduce virus imputation, replication and viral load in vitro, as well as lung inflammation and airways hyper-responsiveness in vivo [29] . doi = 10.1007/s13659-020-00271-z id = cord-304343-m7tbdfri author = Khandia, Rekha title = A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy date = 2019-07-03 keywords = Autophagy; Beclin; LAMP-2A; cancer; cell; disease; inhibit; lc3-ii; pathway; protein; role; virus summary = Similarly, inhibiting the mTOR signaling pathway can prevent apoptosis and even enhance necroptosis, whereas starvation, which induces autophagy, protects cells from zVAD-mediated necroptotic death [194] . For instance, autophagy has been demonstrated to be actively involved in the replication of influenza A virus (IAV), which induces autophagosome formation during the early phase of infection and later inhibits autophagosomal maturation by preventing autophagosomal-lysosomal fusion and promoting autophagosomes to accumulate in virus-infected cells [253] . (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. In addition, the novel anti-cancer molecule HA15, which targets HSPA5/BIP, was shown to induce ER stress and increase the unfolded protein response, resulting in cancer cell death via autophagy and apoptosis [304] . doi = 10.3390/cells8070674 id = cord-326177-zzsaf3bl author = Khatri, Mahesh title = Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model date = 2018-01-29 keywords = MSC; cell; influenza; virus summary = title: Mesenchymal stem cell-derived extracellular vesicles attenuate influenza virus-induced acute lung injury in a pig model In several animal models of human diseases, MSC-EVs mimic the beneficial effects of MSCs. Influenza viruses cause annual outbreaks of acute respiratory illness resulting in significant mortality and morbidity. Next, we examined the anti-influenza activity of MSC-EVs in vitro in lung epithelial cells and anti-viral and immunomodulatory properties in vivo in a pig model of influenza virus. The antiinfluenza activity of MSC-EVs was due to transfer of RNAs from EVs to epithelial cells since pre-incubation of MSC-EVs with RNase enzyme abrogated the anti-influenza activity of MSC-EVs. In a pig model of influenza virus, intratracheal administration of MSC-EVs 12 h after influenza virus infection significantly reduced virus shedding in the nasal swabs, influenza virus replication in the lungs, and virus-induced production of proinflammatory cytokines in the lungs of influenza-infected pigs. doi = 10.1186/s13287-018-0774-8 id = cord-300837-d0a8y5qh author = Khetawat, Dimple title = A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System date = 2010-11-12 keywords = cell; figure; glycoprotein; virus summary = To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP) gene encoding human immunodeficiency virus type-1 (HIV-1) genome in conjunction with the HeV and NiV fusion (F) and attachment (G) glycoproteins. Pseudotyped virus particles generated with the NiV F and G glycoproteins were able to infect and produce luciferase reporter gene activity at various levels on all permissive receptor expressing cells ( Figure 1A ) while no signal was observed with the receptor negative HeLa-USU or with control virus particles generated by transfection with empty vector (pCAGGs). To confirm these findings and demonstrate an expanded utility of the henipavirus envelope glycoprotein pseudotyping systems, NiV and HeV F and G glycoprotein bearing lentivirus particles were prepared with the GFP reporter gene encoding construct pNL4-3-GFP-E-R + and used to infect receptor positive 293T cells ( Figure 2 ). doi = 10.1186/1743-422x-7-312 id = cord-332361-pdoln3nr author = Khor, Chee-Sieng title = Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years date = 2012-03-20 keywords = RSV; respiratory; virus summary = title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years CONCLUSION: Viral RTIs, particularly due to RSV, are commonly detected in respiratory samples from hospitalized children in Kuala Lumpur, Malaysia. In this study, we describe etiological agents, demographic details of patients, and seasonality (including association with meteorological factors) due to viral RTIs in a teaching hospital in Kuala Lumpur, over the last 27 years. Our findings support a previous local study carried out over a year, which showed that RSV was the most commonly detected respiratory virus, followed by parainfluenza viruses, influenza viruses and adenovirus [7] . Respiratory viral infections due to RSV, parainfluenza viruses, influenza viruses and adenovirus are significant causes of morbidity in hospitalized children in Kuala Lumpur, and are likely to be underdiagnosed. doi = 10.1186/1471-2431-12-32 id = cord-328252-dk54w8z9 author = Kikkert, Marjolein title = Innate Immune Evasion by Human Respiratory RNA Viruses date = 2019-10-14 keywords = IFN; RNA; immune; innate; rig; virus summary = Whether PA-X also degrades viral dsRNA species to prevent recognition by cytosolic RNA sensors is not entirely clear, but mutant viruses in which this PA-X protein was expressed in significantly lower amounts elicited higher levels of innate immune response; for example, IFN-beta production was much higher in these infections [71] . This indeed suggests that PA-X, besides having a role in the degradation of cellular mRNAs, may also degrade viral RNA to prevent recognition by innate immune sensors and activation of innate immune responses, similar to what was shown for the CoVs. To my knowledge, an endoribonuclease has not been identified in the RSV genome, so this virus may use alternative innate immune evasion strategies, as discussed elsewhere in this review. [91] suggested that RSV specifically targets mRNA encoding surfactant protein A, an innate immune factor with an important role in the epithelial tissue of the lung, which directly binds to virus particles to cause their destruction by host defense mechanisms. doi = 10.1159/000503030 id = cord-327013-gc6o8ou3 author = Kim, Heui Man title = Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea date = 2020-07-06 keywords = Korea; virus summary = title: Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea The Korea Centers for Disease Control and Prevention operates the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) to monitor epidemics of influenza and Severe Acute Respiratory Infection (SARI) to identify mutated influenza viruses affecting drug resistance, pathogenesis, and transmission. CONCLUSIONS: Our data indicate the utility of monitoring influenza-infected immunocompromised patients in general hospitals for the early detection of emerging neuraminidase inhibitor-resistant viruses and maintaining continuous laboratory surveillance of patients with influenza-like illness in sentinel clinics to monitor the spread of such new variants. If a drug resistance mutation is found in the NA gene, the KINRESS attempts to isolate the virus and perform phenotypic analysis (NA inhibition assay). Here, drug-resistant A(H1N1)pdm09 viruses were detected via the KINRESS in patients with acute hematologic cancer not exhibiting recovery despite oseltamivir and peramivir administration; these were characterized genetically and antigenically following isolation. doi = 10.1186/s12985-020-01375-1 id = cord-000114-f0vud3gu author = Kim, Jeong‐Ki title = Ducks: The “Trojan Horses” of H5N1 influenza date = 2009-05-31 keywords = H5N1; HPAI; duck; virus summary = While the H5N1 HPAI viruses are 100% lethal to chickens and gallinaceous poultry, they often cause asymptomatic infection in some species of domestic and wild ducks. 37 The first indication of the spread of H5N1 HPAI viruses from domestic to wild species of aquatic birds occurred in Kowloon and Penfold Park in Hong Kong, 38 where 19 different duck species were infected. If these wild birds are migratory and experience limited morbidity, they in turn can disperse HPAI viruses widely (Figure 2) , as suggested by the high genetic similarity of HPAI isolates from Africa, Europe, and the Middle East to the Qinghai-H5N1 virus. There is consensus that the migratory waterfowl of the world (predominantly wild ducks) serve as the natural reservoirs of all influenza A viruses, which cause asymptomatic infection in these birds. 51 The continuing co-circulation of multiple subtypes of LPAI viruses in domestic poultry could explain why a small percentage of susceptible domestic species can appear healthy while shedding transmissible levels of H5N1 HPAI virus. doi = 10.1111/j.1750-2659.2009.00084.x id = cord-282344-o1rkx2z4 author = Kim, Seung Won title = Effects of humidity and other factors on the generation and sampling of a coronavirus aerosol date = 2007-07-25 keywords = TGEV; virus summary = The airborne viruses were collected on heating, ventilating, and air conditioning (HVAC) filters in an experimental apparatus and also sampled upstream of these test filters using AGI-30 and BioSampler impinger samplers. To study the effects of relative humidity (RH) on TGEV collection by the filters and samplers, the virus was nebulized into air at 30, 50, 70, and 90% RH. To measure the degree to which the nebulizers generated airborne viruses that could be sampled and remain viable, aerosolization efficiency, g A , was calculated in the same way as Adams et al. The recovery of TGEV from the test filter can be calculated in two ways: (1) relative to the airborne virus concentration, R a , and (2) relative to the nebulizer suspension concentration, R n . TGEV was nebulized, then sampled using AGI-30 impingers and BioSamplers, and finally collected on an HVAC test filter to measure the effects of nebulization stress and the recovery of viable virus from the filter. doi = 10.1007/s10453-007-9068-9 id = cord-285935-5rsk6g7l author = Kinast, Volker title = Hepatitis E Virus Drug Development date = 2019-05-28 keywords = HEV; Hepatitis; RNA; virus summary = Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo doi = 10.3390/v11060485 id = cord-264699-l8db5gll author = Kino, Tomoshige title = Virus-mediated modulation of the host endocrine signaling systems: clinical implications date = 2007-06-30 keywords = AIDS; HIV-1; Vpr; virus summary = For example, HIV-1-encoded gp120 molecules, which are located on the surface of the viral particle and have a major role in the entry of viruses into target cells, demonstrate amino acid sequence similarity to the growth hormone-releasing hormone (GHRH) receptor of the host and suppress the activation of this receptor by GHRH. In addition to their extracellular actions, many viral molecules act inside infected cells to modulate intracellular host signaling systems, including transcriptional regulation of target genes by hormones. In agreement with these findings, one of the HIV-1 proteins, Vpr, which is a 96-amino acid virion-associated accessory protein that has multiple functions (including influencing transcriptional activity and arresting the cell cycle), increases the effects of GR stimulation by several fold, functioning as a nuclear receptor coactivator in cooperation with a host cell coactivator complex containing p300 or its homolog CREB-binding protein (CBP) [29] [30] [31] [32] . doi = 10.1016/j.tem.2007.03.003 id = cord-257064-iafm3pcc author = Kint, Joeri title = Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date = 2014-12-18 keywords = IBV; virus summary = During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs doi = 10.1007/978-1-4939-2438-7_9 id = cord-011457-hqxybv1k author = Kirui, James title = Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date = 2020-05-19 keywords = Gag; HIV-1; virus summary = To enable simple and highly sensitive measurement of virus release from transfected cells, we generated HIV-1 reporter viruses in which Nanoluciferase (NanoLuc) was inserted between the MA and CA domains of Gag (Gag-iNanoLuc). We generated viruses using the pNL4-3 Gag-iNanoLuc vector complemented with different ratios of the WT HIV-1 molecular clone pNL4-3 and tested their infectivity by measuring the HIV-1 Tat-driven firefly luciferase activity in TZM-bl cells. These results demonstrate that the Gag-iNanoLuc vector provides a highly sensitive and quantitative tool for measuring the effects of Gag mutations, host cell restriction factors, and small-molecule inhibitors on HIV-1 particle assembly and release. The Gag-NanoLuc fusion protein is expressed in the cell and released at similar levels to WT Gag, thereby enabling simple yet highly sensitive quantification of viral gene expression and virus particle production by measurement of the NanoLuc reporter protein bioluminescent activity in the cell lysates and supernatants. doi = 10.1186/s12977-020-00521-5 id = cord-005081-kxrzv16n author = Kiselev, O. I. title = Progress in the development of pandemic influenza vaccines and their production technologies date = 2010-11-12 keywords = Fig; influenza; vaccine; virus summary = We are using the following approaches to the development of industrial production: use of nanoparticles and nanoemulsions as functional adjuvants, construction of totally-safe strains for live attenuated influenza vaccines with deletions of molecular determinants of pathogenicity, application of protein and chemical chaperones to provide self-assembly of haemagglutinin molecules of the H1N1v-2009 virus, and impregnation of whole-virion preparations with nanoparticles to enhance antigenicity. Europe and the United States agreed to allot grants and worked out programs for developing novel technologies and vaccine preparations with improved qualities: a new generation of LAIV, that is, delNS1 vaccines with a limited replicative potential, LAIV with deletions of pathogenicity factors in genes, latest variations of subunit vaccines enhanced by adju vants, and capsid nanovaccines and nanovaccines based on inactivated viruses and virus like particles [14] . A marked breakthrough in the construction of recombinant vaccines is related to the use of insect cells and the obtaining of virus like particles (VLPs) based on baculovirus expression vectors. doi = 10.1134/s0003683810090024 id = cord-004774-fvf671jn author = Kjeldsberg, Elisabeth title = Detection of astroviruses in gut contents of nude and normal mice date = 1985 keywords = mouse; virus summary = Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. In this note we report the detection of astrovirus-like partieles in gut contents from nude mice, with and without clinical signs of illness, and from normal symptomless mice in association with an outbreak of diarrhea. The morphology of the virus-like particles detected in gut contents of nude and normal mice corresponds to the previous description of astroviruses. doi = 10.1007/bf01310560 id = cord-326725-0jgw083h author = Klamroth, Robert title = Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date = 2013-09-30 keywords = FVIII; HIV; factor; virus summary = These measures include selection of donors, screening of donations and plasma pools for markers of infection with known viruses, and a manufacturing process with a high capacity to inactivate and/or remove viruses by selected steps validated for their virus reduction capacity. [7] [8] [9] Although screening for viral markers by serology and virus nucleic acid by nucleic acid testing (NAT) ensures that nearly all plasma units entering production are free of HBV, HCV, and HIV, inactivation and removal steps are necessary to reduce any viruses that may enter the plasma pool during a "window period" before markers can be detected. 46 Although B19V was reduced by dry heat in validation studies, the reduction factor may not be sufficient for complete inactivation of the virus load in the final product; asymptomatic B19V infection was detected in a patient who received FVIII concentrate treated at 80°C for 72 hours. doi = 10.1111/trf.12423 id = cord-294585-dl5v9p50 author = Klein, H. G. title = Pathogen‐reduction methods: advantages and limits date = 2009-02-13 keywords = blood; pathogen; plasma; virus summary = However, because blood contains numerous labile proteins and fragile cells, and because there is a wide array of potentially infectious agents, no single method of pathogen-inactivation will likely preserve all blood components, yet effectively remove all viruses, bacteria, spores, protozoa and prions. Riboflavin/ultraviolet light treatment has been evaluated in preclinical studies and found to result in reduction of infectivity by many pathogens including west Nile virus, intracellular HIV, bacteria and protozoa. Therapeutic efficacy and safety of platelets treated with a photochemical process for pathogen inactivation: the SPRINT Trial Clinical safety of platelets photochemically treated with amotosalen HCl and ultraviolet A light for pathogen inactivation: the SPRINT trial Fresh frozen plasma prepared with amotosalen HCl (S-59) photochemical pathogen inactivation: transfusion of patients with congenital coagulation factor deficiencies Therapeutic efficacy and safety of red blood cells treated with a chemical process (S-303) for pathogen inactivation: a Phase III clinical trial in cardiac surgery patients doi = 10.1111/j.1751-2824.2009.01224.x id = cord-020789-slsfhrkx author = Kleines, Michael title = Virale Atemwegserkrankungen – Influenza, RSV und neue Viren date = 2017-10-27 keywords = Influenza; RSV; Viren; Virus; der; die summary = Die Bedeutung der entsprechenden Viren ließ sich nur durch die Anwendung moderner molekularer Methoden erkennen, und sie werden auch am besten durch molekulare Verfahren diagnostisch erfasst. In den letzten Jahren hat es eine Weiterentwicklung der verfügbaren Technologien (ausgehend von der für ein einzelnes Virus spezifischen Standard-PCR mit einem Zeitbedarf von 2-3 h) in 2 Richtungen gegeben: Zum einen sind nun Multiplexverfahren verfügbar, die organsystemorientiert alle relevanten Erreger für ein definiertes Krankheitsbild in einem Reaktionsansatz nachweisen können, z. Aber auch für das Management von RSV-Infektionen und Infektio-nen mit anderen respiratorischen Viren deuten sich substanzielle Fortschritte an. Letzter wichtiger Vertreter dieser Reihe, die von Subtypen mit den Hämagglutininkomponenten H5, H7 und H9 dominiert wird, ist ein Influenza-A-Virus vom Subtyp H7N9, das 2013 in China nachgewiesen wurde und eine größere Zahl humaner Infektionen verursacht hat (▶ Tab. 1). Aufgrund von eingeschränkter Sensitivität und Spezifität der Antikörpernachweisverfahren ist der positive Vorhersagewert positiver Antikörpernachweise für eine frische RSV-Infektion gering. doi = 10.1055/s-0043-114856 id = cord-339172-210dwhgj author = Knoops, Kèvin title = SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date = 2008-09-16 keywords = DMV; RNA; SARS; figure; membrane; virus summary = Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''''inner vesicles,'''' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. doi = 10.1371/journal.pbio.0060226 id = cord-151024-qe7c2uks author = Koca, Caglar title = Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date = 2020-11-07 keywords = ACE2; SARS; respiratory; virus summary = We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . doi = nan id = cord-336212-ueh4q408 author = Koenig, Kristi L. title = Identify-Isolate-Inform: A Tool for Initial Detection and Management of Zika Virus Patients in the Emergency Department date = 2016-04-04 keywords = Ebola; Zika; virus summary = The identify-isolate-inform (3I) tool, originally conceived for initial detection and management of Ebola virus disease patients in the ED, and later adjusted for measles and Middle East Respiratory Syndrome, can be adapted for real-time use for any emerging infectious disease. This paper describes the adaptation of the identify-isolateinform (3I) tool (initially developed for Ebola virus disease 8, 9 and modified for measles 10 and Middle East Respiratory Syndrome (MERS)) 11 for use in the detection and management of potential Zika virus patients presenting to the ED, including women who are pregnant or contemplating pregnancy, and their partners. The identify-isolate-inform (3I) tool, initially developed for Ebola virus disease and subsequently adapted for measles and MERS, can be modified for the ED evaluation and management of patients under investigation for Zika ( Figure 3 ). The identify-isolate-inform (3I) tool is an instrument that can be used real-time on the front lines to rapidly detect and manage patients at risk for Zika virus disease presenting to the ED. doi = 10.5811/westjem.2016.3.30188 id = cord-022383-pz0htccp author = Kohn, Dennis F. title = Biology and Diseases of Rats date = 2013-11-17 keywords = Fig; SDAV; Sendai; animal; colony; disease; infection; lesion; rat; strain; tumor; virus summary = The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. doi = 10.1016/b978-0-12-263620-2.50010-0 id = cord-352054-g7q2z4l5 author = Kolivoška, Viliam title = Electrophoresis on a microfluidic chip for analysis of fluorescence‐labeled human rhinovirus date = 2007-11-15 keywords = SDS; cy5; virus summary = Resolution of the sample constituents (virions, a contaminant present in all virus preparations, and excess dye) was improved upon adaptation of the separation conditions, mainly by adjusting the SDS concentration of the BGE. As the applied instrumentation (a commercial microdevice) utilized a red laser at l ex 630 nm for high-sensitivity detection, virus particles were fluorescence (FL)-labeled prior to analysis and preseparated from the excess of dye by size-exclusion chromatography (SEC). Separation from a contaminant, which also becomes labeled upon reaction of the virus sample with reactive Cy5, and from the excess free dye was improved by addition of SDS and varying its concentration in the BGE. Chip electrophoresis with the finally selected BGE (100 mM borate buffer, pH 8.3, containing 3.1 mM SDS), enabled an extremely rapid assessment of virus purity, and the investigation of bioaffinity reactions of labeled virus with a number of soluble artificial receptor fragments. doi = 10.1002/elps.200700397 id = cord-259505-7hiss0j3 author = Kong, Qingming title = Proteomic analysis of purified coronavirus infectious bronchitis virus particles date = 2010-06-09 keywords = HSP90; IBV; host; protein; virus summary = It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it''s an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. doi = 10.1186/1477-5956-8-29 id = cord-253594-9gbo8viu author = Konieczny, Leszek title = The COVID-19 Puzzle date = 2020-05-31 keywords = alcohol; virus summary = From the epidemiological perspective, an important factor affecting the spread of the virus is the proximity between infection targets. The bacterial genome includes a repository of viral genetic sequences -effectively a "catalogue" of known viruses. Its effects appear to depend on the carrier''s age: many people, particularly young ones, remain asymptomatic, while older individuals frequently develop serious -even life-threateningsymptoms. Variable susceptibility to infection may be a consequence of the general state of health, which, of course, depends on the individual''s age and co-morbidities -particularly metabolic ones (e.g. diabetes). Since the virus preferentially attacks the lungs, we can point to tobacco smoking as a factor, which promotes infection by damaging lung tissue. One mechanism which exhibits clear susceptibility to external disruption (including the presence of unusual substances) is protein folding. Genetic polymorphism undoubtedly results in individual variability, including well-known differences in alcohol tolerance. doi = 10.6026/97320630016418 id = cord-315781-dejh8q22 author = Konishi, Tomokazu title = Re-evaluation of the evolution of influenza H1 viruses using direct PCA date = 2019-12-17 keywords = Fig; virus summary = It should be noted that avian viruses showed lower PC values and appeared around the centre of the PCA, while swine and human viruses exhibited extreme values (Figs. Thus, avian viruses had sequences that were similar to the average among samples at amino acids that were characteristic to the three groups of human and swine viruses: R, M, and U. Avian samples also showed characteristic motifs at other positions, which may appear in lower PCs. The relationships observed among the strains presented here are different from the classic ones 4, [8] [9] [10] [11] [12] in several elements. www.nature.com/scientificreports www.nature.com/scientificreports/ One of the major differences observed was the direct shift from avian to swine or human viruses. Drifts and spreading: the genomes of the R group of human viruses have been changing yearly (Figs. doi = 10.1038/s41598-019-55254-z 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-008556-oetrdm8g author = Kozak, Marilyn title = Regulation of Protein Synthesis in Virus-Infected Animal Cells date = 2008-03-01 keywords = AUG; Kozak; RNA; VSV; cell; protein; translation; virus summary = One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. doi = 10.1016/s0065-3527(08)60265-1 id = cord-021413-1ht1xm88 author = Kraft, Lisbeth M. title = Viral Diseases of the Digestive System date = 2013-10-21 keywords = EDIM; Kraft; MHV; hepatitis; infection; mouse; reovirus; virus summary = Runner and Palm (1953) , studying C3H mice, indicated that there was a higher incidence of diarrhea in December/January (Kraft, 1961; Blackwell et al., 1966) , complement fixation (Wilsnack et al., 1969; Kapikian et al, 1976; Thouless et al., 1977b) , direct immunofluorescent staining or precipitin (Wilsnack et al., 1969; Spence et al., 1975; Foster α/., 1975; Peterson α/., 1976) , immune electron microscopy (Kapikian et al., 1974; Bridger and Woode, 1975) , immunoelectroosmophoresis (Tufvesson and Johnsson, 1976; Middleton et al., 1976) , enzyme-linked im munosorbent assay (ELISA) (Scherrer and Bernard, 1977; El lens etal., 1978; Yolken etal., 1978a,b,c) , radioimmunoas say (Acres and Babiuk, 1978; Kalica et al., 1977; Middleton et al., 1977) , immunodiffusion (Woode et al., 1976) , hemagglutination inhibition (Fauvel et al., 1978) , enzymelinked fluorescence assay (ELISA) (Yolken and Stopa, 1979) , an unlabeled soluble enzyme peroxidase-antiperoxidase method , plaque reduction test (Estes and Graham, 1980) , serologic trapping on antibody-coated electron microscope grids (Nicolaieff et al., 1980) , a solid phase system (SPACE, solid phase aggregation of coupled erythrocytes) for detection of rotaviruses in feces (Bradbume et al., 1979) , and immune electron microscopy with serum in agar diffusion (Lamontagne et al., 1980) . doi = 10.1016/b978-0-12-262502-2.50016-x id = cord-000933-nn9gj0z1 author = Krzyzaniak, Magdalena Anna title = Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein date = 2013-04-11 keywords = FACS; Fig; GFP; RSV; Rab5; cell; virus summary = doi = 10.1371/journal.ppat.1003309 id = cord-003232-nquw7qga author = Kuchipudi, Suresh V. title = Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date = 2018-08-06 keywords = bat; influenza; virus summary = This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection. doi = 10.3390/vetsci5030071 id = cord-329145-424vv8a8 author = Kuhn, Jens H. title = Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae date = 2012-09-23 keywords = filovirus; nomenclature; variant; virus summary = Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). Unfortunately, most ICTV Study Groups or other expert groups have not provided clear guidelines in the past, accepting strain and genetic variant names as they were suggested by different researchers in their publications rather than creating consistent nomenclature schemes that apply at least to all viruses of one family. To differentiate uncultured or passage 0 filoviruses for which near-complete genomic data are available from those that exist in culture, we propose to follow the suggestions of the Rotavirus Classification Working Group and to add the suffix ''''-wt'''' (for ''''wild-type'''') to their genetic variant names as outlined above. doi = 10.1007/s00705-012-1454-0 id = cord-317501-yblzopc3 author = Kuhn, Philipp title = Recombinant antibodies for diagnostics and therapy against pathogens and toxins generated by phage display date = 2016-06-21 keywords = Fab; antibody; display; human; library; phage; single; virus summary = Panning against peptides, recombinant viral proteins, or complete virus particles has led to the identification of antibodies directed against human pathogenic viruses such as Sin nombre virus [100] , Dengue virus [101, 102] , Influenza virus [103, 104] , VEEV [105] , Norovirus [106] , SARS coronavirus [107] , or Hepatitis C [108] from naïve antibody gene libraries. A naïve human Fab-phage library was screened for NS5-specific antibody fragments using various NS5 variants from Dengue Virus serotypes 1-4 as antigens for panning and characterization [128] . [180] reported the isolation of a human monoclonal antibody against the Block 2 region of Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) by phage display from a malaria patient derived scFv library. In this context, the antibody phage display offers a powerful tool for antibody selection and allows the isolation of neutralizing antibodies against complete active toxins or special domains by using different human naïve antibody libraries with high diversity [185] [186] [187] . Single chain variable fragment antibodies against Shiga toxins isolated from a human antibody phage display library doi = 10.1002/prca.201600002 id = cord-327855-txryqil7 author = Kulka, M. title = The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date = 2003 keywords = Fig; HAV; IFN; RNA; cell; virus summary = Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here. doi = 10.1007/s00705-003-0110-0 id = cord-283880-lrrkuist author = Kumar, Arvind title = Evolution of selective-sequencing approaches for virus discovery and virome analysis date = 2017-07-15 keywords = RNA; dna; virus summary = Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches. doi = 10.1016/j.virusres.2017.06.005 id = cord-294323-mryiqmsw author = Kumar, Binod title = The emerging influenza virus threat: status and new prospects for its therapy and control date = 2018-01-10 keywords = H1N1; H3N2; influenza; virus summary = The wide range of hosts provides influenza A viruses greater chances of genetic re-assortment, leading to the emergence of zoonotic strains and occasional pandemics that have a severe impact on human life. Here, we primarily discuss the pathogenesis of influenza virus type A, its epidemiology, pandemic potential, current status of antiviral drugs and vaccines, and ways to effectively manage the disease during a crisis. A genetic shift occurs when two or more different influenza virus strains infect the same cell in a host, leading to recombination of genetic materials, an event that occasionally generates a new strain with a novel combination of hemagglutinin and neuraminidase. The antiviral drugs currently available against influenza viruses are adamantane derivatives (amantadine and rimantadine) and neuraminidase (NA) inhibitors (zanamivir, oseltamivir and peramivir). Due to the increasing burden of vaccine formulations and cases of antiviral-drug-resistant influenza virus isolates turning up every year, it has become necessary to search for alternatives to the current treatment and prevention strategies. doi = 10.1007/s00705-018-3708-y id = cord-320935-3n157yl4 author = Kumar, Manish title = Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date = 2020-09-12 keywords = COVID-19; CoV-2; RNA; SARS; virus summary = This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. doi = 10.1007/s40726-020-00161-5 id = cord-278099-ypov9ha3 author = Kumar, Surender title = Molecular characterization of a novel cryptic virus infecting pigeonpea plants date = 2017-08-03 keywords = 3Dpol; Fig; RNA; motif; virus summary = The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3'' terminus contained the sequence "GCA CCCATATTC". doi = 10.1371/journal.pone.0181829 id = cord-280854-cxpgwwjd author = Kumarasamy, Dhanabal title = Synthesis and in vitro antiviral evaluation of 4-substituted 3,4-dihydropyrimidinones date = 2017-01-15 keywords = RVFV; virus summary = The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The compounds were evaluated in vitro for their antiviral activity against a broad range of DNA and RNA viruses, along with assessment for potential cytotoxicity in diverse mammalian cell lines. The present work was aimed to synthesize 4-substituted 3,4-dihydropyrimidin-2(1H)-ones using various aromatic and aliphatic aldehydes and evaluate their antiviral activity against a broad range of DNA and RNA viruses, along with their cytotoxicity assessment in diverse mammalian cell lines. The antiviral activities and cytotoxicity of the synthesized compounds (4a-m and 5) were determined in CPE reduction assays with a broad and diverse panel of DNA and RNA viruses and using relevant mammalian cell lines. Compound 4m was found to be a selective and potent inhibitor of Punta Toro virus (PTV), a member of the family Bunyaviridae and the genus Phlebovirus. doi = 10.1016/j.bmcl.2016.12.010 id = cord-018639-0g1ov96t author = Kurpiers, Laura A. title = Bushmeat and Emerging Infectious Diseases: Lessons from Africa date = 2015-09-21 keywords = Africa; Cameroon; Congo; Ebola; bushmeat; human; virus summary = Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. In this review, we explore the links between bushmeat-related activities and EIDs in sub-Saharan Africa, where the vast majority of African emerging infectious zoonotic diseases occur (Jones et al. Although research has focused largely on mammals and, to a lesser extent, birds, theoretically any wildlife species harvested for bushmeat could be a potential source of zoonotic disease that can spillover during the hunting, butchering, and preparation process (Wolfe et al. With the increasing prevalence of zoonotic disease emergence and the associated risk for public health, we have to improve our understanding of the dynamics of spillover events of pathogens from animal to human hosts (Rostal et al. doi = 10.1007/978-3-319-22246-2_24 id = cord-347465-yu6oj30v author = Kurskaya, Olga title = Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date = 2018-09-18 keywords = Russia; respiratory; virus summary = METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. doi = 10.1371/journal.pone.0200117 id = cord-345689-5ns1onkw author = Kusters, Inca C. title = Manufacturing Vaccines for an Emerging Viral Infection–Specific Issues Associated with the Development of a Prototype SARS Vaccine date = 2009-01-30 keywords = SARS; Vero; phase; vaccine; virus summary = Taking into account all the uncertainties and anticipating the worst-case scenario, many laboratories and vaccine manufacturers started working on a vaccine approach against SARS infection, largely based on what was known from animal CoVs. In this chapter, we will discuss the necessity for international cooperation and the importance of discretionary funding for rapidly developing a prototype vaccine candidate. When the laboratory work on the SARS-CoV vaccine development started, no data were available on the inactivation characteristics of the virus. The results from the experiments performed to evaluate the viral loss of the SARS-CoV due to drying on glass surface were also surprising: 35 -42 days were necessary to inactivate the virus to the detection limit of the technique. Based on our experience to date, the inactivated, adjuvanted SARS-CoV prototype vaccine seems to be a good candidate for further evaluation in Phase 1 studies. doi = 10.1016/b978-0-12-369408-9.00011-1 id = cord-353290-1wi1dhv6 author = Kustin, Talia title = Biased mutation and selection in RNA viruses date = 2020-09-28 keywords = Fig; RNA; sequence; virus summary = We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. Nevertheless, RNA viruses do share several common features that drive their evolution: (a) their ultimate dependence on the cell, (b) their high mutation rates, (c) strong purifying selection derived from constraints operating on a small and densely coding genome, and (d) sporadic but powerful positive selection driven by an evolutionary arms race with the host they infect. Two non-mutually exclusive hypotheses may be put forth to explain the consistent pattern of A-richness that we observe: there is selection for more A in viral sequences, and/or there is a mutational bias that leads to more A in genomes of viruses. doi = 10.1093/molbev/msaa247 id = cord-263764-2ewz8ok4 author = Kutter, Jasmin S title = Transmission routes of respiratory viruses among humans date = 2018-01-17 keywords = SARS; respiratory; transmission; virus summary = We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] . doi = 10.1016/j.coviro.2018.01.001 id = cord-262722-cz3ce29n author = Kuzmanovic, Deborah A. title = A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology date = 2008-03-31 keywords = IVDS; MS2; Wick; virus summary = Abstract Small-angle scattering (SAS) techniques, like small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), were used to measure and thus to validate the accuracy of a novel technology for virus sizing and concentration determination. Additionally, scattering methods such as classical light scattering, small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) have also been employed to measure the concentration of samples when the molecular weight of the virus is known (Guinier, 1939; Guinier and Fournet, 1955; Jacrot and Zaccai, 1981; Koch et al., 2003) . The primary goal of this study is to explore the utility of using small-angle scattering (SAS) techniques, such as SAXS and SANS, as a general approach to the evaluation and quality assurance testing of virus characterization technology, using the integrated virus detection system (IVDS) instrument as a test technology. Specifically, it was determined using SAXS and SANS that the virus sizing and concentration technology, IVDS, can accurately measure the size of synthetic latex microspheres. doi = 10.1016/j.radphyschem.2007.10.004 id = cord-274765-3wzht843 author = Kweon, Chang-Hee title = Derivation of attenuated porcine epidemic diarrhea virus (PEDV) as vaccine candidate date = 1999-06-04 keywords = PEDV; virus summary = The field isolate of porcine epidemic diarrhea virus (PEDV) was serially passaged in Vero cells. The cell passaged PEDV, designated KPEDV-9, was tested for its pathogenicity in the neonatal pigs, immunogenicity and safety in the pregnant sows. The results of this study supported that the attenuated virus derived from serial passage could be applied as vaccine for protecting suckling piglets against PEDV infection. In this study, we investigated the attenuation of PEDV through serial passages in Vero cell cultures and its prophylactic eect in pregnant sows. Nevertheless, when compared with the wild PEDV, the animals inoculated with the high passage level of virus did not show any severe signs of diarrhea or death in piglets, supporting attenuation. Development of an Elispot for the detection of antibody secreting cells against the porcine epidemic diarrhea virus (PEDV) in dierent tissues doi = 10.1016/s0264-410x(99)00059-6 id = cord-321756-a7eh4dkb author = Kwofie, Theophilus B title = Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date = 2012-04-10 keywords = infection; respiratory; virus summary = The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. Majority of acute lower respiratory tract infections (ALRTI) in developed countries have been reported to be often due to viral pathogens of which most common are RSV, PIV, influenza viruses, Adv, human Coronaviruses and Bocaviruses [5] [6] [7] . This study was done to determine the burden of respiratory viruses among children hospitalized at the Komfo Anokye Teaching Hospital for acute lower respiratory illness using the Real Time Polymerase Chain Reaction (RT-PCR). The overall prevalence is comparable to previous studies done in other developing countries [24] and the predominance of RSV is in accordance with the assertion that this virus is the single most frequent lower respiratory tract pathogen in infants and young children worldwide [25] [26] [27] . doi = 10.1186/1743-422x-9-78 id = cord-018364-b06084r1 author = LaBrunda, Michelle title = The Emerging Threat of Ebola date = 2019-06-07 keywords = Africa; EVD; Ebola; Saa; disease; health; outbreak; virus summary = Transmission of Ebola disease is still being studied, but it is known that person-toperson contact is the most common form of spread. One study found the risk of developing EVD for healthcare workers to be 100 times that of the general community during an outbreak of Ebola in Sierra Leone [67] . After the outbreak of SARS in 2003 many countries starting using boarder screening to try to identify possibly ill people in hopes of limiting spread of infectious disease, others jumped on board after the 2009 H1N1 influenza pandemic. An article by the CDC, published around the same time as the article recommending travel restriction for high-risk individuals, concludes that border screens are expensive and not effective in preventing the spread of disease [100] . Infection Prevention and Control Recommendations for Hospitalized Patients Under Investigation (PUIs) for Ebola Virus Disease (EVD) in U doi = 10.1007/978-3-030-23491-1_6 id = cord-013526-6fip93l2 author = Labadie, Thomas title = A non-enveloped arbovirus released in lysosome-derived extracellular vesicles induces super-infection exclusion date = 2020-10-19 keywords = BTV; Fig; PBS; cell; virus summary = Here we used Bluetongue virus (BTV) as a model of a non-enveloped arthropod-borne virus and discovered that the majority of viruses are released in EVs. Based on the cellular proteins detected in these EVs, and use of inhibitors targeting the cellular degradation process, we demonstrated that these extracellular vesicles are derived from secretory lysosomes, in which the acidic pH is neutralized upon the infection. Virus released in secretory lysosomes infectious EVs. However, inhibition of autophagosome-lysosome fusion with chloroquine (CQ), led to a significant reduction of infectious EVs released as compared to the control ( Fig 2B) , indicating that the late steps of autophagy are necessary for infectious EVs. In addition, inhibition of MVBs regulator protein HSP90 using geldanamycin in BTV-infected cells (MOI = 10) also led to a significant reduction of infectivity measured in the EVs fraction, as compared to the control, indicating a possible role for MVBs in the release of infectious EVs. In contrast, GW4869, a drug that inhibits the release of exosomes (small vesicles~200nm) derived from MVBs, did not affect the secretion levels of EVs containing BTV ( Fig 2B) . doi = 10.1371/journal.ppat.1009015 id = cord-263484-afcgqjwq author = Ladner, Jason T. title = Precision epidemiology for infectious disease control date = 2019-02-06 keywords = Ebola; genomic; pathogen; virus summary = With sufficient sampling, relevant metadata (such as location and date) and an appropriate statistical framework, pathogen genomes can reveal patterns of epidemic transmission at a fine-scale resolution, thus enabling the design of targeted interventions that are more precise than those based on traditional epidemiological data alone. Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42, 43 . This includes changes to research practice regarding the benefits for rapid and open sharing of data and results as well as a focus on building capacity for sequencing and analysis within public health agencies and the regions most severely impacted by infectious disease 57, 58 . One important approach to accelerating responses in the future is to build genome sequencing and analysis capabilities within public health agencies and hospitals as well as in developing countries disproportionately impacted by infectious disease outbreaks. doi = 10.1038/s41591-019-0345-2 id = cord-300810-a1skdp67 author = Lafay, F. title = Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation date = 1991-07-31 keywords = CVS; cell; day; virus summary = title: Spread of the CVS strain of rabies virus and of the avirulent mutant AvO1 along the olfactory pathways of the mouse after intranasal inoculation Abstract After intranasal instillation in the mouse, rabies virus (CVS strain) selectively infected olfactory receptor cells. On the other hand, other neuronal cells permissive for CVS, such as mitral cells or the anterior olfactory nucleus, are completely free of infection with the mutant, indicating that restriction is related to the ability of AvO1 to penetrate several categories of neurons. The G protein plays a pivotal role in the pathogenicity of the virus because of its interaction with the host cells '' Abbreviations used: AON, anterior olfactory nucleus; CNS, central nervous system; GABA, Gamma aminobutyric acid; HDB, horizontal limb of the diagonal band; HRP, horseradish peroxidase; HSVl, herpes simplex type 1; IPL, internal plexiform layer: LC, locus coeruleus; LD50, lethal dose 50%; LPA. doi = 10.1016/0042-6822(91)90145-2 id = cord-328753-qwdxgk4z author = Lafaye, Pierre title = Use of camel single-domain antibodies for the diagnosis and treatment of zoonotic diseases date = 2018-09-25 keywords = antibody; domain; single; vhh; virus summary = The antigen-binding region of such homodimeric heavy-chain only antibodies consists of one single domain, called VHH. VHHs provide many advantages over conventional full-sized antibodies and currently used antibody-based fragments (Fab, scFv), including high specificity, stability and solubility, and small size, allowing them to recognize unusual antigenic sites and deeply penetrate tissues. The active antigen-binding fragment of heavy chain antibodies can be cloned and expressed in the form of VHH, which consists of only one domain (Fig. 1) . Gene therapy with an adenoviral vector expressing a bispecific VHH, consisting of two linked VHHs targeting different PA-neutralizing epitopes, was tested in mice, and found to protect them from anthrax toxin challenge and anthrax spore infection [55] . [92] have been found in the sera of infected camels, whereas antibodies against rabies virus, vesicular stomatitis virus, and FMD virus have been detected in llamas [93] and could lead to the possible isolation of specific broadly neutralizing VHHs. Many neutralizing VHHs that bind to different sites on the same target, including hidden antigenic sites, can be isolated from immunized or infected camelids. doi = 10.1016/j.cimid.2018.09.009 id = cord-303665-l57e54hu author = Lahrich, S. title = Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date = 2020-09-10 keywords = PCR; SARS; virus summary = Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. doi = 10.1016/j.scitotenv.2020.142325 id = cord-001542-f089bs8r author = Lai, Kang Yiu title = Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date = 2014-11-28 keywords = EBOV; Ebola; GP1,2; IFN; RNA; cell; infection; virus summary = These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. doi = 10.1186/2049-9957-3-43 id = cord-352379-q5inrxcm author = Lai, Michael M. C. title = SARS virus: The beginning of the unraveling of a new coronavirus date = 2003-10-17 keywords = MHV; RNA; SARS; coronavirus; virus summary = Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1007/bf02256318 id = cord-003917-bswndfvk author = Lalle, Eleonora title = Pulmonary Involvement during the Ebola Virus Disease date = 2019-08-24 keywords = EBOV; EVD; Ebola; respiratory; virus summary = doi = 10.3390/v11090780 id = cord-076082-4kpkhz0o author = Lam, Tommy Tsan-Yuk title = Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia date = 2008-08-22 keywords = H5N1; Indonesia; Java; figure; virus summary = The H5N1 highly pathogenic avian influenza (HPAI) virus was originally isolated from a farmed goose in Guangdong province of China in 1996 [1] , and soon spread to live-poultry markets in Hong Kong [2] , resulting in 18 cases of human infection in 1997, 6 of which were fatal [3, 4] . We found previously unrecognized phylogenetic discordance between gene trees involving human and cat isolates (n = 25, denoted in red in Figures 1, S1-S3)-the main focus of our study-suggesting that they are reassortant viruses descending from group 2 and 3 lineages. To further investigate the putative reassortant human and cat viruses, a selected dataset (n = 24) of manually concatenated full genomes (Figure 2A ; see Methods) of Indonesian H5N1 HPAI viruses were analyzed using more sophisticated analysis methods, including similarity plots, bootscan analyses and GARD analyses (genetic algorithm for recombination detection). doi = 10.1371/journal.ppat.1000130 id = cord-016171-17ut32bu author = Lane, J. Michael title = Smallpox as a Weapon for Bioterrorism date = 2009 keywords = Centers; Control; Disease; Prevention; Smallpox; virus summary = Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a) . If this algorithm indicates that a patient is high risk to be smallpox, local and national public health authorities should be immediately notified by telephone, and laboratory specimens taken for polymerase chain reaction (PCR), electron photomicroscopy (EM), and viral culture. doi = 10.1007/978-1-4419-1266-4_5 id = cord-336045-8qcj5uiy author = Langlois, Isabelle title = Viral diseases of ferrets date = 2005-03-01 keywords = ADV; aleutian; disease; ferret; infection; virus summary = A tentative diagnosis of canine distemper is based on the presence of typical clinical signs, severe leukopenia, a history of potential exposure to the virus, and questionable vaccination. The severity of disease depends on the origin (mink or ferret) of the ADV strain that is involved as well as the immune status and genotype of the infected individual [25] . Ferrets are used extensively as an animal model for influenza virus pathogenesis and immunity studies because their biologic response to influenza infection is similar to that of humans [53, 54] . Neurologic symptoms, including ataxia, hind-limb paresis, and torticollis, were reported in ferrets that were infected experimentally with avian influenza A (H5N1) viruses that were isolated from the 1997 outbreaks of disease in domestic poultry markets in Hong Kong [50, 65] . Detection of Aleutian disease virus DNA in tissues of naturally infected mink doi = 10.1016/j.cvex.2004.09.008 id = cord-328621-3jda0k2u author = Laporte, Manon title = Airway proteases: an emerging drug target for influenza and other respiratory virus infections date = 2017-04-14 keywords = HA0; TMPRSS2; virus summary = Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenzaand coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. Since the catalytic sites of the diverse serine proteases linked to influenza, parainfluenza-and coronavirus activation are structurally similar, active site inhibitors of these airway proteases could have broad therapeutic applicability against multiple respiratory viruses. The best inhibitor (92 in Table 2 ) had a K i value of 0.9 nM and, interestingly, produced clear inhibition of HA0 cleavage and virus replication in Calu-3 cells, which endogenously express HA0-activating proteases like TMPRSS2. Trypsin-like proteases of the human airways represent unique targets to suppress infections with influenza or other respiratory viruses which rely on these enzymes for their replication. Proteolytic activation of influenza viruses by serine proteases TMPRSS2 and HAT from human airway epithelium doi = 10.1016/j.coviro.2017.03.018 id = cord-260708-l9w5jhsw author = Lasecka, Lidia title = The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date = 2013-12-11 keywords = CCHFV; Congo; Crimean; RNA; protein; virus summary = The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. As several potential cysteine-protease-like cleavage sites have been identified in the L protein sequence of nairoviruses [94] and some viral proteins containing an OTU-like protease domain have also been shown to undergo autoproteolytic cleavage to generate multiple mature proteins, e.g., the replicase of BlScV [98] , it has been suggested that the L proteins of nairoviruses may also be autoproteolytically cleaved into an active RNA polymerase and protein(s) with additional function [85] . Role of actin filaments in targeting of Crimean Congo hemorrhagic fever virus nucleocapsid protein to perinuclear regions of mammalian cells Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection doi = 10.1007/s00705-013-1940-z id = cord-275570-i9fw0afj author = Lau, Susanna K. P. title = Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics date = 2018-01-30 keywords = PRRSV; virus summary = The recent epidemics caused by Zika virus and Middle East respiratory syndrome coronavirus (MERS-CoV) clearly illustrate the ability of emerging viruses to pose huge public health problems within a short time. In this special issue, "Molecular Research on Emerging Viruses: Evolution, Diagnostics, Pathogenesis, and Therapeutics", insights into advances and discoveries in understanding the different aspects of various emerging viruses are given by eight original studies and four review articles. Three articles focus on arthropod-borne viruses (arboviruses) which are important emerging pathogens having caused various epidemics in recent years. In the systematic review and meta-analysis study by Coelho et al., the prevalence of microcephaly in infants born to Zika virus-infected women among all pregnancies was estimated [6] , which may contribute to the understanding of the public health impact of this emerging arbovirus. Two articles report on the virus-host interaction during porcine reproductive and respiratory syndrome virus (PRRSV) infection which causes severe losses in the swine industry worldwide. doi = 10.3390/ijms19020398 id = cord-297339-et2305rz author = Lauber, Chris title = Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences date = 2012-08-31 keywords = figure; ped; virus summary = In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. The DEmARC specifics include (i) the use of pairwise evolutionary distances (PEDs) instead of uncorrected p-distances, and (ii) a quantitative method to devise taxon levels and associated PED thresholds for virus clustering in a systematic and family-wide manner. The first selected threshold (PED of 0.120) results in seven clusters ( Figure 1B ) that match the official or tentative ICTV species of the family Filoviridae. In the high-sampling case of picornaviruses, no PED values with zero frequency are observed which suggests that the current sampling of filovirus genome sequences may strongly underestimate the natural genetic diversity in the family. doi = 10.3390/v4091425 id = cord-000937-8vk89i4h author = Law, John title = Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date = 2013-04-17 keywords = RNA; dna; figure; virus summary = RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix ''D'' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown). doi = 10.1371/journal.pone.0060595 id = cord-023488-jf2xl3vl author = Le Duc, James W. title = Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes date = 2016-02-12 keywords = Africa; Ebola; SARS; disease; human; virus summary = On occasion, a virus that is already widespread in a population can emerge as a cause of epidemic or endemic disease, due to an increase in the ratio of cases to infections. Although many zoonotic viruses can be transmitted to humans on occasion, their relative ability to spread from human to human determines whether or not they emerge as significant new virus diseases of mankind (Table 2 ). In the history of modern virology (the last 50 years) there are very few documented instances where zoonotic viruses have established themselves in the human population and emerged as new viral diseases of mankind (Table 2 ). Rarely, as in the case of HIV, SARS coronavirus, and Ebola filovirus, a zoonotic virus becomes established in humans, causing a disease that is truly new to the human species. doi = 10.1016/b978-0-12-800964-2.00016-1 id = cord-290034-4b0mshqa author = Le, Yen H. title = Virus detections among patients with severe acute respiratory illness, Northern Vietnam date = 2020-05-12 keywords = SARI; Vietnam; virus summary = To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. There was one case of co-infection with enterovirus and coronavirus 229E including a female military hospital patient 28 years of age. Additionally, our results display enterovirus, adenovirus and coronavirus infections among the SARI cases, suggesting that cities in northern Vietnam could benefit also from local surveillance of non-influenza respiratory viruses. doi = 10.1371/journal.pone.0233117 id = cord-013412-gj443yei author = Lebedeva, Natalya Sh. title = The Application of Porphyrins and Their Analogues for Inactivation of Viruses date = 2020-09-23 keywords = P&A; RNA; dna; figure; porphyrin; virus summary = The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. doi = 10.3390/molecules25194368 id = cord-350948-oog6m4h3 author = Leclercq, Loïc title = How to improve the chemical disinfection of contaminated surfaces by viruses, bacteria and fungus? date = 2020-09-17 keywords = RSV; virus summary = The disinfectants, based on equimolar mixtures of didecyldimethylammonium chloride ([DiC(10)][Cl]), dodecyloctaglycol (C(12)E(8)), and cyclodextrin (CD), show synergistic effects against enveloped viruses (RSV, HSV-1, VACV) and fungi (C. In this context, the didecyldimethylammonium chloride ([DiC 10 ] [Cl] ), one of the most widely used quaternary ammonium compounds in healthcare systems to prevent and control viral infections due to its ability to disorganize and to disrupt the envelopes of viruses (Leclercq et al., 2010) , is associated with detergents, such as dodecyloctaglycol (C 12 E 8 ), making the detergent-disinfectant combination ideal for general sanitation purposes (Rauwel et al., 2012) . As, some ethoxylated surfactants (e.g. Triton X-100, Nonoxynol-9 or Brij-97) have been shown to exhibit a virucidal activity due to their ability to solubilize the viral envelope of Epstein-Barr or herpes simplex viruses (Qualtiere and Pearson, 1979; Asculai et al., 1978) , and, as, CDs "are able to participate in the attack of viruses, and specifically SARS-CoV-2, in a large range of different ways" (Garrido et al., 2020) , we have investigated [DiC 10 ][Cl]/C 12 E 8 /CD ternary systems to obtain synergistic effects against enveloped viruses such as RSV instead of hazardous SARS-CoV-2. doi = 10.1016/j.ejps.2020.105559 id = cord-347039-eap592i7 author = Lee, Seung-Hwan title = Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date = 2003-08-31 keywords = MHC; cell; infection; mouse; virus summary = Receptors are recognized as important determinants of virus host range and tissue tropism; and some host resistance/susceptibility loci encode molecules that are expressed on the cell surface. Another example of natural host resistance is the restriction of ecotropic Murine LEUKEMIA VIRUS (MuLV) infection by the mouse Fv4 gene. The effort to understand the genetic basis of susceptibility to viral disease is driven by three considerations: (1) the increased public awareness of the toll imposed by viruses on the host; (2) the increase in susceptible human populations because of longer life expectancy, frequently accompanied by chronic illness, and the consequences of advances in medical technology, including immunosuppressive therapies for organ transplantation or treatment of malignancy; and (3) the need to develop new therapies for infections caused by multidrug-resistant Human killer-cell immunoglobulin-type receptor (KIR) is considered to be a functional homolog of mouse Ly49. Mouse genetics has also demonstrated that recognition and destruction of virus-infected cells by NK cells is mediated by specific interactions between activating NKcell receptors and viral target molecules. doi = 10.1016/s0168-9525(03)00172-0 id = cord-102905-rlee32x7 author = Leis, Jonathan title = Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date = 2020-05-04 keywords = ESCRT; HIV-1; tsg101; virus summary = In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Tenatoprazole and esomeprazole were shown to quantitatively inhibit the release of infectious HIV-1 from 293T cells in culture, and it was suggested that these effects may be mediated via changes in viral interaction with Tsg101, a key component of the cellular ESCRT complex (5, 33) . Given multiple reports suggesting that herpes viruses also use cellular ESCRT proteins in their replication process (20) (21) (22) (23) we tested if the Tsg101-binding prazole drugs, which blocked budding of HIV-1, would also block the release of herpes viruses from cells. doi = 10.1101/2020.05.04.075036 id = cord-333810-57d4oopv author = Leroy, Éric Maurice title = L’Émergence du virus EBOLA chez l’homme: un long processus pas totalement élucidé date = 2015-05-31 keywords = Ebola; des; les; virus summary = Plusieurs études ont montré que la contamination de l''homme s''est parfois produite lors de la manipulation de carcasses infectées de gorilles, chimpanzés et de céphalophes [21, 41] Les grands singes se contamineraient eux-mêmes probablement directement auprès des chauves-souris, en particulier lorsque les animaux de ces espèces animales consomment en même temps les fruits d''un même arbre. Cette diversité génétique des souches virales observées chez les carcasses d''animaux morts exclut par conséquent une transmission du virus d''un individu à l''autre et suggère au contraire que l''infection des grands singes résulterait de contaminations simultanées mais indépendantes à partir de sources animales distinctes, probablement le réservoir naturel du virus Ébola [21, 45] . Je pense que cette impression est purement factuelle, et est amplifiée par la couverture médiatique des maladies dues à certains virus dont les chauves-souris sont réservoirs (SARS, Ébola, Marburg ...). doi = 10.1016/s0001-4079(19)30940-9 id = cord-346906-1wmp43ti author = Lewandowski, Kuiama title = Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date = 2019-12-23 keywords = Nanopore; influenza; sample; virus summary = We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events. doi = 10.1128/jcm.00963-19 id = cord-022830-tvt58gtn author = Li, Dan title = Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce date = 2015-10-08 keywords = HAV; MNV-1; food; fresh; produce; virus summary = In order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In order to determine a basis to identify possible prevention and control efforts, this article reviewed the transmission routes and viral persistence of foodborne viruses (mainly NoVs and HAV) during the farm-to-fork chain of fresh produce, as well as the effect of treatments used in food processing of fresh produce on viruses. In this section the effect of radiation, both nonionizing and ionizing radiation, and high-pressure processing (HPP) will be discussed as nonthermal inactivation treatment options for enteric viruses in fresh produce. doi = 10.1111/1541-4337.12163 id = cord-329902-db7hl770 author = Li, Desheng title = Influenza A(H1N1)pdm09 Virus Infection in Giant Pandas, China date = 2014-03-17 keywords = China; virus summary = We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. We confirmed infection with influenza A(H1N1)pdm09 in giant pandas in China during 2009 by using virus isolation and serologic analysis methods. Analyses showed that each of the 8 gene segments of the virus we isolated were closely related to pH1N1 viruses circulating among humans, including a human representative strain (A/California/04/2009) and a contemporary strain (A/Sichuan/1/2009); these viruses showed 98.6%-100% nt identity to the panda strain (online Technical Appendix Table 1 , wwwnc.cdc.gov/EID/ article/20/3/13-1531-Techapp1.pdf). One panda (Zhangka) had detectable pH1N1 and H3 subtype HI antibodies before infection; this serum sample was collected before the display of overt clinical signs in the animal but after the onset of the human pH1N1 outbreak in China. doi = 10.3201/eid2003.131531 id = cord-278250-dwok857k author = Li, Heng title = The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date = 2019-08-19 keywords = RNA; additional; bacterial; dna; figure; virus summary = We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail. doi = 10.1186/s12985-019-1211-z id = cord-305336-wxiazglk author = Li, Ji Lian title = Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date = 2014-01-21 keywords = PCR; RNA; TRSV; Varroa; bee; virus summary = In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. doi = 10.1128/mbio.00898-13 id = cord-262752-bwofzbwa author = Li, Qianqian title = Current status on the development of pseudoviruses for enveloped viruses date = 2017-12-07 keywords = HIV; VSV; virus summary = Early work by Witte and colleagues showed that when they used VSV to infect the cells in which MLV is packaged, they were able to harvest pseudovirus for use in neutralization antibody assays. Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system Development of a pseudotyped-lentiviral-vector-based neutralization assay for chikungunya virus infection Second generation of pseudotype-based serum neutralization assay for Nipah virus antibodies: sensitive and high-throughput analysis utilizing secreted alkaline phosphatase Use of vesicular stomatitis virus pseudotypes bearing Hantaan or Seoul virus envelope proteins in a rapid and safe neutralization test A neutralization test for specific detection of Nipah virus antibodies using pseudotyped vesicular stomatitis virus expressing green fluorescent protein Truncation of the human immunodeficiency virus-type-2 envelope glycoprotein allows efficient pseudotyping of murine leukemia virus retroviral vector particles Cholesterol supplementation during production increases the infectivity of retroviral and Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) doi = 10.1002/rmv.1963 id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 keywords = IFN; PEDV; RNA; SARS; protein; rig; virus summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. doi = 10.3390/pathogens9050367 id = cord-332046-ihc031ly author = Li, Yan‐Chao title = Neurotropic virus tracing suggests a membranous‐coating‐mediated mechanism for transsynaptic communication date = 2013-01-01 keywords = Fig; HEV; cell; virus summary = This study has systematically examined the assembly and dissemination of HEV 67N in the primary motor cortex of infected rats and provides additional evidence indicating that mem-branous-coating-mediated endo-/exocytosis can be used by HEV for its transsynaptic transfer. Consistent with the results in the previous experiments, the present study showed that at day 4 p.i. HEV-positive cells were observed in only a certain population of neurons with different sizes in layer V of the primary motor cortex (Fig. 1A,B) . Extracellular virions were not enclosed by any vesicular structures, whereas vesicle-enclosed virus particles were otherwise observed in the axonal terminals touching on the infected neurons, so it seemed that the virions within the synapses had acquired new vesicular membrane after entry. D shows a virion within a coated vesicle (arrow; see also the inset for details) in the axon terminal adjacent to an infected pyramidal cell. doi = 10.1002/cne.23171 id = cord-002076-7t4d4vvo author = Li, Yongfeng title = Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology date = 2016-05-06 keywords = EGFP; GFP; reporter; virus summary = Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. Replicating-competent reporter-expressing viruses (RCREVs) are one type of artificially modified viruses that not only retain the viral genetic characteristics but also possess the new properties of the reporter genes, which represent a useful tool for quantitative analysis of viral replication and tracking viral protein transport in both living cells and animals. doi = 10.3390/v8050127 id = cord-278973-82n0d1dh author = Li, Zhijie title = Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date = 2016-05-31 keywords = B/03; MRV; pfu; virus summary = This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. MRV isolates were obtained from hosts with or without clinical signs of disease, and the virus can infect a broad range of mammals (Dermody et al., 2013) . In this study, we report the characterization of a novel MRV strain (called "B/03") isolated from healthy, wild shortnosed fruit bats in Guangdong province, China. In this study, one strain of MRV, B/03, was isolated by in vitro cell culture from thirty wild short-nosed fruit bat samples from Shaoguan city of China''s Guangdong province. Based on sequence comparison and phylogenetic analysis, we conclude that the B/03 isolate is a novel type 1 bat orthoreovirus, and it might have originated from gene segment mixing during infection with more than one MRV strain in nature. doi = 10.1016/j.meegid.2016.05.039 id = cord-342906-51296y8d author = Li, Zhiping title = Aerosolized avian influenza virus by laboratory manipulations date = 2012-08-06 keywords = H5N1; laboratory; virus summary = Many of the routine procedures used to process influenza virus for laboratory research, such as centrifugation or mixing, have a high potential of producing aerosols [21] , and the particle load of each has been estimated to be up to 1-5 μm. To this end, this study was designed to monitor the presence of aerosolized H5N1 virus produced by normal procedures used to process the virus for experimental research and by the most frequently associated "accidents" for each, such as container breakage and accidental subcutaneous injection. None of the aerosol samples collected from any group at the time directly prior to processing of the experiment had detectable levels of H5N1, as evidenced by negative reverse transcription (Rt)-PCR and HA text results. Our results provide evidence that many of the laboratory techniques used to process influenza virus for experimental analysis produce aerosols and, thereby, represent significant risks of infection to laboratory personnel and potential spread beyond the laboratory. doi = 10.1186/1743-422x-9-146 id = cord-336157-aqc9zrrm author = Liang, Guodong title = Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control date = 2015-03-25 keywords = arbovirus; human; mosquito; virus summary = Slave trading of Africans to the Americas, during the 16th to the 19th century was responsible for the first recorded emergence in the New World of two arthropod-borne viruses (arboviruses), yellow fever virus and dengue virus. [2] [3] Chikungunya virus (CHIKV), West Nile virus (WNV) and dengue virus (DENV) are three of a large number of neglected human pathogenic arthropod-borne viruses (arboviruses) whose combined figures for morbidity and mortality far exceed those for Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome viruses. However, many other arthropod species, in which viruses have been identified, may be involved in perpetuating the virus life cycle without having been associated with overt disease in humans or animals. 55 However, implementation of temporary localized arthropod control measures during epidemics, for example in high density urbanized areas, can still play an important but transient role in reducing the impact on humans and animals of emerging arboviruses. doi = 10.1038/emi.2015.18 id = cord-258489-pyfc7jde author = Lico, Chiara title = Viral vectors for production of recombinant proteins in plants date = 2008-03-10 keywords = TMV; expression; plant; protein; virus summary = In this review, we will focus on transient production strategies using plant viral expression systems, with a particular focus on the variety of proteins produced, and their applications. The unique properties of viruses such as ease of manipulation, high level amplification, site specific recombination, strong infectivity, enhanced translation and compact and repetitive morphological structure have enabled their broad application, from basic research to product development, including the generation of robust expression systems. From the discovery of viruses in 1898 (tobacco mosaic virus, TMV) (Bos, 1999) , to the first demonstration of RNAs role in virus replication by turnip yellow mosaic virus (TYMV) (Matthews, 1989) , to the very recent discovery of gene silencing and its implication in host response to infection, gene regulation and transgene expression (Baulcombe, 1999; Lu et al., 2003; Waterhouse and Helliwell, 2003) , plant virology has played a crucial role in the understanding of the most fundamental concepts of modern biology. Thanks to the recent improvements of viral-based vectors, mAbs have been produced with transient expression systems to quickly achieve much higher production levels along with other complex proteins. doi = 10.1002/jcp.21423 id = cord-288930-h13cxuh3 author = Lim, Faye J title = Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date = 2016-07-20 keywords = child; infection; virus summary = METHODS: Children aged 6 to 59 months who presented to a tertiary pediatric hospital between influenza seasons 2008 and 2012 with fever and acute respiratory symptoms were enrolled, and nasal samples were collected. We compared demographics, presenting symptoms, and clinical outcomes of children with a single-virus infection and those in whom 2 or more viruses were detected (virus-virus codetection). With this study, we describe the virology of ARTI in children aged 6 months to 4 years who presented to a tertiary pediatric hospital in Australia with influenza-like illness during influenza season. We conclude that the impact of virus-virus codetection on disease severity in children who present with influenza-like illness is likely to be limited to those infected with specific pathogen pairs. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children doi = 10.1093/jpids/piw042 id = cord-315037-lmur80te author = Lin, Chien-Yu title = Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date = 2020-01-15 keywords = PCR; respiratory; virus summary = We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. This study aims to detect respiratory viruses in children using PCR and to compare the detection power of this technique against that when using traditional antigen tests and virus cultures. For children with respiratory symptoms and with a clinical suspicion of virus infection, a test for RSV antigen test, human parainfluenza virus (PIV) type 3 antigen test, viral PCR for enterovirus, or viral cultures was prescribed by the judgment of pediatricians. The following multiplex PCR assays were performed for each sample to detect RNA/DNA of 15 respiratory viruses, including RSV A or B, FluA, FluB, human enterovirus (EV), MPV, human parainfluenza virus types 1-4, human rhinovirus (RV), coronavirus OC43/NL63/229E, human adenovirus (ADV), and human bocavirus (Boca). The present study demonstrates that PCR has higher detectability for respiratory viruses compared to traditional antigen tests and viral cultures. doi = 10.3390/ijerph17020564 id = cord-269193-a647hwu9 author = Lin, Debby A. title = Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date = 1991-05-31 keywords = Dhori; RNA; virus summary = Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . doi = 10.1016/0042-6822(91)90641-n id = cord-339423-5qym9dsf author = Lina, B. title = Virus émergents ou menaces à répétition date = 2005-05-31 keywords = virus summary = L''analyse des mécanismes ayant permis l''apparition de ces virus montre que pour chaque virus émergent décrit, il ne s''agit en aucun cas de phénomènes purement aléatoires, mais bien de l''accumulation de facteurs qui permettent à ces agents infectieux de diffuser de l''animal vers l''homme. À chaque fois, cette émergence est considérée par le grand public comme un nouveau fléau pouvant potentiellement être responsable d''une mortalité très élevée, ce qui entraîne souvent des comportements irrationnels, ceci d''autant plus que l''importante mortalité autrefois liée aux infections virales et bactériennes a été oubliée (vaccinations et antibiotiques obligent) [2, 3] . Les années 2003 et 2004 ont été particulièrement instructives, permettant d''observer l''épidémie du Syndrome Respiratoire Aigu Sévère ou SRAS [4] , l''émergence de deux épidémies de grippe aviaire transmise à l''homme (influenza A H7N7 en Europe et A H5N1 en Asie) [5, 6] , l''apparition de cas de monkey pox [7] , et la diffusion du virus West Nile sur la quasi totalité du continent Nord Américain [8] . doi = 10.1016/s1294-5501(05)80175-x id = cord-007796-zggk0x2q author = Lindemans, Caroline A. title = The Immune Response to Viral Lower Respiratory Tract Infection date = 2005 keywords = IFN-; RSV; infection; respiratory; virus summary = In respect to the role of viruses in the pathogenesis of acute and chronic airway disease in children, it is of utmost importance that we gain a proper understanding of the underlying mechanisms involved in order to design effective therapeutic and preventive strategies. Epithelial cells are key regulators of the innate immune response against viral infections (Garofalo and Haeberle, 2000) , producing a number of inflammatory mediators in response to RSV infection. In summary, in RSV lower respiratory tract infections, cytotoxic CD8ϩ T-cells are involved in viral clearance while the humoral response is required for the protection against reinfection. The innate immune defense to viral respiratory tract infections consists of the mucosal layer, type 1 interferons, activated phagocytes, and NK-cells. A key question is whether the association with the development of asthma is merely an expression of increased susceptibility to both asthma and RSV-induced lower respiratory tract infections or whether true causality is involved. doi = 10.1007/0-387-25342-4_4 id = cord-003130-p2h8p5bm author = Lindqvist, Richard title = Tick-Borne Flaviviruses and the Type I Interferon Response date = 2018-06-21 keywords = IFN; LGTV; RNA; TBEV; tick; virus summary = There are more than 70 viruses in the genus flavivirus, and they are transmitted by arthropods such as mosquitoes (dengue virus (DENV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV) and ticks (tick-borne encephalitis virus (TBEV), Langat virus (LGTV), Kyasanur forest disease virus (KFDV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), and Louping-ill virus (LIV)) [1] [2] [3] [4] [5] . Two other ISGs which have been shown to be antivirally active against TBEV are virus inhibitory protein endoplasmic reticulum associated interferon inducible (viperin) and tripartite motif-79α (TRIM79α). The role of interferon in tick-borne encephalitis virus-infected l cells. A functional toll-like receptor 3 gene (tlr3) may be a risk factor for tick-borne encephalitis virus (tbev) infection Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection doi = 10.3390/v10070340 id = cord-003004-iif2lnez author = Linster, Martin title = Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1–4 in Children from Viet Nam date = 2018-05-01 keywords = HPIV; Nam; Viet; virus summary = The present study describes species-specific clinical presentation, the genetic variability and HPIV circulation in Viet Nam. The outcome of RSV infection in hospitalized children under 2 years of age presenting with acute lower respiratory infection (ALRI) in Ho Chi Minh City was described previously 17 . Samples were sourced from two previous acute respiratory infection (ARI) cohorts among in-and outpatients, that were conducted at Children''s Hospital 1 and 2 in Ho Chi Minh City, Viet Nam during years 2009 and 2010. For sequencing, HPIV-positive samples were further amplified in a hemi-nested PCR approach with newly designed species-specific primers targeting overlapping regions of the viral genome (Table S2) . In this study, the median age and gender distribution of infected children and frequency of clinical presentation (fever, cough, sore throat, runny nose and nasal congestion) as well as vital signs (pulse and respiratory rate) and duration of illness at presentation were similar between HPIV species (p > 0.05). doi = 10.1038/s41598-018-24767-4 id = cord-017959-g0nf1iwm author = Lipkin, W. Ian title = Diagnosis, Discovery and Dissection of Viral Diseases date = 2014-02-27 keywords = PCR; assay; detection; infection; virus summary = Nested PCR tests that can employ consensus or specifi c primers in two sequential amplifi cation reactions with either one (hemi-nested) or two (fully nested) primers located 3′ with respect to the fi rst primer set may both accommodate sequence variation and be more sensitive than fl uorescent or beacon-based singleplex assays. Whereas multiplex PCR systems support rapid highthroughput diagnosis with highest sensitivity for a limited number of agents, microarray-based systems provide detection of all known pathogens for which sequence information is available, but at the expense of some degree of sensitivity. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fl uid microbead-based assay MassTag polymerasechain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused infl uenza-like illness in New York State during doi = 10.1007/978-1-4899-7448-8_2 id = cord-021116-rh0e4n2w author = Lippens, Ronnie title = Viral Contagion and Anti-Terrorism: Notes on Medical Emergency, Legality and Diplomacy date = 2004 keywords = Empire; September; imaginary; virus summary = This paper traces the main outlines of this emerging imaginary that has left notions of Empire as spheres of integrative production firmly behind, and is now geared towards imagining Empire as a complete, organic body of free-but-organic-and-therefore-orderly flows that however needs to be kept intact by means of epidemiological interventions aimed at excluding or neutralizing viral entities. Law and diplomacy were important technologies (however repressive at times) by which nation-states as well as Empires were held together, or indeed, by which they were produced or maintained, and by which they were made to be productive. There is no need for the productive negotiations of a ''cosmopolitan globalism'' either (to use Mikkel Rasmussen''s words 30 ), nor for reconciliatory efforts (one does not reconcile with viruses): the sanitary exclusion of viral contagion will suffice to keep the body of today''s imperial new world order healthy. doi = 10.1023/b:sela.0000033617.97749.13 id = cord-000708-iuo2cw23 author = Lippé, Roger title = Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date = 2012-05-28 keywords = cell; protein; virus summary = These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection doi = 10.3389/fmicb.2012.00181 id = cord-002337-8v907g24 author = Lipsitch, Marc title = Viral factors in influenza pandemic risk assessment date = 2016-11-11 keywords = H5N1; avian; human; influenza; receptor; virus summary = Preference for a2,6-linked mammalian sialic acid receptors over a2,3-linked avian ones HA pH of activation HA avoids extracellular inactivation and undergoes conformational changes leading to membrane fusion at appropriate pH for human cells (5.0-5.4 or perhaps 5.5) (Russell, 2014) Polymerase complex efficiency Efficient replication in human cells (Cauldwell et al., 2014; Naffakh et al., 2008) Virus morphology Filamentous morphology associated with several adaptations to mammals (Seladi-Schulman et al., 2014; Seladi-Schulman et al., 2013; Campbell et al., 2014; Beale et al., 2014) Length of NA stalk Longer stalk of NA required to penetrate human mucus and deaggregate virions (Blumenkrantz et al., 2013) Antagonism of interferon production Species-specific binding of the NS1 protein to host factors (Rajsbaum et al., 2012) HA-NA "balance" Substrate selectivity and catalytic rate of NA are calibrated to "balance" avidity of HA for the cell-surface glycan receptor (Zanin et al., 2015; Baum and Paulson, 1991; Yen et al., 2011; Handel et al., 2014) DOI: 10.7554/eLife.18491.006 Glaser et al., 2005) ; most human H2 and H3 seasonal isolates (Connor et al., 1994; Matrosovich et al., 2000) *These anomalous results are speculated by the authors to be possibly, or even probably the result of laboratory adaptation to egg passage and may not reflect the properties of the primary isolate. doi = 10.7554/elife.18491 id = cord-273372-69rlh9or author = Litterman, Nadia title = Small molecules with antiviral activity against the Ebola virus date = 2015-02-09 keywords = Ebola; compound; virus summary = In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. We have found that indeed there is much prior knowledge regarding small molecules that have been shown to be active against the Ebola virus in vitro or in animal models 10-13 , including a number of FDA-approved drugs 14-16 . Medicinal chemistry analysis of small molecules active against the Ebola virus We have recently described an expert''s medicinal chemistry 26 analysis of the over 320 NIH probe compounds using public and commercial sources of chemical structures and the issues related to doing this type of analysis 27 . By organizing the data on small molecules tested against the Ebola virus similarly in a central database and using machine learning models based on public data may help identify additional compounds for testing. doi = 10.12688/f1000research.6120.1 id = cord-343350-04e6wvov author = Liu, Haipeng title = Antiviral immunity in crustaceans date = 2009-02-15 keywords = Penaeus; RNA; WSSV; YHV; shrimp; virus summary = White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Preliminary study on haemocyte response to white spot syndrome virus infection in black tiger shrimp Penaeus monodon Time-course and levels of apoptosis in various tissues of black tiger shrimp Penaeus monodon infected with white-spot syndrome virus Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV) Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV) Multiple envelope proteins are involved in white spot syndrome virus (WSSV) infection in crayfish Identification of white spot syndrome virus (WSSV) envelope proteins involved in shrimp infection DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV) doi = 10.1016/j.fsi.2009.02.009 id = cord-264308-y6xuxj16 author = Liu, Rui title = Mouse lung slices: An ex vivo model for the evaluation of antiviral and anti-inflammatory agents against influenza viruses date = 2015-05-26 keywords = Fig; IP-10; lung; slice; virus summary = In this study, we established an ex vivo model using mouse lung slices to evaluate both antiviral and anti-inflammatory agents against influenza virus infection. Our results suggested that mouse lung slices provide a robust, convenient and cost-efficient model for the assessment of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. Our results showed that the lung slice model provides a robust, convenient and cost-economical method for the screening and evaluation of both antiviral and anti-inflammatory agents against influenza virus infection in one assay. To meet the goal of this study in the establishment of an ex vivo mouse slice model for the screening and evaluation of both antiviral and anti-inflammatory drugs against influenza infection in one assay, ensuring that the ex vivo model has similar patterns in influenza-induced cytokine and chemokine responses is critical. doi = 10.1016/j.antiviral.2015.05.008 id = cord-257665-12gyrmh2 author = Liu, Shan-Lu title = Emerging Viruses without Borders: The Wuhan Coronavirus date = 2020-01-22 keywords = virus summary = We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists [3] , as this represents an important first step in curbing the spread of the new virus to other parts of the world. doi = 10.3390/v12020130 id = cord-005258-gps8rzb5 author = Liu, William J. title = The triphibious warfare against viruses date = 2017-12-01 keywords = China; virus summary = Different elements may drive the current trends in emerging and re-emerging infectious diseases, which are as follows: (i) the contact patterns between human beings, their commensal organisms, and wildlife reservoirs are changing due to human behaviors, (ii) the interaction between viruses and their potential hosts and vectors, such as bats and mosquitoes, may cause changes in *Corresponding author (William J. The Chinese Academy of Sciences (CAS) has been one of the backbone forces during this process and has been playing essential roles in the fight against infectious diseases since 2005, when the H5N1 sub-type, a highly pathogenic avian influenza virus (HPAI), was identified among wild birds in Qinghai Lake (Liu et al., 2005) . The majority of emerging infectious diseases in human beings are zoonotic, which indicates the fundamental role of wildlife, especially rodents and bats, as the reservoirs of emerging viruses (Olival et The surveillance of viruses among natural vectors is also an important work, considering the recent global spread of arthropod-borne viruses such as Zika virus and dengue virus. doi = 10.1007/s11427-017-9252-y id = cord-321562-hk4hzl13 author = Liu, Xuan title = Cell membrane-derived biomimetic nanodecoys for viruses date = 2020-05-12 keywords = virus summary = Such pathogenic binding and entry mechanisms offer opportunities for developing broadly applicable anti-viral strategy, which subvert the interaction of specific membrane proteins and viruses. For viral infection inhibition, MVs mimicking cell-surface receptors could compete with native cellular receptors to bind to the specific ligands. To divert Zika virus (ZIKV) away from its intended targets, an anti-ZIKV host-mimicking nanodecoy (ND) constructed by wrapping a polymeric core with mosquito medium host cell membranes was developed (Rao et al., 2019) . What is perhaps most convenient about these cell membrane-based viral decoys is the natural binding ability of host cells that makes the exogenous engineering of receptor moieties unnecessary. Membrane vesicles derived from the modified cells, named hNTCP-MVs, were conferred important surface properties to play a specific biological function. doi = 10.1007/s11427-020-1669-x id = cord-284156-btb4oodz author = Liu, Yiliu title = Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date = 2017-01-03 keywords = MAVS; RNA; TRIM25; rig; virus summary = Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. They function as cytoplasmic sensors for the recognition of a variety of RNA viruses and subsequent activation of downstream signaling to drive type I IFN production and antiviral gene expressions. (c) Interactions between RIG-I-TRIM25 complex and 14-3-3ϵ promote RIG-I translocation to mitochondrial mitochondrial antiviral signaling protein (MAVS) for downstream signaling, leading to interferon production. Protein purification and mass spectrometry analysis identified that phosphorylation of Thr170 in the CARDs antagonizes RIG-I signaling by inhibiting TRIM25-mediated Lys172 ubiquitination and MAVS binding (68) . Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Inhibition of dengue and chikungunya virus infections by RIG-I-mediated type I interferon-independent stimulation of the innate antiviral response doi = 10.3389/fimmu.2016.00662 id = cord-281593-bq12grqo author = Liu, Zheng title = Transmission Electron Microscopy Studies of Cellular Responses to Entry of Virions: One Kind of Natural Nanobiomaterial date = 2012-04-11 keywords = cell; virus summary = For this paper, we chose Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells, as examples to demonstrate the response of eukaryotic cells to two different types of virus from our previous studies. In this paper, we discuss our previous studies on Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells as examples to demonstrate the response of eukaryotic cells to two different types of viruses [11, 12] . It could be seen with ultrathin sectioning and electron microscopy that the virions first attached themselves to the surface of host cell, then their envelopes fused with the cell membrane, and the whole nucleocapsids entered the cell. doi = 10.1155/2012/596589 id = cord-161674-nk0wie0w author = Liu, Zhi title = Implications of the virus-encoded miRNA and host miRNA in the pathogenicity of SARS-CoV-2 date = 2020-04-10 keywords = SARS; figure; miRNA; virus summary = Our results implicated that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Impressively, we found hsa-miR-4661-3p was predicted to target the S gene of SARS-CoV-2, and a virus-encoded miRNA MR147-3p could enhance the expression of TMPRSS2 with the function of strengthening SARS-CoV-2 infection in the gut. In the gut, 54 genes were predicted to be enhanced by 34 miRNAs. The most notable target of the virus miRNA is TMPRSS2, which is reported to enhance SARS-CoV-2 infection together with ACE2 48 In the liver, the virus miRNA mainly regulates genes involved in the function of actin filament severing and regulation of cellular protein metabolic process ( Figure 3E ). There were more than human 800 genes were predicted to be regulated by these miRNA (Figure 4A) , and a notable enrichment at the immune system process was observed There were 27 SARS-CoV-2 encoded miRNA that can target the virus genome ( Figure 5A ). doi = nan id = cord-309048-emmtplv3 author = Lomonossoff, George P. title = TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date = 2018-07-26 keywords = RNA; TMV; mosaic; virus summary = (1999) displayed peptides of either 10 or 15 amino acids from the spike protein of the coronavirus murine hepatitis virus on the surface of assembled particles. coli-produced protein with a minimum of 20% of plant-made TMV CP, an approach that enabled efficient RNA-guided assembly of TMV-CP His6 into particles of the expected length (Eiben et al., 2014) . Assembly of the particle of tobacco mosaic virus from RNA and disks of protein β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli In vitro assembly of tobacco mosaic virus coat protein variants derived from fission yeast expression clones or plants Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications Display of peptides on the surface of tobacco mosaic virus particles Assembly of hybrid RNAs with tobacco mosaic virus coat protein. doi = 10.1016/bs.aivir.2018.06.003 id = cord-322234-1zyy536y author = Lorusso, Alessio title = One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date = 2009-12-17 keywords = H1N1; PCR; RNA; virus summary = To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. doi = 10.1016/j.jviromet.2009.12.002 id = cord-307817-2vy28i4m author = Lou, Zhiyong title = Current progress in antiviral strategies date = 2014-01-14 keywords = HCV; HIV-1; RNA; antiviral; viral; virus summary = The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. doi = 10.1016/j.tips.2013.11.006 id = cord-298051-ej8qxkce author = Louten, Jennifer title = Detection and Diagnosis of Viral Infections date = 2016-05-06 keywords = Fig; PCR; cell; dna; virus summary = Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells. doi = 10.1016/b978-0-12-800947-5.00007-7 id = cord-255181-du6rqc6i author = Louz, Derrick title = Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines date = 2005-06-29 keywords = cell; host; human; influenza; virus summary = This review addresses a number of potential risk factors and their implications for activities with viral vectors from the perspective of cross‐species transfer of viruses in nature, with emphasis on the occurrence of host‐range mutants resulting from either cell culture or tropism engineering. The HIV virus and contemporary human influenza viruses are prominent examples of viruses that have crossed the species barrier and established themselves permanently in the human population without further dependence on the presence of the original animal host reservoir. The emergence of HIV exemplifies how multiple independent cross-species transmissions of simian viruses that are not associated with disease in their natural hosts eventually resulted in the establishment of two types of HIV in the human population. The following examples demonstrate that upon persistent infection and passage in cell culture, cross-species transmissibility may be promoted by selection of virus variants with an altered host range. Adaptation in cell culture may result in changes in receptor specificity and tropism, and leads to the emergence of host-range mutant viruses. doi = 10.1002/jgm.794 id = cord-007717-7x1mqqmf author = Lowen, Anice C. title = Transmission in the Guinea Pig Model date = 2014-07-08 keywords = H1N1; virus summary = This chapter describes influenza virus infection, growth, and transmission in guinea pigs; highlights how these properties differ among influenza viruses adapted to human, swine, and avian hosts; and provides an overview of knowledge gained through the study of influenza virus transmission in the guinea pig model. By virus histochemistry, the H3N2 subtype human influenza viruses studied (Pan/99 and A/Netherlands/213/03) attached mainly to the guinea pig upper respiratory tract and the trachea, with little to no binding detected on bronchiolar and alveolar epithelia. Seasonal H3N2 viruses and 2009 H1N1 pandemic strains show similar and high efficiency of transmission in both contact and respiratory droplet models (Lowen et al. Reverse genetics-derived Pan/99 viruses with and without the NA-E119V mutation were found to transmit with equal efficiency in the guinea pig contact transmission model, as had been seen with similar isolates in the ferret model (Herlocher et al. doi = 10.1007/82_2014_390 id = cord-031840-k9l91unc author = Lu, Li title = Forum: COVID-19 Dispatches date = 2020-09-11 keywords = Asia; COVID-19; China; East; Japan; Korea; South; chinese; coronavirus; pandemic; virus summary = With death count worldwide reaching 586,000 merely 7 months after its first outbreak in China in late December 2019 and 13.6 million cases reported in 188 countries and territories as of July 2020, this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. On one hand, the eagerness to build solidarity with East Asian countries represented by Japan and South Korea might be a strategy to react to the racialization of COVID-19 as a "Chinese virus" and the demonization of China as a "public enemy" and "trouble maker" in the Euro-American political and media agenda (Viala-Gaudefroy & Lindaman, 2020). On the other hand, the rise of this East Asian imaginary centering around China''s historical and cultural bonds with Japan and South Korea has far-reaching implications for China''s geopolitical strategies beyond the COVID-19 pandemic and the realm of public health. doi = 10.1177/1532708620953190 id = cord-007575-5ekgabx5 author = Luby, James P. title = Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date = 2016-01-14 keywords = CMV; infection; influenza; patient; pneumonia; virus summary = Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. doi = 10.1097/00000441-198707000-00007 id = cord-287337-2ljbsia2 author = Ludwig, Christine title = Virus-like particles—universal molecular toolboxes date = 2008-01-04 keywords = Gag; HIV; VLP; immune; virus summary = It is noteworthy that VLPs assembled from HPV major capsid protein L1 in yeast were capable of inducing protective immune responses against HPV subtypes 16 and 18 causing cervical cancer in humans, thus resulting in a safe, well tolerated and highly immunogenic vaccine that received approval for marketing in 2006 [13] . Since particulate antigens had been demonstrated to induce better cellular and humoral immune responses than soluble antigens, the detection that HIV-1 Pr55Gag polyprotein self-assembles into particulate spheres provided a new rationale for generating a Gag-based VLP vaccine [15, 16] . The authors demonstrated efficient expression of murine leukemia virus (MLV) Gag-Env VLPs from plasmid DNA in vitro and used these plasmo-retroVLPs to induce strong specific CTL responses towards displayed T cell epitopes, protecting mice from lethal virus challenge. [52] have formerly shown that virosome-mediated targeting of mumps virus DNA to APCs induces specific CTL responses suggesting efficient expression and presentation of the encoded mumps antigens. DNA vaccines encoding retrovirusbased virus-like particles induce efficient immune responses without adjuvant doi = 10.1016/j.copbio.2007.10.013 id = cord-005246-cskb0njm author = Ludwig, George V. title = Insect-transmitted vertebrate viruses: Flaviviridae date = 1993 keywords = cell; culture; flavivirus; japanese; vaccine; virus summary = Additionally, these culture systems permit the study of flavivirus attachment, penetration, replication, and release from cells and have been instrumental in the production and characterization of live-attenuated vaccines. Cell culture is essential for the study of flaviviruses, and will continue to play a pivotal role in the isolation, characterization, and development of new vaccines against current and future flavivirus health threats. More recent research has shown that fusion of dengue, yellow fever, and Japanese encephalitis viruses may in fact involve fusion of virus directly to the cell''s plasma membrane (52, 108) . The observation that persistent dengue virus infections can be established in a non-vector mosquito cell line associated with changes in several of the important biological characteristics, such as temperature sensitivity and antigenic structure (64) , presents the possibility that genetic selection of attenuated virus strains may be possible with insect cell lines. doi = 10.1007/bf02633958 id = cord-304481-yqc8r3ll author = Luis, Angela D. title = Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date = 2015-08-24 keywords = Fig; bat; specie; virus summary = Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19). doi = 10.1111/ele.12491 id = cord-264794-bgygebgx author = Lundgren, A.-L. title = Feline non-suppurative meningoencephalomyelitis. A clinical and pathological study date = 1992-11-30 keywords = CNS; cat; disease; feline; virus summary = It has been argued that the syndrome may include several aetiologically unrelated conditions affecting the central nervous system of cats, e.g. toxoplasmosis (Hirth and Nielsen, 1969) and the cerebral form of feline infectious peritonitis (Slauson and Finn, 1972; Kornegay, 1978) . Histopathological examination revealed throughout the central nervous system a non-suppurative inflammation characterized by perivascular mononuclear cuffing, presence of inflammatory nodules and neuronal degeneration in all cats. Neuropathological examination of the cats of the present study showed a marked inflammatory reaction in the cerebral leptomeninges as well as in the grey matter of the brain and spinal cord. Neither the serological results nor the clinical and histopathological findings in the cats with staggering disease indicate a FeLV infection. Feline immunodeficiency virus (FIV) has emerged as an important cause of neurological disease in cats (Dow, Poss and Hoover, 1990; Sparger, 1991) , often in association with clinical syndromes typical of an immunodeficient state (chronic stomatitis, enteritis, dermatitis, etc). doi = 10.1016/0021-9975(92)90015-m id = cord-007792-596jxrm5 author = Luo, Ming title = Influenza Virus Entry date = 2011-08-26 keywords = HA2; infl; uenza; virus summary = The key player in virus entry is the surface glycoprotein HA that contains the host receptor binding site to allow the virus particle to attach to specifi c host cells, the fusion peptide that is inserted into the target cellular membrane during membrane fusion, and other structural elements that may refold during the membrane fusion process. When the HA amino acid substitutions are accumulated in the repertoire of infl uenza virus strains, they are mostly on the exposed surface of the HA glycoprotein except for the receptor binding site, the fusion peptide, and the amino acids that accommodate the fusion peptide before HA structural changes for membrane fusion (Wilson et al. The next 18 amino acids form part of the pocket that accommodates the hydrophobic fusion peptide in the metastable HA structure on the infl uenza virion prior to virus entry. doi = 10.1007/978-1-4614-0980-9_9 id = cord-332632-u2ud0vmq author = Lussi, Carmela title = What can pestiviral endonucleases teach us about innate immunotolerance? date = 2016-03-17 keywords = BVDV; IFN; RNA; viral; virus summary = In particular, the unique extension of ''self'' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host''s own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Thus, the survival strategy of BVDV consists of being non-cytopathogenic and producing less dsRNA than its cp counterpart, and expressing the IFN antagonists N pro as the first protein in order to reduce or even avoid IFN production in infected cells and E rns to degrade immunostimulatory viral RNA before they might activate the host''s PRRs. Notably, both pestiviral IFN antagonists are not only required to constantly maintain innate immunotolerance during persistent infections, but they also play an important role in acute infections [25] . doi = 10.1016/j.cytogfr.2016.03.003 id = cord-331714-2qj2rrgd author = Lvov, Dimitry Konstantinovich title = Single-Stranded RNA Viruses date = 2015-05-29 keywords = Aedes; Africa; Asia; Bunyaviridae; Congo; Crimean; East; Eurasia; Europe; Influenza; Ixodes; Nile; Northern; Republic; Russia; Sea; Siberia; TBEV; USSR; WNV; West; figure; isolate; isolation; tick; virus summary = Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Artashat virus (ARTSV, strain LEIV-2236Ar) was originally isolated from Ornithodoros alactagalis ticks (family Argasidae) collected in the burrows of a small five-toed jerboa (Allactaga elater) near Arevashat village (40 02 absence of antigenic relationships with any known viruses, it was referred to as an "unclassified bunyavirus." 1À3 Taxonomy. doi = 10.1016/b978-0-12-801742-5.00008-8 id = cord-018804-wj35q88f author = Lázaro, Ester title = Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date = 2007 keywords = RNA; genome; mutation; virus summary = High error prone replication, together with the short replication times and large population sizes typical of RNA viruses, instead of being a handicap for survival provides an extraordinary evolutionary advantage by permitting the generation of a wide reservoir of mutants with different phenotypic properties [7] . However, the fact that DNA organisms, which usually live in constant environments, have evolved corrector activities, whereas RNA viruses have not, suggests that replication with high error rates is a selected character that strongly favours viral adaptation to fast changing conditions. Quasi-species replicating during a long time in a near-constant environment in the absence of large population size fluctuations can present a low rate of fixation of mutations in the consensus sequence, despite the continuous occurrence of mutants that is characteristic of the underlying dynamics of the population. The infection of a new host constitutes a sudden change in the environment in which viral replication takes place, usually with the consequence of a drastic decrease in the average fitness of the virus population, which prevents further transmission. doi = 10.1007/978-3-540-35306-5_15 id = cord-309346-4mdxe6ri author = López-Medrano, Francisco title = Virus respiratorios: los más frecuentes, los más olvidados date = 2008-02-29 keywords = virus summary = Los estudios de descripción epidemiológica, como el de Reina et al 10 son el primer paso para el desarrollo de nuevas posibilidades terapéuticas (antivirales) y profilácticas (vacunas) frente a metapneumovirus y VRS, que a buen seguro tendrían una importante repercusión sobre el control de la patología respiratoria de la población pediátrica. También en este número de ENFERMEDADES INFECCIOSAS Y MICROBIOLOGÍA CLÍNICA se publica un artículo de Perelló et al 12 sobre la implicación de los virus respiratorios en la neumonía adquirida en la comunidad (NAC) en sujetos infectados por el virus de la inmunodeficiencia humana (VIH). Sin embargo, es importante recordar que las infecciones por virus respiratorios pueden complicarse con infección de vías respiratorias bajas y neumonía en sujetos inmunodeprimidos, con una morbimortalidad no despreciable, como se ha demostrado recientemente en cohortes de pacientes con enfermedades hematológicas 5,6 y en portadores de trasplante de órgano sólido 7 . doi = 10.1157/13115538 id = cord-336948-8yqdhcnz author = Löhner, Rainald title = Detailed simulation of viral propagation in the built environment date = 2020-08-05 keywords = flow; numerical; particle; virus summary = If, for the sake of argument, we consider Stoke''s law for the drag of spherical particles, valid below Reynolds numbers of Re = 1, the terminal sink velocity (also known as the settling velocity) of particles will be given by [26] : where ρ p , ρ g , g, μ, d denote the density of the particles (essentially water in the present case), density of the gas (air), gravity, dynamic viscosity of the gas and diameter of the particle respectively. -Spatial discretization using unstructured grids (in order to allow for arbitrary geometries and adaptive refinement); -Spatial approximation of unknowns with simple linear finite elements (in order to have a simple input/output and code structure); -Edge-based data structures (for reduced access to memory and indirect addressing); -Temporal approximation using implicit integration of viscous terms and pressure (the interesting scales are the ones associated with advection); -Temporal approximation using explicit, high-order integration of advective terms; -Low-storage, iterative solvers for the resulting systems of equations (in order to solve large 3-D problems); and -Steady results that are independent from the timestep chosen (in order to have confidence in convergence studies). doi = 10.1007/s00466-020-01881-7 id = cord-331020-lyxje82u author = M. Najimudeen, Shahnas title = Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date = 2020-09-24 keywords = Bronchitis; IBV; Infectious; Virus; chicken summary = The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] . doi = 10.3390/pathogens9100779 id = cord-290855-6umgvt28 author = Ma, Li title = Antiviral Effects of Plant-Derived Essential Oils and Their Components: An Updated Review date = 2020-06-05 keywords = antiviral; virus summary = Previous studies have demonstrated essential oils to be excellent candidates to treat antiviral-resistant infection associated with their chemical complexity which confers broad-spectrum mechanisms of action and non-specific antiviral properties. This review provides an up-to-date overview of the antiviral efficacy of essential oils from a wide range of plant species and their characteristic components, as well as their overall mechanisms of action, focusing on the last decade. Virucidal effects of EOs extracted from numerous aromatic and herbal plants are also well documented on a variety of viruses, such as IFV, HSV, HIV, yellow fever virus, and avian influenza, etc. Essential oils from Star Anise, Australian tea tree, oregano, Eucalyptus caesia, to name a few, have been demonstrated to exhibit high anti-HSV-1 activities in vitro (Table 1 ). doi = 10.3390/molecules25112627 id = cord-354582-fniymnmf author = Ma, Zhiqian title = Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date = 2020-06-30 keywords = MERS; RNA; SARS; virus summary = In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . doi = 10.1016/bs.aivir.2020.06.003 id = cord-000180-howix091 author = MacLeod, Iain J. title = Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date = 2010-03-05 keywords = PCR; Virus; cell; hsv-1 summary = By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. doi = 10.1371/journal.pone.0009560 id = cord-016499-5iqpl23p author = Mackay, Ian M. title = Rhinoviruses date = 2014-02-27 keywords = ARI; HRSV; HRV; IFN; PCR; RNA; human; infection; respiratory; rhinovirus; viral; virus summary = A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines doi = 10.1007/978-1-4899-7448-8_29 id = cord-351571-gwtkrt5u author = Mackay, Ian M. title = Community-Wide, Contemporaneous Circulation of a Broad Spectrum of Human Rhinoviruses in Healthy Australian Preschool-Aged Children During a 12-Month Period date = 2013-05-01 keywords = HRV; virus summary = Human rhinovirus (HRV) infections trigger exacerbations of asthma and chronic obstructive pulmonary disease and the majority of acute respiratory illnesses (ARIs), some of which meet criteria for influenza-like illness. Nevertheless, each available majority sequence of an HRV-C type has to date represented a genetically unique, phylogenetically distinct, and globally distributed virus detected in patients with ARIs. There are specific seasonal and annual variations in respiratory virus circulation and interactions [11] [12] [13] . We sought to quantify the genetic diversity, epidemiology, and impact of HRV and enterovirus species, conjointly referred to hereafter as picornaviruses, circulating among a community cohort of preschool-aged children who provided respiratory samples over a 1-year period. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children doi = 10.1093/infdis/jis476 id = cord-317244-4su5on6s author = Maganga, Gael D. title = Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date = 2014-12-31 keywords = PCR; RNA; bat; virus summary = In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. doi = 10.1371/journal.pone.0115588 id = cord-002581-r7mskri0 author = Magnani, Diogo M. title = A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus date = 2017-06-12 keywords = DENV; P1F12; ZIKV; Zika; virus summary = title: A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus The isolation of neutralizing monoclonal antibodies (nmAbs) against the Zika virus (ZIKV) might lead to novel preventative strategies for infections in at-risk individuals, primarily pregnant women. Here we describe the isolation of 18 plasmablast-derived human mAbs, sorted 12 days post onset of symptoms from a ZIKV-patient in São Paulo, Brazil. Interestingly, one of these mAbs (P1F12) exhibited no nucleotide mutations when compared to its corresponding germline sequences, but still recognized a ZIKV immunodominant epitope and neutralized the virus. Virus capture assay and recombinant E protein ELISA P1F12 binding was determined by both virus capture assay (VCA) and recombinant (r)E ELISAs. The VCA plates were coated overnight with the mouse-anti-Flavivirus monoclonal antibody 4G2 (clone D1-4G2-4-15, EMD Millipore) followed by incubation with viral stocks (ZIKV or DENV). Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus doi = 10.1371/journal.pntd.0005655 id = cord-007094-ur9sz21s author = Mahabir, Esther title = Rodent and Germplasm Trafficking: Risks of Microbial Contamination in a High-Tech Biomedical World date = 2008-01-01 keywords = embryo; mouse; virus summary = Preservation of mouse germ-plasm is achieved by cryopreservation of spermatozoa, embryos, or ovaries, and embryonic stem cells are used for the production of genetically engineered mice. In this article, we discuss regulations and practical issues in the shipping of live mice and mouse tissues, including spermatozoa, embryos, ovaries, and embryonic stem cells, and review work on microbial contamination of these biological materials. The importation paperwork for cryopreserved laboratory mouse tissues and cell lines is similar to that required for live animal importation to the United States (i.e., a pro forma invoice and declaration statements). Embryo transfer recipients in rederivation programs should be held in individually ventilated cages (IVCs 1 ) until testing shows that they are free of all unwanted microorganisms, including those listed in Appendix 3 of the Federation of Laboratory Animal Science Associations (FELASA) recommendations (Nicklas et al. Risk assessment of mouse hepatitis virus infection via in vitro fertilization and embryo transfer by the use of zona-intact and laser-microdissected oocytes doi = 10.1093/ilar.49.3.347 id = cord-314201-6njwigco author = Maher-Sturgess, Sheryl L title = Universal primers that amplify RNA from all three flavivirus subgroups date = 2008-01-24 keywords = PCR; primer; virus summary = Tanaka [3] published the first universal primer pair specific for mosquito borne flaviviruses in 1993; the YF1 and YF3 primers targeted the NS5/3''UTR of the genome and were based upon the six flavivirus sequences available at the time. In 2005 Gaunt and Gould designed a universal nested PCR, using six primers targeting the E gene, capable of amplifying cDNA from 60 flavivirus strains. In the present study, we identified conserved sites and developed a universal, non-nested primer pair that amplifies cDNA from each of the major subgroups of flaviviruses, and also TABV, under standard reaction conditions. Since the amplified products represent 8% of the genome, this is sufficient sequence to determine the species of the virus and thus potentially to identify unrecognised flaviviruses. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis doi = 10.1186/1743-422x-5-16 id = cord-021034-hnw7a3a1 author = Mahony, James B. title = Negative staining in the detection of viruses in clinical specimens date = 2002-10-09 keywords = IEM; PAG; virus summary = In our experience the serum-in-agar (SIA) method is the most sensitive of the PAG IEM techniques for detection of rotavirus particles in clinical specimens. SPEIMDAGT employing colloidal gold-labeled secondary antibody has increased sensitivity and offers the advantage of detecting viral antigen when whole virus particles are not visible. Prior to the development of immunoassay techniques for detecting viral antigens, direct electron microscopy (DEM) with negative staining was the only method of providing a definitive diagnosis of several viral infections. We have used this method to detect rotavirus in fecal specimens (Wu et a!., 1989) (Fig. 2) Solid phase JEM Although IEM is considerably more sensitive than DEM, it is dependent upon the optimal concentrations of antibody and antigen and is susceptible to a prozone phenomenon. Development of a sensitive protein A-gold immunoelectron microscopy method for detecting viral antigens in fluid specimens doi = 10.1016/0739-6260(91)90062-5 id = cord-279694-25rblhwb author = Mahy, B.W.J title = Emerging and Reemerging Virus Diseases of Vertebrates date = 2014-11-28 keywords = cause; disease; human; virus summary = Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. It will be important in the future to detect new viruses before they can emerge to cause disease in the population. doi = 10.1016/b978-0-12-801238-3.02564-2 id = cord-331584-z43ifmr3 author = Mahy, B.W.J. title = Emerging and Reemerging Virus Diseases of Vertebrates date = 2008-07-30 keywords = disease; human; virus summary = The threat of a new pandemic of influenza virus in the human population stresses the need for development of better methods for detection, surveillance, and control of emerging virus diseases. Although it is still important to isolate viruses in cell culture for their complete characterization, it is now possible directly to detect viruses in diseased tissues by PCR, then, by sequencing the amplicon, to determine whether a new virus has emerged to cause the disease. For example, when hantavirus pulmonary syndrome, caused by a bunyavirus of rodents, Sin Nombre virus, was initially detected in 1993 in the Four Corners region of Western USA, it was found that rodents inside a house where people had been infected carried a virus identical in sequence to virus isolated from human cases. Then, in 1993, a new hantavirus emerged in the Four Corners region of Southwestern USA as the cause of a severe acute respiratory disease syndrome, with a fatality rate close to 40%, and named Sin Nombre virus. doi = 10.1016/b978-012374410-4.00383-6 id = cord-280986-i27mge10 author = Mallia, Patrick title = How Viral Infections Cause Exacerbation of Airway Diseases date = 2017-01-25 keywords = COPD; exacerbation; virus summary = Exacerbations are associated with increased airway inflammation in patients with both asthma and COPD, but many questions remain unanswered regarding the key inflammatory cells and mediators involved. 24, 25 In the lower respiratory tract, increases in Il-6, IL-8, and the chemokine regulated on activation, normal T-cell expressed and secreted (RANTES) have been documented in the sputum of asthmatic patients after experimental rhinovirus infection, 10, 26 and IL-8 has been detected in the sputum of children with naturally occurring exacerbations. A recent study 10 in patients with naturally occurring virusassociated asthma exacerbations found increased levels of IL-10 messenger RNA in the sputum of asthmatic patients compared to virus-infected healthy subjects, but no differences in the level of RANTES or IL-8 between the two groups. Studies 38 of airway inflammation in stable patients with COPD have shown that the disease is characterized by pulmonary infiltration of macrophages, neutrophils, and CD8ϩ T lymphocytes, together with increased expression of cytokines, chemokines, and adhesion molecules. doi = 10.1378/chest.130.4.1203 id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 keywords = RNA; ZIKV; Zika; bat; virus summary = Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. doi = 10.1371/journal.pntd.0007071 id = cord-027550-yyqsatqw author = Mammas, Ioannis N. title = Update on current views and advances on RSV infection (Review) date = 2020-06-15 keywords = RSV; bronchiolitis; child; infection; respiratory; virus summary = doi = 10.3892/ijmm.2020.4641 id = cord-268417-6eyetb5i author = Mandel, Benjamin title = Neutralization of Animal Viruses date = 1978-12-31 keywords = Fab; Mandel; Yoshino; antibody; complement; neutralization; study; virus summary = Somewhat earlier, Morgan (1945''1 had reported that discrepancies in the quantitative aspects of the neutralization of WEE virus by immune rabbit sera were related to the use of fresh or heated serum, and that the addition of complement to the latter tended to eliminate the discrepancies. Further studies (Radwan et al., 1973) showed that the addition of complement to virus complexed with dependent antibody eventually resulted in lysis of the viral membrane. It was also shown (Yoshino and Taniguchi, 1966 ) that antibodies induced in guinea pigs by immunization, and in humans following herpes infection, were initially dependent and later independent of complement for neutralizing activity. A relevant observation has been made in several studies; neutralization of infectious virus-antibody complexes by antiglobulin also shows a single-hit mechanism, and at a rate that exceeds the rate of the homotypic reaction. doi = 10.1016/s0065-3527(08)60101-3 id = cord-297790-tpjxt0w5 author = Mandl, Judith N. title = Going to Bat(s) for Studies of Disease Tolerance date = 2018-09-20 keywords = IFN; RNA; bat; dna; infection; virus summary = Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. doi = 10.3389/fimmu.2018.02112 id = cord-293732-rxd1lyi7 author = Manoj, M.G. title = Potential link between compromised air quality and transmission of the novel corona virus (SARS-CoV-2) in affected areas date = 2020-08-01 keywords = COVID-19; SARS; virus summary = Through a critical review of the current literature and a preliminary analysis of the link between SARS-CoV-2 transmission and air pollution in the affected regions, we offer a perspective that polluted environment could enhance the transmission rate of such deadly viruses under moderate-to-high humidity conditions. The aqueous atmospheric aerosols offer a conducive surface for adsorption/absorption of organic molecules and viruses onto them, facilitating a pathway for higher rate of transmission under favourable environmental conditions. Analysis of the air quality index (AQI, Fig. S1 , acquired on 16 th March 2020) reveals that the effected countries or regions had witnessed enhanced level of pollution ( frequently AQI > 100) which are qualified as "unhealthy" and even "hazardous", in the cold winter period. (2020) reports that air pollutants measured over Italy (PM 10 and PM 2.5 ) have a substantial influence on the COVID-19 transmission and infection rate there. doi = 10.1016/j.envres.2020.110001 id = cord-257299-z9u12yqb author = Mansi, N. title = Ear, nose and throat manifestation of viral systemic infections in pediatric patients date = 2009-12-31 keywords = EBV; cause; child; infection; respiratory; virus summary = Common childhood viral infections, such as measles and mumps are probably an unrecognized cause of acute or progressive damage to hearing [5] . Measles infection can be avoided by administering a reduced, live-virus vaccine to children between the ages of 12 and 15 months (MMR). The etiology of the acute forms in the respiratory airways is, initially, of a viral nature in most patients, with later, secondary bacterial infections on the mucous lesions caused by the viral agents [31] . Herpangina is an extremely contagious illness caused by a coxackievirus characterized by a presence of a vesicular exanthema at the velopharyngeal mucous level and acute or croup laryngotracheitis [38] [39] [40] [41] when viral infections are associated. The most common manifestation of the primary infection of this organism is infective mononucleosis (IM), a sometimes acute, but often asymptomatic clinical syndrome which more often strikes children, adolescents, and young adults [82] . Viral etiology and epidemiology of acute lower respiratory tract infections in children doi = 10.1016/s0165-5876(09)70006-0 id = cord-000729-iq30z094 author = Marsh, Glenn A. title = Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date = 2012-08-02 keywords = CedPV; Fig; Nipah; RNA; virus summary = The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrinB2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. As part of our on-going field studies on HeV genetic diversity and infection dynamics in the Queensland flying fox populations, urine samples were collected on a regular basis for PCR and virus isolation. CedPV is more closely related to HeV and NiV than henipavirus-like sequences detected in African bats [26, 32] as shown in a phylogenetic tree based on the only sequences available of a 550-nt L gene fragment (Fig. S5) . doi = 10.1371/journal.ppat.1002836 id = cord-295062-8rl4kswe author = Marsh, Mark title = Virus Entry: Open Sesame date = 2006-02-24 keywords = HIV; cell; entry; virus summary = Virus Particles as Devices for Targeted Gene Transfer A viral particle is composed of nucleic acids (RNA or DNA), protein, and, in the case of enveloped viruses, membrane lipids. Viruses use signaling activities to induce changes in the cell that promote viral entry and early cytoplasmic events, as well as to optimize later processes in the replication cycle. Like cholera toxin, these viruses bind to the sugar moiety of gangliosides and enter cells via caveolar/raft pathways that are dependent on cholesterol ( Figures 2D and 2E ) and the activation of tyrosine-kinase signaling cascades (Anderson et al., 1996; Pelkmans et al., 2001; Smith et al., 2003a; Stang et al., 1997; Tsai et al., 2003) . Nevertheless, in the majority of cases, the transfer of viral genomes from cell to cell appears to occur through the formation of virus particles that are released from infected cells and use the mechanisms described above to enter new uninfected hosts. doi = 10.1016/j.cell.2006.02.007 id = cord-312688-12san3m7 author = Martin, Baptiste title = Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date = 2016-09-14 keywords = Ebola; Marburg; RNA; virus summary = title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry After replication of the viral genome and RNA transcription, nascent viral particles are assembled in a process mediated by the matrix protein VP40, and virus budding occurs at the cell surface membrane in a process that involves hijacking the host ESCRT machinery (Hartlieb and Weissenhorn, 2006; Noda et al., 2006) . However, no direct interaction between both molecules has been demonstrated yet, and recent studies suggest that a 5 b 1 -integrin is not required for GP-mediated binding of internalization, but rather is a positive regulator of cathepsins, which play an important role in processing GP 1 into its fusion-competent form within the endosomes of infected cells (Schornberg et al., 2009) . After attachment mediated by interaction between the filovirus surface protein GP 1,2 (PDB: 3CSY) and various attachment factors, the complex is internalized and routed to the endosome, where GP 1,2 is processed to trigger fusion of viral and host membranes. doi = 10.1016/j.antiviral.2016.09.001 id = cord-310439-z0bxsjug author = Martin, R. R. title = Pathogen-Tested Planting Material date = 2014-12-31 keywords = certification; pathogen; plant; program; virus summary = Buffer zone An area surrounding or adjacent to an area for production of plants in a certification scheme designed to minimize the probability of spread of the target pathogens, pollen, or seed into or out of the block, to meet phytosanitary or other control measures as defined in a certification standard. Many certification programs are based on a published standard that defines site selection and preparation, isolation distances from plants of the same species and other vegetation, number of inspections, record keeping on plant traceability so that tracebacks or traceforwards can be done if a problem should arise, a pest and disease management plan, records of all pest management activities, the conditions and protocols to be followed during plant or seed production, and types and amount of testing that needs to be done at each level in the propagation cycle. doi = 10.1016/b978-0-444-52512-3.00173-x id = cord-287348-00yaxpkp author = Martinez, Maria Jose Abad title = Antiviral Activities of Polysaccharides from Natural Sources date = 2005-12-31 keywords = HIV; activity; antiviral; sulphate; virus summary = Although many compounds with potent antiviral activity in cell cultures and in experimental animals have been detected, at present only several molecules and a-interferon have been approved by the health authorities for therapy of viral infections in humans. Furthermore, several soluble derivatized dextrans with different percentages of carbomethyl, benzylamide and sulphonate/sulphate groups were also evaluated for possible inhibitory effects on HIV-1 infection, and from the results obtained, their use as anti-HIV therapeutic agents can be proposed [56] . Carrageenans and fucoidan are sulphated PS extracted from red seaweed and brown algae, which have shown potent inhibitory activity against different viruses including HIV. These compounds act as potent inhibitors of different enveloped viruses, including members of Herpesviridae, and their activity is linked to the anionic features of the molecule which hinder the attachment of viral particles to host cells. doi = 10.1016/s1572-5995(05)80038-9 id = cord-263315-g7os15m1 author = Martins-da-Silva, Andrea title = Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date = 2018-01-18 keywords = RNA; Virus; cell; ll5; protein; response summary = title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. doi = 10.3390/v10010043 id = cord-263157-8jin6oru author = Martínez, Miguel Angel title = Progress in the Therapeutic Applications of siRNAs Against HIV-1 date = 2008-10-13 keywords = HIV-1; RNA; Tat; cell; target; virus summary = Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Importantly, this study made the extraordinary demonstration that cell transfection of synthetic 21 base pairs (bp) short interfering RNA (siRNA) duplexes can mediate RNAi in a sequence-specific manner; this finding enabled the specific regulation of gene expression in a variety of biological systems, including diseased cells. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication. To counteract this strategic weakness, co-expression of multiple siRNAs or shRNAs that target conserved RNA sequences could reduce the emergence of single siRNA-resistant virus with a comparable effect to that achieved by the multiple anti-HIV drug combination approach employed by HAART. doi = 10.1007/978-1-60327-547-7_17 id = cord-300133-yc2wxgid author = Martínez, Miguel J. title = Ebola Virus Infection: Overview and Update on Prevention and Treatment date = 2015-09-12 keywords = EBOV; EVD; Ebola; virus summary = In 2014 and 2015, the largest Ebola virus disease (EVD) outbreak in history affected large populations across West Africa. Relevant information was identified through a comprehensive literature search using Medline, PubMed and CINAHL Complete and using the search terms Ebola, Ebola virus disease, Ebola hemorrhagic fever, West Africa outbreak, Ebola transmission, Ebola symptoms and signs, Ebola diagnosis, Ebola treatment, vaccines for Ebola and clinical trials on Ebola. Over the past 17 months, the West Africa EVD outbreak has provided an important opportunity to consider use of and evaluate several therapeutic and prophylactic agents (e.g., vaccines) to determine their safety and efficacy [5, 6] . FGI-103, FGI-104, and FGI-106 are a group of broad-spectrum antiviral agents that inhibit viral replication in a dose-dependent manner among multiple and genetically distinct viruses including EBOV, bunyaviruses, dengue virus, Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an emprical treatment during outbreaks doi = 10.1007/s40121-015-0079-5 id = cord-003926-ycdaw2vh author = Maslow, Joel N. title = Zika Vaccine Development—Current Progress and Challenges for the Future date = 2019-07-14 keywords = Zika; infection; vaccine; virus summary = Of note, the first demonstration of immunoprotection was as part of a 1953 study to define the ultrastructural characteristics of Zika virus, that found intramuscular vaccination of mice with infectious viral filtrates protected against cerebral infection [36] . In pre-clinical studies, vaccinated mice and non-human primates were shown to develop B and T-cell immune responses against the Zika virus envelope and protected against development of neurologic disease and death in immunosuppressed, interferon α, β receptor deficient (IFNAR) mice [43] . A subsequent study in non-human primates vaccinated twice at four-week intervals with alum generated binding and microneutralization antibody titers of 3.54 and 3.55 log10, respectively, and complete protection against viremia and viruria following challenge with either Brazilian or Puerto Rican strains of Zika virus [47] . Guillain-Barre Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study doi = 10.3390/tropicalmed4030104 id = cord-331343-qzvwwca9 author = Mason, Andrew L. title = Metagenomics and the case of the deadly hamster date = 2008-06-09 keywords = LCMV; human; virus summary = 1 The authors then tried panmicrobial microarray analysis with 29,455 oligonucleotide probes reactive to known vertebrate viruses, bacteria, fungi, and parasites, 5 and after drawing a blank with all these studies, they resorted to brute sequencing of all RNA in the infected tissue to discover the new virus. 8 In humans, metagenomic analysis has been used to study viral communities in blood and respiratory secretions, 6 to differentiate bacterial species in gut flora, 9 and to catalog the collective DNA and RNA viral species in stool samples of healthy subjects 10, 11 and patients with diarrhea. 16 They would have saved a considerable amount of time and effort if they could have sequenced RNA from a few "non-A non-B virus" infected livers (assuming that they could have had access to human genome data that were not available at the time). doi = 10.1002/hep.22452 id = cord-029419-b0w9nomq author = Matthews, Adam title = Review of Mark Honigsbaum (2020). The Pandemic Century—A History of Global Contagion from the Spanish Flu to Covid-19: Cambridge, MA: Penguin. 321 pp. ISBN 9780753558287 date = 2020-07-20 keywords = Honigsbaum; SARS; covid-19; virus summary = Honigsbaum surveys with biological detail the genealogy and history of influenza, the plague, Parrot Fever, Legionnaires Disease, Aids, SARS, Ebola, Zika and Covid-19. Honigsbaum describes ecological disruption amplifying the mutation and spread of a virus which had existed in its natural environment for centuries. From a postdigital perspective, the ten cases detailed by Honigsbaum in The Pandemic Century (2020) show how digital and wider technologies are not separate from the natural and social world. The questions then, which The Pandemic Century (Honigsbaum 2020) illustrates is whether to take a posthuman perspective and pull back from technological and human development and reduce ecological disruption and work with the natural environment as equals or to push on unabated with technological developments to go beyond what has been done already to ''fix'' ourselves and the planet, including new viral outbreaks. doi = 10.1007/s42438-020-00170-z id = cord-016652-x8t3lf1x author = Matthews, David title = Viruses and the Nucleolus date = 2011-05-23 keywords = RNA; protein; virus summary = This process is crucial for virus biology because if the viral proteins that are required for cytoplasmic functions such as RNA synthesis and encapsidation are sequestered in the nucleolus or nucleus, then progeny virus production will be affected as has been revealed by inhibitor and genetic studies (Lee et al. Viruses may interact with the nucleolus to usurp host cell functions and recruit nucleolar proteins to facilitate virus replication. Initial studies utilising the prototype g-2 herpesvirus, herpes virus saimiri (HVS), demonstrated that the HVS nucleolar trafficking ORF57 protein induces nucleolar redistribution of the host cell human TREX proteins, which are involved in mRNA nuclear export (Boyne and Whitehouse 2006) . The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing doi = 10.1007/978-1-4614-0514-6_14 id = cord-318786-qd0k8174 author = Mauriz, Elba title = Recent Progress in Plasmonic Biosensing Schemes for Virus Detection date = 2020-08-22 keywords = LSPR; SARS; SERS; detection; figure; virus summary = Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Technological advancements in plasmonic biosensing including colorimetric and fluorescence enhancement as well as the utilization of nanomaterials and optical aperture nanostructures for achieving highly sensitive virus detection are described in this section. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. Typically, most of quantum dots'' applications have been exploited in LSPR-based biosensors because the distance and dimensions of the adjacent gold nanoparticles can affect the fluorescence signal and, therefore, be quenched depending on the analyte concentration. doi = 10.3390/s20174745 id = cord-290993-bsnja161 author = McAuliffe, Josephine title = Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys date = 2004-12-05 keywords = SARS; TCID; virus summary = Serologic evidence of infection, defined as a four-fold rise in Nt Ab titer, was observed in 4 of 4 rhesus, 3 of 4 cynomolgus, and 4 of 4 AGMs. Although the study described above indicated that all three species of monkeys were infected with SARS-CoV, there were significant discrepancies between our findings and published reports of cynomolgus macaques infected with SARS-CoV; Kuiken et al. Mean titers of virus (expressed as log 10 TCID 50 /ml of sample; y axis) detected on indicated days (x axis) in the upper respiratory tract (left panels, A, C, and E, closed symbols) and lower respiratory tract (right panels, B, D, and F, open symbols) of rhesus (panels A and B, x, w), cynomolgus (panels C and D, E, 4), and African Green (panels E and F, n, 5) monkeys following intranasal and intratracheal administration of 10 6 TCID 50 of SARS-CoV. doi = 10.1016/j.virol.2004.09.030 id = cord-273343-als886fe author = McClenahan, Shasta D. title = Discovery of a Bovine Enterovirus in Alpaca date = 2013-08-12 keywords = PCR; virus summary = A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. doi = 10.1371/journal.pone.0068777 id = cord-252012-hdjbxah8 author = McErlean, Peter title = Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date = 2010-11-01 keywords = ARI; asthma; respiratory; virus summary = Traditionally associated with acute respiratory illness (ARI) or symptoms of the "common cold," the respiratory viruses implicated in asthma exacerbations predominantly possess RNA genomes with a distinct genome organization (positive [1] or negative [À] sense), virus particle (virion) morphology (enveloped or nonenveloped), host cell receptor interaction, and well-defined annual or seasonal prevalence. These "newly identified viruses" (NIVs) including human metapneumovirus (HMPV; described pre-SARS), the human rhinovirus (HRV) species C (HRV-Cs), human coronaviruses (HCoVs)-NL63 and -HKU1, human bocavirus (HBoV), and the KI and WU polyomaviruses (KIPyV and WUPyV) are now the focus of intense research, and their involvement in asthma exacerbations is slowly beginning to be determined. 34 In a retrospective study of clinical samples taken over a 20-year period from young children (median age 14.5 months), the percentage of lower respiratory tract illness (LRTI; including asthma exacerbations and bronchiolitis) associated with any HCoV, HCoV-NL63, or HCoV-OC43 was estimated to be 4.6%, 2.6%, and 1.9%, respectively. doi = 10.1016/j.iac.2010.08.001 id = cord-341303-1iayp8oa author = McINTOSH, KENNETH title = Immunofluorescence in Diagnostic Virology date = 2006-12-16 keywords = specimen; virus summary = In the 1930s Parker and Muckenfuss first developed the complement fixation reaction using lymph mixed with antibody and a fresh source of complement.s I n fact, this became the procedure of choice for the laboratory diagnosis of smallpox before and even after the general use of tissue culture for viral isolation. Immunofluorescence (IF) was also recognized early as a potentially valuable tool for detection of viral antigen^,''.^.^ but its use as a procedure that could supplement and, at times, replace tissue culture in diagnostic laboratories has been only gradually gaining acceptance. IF has, of course, been used at several stages in the diagnosis of viral diseases: the measurement of antibody, particularly when there is some highly specific antigen in question, as with Epstein-Barr virus or cytomegalovirus; the identification of viruses in tissue culture; and the direct detection of viruses in body fluids. doi = 10.1111/j.1749-6632.1983.tb22226.x id = cord-339386-sxyeuiw1 author = McIntosh, Kenneth title = 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date = 2015-12-31 keywords = MERS; OC43; SARS; human; respiratory; virus summary = The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. doi = 10.1016/b978-1-4557-4801-3.00157-0 id = cord-252048-ftbjsoup author = McKinley, Enid T. title = Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date = 2011-04-22 keywords = Conn; IBV; Mass; virus summary = The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. doi = 10.1016/j.virusres.2011.04.006 id = cord-017764-h1w9gbxk author = Meanwell, Nicholas A. title = The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date = 2018-06-08 keywords = Daclatasvir; HCV; NS5A; RNA; virus summary = A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. The discovery of the hepatitis C virus (HCV) nonstructural 5A (NS5A) replication complex inhibitor daclatasvir (1) began with the development of a genotype 1b (GT-1b) replicon that was implemented as a phenotypic screen using a design that conferred a stringent triaging of hit molecules [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] . A screen of compounds selected from the library of HCV NS5A inhibitors assessed in the presence of 1 using the Tyr93Asn GT-1aresistant replicon, followed by SAR optimization, identified Syn-395 (52) as a molecule capable of restoring the sensitivity of resistant virus to the inhibitory effects of 1. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect doi = 10.1007/7355_2018_47 id = cord-280429-4fota9rl author = Medvedev, Kirill E. title = Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold date = 2018-06-13 keywords = ECOD; Fig; Rossmann; dna; protein; virus summary = 10 However, structural analyses of virion architecture and coat protein topology have revealed unexpected similarities, not visible in sequence comparisons, suggesting a common origin for viruses that infect hosts residing in different domains of life. In this current work, we provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold that can be found in the Evolutionary Classification of protein Domains (ECOD) database developed in our lab. The structures represented gene products from 21 viral taxonomical families with host ranges from all kingdoms of life (http://prodata.swmed.edu/rossmann_fold/viruses/). Our analysis detected 14 different bacterial virus structure topology types defined by ECOD T-groups that contain a Rossmann-like fold (Fig. 2, 12 topology groups shown). Like the bacterial and eukaryotic branches in the tree of life, the Archea are host to a multitude of Functional and Evolutionary Analysis of Viral Proteins viruses. 61 Among viral protein structures containing the minimal Rossmann fold, 14 protein families are known helicases (http://prodata.swmed.edu/ross-mann_fold/viruses/). doi = 10.1002/pro.3438 id = cord-023721-e0zp2gux author = Meissner, H. Cody title = Bronchiolitis date = 2013-02-10 keywords = RSV; bronchiolitis; infant; respiratory; virus summary = Bronchiolitis may be defined as an episode of obstructive lower airway disease precipitated by a viral infection in infants younger than 24 months of age. Monthly administration of monoclonal antiF anti body (palivizumab) throughout the RSV season reduces the inci dence of hospitalization due to RSV infection in infants with bronchopulmonary dysplasia, congenital heart disease, and pre maturity by about 50% (see Chapter 225, Respiratory Syncytial Virus). Early trials indicated that ribavirin therapy was associated with modest improvement in clinical scores, oxygenation, and duration of mechanical ventilation for infants with severe bron chiolitis due to RSV infection. Duration of hospitalization in previously well infants with respiratory syncytial virus infection Ribavirin aerosol treatment of bronchiolitis associated with respiratory syncytial virus infection in infants Intravenous immunoglobulin treatment of respiratory syncytial virus infections in infants and young children Respiratory syncytial virus immune globulin treatment of RSV lower respiratory tract infection in previously healthy children doi = 10.1016/b978-1-4377-2702-9.00033-7 id = cord-252769-fe50u028 author = Mendes, J. Pinto title = Infecção na modulaçâo da asma 1 1 Trabalho apresentado no XXIII Congresso de Pneumologia da SPP – Guarda, Novembro 2007 / Paper presented at the XXIII Congresso de Pneumologia da SPP / PSP Pulmonology Congress, Guarda, November 2007 date = 2008-10-31 keywords = CD14; Mendes; Pinto; RSV; asma; asthma; que; virus summary = Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. This phenomenon has been put to the test in inhalatory challenge tests which could bring on asthma episodes or exacerbations in children and adults 82, 102 , but, to test this seeming paradox, it is not necessary to resort to these arguments as in a German study 82 , the degree of early life exposure to domestic endotoxins was in direct correla-Infecção na modulaçâo da asma J Pinto Mendes fende um efeito daquelas células na supressão simultânea das respostas Th 1 e Th 2 . doi = 10.1016/s0873-2159(15)30275-0 id = cord-355489-tkvfneje author = Mendez, Jairo A title = Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date = 2010-09-14 keywords = Colombia; DENV-1; PCR; dengue; virus summary = Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Due to the importance of DENV in public health, the particular goals of this research were to reconstruct the phylogenetic history of DENV-1 and to date the phylogenetic tree using isolation time as calibration points to establish date of introduction of virus and rate evolution patterns of virus in Colombia. Previously reported genotypes were represented in the tree and placed most of the Colombian isolates nesting in the genotype V clade (America, Africa) and were closely related to Argentina, Brazil and Paraguay virus strains. doi = 10.1186/1743-422x-7-226 id = cord-102908-sr7j8z9c author = Mersmann, Sophia F. title = Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date = 2020-07-24 keywords = antibody; figure; particle; virus summary = We used differential binary labelling and statistical modelling to extract estimates of stoichiometry, our strategy is outlined in Figure 1 ; note that this approach can be generalised to apply to many other multi-component systems (i.e. how many protein x are found in assembly y?). As described above, our experimental design utilizes antibody labelled with spectrally distinct dyes allowing binary scoring of individual virus particles as positive if they interact with at least one Ab B molecule ( Figure 1 ). We have demonstrated quantitative analysis of 9C12 interaction with individual Adv particles ( Figure 3) ; we have confirmed that differential labelling of antibody does not bias binding ( Figure 4A & B) ; and that we could detect single molecules of 9C12 Biotin allowing discrimination of positive and negative AdV-9C12 complexes ( Figure 4C & D). However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. doi = 10.1101/2020.07.23.217745 id = cord-000777-7cty5s6o author = Merten, O.-W. title = Virus contaminations of cell cultures – A biotechnological view date = 2002-01-01 keywords = BVDV; CHO; CRL; animal; cell; contamination; line; virus summary = These may include the use of production media devoid of animal derived substances, validation of viral clearance in downstream processing or analytics for detecting adventitious viruses in cell culture and final biological product. However, the best means to increase the biological safety of the produced viral vaccines is the use of diploid or continuous cell lines, because it can be determined that such cells are free of animal derived viruses: This can be achieved by establishing master (seed stock) and working (distribution and user stocks) cell banks which have been rigorously tested and validated for the absence of microbial as well as viral contaminants (see chapter by Freshney and the section on ''Testing-virus screening in cell banks'' of this article). As animal derived substances such as serum can be contaminated by adventitious viruses, γ irradition is, after routine quality control for virus detection, the best method to increase the safety of using serum in the production of animal cell culture derived biologicals. doi = 10.1023/a:1022969101804 id = cord-001958-2gt3fwpy author = Meseda, Clement A. title = Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date = 2016-02-19 keywords = Ankara; MVA; mouse; virus summary = Our data suggest that MVA administered by percutaneous inoculation, elicited vaccinia-specific antibody responses, and protected mice from lethal vaccinia virus challenge, at levels comparable to or better than subcutaneous or intramuscular inoculation. In the work described here, we demonstrate in mouse models that percutaneous inoculation of MVA elicited protective immune responses against lethal intranasal challenge with the Western Reserve (WR) strain of vaccinia virus, and at low doses of MVA, lower morbidity was recorded in mice that were vaccinated via the percutaneous route than in those immunized via the intramuscular or subcutaneous routes. In a preliminary experiment to investigate the utility of the percutaneous route for the delivery of MVA, we observed that MVA delivered by tail scarification, while statistically insignificant (p = 0.298), elicited a higher vaccinia-specific IgG response and protection in mice than the same dose (10 6 pfu) delivered by the intramuscular route (S1 Fig) . doi = 10.1371/journal.pone.0149364 id = cord-353297-jizitnfl author = Meyer, R.F. title = Viruses and Bioterrorism date = 2008-07-30 keywords = agent; dna; viral; virus summary = The requirements for an ideal biological warfare agent include availability, ease of production, stability after production, a susceptible population, absence of specific treatment, ability to incapacitate or kill the host, appropriate particle size in aerosol so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims, ability to be disseminated via food or water, and the availability of a vaccine to protect certain groups. Instead, the ectromelia virus vector expressing IL-4 altered the host''s immune response to this virus resulting in lethal infections in normally genetically Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs resistant mice (e.g., C57BL/6). doi = 10.1016/b978-012374410-4.00549-5 id = cord-311012-wyglrpqh author = Meyers, Craig title = Ethanol and Isopropanol Inactivation of Human Coronavirus on Hard Surfaces date = 2020-09-28 keywords = IPA; SARS; virus summary = AIM: There are few data showing the efficacy of multiple concentrations of EtOH, IPA, and SH on a human coronavirus (HCoV) dried on surfaces using short contact times. FINDINGS: Concentrations of EtOH and IPA from 62% to 80% were very efficient at inactivating high numbers of HCoV dried on tile surfaces even with a 15 sec contact time. CONCLUSIONS: EtOH, IPA, and SH at multiple concentrations efficiently inactivated infectious virus on hard surfaces, typical of those found in public places. Interestingly, at the highest concentrations tested, 95% EtOH and 95% IPA, we observed significant reductions in inactivating, with some contact times producing less than a 2 log 10 reduction of infectious virus. Our studies demonstrate that EtOH and IPA at concentrations ranging from 62% to 80% are highly effective at inactivating HCoV on tile surfaces even with contact times as low as 15 sec. doi = 10.1016/j.jhin.2020.09.026 id = cord-102704-wfuzk2dp author = Meza, Diana K. title = Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date = 2020-04-30 keywords = Rabies; antibody; test; virus summary = Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 doi = 10.1101/2020.04.24.060095 id = cord-290556-x7t7zqjd author = Middleton, Peter J title = Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis date = 1996-08-31 keywords = Norwalk; virus summary = Objective: To nominate the various viral agents that cause enteritis, discuss the pathogenesis, clinical features, epidemiology and diagnostic procedures employed. Results: The viruses causing gastroenteritis include: Rotaviruses; Adenoviruses-especially Ad 31, Ad 40 and Ad 41; members of the Caliciviridae, e.g. Norwalk virus, Hawaii virus, Snow Mountain virus, Taunton virus, Southampton virus, Toronto virus (formerly mini-reovirus) and others; Astrovirus; Coronavirus; Torovirus; Cytomegalovirus (CMV) and possibly Picobirnavirus. Rotavirus eventually became established as the leading worldwide cause of serious viral enteritis in infants and young children. Antigens or virions that form the basis of these serological tests may be obtained by purification procedures on infected stools; by cell culture cultivation, e.g. adenovirus, rotavirus and, in the case of Norwalk virus (NV), by self-assembled recombinant NV (rNV) particles expressed in a baculovirus system (Jiang et al., 1990 (Jiang et al., , 1993 . Enteric viruses and diarrhea in HIV-infected patients doi = 10.1016/0928-0197(96)00231-0 id = cord-319761-bu5pzbnv author = Miller, Craig S. title = Pleiotropic mechanisms of virus survival and persistence date = 2005-07-16 keywords = IFN; MHC; cell; viral; virus summary = Accordingly, this review focuses on specific viral cell interactions that allow the virus to survive the cellular attack and evade the immune system, establish persistent infections, and cause chronic disease. 13, 14 Viruses regulate apoptosis by several mechanisms including the targeting of the tumor suppressor gene product p53, the Fas death receptor, and by producing caspase inhibitors and viral Bcl-2 homologs. 24, 25 The alpha herpesvirus HSV-1 encodes several antiapoptotic gene products (ie, ICP4, ICP27, c34.5, U s 3, gJ) [26] [27] [28] [29] [30] that modulate apoptosis at several levels, including antagonism of double-stranded RNA-activated protein kinase (PKR), a downstream induction molecule of the interferon signaling pathway 31, 32 Of note, all c-herpesviruses express viral homologues of cellular antiapoptotic genes, including 1 or 2 Bcl-2 homologues. In the majority of infections, viruses encode products that antagonize either the IFN signal transduction pathway or cellular proteins induced by IFN that are responsible for inhibiting virus replication (Fig 2) . doi = 10.1016/j.tripleo.2005.03.017 id = cord-022252-9yiuuye3 author = Mims, Cedric A. title = Mechanisms of Cell and Tissue Damage date = 2013-11-17 keywords = Fig; LPS; antigen; cause; cell; damage; disease; infection; response; toxin; virus summary = A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. doi = 10.1016/b978-0-12-498262-8.50015-1 id = cord-002482-2t09zqqi author = Miras, Manuel title = Non-canonical Translation in Plant RNA Viruses date = 2017-04-06 keywords = -utr; IRES; RNA; translation; virus summary = Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. In this review, we describe current knowledge on the mechanisms used by positive-sense single-stranded (+ss) RNA plant viruses to initiate translation, focusing on cis-acting sequences present in viral mRNAs. We also describe other protein translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. doi = 10.3389/fpls.2017.00494 id = cord-264406-s5c0grz0 author = Miró-Cañís, Sílvia title = Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis date = 2016-11-13 keywords = cystic; virus summary = Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. This study aimed to evaluate the frequency viruses and bacteria in respiratory specimens and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses in children with cystic fibrosis. doi = 10.1016/j.jcv.2016.11.004 id = cord-302055-s155i4e9 author = Mitchell, Edith P. title = Corona Virus: Global Pandemic Causing World-Wide Shutdown date = 2020-04-03 keywords = virus summary = Human coronaviruses constitute a large family of viruses that usually cause mild to moderate upper respiratory illnesses in people such as the common cold. 1 Initial characterization of the coronavirus occurred in the 1960''s when Tyrell and Bynoe described passage of a virus named B814 at the time, as a group of viruses causing a large proportion of respiratory tract infections in humans. Strategies to prevent infection with the new coronavirus from World Health Organization (WHO) and the Center for Disease Control (CDC) recommend following these precautions for avoiding COVID-19: The Publisher of Journal of the National Medical Association, Elsevier, has compiled an extensive list of publications that may also be useful to physicians and other clinicians and can be found at: Elsevier''s Novel Coronavirus Information Center. A previously undescribed coronavirus associated with respiratory disease in humans doi = 10.1016/j.jnma.2020.03.015 id = cord-018437-yjvwa1ot author = Mitchell, Michael title = Taxonomy date = 2013-08-26 keywords = RNA; dna; genome; human; protein; virus summary = Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . doi = 10.1007/978-3-642-40605-8_3 id = cord-329429-ur8g68vp author = Miłek, Justyna title = Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date = 2018-12-10 keywords = IBV; RNA; bird; virus summary = Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . doi = 10.2478/jvetres-2018-0035 id = cord-001397-nrq4ncdf author = Mlera, Luwanika title = The role of viral persistence in flavivirus biology date = 2014-05-12 keywords = IFN; JEV; Nile; RNA; WNV; West; infection; virus summary = doi = 10.1111/2049-632x.12178 id = cord-018058-n3majqes author = Modrow, Susanne title = Historical Overview date = 2013-08-12 keywords = Sect; disease; infection; viral; virus summary = Many of the steps that characterize a viral infection were first discovered in experiments with bacterial viruses: such processes include attachment and penetration, the reproduction-cycledependent regulation of gene expression that results in early and late synthesized proteins, and lysogeny, which is associated with the existence of prophages. Besides the importance for tumour virus research, these observations aroused interest in the question concerning the basis of the high susceptibility of newborn animals to viral infections, and suggested investigations on the innate resistance of an organism to infections as well as the time and the causes of its formation. Between 1918 and 1920, a pandemic emerging viral disease, Spanish flu, claimed more than 20 million lives, i.e., more than in the First World War. After cultivation of the virus responsible in embryonated chicken eggs in 1933, their haemagglutinating properties were discovered in 1941 (i.e., their ability to agglutinate red blood cells), thereby laying the basis for the development of haemagglutination tests to detect viruses. doi = 10.1007/978-3-642-20718-1_1 id = cord-018165-afzjx2ci author = Modrow, Susanne title = Vaccines date = 2013-08-12 keywords = Sect; vaccine; virus summary = Live vaccines contain attenuated, replication-competent pathogens that can replicate in the vaccinated person, i.e. they are able to infect certain cells and initiate the synthesis of viral proteins and particles, but without triggering the respective clinical picture. Therefore, the immune response that is triggered by attenuated viruses is suitable to induce a long-lasting, effective protection against infections with the respective pathogen. Similarly, vaccinia viruses that were originally used to produce a protective immune response against smallpox virus induced local infections in humans, which in very rare cases had a generalized or fatal course. It is being attempted to modify well-explored, less pathogenic viruses (e.g. adenoviruses) and vaccine viruses that were used successfully in the past (usually vaccinia viruses) by using genetic engineering methods in such a way that they encode proteins of other viral species, in addition to their own gene products necessary for infection and replication (▶ Sects. doi = 10.1007/978-3-642-20718-1_10 id = cord-018477-hgvqd1ej author = Modrow, Susanne title = Pathogenesis date = 2013-08-12 keywords = Sect; virus summary = These cells are loaded with the virus particles and proteins and migrate to the immunologically active centres of the nearest lymph nodes, encountering there other immune cells such as CD4 + and CD8 + T lymphocytes, B lymphocytes and macrophages, which start to proliferate by contact with the pathogen proteins or with MHC-peptide complexes and by the influence of cytokines secreted by activated immune cells (▶ Chaps. During herpes simplex virus infections of the conjunctiva and the cornea, reactivated pathogens migrate from the ganglia of the nerve fibres into the eye, where they may spread in the epithelium of the cornea and cause inflammations. In pregnant women, haematogenously disseminated viruses such as rubella virus, cytomegalovirus and parvovirus B19 are transported via the bloodstream into the placenta and infect the endothelial cells of this organ. Other viruses, such poliovirus and tick-borne encephalitis virus, overcome the barriers probably by infection of endothelial cells, as occurs by infecting other organs (▶ Sects. doi = 10.1007/978-3-642-20718-1_4 id = cord-291063-de7v4e5s author = Moens, Ugo title = Silencing Viral MicroRNA as a Novel Antiviral Therapy? date = 2009-05-28 keywords = EBV; HIV-1; K12; RNA; viral; virus summary = The expressions of EBV-encoded miRNAs in clinical samples and computational analysis to predict putative targets were applied to unravel the biological functions of EBV miRNAs. These approaches showed that the miR-BARTs are abundantly expressed in latently infected epithelial cells, nasopharyngeal carcinomas, EBV-associated gastric carcinoma cell lines and tissues, Burkitt''s lymphomas latency type I, EBV positive primary effusion lymphomas, and diffuse large B-cell lymphomas, but at a significantly lower level in B cells. However, computational alignment of the potential HIV-1 miRNAs with specific human T-cell mRNAs identified potential cellular targets including genes encoding CD4, CD28 and interleukin-2, IL-3, and IL-12 [119] . The idea of targeting viral transcripts is not new, and RNA interference has been demonstrated to efficiently mediate inhibition of replication of human pathogenic viruses such as HIV-1, HCV, dengue virus, severe acute respiratory syndrome (SARS) coronavirus, poliovirus, human rhinovirus, influenza A virus, hepatitis D virus, HBV, HSV-1, HPV, JCV, EBV, and CMV in cell culture (reviewed in [12] ). doi = 10.1155/2009/419539 id = cord-327199-ggomuomb author = Moerdyk-Schauwecker, Megan title = Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date = 2014-08-08 keywords = RNP; VSV; protein; virion; virus summary = In another example, the presence of host complement control proteins such as CD46, CD55 and CD59 in the viral envelope has been shown to protect against antibody dependent complement mediated virus lysis in several viruses including human T cell leukemia/ lymphoma virus type I [16] , human cytomegalovirus [16] , hepatitis C virus [17] , HIV-1 [18, 19] , extracellular enveloped vaccinia virus [20] , simian virus 5 [21] and mumps virus [21] . As discussed in the previous section, proteins not associated with the interior of the virion, including proteins embedded in the host derived viral envelope, can be identified by their absence in ProK treated samples or by a size shift upon ProK treatment. While many of the proteins identified in VSV virions appear to be associated with viral assembly, budding or the host-derived viral envelope, they may also have additional functions that affect virus replication. doi = 10.1371/journal.pone.0104688 id = cord-285330-td4vr0zv author = Mohammadi, Ali title = Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date = 2015-11-12 keywords = IBV; RNA; virus summary = title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens doi = 10.1007/s13337-015-0286-4 id = cord-313312-h607itv2 author = Mok, Darren Z. L. title = The Effects of Pre-Existing Antibodies on Live-Attenuated Viral Vaccines date = 2020-05-08 keywords = LAV; antibody; existing; virus summary = Pre-existing antibodies, derived from either from maternal–fetal transmission, or by previous infection or vaccination, have been demonstrated to interfere with vaccine immunogenicity of measles, adenovirus, and influenza LAVs. Immune interference of LAVs can be caused by the formation of virus–antibody complexes that neutralize virus infection in antigen-presenting cells, or by the cross-linking of the B-cell receptor with the inhibitory receptor, FcγRIIB. The clinical trial finding that subjects with a limited range of cross-reactive antibodies from a prior Japanese Encephalitis vaccine were able to enhance yellow fever vaccination, by prolonging vaccine viremia duration that leads to higher antibody titers, thus hints at the possibility that whether pre-existing antibodies inhibit or augment flavivirus infection will depend on both antibody titers and the type/specificity of antibodies produced [85] . By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. By contrast, at sub-neutralizing titers, pre-existing antibodies can enable viruses to better infect cells and increase innate immune responses that augment LAV immunogenicity. doi = 10.3390/v12050520 id = cord-340503-zwdewiu1 author = Mokhtarzadeh, Ahad title = Nanomaterial-based biosensors for detection of pathogenic virus date = 2017-10-13 keywords = HBV; biosensor; detection; dna; virus summary = Electron microscopy Viral particle Hours Broad spectrum; rapid method Necessity for presence of around 10 6 virus particles/mL for detection; similarity of morphologies [11] Hemagglutination assay Viral protein Hours Easy; inexpensive Poor sensitivity; necessity for fresh reagents [12] ELISA Viral protein Hours Only one incubation step; no hook effect at high analyte concentrations Limited concentration range in which the analyte can be quantified without sample dilution; and that the antigen or antibody produce the same response and not distinguishable in a one step [13] PCR Viral nucleic acid Hours Extremely high sensitivity; Easy to set up Extremely liable to contamination; Not easy to quantitate results; High degree of operator skill required [14] As an example for HIV, a type of virus that gradually attacks the immune system and makes it harder to fight off infections and diseases in infected body, a QDs-based rapid capture and imaging system was developed by Kim et al. doi = 10.1016/j.trac.2017.10.005 id = cord-325750-x7jpsnxg author = Mokili, John L title = Metagenomics and future perspectives in virus discovery date = 2012-01-20 keywords = Koch; dna; figure; metagenomic; sequence; viral; virus summary = In this article, we review virus discovery techniques with a focus on metagenomic approaches that employ high-throughput sequencing technologies to characterize novel viruses. This method lacks sufficient sensitivity to detect viruses when the viral burden is low or when the DNA sequence of the suspected etiological agent is not clearly distinguishable from the control sample [31] . The following items should be included in any report on viral metagenomic studies: firstly, the sequencing platform and its version number; secondly, raw sequence data accession numbers in a public database; thirdly, details about the bioinformatic analysis, including the homology search tool and the database being used to assign the taxonomy, and their versions; fourthly, a list of known and previously unknown viruses found, clearly showing if the ''novel'' viruses are new strains of a previously described species or completely different viruses; and fifthly, causality evidence if any. doi = 10.1016/j.coviro.2011.12.004 id = cord-260496-s2ba7uy3 author = Moncany, Maurice L.J. title = Identification of conserved lentiviral sequences as landmarks of genomic flexibility date = 2006-08-08 keywords = CLS; HIV-1; gene; virus summary = Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). Immunodeficiency lentiviral genomes correspond to 171 human viruses (155 HIV-1s and 16 HIV-2s), 33 simian viruses (3 CPZ, 9 AGM, 8 Macaque, 2 Mandrill, 10 Sooty Mangabey, 1 Sykes'' monkey viruses) and 33 non-primate mammal viruses (2 bovine, 2 caprine, 11 equine, 9 feline, 3 ovine and 6 ovine/caprine viruses). From the particular organization of the HIV-1 and HIV-2 ( Fig. 1) , AGM and macaque (Fig. 2) , CPZ, feline, equine and D-particle-forming viruses (Fig. 3) and that of sooty mangabey, mandrill and other non-primate lentiviruses (supplementary data), it appears that a given CLS occupied on the viral genome a specific position that was roughly conserved in the different viral families. doi = 10.1016/j.crvi.2006.07.001 id = cord-275795-ee7qyw5h author = Monette, Anne title = T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date = 2018-10-24 keywords = CD4; CD8; CNS; HBV; IFN; RNA; RSV; VZV; cell; infection; virus summary = We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. doi = 10.1016/bs.ircmb.2018.07.006 id = cord-214795-8jweuq50 author = Mongia, Aanchal title = DeepVir -- Graphical Deep Matrix Factorization for"In Silico"Antiviral Repositioning: Application to COVID-19 date = 2020-09-22 keywords = drug; matrix; virus summary = Results on our curated RNA drug virus association (DVA) dataset shows that the proposed approach excels over state-of-the-art graph regularized matrix completion techniques. It shows how the matrix completion framework can be used to computationally predict the drugs that could be effective against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus responsible for the ongoing pandemic, COVID-19 (COrona VIrus Disease-2019). In this present work, we propose to solve the problem of drug-virus association prediction via graph regularized deep matrix factorization. Among all the methodologies compared in [52] , graph regularized matrix factorization based technique (GRMF) provided the best results for the validation setting where drugs are predicted for novel viruses. In our proposed technique, multi-graph regularization is incorporated in the deep matrix factorization formulation with the aim to incorporate the metadata associated with the drugs and viruses in the form of similarity information as shown below: doi = nan id = cord-232446-vvb2ffhv author = Mongia, Aanchal title = A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials date = 2020-07-03 keywords = SARS; covid-19; drug; matrix; virus summary = In view to assist acceleration of this process (by pruning down the search space), we create and share a publicly available DVA database, along with a number of matrix completion techniques (mentioned above) for drug-virus association prediction. Such a computational approach requires the chemical structure of the drugs and, in case of graph-regularized matrix completion techniques, the genome of the viruses, or existing associations otherwise. A clear observation from the experiments is that the graph regularized-based matrix completion algorithms that incorporate the similarity information associated with the drugs and viruses, perform fairly well giving an AUC greater or equal than 0.83 in CV1. It can be noted that the standard matrix completion methods, which do not take into account the metadata, fail to learn from the association data giving a near-random performance as far as the prediction on novel viruses is concerned, depicting how very important the similarity information is. doi = nan id = cord-003492-rodqdtfj author = Montaner-Tarbes, Sergio title = Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV) date = 2019-02-20 keywords = IFN; PRRSV; porcine; reproductive; respiratory; virus summary = PRRSV is a complex disease and several gaps in the knowledge of its economic impact, biology and evolution, genetic polymorphism, mechanism of viral infections, elicitation of protective immune responses and novel control strategies, have been reviewed here (Box 1). Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses Immune responses in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV) Immunodominant epitopes in nsp2 of porcine reproductive and respiratory syndrome virus are dispensable for replication, but play an important role in modulation of the host immune response Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells Immune response to ORF5a protein immunization is not protective against porcine reproductive and respiratory syndrome virus infection doi = 10.3389/fvets.2019.00038 id = cord-320030-ojtp90na author = Montero, Antonio title = Fiebre chikungunya - Una nueva amenaza global date = 2015-08-07 keywords = chikungunya; virus summary = Resumen Las epidemias causadas, entre otros, por los virus Ébola, Marburgo, Nipah, Lassa, coronavirus, virus del Nilo Occidental, virus de Saint Louis, virus de la inmunodeficiencia humana, dengue, fiebre amarilla y fiebre hemorrágica venezolana han puesto sobre el tapete el riesgo que estos agentes representan para la salud pública global. El riesgo de epidemias y endemicidad en las Amé ricas parece muy elevado debido a la existencia de una població n sensible a la enfermedad, la ubicuidad de los mosquitos vectores y la introducció n cada vez má s frecuente de casos importados. Debido a la amplia distribució n de los Aedes en las Amé ricas, toda la regió n es susceptible a la invasió n y la diseminació n de este virus, y la aparició n reciente de epidemias urbanas de dengue en Sudamé rica destaca el peligro potencial de fiebre chikungunya. doi = 10.1016/j.medcli.2014.05.031 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-007149-m4xsx9ev author = Morahan, Pages S title = VIRUSES AND THE VERSATILE MACROPHAGE date = 1985-01-17 keywords = cell; virus summary = 5S~63 Enhanced infection requires monocytes, peritoneal MuJ>or M(J>-like cell lines with Fc receptors, and non-cytophilic IgG antibody that exhibits virus serotype or cross-reactive specificity. Monocytes or M4> infected with CMV, influenza, Sendai or poliovirus have been shown to be suppressive Functions of mononuclear phagocytes that may be affected by virus infection Chemotaxis Attachment and phagocytosis of particles through nonspecific, Fc or complement receptors Intracallular oxidatrve response Lysosome-phegosome fusion Intracellular microbicidaJ activity Synthesis and/or secretion of txologicalry active molecules, e.g. prostaglandini, neutral proteases, interferon and complement Antigen presentation Regulation of immune responses, i e accessory and suppressor activity M$ activation procees for microbicidai and tumoncidal activity Antibody dependent cytotoxicrty (ADCC) by M$ Wound healing ONA synthesis and M$ proliferation in response to macrophage growth factor Mi) differentiation for certain lymphocyte responses. Antibody-mediated enhancement of dengue virus infection in mouse macrophage cell lines, Mkl and Mini (41802) doi = 10.1093/oxfordjournals.bmb.a072017 id = cord-325925-010xj69x author = Mordecai, Gideon J title = Endangered wild salmon infected by newly discovered viruses date = 2019-09-03 keywords = Chinook; Pacific; RNA; salmon; virus summary = Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations. High-throughput RT-PCR screening of >6000 wild juvenile Chinook and sockeye salmon showed dissimilar geographical distributions of infected fish, reflecting differences in epidemiological patterns of transmission and infection dynamics for each of the viruses ( Figure 2) . doi = 10.7554/elife.47615 id = cord-002921-i5jxn1vj author = Morens, David M title = Pandemic Zika: A Formidable Challenge to Medicine and Public Health date = 2017-12-15 keywords = Zika; virus summary = Because of the pandemic''s uniqueness and the insidious ability of Zika virus to harm unborn children, the pandemic has captured the attention of infectious disease researchers and practitioners of clinical and public health medicine around the world, as well as the attention of allied colleagues working in entomology, vector control, informatics, teratology, immunology, and a host of other disciplines [3] [4] [5] . Furthermore, some studies have suggested that preexisting flavivirus immunity (eg, from prior dengue virus infection) might potentiate Zika [16] via antibody-dependent infection enhancement in some circumstances [17] , while other research has countered this view [18] . As with most flaviviruses, small-animal models of Zika virus infection and disease have been problematic, but considerable progress has nonetheless been made, including important new information bearing on teratogenicity and vaccine design strategy [20] . Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes doi = 10.1093/infdis/jix383 id = cord-316063-9bg2dm8e author = Morgan, Marcus title = Why meaning-making matters: the case of the UK Government’s COVID-19 response date = 2020-10-15 keywords = COVID-19; Cummings; Guardian; Johnson; March; NHS; PPE; SAGE; Turner; british; government; public; virus summary = The paper also offers more specific contributions to cultural sociology by showing why social performance theory needs to consider the effects of casting non-human actors in social dramas, how metaphor forms a powerful tool of political action through simplifying and shaping complex realities, and how casting can shift responsibility and redefine the meaning of emotionally charged events such as human death. On 28th February, the first death of a British national occurred on the quarantined Diamond Princess cruise ship, and the Sunday Times reported that around the same time Dominic Cummings (Johnson''s Chief Advisor, and former director of the successful Vote Leave campaign) had ''outlined the government''s strategy'' for the UK''s national response to the virus ''at a private engagement'', quoting those present as claiming that it was ''herd immunity, protect the economy, and if that means some pensioners die, too bad'' (Shipman and Wheeler 2020) . doi = 10.1057/s41290-020-00121-y id = cord-295873-kykyubdq author = Morikawa, Saeko title = Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date = 2015-10-22 keywords = infection; virus summary = authors: Morikawa, Saeko; Kohdera, Urara; Hosaka, Taisuke; Ishii, Kousuke; Akagawa, Shohei; Hiroi, Satoshi; Kase, Tetsuo STUDY DESIGN: Nasal aspirate samples were obtained from outpatients and inpatients of a children''s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. PCR makes it possible to detect uncultivable viruses such as human bocavirus and rhinovirus C and discover concurrent viral infections. Though there was no significant difference in the number of hospitalization days of patients with single infections by rhinoviruses or other respiratory viruses, our data suggested the importance of rhinoviruses as a potential cause of pediatric pneumonia. doi = 10.1016/j.jcv.2015.10.001 id = cord-017158-w2tlq6ho author = Moriones, Enrique title = Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development date = 2007 keywords = Spain; TYLCV; virus summary = The potential of begomoviruses to generate genetic diversity through recombination can be relevant for their ecological fitness, because greater sequence heterogeneity provides a reservoir of virus variants in the population that enables rapid adaptation to changing environmental conditions. Thus, begomoviruses like those in the Tomato yellow leaf curl virus (TYLCV) complex exploit gene flow provided by recombination as a mechanism to increase their evolutionary potential and local adaptation. Also, when region I was analyzed, phylogenetic analyses revealed that all TYLCV isolates grouped in a single clade related to Tomato yellow leaf curl Sardinia virus (TYLCSV), another species of the TYLCV complex causing the TYLCD. Tomato yellow leaf curl Sardinia virus (TYLCSV) is another monopartite begomovirus species of the TYLCV complex that comprises isolates infecting tomato in the Mediterranean Basin, both in southern Europe and northern Africa (Noris et al., 1994; . doi = 10.1007/978-1-4020-4769-5_7 id = cord-021069-v9f9874x author = Morrison, Lynda A. title = Viral pathogenesis and central nervous system infection date = 2004-11-23 keywords = CNS; infection; virus summary = Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Genetic determinants of disease susceptibility have been found for infection of mice with strains of most neurotropic viruses, in at least one case of coronavirus reflecting lack of a gene encoding a virus receptor protein . doi = 10.1016/1044-5765(91)90002-6 id = cord-341298-mqpovrms author = Morse, S.A. title = Viruses and Bioterrorism date = 2016-10-31 keywords = FMD; HIV; virus summary = Requirements for an ideal biological warfare agent may include: availability; ease of production; stability after production; a susceptible population (human or animal); absence of specific treatment; ability to incapacitate or kill the host; appropriate particle size in aerosols so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims; ability to be disseminated via food or water; and, the availability of a vaccine to protect certain groups. Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs incapacitating (eg, VEE) or lethal infections (EEE case fatality rates range from 50 to 75%) (Sidwell and Smee, 2003) . An Australian research group (Jackson et al., 2001) was investigating virally vectored immunocontraceptive vaccines based on ectromelia virus, the causative agent of the disease termed mousepox. doi = 10.1016/b978-0-12-809633-8.11007-6 id = cord-308686-tbwecf7o author = Mortamet, G. title = Étude prospective de l’écologie virale hivernale dans un service de réanimation pédiatrique date = 2015-04-30 keywords = PICU; virus summary = Résumé Le but de cette étude prospective était d''évaluer l''épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatriques pendant 3 mois d''hiver, en 2012–2013. Ont été inclus tous les enfants admis en réanimation pédiatrique du centre hospitalier universitaire (CHU) de Caen et ayant bénéficié d''une recherche d''infection par un virus respiratoire à partir d''un prélèvement nasal analysé par amplification génique (PCR) multiplex. Cette étude révèle cependant un taux élevé d''infections respiratoires causées par des virus chez les enfants qui ne présentent pas de symptômes respiratoires à leur admission en unité de réanimation et soins continus. Le but de cette étude prospective était d''évaluer l''épidémiologie des virus respiratoires chez les enfants hospitalisés dans une unité de réanimation et de soins continus pédiatrique pendant 3 mois d''hiver. doi = 10.1016/j.arcped.2014.10.025 id = cord-260705-huyyw5z6 author = Moshe, Adi title = Virus-Induced Aggregates in Infected Cells date = 2012-10-17 keywords = PML; RNA; dna; virus summary = During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense. doi = 10.3390/v4102218 id = cord-263619-p17oomzn author = Moss, William J. title = Measles date = 2009-01-30 keywords = child; measle; vaccine; virus summary = Although providing passive immunity to young infants, maternally acquired antibodies can interfere with the immune responses to the attenuated measles vaccine by inhibiting replication of vaccine virus. Women with vaccine-induced immunity tend to have lower antimeasles virus antibody titers than women with naturally acquired immunity, and their children may be susceptible to measles at an earlier age. The cumulative distribution can reach 50% by 1 year of age, with a significant proportion of children acquiring measles virus infection before 9 months, the age of routine vaccination. Infants and younger children, although susceptible if not protected by immunization, are not exposed to measles virus at a rate sufficient to cause a large disease burden in this age group. The only documented case of disease induced by vaccine virus in an HIV-infected person was in a 20-year-old man who died 15 months after receiving his second dose of measles vaccine ( Angel et al., 1998 ) . doi = 10.1016/b978-0-12-369408-9.00030-5 id = cord-004751-4vl0cvyq author = Mostow, S. R. title = The behaviour in vitro of attenuated recombinant influenza viruses date = 1973 keywords = strain; virus summary = Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Attenuated influenza viruses have been produced recently by genetic recombination of avirulent laboratory-adapted strains and virulent parents (BEARE and HALL, 1971; McCAHo~ and SCHILD, 1972) . This method, which is the most rapid means of producing attenuated influenza strains to date, results in a spectrum of both attenuated and virulent clones as judged by their effects in human volunteers. The use of L-15 medium and rolling the screw-topped tubes prolonged the survival of the ciliated epithelium beyond that obtained using other standard media, and, in the conditions finally used, the human embryo trachea regularly survived for periods of 30--50 and occasionally 90 days. The recombinant viruses did not cause ciliary damage, but at 5 days the growth in ferret epithelium was similar to that in human tissue. doi = 10.1007/bf01556156 id = cord-018089-m94q75xn author = Mubareka, Samira title = Influenza Virus: The Biology of a Changing Virus date = 2010-06-18 keywords = H1N1; H5N1; influenza; virus summary = The genetic diversity of influenza A viruses and their capability to successfully infect an array of hosts, including avian and mammalian species, are highlighted in a discussion about host range and evolution. In contrast, avian hosts including waterfowl and domestic poultry harbor sialic acid with a2,3 linkage (SAa2,3Gal) which is distributed in the gastrointestinal tract, reflecting the fecal-oral mode of transmission of avian influenza strains in these species [23] . Specifically, changes at amino acid position 225 impart the ability of A/New York/1/18 to bind both avian and human host influenza virus receptors [26] . Since 1997, several avian influenza viruses, including H5N1, H7N2, H7N3, H7N7, H9N2, and H10N7 subtypes, have infected humans [76], though limited evidence for person to person spread exists [77, 78] . Pathology of fatal human infection associated with avian influenza A H5N1 virus doi = 10.1007/978-3-0346-0279-2_1 id = cord-260420-4s7akmdp author = Mubareka, Samira title = Bioaerosols and Transmission, a Diverse and Growing Community of Practice date = 2019-02-21 keywords = MERS; bioaerosol; pathogen; virus summary = There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate interand intra-species pathogen transmission via bioaerosols. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter-and intra-species pathogen transmission via bioaerosols. A network approach has proven successful in other cross-disciplinary fields, including One Health and eco-health whereby wildlife, computational and evolutionary biologists, microbiologists, virologists, epidemiologists, ecologists, environmental scientists, climatologists, and human, animal, and public health practitioners are collaborating to address challenges in zoonotic diseases research and control (17, 18) . doi = 10.3389/fpubh.2019.00023 id = cord-269324-zh1a3gwh author = Mubareka, Samira title = Human Genes and Influenza date = 2008-01-01 keywords = influenza; virus summary = Specific genes responsible for the host immune response have been invoked as major determinants of the clinical course of HIV-associated disease and hepatitis B and C virus infections [2, 3] . Clinical and animal studies indicate that cytokine dysregulation is associated with acute respiratory distress syndrome and death among hosts infected with avian influenza virus (H5N1) [4 -6] . TLR4 has been implicated in the innate immune response to respiratory syncytial virus (RSV) infection, and polymorphisms in the TLR4 gene have been associated with severe bronchiolitis in RSV-infected infants, although the significance of the Asp299Gly polymorphism appears to be a matter of ongoing debate [9 -12] . All of these genes would be excellent candidates for an analysis to iden-tify determinants of severity of disease after influenza virus infection. Association between common Toll-like receptor 4 mutations and severe respiratory syncytial virus disease Association between mannose-binding lectin gene polymorphisms and susceptibility to severe acute respiratory syndrome coronavirus infection doi = 10.1086/524067 id = cord-315918-12rbbe8c author = Mukherjee, Pulok K. title = Antiviral Evaluation of Herbal Drugs date = 2019-06-21 keywords = HIV; activity; antiviral; cell; drug; plant; virus summary = To test the inhibitory activity of a new antiviral agent, it is first necessary to select the host cell system(s) in which the virus replication can be measured. (d) Assay systems based on the measurement of specialized functions and viral products; a number of viruses do not produce plaques nor do they cause CPE readily, but they may be quantified by certain specialized functions based on their unique properties, for example, hemagglutination and hemadsorption tests used to study the antiviral activity against myxoviruses and ELISA, used to determine the extent of virus replication and, thus, obtain a measure of the inhibitory effect of various antiviral agents on virus replication, etc. On the other hand, the antiviral activity is determined by comparing the virus titers of infected cells, which have been cultured with a maintenance medium containing plant extracts or test substances and a maintenance medium without test material (Colegate and Molyneux, 1993) . doi = 10.1016/b978-0-12-813374-3.00016-8 id = cord-335774-15fhg8o9 author = Mull, Nathaniel title = Ecology of Neglected Rodent-Borne American Orthohantaviruses date = 2020-04-26 keywords = SNV; american; host; orthohantaviruse; virus summary = Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. However, mammals, particularly rodents, are still the most common natural hosts of hantaviruses, encompassing viruses in the largest subfamily (Mammantavirinae) and genus (Orthohantavirus) [9] , and only rodent-borne orthohantaviruses have been linked to human disease [10] . For example, range expansion of a North American grassland rodent species, Baiomys taylori, was recently found in New Mexico, United States, likely due to an increase in grassland areas, particularly along roadsides, due to climate change and habitat disturbance [61] . In the absence of empirical data, we shed light on the diversity, transmission, and risk of spillover for neglected American orthohantaviruses and viral genotypes using the ecology of their hosts and information on ANDV and SNV. Since multiple rodent species are commonly found RT-PCR positive for particular American orthohantavirus strains (Table A1) , virus-host relationships are unclear. doi = 10.3390/pathogens9050325 id = cord-314325-nquov2i0 author = Murphy, F.A. title = Epidemiology of Human and Animal Viral Diseases date = 2008-07-30 keywords = disease; host; population; transmission; virus summary = Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Epidemiology is also effective in (1) clarifying the role of particular viruses and viral variants as the cause of disease, (2) clarifying the interaction of viruses with environmental determinants of disease, (3) determining factors affecting host susceptibility, (4) unraveling modes of transmission, and (5) field testing of vaccines and antiviral drugs. doi = 10.1016/b978-012374410-4.00390-3 id = cord-331217-uup16bhm author = Murphy, Frederick A. title = Adventitious Agents and Smallpox Vaccine in Strategic National Stockpile date = 2005-07-17 keywords = vaccine; virus summary = In keeping with current standards, we urge that old smallpox vaccines that were made in animal skin and are still a key part of our strategic national stockpile be tested for adventitious infectious agents. However, if these old vaccines are to be considered valid parts of our national stockpile we should expect not only continuing testing of potency and sterility but also testing for adventitious agents with methods that reflect the standards of today. We were unable to find a comprehensive list of possible adventitious agents when ovine materials are used, as is the case for the Lister strain smallpox vaccine produced in Europe and old vaccine stocks held by some European countries for biologic defense. Concerns about the possible presence of adventitious agents in old smallpox vaccine stocks are amplified further by current concerns about prions and the zoonotic potential of prion diseases. doi = 10.3201/eid1107.050277 id = cord-329078-gnnis7pl author = Musella, Simona title = Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor date = 2016-11-29 keywords = DCM; VZV; compound; virus summary = title: Identification of an indol-based derivative as potent and selective varicella zoster virus (VZV) inhibitor Tryptamine derivative 17a was found to have a selective inhibitory activity against human varicella zoster virus (VZV) replication in vitro, being inactive against a variety of other DNA and RNA viruses. Arbidol [34] and delavirdine [35] , are examples of marketed indole-containing antiviral drugs, whereas Panobinostat (LBH589) [36] , being a HDAC (histone deacetylase) inhibitor, is actively undergoing clinical evaluation against human immunodeficiency virus (HIV) type 1 (See Fig. 1 ). The antiviral activity was expressed as EC50, being the compound concentration required to reduce virus-plaque formation (VZV) by 50%. The mixture was stirred for 3 h at room temperature, then was washed with water (3  50 mL), dried over anhydrous Na2SO4, filtered, concentrated and purified by column chromatography using DCM/MeOH (9:1 v/v) as mobile phase. 4-Benzyloxy-gamma-sultone derivatives: discovery of a novel family of non-nucleoside inhibitors of human cytomegalovirus and varicella zoster virus doi = 10.1016/j.ejmech.2016.09.014 id = cord-004719-3stcx0dd author = Mushegian, A. R. title = Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date = 1993 keywords = RNA; movement; protein; virus summary = doi = 10.1007/bf01313766 id = cord-288734-xinkqs6u author = Muñoz-Fontela, César title = Ebola Virus Disease in Humans: Pathophysiology and Immunity date = 2017-03-30 keywords = EBOV; EVD; Ebola; Virus summary = Discovered in 1976 during the first documented outbreak of Ebola virus disease (EVD) in the town of Yambuku in northern Zaire (today Democratic Republic of the Congo), EBOV has since caused sporadic human disease outbreaks of varying magnitude in Equatorial African countries (Sanchez et al. Antigen-presenting cells are a putative initial target of EBOV infection and previous research in animal models of disease has indicated that dendritic cells (DCs) and macrophages are early and preferred targets of EBOV and support virus replication (Geisbert et al. Clinical presentation, biochemical, and haematological parameters and their association with outcome in patients with Ebola virus disease: an observational cohort study Sequence-based human leukocyte antigen-B typing of patients infected with Ebola virus in Uganda in 2000: identification of alleles associated with fatal and nonfatal disease outcomes doi = 10.1007/82_2017_11 id = cord-017008-c7skxte0 author = Méthot, Pierre-Olivier title = Emerging Disease and the Evolution of Virulence: The Case of the 1918–1919 Influenza Pandemic date = 2014-08-22 keywords = Ewald; Taubenberger; host; infl; pandemic; spanish; uenza; virulence; virus summary = Next, we describe the biology of infl uenza viruses with a focus on the 1918-19 pandemics and we move on to the ecological-evolutionary explanations of its exceptional virulence, paying attention to the trade-off model, before turning to molecular 4 On the history, epistemology, and social aspects of the concept of emerging disease see Grmek ( 1993 ); Farmer ( 1996 ) , King ( 2004 ) ; and Weir and Mykhalovski ( 2010 ) . 6 Whereas the ecological (or exogenous) style focuses on processes (e.g. selective pressures, population density, within and between host competition, and so on) acting on the hosts and the pathogen, the molecular (or endogenous) style traces the evolutionary pathway, or patterns, of the infl uenza virus from animal(s) to man, and, by constructing molecular phylogenies, identifi es particular genes for pathogenesis and mutation sites within lineages. doi = 10.1007/978-94-017-8887-8_5 id = cord-263165-bv4dh9eu author = Möstl, Karin title = Coronaviridae, pathogenetic and clinical aspects: An update date = 1990-12-31 keywords = FIPV; Ref; TGEV; virus summary = The recent detection of previously unknown coronaviruses or mutants, like the "Porcine Epidemic Diarrhea"-virus (PEDV) and the TGE-like "Porcine Respiratory Coronavirus" (PRCV) on one hand and new knowledge about pathogenetic mechanisms, for example in FIPV-infections, on the other hand are the basis for this review article. For diagnosis TGEV antigen can be detected by immunofluorescence in the small intestine of piglets at an early stage of disease, by virus isolation in tissue culture or by ELISA. As it causes a respiratory infection and does not replicate in the enteric tract, it was named "Respiratory Variant" of TGEV [16] and recently "Porcine respiratory coronavirus". Pedersen [51] assumed that not only the properties of the infecting virus strain were responsible for the outcome of the disease, but that also the immunologic situation of the host and the type and degree of developing immunity may be of great importance. Natural infection with the Porcine Respiratory Coronavirus induces protective lactogenic immunity against Transmissible Gastroenteritis doi = 10.1016/0147-9571(90)90085-8 id = cord-323710-cmbg0ty8 author = Mühlebach, Michael D. title = Development of Recombinant Measles Virus-Based Vaccines date = 2016-11-26 keywords = recombinant; vaccine; virus summary = For this purpose, the foreign antigen-encoding genes are cloned into additional transcription units of plasmid based full-length MV vaccine strain genomes, which in turn are used to rescue recombinant MV by providing both full-length viral RNA genomes respective anti-genomes together with all protein components of the viral ribonucleoprotein complex after transient transfection of the so-called rescue cells. After demonstrating efficacy in appropriate mouse and primate animal models [8] , this recombinant vaccine delivered proof of Triggered antigen-specific immune responses after immunization determined by measuring total antibodies (ELISA), neutralizing antibodies (nAbs), or reactive T cells determined by ELISpot or intracellular cytokine staining (ICS) c Protective capacity of vaccine-induced immune responses after challenge of the appropriate animal model determined by reduction of pathogen load or attenuation of etiopathology principle for safety and immunogenicity in human patients, irrespective of preformed anti-measles immunity [9] . doi = 10.1007/978-1-4939-6869-5_9 id = cord-346673-kyc1wks5 author = NICKBAKHSH, S. title = Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date = 2016-03-02 keywords = infection; respiratory; virus summary = In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. We analysed diagnostic data generated by NHSGGC using multiplex PCR from 2005 to 2013 with the following objectives: (i) to describe testing and virus prevalence trends, (ii) to examine temporal and patient subgroup distributions for each individual virus, and (iii) to compare factors associated with overall viral infection and co-infection using statistical modelling, in order to provide robust and timely estimates of who is most at risk of viral-associated respiratory illness, and when, within a major urban UK population. doi = 10.1017/s0950268816000339 id = cord-027654-k0uby99n author = Nabel, Gary J. title = The development of gene-based vectors for immunization date = 2020-06-22 keywords = dna; vaccine; vector; virus summary = The advantages of their ability to induce cellular immunity, immunogenicity, safety, mode of antigen presentation, and other attractive features are countered by limitations in knowledge about clinical effi cacy, production methodologies, DNA vaccination as the initial vaccine constituent and replication-defective viral vectors, including modifi ed vaccinia Ankara virus (MVA), 21,28 rAd 22,23,27,29 or proteins to boost the initial response. 31, 32 In addition, the development of improved enhancer/ promoter regions can allow for even higher expression 5 and these vaccines have advanced into multiple human Phase I studies, alone or in combination with other gene-based vectors. Depending on their ability to target antigen presenting cells, ability to develop packaging lines, inherent immunogenicity of both the vector and insert, and other factors (Table 62 -2), these viral vectors are helping to improve vaccine effi cacy in a variety of infectious disease models. Comparative immunogenicity in rhesus monkeys of DNA plasmid, recombinant vaccinia virus, and replication-defective adenovirus vectors expressing a human immunodefi ciency virus type 1 gag gene doi = 10.1016/b978-1-4160-3611-1.50066-0 id = cord-329050-vzsy6xw1 author = Nabi, Ghulam title = Bats and birds as viral reservoirs: A physiological and ecological perspective date = 2020-09-22 keywords = bat; bird; virus summary = These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics. This paper reviews convergent traits in the physiology, immunology and flight-related ecology of birds and bats with the aim of a better understanding of why these species are such important reservoirs of viral zoonoses, and the potential risk of bat and bird viruses infecting humans. The convergent traits of miniaturized body size, enhanced metabolic rate and antioxidant capacity, prolonged lifespan, a short but efficient digestive tract, and possessing some specific immunological features relative to non-flying mammals are thought to be the result of functional constraints on evolution imposed by the demands of powered flight (Thomas and Suthers, 1972; Norberg, 1990; Caviedes-Vidal et al., 2007; Costantini, 2008; Munshi-South and Wilkinson, 2010; Song et al., 2020; ) . doi = 10.1016/j.scitotenv.2020.142372 id = cord-285856-0sw3wt1i author = Naesens, Lieve title = Anti-influenza virus activity and structure–activity relationship of aglycoristocetin derivatives with cyclobutenedione carrying hydrophobic chains date = 2009-02-05 keywords = activity; influenza; virus summary = We here report on the chemical synthesis, anti-influenza virus activity and structure-activity relationship of novel glycopeptide compounds carrying a hydrophobic side chain on an aglycoristocetin backbone ( Fig. 1) . b HPLC conditions: instrument: Waters 600 with UV230nm detection; column: Lichrospher RP-8 (4 mm × 250 mm; 10 m); injection volume: 20 l (corresponding to 2 g compound); solvents: Table 2 , several asymmetric squaric diamides derived from aglycoristocetin exerted marked activity against influenza virus, the most potent compounds being the phenylbenzyl derivative 8e [average antiviral EC 50 : 0.4 M; selectivity index (SI), defined as the ratio of MCC to EC 50 : 50]; the hexanol deriva-tive 8a (EC 50 : 1 M; SI: 14) and the naphthyl derivative 8f (EC 50 : 1.4 M; SI: 10). With regard to the antiviral mode of action, time-of-addition studies suggested that 8e blocks the viral entry process, since optimal anti-influenza virus activity was obtained when the compound was added to MDCK cells 30 min prior to or simultaneously with virus infection. doi = 10.1016/j.antiviral.2009.01.003 id = cord-004743-ido065mh author = Nagy, Éva title = Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories date = 1979 keywords = virus summary = doi = 10.1007/bf01315022 id = cord-323009-frej2qmb author = Nakouné, Emmanuel title = First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic date = 2013-02-08 keywords = car; respiratory; virus summary = FINDINGS: A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. The aim of the study reported here was to determine the circulation of 2009 pandemic influenza A/H1N1 virus (H1N1pdm09) by molecular methods and to identify the causative viruses, the incidence and the clinical features of acute respiratory illness among infants and young children at sentinel sites in Bangui and three rural areas. All infants and children aged between 0-15 years who attended sentinel sites in Bangui and three rural areas ( Figure 1 ) for influenza-like illness (ILI) or severe acute respiratory illness between January and December 2010 were included in the study (Figure 2A ). Abbreviations CAR: Central African Republic; ILI: Influenza-like illness; HRSV: Human respiratory syncytial virus; PIV: Parainfluenza viruses. doi = 10.1186/1743-422x-10-49 id = cord-298032-3zlu8g8y author = Nan, Yuchen title = Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date = 2018-04-20 keywords = PMO; PPMO; RNA; Vivo; virus summary = An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 doi = 10.3389/fmicb.2018.00750 id = cord-252871-qfrpuy3t author = Nasir, Arshan title = Investigating the Concept and Origin of Viruses date = 2020-11-03 keywords = RNA; cell; dna; virus summary = We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells. doi = 10.1016/j.tim.2020.08.003 id = cord-277400-w7mvk3x4 author = Nasir, Arshan title = Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date = 2017-03-10 keywords = Abrescia; FSF; SCOP; virus summary = While the member viruses within a lineage exhibit strong 3D structural similarities in capsid/coat fold architectures (or principles in constructing a functional virion) regardless of the viral replicon (i.e., DNA or RNA) and/or infected host type, the lineages however are believed to be unrelated to each other indicating the polyphyletic origin of viruses (Bamford, 2003) . The b.121 fold in the SCOP hierarchy includes 7 children FSFs (that are not necessarily related in evolution according to SCOP definitions): (i) "PHM/PNGase F" FSF (b.121.1) involved in oxidation-reduction metabolic processes (not detected in any of our sampled viral proteomes), (ii) "Group II dsDNA viruses VP" FSF (b.121.2), which is the "double β-barrel" fold signature of the PRD1/Adenovirus-like lineage (read below), (iii) "Nucleoplasmin-like core domain" FSF (b.121.3) involved in the assembly of nucleosomes in cells, and (iv-vii) FSFs b.121.4, b.121.5, b.121.6, and b.121.7 (Figure 1 ) that define the picornavirus-like lineage and are individually described below. doi = 10.3389/fmicb.2017.00380 id = cord-341029-49360l2a author = Nasir, Arshan title = A phylogenomic data-driven exploration of viral origins and evolution date = 2015-09-25 keywords = Archaea; FSF; Fig; RNA; Venn; dna; virus summary = Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Here, we analyzed a total of 5080 completely sequenced proteomes from cells and viruses and assigned FSF domains to their proteins using structure-based hidden Markov models (HMMs) defined by the SUPER-FAMILY database (version 1.75) (20) . Viral supergroup behaves similarly to cellular superkingdoms in terms of FSF sharing patterns A total of 1995 significant FSF domains (E < 0.0001) were detected iñ 11 million proteins of 5080 proteomes sampled from cells and viruses. It also suggests that viruses are very ancient and most likely infected the last common ancestor of each superkingdom because viral FSFs were present in a diverse array of cellular organisms ranging from small microbes to large eukaryotes. doi = 10.1126/sciadv.1500527 id = cord-325712-9kbnyqt3 author = Nathan, Lakshmi title = Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms date = 2019-07-18 keywords = cell; fusion; membrane; single; virion; virus summary = title: Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms In addition, for HIV [9] , influenza [10] , and Ebola virus [11] , most virions that encounter a cell are not involved in productive entry so the ability of single virion techniques to distinguish entry-competent particles from non-competent ones and characterize their individual behavior provides valuable data on heterogeneity in viral populations and its ultimate impact on infection. The remaining part of the chapter will focus on single particle tracking microscopy techniques compatible with dynamic/temporal data acquisition, their salient features, and how the data generated complement ensemble methods for studying viral entry processes and their intermediate steps and mechanisms. Here, binding and fusion is studied by monitoring liposomes decorated with host cell receptors interacting with the planar virus-like bilayer containing embedded viral proteins [59] [60] [61] . doi = 10.1007/978-3-030-14741-9_2 id = cord-344009-hm36pepp author = Nathanson, N. title = Virus perpetuation in populations: biological variables that determine persistence or eradication date = 2005 keywords = infection; population; virus summary = However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Measles has several attributes that -in the aggregate -are not seen for other common viral diseases: (i) There are longterm records of measles incidence, collected by many health departments in the United States and other countries; (ii) 95% of all measles infections manifest as illness (in contrast to 1% for poliomyelitis for example); (iii) the symptoms of measles are sufficiently pathognomonic so that it can be distinguished from other viral infections by clinical observers; and (iv) population-wide reports can be corrected for under-reporting (about 15% of measles cases were reported in most cities in the United States prior to the introduction of measles vaccine in 1963). Vaccine-induced reduction of susceptible individuals in such a population can be guesstimated to reduce the number of new infections per trough generation period below the threshold for virus perpetuation. doi = 10.1007/3-211-29981-5_2 id = cord-022254-8y5sq72c author = Nathanson, Neal title = IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date = 2012-12-02 keywords = infection; virus summary = One example of specific deletion is the use of anti-mu antiserum to delete IgM bearing B cells from neonatal animals, thus blocking the B cell arm of the immune response (43-46). Complement plays an important ancillary role as a host defense, since in conjunction with specific antiviral antibody, it can lyse either virions or virus-infected cells (60). The recent development of methods for the cloning of T cells and the culture of T cell lines (88) (89) (90) (91) (92) , has made it possible to study the effect of specific T cell subsets upon virus infection (93) (94) (95) (96) . I. Comparative effectiveness of antibody and reconstitution of immune spleen cells on immunosuppressed mice Protection of mice from fatal herpes simplex virus type 1 infection by adoptive transfer of cloned virusspecific and H-2-restricted cytotoxic T lymphocytes Dual role of the immune response in street rabies virus infection of mice doi = 10.1016/b978-0-12-095785-9.50036-6 id = cord-355906-yeaw9nr8 author = Nedjadi, Taoufik title = Tackling dengue fever: Current status and challenges date = 2015-12-09 keywords = Aedes; DENV; dengue; infection; vaccine; virus summary = Recent advances in molecular biology have revealed that the genetic makeup of the three elements of dengue infection (the virus, the vector, and the host) plays a primordial role in the pathogenesis of the disease and could potentially contribute to the DHF progression [19, 24, 35] . Dengue virus serotype-1 antigen was expressed in a vector based on pediatric live-attenuated Schwarz measles vaccine (MV) by using the envelope domain III (EDIII) fused with the ectodomain of the membrane protein (ectoM). The Centers for Disease Control and Prevention (USA) have also developed a live-attenuated vaccine named DENVax, which was found to be highly immunogenic in both children and adults and has currently entered phase I clinical trial in the United States [96, 97] . doi = 10.1186/s12985-015-0444-8 id = cord-326225-crtpzad7 author = Neill, John D. title = Simultaneous rapid sequencing of multiple RNA virus genomes date = 2014-06-01 keywords = RNA; sequence; virus summary = This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. There is a wealth of information in these isolates, but up till now, it has been time consuming and expensive to sequence these viral genomes, often requiring sets of strain-specific primers for PCR amplification and sequencing. These primers were developed so that the 20 base known sequence was used for PCR amplification of the library as well as served as a barcode for identifying each viral library following pooling and sequencing. This virus, a BVDV 1b strain isolated from alpaca (GenBank accession JX297520.1; Table 2 , library 3, barcode 10), was assembled from Ion Torrent data and was found to have only 1 base difference from the sequence determined earlier (data not shown). One virus, library 1, barcode 9, had only 658 viral sequence reads but 94.4% of the genome was assembled. doi = 10.1016/j.jviromet.2014.02.016 id = cord-325830-mrtpihc7 author = Nelson, Philipp P. title = Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date = 2020-04-29 keywords = SARS; respiratory; virus summary = In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. doi = 10.3389/fcimb.2020.00181 id = cord-346290-my8ow5ee author = Nelson, Philipp P. title = Respiratory Viral Pathogens date = 2020-05-28 keywords = respiratory; viral; virus summary = Respiratory viruses are responsible for a variety of clinical syndromes including the common cold, acute otitis media, laryngitis, sinusitis, pneumonia, bronchiolitis, influenza-like illness, and exacerbations of asthma and chronic obstructive pulmonary disease. Treatment modalities include over-the-counter and non-specific remedies along with a small number of specific antiviral medications such as the influenza neuraminidase inhibitors or palivizumab against respiratory syncytial virus. Viruses of the family of Pneumoviridae form enveloped, spherical or filamentous virions with 100-200 nm in diameter, which contain a single, linear, negative-sense RNA genome. Human bocavirus 1 (HBoV1), a member of the species Primate bocaparvovirus 1, in the genus Bocaparvovirus and the subfamily of Parvovirinae, is strongly associated with upper and lower respiratory tract infections in young children. The common cold is a rather benign clinical entity, which may however be complicated by secondary bacterial infections, otitis media, sinusitis, pneumonia, and asthma exacerbations; severe courses of disease and death may occur in young children and immunocompromised patients. doi = 10.1016/b978-0-12-801238-3.11635-6 id = cord-253466-7gpije5d author = Netherton, Christopher title = A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date = 2007-08-31 keywords = ASFV; Fig; Golgi; Poliovirus; RNA; african; dna; protein; replication; virus summary = Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein doi = 10.1016/s0065-3527(07)70004-0 id = cord-322904-9mta0aem author = Neu, Ursula title = The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry date = 2009-02-01 keywords = SV40; VP1; virus summary = The mPyV and the two human polyomaviruses, JCV and BKV are known to require sialic acid for binding to host cells as "receptor destroying enzyme" or neuraminidase inhibits the viruses'' ability to agglutinate red blood cells and to infect cells (Table 1) . High-resolution structural information on the interaction of viral attachment proteins with sialylated carbohydrates is available for the following systems: Influenza virus A haemagglutinin (HA) in complex with oligosaccharides containing α2,3-linked and α2,6linked NeuNAc (Eisen et al., 1997; Gamblin et al., 2004; Ha et al., 2001; Ha et al., 2003; Russell et al., 2006; Sauter et al., 1992; Stevens et al., 2006; Stevens et al., 2004; Weis et al., 1988) , mPyV VP1 with a fragment of ganglioside GD1a (Stehle and Harrison, 1997) , rhesus, swine and human rotavirus VP8⁎ with methyl-α2,3-sialoside (Blanchard et al., 2007; Dormitzer et al., 2002a) , adenovirus Ad37 fiber knob (Ad37) with α2,3and α2,6-sialyllactose (Burmeister et al., 2004) and SV40 VP1 with ganglioside GM1 (Neu et al., 2008) . doi = 10.1016/j.virol.2008.12.021 id = cord-303533-6s01qplg author = Neuman, Benjamin W. title = Does form meet function in the coronavirus replicative organelle? date = 2014-07-15 keywords = RNA; organelle; virus summary = This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. Whatever their purpose, it is clear that the coronavirus organelle is dynamic [9] , closely tied to vesicular transport in the host cell [5, 10] , and consists mainly of paired membranes that form a variety of complex shapes including convoluted membranes and double-membrane vesicles (DMVs) [2, 11] . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein doi = 10.1016/j.tim.2014.06.003 id = cord-279418-3r1ijafm author = Nevers, Quentin title = Negri bodies and other virus membrane-less replication compartments() date = 2020-08-21 keywords = PML; Protein; RNA; Virus summary = We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription doi = 10.1016/j.bbamcr.2020.118831 id = cord-304569-o39kl5k4 author = Nguyen-Van-Tam, Jonathan S title = From the Editor''s desk date = 2015-04-23 keywords = influenza; virus summary = If one shifts the focus away from influenza, the ongoing MERS-CoV outbreak in the Middle East, is also of substantial concern, because despite its likely introduction into humans via close contact with dromedary camels, 9 nosocomial transmission appears to be a central concern, 10,11 case-fatality is high, household transmission is also described, 12 and there are currently no vaccines or specific therapies available. Papers considered for rapid peer-review will need to be of immediate relevance, interest, or importance to scientists, clinicians, public health practitioners or policy makers, usually in relation to a current or evolving event related to respiratory virus activity. Accepted Articles are published online a few days after final acceptance, appear in PDF format only, are given a Digital Object Identifier (DOI), which allows them to be cited and tracked, and are indexed by PubMed. 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 = 10.1111/irv.12311 id = cord-309120-05bg7rfa author = Niazi, Sadegh title = The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date = 2020-11-06 keywords = SARS; respiratory; virus summary = title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses'' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs doi = 10.1016/j.envpol.2020.115767 id = cord-316996-8yimrpaz author = Nicholls, John M. title = The use of sialidase therapy for respiratory viral infections date = 2013-04-17 keywords = DAS181; Sia; virus summary = DAS181 is an inhaled bacterial sialidase which functions by removing sialic acid (Sia) from the surface of epithelial cells, preventing attachment and subsequent infection by respiratory viruses that utilize Sia as a receptor. DAS181 is the first antiviral compound in Phase II development that functions by blocking this pathogen-host interaction, by destroying the influenza host-cell receptor, sialic acid (Sia), on the surface of respiratory epithelial cells. In this paper, we provide background information on Sia and sialidases; discuss the potential role of bacterial sialidases as antiviral agents; review the in vitro and Phase II evaluation of DAS181 for the treatment of influenza; and note evidence that the drug would also be useful against parainfluenza virus infections. Even though influenza virus has been the most well characterized of the pathogens studied, it must be noted that other viruses, including cytomegalovirus (Taylor and Cooper, 1989) , rhinovirus 87 (Blomqvist et al., 2002) , mumps Urabe AM9 (ReyesLeyva et al., 2007) and the paramyxoviruses all utilize Sia (Suzuki et al., 2001) (Paulson et al., 1979) , suggesting that sialidase treatment may potentially be useful for these infections. doi = 10.1016/j.antiviral.2013.04.012 id = cord-269623-9pxdeva3 author = Nicholson, Karl G title = Influenza date = 2003-11-22 keywords = H5N1; Hong; influenza; vaccine; virus summary = The contrast between recent cases of H5N1 infection, associated with high mortality, and the typically mild, self-limiting nature of human infections with avian H7N7 and H9N2 influenza shows the gaps in our understanding of molecular correlates of pathogenicity and underlines the need for continuing international research into pandemic influenza. We gave priority to randomised controlled trials when available, to larger studies, articles published in high-impact journals that have a wide readership, and the systematic review and economic decision modelling, for the prevention and treatment of influenza, commissioned by the Health Technology Assessment Programme on behalf of the National Institute of Clinical Excellence. A meta-analysis of reports published before 2001 showed that vaccination reduces numbers of cases of influenza-like illness by 35%, hospital admissions for pneumonia and influenza by 47%, and all-cause mortality by 50%. doi = 10.1016/s0140-6736(03)14854-4 id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 keywords = ELISA; IFA; LCMV; LDV; MHV; MPV; PCR; TMEV; infection; mouse; strain; virus summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. doi = 10.1016/b978-0-12-382008-2.00019-2 id = cord-003466-599x0euj author = Nickol, Michaela E. title = A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919 date = 2019-02-06 keywords = H1N1; influenza; pandemic; virus summary = MAIN TEXT: The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). Influenza viruses have posed a continual threat to global public health since at least as early as the Middle Ages, resulting in an estimated 3-5 million cases of severe illness and 291,243-645,832 deaths annually worldwide, according to a recent estimate [1] . To be considered a pandemic, an influenza virus must: i) spread globally from a distinct location with high rates of infectivity resulting in increased mortality; and ii) the hemagglutinin (HA) cannot be related to influenza strains circulating prior to the outbreak nor have resulted from mutation [14, 15] . doi = 10.1186/s12879-019-3750-8 id = cord-300020-edolh7ww author = Nielsen, Anne Ahlmann title = Persistence of Low-Pathogenic Avian Influenza H5N7 and H7N1 Subtypes in House Flies (Diptera: Muscidae) date = 2011-05-01 keywords = AIV; virus; ßie summary = The objective of the present work was to investigate the potential transmission of LPAIV by persistence of the virus in the alimentary tract of house flies, Musca domestica L. The persistence of HPAIV H5N1 in house ßies and blow ßies as well as Newcastle disease virus (family Paramyxoviridae, genus avulavirus, NDV), turkey coronavirus (family Coronaviridae, genus Coronavirus, TCV), and reticuloendotheliosis virus (family Retroviridae, genus Gammaretrovirus, REV) has been studied in the laboratory (Calibeo-Hayes et al. The current study investigated the persistence of LPAIV in the alimentary tract of house ßies that were fed various concentrations of subtypes H5N7 and H7N1 viruses and incubated at different temperatures for up to 24 h. Our study demonstrated that infective low-pathogenic avian inßuenza virus of the H7N1 and H5N7 subtypes can be isolated from the alimentary tract of house ßies for at least 24 h postfeeding and that factors such as temperature, incubation period postfeeding, and load of ingested virus play an important role in the persistence of infective virus. doi = 10.1603/me11017 id = cord-342124-jdv17u86 author = Nieto‐Rabiela, Fabiola title = Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date = 2019-06-20 keywords = bat; virus; zoonotic summary = title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential. doi = 10.1111/zph.12618 id = cord-013176-6ckuya1w author = Ninfali, Paolino title = Antiviral Properties of Flavonoids and Delivery Strategies date = 2020-08-21 keywords = HCV; RNA; activity; antiviral; effect; flavonoid; virus summary = Quercetin, extracted from Embelia ribes (Mirsinaceae), exhibited antiviral effects against HCV, exerted through activity inhibition of the viral protease Non-Structural protein 3 (NS3), leading to a decrease in HCV replication [36] . The natural extract of Tetrastigma hemsleyanum (Vitaceae) contains many flavonoids, including vitexin, vitexin-2-O-rhamnoside, isorhamnetin, rutin, kaempferol, astragalin, quercitrin, quercetin and iso-quercetin, which were shown to be able to exert anti-influenza virus activity, with different efficiency, through the reduction of the number of plaques induced by the influenza virus in infected Madin-Darby Canine Kidney (MDCK) cells [21] . In future perspective, this approach could be considered in order to possibly improve the antiviral activity of some flavonoids, like baicalin, that was able, like fludarabine [65] , to act against HIV-1 chronic infection of human monocytes and macrophages, inhibiting the fusion of HIV virus envelope proteins with these cells [73] . doi = 10.3390/nu12092534 id = cord-024188-d7tnku8z author = Nissen, Michael D. title = Respiratory Infections date = 2010-03-27 keywords = RSV; infection; respiratory; virus summary = For example, recent findings from the New Vaccine Surveillance Network in the United States show that despite respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), and human coronaviruses (HCoVs) all being common in early childhood; RSV and PIVs are more common causes of hospital admission with acute febrile and respiratory illness than HCoVs [33, 41] . A review of healthy adult human volunteer studies showed that viral shedding increased sharply between 0.5 and 1 day after influenza virus challenge, peaking on day two; shedding can be detected 24 to 28 h before clinical onset, and has a mean duration of 4.8 days; two-thirds of subjects had symptomatic infection, and total symptom scores peaked on day three [11] . Infections due to common viruses that result in disease severe enough to warrant laboratory testing, notification, or hospitalisation occur in the young, the very old, or both, such as with RSV and influenza [9, 14] . doi = 10.1007/978-90-481-9039-3_5 id = cord-001748-7e8px4vx author = Nobach, Daniel title = Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date = 2015-08-27 keywords = Borna; RNA; shrew; virus summary = The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species doi = 10.1371/journal.pone.0137018 id = cord-002407-25cawzi0 author = Nogales, Aitor title = Reverse Genetics Approaches for the Development of Influenza Vaccines date = 2016-12-22 keywords = IAV; IBV; influenza; virus summary = To date, three types of influenza virus vaccines are approved by the Food and Drug Administration (FDA) for human use: recombinant viral HA, inactivated virus and live-attenuated viruses [65] [66] [67] [68] [69] . Plasmid-based reverse genetics for influenza virus allows for the simultaneous expression of the viral components involved in viral genome replication and gene transcription (PB2, PB1, PA and NP) and the eight negative-stranded vRNAs in transfected susceptible cells, which together generate de novo, recombinant IAVs or IBVs (Figure 3 ) [48] . Plasmid-based reverse genetic technologies have allowed the engineering of recombinant influenza viruses that contain single or multiple mutations in the viral genome, which can be potentially implemented as novel or improved vaccine approaches. Importantly, influenza viruses generated by codon deoptimization showed similar viral replication kinetics to WT virus in MDCK cells, which is important for their effective use for vaccine production. doi = 10.3390/ijms18010020 id = cord-309381-cb80ntxs author = Nogales, Aitor title = Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans date = 2019-09-30 keywords = IAV; IFITM3; IFN; Influenza; NCR; SNP; virus summary = IAV RNAs are mainly recognized by the endosomal, membrane-associated PRR Toll-like receptors (TLRs) 3 (double-stranded RNAs, dsRNAs) or 7/8 (ssRNAs), respectively [50, 51] , by the cytoplasmic PRR retinoic acid-inducible gene I (RIG-I), which detects dsRNA and 5 -triphosphates of the negative ssRNA viral genome [50, 52] , generated during replication of multiple viruses, by the NOD-like receptor family member NOD-, LRR-and pyrin domain-containing 3 (NLRP3), which recognizes various stimuli (see below) [53] and by the absent in melanoma 2 (AIM2) protein, recognizing not well-characterized influenza stimuli [54] . Another important SNP (rs34481144) associated with risk of severe influenza in humans from the United States (US) infected with seasonal IAVs is located in the 5 -UTR of the IFITM3 gene [123, 124] . doi = 10.3390/pathogens8040168 id = cord-003166-k3jxvzfi author = Noh, Ji Yeong title = Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date = 2018-08-22 keywords = B16; KBPV; bat; virus summary = Even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus showing (Table 1) . In addition, among three pooled sera (two mouse sera each) against human parainfluenza virus 1 (KBPV-VR-44), one pooled serum was cross-reactive to the bat paramyxovirus B16-40 with 40 as the end-point titer for the fluorescent signal ( Table 2 , Fig. 4 ). Notably, even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus (Table 1) . In fact, in this study, when mouse antisera were made and tested against bat paramyxovirus B16-40 and human parainfluenza virus 1 (KBPV-VR-44), the two viruses were partially cross-reactive to each other in an indirect immunofluorescence assay. doi = 10.1038/s41598-018-30319-7 id = cord-285547-7m3dh8hu author = Nomura, Naoki title = Characterization of avian influenza viruses isolated from domestic ducks in Vietnam in 2009 and 2010 date = 2011-11-09 keywords = H9N2; virus summary = In the present study, a surveillance of avian influenza was carried out in Vietnam in domestic ducks and wild birds in 2009 and 2010, and the isolates were antigenically and phylogenetically analyzed and their pathogenicity in birds and mammals was assessed. One hundred tracheal and cloacal swab samples that were viral gene positive from 600 domestic ducks and 207 wild birds (night heron, Nycticorax nycticorax; grey heron, Ardea cinerea; purple heron, Ardea purpurea; chinese pond heron, Ardeola bacchus; chinese egret, Egretta eulophotes; little egret, Egretta garzetta; intermediate egret, Egretta intermedia; cormorant, Phalacrocorax carbo; little cormorant, Microcarbo niger; Japanese bush warbler, Cettia diphone; black-browed reed warbler, Acrocephalus bistrigiceps; olive bulbul, Iole virescens; black capped kingfisher, Halcyon pileata; collared kingfisher, Halcyon chloris; racket tailed treepie, Crypsirina temia; oriental magpie robin, Copsychus saularis; tiger shrike, Lanius tigrinus; yellow bittern, Ixobrychus sinensis; indian cuckoo, Cuculus micropterus; common koel, Eudynamys scolopacea; and black collared starling, Sturnus nigricollis) in April 2009 and March 2010 in southern Vietnam were inoculated into the allantoic cavities of 10-day-old embryonated chicken eggs. doi = 10.1007/s00705-011-1152-3 id = cord-030279-pv770doe author = Novossiolova, Tatyana title = Twenty-first Century Governance Challenges in the Life Sciences date = 2016-11-29 keywords = H5N1; Influenza; Research; biology; biotechnology; change; development; human; life; risk; science; virus summary = From ''dual-use life science research of concern'' through the rise of amateur biology to the advent of personalised medicine, the chapter exposes the limitations of the existing governance mechanisms in accommodating the multifaceted ethical, social, security, and legal concerns arising from cutting-edge scientific and technological developments. Indeed, rapid advances in the field have produced a knowledge base and set of tools and techniques that enable biological processes to be understood, manipulated and controlled to an extent never possible before 5 ; they have found various applications in numerous spheres of life, generating enormous benefits and offering bright prospects for human betterment; and they have come to be regarded as a key driver of economic development with potential to close the gap between resource-rich and resource-poor countries. doi = 10.1007/978-3-319-51004-0_4 id = cord-353509-yfkiaq80 author = Nugraha, Rhea Veda title = Traditional Herbal Medicine Candidates as Complementary Treatments for COVID-19: A Review of Their Mechanisms, Pros and Cons date = 2020-10-10 keywords = ACE2; COVID-19; SARS; cytokine; virus summary = This review discusses some herbal agents extracted from various plants, including Echinacea, Cinchona, Curcuma longa, and Curcuma xanthorrhiza, which are considered for the treatment of COVID-19. e single cause of this highly communicable disease is a novel coronavirus, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the seventh known virus of the Coronaviridae family capable of infecting humans [2] . Studies that describe the relation of some herbal drugs with the molecular mechanisms of COVID-19 infection, treatment, and prevention remain to be explained. in their systematic review about convalescent plasma transfusion (CPT) for the treatment of COVID-19 suggested that CPT could be an effective therapeutic option with promising evidence on safety, improvement of clinical symptoms, and reduced mortality, in addition to antiviral/antimicrobial drugs. A clinical trial study is needed to confirm the effect of using curcumin as a preventive agent against COVID-19. doi = 10.1155/2020/2560645 id = cord-002136-mkl89qkt author = Nunes, Sandro F. title = An ex vivo swine tracheal organ culture for the study of influenza infection date = 2009-12-09 keywords = EVOC; figure; influenza; virus summary = Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. 1, 3 Influenza infection in humans and pigs is primarily restricted to the upper and lower respiratory tract with viral replication occurring in the epithelial cells present on the surface of the respiratory mucosa. Ex vivo organ cultures (EVOC) of tracheal explants with an air interface system have been successfully developed and used in the study of both human and animal respiratory pathogens. To determine if the swine tracheal explants supported productive viral replication, explants were infected with 2AE5 · 10 2 pfu of swine influenza virus and maintained in organ culture for 5 days. Cultures of equine respiratory epithelial cells and organ explants as tools for the study of equine influenza virus infection doi = 10.1111/j.1750-2659.2009.00119.x id = cord-035015-slgywe0c author = Nunn, Alistair V. W. title = SARS-CoV-2 and mitochondrial health: implications of lifestyle and ageing date = 2020-11-09 keywords = ACE2; COVID-19; ROS; SARS; age; cell; function; mitochondrial; virus summary = Data is now showing that COVID-19 patients do have populations of T-cells displaying mitochondrial dysfunction, as well as altered mitochondrial markers in monocyteshinting that immune-metabolic phenotyping could be used to understand disease pathogenesis and possible treatments; this could include targeting mitochondria [32] . The underlying aetiology for "inflammaging" has long thought to be associated with mitochondrial dysfunction as suggested by Nick Lane in 2003 in his "double agent" theory [5] , and is now receiving renewed interest, for instance, in how decreasing mitochondrial function can reduce T-cell function and enhance immune senescence, as mitochondria are pivotal in metabolic reprogramming towards the Warburg effect [40] . Furthermore, as evidence indicates that many viruses, which most likely include SARs-CoV-2, modulate bioenergetics and redox in both the immune system and other cells they infect to enhance their own replication, they could potentially induce excessive stress in these systems if their mitochondria are already sub-optimally functional. doi = 10.1186/s12979-020-00204-x id = cord-317619-o7qfugjw author = Nye, Steven title = Viral Infection in the Development and Progression of Pediatric Acute Respiratory Distress Syndrome date = 2016-11-24 keywords = ARDS; H1N1; RSV; respiratory; virus summary = While the overall incidence of respiratory virus infection, in particular RSV and influenza A (H1N1) virus, leading to lower respiratory tract disease is widely studied (12, 13), the frequency of progression to pediatric ARDS has yet to be clearly determined. While post-pandemic studies suggest a decrease in influenza A (H1N1) virus disease severity and burden (20, 21), it continues to be a significant cause of severe illness and pediatric ARDS (22). In RSV infection, development of lower respiratory track disease in premature infants, with or without chronic neonatal lung disease is associated with a significantly higher risk of hospitalization, intensive care unit admission, need for mechanical ventilation, and death (12, [70] [71] [72] [73] . Disease severity and viral load are correlated in infants with primary respiratory syncytial virus infection in the community Motavizumab treatment of infants hospitalized with respiratory syncytial virus infection does not decrease viral load or severity of illness doi = 10.3389/fped.2016.00128 id = cord-290149-eed4v2jl author = ODEND''HAL, STEWART title = Porcine Hemagglutinating Encephalomyelitis Virus date = 2012-12-02 keywords = virus summary = key: cord-290149-eed4v2jl title: Porcine Hemagglutinating Encephalomyelitis Virus This chapter provides an overview of the classification, description, hosts, key developments, diagnostic techniques, and diagnostic reagents for porcine hemagglutinating encephalomyelitis virus. Porcine hemagglutinating encephalomyelitis virus causes two distinct syndromes; one is known as vomiting and wasting disease, and the other involves encephalomyelitis. The hosts of porcine hemagglutinating encephalomyelitis virus are pigs. Vomiting and wasting disease and encephalomyelitis were initially reported as two separate diseases in Canada in the late 1950s. Porcine hemagglutinating encephalomyelitis virus was isolated in 1962, and the common etiology of the two syndromes was shown in 1969. The diagnostic techniques for porcine hemagglutinating encephalomyelitis virus are virus neutralisation (VN) and agar gel immunodiffusion (AGID). To day in Canada the virus is endemic and antibodies can be demonstrated, but the disease syndrome is no longer evident (5). doi = 10.1016/b978-0-12-524180-9.50087-x id = cord-303297-fiievwy7 author = Oberemok, Volodymyr V. title = SARS-CoV-2 will continue to circulate in the human population: an opinion from the point of view of the virus-host relationship date = 2020-04-30 keywords = COVID-19; CoV-2; SARS; virus summary = In this article, we will concentrate on the facts currently available about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused COVID-19 (coronavirus disease 2019) pandemic and try to predict its development and consequences based on the virus-host relationship. In addition, it seems that the virus is also more likely to affect the heart than any other similar viruses, so although pneumonia is often the main cause of death, cardiologists and infectionists, for example in Russia, are seeing infected patients whose worst symptoms are not respiratory, but cardiac and many people infected with COVID-19 are dying from heart attacks, as a possible complication of SARS-CoV-2 infection. Despite the initial reports stating that most of the laboratory-confirmed infected patients (27 of 41 cases) had links to the Wuhan seafood market where different animals, including bats, snakes, birds, pangolins, and other small mammals are normally traded within the market [6] , it is now obvious that the newly identified coronavirus SARS-CoV-2 is transmitted with enormous efficacy from human to human via respiratory droplets or close contact. doi = 10.1007/s00011-020-01352-y id = cord-000238-om92cx5q author = Ogbunugafor, C. Brandon title = On the possible role of robustness in the evolution of infectious diseases date = 2010-06-30 keywords = RNA; UVC; robustness; virus summary = We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. [14] [15] [16] In reviewing these results, we hope to highlight the importance of empirical work in RNA viruses for testing theory pertaining to robustness, as well as for better understanding the evolutionary biology and evolvability of infectious organisms in general. 1 However, theory and artificial-life data 9 support the idea that genetic robustness should be strongly favored when populations experience elevated mutation rates, suggesting that RNA viruses would be fruitful systems to explore how genetic robustness evolves. [33] [34] [35] Regardless, preliminary experiments showed that UVC exposure for periods up to 30 min greatly increased mortality in wild type phage 6 ͑Fig. 2͒, indicating that this environmental effect should produce strong selection for UVC resistance in populations of the virus. doi = 10.1063/1.3455189 id = cord-276348-vr5fit8r author = Ogra, Pearay L. title = Respiratory syncytial virus: The virus, the disease and the immune response date = 2004-01-31 keywords = RSV; infection; respiratory; virus summary = Premature babies born at 30–35 weeks of gestation, infants with cyanotic congenital heart disease, HIV-infected subjects, and patients on intensive immunosuppressive therapy especially after bone marrow transplant are considered to be at risk for increased mortality and morbidity during RSV infection. Recurrent wheezing for up to 5 to 7 years of age and established airway disease has been observed in a significant number of children with a strong family history of allergy, after primary infection or reinfection with RSV. Children at increased risk from RSV infection include young infants with prematurity, bronchopulmonary dysplasia, congenital heart disease, congenital or acquired immunodeficiency, subjects with hematologic malignancies, patients with bone-marrow or organ transplants, and cystic fibrosis. 6 It is important to recognise that virtually all children who get infected with RSV develop virus-specific IgE homocytotropic antibody in the respiratory tract. doi = 10.1016/s1526-0542(04)90023-1 id = cord-020712-l9cn0n99 author = Ohnishi, Shun-Ichi title = Chapter 9 Fusion of Viral Envelopes with Cellular Membranes date = 2008-05-30 keywords = Fig; HVJ; Sendai; fusion; membrane; virus summary = Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin doi = 10.1016/s0070-2161(08)60137-9 id = cord-345359-okmkgsbr author = Ohno, Marumi title = Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice date = 2020-07-02 keywords = PR8; TCA; acid; mouse; virus summary = After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. www.nature.com/scientificreports/ investigated metabolic changes by determining the serum levels of metabolites, insulin sensitivity in the liver, glucose availability, and hepatic gene expressions in the early stages of symptom onset as well as the lethal phase of influenza in a mouse model. The results of this study indicate that influenza virus infection dysregulates glucose and fatty acid metabolism and decreases tricarboxylic acid (TCA) cycle activity, leading to enhanced degradation of adenosine triphosphate (ATP) and guanosine triphosphate (GTP). Metabolites that were present at reduced levels in the sera of PR8 virus-infected mice were mainly related to the TCA cycle, urea cycle, and amino acid metabolism, as indicated by the serum levels of metabolite in these pathways at 1, 3, and 6 dpi (Fig. 2) . doi = 10.1038/s41598-020-67879-6 id = cord-355771-pxkkd3s1 author = Olagnier, David title = Oncolytic Viral Immunotherapy in the Time of COVID-19 date = 2020-11-04 keywords = virus summary = The 2020 global pandemic of Covid-19 has refocused the entire scientific community towards understanding the SARS coronavirus-2 (SARS-CoV-2) and developing urgently needed therapies and vaccines to halt the spread of this newly emerging virus. In this special issue of Cytokines and Growth Factor Reviews -Oncolytic Viral Immunotherapy 2020, international experts discuss the innovative approaches developed for OV-based immunotherapies. Interferons (IFNs) are the most potent anti-viral cytokines induced by virus-infected cells and can reduce the efficacy of OVs. However, many types of cancer cells have been shown to be compromised in terms of generating a potent IFN antiviral state, thus making these tumours a particularly sensitive niche population for oncolytic virus replication. Four reviews in this issue describe our current understanding of the factors that can contribute to a successful super-spreading oncolytic and immune stimulating event within tumours. doi = 10.1016/j.cytogfr.2020.10.009 id = cord-317508-03u2vtzk author = Oldstone, M.B.A. title = History of Virology date = 2019-08-28 keywords = Discovery; virus summary = were clinically evident in early human history, the initial isolation of individual viruses and their assignment to specific diseases did not occur until about 1898, 120 years ago, a proverbial drop in the bucket of time. Although the majority of life-threatening and debilitating acute virus infections are now controlled through vaccination, it is worthwhile considering the consequences of acute infections like smallpox, measles, and yellow fever in the prevaccine era. This devastating depopulation came primarily from smallpox and measles infections, since these viruses had never before existed in the New World (Oldstone, 2010) . However, measles virus infection was and remains a serious disease today with approximately one per thousand infected persons developing severe destruction of the central nervous system requiring institutionalization. Now these and many other acute virus infections are controlled by vaccination or antivirals and public health policies when and where they are instituted. doi = 10.1016/b978-0-12-801238-3.00078-7 id = cord-010222-5oxie0zc author = Oldstone, Michael B.A. title = Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date = 2004-04-11 keywords = B27; HLA; virus summary = Because the studies described above indicate that many viruses share antigenic determinants (linear or conformation) with normal host proteins, the next step was to determine experimentally whether molecular mimicry could elicit autoimmune diseases. The most likely explanation for how molecular mimicry causes disease is that an immune response against the determinant shared by host and virus takes the form of a tissue-specific attack, presumably capable of destroying cells and eventually the tissue. In any case, molecular mimicry would occur only when the virus and host determinants are sufficiently similar to induce a cross-reactive response yet different enough to break B or T-cell immunologic tolerance. Thus, the human AChR a-chain 160-167 peptide specifically cross-reacts with a shared homologous domain on herpes simplex virus glycoprotein D, residues 286-293, by binding and inhibition studies, and elicits antibodies in myasthenic patients that bind to the native AChR protein; these antibodies are capable of causing a biologic effect. doi = 10.1016/0896-8411(89)90130-3 id = cord-023740-g84fa45m author = Oldstone, Michael B.A. title = Mimicry by Virus of Host Molecules: Implications for Autoimmune Disease date = 2014-06-27 keywords = protein; virus summary = Monoclonal antibodies against 11 different viruses including DNA and RNA viruses known to cause human infection from the herpes virus group, vaccinia virus, myxoviruses, paramyxoviruses, arenaviruses, flaviviruses, alphaviruses, rhabdovirus, and coronaviruses cross-react with host cell determinants expressed on uninfected tissues. other examples (reviewed in Oldstone and Notkins, 1986 ) suggest a mechanism whereby immune reactants directed against a viral or microbial component may cross-react with a host component and generate autoimmune disease. Since, on the basis of antibody cross-reactivity, many viruses share antigenic sites with normal host cell components, the next step was to look for crossreactive capability in eliciting autoimmunity and related disease. The most likely mechanism by which molecular mimicry would cause disease is by eliciting an immune response against a determinant shared between the host and the virus to bring forth a tissue-specific immune response, presumably capable of destroying cells and eventually the tissue. doi = 10.1016/b978-0-12-174685-8.50079-2 id = cord-307918-8y89p11a author = Onyango, Clayton O. title = Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010 date = 2012-12-15 keywords = Kenya; influenza; virus summary = Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. The following clinical and laboratory features obtained on admission or that relate to discharge outcome were compared between influenza-positive and influenza-negative children: duration of hospitalization >14 days, very severe pneumonia, wheezing, hypoxia (oxygen saturation level <90%, by fingertip pulse oximetry), circulatory shock (capillary refill time ≥3 seconds), severe anemia (hemoglobin level <5 g/dL), prematurity, congenital heart disease, positivity for HIV antibody (by 2 rapid tests), severe underweight (weight for age Z score ≤3), slide positivity for Plasmodium species, bacteremia, concurrent viral infection diagnosis, and death before discharge [2] . Our study identified all 3 influenza viruses in circulation in this rural coastal Kenya location among patients hospitalized with severe or very severe pneumonia and among outpatients with URTI. doi = 10.1093/infdis/jis536 id = cord-317971-kuwargnp author = Opatz, Till title = Thoughts on What Chemists Can Contribute to Fighting SARS‐CoV‐2 – A Short Note on Hand Sanitizers, Drug Candidates and Outreach date = 2020-05-08 keywords = SARS; drug; virus summary = [11] Exposure to concentrations of just 30 % of either ethanol or isopropanol for 30 seconds fully suppressed viral infectivity.Likewise,the virucidal activity of the hand rub solutions known as WHO formulation 1, with 85 % ethanol, and WHO formulation 2, with 75 %i sopropanol, against SARS-CoV-2 was found to be excellent, with full inactivation of the coronavirus at 40 %or30%concentration, respectively.W hile the alcohol component is the main virucide,0 .125 % v/v H 2 O 2 is added to kill bacterial spores that may be present in the raw materials or the container.The addition of 1.45 % v/v glycerol as ah umectant improves the dermatological properties and thus the acceptance of the product. doi = 10.1002/anie.202004721 id = cord-290282-oxyzndsj author = Ortego, Javier title = Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date = 2003-03-30 keywords = TGEV; gene; virus summary = Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3′-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5′ end of each gene using an infectious cDNA clone. All the rTGEV viruses conserved the modifications engineered in the cDNAs (data not shown), indicating that the ORF separation and the insertion of unique endonuclease restriction sites between genes were stably maintained in the rTGEV genomes. Interestingly, analysis of viral growth in the gut of infected piglets showed a 100-to 5000-fold reduction of recombinant viruses containing one or more restriction sites in relation to the rTGEV-wt virus ( Fig. 5D and E) . doi = 10.1016/s0042-6822(02)00096-x id = cord-356188-rwf78stz author = Oshansky, Christine M. title = The human side of influenza date = 2012-07-01 keywords = H1N1; cell; infection; influenza; virus summary = Few studies have examined the role of monocytes during influenza infection in humans, particularly regarding the specific subsets mentioned above, but comparison of IFN-␥ production from T cells cocultured with CD64 ϩ CD16 Ϫ and CD64 Ϫ CD16 ϩ monocytes [119, 120] Cellular immunity Class I HLA presents peptides from internal and external viral proteins. As influenza primarily infects epithelial cells lining the respiratory tract, lung-resident DCs and macrophages are particularly important for efficient development of an adaptive immune response. [189] ), and in vitro studies suggest that activated human V␥9V␦2 T cells may have a role in the antiviral response by killing influenza-infected, monocyte-derived macrophages and producing high levels of IFN-␥ [190, 191] . Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection Characterization of the human CD8ϩ T cell response following infection with 2009 pandemic influenza H1N1 virus doi = 10.1189/jlb.1011506 id = cord-009791-k09vcq96 author = Osterhaus, A. title = Antiviral Antibodies in Dogs in the Netherlands date = 2010-05-13 keywords = CAV; HA1; virus summary = SUMMARY: Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses, parainfluenza viruses, equine influenza viruses and vomiting and wasting disease virus of pigs. Sera from six animal attendants from a CP kennel, cornprizing a total of at least 170 dogs, were tested for the prevalence of HA1 antibodies to CAV,, CAV, , REOvirus types 1, 2 and 3, parainfluenzavirus types 1, 2 and 3 and VW virus. Summary Antiviral antibodies in dogs in the Netherlands A collection of more than 700 canine sera, coming from open and closed populations and from kennels with frequent neonatal mortality, were screened for the prevalence of antibodies to canine adenoviruses, canine herpesvirus, polyoma virus, REOviruses,. doi = 10.1111/j.1439-0450.1977.tb00982.x id = cord-023034-j8zwcfys author = Osterhaus, Albert D. M. E. title = Feline Infectious Peritonitis Virus: II. Propagation in Suckling Mouse Brain date = 2010-05-13 keywords = FIP; SPF; virus summary = SUMMARY: Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one‐day‐old laboratory mice using direct immunofluorescence tests. In order to determine the specificity of the observed fluorescence for FIP virus, indirect IFT were carried out in parallel on poslitive mouse brain sections (homologous reaction) and on porcine kidney cells infected with TGE virus (heterologous reaction). The conclusive experiment for establishing the FIP virus specificity of the immunofluorescence in mouse brain was performed by inoculating SPF kittens with fluorescence-positive material of the 6th mouse passage (isolation series A, Table 1 ). Feline infectious peritonitis (FIP) virus multiplication was demonstrated in the brains of one-day-old laboratory mice using direct immunofluorescence tests. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. Specificity was assessed by virus reisolation, indirect immunofluorescence and reproduction of FIP after inoculation of SPF kittens using brain material from the 6th mouse passage. doi = 10.1111/j.1439-0450.1978.tb01683.x id = cord-339854-scb7pz87 author = Overend, Christopher title = The synthetic futures of vesicular stomatitis virus date = 2012-07-11 keywords = VSV; virus summary = Vesicular stomatitis virus (VSV) is one of the most promising viruses for engineering vaccines and oncolytic therapies [2] . Of particular interest is a study in which VSV expressing the H5 antigen from highly pathogenic avian influenza induced sterilizing immunity against heterologous challenge in mice [4] . This demonstrates the safety and efficacy potential of VSV when live virus vaccination would otherwise be contraindicated. Even more promising, recombinant VSV expressing a secreted form of a virulence factor protein for Yersinia pestis, LcrV, induced high levels of LcrV-specific antibodies, protecting 90% of the mice challenged with 10 LD 50 [6] . Vesicular stomatitis virus-based Ebola vaccine is well-tolerated and protects immunocompromised nonhuman primates Potent vesicular stomatitis virus-based avian influenza vaccines provide long-term sterilizing immunity against heterologous challenge Heterologous boosting of recombinant adenoviral prime immunization with a novel vesicular stomatitis virus-vectored tuberculosis vaccine SARS vaccine based on a replicationdefective recombinant vesicular stomatitis virus is more potent than one based on a replication-competent vector doi = 10.1016/j.tibtech.2012.06.002 id = cord-018555-3lta1tbp author = Overstreet, Robin M. title = Host–Symbiont Relationships: Understanding the Change from Guest to Pest date = 2016-01-06 keywords = Litopenaeus; Overstreet; fish; host; infection; shrimp; symbiont; virus summary = We provide examples involving multiple triggers for organisms associated with termites, for an endemic virus being affected by multiple factors and having multiple effects on its commercial penaeid shrimp hosts, and for contrasting variables associated with two exotic viruses in wild and cultured commercial penaeid shrimps with an emphasis on hypothesizing how the pathogenicity developed in these two viruses. Atypical temperatures, such as warm water associated with power plants, can cause infections of a specific parasite during periods when the hosts are more likely to be consumed by predators, more susceptible to disease, or more susceptible to interactions among parasites that can occur and result in unusual pathogenic conditions. The transformation triggers phenotypic and behavioral changes specifically attracting infective specimens to predatory birds in which the trematode matures considerable detail the host-symbiont relationships affecting the outcome of pathogenic viruses in populations of commercial penaeid shrimp. doi = 10.1007/978-3-319-28170-4_2 id = cord-018811-zhwr3h07 author = Oxford, John title = Influenza Vaccines Have a Short but Illustrious History of Dedicated Science Enabling the Rapid Global Production of A/Swine (H1N1) Vaccine in the Current Pandemic date = 2010-06-18 keywords = H1N1; H3N2; antibody; influenza; vaccine; virus summary = The international investment into public health measures for a global human outbreak of avian H5N1 influenza together with a focus of swine influenza H1N1 is leading to enhanced production of conventional vaccine and to a new research searchlight on T-cell epitope vaccines, viral live-attenuated carriers of influenza proteins, and even more innovative substrates to cultivate virus, including plant cells. This was particularly well demonstrated by studies during the swine influenza campaign in the USA in 1976, when many observers reported results, which ultimately led to the recommended use in children of two doses of split-type rather than whole-virus vaccines. It has been known for many years that the serological response to inactivated vaccine depends on the previous experience of the recipient to infection by viruses of the same subtype of influenza A virus as that present in the vaccine. Comparison of inactivated vaccine A/HongKong/68 (H3N2) given intranasally or subcutaneously showed that following challenge with live virus only those who had developed a serum antibody response after vaccine by either route resisted infection. doi = 10.1007/978-3-0346-0279-2_6 id = cord-334082-fyxn0g3v author = O’Carroll, I.P. title = Viral Nucleic Acids date = 2015-08-20 keywords = RNA; dna; virus summary = This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to ''rolling circle'' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or ''reverse transcriptase'' in the virus copies this RNA into dsDNA. doi = 10.1016/b978-0-12-394447-4.10061-6 id = cord-290432-4dli5emd author = O’Grady, Kerry-Ann F. title = Upper airway viruses and bacteria in urban Aboriginal and Torres Strait Islander children in Brisbane, Australia: a cross-sectional study date = 2017-04-04 keywords = child; indigenous; virus summary = We aimed to describe the prevalence of upper airway viruses and bacteria in symptomatic and asymptomatic urban-based Australian Indigenous children aged less than 5 years. METHODS: A cross-sectional analysis of data collected at baseline in an ongoing prospective cohort study of urban Aboriginal and Torres Strait Islander children registered with a primary health care service in the northern suburbs of Brisbane, Australia. Thus, in 164 urban-based Indigenous children presenting to an urban primary health care service, we described the prevalence of upper airway respiratory viruses and bacteria. We analysed data from a cohort of urban Aboriginal and Torres Strait Islander children aged less than 5 years collected at time of enrolment into a prospective study of ARIwC. In a study of upper airway viruses and bacteria in Central Australian Aboriginal children hospitalised for pneumonia [8] , a population with high rates of hospitalised lower ARI [15] and nasal colonisation [16] , the [8] . doi = 10.1186/s12879-017-2349-1 id = cord-259458-o2yts5pq author = O’Grady, Kerry‐Ann F. title = Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date = 2011-03-21 keywords = PCR; specimen; virus summary = This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. To inform the design of surveillance and intervention studies addressing respiratory infections in remote communities, we compared the sensitivity of a simple, cost-efficient method for transporting respiratory samples from a remote setting for viral real-time PCR with transport using frozen specimens. Given the sensitivity and specificity of real-time PCR diagnosis, we considered a specimen from either nostril positive for any virus to represent a true-positive, similar to previous studies (Lambert et al. Determining the aetiology and burden of viral respiratory infections in remote communities has to date been limited by the inability to store and transport clinical specimens requiring freezing ⁄ refrigeration to urban laboratories. We propose that this method, combining standard clinic refrigeration and weekly surface mailing of specimens combined with real-time PCR, can be used for viral respiratory research in remote locations. doi = 10.1111/j.1365-3156.2011.02757.x id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 keywords = Nipah; SARS; human; infection; virus summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. doi = 10.1016/b978-0-12-809633-8.90273-5 id = cord-021465-2pj26fmv author = PERDUE, MICHAEL L. title = Impact of Avian Viruses date = 2007-05-09 keywords = NDV; Newcastle; avian; bird; disease; host; infection; virus summary = Although there is variation in the economic or ecological impact of various viral groups from year to year and among geographic sites, the "Top Ten" list of virus groups exhibiting routine significant impact on commercial poultry worldwide (not necessarily in order of impact) are paramyxoviruses (Newcastle disease); coronaviruses (infectious bronchitis); herpesviruses (infectious laryngotracheitis; Marek''s disease; duck enteritis); reoviruses (viral arthritis); picornaviruses (avian encephalomyelitis); adenoviruses (egg drop syndrome); retroviruses (lymphoid leukosis); orthomyxoviruses (avian influenza); poxviruses (fowlpox); and birnaviruses (infectious bursal disease). With the recent documented transmission of a lethal avian influenza virus from commercial poultry to humans, these ecological relationships take on new significance. Lymphomas caused by MDV and retroviruses are still the most common viral neoplastic diseases of poultry, and a recent increase in mortality and evolution of more virulent MDV strains indicates that the impact of these viruses will continue to be felt (Witter, 1996) . doi = 10.1016/b978-012362675-2/50016-1 id = cord-335279-cfv18qn0 author = Paillot, Romain title = Special Issue “Equine Viruses”: Old “Friends” and New Foes? date = 2020-01-29 keywords = Equine; horse; virus summary = With this Special Issue, which assembles a collection of communications, research articles, and reviews, we intend to explore our understanding of a panel of equine viruses, looking at their pathogenicity, their importance in terms of welfare and potential association with diseases, their economic importance and impact on performance, and how their identification can be helped by new technologies and methods. The authors highlight the potential protective role of eqMx1, which primarily targets the virus nucleoprotein (NP), against the transmission of new IAVs in horses (i.e., eqMx1 could only inhibit the polymerase activity of IAVs of avian and human origin but remained inactive against the equine IAVs tested). To date, equine influenza virus remains one of the most important respiratory pathogens of horses worldwide, with a potential damaging impact on the equine industry, as clearly illustrated in 2007 in Australia and in 2019 in Europe [20, 21] . doi = 10.3390/v12020153 id = cord-268501-z4oztgi0 author = Palatnik-de-Sousa, Clarisa B. title = What Would Jenner and Pasteur Have Done About COVID-19 Coronavirus? The Urges of a Vaccinologist date = 2020-08-26 keywords = Chadox1; SARS; Sinovac; vaccine; virus summary = In fact, by May 11th, 2020 seven vaccines had already entered Phase I clinical trials: (1) encapsulated mRNA encoding protein S (Moderna and NIAID, USA); (2) Adenovirus expressing protein S (Cansino Biologics, China); (3) DCs modified with lentivirus expressing several proteins and CTLs (Shenzen Geno-Immune Medical, China); (4) an APC modified with lentivirus expressing several viral proteins (35); (5) Inno 4800, SARS CoV2 DNA Injection (Innovio, USA); (6) ChAdOx1 vaccine from the Jenner Institute, Oxford University, (UK) which is a genetically modified Adenovirus expressing Coronavirus proteins (39) , and is also being tested in a Phase II trial; and finally (7) the whole inactivated coronavirus with Alum by Sinovac, China (40) . Furthermore, in vaccinated monkeys, seven days after infection, the Sinovac inactivated vaccine at 6 µg/dose induced high titers of IgG antibodies directed against the S, RBD and lower levels of anti-N protein antibodies, high titers of virus neutralizing antibodies with no detected antibodydependent enhancement of disease (ADE) (40) . doi = 10.3389/fimmu.2020.02173 id = cord-323793-c69joaqs author = Palmieri, V. title = Can graphene take part in the fight against COVID-19? date = 2020-05-07 keywords = COVID-19; graphene; virus summary = In response to this global outbreak, we summarized the current state of knowledge of graphene and virus interaction as well as possible successful applications to fight COVID-19. Antibody-conjugated graphene sheets can rapidly detect targeted virus proteins and can be useful for large population screening, but also for the development of environmental sensors and filters, given the low cost of graphene materials. While government bodies are struggling in preventing further spread of COVID-19, researchers immediately started tests on vaccines and a clinical trial is currently underway with potential treatments for severe acute respiratory syndrome coronavirus -2 (SARS-CoV-2) [1] . Ziem and colleagues synthesized thermal rGO sulfate derivatives and demonstrated their antiviral activity against African swine fever virus, orthopoxvirus and herpesvirus strains [14, 15] . Synergistic antiviral effect of curcumin functionalized graphene oxide against respiratory syncytial virus infection doi = 10.1016/j.nantod.2020.100883 id = cord-254932-b447w202 author = Panda, Aruna title = Role of fusion protein cleavage site in the virulence of Newcastle disease virus date = 2003-11-18 keywords = NDV; V.F.; virus summary = The genetic stability of the mutations introduced into the genome of LaSota V.F. virus was determined by sequence analysis of the RT-PCR fragment that covered the region of the F protein cleavage site of the mutant virus that was passed five times in 9-day-old chicken embryos, and also from the mutant virus that was passaged once in chicken brains. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. These results demonstrated that the efficiency of cleavage of the F protein plays an important role if the NDV is delivered directly into the brains of chicks, but there could be other viral factors that probably affect peripheral replication, viremia, or entry into the central nervous system. doi = 10.1016/j.micpath.2003.07.003 id = cord-259927-xh9cw9ao author = Papadopoulos, Nikolaos G. title = Promising approaches for the treatment and prevention of viral respiratory illnesses date = 2017-07-21 keywords = RNA; RSV; ifv; respiratory; vaccine; virus summary = When considering prevention or treatment of viral respiratory tract infections, potential targets include the causative pathogens themselves but also the immune response, disease transmission, or even just the symptoms. Here we provide an overview of the options and highlight some of the most promising approaches in vRTI treatment, including symptomatic medication, immunomodulatory drugs, antiviral agents, and natural products, as well as in vRTI prevention, ranging from vaccines to immunostimulators and public health policies. Early in vivo evidence suggested that azithromycin has anti-inflammatory and antiviral effects through induction of interferon-stimulated gene mRNA expression and reduced viral replication and release in patients with asthma and chronic obstructive lung disease. mAb therapies to viral infections, such as EBV (rituximab) or RSV (palivizumab), provide passive immunization and are licensed, whereas similar agents targeting influenza and other viruses are in preclinical development. doi = 10.1016/j.jaci.2017.07.001 id = cord-260472-xvvfguht author = Papadopoulos, Nikolaos G. title = Antimicrobial strategies: An option to treat allergy? date = 2007-01-31 keywords = asthma; infection; respiratory; virus summary = The association between upper respiratory viral infections and asthma exacerbations in children was demonstrated almost three decades ago using virus cultures and serological techniques [5] . Abbreviations: RTePCR, reverse transcriptionepolymerase chain reaction; RV, rhinovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus; MPV, human metapneumovirus; ICAM-1, intracellular adhesion molecule-1; IFN-b, interferon-beta; NGF, nerve growth factor; SP, substance P; NK1, neurokinin 1 receptor; MBL, mannose-binding lectin; LABA, long-acting b 2 agonists. In the human respiratory tract, all the above agents are able to produce a spectrum of clinical acute infection phenotypes, ranging from the common cold, croup and acute bronchiolitis, to pneumonia, although each virus has increased propensity for a particular clinical disease (e.g. parainfluenza for croup, RSV for severe bronchiolitis, influenza for pneumonia) [21, 22] . Rhinovirus is the key virus accounting for the majority of exacerbations both in children and adults and thus the effective treatment or prevention of that infection would be a major asset in asthma therapy. doi = 10.1016/j.biopha.2006.10.004 id = cord-286741-h3oix9zc author = Park, Mee Sook title = Animal models for the risk assessment of viral pandemic potential date = 2020-04-22 keywords = H1N1; IAV; MERS; virus summary = Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses. When a virus with a nonhuman origin HA and an efficient human transmissibility gets transmitted from the adaptation host swine to human (4), a pandemic might ensue (5) of IAVs, avian and swine species should be considered the natural reservoir animals, and in case of MERS-CoVs, bats and dromedary camels [32, 87, 90] . In addition to NHP and hDPP4-mouse models, rabbits might be a good candidate for MERS-CoV transmission experiments due to its camel-like receptor distribution in the upper respiratory tract (Table 2 ) [142, 150] . Human-like symptoms of MERS-CoV infection have not been reproduced in other animals than hDPP4-mice and NHPs. Starting from the distinct receptor specificities of the HA proteins between avian and human IAVs, host restriction determinants of IAVs have been documented [56] . doi = 10.1186/s42826-020-00040-6 id = cord-303040-ha8gufh8 author = Park, Won-Ju title = Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force date = 2015-01-14 keywords = RSV; respiratory; virus summary = In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents. Recent studies indicate that RSV is an important cause of respiratory infection in elderly patients, either those with compromised immunity or inflicted with chronic illness, as well as in adult populations in a special environment, such as military personnel [7] [8] [9] [10] [11] . A case patient was a person, among military recruits in this boot camp, who was admitted to the medical care center in the boot camp with chief complaints of fever and symptoms of upper respiratory tract illness after May 26, 2011. In the event of an epidemic of acute febrile respiratory illness of a highly infective nature, it is recommended to conduct a test for RSV in the young adult population in the military facilities. doi = 10.3961/jpmph.14.037 id = cord-268540-wrjzr3ws author = Park, You Jeong title = Fighting the War Against COVID-19 via Cell-Based Regenerative Medicine: Lessons Learned from 1918 Spanish Flu and Other Previous Pandemics date = 2020-08-13 keywords = ACE2; COVID-19; Cov-2; SARS; cell; patient; spanish; virus summary = A potential target for drug development for COVID-19 also involves inhibition of ACE2, the host cell receptor for the S protein of SARS-CoV-2 that is primed by TMPRSS2 protease and may prevent the entry of the virus. As previously described, the intermolecular interaction between the viral SP and human ACE2 Phase II CAStem cells will be intravenously injected into patients with or without acute respiratory distress syndrome (ARDS) induced by COVID-19. Phase II Patients with acute respiratory distress syndrome caused by COVID-19 will be treated with intravenous UC-MSCs at a dose 1 million xKg. Patient improvement will be evaluated over three weeks, along with the assessment of the immune profile, investigating the stem cells'' effect on the cytokine storm. The similarities in systemic multi-organ complications between H7N9 and Sars-Cov-2 infections, along with direct evidence of the benefits of MSCs transplantation for COVID-19, further supports the potential of stem cells as an effective treatment [138] . doi = 10.1007/s12015-020-10026-5 id = cord-104317-t30dg6oj author = Parker, Michael T. title = An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date = 2016-09-30 keywords = host; human; infection; interaction; pathogenic; virome; virus summary = However, the obvious importance of viruses in the composition of all biomes has not (yet) been met with an appropriate fervor for the characterization of the viral REVIEW Recent advances in sequencing technologies have opened the door for the classification of the human virome. The discovery of intimate interactions of viruses with humans, like the role of endogenous retrovirus (ERV †) syncytins in placentation [27] , are categorically dissimilar to the classical view of viruses only as parasites and brings to issue how scientists are approaching the study of the virome. The application of this scaffold will not only deepen the understanding of known virus-host interactions in the ecological context of the virome, but will also identify logical next steps and gaps in current knowledge that are tantalizing areas for future exploration. Additionally, further characterization of the human virome is likely to uncover more viruses that persistently infect humans [31] , and such discoveries could pave the way for the treatment of diseases of currently unknown etiology. doi = nan id = cord-008551-yu71iewp author = Parrish, Colin R. title = Emergence, Natural History, and Variation of Canine, Mink, and Feline Parvoviruses date = 2008-04-11 keywords = CPV; FPV; MEV; Parrish; virus summary = This chapter discusses the emergence of canine parvovirus (CPV), the evidence concerning the previous emergence of mink enteritis virus (MEV) as the cause of a new disease in minks in the 1940s, and the mechanisms that determine the host ranges and other specific properties of the viruses of cats, minks, and dogs. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. Feline panleukopenia virus (FPV), MEV, and CPV are classified as "host range variants." In addition to the viruses of cats, minks, and dogs, similar viruses naturally infect many species within the families Felidae, Canidae, Procyonidae, Mustelidae, and possibly the Viverridae. doi = 10.1016/s0065-3527(08)60867-2 id = cord-272405-jmwn8pdn author = Parvez, Mohammad K. title = Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future date = 2017-08-04 keywords = SARS; ZIKV; human; virus summary = Despite substantial advancements in the understanding of the biology of pathogens, the breakthroughs in prevention, and their effects on public health and the global economy, the emergence of novel pandemic viruses remains an enduring puzzle. This review presents an update on the knowledge of important emerging/re-emerging viral infections worldwide, discussing their possible origin, evolution, natural reservoirs, human adaptations, and risk factors ( Fig. 1 ). To understand this further, a recently isolated HEV genotype 3 from a chronic hepatitis E patient containing a recombinant virus-host RNA genome was shown to infect cultured human, pig, and deer hepatocytes [39] . The field of phylodynamics, combining a modeling framework for host, epidemiological, and molecular data, especially for RNA viruses, shows particular promise for Parvez understanding the patterns of viral evolution during epidemics [40, 41] . Despite landmark advances in understanding the nature and biology of many pathogenic viruses, there is limited knowledge on emerging novel viruses, their potential reservoirs, and their modes of transmission. doi = 10.1159/000478729 id = cord-317496-6o2upns3 author = Pascual-Iglesias, Alejandro title = Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV date = 2019-07-25 keywords = PEDV; TGEV; figure; virus summary = In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). Interestingly, Viruses 2019, 11, 682 9 of 18 when viral RNA was isolated from feces of 21-day-old piglets at seven days post-vaccination (see below) and rTGEV-RS-SPEDV virus was sequenced, the same modifications were observed. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. doi = 10.3390/v11080682 id = cord-254963-cnvxlv6h author = Paskey, Adrian C. title = Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date = 2019-02-26 keywords = RNA; sample; sequencing; virus summary = In order to test this newly expanded probe panel and to specifically assess the effect of hybridization-based viral enrichment on the sensitivity of HTS for detection of a single virus within a complex environmental sample, commercial bat guano was spiked with increasing concentrations of Influenza virus (IFV). As expected, a dose-dependent effect in the proportion of sequencing reads derived from IFV was observed as the number of spiked genome copies increased ( Fig. 1a and Additional file 1: Table S1 ), in both the unbiased shotgun sequence data as well as the virus enriched sequence data. Such limitations have been of particular concern for U.S. Department of Defense (DoD) laboratories tasked with biosurveillance and biodefense activities in regions with limited material resources and human We demonstrate here that hybridization-based viral target enrichment yields robust coverage of small genomes from clinical samples, even yielding full-length, deeply covered genomes at concentrations whereby Fig. 3 Detection of close relative viruses irrespective of extensive multiplexing. doi = 10.1186/s12864-019-5543-2 id = cord-319379-qe56u93a author = Patil, Vaishali M. title = A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: Efficacy, safety and clinical trials date = 2020-05-11 keywords = COVID-19; chloroquine; hydroxychloroquine; virus summary = The well reported and clinically used anti-malarial aminoquinoline drugs (chloroquine and hydroxychloroquine) have shown potential to be repurposed to control the present pandemic by inhibition of COVID-19. The review elaborates the mechanism of action, safety (side effects, adverse effects, toxicity) and worldwide clinical trials for chloroquine and hydroxychloroquine to benefit the clinicians, medicinal chemist, pharmacologist actively involved in the management of COVID-19 infection. In vitro inhibition of human influenza A virus replication by chloroquine Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model Inhibition of human immunodeficiency virus type 1 replication by hydroxychloroquine in T cells and monocytes Inhibition of A/Human/Hubei/3/2005 (H3N2) influenza virus infection by silver nanoparticles in vitro and in vivo Mycophenolic acid inhibits dengue virus infection by preventing replication of viral RNA Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro doi = 10.1016/j.lfs.2020.117775 id = cord-271076-436nxsua author = Paul-Pierre, Pastoret title = Emerging diseases, zoonoses and vaccines to control them date = 2009-10-30 keywords = infection; specie; virus summary = In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals. doi = 10.1016/j.vaccine.2009.06.021 id = cord-025704-icedihm2 author = Pawestri, Hana A. title = Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date = 2020-06-01 keywords = H5N1; HPAI; Indonesia; virus summary = Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. Sequencing data contain valuable information about viral genetic characteristics, including presence of known human adaptive markers, resistance against available antiviral drugs or other changes that can explain the high and rising mortality, while antigenic characterization will help assess the potential protection of pre-pandemic vaccines. Amino acid sequences were analyzed to identify substitutions potentially linked to human adaptation, virulence, antiviral resistance and antigenic properties as listed in the CDC H5N1 Genetic Change Inventory [37] . Although some genetic diversity was observed in the polymerase genes, well-known substitutions such as PB2-E627K and PB2-D701N, which are often selected upon infection of humans and affects the virulence of avian influenza viruses such as H5N1 [12, 66, 67, 79] , were not commonly found in the new samples. doi = 10.1007/s11262-020-01765-1 id = cord-352619-s2x53grh author = Payne, Natalie title = Novel Circoviruses Detected in Feces of Sonoran Felids date = 2020-09-15 keywords = Rep; dna; genome; virus summary = Genomes from several families of circular Rep-encoding single-stranded DNA viruses (CRESS-DNA viruses) are part of the phylum Cressdnaviricota [22] and have been identified in fecal samples of other mammals, including domestic cats [23, 24] , bobcats, African lions [25] , capybaras [26] , and Tasmanian devils [27] . Here we used a metagenomic approach to identify novel circoviruses in the feces of two species of Sonoran felids, the puma and bobcat; although not endangered, knowledge of viral threats facing these species could help prevent future population decline, as well as indicate potential threats to the endangered ocelot and jaguar. Based on the species-demarcation threshold for circoviruses which is 80% genome-wide identity [28] , both of these belong to a new species which we refer to as Sonfela (derived from Sonoran felid associated) circovirus 1. As the viral genomes were derived from scat samples, the circoviruses could have infected the bobcat prey species or the felids themselves or be environmentally derived. doi = 10.3390/v12091027 id = cord-352475-cmmpy5u7 author = Pemmada, Rakesh title = Science-Based Strategies of Antiviral Coatings with Viricidal Properties for the COVID-19 Like Pandemics date = 2020-09-11 keywords = COVID-19; antiviral; coating; metal; oxide; virus summary = The worldwide, extraordinary outbreak of coronavirus pandemic (i.e., COVID-19) and other emerging viral expansions have drawn particular interest to the design and development of novel antiviral, and viricidal, agents, with a broad-spectrum of antiviral activity. Hence, it is highly desirable to search for potential antiviral and viricidal elements (materials and coatings) to design personal protective equipment (PPE), hygienic implements, and other devices to fight against the rise of viral pandemics and virus-associated fatal risks [22] . In addition, a large number of studies have reported coating materials containing metal ions (i.e., silver, copper, zinc), which have demonstrated an excellent antiviral ability with long-term, persistent effects [30] [31] [32] [33] [51] [52] [53] [54] [55] . Various strategies involved in the development of antiviral and viricidal coatings, like modifying the surface of a substrate via antiviral polymers, incorporation of metal ions/oxides, and functional nanoparticles were discussed. doi = 10.3390/ma13184041 id = cord-351482-hzh5tyoo author = Peng, Xinxia title = Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date = 2011-11-15 keywords = Fig; RNA; SARS; small; virus summary = The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). doi = 10.1128/mbio.00198-11 id = cord-016070-e9ix35x3 author = Perret Pérez, Cecilia title = Pneumonia Caused by Emerging Viral Agents date = 2020-02-01 keywords = human; respiratory; virus summary = The SARS coronavirus and MERS-CoV are two pathogens from the coronavirus family that predominantly cause serious lower tract respiratory infections with a high mortality rate, but they are genetically different viruses. This observation suggests that camels are the reservoirs of the virus, which can be transmitted to humans through direct contact with these animals or through consumption of their milk: 1599 cases had been diagnosed by July 2015, with 574 deaths [World Health Organization (WHO)]. HCoV-NL63 and HCoV-HKU1 are viruses that tend to manifest as a common cold, just as the usual coronaviruses HCoV-229E and HCoV-OC43; nevertheless, in small children, elderly patients, and immunosuppressed patients, they can cause serious respiratory disease with a high mortality rate. Isolated cases of avian origin in humans caused by the influenza H10N8 virus and H6N1 have been observed in China. doi = 10.1007/978-3-030-26961-6_34 id = cord-278093-0twnkv93 author = Perveen, Shagufta title = Coronavirus nCOVID-19: A Pandemic Disease and the Saudi precautions date = 2020-06-18 keywords = SARS; disease; virus summary = Recently a novel coronavirus (nCOVID-19) has first emerged in China, causing multiple symptoms in humans and closely related to those caused by SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In these circumstances, rapid reviews which recommended by WHO (World Health Organization), and these recommendations are very significant, helpful and cover current data with different preventive measures developed by the Saudi CDC (Saudi Centre for Disease Prevention and Control). Taking into consideration the preventive measures by pharmacists as part of health care professions, however, the number of infected people, especially those with close contact with nCOVID-19 patients, are rise day by day and currently seems unstoppable. In comparison to other members of coronaviruses ,which cause humans respiratory infections, SARS-CoV (first then it has spread to 216 different countries and territories all over the world, and it seems more deadly. doi = 10.1016/j.jsps.2020.06.006 id = cord-344093-3bniy5b5 author = Peteranderl, Christin title = The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date = 2017-03-22 keywords = IAV; IFN; TRAIL; cell; infection; type; virus summary = A prominent regulator of disease outcome, especially in-but not limited to-respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. (73) Cell death induction, e.g., Bcl-2-associated X protein, caspase-8, Fas-associated protein with death domain, Fas ligand, and TNF-related apoptosis-inducing ligand (TRAIL) dsRNA, polyI:C (4, 110) IAV (4, 5, 10, 115) Sendai virus (110) TRAIL Virus control by apoptosis induction in infected cells IAV (6, 170, 171) Tissue injury by apoptosis of both infected and non-infected alveolar epithelial cells, lung macrophages IAV (5, 7, 10) RSV (137) Necrosis of fibroblasts, dendritic cells, and epithelial cells IAV (146, 147, 168) Increased cellular infiltration CoV (175) Decreased expression of Na,K-ATPase, impaired epithelial fluid reabsorption IAV (11) iNTRODUCTiON In 1957, Isaacs and Lindenmann (1) first recognized the potential of a soluble and probably cell-derived factor to combat influenza virus infection and named this factor interferon [(IFN) from latin interferre, to interfere]. doi = 10.3389/fimmu.2017.00313 id = cord-348161-757c51xw author = Petrosova, A. title = Development of a highly sensitive, field operable biosensor for serological studies of Ebola virus in central Africa date = 2007-03-26 keywords = ELISA; Ebola; Sudan; Zaire; virus summary = We employed a photo immobilization methodology based on a photoactivatable electrogenerated poly(pyrrole-benzophenone) film deposited upon an indium tin oxide (ITO) modified conductive surface fiber-optic. The photochemically modified optical fibers were tested as an immunosensor for detection of antibodies against Ebola virus, in animal and human sera, by use of a coupled chemiluminescent reaction. In this study we present a newly developed optical immunosensor for detection of antibodies to Ebola virus strains Zaire and Sudan, by using a photoimmobilization methodology based on a photoactivable electrogenerated polymer film. The optical fibers coated with poly(pyrrole-benzophenone) were soaked in diluted solution containing inactivated Ebola virus antigen (approximately 7.5 g/ml, the concentration was determined by Micro BCA Protein assay kit, PIERCE) and irradiated with UV light. The calibration curve obtained from the optical fiber immunosensor and ELISA for the detection of anti-Ebola subtype Zaire antibodies. doi = 10.1016/j.snb.2006.07.005 id = cord-298678-hjxph9jm author = Petrović, T. title = Viral Contamination of Food date = 2016-02-05 keywords = EFSA; HAV; HEV; food; outbreak; virus summary = Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. These viruses have been identified in a variety of environmental samples, including wastewater, sludge, in marine, surface, and drinking waters, and shellfish, but no foodborne or waterborne outbreaks associated with the enteric HAdV have been reported (Greening, 2006) . The presented data suggest a high prevalence of different human enteric viruses, but mostly NoV, HAV, EV, HAdV, and HRV were found in shellfish samples collected from growing areas, as well as from the market in different countries. doi = 10.1016/b978-0-12-800723-5.00005-x id = cord-314254-9ye8tfvz author = Pfaender, Stephanie title = Natural reservoirs for homologs of hepatitis C virus date = 2014-03-26 keywords = GBV; HCV; NPHV; RNA; virus summary = To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse. doi = 10.1038/emi.2014.19 id = cord-013073-siy7dvlo author = Pfäfflin, Albrecht title = Influenza virus-flow from insects to humans as causative for influenza seasonality date = 2020-10-09 keywords = influenza; virus summary = title: Influenza virus-flow from insects to humans as causative for influenza seasonality A model of viral flow is described and specified to explain influenza virus seasonality, which, in temperate climate, usually evolves when insects have mostly disappeared. The incidence of influenza under different circumstances e.g. temperature, humidity, or tropical conditions and different aspects like synchronicity of infections or in respect to evolutionary conditions do sustain this hypothesis if the behaviour of insects is considered. When influenza virus has reached humans and persists there, it disappears during off-season but re-emerges regularly. Seasonality of influenza is explainable using this insect-compartment model in temperate climate conditions. Associations of global weather conditions to the dynamics of seasonal influenza are found regularly, but the biological mechanism between climate variations and influenza epidemics is dubious [27] . Here, an viral-flow model contributory to explain seasonality of influenza is applied to elucidate questions and circumstances concerning influenza infections like synchronicity, environmental factors. doi = 10.1186/s13062-020-00272-5 id = cord-255623-qdpdsye9 author = Pham, Hien T. title = Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children''s Hospital date = 2020-03-11 keywords = infection; respiratory; virus summary = We collected 194 nasopharyngeal aspirates from infants (2–24 months old) with lower respiratory tract infections treated at the Vietnam National Children''s Hospital between November 2014 and June 2015 and assessed the presence of 16 virus types and subtypes by multiplex PCR using the xTAG Respiratory Viral Panel (RVP) assay. e clinical presentation depends on the specific causative agent but typically includes fever and lower respiratory tract symptoms, such as tachypnoea, nonproductive cough, wheeze, and increased breath sound [7, 8] . In the present study, we used the xTAG RVP FAST assay to identify the viruses causing RI in children and the relationship between specific viruses and clinical outcome. We enrolled 194 pediatric infants (2-24 months old) who had lower respiratory tract infections and were treated at the Vietnam National Children''s Hospital. Bronchiolitis was the most common clinical characteristic of lower respiratory tract infection at the Vietnam National Children''s Hospital. doi = 10.1155/2020/7931950 id = cord-022960-u4s23x1r author = Pihlstrom, Bruce Lee title = Selections from the current literature date = 2020-04-17 keywords = virus summary = In the context of the novel coronavirus pandemic, the authors reviewed relevant literature about the virus and made recommendations for controlling its transmission in dental offices. 2 In light of these reports, the authors noted that dental patients and personnel can be exposed to this virus because of face-to-face communication with patients, frequent exposure to saliva, blood, and aerosols, and by handling sharp instruments. They also noted that the virus could be spread by direct or indirect contact with human fluids, patient materials, contaminated dental instruments, and environmental surfaces. [3] [4] Because of the likelihood of 2019-nCoV transmission in the dental office, the authors made several recommendations to help mitigate the spread of the virus in this setting. This is an important study because as the authors noted, it may explain why this virus appears to persist in the environment and is more transmissible than other coronaviruses. doi = 10.1016/j.aime.2020.04.020 id = cord-271790-3s8o774l author = Pinto Mendes, J. title = The role of infection in asthma date = 2008-10-31 keywords = CD14; Mendes; Pinto; RSV; asma; asthma; que; virus summary = Animal research is difficult to extrapolate to man but suggests RSV can induce allergic sensitisation 28 , increase bronchial and interleukin (IL)-13 hyperresponsiveness, and rão, na maioria dos casos, consequências remotas, embora algumas vezes descrevam sibilâncias que irão desaparecer aos 3 -5 anos e só raramente se prolongam, instalando -se ou não uma asma. If viral infection in acute asthma, particularly RV -the most studied -is associated with neutrophilic inflammation, cellular lysis and production of interferons (IFNs) 46 and if the environment is rich in IL-4, the production of IL-5, RANTES (Regulated upon Activated T cell Expressed and Selected), eotaxin, eosinophilic infiltration and IgE production 47 generally occur. While children at risk at allergic asthma have long been told to avoid contact with these animals, it is concluded that prolonged early life exposure to Feld-1 induces a form of immune tolerance specific to that allergen 89 . doi = 10.1016/s2173-5115(08)70297-5 id = cord-336447-hpnkou41 author = Pitlik, Silvio Daniel title = COVID-19 Compared to Other Pandemic Diseases date = 2020-07-31 keywords = COVID-19; RNA; SARS; disease; pandemic; virus summary = Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. doi = 10.5041/rmmj.10418 id = cord-016475-7ldxvbpz author = Pleschka, Stephan title = Anti-viral approaches against influenza viruses date = 2006 keywords = MEK; influenza; vaccine; viral; virus summary = After influenza virus infection antibodies directed against all major viral proteins can be detected in humans and the level of serum antibodies correlate with resistance to disease (Couch, 2003; Couch and Kasel, 1983; Coulter et al., 2003; Nichol et al., 1998; Potter and Oxford, 1979) . Nevertheless, IKK and NFκB might not only have anti-viral functions as two recent studies demonstrate that influenza viruses replicate much better in cells where NFκB is pre-activated (Nimmerjahn et al., 2004; Wurzer et al., 2004) . Apoptosis is mainly regarded to be a host cell defense against virus viruses (reviewed in: Julkunen et al., 2000; Ludwig et al., 2003; infections since many viruses express anti-apoptotic proteins to prevent this cellular response. Influenza virus-induced NF-kappaB-dependent gene expression is mediated by overexpression of viral proteins and involves oxidative radicals and activation of IkappaB kinase doi = 10.1007/978-0-387-31047-3_5 id = cord-355181-affuyn8z author = Poggio, Claudio title = Copper-Alloy Surfaces and Cleaning Regimens against the Spread of SARS-CoV-2 in Dentistry and Orthopedics. From Fomites to Anti-Infective Nanocoatings date = 2020-07-22 keywords = COVID-19; SARS; copper; surface; virus summary = SARS-CoV-2 (acronym for severe acute respiratory syndrome coronavirus 2), responsible for the current outbreak that causes COVID-19 (acronym for "corona virus disease 2019"), is reported to be able of surviving on inanimate surfaces for days. An interesting 2008 article that dealt with environmental hygiene focused on the importance of the transmission of respiratory tract infections Genetic material of SARS-CoV-2 has recently been demonstrated in the plasma of patients with COVID-19, thus feeding concerns for virus shedding during surgical procedures [16] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . Incorporation of copper alloy surfaces in conjunction with effective cleaning regimens and good clinical practice could help to control transmission of respiratory coronaviruses, including MERS and SARS [52, 53] . doi = 10.3390/ma13153244 id = cord-015764-ly68q5z0 author = Poissy, J. title = La modulation de la signature transcriptomique de l’hôte infecté : une nouvelle stratégie thérapeutique dans les viroses graves ? Exemple de la grippe date = 2016-04-07 keywords = influenza; virus summary = Une des approches possibles pour le développement de nouveaux antiviraux à plus large spectre d''action est de cibler non pas le virus, mais la cellule de l''hôte infecté, en utilisant la signature transcriptomique cellulaire de l''infection pour sélectionner et repositionner des molécules déjà sur le marché qui vont moduler ce profil transcriptomique, supposé comme étant favorable à l''infection. Les admissions en réanimation pour détresse respiratoire associée à une infection par influenza de type A sont estimées à 12/100 000 personnes.an chez l''adulte [13] . Par ailleurs, plusieurs méthodes de criblage à haut débit (petits ARN interférents [siRNA], interaction protéine-protéine) ont été menées ces dernières années et ont identifié plusieurs centaines de facteurs cellulaires impliqués dans la réplication des virus influenza et/ou la pathogenèse associée à l''infection, proposant ainsi autant de cibles thérapeutiques potentielles [43, 44] . Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus doi = 10.1007/s13546-016-1188-1 id = cord-267567-w39f584z author = Pombo, Joao Palma title = Perturbation of Intracellular Cholesterol and Fatty Acid Homeostasis During Flavivirus Infections date = 2018-06-04 keywords = SCAP; cholesterol; virus summary = Upon flavivirus infections, these are significantly altered: on the one hand, these viruses can co-opt lipid metabolic pathways to generate ATP to facilitate replication, or to synthesize membrane components to generate replication sites; on the other hand, more recent evidence suggests counter strategies employed by host cells, which actively modulate several of these networks in response to infection, enhancing interferon signaling by doing so, and thus creating an antiviral environment. In this review, we discuss recent data on mechanisms of alteration of lipid metabolic pathways during infection by flaviviruses, with a focus on cholesterol and fatty acid biosynthesis, which can be manipulated by the invading viruses to support replication, but can also be modulated by the host immune system itself, as a means to fight infection. doi = 10.3389/fimmu.2018.01276 id = cord-302716-wfla3l20 author = Popov, Vsevolod L. title = Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) date = 2019-05-25 keywords = figure; virion; virus summary = Viruses can be differentiated by their specific morphology (ultrastructure): shape, size, intracellular location, or from the ultrastructural cytopathic effects and specific structures forming in the host cell Upolu, Aransas Bay [22] , Sinu [23] , and Trinity [24] orthobunyaviruses [25] [26] [27] , nyamiviruses [28] , a new reovirus from Cameroon (Fako virus) [29] and Colombia [30] , a new paramyxovirus [31] , an insect-specific (capable of replication in insects but not in vertebrates) alphavirus [32] , a new flavivirus genus [33] and other novel flaviviruses [34] [35] [36] [37] and rhabdoviruses [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] . Insect-specific viruses isolated recently from mosquitoes and phlebotomine sandflies have been characterized and proposed to represent a new genus (Negevirus) related to genera of mite-infecting plant viruses (Blunervirus, Cilevirus, and Higrevirus) in the new family Kitaviridae [49, 73] , or novel members of Entomobirnavirus, family Birnaviridae ( Figure 10D ). doi = 10.3390/v11050477 id = cord-309642-wwaa6ls0 author = Potgieter, Leon N.D. title = Pathogenesis of Viral Infections date = 1986-11-30 keywords = cell; dna; host; infection; result; viral; virus summary = 7 · 18 · 84 · 133 Such restrictions function at the cellular level either as the presence or absence of appropriate cell surface receptors (in some instances, they have been shown to be inherited as dominant alleles in a Mendelian manner) 9 · 18 · 26 · 46 · 68 · 97 ·u 9 · 120 or the intracellular hospitality of the cell (several genetic host restrictions on virus replication have been identified).18·32·59·80·82·108·109·120·126 Restricted growth of several DNA viruses in some cells results in transformation without production of progeny viruses. 112 The phenomenon appears to be mediated by virus-induced receptors on the surface membrane of cells and may be one mechanism of the often-encountered secondary bacterial infections associated with viral diseases. 51 · 52 · 104 Viral respiratory tract disease is a consequence of mechanical and biochemical injury to epithelial cells and alveolar macrophages, which can, in the most severe instances, result in secondary bacterial infection, pneumonia, and death. doi = 10.1016/s0195-5616(86)50129-7 id = cord-271172-y48dovux author = Potter, Christopher William title = Chapter 25 Respiratory tract viruses date = 1998-12-31 keywords = cell; infection; influenza; respiratory; virus summary = Adenoviruses, spread by droplet infection, impinge on epithelial cells in the pharynx or in the lower respiratory tract to enter and kill cells by a combination of inhibition of cellular metabolism, virus replication and the toxic effects of the penton: the results are extensive desquamation of affected areas, causing sore throat, necrotizing bronchitis, bronchiolitis and interstitial pneumonia. The illnesses vary from relatively mild common colds caused by rhinoviruses and coronaviruses, to severe bronchiolitis and pneumonia caused by adenoviruses and influenza viruses and respiratory syncytial virus (RSV) in infants: the former is associated with little morbidity and no mortality, while influenza is responsible annually for between 1 and 25 thousand deaths per 50 million population. The illnesses vary from relatively mild common colds caused by rhinoviruses and coronaviruses, to severe bronchiolitis and pneumonia caused by adenoviruses and influenza viruses and respiratory syncytial virus (RSV) in infants: the former is associated with little morbidity and no mortality, while influenza is responsible annually for between 1 and 25 thousand deaths per 50 million population. doi = 10.1016/s1569-2582(97)80009-8 id = cord-290617-45be6gxe author = Poulain, Florian title = Footprint of the host restriction factors APOBEC3 on the genome of human viruses date = 2020-08-14 keywords = Fig; NTC; dna; virus summary = Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. By breaking down the human viruses into their respective Baltimore''s group (S3 Fig), we observed that NTC depletion is not present in reverse transcribing nor in negative sense single strand RNA viruses. We also observed a mild general NCC depletion in single strand DNA and double strand RNA viruses, justifying further investigation for a possible A3G-induced footprint (S1 Fig). In order to identify A3-footprinted viruses, we detailed the NTC and NNGANN ratios for 870 human viral species (Fig 4A) . B. The observed/expected ratios of TC dinucleotide at various codon positions and on both strands (i.e. NNTCNN, TCN, NTC, GAN, NGA and NNGANN) were calculated for the putative A3-footprinted viral species and depicted by a heatmap. doi = 10.1371/journal.ppat.1008718 id = cord-007530-eyk015n3 author = Powell, H.C. title = Electron-microscopic appearance of the DA virus, a demyelinating murine virus() date = 2003-03-06 keywords = BHK-21; virus summary = doi = 10.1016/0022-510x(77)90087-9 id = cord-340481-i3qrxnpr author = Pozo, Francisco title = Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date = 2008-07-31 keywords = IRA; PCR; los; virus summary = En comparación con las técnicas de diagnóstico clásicas, como son el cultivo de virus en líneas celulares (CC) o la detección de antígenos mediante ensayos de inmunofluorescencia (IF) u otros métodos, la reacción en cadena de la polimerasa (PCR), en sus múltiples variantes, ha permitido incre-mentar de manera considerable el número de muestras respiratorias en las que se detecta la presencia de alguno de los virus asociados con IRA. La elevada sensibilidad de los ensayos de PCR también comporta algunos inconvenientes para el diagnóstico etiológico de la IRA, como son la detección de virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas o la detección, a consecuencia de excreción prolongada, del virus en secreciones de pacientes que ya se han recuperado de una infección. doi = 10.1016/s0213-005x(08)76537-6 id = cord-345020-ai5tib7h author = Price, O. H. title = Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia date = 2019-06-17 keywords = RSV; influenza; virus summary = Studies investigating viral interference since the pandemic are sparser, though two studies reported that the timing and magnitude of respiratory virus epidemics were affected by the timing of the seasonal influenza A peak [15, 16] . We used routine diagnostic testing data of specimens from both the community and hospitals at the Victorian Infectious Diseases Reference Laboratory (VIDRL) between 2002 and 2017 to describe relationships between respiratory viruses, with a focus on influenza A and RSV. Seasonality of viruses was assessed visually by time series analysis and for further investigation each virus was compared with influenza A and RSV using cross-correlations that estimated the association between peaks in epidemic curves at a lag or lead of up to 15 weeks. Results of further investigation by logistic regression adjusted for covariates that are predictors of codetection (sex, age and season) were compatible with influenza A, RSV and picornavirus conferring temporary immunity against infection by another respiratory virus. doi = 10.1017/s0950268819001055 id = cord-335116-c83xyev5 author = Proença-Módena, José Luiz title = Respiratory viruses are continuously detected in children with chronic tonsillitis throughout the year date = 2014-07-21 keywords = HEV; respiratory; virus summary = Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. We have previously reported high rates of detection of respiratory virus genomes in tonsils and adenoids from patients with chronic adenotonsillar diseases, suggesting a significant association of viruses, particularly picornaviruses, with severe tonsillar hypertrophy [3] . doi = 10.1016/j.ijporl.2014.07.015 id = cord-276585-m1dkkbq7 author = Pulliam, Juliet R. C. title = Viral Host Jumps: Moving toward a Predictive Framework date = 2008-02-13 keywords = host; specie; virus summary = Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. Although he makes no attempt to quantitatively determine the relative frequency of emergence for different types of pathogens, Burke claims that recent pandemics in humans and wildlife have mostly been caused by RNA viruses, citing multiple examples (influenza A, HIV-1, enteroviruses 70 and 71, human T-cell lymphoma virus, three paramyxoviruses, porcine respiratory coronavirus, and a calicivirus that causes hemorrhagic disease in rabbits). doi = 10.1007/s10393-007-0149-6 id = cord-325611-tu1bn4hu author = Pérez-Sautu, Unai title = Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date = 2019-07-23 keywords = HTS; PCR; respiratory; virus summary = We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group. doi = 10.1080/22221751.2019.1640587 id = cord-345157-fhmhpobi author = Qi, Dan title = Virus infection-induced host mRNA degradation and potential application of live cell imaging date = 2018-12-12 keywords = RNA; host; virus summary = Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. Many viruses also impair the translation of cellular mRNA [1e3], one of the mechanisms during the shift of gene expression from host to virus, a process termed "host shutoff", in order to prevent the production of anti-viral, host protecting proteins [4] . Moreover, Gaglia et al.''s work showed that viral encoded proteins trigger host mRNA degradation by a primary endonucleolytic cleavage causing shutoff of host gene expression and a host exonuclease such as Xrn1, an important 5 0 to 3 0 exonuclease in human cells, were required in subsequent completion of host mRNA turnover [5] . doi = 10.1016/j.jrid.2018.12.002 id = cord-278456-gsv6dh36 author = Qureshi, Abid title = AVCpred: an integrated web server for prediction and design of antiviral compounds date = 2016-09-09 keywords = HIV; QSAR; virus summary = In this study, we have developed quantitative structure–activity relationship (QSAR)‐based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. We have integrated these models in the AVCpred web server, which will be helpful for virtual screening of AVCs and designing new compounds to target the viruses. The QSAR models have been integrated into a freely available and easy to use web server, ''AVCpred'', where users can predict the antiviral potential of their query molecules against the different viruses in terms of percent inhibition value. In this study, we developed virus specific as well as general prediction models to identify the likelihood of a compound being antiviral using selected chemical attributes of experimentally validated AVCs. PaDEL, an open-source software, was used to calculate molecular descriptors and fingerprints. doi = 10.1111/cbdd.12834 id = cord-310141-2jofy8fo author = Qureshi, Abid title = A review on current status of antiviral siRNA date = 2018-04-15 keywords = RNA; cell; short; virus summary = Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. For example, siRNAs directed against different genes of deadly viruses like human immunodeficiency virus (HIV), 9, 10 influenza virus (INFV), 11, 12 hepatitis B virus (HBV), 13 SARS coronavirus (SARS-CoV), 14, 15 human papillomavirus (HPV), 16 and West Nile virus (WNV) 17 in infected cells displayed encouraging results in inhibiting viral replication. 18, 19 Short interfering RNAs for various human viruses like respiratory syncytial virus (RSV), hepatitis C virus (HCV), HBV, and HIV are also appearing in clinical trials, which further elucidate their importance in inhibiting viral infections. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice doi = 10.1002/rmv.1976 id = cord-276715-d1nh2dvb author = Raha, Syamal title = Is Copper beneficial for COVID-19 patients? date = 2020-05-05 keywords = virus summary = Besides, Cu can kill several infectious viruses such as bronchitis virus, poliovirus, human immunodeficiency virus type 1(HIV-1), other enveloped or nonenveloped, singleor double-stranded DNA and RNA viruses. Based on available data, we hypothesize that enrichment of plasma copper levels will boost both the innate and adaptive immunity in people. Copper exposure to human coronavirus 229E destroyed the viral genomes and irreversibly affected virus morphology, including disintegration of envelope and dispersal of surface spikes [16] . Copper deficiency could lead a decreased number of circulatory blood cells with a greater susceptibility towards infection in older people In a study of 11 men on a low-Cu diet (0.66 mg Cu/day for 24 days and 0.38 mg/day for another 40 days) showed a decreased proliferation response of their white blood cells when presented with an immune challenge in cell culture [33] . Thujaplicin-copper chelates inhibit replication of human influenza viruses Effects of low-copper diets on human immune response doi = 10.1016/j.mehy.2020.109814 id = cord-304278-0qy1nngs author = Raj, G. Dhinakar title = Infectious bronchitis virus: immunopathogenesis of infection in the chicken date = 2007-11-12 keywords = IBV; Jones; Raj; bronchitis; infectious; virus summary = While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens doi = 10.1080/03079459708419246 id = cord-334771-uy3s6443 author = Rao, BL title = A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date = 2004-09-09 keywords = Chandipura; India; RNA; virus summary = Samples obtained were: 54 blood samples, 22 throat swabs, ten CSF samples, and one brain aspirate from 55 patients with encephalitis; five blood samples and nine throat swabs from 13 fever cases; and ten blood samples and one throat swab from ten family contacts (including specimens from the brother and mother of a patient who Methods Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. The confirmed Chandipura virus encephalitis group consisted of individuals from whose samples we isolated the virus, viral RNA, or reactive IgM antibodies. The viruses isolated in different cell lines from clinical samples from patients with encephalitis were confirmed as Chandipura virus with various techniques including complement fixation, neutralisation test, and immunofluorescence assay. Moreover, the presence of Chandipura virus RNA in nine patients with encephalitis, all from samples obtained before day 4 after onset of illness, suggests an early viraemic phase of the infection process. doi = 10.1016/s0140-6736(04)16982-1 id = cord-000050-tfcerilc author = Rao, Srinivas title = Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date = 2008-06-18 keywords = H5N1; dna; vaccine; virus summary = METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. After optimization of injection conditions, alternative multivalent DNA vaccine regimens were analyzed and compared for magnitude and breadth of neutralizing antibodies, as well as protective efficacy after challenge in mouse and chicken models of HPAI H5N1 infection. The ability of chickens to generate specific antibodies was assessed with three strains that showed broad cross protection in mouse studies (A/Vietnam/1203/2004, A/Anhui/ 1/2005 and A/Indonesia/05/2005), administered individually or in combination, by different injection methods. doi = 10.1371/journal.pone.0002432 id = cord-266822-ecq50ye2 author = Rath, Barbara title = Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials date = 2017-05-12 keywords = Disease; Score; Severity; ViVI; respiratory; virus summary = Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Standardized measures of disease severity are urgently needed for clinical trials of vaccines and antivirals currently in development for ARI caused by influenza (FLU), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), adenovirus (ADV), or human rhinovirus (HRV) [9] [10] [11] [12] [13] [14] [15] [16] [17] . Considering the variability in disease presentations and courses of illness with influenza and other respiratory viral infections in children, the ViVI Disease Severity Score is not intended to be validated against future clinical events or outcomes. Our contributions are the following: (A) The design of a hospital-based surveillance program and a unique QM cohort of more than 6000 children, where an independent QM team monitored patients daily using standardized clinical assessments and virology at the National Reference Centre for Influenza and Other Respiratory Viruses. doi = 10.1080/14787210.2017.1295847 id = cord-348860-zaimorg0 author = Ratra, Ruchi title = Functional genomics as a tool in virus research date = 2008-06-01 keywords = RNA; dna; virus summary = The genomics era has revolutionized the biological sciences and has heralded the emergence of new ''omics'' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] . doi = 10.1007/s12088-008-0032-3 id = cord-004781-ajf9zig0 author = Ray, N. B. title = Rabies viruses infect primary cultures of murine, feline, and human microglia and astrocytes date = 2014-03-07 keywords = cell; virus summary = Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. In addition, a number of studies have reported rabies viral antigens and virions in human [1, 13, 29] and murine astrocytes [10, 18, 23] , and in murine rami®ed microglial cells [27] , begging the question of the role of these cells in viral replication and persistence, as well as pathogenesis. In the present study, as an initial step toward evaluation of the potential involvement of these glial cells in rabies virus infections, we have directly examined the ability of different rabies virus strains and isolates to infect and replicate in primary cultures of microglia and astrocytes. doi = 10.1007/s007050050136 id = cord-003216-5qioku84 author = Rehman, Zaib Ur. title = Pathobiology of Avian avulavirus 1: special focus on waterfowl date = 2018-09-19 keywords = APMV-1; Newcastle; disease; virus summary = Besides the strong innate immune responses, waterfowl are generally considered long-term carrier of APMV-1 and disease outbreaks have been reported since 1997 [12] [13] [14] , and were confirmed by follow up experimental studies. Host innate immune responses of ducks infected with Newcastle disease viruses of different pathogenicities Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during Histopathological alterations in immune organs of chickens and ducks after experimental infection with virulent 9a5b newcastle disease virus Experimental co-infections of domestic ducks with a virulent Newcastle disease virus and low or highly pathogenic avian influenza viruses Phylogenetic diversity among low-virulence newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates Genomic characterizations of a Newcastle disease virus isolated from ducks in live bird markets in China doi = 10.1186/s13567-018-0587-x id = cord-270161-vaejyy4i author = Reicks, Darwin L. title = Effective biosecurity to protect North American studs and clients from emerging infectious disease date = 2019-10-01 keywords = PRRS; boar; virus summary = Circumstances in North America in the period of 1999–2004 resulted in numerous PRRS virus (Porcine Reproductive and Respiratory Syndrome) negative boar studs becoming infected and disseminating virus to sow farms. Cleary defined physical barriers for people and animal entry and exit, sanitization and/or down time on incoming supplies, risk mitigation and testing of feed ingredients, and filtration have been keys to changing the incidence of emerging infectious disease introduction into boar studs. Biosecurity measures to prevent PRRS (Porcine Reproductive and Respiratory Syndrome) virus transfer among farms has largely influenced the biosecurity practices of boar studs in North America and worldwide. The purpose of this paper is to review practical effective biosecurity procedures that have made an impact in reducing the risk of emerging infectious disease entering boar studs and infecting sow farms through semen. Air filtration can be an effective way to prevent aerosol transmission of important swine viral diseases that can spread from the boars through the semen and infect sow farms. doi = 10.1016/j.theriogenology.2019.05.041 id = cord-331673-xv1tcugl author = Reina, Giacomo title = Hard Nanomaterials in Time of Viral Pandemics date = 2020-07-15 keywords = HIV; Nanoparticles; ROS; SARS; Virus; antiviral; cell; infection; viral summary = For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). doi = 10.1021/acsnano.0c04117 id = cord-018302-lmly43rd author = Renaud, Christian title = Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date = 2016-02-15 keywords = HSCT; RSV; infection; recipient; respiratory; virus summary = Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. Surveillance studies of respiratory viruses from transplant centers have established the high frequency and the signifi cant clinical impact of respiratory viral infections in HSCT recipients overall [ 8 -15 , 46 , 47 ] as well as the relative importance of RSV in terms of morbidity and mortality (Table 31 -2 ). A retrospective MDACC study of confi rmed RSV infections in 280 allogeneic HSCT recipients from 1996 to 2009 utilized multivariable logistic regression to demonstrate that lack of ribavirin aerosol therapy at the upper respiratory tract disease stage was an important risk factor associated with RSV LRTI and all-cause mortality [ 99 ] . doi = 10.1007/978-3-319-28797-3_31 id = cord-016882-c9ts2g7w author = Ribeiro, Edna title = Viruses Present Indoors and Analyses Approaches date = 2017-06-12 keywords = PCR; Rosa; infection; respiratory; virus summary = It''s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Viruses'' inductors of Severe Acute Respiratory Syndrome (SARS), influenza and norovirus are transmitted from patients primarily by contact and/or droplet routes, while airborne transmission occurs over a limited distance (Srikanth et al., 2008) . It is well-known that viruses are shed in large numbers, with transmission routes extraordinary diverse, including direct contact with infected persons, faecal-oral transmission (through contaminated food and water), droplet and airborne transmission, and can survive for long periods on surfaces or fomites, emphasizing the possible role of surfaces in the transmission of viruses (Barker et al., 2001; La Rosa et al., 2013) . doi = 10.1007/978-3-319-61688-9_7 id = cord-017489-ftz9190a author = Richards, Guy A. title = Viruses in the Intensive Care Unit (ICU) date = 2005 keywords = ICU; SARS; patient; pneumonia; virus summary = Pneumonia is the most common complication, which occurs in high-risk patients including those with comorbid illness such as cardiovascular or pulmonary disease, diabetes, renal failure, immunosuppression, the elderly, or residents of nursing homes. A study performed in our ICU indicates that corticosteroids may dramatically alter the course of the most severe disease and should be considered in addition to antiviral therapy along with appropriate supportive care in any previously well patient with life threatening varicella pneumonia (42). Patients with HIV or AIDS (acquired immunodeficiency syndrome) who are hospitalized with chickenpox appear to be at high risk for developing varicella pneumonia, which manifests in a similar clinical fashion to that in immunocompetent individuals. In another study of 68 adult patients admitted with measles diagnosed on clinical and serological grounds, 9 required intensive care, six mechanical ventilation for approximately 15 days, and two deaths occurred. doi = 10.1007/0-387-23380-6_3 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-102898-eyyd7ent author = Rizvi, Vaseef A. title = Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date = 2020-07-17 keywords = JEV; RNA; UTR; virus summary = Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. downstream polyprotein, 2) Significant modulation in levels of a distinct subset of ribosome-bound tRNAs 48 that cannot be explained by virtue of codon usage and 3) Translation from an upstream ORF (uORF) using 49 a non-canonical initiation codon in the 5 UTR region of JEV. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . Interestingly, JEV infection appears to stimulate 251 expression from UUG start site by almost 67% suggesting viral or virus-induced host trans-regulatory factors 252 promoting uORF translation (Fig.4D) . We also identify a subset of ribosome associated 286 tRNAs whose levels are modulated globally upon JEV infection (Fig.3) . doi = 10.1101/2020.07.16.206920 id = cord-003403-ypefqm71 author = Roberts, Christine C. title = Assay Challenges for Emerging Infectious Diseases: The Zika Experience date = 2018-10-02 keywords = Virus; ZIKV; Zika; vaccine summary = doi = 10.3390/vaccines6040070 id = cord-320713-b37c8aye author = Roberts, Lisa O. title = Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date = 2009-10-27 keywords = IRES; PABP; PKR; RNA; protein; translation; viral; virus summary = 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). doi = 10.1016/s1877-1173(09)90009-6 id = cord-333262-xvfl7ycj author = Robson, B. title = COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles’ heel conserved region to minimize probability of escape mutations and drug resistance date = 2020-04-11 keywords = ACE2; COVID-19; KRSFIEDLLFNKV; SARS; Wuhan; bind; peptide; protein; spike; virus summary = The Wuhan and related isolates revealed a coronavirus that resides in the subgenus Sarbecovirus of the genus Betacoronavirus [2] , and although genetically distinct from its predecessor SARS-CoV it appeared to have similar external binding proteins, meaning here the spike glycoprotein discussed extensively in the present paper. In brief summary, the justifications for the ensemble pharmacophore in the coronavirus case, i.e. the contributions to "fuzziness", include parsimony, that proteins and parts of proteins sometimes have more than one function [12] encouraged by limited numbers of accessible sites (due to e.g. glycosylation) and exemplified by parallel alternative mechanisms of cell entry, multiple methods of drug action, escape from scientific defense measures by virus mutation, polymorphism of human proteins involved, different expression levels of human proteins involved, and the potential problem of the "specter of vaccine development" (concerns about missing the appropriate region of the virus that allows common cold viruses to escape the appropriate immune response). doi = 10.1016/j.compbiomed.2020.103749 id = cord-333351-homxj9uz author = Rodhain, F. title = Bats and Viruses: complex relationships date = 2015-10-10 keywords = Chiroptères; chauves; des; les; souris; virus summary = Plus d''une soixantaine de virus a été isolée ou détectée chez des chauves-souris qui, selon différentes modalités, se trouvent ainsi impliquées dans la circulation de beaucoup d''entre eux ; c''est le cas, notamment, de Rhabdoviridae du genre Lyssavirus, de Paramyxoviridae comme les virus Nipah et Hendra, de Filoviridae (virus Ebola et Marburg) ou de Coronaviridae comme les agents du syndrome respiratoire aigu sévère (SRAS) et du syndrome respiratoire du Moyen-Orient (MERS). Cependant, même si les contacts entre les Hommes et les chauves-souris sont faibles, la rareté des infections humaines par des Lyssavirus n''appartenant pas au génotype 1 n''est pas clairement expliquée car certains au moins de ces virus sont très largement répandus depuis longtemps ; sans doute leur véritable pathogénicité pour l''Homme est-elle faible (l''observation de cas non mortels et de sujets en bonne santé apparente porteurs d''anticorps semble en témoigner), mais les déterminants de cette pathogénicité demeurent inconnus. doi = 10.1007/s13149-015-0448-z id = cord-008700-knbf8m4x author = Rodrigues, Merlyn R. title = Methods for Rapid Detection of Human Ocular Viral Infections date = 2013-10-30 keywords = Fig; type; virus summary = Simple techniques of immunofluorescence and negative stain electron microscopy are used for the rapid detection of viruses in human adenoviral, herpetic, rubella, molluscum contagiosum, and vaccinial infections. Lens aspirate from a 2-year-old patient with clinical ocular rubella was examined by immunofluorescence and negative stain electron microscopy. 10 In a recent epidemic of EKC at a Vietnamese refugee camp in Florida, adenovirus type 8 was recovered in 81% of cases cultured within two weeks of onset of infection.U Dawson et aP 2 described adenovirus-like particles in the conjunctiva of one patient and in the corneal epithelium of another by transmission electron microscopy of tissue culture preparations. In the present study, the typical virions of herpes simplex keratitis were readily identified both by immunofluorescence and by negative stain transmission electron microscopy. Herpes simplex hominis type 1 was recovered in culture and demonstrated by direct immunofluorescence and negative stain electron microscopy in three patients with herpetic dendritic keratitis. doi = 10.1016/s0161-6420(79)35507-5 id = cord-293421-0ksn0fc7 author = Rodriguez, J. M. title = Detection of animal pathogens by using the polymerasechain reaction (PCR) date = 1997-05-31 keywords = PCR; chain; detection; disease; dna; reaction; virus summary = Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Althougla PCR has some shortcomings, such as the problems caused by contaminants and inhibitors or the lack of suitable sequences for designing specific primers, the outstanding research effort focused on tiffs technique, together with the remarkable development of molecular biology have minimized the deficiencies and allowed its increased general use as a diagnostic tool. Sensitive studies using reference strains of BVDV fi-om persistently infected carriers have shown that reverse transo-iption (RT)-PCR has greater sensitivity than other tests, including enzyme-linked immunosorbent assay (ELISA) (Horner el aL, 1995) ; unfortunately, cost currently makes this technique unsuitahle for large-scale testing but it should be valuahle as a coniirmatm T test in cases where ELISA resuhs are in the ''suspicious range'' or where the viral titre is low, such as in batches of foetal bovine serum. Comparison of polymerase chain reaction and virus isolation for detection of epizootic hemorrhagic disease in clinical samples from naturally infected deer doi = 10.1016/s1090-0233(97)80063-9 id = cord-294312-ju6vuywm author = Rohde, Rodney E. title = Common Myths and Legends of Rabies date = 2019-04-19 keywords = animal; disease; rabie; virus summary = While in fact, today''s treatment regimen is typically only four vaccinations (five for immunocompromised individuals) in the arm, plus a dose of humane rabies immune globulin (HRIG). A viral disease of the central nervous system, rabies transmits between animals, including humans, when saliva containing the virus enters an opening in the skin. Usually, the rabies virus enters through the bite of a rabid animal, but transmission can also occur when infected saliva enters through mucous membranes or a break in the skin. According to the Centers for Disease Control and Prevention (CDC), the first clinical signs and symptoms of rabies may be very similar to those of the flu including general weakness or discomfort, fever, or headache. For the rabies virus to get to the salivary glands, it has to travel first from the site of entry (usually a bite wound) through the animal''s nervous system, then to the brain. doi = 10.1016/b978-0-323-63979-8.00005-2 id = cord-261171-iknoqb4d author = Roingeard, Philippe title = Viral detection by electron microscopy: past, present and future date = 2012-01-09 keywords = TEM; virus summary = In research, new imaging techniques for fluorescence light microscopy have supplanted TEM, making it possible to study live cells and dynamic interactions between viruses and the cellular machinery. This large diversity of viruses potentially involved in human gastroenteritis contributed to the use of TEM on negatively stained samples for routine diagnosis by this rapid ''catch-all'' method in clinical virology ( Figures 2C and 2D ). The new techniques, which can be used on living cells, make it possible to follow the fate of individual viral particles and to monitor dynamic interactions between viruses and cellular structures, making it possible to study steps in infection that could previously not be observed. HIV morphogenesis also provides a remarkable example of intensive research into virus-host cell interactions, for which the debate concerning the Figure 6 Budding of HCV Ultrastructural analysis of cells producing the HCV core protein shows that this protein self-assembles into HCV-like particles (arrows) at convoluted and electron-dense ER membranes surrounding the lipid droplets (LD) present in the perinuclear area. doi = 10.1042/bc20070173 id = cord-275719-ru33ubss author = Roingeard, Philippe title = Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety date = 2018-11-09 keywords = TEM; cell; virus summary = Despite the lack of established methods of biological sample preparation for transmission electron microscopy (TEM) at this time, Helmut Ruska was able to characterize the morphology of several viruses and he developed a rough viral classification based on the size and shape of the viral particles. 4 TEM was rapidly adopted for its first major use in clinical virology: the differential diagnosis of smallpox, caused by the variola virus Abbreviations: ELISA, enzyme-linked immunosorbent assay; EM, electron microscopy; EMEA, European Medicines Agency; FDA, Food and Drug Administration; FPERT, fluorescent product-enhanced reverse transcription; LCMV, lymphocytic choriomeningitis virus; PCR, polymerase chain reaction; SARS, severe acute respiratory syndrome; SFTS, severe fever with thrombocytopenia syndrome; TEM, transmission electron microscopy from the poxvirus family, and chickenpox, caused by the varicellazoster virus of the herpes family, based on investigations of fluid samples from the vesicles on the patients'' skin. Detection of retrovirus-like particles by transmission electron microscopy (TEM) with negative staining in bulk harvests of rodent cells used for the production of biological products. doi = 10.1002/rmv.2019 id = cord-341324-f9g9gitn author = Rojas, José M. title = Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date = 2020-10-21 keywords = IFN; IRF3; PRR; RNA; protein; rig; virus summary = This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). doi = 10.1007/s00018-020-03671-z id = cord-255690-xc4bxin4 author = Rolain, Jean-Marc title = Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date = 2007-07-16 keywords = HCQ; HIV-1; inhibition; virus summary = Here we review available in vitro and in vivo data on the effects of CQ/HCQ on bacterial, fungal and viral infections, with the concept that manipulation of the intracellular pH in cells and modification of glycosylation of proteins by lysosomotropic agents instead of antimicrobial compounds is a powerful approach as new therapeutic strategies for the prevention and therapeutic management of several infectious diseases, including some of great public health concern worldwide. Coxiella burnetii [5, 13] Histoplasma capsulatum [24] HIV [2, [29] [30] [31] [32] ] Tropheryma whipplei [7, 8] Cryptococcus neoformans [15, 25] SARS-CoV [33, 34] Legionella pneumophila [11] Paracoccidioides brasiliensis [26] Influenza viruses [35] [36] [37] [38] Francisella tularensis [12] Penicillium marneffei [15, 27] Flavivirus, including yellow fever virus [39] Mycobacterium tuberculosis [14] Aspergillus fumigatus [28] Rubella virus [ tetracycline and quinolone regimen for at least 4 years, with a high percentage of relapses [6] . doi = 10.1016/j.ijantimicag.2007.05.015 id = cord-102383-m5ahicqb author = Romano, Alessandra title = Energy dynamics for systemic configurations of virus-host co-evolution date = 2020-05-15 keywords = host; system; virus summary = A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. A systems-thinking representation, based on stock-flow diagramming of virus-host interaction at the cellular level, is used here for the first time to simulate the system energy dynamics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. Viral load and early addressing (in the first two days from infection) of leverage points are the most effective strategies on stock dynamics to minimize virion assembly and preserve host-cell bioenergetics. doi = 10.1101/2020.05.13.092866 id = cord-294842-aesiff1f author = Romero-Brey, Inés title = Membranous Replication Factories Induced by Plus-Strand RNA Viruses date = 2014-07-22 keywords = DENV; HCV; RNA; membrane; replication; virus summary = Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein doi = 10.3390/v6072826 id = cord-270647-vn4kirrx author = Romero-Espinoza, Jose A. title = Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date = 2018-02-15 keywords = asthma; respiratory; virus summary = OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Both groups differ with respect to the associated virus and bacteria: while asthma exacerbations have been associated to a specific rhinovirus infection, pneumonia can be related to a wide range of bacterial, fungal and viral agents, with a high prevalence of Respiratory Syncytial Virus (RSV) [2, 7] . Here we describe the virome and bacteriome present in the Upper Respiratory Tract of hospitalized children clinically diagnosed with asthma and pneumonia, during an acute exacerbation and an ARI episode respectively, at the National Institute of Respiratory Diseases (INER, Mexico City) during 2014 and 2015 winter seasons. Prevalence of respiratory viral infection in children hospitalized for acute lower respiratory tract diseases, and association of rhinovirus and influenza virus with asthma exacerbations doi = 10.1371/journal.pone.0192878 id = cord-330296-706hf4qw author = Romette, J. L. title = The European Virus Archive goes global: A growing resource for research date = 2018-10-31 keywords = EVAg; European; virus summary = Abstract The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry (Gould et al., 2012) . In fact, besides the EVAg, we are unaware of any non-profit organization that is concerned with facilitating reliable access globally to viruses and associated reagents from individual virus collections for research and/or diagnostic laboratories, teaching centres or industries involved in the production of diagnostic reagents, pharmaceuticals and vaccines solely for the benefit of science, in a safe and carefully regulated manner. doi = 10.1016/j.antiviral.2018.07.017 id = cord-027473-8zerjwa0 author = Roos, Yrjö H. title = Water and Pathogenic Viruses Inactivation—Food Engineering Perspectives date = 2020-06-20 keywords = HAV; food; virus summary = The large number of virus species, differences in spreading, likelihood of foodborne infections, unknown infective doses, and difficulties of infective virus quantification are often limiting experimental approaches to establish accurate data required for detailed understanding of virions'' stability and inactivation kinetics in various foods. The stability of enteric viruses, human norovirus (HuNoV), and hepatitis A (HAV) virions in food materials and their resistance against inactivation in traditional food processing and preservation is well recognized. The small size, concentration, and a tiny infective dose of virions besides the need of host cells for reproduction of viral material result in challenges in studies analyzing virus survival and infectiousness in food, water, and the environment [60] . Here, we summarize studies reporting on virus survival and degradation kinetics with critical evaluation of the importance of known data to understanding losses of virus infectivity in normal circumstances, and particularly as affected by water from a food engineering and safety perspective. doi = 10.1007/s12393-020-09234-z id = cord-306733-df36w6l7 author = Rosales-Mendoza, Sergio title = What Does Plant-Based Vaccine Technology Offer to the Fight against COVID-19? date = 2020-04-14 keywords = COVID-19; SARS; plant; protein; vaccine; virus summary = Transient nuclear genome transformation Rapid production; high productivity; implemented at the industrial level Seed bank cannot be generated; requires purification of the antigen to eliminate toxic compounds from the host and ag-robacteria residues S protein; multiepitope vaccines A chimeric protein of GFP and amino acids 1-658 of the SARS-CoV-1 S protein (S1:GFP) was transiently expressed in tobacco leaves and stably transformed in tobacco and lettuce. No immunization assays were performed The SARS-CoV-1 N protein was transiently expressed in Nicotiana benthamiana, which induced in mice high levels of IgG1 and IgG2a and up regulation of IFN-γ and IL-10 in splenocytes. The precedents of SARS-CoV-1 and MERS antigens expressed in recombinant systems leading to the formation of VLPs constitute important guides for the topic of COVID-19 vaccine development. Thus, VLPs based on the main SARS-CoV-2 structural proteins is an attractive approach for vaccine development against coronavirus infections. doi = 10.3390/vaccines8020183 id = cord-023831-93xqrblk author = Rosenberg, Helene F. title = Pneumonia Virus of Mice (PVM): Exploring Novel Therapeutic Options In a Severe Respiratory Disease Model date = 2010-03-30 keywords = PVM; RSV; virus summary = Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. Our laboratories have pioneered the use of the PVM model for the study of human clinical disease, which has provided important insights into the role of the inflammatory response in the pathogenesis of severe respiratory virus infection. With these factors in mind, around 1997, we began our collaborative exploration of the pneumonia virus of mice (PVM) pathogen for the study of respiratory virus replication and the ensuing inflammatory response within a natural, evolutionarily relevant host-pathogen relationship. In a study performed using young adult (eight-12 weeks) through aged (up to 78 weeks), but otherwise immunologically naïve mice, we observed no change in the kinetics of PVM replication, but diminished local production of several proinflammatory mediators, including MIP-1a, MCP-1, and IFN-g, along with diminished recruitment of granulocytes to the lung tissue [35] . doi = 10.1007/978-1-60761-512-5_35 id = cord-256615-gvq8uyfk author = Rosenberg, Ronald title = Detecting the emergence of novel, zoonotic viruses pathogenic to humans date = 2014-11-22 keywords = RNA; animal; human; pathogen; virus summary = RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. doi = 10.1007/s00018-014-1785-y id = cord-316295-x636ux34 author = Roth, Bernhard title = Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date = 2012-01-11 keywords = MDCK; PCR; virus summary = Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. In a similar way, samples with positive and questionable multiplex PCR results only for viruses other than influenza virus were also cultivated for 2 or 3 passages in MDCK 33016PF cells. Considering the selection of specimens, the high percentage of influenza-positive results is not surprising, but a significant number of samples (66/370 or 17.8%) also tested positive for other viruses, such as adenovirus, bocavirus, coronavirus, enterovirus, metapneumovirus (HMPV), parainfluenza virus (PIV), rhinovirus, and respiratory syncytial virus (RSV). doi = 10.1016/j.vaccine.2011.11.063 id = cord-290540-r0d6oaez author = Rottier, Peter J.M. title = The molecular dynamics of feline coronaviruses date = 1999-09-01 keywords = FIPV; PCR; virus summary = Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that''feline enteric coronaviruses'' are indeed restricted in tropism, while''FIP viruses'' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an''early death'' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR doi = 10.1016/s0378-1135(99)00099-1 id = cord-266762-z08rn959 author = Rouse, Barry T. title = 25 Host Defenses to Viruses date = 2019-12-31 keywords = CD4; CD8; cell; virus summary = authors: Rouse, Barry T.; Mueller, Scott N. However, broadly neutralizing antiviral antibodies have the potential to be effective therapies against many different human infections, including HIV, influenza viruses, and Ebola virus. Initiation of adaptive immunity is closely dependent on early innate mechanisms that activate antigen-presenting cells (APCs), principally subsets of DCs. APCs and lymphocytes are drawn into lymphoid tissues by chemokine and cytokine signals and are retained there for a few days to facilitate effective intercellular interactions. 19 T-cell immunity against a particular virus involves both CD4 + and CD8 + T-cell subsets that recognize peptides derived from viral antigens bound to surface MHC proteins (class II and class I, respectively) (Chapters 5, 6). Immune responses against virus-infected cells often result in tissue damage, especially if cell killing is involved or if there is extensive recruitment and activation of inflammatory cell types, such as macrophages and sometimes neutrophils. doi = 10.1016/b978-0-7020-6896-6.00025-9 id = cord-275683-1qj9ri18 author = Roux, Simon title = Metagenomics in Virology date = 2019-06-12 keywords = RNA; genome; viral; virus summary = Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. However, these techniques can only detect previously known viruses, and often require Box 1 Use of complementary methods to target different types of viruses A number of approaches have been developed to specifically select and survey the genetic material contained by virus particles in a given sample. Virus sequences obtained from "bulk" metagenomes will typically reflect viruses infecting their host cell at the time of sampling, either actively replicating or not, while viromes enables a deeper and more focused exploration of the virus diversity in a specific site or sample. With viral metagenomics being applied to a larger set of samples and environments, and with bioinformatic analyses including genome assembly and interpretation constantly improving, novel groups of dominant and widespread viruses may thus be progressively revealed across many environments. doi = 10.1016/b978-0-12-809633-8.20957-6 id = cord-006997-sghhdjyi author = Rowland, M.G.M. title = Viruses and diarrhoea in West Africa and London: a collaborative study date = 1978-01-17 keywords = diarrhoea; virus summary = Rotaviruses and, in some cases, adenoviruses are found on electron microscopy of faeces of a substantial proportion of children with acute diarrhoea in various parts of the world and there is evidence that these organisms can cause the disease (BISHOP et al., 1974; BRYDEN et al., 1975; MIDDLETON et al., 1974; SEXTON et al., 1974; FLEWETT et al., 1975; SCHOUB et al., 1975) . This study was undertaken to look systematically and by comparable techniques for the viral causes of childhood diarrhoea in a typical village in rural Africa and a comparison group of children and adults in north-west London. doi = 10.1016/0035-9203(78)90308-5 id = cord-261160-g92zhv19 author = Rowland, Raymond R.R title = Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date = 2003-10-30 keywords = PCR; PRRSV; RNA; virus summary = title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. doi = 10.1016/j.vetmic.2003.07.006 id = cord-001831-3aonqyub author = Royle, Jamie title = Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? date = 2015-10-16 keywords = SV40; TMD; virus summary = Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention. Research over recent decades has identified a group of virus-encoded proteins able to mediate the passage of ions and solutes across cellular membranes, termed viroporins [1, 2] . Due to these broad perturbations to host cell physiology, it is not surprising that viroporin function has been shown to assist in all stages of the virus life cycle including entry, membrane penetration, genome replication and virus egress [1, 2] . This review will summarize our understanding of these putative viroporins, describe their known functions and attempt to highlight how possible ion channel activity may aid the life cycles of these small DNA tumor viruses. doi = 10.3390/v7102880 id = cord-334947-pa0p5dif author = Rozen-Gagnon, Kathryn title = Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date = 2014-01-16 keywords = CHIKV; RNA; SINV; cell; figure; virus summary = Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. To estimate the population diversity of variants by deep sequencing, cDNA libraries were prepared by Superscript III from RNA extracted from virus generated in BHK-21 or C6/36 cells, and the viral genome was amplified using a high fidelity polymerase (Phusion) to generate 5 overlapping amplicons 2-3 kb in length. To address the possibility that the fitness cost of defective replication, observed in mosquito cell culture, would favor the reversion of these mutant polymerases to wildtype, we deep sequenced virus from the body of an individual mosquito that presented the median titer from each group. doi = 10.1371/journal.ppat.1003877 id = cord-276039-nqqwnmwc author = Rua, Rejane title = Origin, evolution and innate immune control of simian foamy viruses in humans date = 2015-02-17 keywords = SFV; foamy; human; virus summary = In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence. In this brief review, we will present the current available data on the discovery, cross-species transmission and molecular evolution of the simian foamy viruses (SFV) present in different human populations at risk for zoonotic emergence. They were mostly hunters who reported direct contacts with blood and/or body fluids from wild NHPs. We extended such studies into different areas and populations of this Central African country and found the presence of SFV infection in at least 50 persons [12 ] . Origin, evolution and innate immune control of simian foamy viruses in humans Rua and Gessain 51 Table 1 SFV tropism and viral load in the blood of SFV-infected humans and NHPs. The proportion of SFV DNA positive samples among leukocyte populations in SFV-infected NHP and SFVinfected humans is indicated. doi = 10.1016/j.coviro.2014.12.003 id = cord-030028-s6sxi8uj author = Rubio, Luis title = Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date = 2020-07-17 keywords = PCR; RNA; detection; dna; plant; virus summary = This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. doi = 10.3389/fpls.2020.01092 id = cord-264408-vk4lt83x author = Ruiz, Sara I. title = Animal Models of Human Viral Diseases date = 2017-06-23 keywords = H5N1; HIV; HIV-1; MPXV; Mers; NHP; Nipah; West; animal; disease; human; infection; model; mouse; virus summary = Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . doi = 10.1016/b978-0-12-809468-6.00033-4 id = cord-319933-yp9ofhi8 author = Ruiz, Sara I. title = Chapter 38 Animal Models of Human Viral Diseases date = 2013-12-31 keywords = Nipah; SARS; animal; clinical; day; disease; experimental; human; infection; model; mouse; virus summary = An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. doi = 10.1016/b978-0-12-415894-8.00038-5 id = cord-274080-884x48on author = Rumlová, Michaela title = In vitro methods for testing antiviral drugs date = 2018-06-30 keywords = HBV; HCV; HIV-1; RNA; cell; dna; protein; viral; virus summary = For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. doi = 10.1016/j.biotechadv.2017.12.016 id = cord-003707-fbe47bgi author = Russo, Alice G title = Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date = 2019-06-18 keywords = Fig; NIRVS; RNA; Table; virus summary = I. scapularis NIRVS are enriched in bunyaand orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. NIRVS arise from the reverse transcription of viral RNA into cDNA and its integration into the genome of a host germ cell, followed by vertical transmission to offspring (Katzourakis and Gifford 2010) . Yet recent evidence has highlighted the abundance of NIRVS in some arthropod genomes-e.g., Ae. aegypti and Ae. albopictus contain >100 NIRVS from over eight RNA virus families encompassing þssRNA, ÀssRNA, and dsRNA viral groups (Palatini et al. Using the well-studied genomes of Aedes mosquitoes to validate our analysis, we employed a bioinformatic pipeline to characterise NIRVS in seven non-Aedes arbovirus vectors that have representative genomic sequences (Table 1 and Fig. 1 ). scapularis lacked NIRVS from positive-sense RNA viruses, which comprise about one tenth of NIRVS in Aedes mosquitoes ( Fig. 3; Supplementary Table S2 ). doi = 10.1093/ve/vez010 id = cord-332165-31tbc31x author = Rustmeier, Nils H. title = The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies date = 2019-10-14 keywords = acid; figure; sialic; site; virus summary = In this review, we will evaluate the structures of non-enveloped virus capsid proteins bound to sialylated glycan receptors and discuss the potential of these structures for the development of potent antiviral attachment inhibitors. This concept of targeting multiple, symmetric receptor binding sites by multivalent inhibitors is also applicable for many viruses, since viral capsids are often icosahedral and, therefore, highly symmetric structures. Many members of the polyomavirus family bind sialic acid-based glycans using their VP1 proteins, so the binding sites on individual pentamers are always linked by local five-fold symmetry (Figure 4a , TSPyV). The glycooligopeptide-VP1 complex structures displayed a similar ligand binding mode that was reported for sialic acid in an earlier study [50] and showed, for the compounds, that the linker between the ligand and the scaffold occupies the space that is usually targeted by the natural glycan receptor moieties (Figure 5a,b, right) . doi = 10.3390/v11100947 id = cord-009702-02bo7pnl author = SCOTT, G. R. title = Guidelines for the Control of Equine Viral Infections date = 2010-04-23 keywords = disease; equine; horse; virus summary = At least twenty‐eight of the fifty‐eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. There is possibly one Coronavirus infecting horses; Ditchfield (1969) isolated a virus from a Thoroughbred with undifferentiated respiratory disease and found that it possessed a morphology similar to that of infectious bronchitis virus of poultry, the type-virus of the Coronavirus group. Equine infectious anaemia virus probably belongs to the Oncornavirus group, i.e. the RNA tumour viruses. Eleven of the thirty-four known vector-transmitted viruses cause disease and vaccines have been developed against six of them (Table VII) . Seventeen of the twenty known viral contagions of horses cause disease and vaccines have been developed against five of them (Table VIII ). At least twenty-eight of the fifty-eight viruses induce clinical disease but the range of syndromes is limited; eleven provoke respiratory symptoms and eleven cause encephalitis. The vector-transmitted virus diseases are best controlled by prophylactic vaccination. doi = 10.1111/j.2042-3306.1971.tb04431.x id = cord-020969-lh2ergpm author = STRAUSS, JAMES H. title = Gene Therapy date = 2012-07-27 keywords = RNA; cell; dna; gene; virus summary = Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. doi = 10.1016/b978-0-12-373741-0.50014-3 id = cord-023726-2fduzqyb author = STRAUSS, JAMES H. title = The Structure of Viruses date = 2012-07-27 keywords = Fig; RNA; protein; structure; virus summary = Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. doi = 10.1016/b978-0-12-373741-0.50005-2 id = cord-324950-ux7shvji author = Saade, Georges title = Coinfections and their molecular consequences in the porcine respiratory tract date = 2020-06-16 keywords = PCV2; PRRSV; cell; infection; porcine; respiratory; virus summary = In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] . doi = 10.1186/s13567-020-00807-8 id = cord-001207-yjaiybwf author = Sachsenröder, Jana title = The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date = 2014-02-19 keywords = NCIMB; sample; virus summary = faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. doi = 10.1371/journal.pone.0088888 id = cord-273326-gmw8gl2r author = Saiz, Juan-Carlos title = Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date = 2018-08-24 keywords = RNA; ZIKV; Zika; cell; infection; virus summary = In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . doi = 10.3390/v10090453 id = cord-267134-5gz2dotn author = Sallenave, Jean-Michel title = Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? date = 2020-05-28 keywords = ACE2; CoV; SARS; cell; virus summary = The first anatomical/histological reports from the lungs of severely SARS-CoV-2-affected patients experiencing acute respiratory disease syndrome (ARDS) revealed excessive inflammatory activation and destruction of the bronchial and alveolar epithelium, features already observed during the first SARS pandemics in 2003 (3, 4). The following sections will give an overview of the molecular and cellular mechanisms underpinning SARS-CoV virus infections and how lung and systemic host innate immune responses affect survival either positively, through downregulating the initial viral load, or negatively, by triggering uncontrolled inflammation. Regarding the lung, the differentiated Calu-3 cell line [when cultured at the air-liquid interface (ALI)] is the model of choice: in that set-up, SARS-CoV infection triggered an inflammatory response characterized by increased production of interleukin (IL)-6, IL-8, gamma interferon (IFN-γ), inducible protein 10 (IP-10), and activation of the transcription factor NF-κB (56) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus doi = 10.3389/fimmu.2020.01229 id = cord-318853-mxyxwkhx author = Sallie, Richard title = Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date = 2005-08-22 keywords = HBV; HCV; RNA; cell; protein; receptor; viral; virus summary = Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? doi = 10.1186/1743-422x-2-70 id = cord-284941-wfn0pnev author = Samal, S.K. title = Paramyxoviruses of Animals date = 2008-07-30 keywords = RNA; paramyxovirus; virus summary = The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. A number of animal paramyxoviruses have been recovered from cDNAs using reverse genetics, including simian virus 5, NDV, bovine parainfluenza virus 3, Sendai virus, canine distemper virus, rinderpest virus, bovine respiratory syncytial virus, and avian metapneumovirus. Infection occurs by several different routes, including aerosols (NDV, bovine respiratory syncytial virus, avian metapneumovirus) and contaminated feed and water (Newcastle disease, canine distemper, and rinderpest viruses). doi = 10.1016/b978-012374410-4.00460-x id = cord-017331-ru7mvfc0 author = Samanta, Indranil title = Infectious Diseases date = 2017-02-25 keywords = AIV; Amazon; Borrelia; Campylobacter; Chlamydia; Fig; Giardia; Mycobacterium; PCR; PDD; Salmonella; USUV; WNV; avian; bird; clinical; infection; parrot; pet; virus summary = The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. doi = 10.1007/978-981-10-3674-3_2 id = cord-296819-gztmidn2 author = Sambri, Vittorio title = Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date = 2013-09-25 keywords = Nile; PCR; WNV; West; virus summary = title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ''Imported'' Viral Diseases (ENIVD). For the routine detection of WNV RNA using molecular techniques there are two distinct diagnostic settings: the first involves blood and organ donation screening from subjects living in an area where WNV circulation is known to be occurring, and the second involves the identification of viral genomes in serum, plasma and CSF samples from patients presenting with a clinical picture typical of WNV infection [21] . doi = 10.3390/v5102329 id = cord-278479-vl296i1b author = Samuel, Arthur S title = Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 date = 2011-02-23 keywords = APMV; APMV-1; Newcastle; virus summary = In this study, groups of hamsters were infected with a prototype strain of each APMV serotype by the intranasal route and monitored for virus replication, clinical symptoms, histopathology, and seroconversion. Our results showed that each of the APMV serotypes replicated in hamsters without causing adverse clinical signs of illness, although histopathologic evidence of disease was observed in some cases, and also induced high neutralizing antibody titers. Necropsies were performed immediately postmortem and the following tissue samples were collected for immunohistochemistry (IHC), histopathology, and virus isolation: brain, nasal turbinates, lung, spleen, kidney and small intestine. Deparaffinized sections of the virus-infected and uninfected control tissue (brain, lungs, nasal turbinates, small intestine, kidney, and spleen) were immunostained using polyclonal antisera against the N protein of the homologous APMV serotypes. In animals infected with any of the other APMV serotypes, virus-specific antigens were detected on 3 dpi in the lungs and nasal turbinates (Figure 3 ). doi = 10.1186/1297-9716-42-38 id = cord-256036-gd53s4dv author = Sandmann, Lisa title = Barriers of hepatitis C virus interspecies transmission date = 2013-01-01 keywords = CD81; HCV; RNA; virus summary = In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease doi = 10.1016/j.virol.2012.09.044 id = cord-279798-b5tduubu author = Sano, Daisuke title = Risk management of viral infectious diseases in wastewater reclamation and reuse: Review date = 2016-03-14 keywords = Water; virus; wastewater summary = The objectives of this review were to calculate representative values of virus removal efficiency in wastewater treatment units based on published datasets, and to identify research topics that should be further addressed for improving implementation of the multiple-barrier system. In this review article, current guidelines for designing wastewater reclamation and reuse systems from the viewpoint of virus risk management are overviewed, and the efficiency of virus removal from wastewater by currently employed wastewater treatment units are shown by the results of meta-analysis. The United States Environmental Protection Agency (USEPA) (2012) guideline explicitly notes that setting a tolerable virus concentration in reclaimed wastewater (virus limit) is not recommended for the following reasons: 1) viruses are well reduced by appropriate wastewater treatments, 2) identification and enumeration of viruses is time-and labor-consuming, 3) detection of infectious viruses in water is further labor-and time-consuming, 4) molecular-based virus detection does not always indicate the presence of infectious viruses, and 5) waterborne viral infections due to reclaimed water have not been documented. doi = 10.1016/j.envint.2016.03.001 id = cord-300522-okbupw61 author = Sansone, Clementina title = Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date = 2020-05-07 keywords = HIV; activity; antiviral; cell; virus summary = Given the ability of various algal molecules—mainly sulfated polysaccharides—to inhibit viral infection at Stage I (adsorption and invasion of cells), we envisage a need to further investigate the antiviral ability of algae, and their mechanisms of action. Oxidative stress-a loss in the balance between the production of free radicals including reactive oxygen species (ROS) and antioxidant cell signaling pathways [2] -can be a key factor of the pathogenesis in many acute or chronical human diseases [3] . For that, we explore the relationship between oxidative stress and viral infections, looking for solutions through the deciphering of cell signaling pathways that can inhibit virus replication and infections, and the mechanisms of action of potential antiviral molecules. Three polysaccharides extracted from marine microalgae, naviculan from the diatom Navicula directa, and two others (named A1 and A2) from the dinoflagellate Cochlodinium polykrikoides also displayed antiviral activities against several enveloped viruses, such as HIV-1, HSV-1 or influenza virus type A (IFV-A) [71] . doi = 10.3390/antiox9050392 id = cord-350235-yoy3hj3j author = Sansonetti, Philippe J title = COVID‐19, chronicle of an expected pandemic date = 2020-05-04 keywords = SARS; disease; virus summary = Philippe Sansonetti, Infectious disease specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands.[Image: see text] Philippe Sansonetti, Infectious Disease Specialist and Chief Editor of EMBO Molecular Medicine, explains why the fate of the epidemic is in our hands. Beta-coronaviruses like SARS-CoV-2 (the official name of COVID-19 virus) on the other hand are well adapted to their reservoir, the bat, but not to humans, which explains why human infections are so damaging. Molecular diagnosis has revolutionized this field, and despite the initial delays in communicating about this epidemic, Chinese doctors and biologists quickly reported the first evidence for SARS-CoV-2, and provided the first sequences, clearing the way for the global scientific community to further develop diagnostic tools and engage in a race to discover dedicated drugs and vaccines. doi = 10.15252/emmm.202012463 id = cord-317404-jvtozj4v author = Santos, Marfran C.D. title = Spectroscopy with computational analysis in virological studies: A decade (2006–2016) date = 2017-09-21 keywords = PCA; Raman; spectroscopy; virus summary = The potential of spectroscopic techniques in the detection and identification of virus-infected cells has been studied using statistical methods as a sensitive, rapid and reliable methodology. First, we will discuss the most commonly used spectroscopic techniques, then we will discuss the computational processes used to extract useful information from the obtained spectra (spectral preprocessing, multivariate classification algorithms, performance evaluation), and finally we will discuss some works published in the period from 2006 to 2016 using spectroscopy and multivariate analysis in studies involving viruses. For example, the potential of Raman spectroscopy followed by statistical methods in detecting and identifying Herpes Simplex Virus type 1 (HSV-1) infections as a sensitive, rapid and reliable method has been evaluated by Salman et al. (2014) [25] evaluated the potential of Raman spectroscopy as a sensitive, reliable and rapid method for detecting and identifying viral infection by Herpes simplex virus type 1 (HSV-1) in cell culture. doi = 10.1016/j.trac.2017.09.015 id = cord-257163-hodykbcb author = Sanz, Ivan title = Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period date = 2015-05-07 keywords = COPD; virus summary = During the study period (2009–2012), respiratory viruses were identified in 48.7% of samples, and the proportion of viral detections in AE-COPD was higher in patients aged 30–64 years than ≥65 years. Studies conducted before emergence of the pandemic H1N1pdm09 strain showed that half of all AE-COPD cases were associated with viral infections and that picornaviruses (especially human rhinovirus and enterovirus (HREV)) were the dominant viral pathogens diagnosed in these patients [15, 16] . The aim of this study is to describe the etiological characteristics of respiratory viruses linked to COPD exacerbations after a singular pandemic period caused by a new influenza virus. We used the OR to analyze the probability of detection of viral categories (ORP, HREV, any influenza virus, and RSV) as well as viral coinfections in AE-COPD patients among different demographic and epidemiological characteristics such as gender, age groups, and the different periods analyzed. doi = 10.1155/2015/560679 id = cord-292416-3hhi4wps author = Sarid, Ronit title = Investigating an Emerging Virus During a Sudden Pandemic Outbreak date = 2020-07-31 keywords = RNA; SARS; viral; virus summary = Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. doi = 10.5041/rmmj.10414 id = cord-319746-6bccxgbd author = Saxena, Latika title = Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors date = 2015-12-31 keywords = antibody; cell; virus summary = title: Production and Characterization of Human Monoclonal Antibodies from the Cells of A(H1N1)pdm2009 Influenza Virus Infected Indian Donors Abstract Analysis of human monoclonal antibodies (mAbs) developed from influenza infected donors have enormously contributed to the identification of neutralization sensitive epitopes of influenza virus. In this study, we generated strongly neutralizing novel human monoclonal antibodies that were selected from the immune repertoire of influenza infected seropositive patients. Monoclonal antibody 2D8 showed the maximum binding in the in vitro assays and neutralized the human isolate of the pandemic strain as well as the reference strain at lowest concentrations when compared to the 2F12 antibody. The antibodies however, showed comparative neutralization and HAI activity between the laboratory isolates of the pandemic virus and the reference strain A/Cal/07/2009(H1N1). To, the best of our knowledge, these antibodies are the first fully human monoclonal antibodies generated from the immune repertoire of Indian patients infected with A(H1N1)pdm09 virus. doi = 10.1016/j.provac.2015.05.009 id = cord-352178-irjhmxsg author = Saxton-Shaw, Kali D. title = O''nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date = 2013-01-24 keywords = CHIKV; ONNV; RNA; infection; virus summary = Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV''s unique vector specificity for An. gambiae mosquitoes (Figure 2) . doi = 10.1371/journal.pntd.0001931 id = cord-354848-7aakik9a author = Sayres, Lauren title = Contemporary Understanding of Ebola and Zika Virus in Pregnancy date = 2020-10-16 keywords = Ebola; Zika; virus; woman summary = In particular, Ebola virus is associated with high case fatality and pregnancy and neonatal loss rates, while Zika virus has been associated with multiple congenital anomalies; these features present critical clinical dilemmas for management of pregnant and reproductive aged women. The Monitored Emergency Use of Unregistered and Investigational Interventions ethical framework recommends that vulnerable Contemporary Understanding of Ebola and Zika Virus populations including pregnant women be offered similar treatments to the nonpregnant population when potential benefits can outweigh risks. 75 Attention must be paid to the successes and failures of the response to the Ebola and Zika outbreaks as physicians strive to provide excellent care for pregnant women who are affected by or at risk for emerging infectious diseases. Prevention of Ebola virus includes containment of infected substances and personal protection equipment use, and prevention of Zika virus entails protection against mosquito bites, avoidance of high-risk regions, and delay of childbearing. doi = 10.1016/j.clp.2020.08.005 id = cord-288879-rj03dsib author = Schein, Catherine H. title = Polyglutamine Repeats in Viruses date = 2018-09-04 keywords = RNA; dna; polyQ; repeat; virus summary = While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). doi = 10.1007/s12035-018-1269-4 id = cord-284266-tbndldhr author = Schippa, Serena title = Nasal Microbiota in RSV Bronchiolitis date = 2020-05-13 keywords = RSV; group; respiratory; virus summary = Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSV-positive subjects (Figure 1a) . Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSVpositive subjects (Figure 1a) . The main aim of the present study was to characterize the nasal microbiota in pediatric patients hospitalized for bronchiolitis from RSV and in infants affected by bronchiolitis but negative for a respiratory virus. doi = 10.3390/microorganisms8050731 id = cord-323333-keshu99t author = Schleis, Thomas G. title = The Process: New Methods of Purification and Viral Safety date = 2013-01-16 keywords = igiv; virus summary = From the transmission of hepatitis C virus by gammaglobulins in 1994 to the emergence of new viruses and concern over prions, intravenous immunoglobulin (IGIV) manufacturers have continued to address safety issues and respond to changing needs. Because the different techniques can affect the biologic function of the IgG molecule, the methods of viral inactivation may account for some of the differences among IGIV products in terms of side effects and efficacy (Table 1) . Because intravenous immunoglobulins are derived from human plasma, they are potentially susceptible to contamination by a variety of blood-borne pathogens; consequently, patients receiving and clinicians administering IGIV are concerned about disease transmission. From the transmission of HCV by gammaglobulins in 1994 to the emergence of new viruses or concern over prions, IGIV manufacturers have continued to address safety issues and respond to changing needs. doi = 10.1592/phco.2005.25.11part2.73s id = cord-010188-884d196k author = Schlesinger, Sondra title = Alphaviruses — vectors for the expression of heterologous genes date = 2004-08-26 keywords = RNA; virus summary = Sindbis virus and Semliki Forest vires are best known as valuable models for molecular and cell biology, and it is these two viruses that are presently being developed as vectors for the expression of heterologous genes. The basic strategy for using alphaviruses as vectors for the expression of heterologous genes has been to construct cDNAs of the alphavirus genome, in which the heterologous gene is placed downstream from the promoter used to transcribe a subgenomic RNA 13 (Fig. 2a) . A second potential problem is recombination between the packaging helper virus RNA and vector RNAs. The two Sindbis RNAs can undergo recombination to produce a single molecule of RNA containing the genes that encode both the nonstructural and structural proteins m. The initial studies with Sindbis and Semliki Forest virus suggest that both viruses are promising as vectors for heterologous gene expression. doi = 10.1016/0167-7799(93)90070-p id = cord-008716-38sqkh9m author = Schmidt, Alexander C title = Current research on respiratory viral infections: Third International Symposium date = 2001-06-01 keywords = H5N1; RSV; infection; influenza; respiratory; vaccine; virus summary = Renewed efforts in vaccine development against respiratory viruses began in the 1960s with the observation that infants and young children, after having recovered from respiratory tract infection with adenoviruses, shed virus from their gastrointestinal tract for an extended period of time without experiencing gastrointestinal symptoms. Earlier studies of viral pathogens in immunocompromised adults indicated that CMV, herpes simplex, influenza, parainfluenza, rhinovirus, adenovirus, enterovirus, and RSV cause lower respiratory infection (Connolly et al., 1994) . Children with RSV, adenovirus or influenza virus infections have a 30% risk of developing AOM within 2 weeks of the onset of the respiratory tract infection (Henderson et al., 1982) , and coinfection with bacteria and viruses also adversely influences the outcome of AOM. Populations at high risk for complications resulting from respiratory viral infections are now better defined and a more targeted prophylaxis is possible, be it passive prophylaxis against RSV disease with monoclonal antibody preparations or active prophylaxis with influenza-or adenovirus vaccines. doi = 10.1016/s0166-3542(01)00136-x id = cord-297834-me1ajoyb author = Schountz, Tony title = Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date = 2014-03-14 keywords = RNA; infection; reservoir; response; virus summary = The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. doi = 10.3390/v6031317 id = cord-012418-6ralcn8p author = Schwanke, Hella title = Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression date = 2020-07-07 keywords = CBP; IFN; IRF3; IRF7; dna; factor; ifnb1; virus summary = Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). doi = 10.3390/v12070733 id = cord-304251-dohglrm1 author = Scully, C title = Emerging and changing viral diseases in the new millennium date = 2015-08-06 keywords = HIV; infection; oral; virus summary = Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. doi = 10.1111/odi.12356 id = cord-306424-gf0bglm0 author = Scutigliani, Enzo Maxim title = Interaction of the innate immune system with positive-strand RNA virus replication organelles date = 2017-06-27 keywords = IFN; RNA; SARS; viral; virus summary = Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus doi = 10.1016/j.cytogfr.2017.05.007 id = cord-017326-1caeui30 author = Seay, Montrell title = Digesting Oneself and Digesting Microbes: Autophagy as a Host Response to Viral Infection date = 2005 keywords = Beclin; PKR; autophagy; cell; protein; virus summary = Genetic studies in yeast and mammalian cells have also shown that the eIF2 kinase signaling pathway is required for starvation and herpes simplex virus-induced autophagy 18 . The role of some of the Atg proteins, including ones that act in the lipid kinase signaling complex and in the ubiquitin-like conjugation pathways, has been studied in plant and mammalian viral infections (see Table 1 ). Together, the studies of Sindbis virus infection in neurons overexpressing beclin 1 or in cultured cells lacking beclin 1 or atg5 demonstrate a role for mammalian autophagy genes in both restricting viral replication and in protection against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. doi = 10.1007/1-4020-3242-0_11 id = cord-270335-8vqi9c68 author = Seifert, Stephanie N title = Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date = 2019-11-04 keywords = EFB; Nipah; bat; virus summary = Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Studies of wild caught Pteropus spp suggest potential for viral recrudescence [16, 23] ; however, the hypothesis that NiV may persist in an individual bat and re-emerge under times of stress has yet to be confirmed experimentally. In contrast, the Egyptian fruit bat (EFB), Rousettus aegyptiacus, belongs to the same taxonomic family as Pteropus spp, Pteropodidae, and has been successfully used to model Marburg virus transmission [24, 25] and serological cross-reactivity after filovirus challenge [26] . Previous studies have demonstrated that EFB cells are permissive to Ebola virus, but experimentally challenged bats did not shed virus or support productive replication [38, 39] despite compatibility between the Ebola virus glycoprotein and the host receptor, NPC1 [40] . doi = 10.1093/infdis/jiz429 id = cord-334108-4ey725dv author = Seymour, I.J. title = Foodborne viruses and fresh produce date = 2008-07-07 keywords = United; hepatitis; outbreak; virus summary = The most frequently reported foodborne viral infections are viral gastroenteritis and hepatitis A: both have been associated with the consumption of fresh fruit or vegetables. There are many groups of viruses which could contaminate food items, but the major foodborne viral pathogens are those that infect via the gastrointestinal tract, such as the gastroenteritis viruses and hepatitis A virus. There is a need to develop more effective quantitative methods in order to assess the survival of viruses on fresh produce and to determine the decontamination ef®ciencies of current commercial washing systems for fruit and vegetables. Mounting evidence suggests that viruses can survive long enough and in high enough numbers to cause human diseases through direct contact with polluted water or contaminated foods (Nasser 1994; Bosch 1995) . When hepatitis A virus was detected in lettuce from Costa Rica, it was suggested that the possible source of contamination was the discharge of untreated sewage into river water used to irrigate crops, which is common practice in some less well-developed countries (Hernandez et al. doi = 10.1046/j.1365-2672.2001.01427.x id = cord-007843-yqdqm4rh author = Shader, Richard I. title = Zoonotic Viruses: The Mysterious Leap From Animals to Man date = 2018-07-26 keywords = human; virus summary = Nipah and Hendra viruses are both members of the Paramyxoviridae family; neither virus is known to cause disease in their host bats. Similarly, although infrequent, the H1N1 influenza virus can be transmitted from infected pigs to humans, hence its common name of swine flu. 8 Even more uncommon is for a virus to be transmitted from an infected human to an animal. In theory, infected humans could transmit the rabies virus to animals; no cases have been documented. For this issue of Clinical Therapeutics, our Infectious Diseases Topic Editor Dr Ravi Jhaveri has assembled a collection of articles entitled "Hot Topics in Viral Diseases." The collection highlights recent controversies in vaccine licensure and recommendation, as well as advances in antiviral therapies for herpesvirus, hepatitis B and C, respiratory syncytial virus, and influenza, with an emphasis on pediatric patients. A review of therapeutics in clinical development for respiratory syncytial virus and influenza in children doi = 10.1016/j.clinthera.2018.06.016 id = cord-265751-q1ecpfyg author = Shahani, Lokesh title = Antiviral therapy for respiratory viral infections in immunocompromised patients date = 2017-01-16 keywords = H1N1; PIV; RSV; infection; influenza; respiratory; virus summary = â�¢ High prevalence of M2 inhibitors resistance detected in influenza A (H3N2) and 2009 H1N1 virus strains preclude their use for prophylaxis or empiric treatment of seasonal influenza â�¢ Neuraminidase inhibitors are the first line agents for treatment of Influenza and treatment is most likely to provide the most benefit when initiated within the first 48 h of illness â�¢ Zanamivir is currently the therapy of choice for the treatment of oseltamivir-resistant influenza infection â�¢ An immunodeficiency scoring index for RSV, that accounts for the number of risk factors, can be used to identify HSCT recipients who are at high risk for progression to RSV LRTI and RSV associated mortality â�¢ Ribavirin-based therapy (alone or in combination with immunomodulators) can be effective in preventing progression from URTI to LRTI and may improve mortality in highly immunosuppressed adult HSCT recipients â�¢ The safety and efficacy of DAS181 in immunocompromised patients with PIV pneumonia, is currently being studied in an ongoing phase 2 double-blind, placebo-controlled trial. doi = 10.1080/14787210.2017.1279970 id = cord-324280-e8mj6ecl author = Shaman, Jeffrey title = Asymptomatic Summertime Shedding of Respiratory Viruses date = 2018-04-01 keywords = virus summary = Here, we explore respiratory virus infection rates in a segment of this population through a convenience survey and sampling study of adult visitors to a New York City tourist attraction during spring and summer 2016. Among all participants there was a statistically significant positive association between reporting a greater tendency to get sick and total self-reported symptom score (P < .0001 by the Tukey test); however, there was no significant association between reporting a greater tendency to get sick and actual detection of respiratory virus shedding (P = .10 by χ 2 analysis). The best-fit logistic regression model supported an association between an increased likelihood of testing positive for respiratory virus infection and a higher total symptom score (P < .0001) and being Hispanic (P < .005). doi = 10.1093/infdis/jix685 id = cord-330827-gu2mt6zp author = Shanmugaraj, Balamurugan title = Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development date = 2020-02-22 keywords = China; SARS; plant; virus summary = The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV. doi = 10.3390/pathogens9020148 id = cord-026130-ki7bn67o author = Sharma, Anand Kumar title = Novel Coronavirus Disease (COVID-19) date = 2020-06-05 keywords = COVID-19; SARS; people; virus summary = In humans, coronaviruses cause respiratory tract infections that are typically mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), though rarer forms such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), and COVID-19 can be lethal [4] . Based on currently available information and clinical expertise, older adults of over 60 years and people of any age who have serious underlying medical conditions (comorbidities) might be at higher risk of developing the severe disease with SARS-CoV-2, which may even lead to death. As of April 22, 2020, more than 2.5 million people all over the world have tested positive for COVID19 countries including India have evaluated the pandemic situation and have taken the "extraordinary measures" of complete lockdown to contain the virus. doi = 10.1007/s12045-020-0981-3 id = cord-257008-7q5s1vu1 author = Sharma, Virender K. title = Environmental chemistry is most relevant to study coronavirus pandemics date = 2020-05-20 keywords = SARS; virus summary = In the environment, SARS-CoV-2 may survive in the air, on the surfaces, in water and wastewater (Qu et al. Systematically designed experiments will help us gain insight into the virus survival on various surfaces, thus minimizing the exposure of the novel coronavirus to the humans. During wastewater treatment, oxidants and disinfectants can inactivate enveloped viruses (Manoli et al. Research on enveloped-virus transmission and on the treatment of wastewater must include a wide range of enveloped viruses. The recommendation of using oxidants and disinfectants to inactivate SARS-CoV-2 must be experimentally based, which includes testing dose demand and contact time under the environmental conditions at which the virus would be presented. Overall, research in environmental chemistry is disclosing unique knowledge that may help to understand the behavior of viruses and other microbial pathogens in the environment. An imperative need for research on the role of environmental factors in transmission of novel coronavirus (COVID-19) doi = 10.1007/s10311-020-01017-6 id = cord-300711-yibdumij author = Shatizadeh, Somayeh title = Epidemiological and clinical evaluation of children with respiratory virus infections date = 2014-09-22 keywords = respiratory; virus summary = This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. Methods: In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. Results: Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. In this study, AdVs followed by RSV were the most frequently detected viral agents in our patients (14.4%) which occurred mostly in the summer and winter months (August, September and February) in male children in all age groups. doi = nan id = cord-021966-5m21bsrw author = Shaw, Alan R. title = Vaccines date = 2009-05-15 keywords = HIV; antigen; development; dna; immune; infection; pathogen; response; vaccine; virus summary = Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? doi = 10.1016/b978-0-323-04404-2.10092-2 id = cord-277641-nb1p1akx author = Shaw, D. M. title = Invisible Enemies: Coronavirus and Other Hidden Threats date = 2020-08-25 keywords = invisible; virus summary = Fourth, I go on to explore the underlying structural weaknesses and disparities in society that have been exposed by the virus but previously remained unconsidered for so long that they too have become camouflaged, even if their effects are all too apparent; like the virus, neoliberal capitalism is an invisible enemy that has made prisoners of us all. Only by rendering the rest of humanity morally visible to ourselves can we overcome capitalism and stop treating other people as invisible enemies. Socio-economic inequalities existed for centuries before coronavirus came along, but the crisis exposes the invisible enemy that underlies all our lives. The essential flaw of capitalism is that it forces us to treat other people as invisible enemies against whom we are always competing, day in, day out, in a battle to the death. But despite the necessity of physical distancing, coronavirus has reduced our moral distance from the people we share our planet with, revealing them to be not invisible enemies but friends in need. doi = 10.1007/s11673-020-10015-w id = cord-003880-uuuzfyjm author = Shen, Meng-xin title = Antiviral Properties of R. tanguticum Nanoparticles on Herpes Simplex Virus Type I In Vitro and In Vivo date = 2019-09-04 keywords = ICP4; hsv-1; nanoparticle; tanguticum; virus summary = We first conducted plaque reduction assays using HEp-2 cells to test the capacity of these nanoparticles to inactivate the HSV-1 virions and block the viral attachment and entry into cells, following the evaluation of inhibitory effect on viral replication using real-time quantitative PCR, Western blot, and immunofluorescence methods. tanguticum nanoparticles were added to HEp-2 cell monolayers at indicated time periods after HSV-1 infection (MOI = 0.01). tanguticum nanoparticles could suppress HSV-1 viral plaque formation in a dose-dependent manner ( Figure 3B ) and with the increase of drug concentrations, a noted increased antiviral activity was observed. Our previous study showed that the ethanol extracts of Rheum tanguticum, emodin inhibit the herpes simplex virus in vitro and in vivo, which the most effective dose orally administered to mice was 6.7 g/kg/day (Xiong et al., 2011) . doi = 10.3389/fphar.2019.00959 id = cord-009383-ozx5u0t3 author = Sheppard, Michael title = Viral Vectors for Veterinary Vaccines date = 2007-09-28 keywords = vaccine; vector; virus summary = Second, genes from pathogens that encode proteins that will induce an appropriate protective immune response and can be stably integrated into the vector''s genome and expressed need to be identified. The vector only expresses the antigens from the pathogen that are required to elicit a protective immune response and therefore reduces or eliminates the chance of disease by being exposed to the whole pathogen as with a killed or modified live vaccine. One of the main disadvantages of using viral vectors for vaccine delivery is that like subunit vaccines each vector can only deliver one or a relatively small number of foreign antigens to the host animal and therefore rely on those being able to elicit a completely protective immune response. Construction of a defective adenovirus vector expressing the pseudorabies virus glycoprotein gp50 and its use as a live vaccine Expression in recombinant vaccinia virus of the equine herpesvirus 1 gene encoding glycoprotein 13 and protection of immunized animals doi = 10.1016/s0065-3519(99)80014-7 id = cord-302614-siyyve9e author = Shigeta, Shiro title = Anti-RNA virus activity of polyoxometalates date = 2006-05-24 keywords = PM-523; RSV; virus summary = Among these, HS-054 exhibited broad spectrum anti-myxovirus activity and its selectivity indices (SI) for FluV-A, RSV-A, MLSV and PfluV-2 were 333, 31, 167, and 111, respectively, which exceeded those of ribavirin for each virus. We examined anti-FluV A activity with several different ratio combination of PM-523 and ribavirin in vitro and compared this with the individual respective compounds in terms of the effective dose by several parameters of inhibition. We examined seven titanium or vanadium substituted polyoxotungstates (all have Keggin or Keggin All of the compounds exhibited broad spectrum anti-RNA virus activity except that PM-43, PM-518 and PM-523 did not have antiviral activities against PfluV 2, CDV and DFV, respectively. Although, as yet there are no reports of POMs in clinical use, most of the in vitro and some of the in vivo experiments have shown these compounds to be potent and broad spectrum in terms of their antiviral activities against acute respiratory disease viruses. doi = 10.1016/j.biopha.2006.03.009 id = cord-272066-f6q6q3io author = Shim, Byoung-Shik title = Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity date = 2013-06-30 keywords = sublingual; virus summary = These studies have successfully demonstrated the safety and efficacy of sublingual immunization in inducing antigen-specific systemic and mucosal immune responses and protection against pathogen challenges. Taken together, these studies recognized the sublingual mucosa as a potential route of vaccine delivery, which promotes the induction broadly distributed humoral and cell-mediated immune response in systemic lymphoid tissues as well as various mucosal compartments, to offer protection against pathogens that possess tropism for mucosal epithelia. In one study, a recombinant influenza virus M2 protein-based subunit vaccine containing three tandem copies of the M2e (3M2eC) was expressed in Escherichia coli, and the protective efficacy of parenteral and sublingual immunizations was compared (7) . Sublingual sHA1 immunization induced neutralizing antibody responses in the serum and in the respiratory mucosa and provided complete protection against a lethal challenge with pandemic H1N1 influenza A/CA/04/09 virus. In this report, sublingual administration of rADV-S in mice induced SARS virus-specific neutralizing antibody response in the serum and secretory IgA response in the respiratory mucosa. doi = 10.4110/in.2013.13.3.81 id = cord-001676-68y733y3 author = Shoemaker, Jason E. title = An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation date = 2015-06-05 keywords = Fig; H5N1; IFN; pfu; virus summary = After filtering transcripts for minimally confident variation (we required at least one time-matched, infected condition compared with mock-infected absolute fold change 2 and a false discovery rate [FDR]-adjusted P-value < 0.01), the log 2 of the normalized intensity of the retained transcripts (16, 063) for all 167 samples were then clustered by using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm [18] . Data corresponding to macrophage signatures in different cellular states are colored red (see S3 Table for Within the inflammation-associated modules (N1 and N2), the H5N1 virus induced the earliest gene expression changes and the highest peak expression levels, corroborating previous observations that H5N1 viruses are strong inducers of inflammatory and IFN response signaling in vivo [10, 24, 25] . We infected mice with 10 3 PFU of the H5N1 virus (a 100-fold reduced dose compared with that used in the experiments to fit the model), determined lung virus titers at the same time points used for the initial experiment (S3 Fig), and then evaluated the segmented linear model''s ability to predict cytokine-associated gene expression. doi = 10.1371/journal.ppat.1004856 id = cord-310870-w8wu8vno author = Shorten, Robert J. title = The risk of transmission of a viral haemorrhagic fever infection in a United Kingdom laboratory date = 2017-05-18 keywords = laboratory; virus summary = [9] [10] [11] [12] In addition, over 9,000 cases of Crimean Congo Haemorrhagic Fever (CCHF) were reported in Turkey between 2002 and 2014, with an estimated minimum 180,000 blood samples processed in routine laboratories with no additional precautions. Although it is reassuring that large numbers of samples from patients with CCHF infection have been processed safely in routine laboratories in Turkey, it should be noted that this bunyavirus is rarely transmitted person to person, so the parallels between this and other VHF viruses need to be carefully considered. Manufacturers must validate their decontamination method against appropriate surrogate model enveloped viruses. Viral inactivation validation studies have successfully used surrogate model viruses with properties similar to wildtype viruses to provide evidence for the safety of human blood plasma products for over a decade. Once assessed by appropriately designed viral inactivation validation studies on relevant surrogate model enveloped viruses, the decontamination process has been shown to be effective against all known and future emerging enveloped viruses, which includes Ebola, CCHF, Lassa fever, and Marburg virus. doi = 10.1371/journal.pntd.0005358 id = cord-004841-wf0o3whi author = Sibalin, M. title = Herpesvirus strigis, a new avian herpesvirus: II. Biochemical and biophysical properties date = 1974 keywords = HSIS; virus summary = Tissue cultured virus proved sensitive to ether, chloroform, 0.5 per cent trypsin, and to pH levels of 4.0 or lower. Biological properties described in a foregoing paper sustained such grouping, and indicated that the agent was a new avian herpesvirus for which the nameherpesvirus strigis was proposed. According to Table 1 , both herpesviruses tested, i.e. HSIS and IBI~, got completely inactivated by ether as well as chloroform indicating that their virions were sensitive to lipid solvents. Other authors had observed similar core structures with some of their herpesviruses (12, 20) , and also fringes on the viral envelope (3, 12, 20) , of the size recorded here for herpesvirus strigis. Based on its biological properties described in our first paper (7), which allowed to differentiate it from other herpesviruses, we proposed tISIS as a new avian virus species to be named herpesvirus strigis. doi = 10.1007/bf01251017 id = cord-010374-z9ygudv6 author = Siddell, S.G. title = Coronaviridae1 date = 2008-07-24 keywords = RNA; virus summary = The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Recently, there have been reports of virus-specific RNA poly merases in coronavirus-infected cells, but the components of the enzyme have not been iden tified. UV inactivation studies in dicate that coronavirus mRNAs are not pro duced by the processing of a larger RNA, although extensive sequence homologies have been detected at the 5'' ends of ail murine hepatitis virus-specific subgenomic RNAs. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. doi = 10.1159/000149390 id = cord-282204-j1slaefb author = Silva, José V.J. title = A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date = 2018-12-31 keywords = Aedes; CHIKV; Chikungunya; DENV; infection; virus summary = de; Oliveira, Renato A.S.; Durães-Carvalho, Ricardo; Lopes, Thaísa R.R.; Silva, Daisy E.A.; Gil, Laura H.V.G. title: A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control Laboratory tests for specific diagnosis of CHIKV infection are based on virus isolation, viral RNA detection and serology (Johnson et al., 2016) . Anti-CHIKV candidates that have been already tested in humans and/or animals include inactivated-, attenuated-, virus like particle-(VLP), DNA-and chimeric vaccines (Eckels et al., 1970; Levitt et al., 1986; Muthumani et al., 2008; Wang et al., 2008; Tiwari et al., 2009; Sharma et al., 2012 Akahata et al., 2010 Plante et al., 2011; Wang et al., 2011; Gorchakov et al., 2012; Brandler et al., 2013; Chang et al., 2014; García-Arriaza et al., 2014; Tretyakova et al., 2014; van den Doel et al., 2014; Erasmus et al., 2017) . doi = 10.1016/j.actatropica.2018.09.003 id = cord-010273-0c56x9f5 author = Simmonds, Peter title = Virology of hepatitis C virus date = 2001-10-10 keywords = HCV; RNA; hepatitis; sequence; virus summary = 1,2 The identification of HCV led to the development of diagnostic assays for infection, based either on detection of antibody to recombinant polypeptides expressed from cloned HCV sequences or direct detection of virus ribonucleic acid (RNA) sequences by polymerase chain reaction (PCR) using primers complimentary to the HCV genome. 6 ''13 Remarkably, a series of plant viruses that are structurally distinct from each of the mammalian virus groups, and with different genome organizations, have RNA-dependent RNA polymerase amino acid sequences that are perhaps more similar to those of HCV than are the flaviviruses. In contrast to the highly restricted sequence diversity of the 5''NCR and adjacent core region, the two putative envelope genes are highly divergent between different variants of HCV (Table III) 111-114 and show a three-to-four-times higher rate of sequence change with time in persistently infected patients, ll5 Because these proteins are likely to lie on the outside of the virus, they would be the principal targets of the humoral immune response to HCV elicited on infection. doi = 10.1016/s0149-2918(96)80193-7 id = cord-283756-ycjzitlk author = Simons, Robin R. L. title = Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date = 2014-05-16 keywords = Africa; Bangladesh; MARV; Nipah; bat; virus summary = Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. Bats are known to have varying degrees of contact with domestic animals and commercial food crops [20, 21] , in particular contact of Pteropus giganteus bats with date palm sap producing trees in Bangladesh is considered a risk factor for human NiV infection [22] . It can be seen that while recent human infections of both NiV and MARV appear to be limited in geographical range (the red areas in Figure 2 ), there are a number of countries where bats have been identified as having the virus, but no human infection has been reported. doi = 10.3390/v6052084 id = cord-285148-bch7814v author = Singanayagam, Aran title = Viruses exacerbating chronic pulmonary disease: the role of immune modulation date = 2012-03-15 keywords = COPD; IFN; infection; virus summary = However in vitro RV infection of epithelial cells from COPD patients resulted in higher virus load and increased inflammatory mediators, but no differences in interferon production compared to cells from control subjects [87] . List of abbreviations ATF: activating transcription factor; BAL: bronchoalveolar lavage; CF: cystic fibrosis; CFTR: cystic fibrosis transmembrane regulator; COPD: chronic obstructive pulmonary disease; ENA-78: epithelial-derived neutrophilactivating peptide 78; ICAM-1: intercellular adhesion molecule; IFN-α: interferon-alpha; IFN-β: interferon-beta; IFN-λ: interferon-lambda; IFN-γ: interferon-gamma; IL: interleukin; IP-10: IFN-γ-induced protein-10; IRF: interferon regulatory factor; ISG: interferon stimulated genes; MDA-5: melanoma differentiation-associated protein-5; NF-κB: nuclear factor-kappa B; NO: nitric oxide; NOS2: nitric oxide synthase 2; PCR: polymerase chain reaction; PEF: peak expiratory flow; PIV: parainfluenza virus; RANTES: regulated on activation: normal T-cell expressed and secreted; RIG-I: retinoic acid inducible gene I; RSV: respiratory syncytial virus; RV: rhinovirus; SLPI: secretory leukoprotease inhibitor; SOCS: suppressor of cytokine signaling family; Th1/2: T helper 1/2; TLR: toll-like receptors; TNF-α: tumor necrosis factor-alpha -1. doi = 10.1186/1741-7015-10-27 id = cord-263245-2qub96mz author = Singh, D. title = Alcohol-based hand sanitisers as first line of defence against SARS-CoV-2: a review of biology, chemistry and formulations date = 2020-09-29 keywords = SARS; alcohol; hand; virus summary = This review summarises the studies on alcohol-based hand sanitisers and their disinfectant activity against SARS-CoV-2 and related viruses. The literature shows that the type and concentration of alcohol, formulation and nature of product, presence of excipients, applied volume, contact time and viral contamination load are critical factors that determine the effectiveness of hand sanitisers. When soap and water are not available, the Food and Drug Administration (FDA) recommends sanitising of non-visibly soiled hands with an alcoholbased agent containing 80% v/v ethanol or 75% v/v isopropanol [4] . This review assesses available information on the composition, formulation and effectiveness of alcohol-based hand disinfection products with specific reference to their activity against SARS-CoV-2. Alcohol-based hand rubs in the form of foam, rinse and gel did not differ significantly in trials of antimicrobial activity but the application volume and drying time had a profound effect on their efficacy [54] . doi = 10.1017/s0950268820002319 id = cord-349249-jwvz1ux2 author = Singh, Gagandeep title = A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date = 2019-10-22 keywords = PEDV; RNA; figure; vaccine; virus summary = To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. to that of the spike protein-specific Abs. Strong virus neutralizing Ab responses, were detected in animals vaccinated with the heat and RNAse treated virions but not in the pigs which received the irradiated viral vaccine. Although the heat and RNAse treated virus culture was amplified after 3 passages in cell culture (Figure 2) , the absence its detection by RT-qPCR (Figure 4) , or immunohistochemistry (Table 1 and Figure 5 ) and the lack of strong Ab responses to the non-structural NP (Figure 3) , in vaccinated pigs prior to challenge indicates that active vaccine viral replication was absent in the host or was undetectable by the techniques used. doi = 10.3389/fvets.2019.00347 id = cord-275013-na6319rg author = Singh, Indra P. title = Innate defences against viraemia date = 2000-11-23 keywords = HDL; inhibitor; virus summary = Recently, two naturally occurring nonspecific broad‐spectrum antiviral agents, University of Texas Inhibitor β (UTIβ) glycoprotein and high density lipoprotein, have been described in human serum. In this review, we emphasise the properties of broadly active antiviral molecules in human serum and explore the possibility that they can be important as natural defence mechanisms. Based on this protection and other correlations, the authors suggested a natural defensive role for this broadly antiviral inhibitor that is present widely and in high concentration in tissues and extracellular¯uid of human nervous system [25] . The mechanisms of action of these inhibitors are competitive inhibition of virus attachment to cells and neutralisation of viral infectivity by a mechanism unlike classical antibody because complement is not needed for their activity. These observations point to a relationship in vivo between the level of serum inhibitors and in¯uenza virus multiplication and thus support the notion that the narrowly active, nonspeci®c viral inhibitors can be a factor in innate resistance to speci®c viruses. doi = 10.1002/1099-1654(200011/12)10:6<395::aid-rmv298>3.0.co;2-v id = cord-026340-2nf97zvc author = Singh, Ranjana title = Chloroquine: A Potential Drug in the COVID-19 Scenario date = 2020-06-07 keywords = COVID-19; HCQ; SARS; virus summary = In this review article, we have systematically searched for details of COVID-19 pandemic till May 2020 and assembled few data pertaining to (i) Corona viruses; (ii) SARS-CoV2, the virus that causes COVID-19'' and (iii) How chloroquine and hydroxychloroquine mediates anti-viral effect in both prophylactic and therapeutic setting. The Corona Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) after assessing the etiological agent named it SARS-CoV2 (Severe Acute Respiratory Syndrome Corona Virus2) and the disease outbreak as COVID-19 (Corona Virus Disease-Year of Identification). During COVID-19, SARS-CoV2 S-protein binds to host cell''s receptor ACE2 (Belouzard et al. As for the case of SARS-CoV, it was shown that the binding specificity of virus to host cell was due to 3 prime amino acid residues in S1 protein at positions 360, 479, and 487. doi = 10.1007/s41403-020-00114-w id = cord-336554-n8n5ii5k author = Singh, Thakur Uttam title = Drug repurposing approach to fight COVID-19 date = 2020-09-05 keywords = ACE2; COVID-19; RNA; SARS; clinical; drug; patient; treatment; virus summary = Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . doi = 10.1007/s43440-020-00155-6 id = cord-280427-smqc23vr author = Singla, Rubal title = Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date = 2020-09-14 keywords = COVID-19; RNA; SARS; animal; virus summary = The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. doi = 10.1007/s11259-020-09781-0 id = cord-010248-ln800g5z author = Sissons, J.G. Patrick title = Antibody-Mediated Destruction of Virus-Infected Cells date = 2008-02-29 keywords = ADCC; Oldstone; PBL; antibody; cell; virus summary = When lz5I-1abeled IgG antibody was bound to the surface of measles virus-infected cells at the start of the culture period, under the conditions described above for antigenic modulation, about 40% of the radioactivity was still cell associated at 12 hours and nearly all was protein bound Perrin and Oldstone, 1977) . Lysis by human serum of cells infected with HSV types 1 and 2, influenza A, parainfluenza 1, 2, 3, and 4, mumps, and measles viruses was dependent on the presence in serum of IgG antibody specific for the relevant virus and of complement (reviewed by Oldstone and Lampert, 1979) . The use of this system, composed of 11 highly purified complement proteins, provided conclusive evidence that the known proteins of the alternative and membrane attack pathways with IgG antibody are sufficient for lysis of the measles virus-infected cell, without other serum factors. It is apparent that considerably more surface-bound IgG is required to induce complement-dependent lysis of virus-infected cells than is required for antigenic modulation or antibody-dependent cell-mediated cytotoxicity. doi = 10.1016/s0065-2776(08)60045-0 id = cord-258333-jmk8hdk2 author = Sivier, V title = Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date = 2001-12-10 keywords = des; infection; virus summary = Sur les 129 malades ayant présenté une hyperthermie, 12 décès ont été observés, soit un taux de mortalité de 9,3 % : un décès dans le groupe « virose respiratoire » par surinfection bactérienne pulmonaire, sept décès dans le groupe « infection respiratoire non virale » (un choc septique, cinq décompensations respiratoires aiguës, une décompensation cardiaque aiguë) et quatre décès dans le groupe « autre » (deux cancers en phase terminale, un accident vasculaire cérébral et une cause indéterminée). L''épidémie nosocomiale de virus respiratoire syncytial est survenue dans un service de long séjour avec des locaux communs et exigus, chez des patients porteurs de multiples maladies et souvent déments. En conclusion, les infections respiratoires, qu''elles soient virales, bactériennes ou non documentées, apparaissent comme la principale cause d''hyperthermie chez le sujet âgé institutionnalisé pendant la saison hivernale et sont à l''origine de nombreuses complications, voire de décès. doi = 10.1016/s0248-8663(01)00489-1 id = cord-011917-6u0t4hy8 author = Skarlupka, Amanda L. title = Immune Imprinting in the Influenza Ferret Model date = 2020-04-08 keywords = A(H1N1; A(H3N2; Influenza; ferret; virus summary = Therefore, the use of naïve ferret sera for vaccine strain selection is potentially misrepresentative of the pre-immune human population that receives each season''s influenza virus vaccines, contributing to the observed VE. Unique to sequentially infected ferrets, the elicited antibody profile was broader and interacted with pandemic A(H1N1) HA compared to the single pre-immunity groups as measured with HA-specific ELISA binding. In contrast to previous reports that pre-immunity induced protection does not wane [68] , the boosts in anti-HA stalk antibodies and the cross-reactivity induced from sequential infection with antigenically distinct seasonal A(H1N1) declined over time [74] . The current pre-immunity models are moving away from investigating the differences in disease symptoms and vaccine effectiveness observed in the human population in response to the pandemic virus. Pre-immunity to a historical A(H3N2) virus helped boost the magnitude and breadth of the broadly neutralizing antibodies elicited by computationally optimized broadly reactive antigen (COBRA) immunogens compared to a naïve ferret group [37] . doi = 10.3390/vaccines8020173 id = cord-325325-xw7627x9 author = Skeik, Nedaa title = Influenza viruses and the evolution of avian influenza virus H5N1 date = 2007-10-02 keywords = H5N1; influenza; virus summary = While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. doi = 10.1016/j.ijid.2007.07.002 id = cord-021770-zn7na974 author = Slifka, Mark K. title = Passive Immunization date = 2017-07-17 keywords = antibody; human; infection; monoclonal; passive; serum; treatment; virus summary = [26] [27] [28] [29] Recent studies verify these earlier results, demonstrating a 90% to 91% vaccine efficacy against whooping cough among infants younger than 2 months of nonlymphoid tissues and to penetrate mucosal sites of infection is likely to explain why it is often considered the best immunoglobulin isotype for routine passive immunization and has shown clinical benefit ranging from reduced clinical symptoms to nearly complete protection from lethal infection in a number of infectious disease models (Table 8 .3). 118 With the recent development of polyclonal and monoclonal antibodies that show protective efficacy against tularemia in animal models, [119] [120] [121] it may be possible to incorporate both passive immunotherapy and antibiotic treatment into clinical practice not only for tularemia, but for other bacterial diseases, especially in cases in which antibiotic resistance is becoming more widespread. doi = 10.1016/b978-0-323-35761-6.00008-0 id = cord-003767-9xbu4hnq author = Slingenbergh, Jan title = Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern date = 2019-05-25 keywords = host; transmission; virus summary = The synthesis of the findings reveals a predictive virus evolution framework, based on the outerto inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . doi = 10.3390/pathogens8020072 id = cord-341155-3d64mso0 author = Slots, Jørgen title = Bacterial and viral pathogens in saliva: disease relationship and infectious risk date = 2010-12-07 keywords = Barr; Epstein; HIV; human; oral; saliva; virus summary = Human viruses are also frequent inhabitants of the human mouth, and their presence in saliva may be caused by the direct transfer of saliva from infected individuals, a bloodborne infection of the salivary glands, infection of the oral mucosa, or serumal exudates from diseased periodontal sites. Caries risk is assessed by the levels of mutans streptococci and lactobacilli in stimulated saliva (94, 96) , and salivary transmission of cariogenic bacteria frequently occurs from the mother to her child (92, 100) . As high quantities of salivary Epstein-Barr virus DNA can be recovered from fully edentulous patients (155) , the occurrence of the virus in saliva may not be a reliable indicator of its subgingival level or of the periodontitis disease status. Taken together, the saliva of HIV-infected persons is a risk factor for the transmission of several virulent herpesvirus species, and patients receiving HAART cannot be assumed to be less infectious for herpesviruses than individuals not receiving HAART. doi = 10.1111/j.1600-0757.2010.00361.x id = cord-333853-p2kbjwpy author = Smee, Donald F. title = Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date = 2011-10-13 keywords = infection; pfu; virus summary = title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. Ad5-vectored mouse interferon (mDEF201) resulted in sustained IFN levels [16] , that completely protected mice from a lethal Western equine encephalitis virus infection when given intramuscularly at 10 7 plaque forming units (PFU)/ mouse up to 7 days prior to virus challenge [16] . The extent of inhibition of lung Intranasal treatments with mDEF201 (10 7 PFU/mouse) were given one time only on the indicated day prior to virus exposure. doi = 10.1371/journal.pone.0026330 id = cord-006285-kkxdmzk9 author = Smirnova, S. S. title = Long-Term Maintenance of the Functional Changes Induced by Influenza A Virus and/or LPS in Human Endothelial ECV-304 Cell Sublines date = 2019-08-26 keywords = LPS; cell; virus summary = The present work reports the comparative assessment of the functional changes which take place in human ECV-304 endothelial cell sublines obtained previously by the long-term culturing of cells after exposure to varying infectious doses (IDs) of influenza A virus, and/or bacterial lipopolysaccharide (LPS). It has been demonstrated that, in the course of long-term culturing (six passages) after exposure to pathogenic agents (influenza virus and/or LPS), endothelial cells maintain changes in their migratory activity, permeability, and expression of mRNA for cytokines TNFα and TGFβ (along with the changes in their proliferation activity, which has been demonstrated earlier). The comparative study of the human endothelial ECV-304 cell sublines carried out in the present work and in our previous work (Smirnova et al., 2018) has demonstrated that the infection of nonpermissive cells with influenza A virus (both in high and in very low doses) and exposure to LPS can change migratory, proliferation, and apoptotic activity of cells and impair cell barrier function. doi = 10.1134/s1990519x19040084 id = cord-339230-cc7gcy5b author = Smith, Amber M. title = Secondary Bacterial Infections in Influenza Virus Infection Pathogenesis date = 2014-07-16 keywords = PB1-F2; bacterial; influenza; streptococcus; virus summary = Several different animal models have been used to study the effect that influenza viruses have on bacterial transmission and colonization and on invasive diseases, such as acute otitis media and pneumonia (Wherry and Butterfield 1921; Shope 1931; Francis and de Torregrosa 1945; Berendt et al. Although the precise mechanisms responsible for enhancing the transmission profile that influenza viruses provide pneumococci are currently unknown, it is likely due to an increase in pathogen density and frequency of secretion events (e.g., sneezing and coughing) in the infected individual combined with a decrease in immunity and resistance from natural barriers breaking down in the person who is newly exposed. The PB1-F2 protein of some influenza viruses increases pathologic effects by causing cell death, increasing viral replication, and altering inflammatory responses to primary viral infections and to bacterial coinfections (Conenello et al. doi = 10.1007/82_2014_394 id = cord-007764-7750z41g author = Smith, M. L. title = Display of Peptides on the Surface of Tobacco Mosaic Virus Particles date = 2009 keywords = TMV; fusion; virus summary = In this review, we focus on the potential that tobacco mosaic virus (TMV) has as a carrier for immunogenic epitopes, and the factors that must be considered in order to bring products based on this platform to the market. There are well-established methodologies for recombinant production of VLP-epitope display systems that use self-assembling capsid proteins of several different viruses, most notably papillomaviruses, hepatitis B core and surface antigens, and various bacteriophages, including the leviviruses MS2 and Qβ. The focus of this review is on some of the practical issues that must be considered in order to bring plant-produced virus particle and VLP-based epitope display systems into commercial use. Commercial-scale biomanufacturing allows translation of the body of data providing proof of the concept that TMV can function as an effective carrier for antigenic peptides into vaccine products for human and veterinary applications (Pogue et al. doi = 10.1007/978-3-540-70868-1_2 id = cord-256837-100ir651 author = Smith, Steven B. title = Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date = 2012-03-14 keywords = Parkin; RSV; TNF; figure; gene; pathway; virus summary = Several recent studies have generated multiple mRNA microarray gene expression datasets derived from experiments involving the infection of human cell-lines or animal models with one or more of the major respiratory viruses [21] [22] [23] . Through a systematic analysis of these respiratory virus-human host gene expression datasets, we determined common sets of genes and pathways involved in host responses to viral infections. A total of seven different respiratory viruses were analyzed, represented by fifteen unique Gene Expression Omnibus (GEO) datasets (indicated by GEO Series or GSE accession numbers), nine different human cell types, and seven different array platforms for a total of 28 unique comparisons. This assumption is based on the occurrence of genes that are differentially expressed in infection models for at least five of the seven respiratory viruses, have involvement in a number of relevant pathways related to host immune response, and encode for known drug targets. doi = 10.1371/journal.pone.0033174 id = cord-323930-pl3qlcpo author = Sohail, Ayesha title = Forecasting the timeframe of coronavirus and human cells interaction with reverse engineering date = 2020-04-29 keywords = SARS; virus summary = The purpose of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane fusion [10]. The purpose 11 of this article is to review and investigate further the molecular mechanism by which the SARS-CoV2 12 virus infection proceeds via the formation of a hetero-trimer between its protein S, the ACE2 receptor 13 and the B0AT1 protein, which is the "entry receptor" for the infection process involving membrane "animal to man" and then "man to man " transmission. Our hypothesis is supported by 128 the need for activation of the infection system by the virus, given by the particular molecular kinetics that 129 leads to the formation of the "infection trimer" given by the viral S1 protein and the ACE-2 receptor While developing the computational framework, the virus-target cell interaction was studied in depth. doi = 10.1016/j.pbiomolbio.2020.04.002 id = cord-022348-w7z97wir author = Sola, Monica title = Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date = 2007-09-02 keywords = HIV-1; RNA; figure; sequence; virus summary = An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. Under the rubric replication, a virus could vary to increase its fitness, exploit different target cells or evade adaptive immune responses. For a given virus, different protein sequence sets were compared to a given reference such as RT in the case of HIV/SIV. Although these data were derived from completely sequenced primate immunodeficiency viral genomes, analyses on larger data sets, such as p17 Gag/p24 Gag or gp120/gp41, yielded relative values that differed from those given in Table 6 .1 by at most 14%. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships (Table 6 .1). In the clear cases where genetic variation is exploited by RNA viruses, it is used to overcome barriers to transmission set up by the host population, e.g. herd immunity. doi = 10.1016/b978-012220360-2/50007-6 id = cord-006790-lye0qjw8 author = Song, R. title = Surveillance of the first case of human avian influenza A (H7N9) virus in Beijing, China date = 2013-10-16 keywords = H7N9; case; virus summary = A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case''s illness. A number of specimens from the environment of this cluster and from the feces specimens tested positive for viral RNA of the H7N9 virus on the fourth day following onset of the index case''s illness. Fifteen hours after the fever began, the pharyngeal swab collected from the index case tested positive for the H7N9 virus by RT-time PCR. Pharyngeal swabs collected from the index case''s mother tested positive for the H7N9 virus on 12 April and 14 April and were negative after 15 April. Although the family members of the index case were all exposed to asymptomatic chickens infected with H7N9 virus, they presented with distinct outcomes. doi = 10.1007/s15010-013-0533-9 id = cord-288945-c9ow1q5c author = Spengler, Ulrich title = Liver Disease Associated with Non-Hepatitis Viruses date = 2019-11-01 keywords = CMV; EBV; infection; virus summary = Although exotic diseases, in particular viral hemorrhagic fevers are a severe threat in certain regions of the world, liver disease due to exotic infections such as Ebola virus, Rift valley fever or Lassa fever have been reported only sporadically but do not represent a frequent health problem in returning travelers. Clinically more severe diseases, for example, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) can follow from secondary infection with dengue virus of different serotype. Herpes simplex virus (HSV), varizella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV) and Human Herpesvirus type 6 or 7 (HHV6, HHV7) can directly affect the liver and are infections in the human population usually acquired during childhood or adolescence. In patients with severe immunodeficiency lymphomatoid granulomatosis is a further unusual complication of Epstein-Barr virus infection leading to granuloma formation in multiple organs including the liver, which may require interferon-alpha antiviral therapy (Wilson et al., 1996) . doi = 10.1016/b978-0-12-801238-3.65782-3 id = cord-009589-xfdgk2j6 author = Spradbrow, P. B. title = VIRUS DISEASES OF DOMESTIC ANIMALS date = 2008-03-10 keywords = virus summary = Viruses multiply solely from their genetic material of DNA or RNA when this is introduced into a susceptible cell and provides a code for the production of new virus genetic material and structural components. Much progress has been made towards the grouping (classifying) of related viruses by a consideration of the nature of their genetic material and of certain stable features of the infectious particle or virion. Surprisingly, many veterinary viruses that produce severe disease in conventional animals cause only mild disease in the germ-free host. In fact, the herpesvirus of feline rhinotracheitis is an unusual virus in producing a disease in germ-free animals comparable in severity with that seen naturally (Hoover et a1 1970) . group of agents, and the relative importance of the various defence mechanisms will probably vary with the nature of the infecting virus and of the host. doi = 10.1111/j.1751-0813.1972.tb05117.x id = cord-327392-9psblokc author = Srivastava, A.K. title = Potential of Graphene-based Materials to Combat COVID-19: Properties, Perspectives and Prospects date = 2020-10-21 keywords = SARS; SPR; graphene; virus summary = Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. Thus, the effectiveness of graphene-based electrochemical biosensors for the detection of biomolecules, in particular for the viruses, suggests that these biosensors have the potential to effectively detect the novel coronavirus SARS-CoV-2 as well [51] but a lot of high-end research needs to be performed to develop reliable diagnostic devices. We present a hypothetical mechanism in Figure 4 that shows how electrochemical biosensors based on graphene and GRMs could be used for the detection of SARS-CoV-2 virus. These findings reinforce that graphene-based SPR substrates could be used for designing and development of the sensitivity devices for the detection of SARS-CoV-2 and other viruses. doi = 10.1016/j.mtchem.2020.100385 id = cord-263868-ewnf96cz author = Srivastava, Mayank title = Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor date = 2020-08-04 keywords = Fig; NCAM1; Supplementary; ZIKV; virus summary = ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We used the labeled ZIKV to infect Vero cells and interacting proteins were crosslinked at fixed time points to identify the virus-host factors and elucidate the virus entry mechanism (Fig. 1c) . To further investigate whether the strategy was also capable of correlating spatial information with the virus crosslinked proteins, we performed the STRING analysis to determine whether there is statistical overrepresentation of specific genes or proteins in the sample at specific time points and identify proteins specific at the attachment or cellular entry stages ( Supplementary Fig. 6 ). doi = 10.1038/s41467-020-17638-y id = cord-007731-wu7i548j author = Sriwilaijaroen, Nongluk title = Molecular Basis of a Pandemic of Avian-Type Influenza Virus date = 2014-05-27 keywords = H5N1; HPAI; infl; uenza; virus summary = Change in HA antigen either by accumulation of mutations in HA1 of fi ve proposed antigenic sites (based on amino acid sequence comparison among viruses isolated from different years or among variants grown in the presence of mouse monoclonal antibodies) as shown in Fig. 7c [ 56 -59 ] or by intrasubtypic reassortment between distinct clades of co-circulating infl uenza A viruses [ 35 ] is responsible for evasion of recognition by the host antibodies and thus Cleavage site 324P-X-X/R/K-X-X-R/K↓GLF X = nonbasic residue 324P-X-R/K-X-R/K-R↓GLF (due to insertion/substitution) Host proteases Extracellular tissue-restricted trypsin-like proteases Ubiquitously expressed intracellular proteases (e.g., furin and PC6) continuous circulation of the virus in host populations. However, highly mutable avian infl uenza A viruses that have sporadically continued direct transmission to and infection in humans have raised concerns for pandemic potential with unpredictable pathogenesis (depending on virus-host interactions). doi = 10.1007/978-1-4939-1292-6_38 id = cord-253705-utp8po48 author = Sriwilaijaroen, Nongluk title = Sialoglycovirology of Lectins: Sialyl Glycan Binding of Enveloped and Non-enveloped Viruses date = 2020-04-19 keywords = D37; Fig; Neu5Ac; Sia; cell; receptor; virus summary = While HEF glycoproteins of influenza C and D viruses attach to 9-O-acetyl-Neu5Accarrying sugar chains found in the respiratory tract of animals [31] as a receptor determinant for infection in cattle and pigs (only C virus has been detected in humans), HAs of influenza A (Fig. 3a) and B viruses recognize α2-6Neu5Ac-carrying sugar chains and Fig. 3 (continued) σ1 containing a Sia-binding site in its body) interacts with a sialoglycan on a glycoprotein/ glycolipid (a brown dash), which is anchored to the host cell membrane. Variants with the HE gene, which have become circulating strains, could be explained by the finding that the HE protein increases the efficiency of production of infectious virus [78] possibly by acting as a lectin for enhancing viral binding and as an enzyme that destroys receptors by de-O-acetylation (esterase) for enhancing release of trapped virions from the host mucosa and of budding virions from infected cells. doi = 10.1007/978-1-0716-0430-4_47 id = cord-261961-u4d0vvmq author = St-Germain, Jonathan R. title = A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date = 2020-08-28 keywords = SARS; protein; virus summary = To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. The resulting viral tryptic peptides were identified using nanoflow liquid chromatography -tandem mass spectrometry (LC-MS/MS; Fig 1A, Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12] [13] [14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches. To this end, we also undertook an analysis of SARS-CoV-2 virions and infected Vero cell lsyates using data-dependent acquisition tandem mass spectrometry, and identified 189 unique tryptic peptides, assigned to 17 different virus proteins. doi = 10.1101/2020.08.28.269175 id = cord-002933-zmx4k46v author = Stabell, Alex C title = Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir date = 2018-03-20 keywords = dengue; figure; human; sting; virus summary = The dengue virus 2 (DENV2) encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We show that an ''RG'' motif at positions 78/79 of STING is critical for susceptibility to cleavage, and conversion of these residues to ''RG'' renders all nonhuman primate STING proteins tested, as well as mouse STING, sensitive to dengue virus proteases. Out of the entire Genbank database, along with our sequencing of STING from 16 additional primate species, we identify only a small number of apes (gorillas, orangutans, and gibbons), and three small rodent species (chinchillas, naked mole rats, and desert woodrats) as encoding a functional dengue virus cleavage determinant in STING. Further, the restoration of the ''RG'' motif at positions 78/79 again renders all of these STING proteins susceptible to cleavage ( Figure 5B) , indicating that the sylvatic protease is targeting (i.e. binding or cleaving) the same cleavage determinant as the proteases from human dengue viruses. doi = 10.7554/elife.31919 id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 keywords = CoV; RNA; SARS; protein; virus summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection doi = 10.1038/nrmicro775 id = cord-302021-42vqmndl author = Stanley, Mathew title = Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases date = 2011-04-08 keywords = virus summary = Besides sialidases, the haemagglutinin-esterases (HE) of influenza C virus, isavirus, betacoronaviruses and toroviruses represent another class of RDEs. They are sialate-O-acetylesterases (SOAE) hydrolysing O-acetyl esters of O-acetylated sialic acid derivatives (Fig. 1) . Alkylation of 7 under Williamson-conditions followed by acid-mediated ketal hydrolysis and basic saponification of the methyl ester gave crude inhibitor 1 which was purified by gel permeation chromatography. Inhibition of the SOAE activity of three viruses, influenza C virus (INF-C), bovine coronavirus (BCoV) and mouse hepatitis virus strain S (MHV-S) and of two chimeric recombinant viral haemagglutinin esterases, from influenza C/Cal/78 virus (HE12-GFP) and sialodacryoadenitis virus (SDAV-HE) was investigated. The crude product was purified by flash chromatography (EA / EA:MeOH; 5:1) to yield the 9-O-methyl ether ( The ether (5 mg, 0.0132 mmol) was dissolved in dioxane (0.5 mL) and NaOH (0.05M, 0.5 mL) was added with stirring. doi = 10.1016/j.ejmech.2011.04.008 id = cord-271927-u8p6c9w4 author = Stefanacci, Richard G. title = Learnings to Operate LTC Better from the COVID-19 Crisis date = 2020-09-07 keywords = LTC; medication; virus summary = But the indirect impact of COVID and LTC residents from social isolation causing weight loss, falls, delirium, dementia and depression as well as staff burn out will likely cause early deaths that may be even more significant. And what I mean by that it''s an opportunity to do things you think you could not do before.‖ This COVID-19 is a serious crisis that we should not let go to waste but rather use as an opportunity operate differently around improving socialization, senses and staff support. For residents of health care facilities and staff the COVID-19 pandemic has added to our existing burden of daily stressors. As we navigate the COVID-19 pandemic, the need or deprescribing and optimizing medication management is more critical than it has ever been as reducing medications will potentially reduce opportunities for transmission of the virus between staff and residents. doi = 10.1016/j.gerinurse.2020.07.014 id = cord-287151-4hlvrfeh author = Steinmann, J title = Surrogate viruses for testing virucidal efficacy of chemical disinfectants date = 2004-04-30 keywords = HBV; virus summary = Abstract Since important agents of viral nosocomial infections like hepatitis B and C viruses and norovirus do not replicate sufficiently in cell culture systems, disinfectants with suspected efficacy against these viruses must be evaluated by different methods. Besides molecular approaches and indirect tests, the use of surrogate viruses with similar biophysical properties and genomic structure allows the assessment of virucidal efficacy of chemical disinfectants in quantitative suspension tests. By including these viruses in inactivation experiments, valuable data from suspension tests can be derived on the virucidal efficacy of chemical disinfectants. Besides the viruses mentioned in the guidelines, there are other important pathogens such as Hepatitis B virus (HBV), Hepatitis C virus (HCV) and norovirus which cause nosocomial infections but cannot be propagated sufficiently by cell culture techniques. Inactivation of hepatitis B virus in plasma by hospital in-use chemical disinfectant assessed by a modified HepG2 cell culture doi = 10.1016/j.jhin.2003.12.030 id = cord-331244-zaguyxm5 author = Stephenson, Iain title = Confronting the avian influenza threat: vaccine development for a potential pandemic date = 2004-07-30 keywords = H5N1; H9N2; Hong; influenza; virus summary = In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. In clinical trials, conventional surfaceantigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. The main antigenic determinants of influenza A and B viruses are two surface glycoproteins: the neuraminidase and the haemagglutinin, both capable of eliciting immune responses in human beings. Pandemic influenza viruses arise by this process of "antigenic shift", when a virus with a new haemagglutinin subtype emerges and spreads efficiently in a naive human population. 14 These reassortant viruses have haemagglutinin receptor-binding sequences potentially capable of human infection, suggesting that new viruses may emerge directly from the avian pool. Improved understanding of the antigenic and molecular associations between potential pandemic strains of same subtype Improved understanding of immunogenicity against drifted avian influenza strains is required as the ability to generate broad crossprotective immunity is desirable in vaccine candidate. doi = 10.1016/s1473-3099(04)01105-3 id = cord-316894-zhmuzv7z author = Stetzenbach, L.D. title = Airborne Infectious Microorganisms date = 2009-02-17 keywords = SARS; disease; infection; virus summary = Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. doi = 10.1016/b978-012373944-5.00177-2 id = cord-006089-08g206kf author = Stevens, James title = Glycan microarray technologies: tools to survey host specificity of influenza viruses date = 2006-10-02 keywords = H5N1; influenza; virus summary = These proteins are rich in α2-3-linked sialosides (sialylated glycans), and function to trap avian influenza viruses and prevent their attachment to epithelial cells 12 Recent studies have revealed that some human epithelial cells in the lower respiratory tract contain α2-3-linked sialic acids and can be directly infected by avian influenza viruses 10, 11, 13 . Therefore, it is clear that, although human and avian virus HAs have a primary specificity for either α2-6or α2-3-linked sialosides, each virus might use a different range of glycan receptors for cell entry, and the ability of a virus to infect a host cell might depend on features in the glycan structure, other than simply the type of sialic-acid linkage. By working together, future development of DNA and glycan microarray technologies could enable rapid assessment of emerging viruses to detect virus subtypes and receptor specificities that increase the risk to the human population, and to eliminate guesswork from sequence analyses alone. doi = 10.1038/nrmicro1530 id = cord-256325-q70rky3r author = Stewart, Cameron R. title = A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date = 2017-07-04 keywords = IFN; RNA; protein; virus summary = title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. doi = 10.1007/82_2017_28 id = cord-018724-ss8x2g3b author = Stobbe, Anthony title = Plant Virus Diversity and Evolution date = 2016-06-22 keywords = RNA; Roossinck; plant; virus summary = The variation we see within a single plant host has profound effects on the how the virus responds to selective pressures associated with new hosts, and factors such as the bottleneck events associated with cell-to-cell movement or vectoring. However, several forms of virus variation, such as the high mutation rates of RNA and some DNA viruses, recombination, and reassortment lead to resistance breaking (Duffy and Holmes 2008; McDonald and Linde 2002; Harrison 2002) . For example, genetic diversity (heterosis) induced tolerance to Turnip mosaic virus in wild cress (Lepidium sp.) hybrids, while plants that were selfed were more susceptable to disease, suggesting that small populations with low genetic diversity could lead to increased disease symptoms, and infection rates (Houliston et al. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus doi = 10.1007/978-3-319-32919-2_8 id = cord-280781-u3wd27rn author = Stohlman, S. A. title = Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells date = 1978 keywords = JHM; virus summary = title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells A line of mouse neuroblastoma cells which was chronically infected with the neurotropic strain (JHM) of MHV, a member of the coronavirus group, was established. The addition of low concentration antiviral antibody modulated the infection to a carrier culture with viral antigen in the cytoplasm of the cells, but no infectious virus was produced, and the cells lacked both surface viral antigen and CPE. Following incubation at room temperature for 30 minutes in the presence of anti-JHM hyperimmune aseitie fluid (50 per cent plaque reduction neutralization titer = 1/1~00), serial dilutions were plated on the indicator monolayers and fixed with 0.5 ml of DMEM plus 5 per cent FBS containing 0.6 per cent agarose. Figure 3 shows that following the initial passage in the presence of antibody, there was an increase in both the supernatant and cell associated virus titer, which rapidly declined until after 4 serial passages no infectious virus was detectable. doi = 10.1007/bf01315637 id = cord-009615-xcz8m9a7 author = Stoner, Gerald L. title = Polyomavirus Models of Brain Infection and the Pathogenesis of Multiple Sclerosis date = 2008-01-28 keywords = JCV; PML; dna; virus summary = Animal models of viral demyelination and studies showing that JC virus (JCV), the polyomavirus which causes progressive multifocal leukoencephalopathy (PML), may be latent in some normal human brains suggest another possibility. It is thought that an MS virus could be one of two basic types: 1) A rare agent which infects relatively few individuals but is frequently pathogenic, or 2) A common agent which infects a majority of the population and perhaps a significant number of normal brains, but, in which the virus expression and the host response to the infection ( Immunocytochemical studies in our laboratory indicate that perivascular cellular infiltration, apparently due to immunological reactivity to SV40 antigens, occurs in this model (Fig. 1) . Thus, simian immunodeficiency virus (S1V)-infected macaques should be observed regularly for the possible occurrence of MS-like signs with demyelination attributable to mononuclear cell infiltration in response to abortively infected glial cells, rather twa-stage process of deletion and duplication known as "brain adaptation" to generate the progressive multifocal leukoencephalopathy (PML)-type viral genome capable of replicating in glial cells of the human brain. doi = 10.1111/j.1750-3639.1993.tb00748.x id = cord-281158-vjh9z7l4 author = Storch, Gregory A title = Respiratory Viruses in Babies: Important Insights From Down Under date = 2018-02-01 keywords = HRV; virus summary = Impressive study attributes include large size, community base, enrollment from birth, scheduled frequent longitudinal sampling with or without illness, high percentage of specimen acquisition rate, even enrollment of subjects throughout the year to account for virus seasonality, and testing of samples with an extensive panel of real-time polymerase chain reaction (PCR) assays. This intensive prospective study of respiratory viruses in infants finds that human rhinovirus (HRV) is by far the most frequent virus detected in the infant respiratory tract. Of the 152 infants followed, 81% experienced a first infection with HRV by 6 months of age, compared to 8.5% for RSV, and 0.7%-9.4% for the other respiratory viruses. Timing of first respiratory virus detection in infants: a community-based birth cohort study Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study Etiology of acute respiratory infections in infants: a prospective birth cohort study doi = 10.1093/infdis/jix600 id = cord-293375-qcy56ui7 author = Strauss, Ellen G. title = Identification of the active site residues in the nsP2 proteinase of sindbis virus date = 1992-12-31 keywords = RNA; Sindbis; proteinase; virus summary = coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. doi = 10.1016/0042-6822(92)90268-t id = cord-267261-8z4aqfff author = Su, John R. title = Emerging viral infections date = 2005-03-01 keywords = Ebola; Nile; SARS; WNV; West; virus summary = In 1999, a similar outbreak in pigs caused an outbreak of human encephalitis in Malaysia with a case-fatality rate approaching 40% [70] ; the causative agent was identified as a distinct but Hendra-like virus later named Nipah virus (NiV) [70] . In November 2002, cases of a new pulmonary disease, later named severe acute respiratory syndrome (SARS), were noted in the Guandong Province of China. In humans, about 20% of cases of infection with WNV lead to clinical disease, typically after an incubation period of 2 to 6 days. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome Detection of Severe Acute Respiratory Syndrome coronavirus in blood of infected patients doi = 10.1016/j.cll.2004.05.002 id = cord-002757-upwe0cpj author = Sullivan, Kathleen E. title = Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date = 2017-08-07 keywords = Africa; CNS; Europe; HIV; Leishmania; PCR; PIDD; USA; disease; infection; patient; severe; virus summary = The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . doi = 10.1007/s10875-017-0426-2 id = cord-003503-t6cnjwpd author = Sung, Ming-Hua title = Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date = 2019-03-06 keywords = PEDV; Taiwan; virus summary = Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government''s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. To determine specific temporal and geographic relationships associated with PEDV strain transmission, we used phylogenetic, phylodynamic and phylogeographic methods to systematically evaluate potential temporal and spatial transmission routes among Taiwanese swine farms during the 2014 outbreak. However, to date very few research efforts in Asia have utilized full genome sequencing for determining geographic structures due to the high costs and enormous amounts of computational time Phylogeographic investigation of 2014 porcine epidemic diarrhea virus transmission in Taiwan required for analyses [33, 34] . doi = 10.1371/journal.pone.0213153 id = cord-001834-6xf4o3oy author = Sung, Pil Soo title = Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection date = 2015-10-07 keywords = HCV; IFN; virus summary = In HCV-infected cells, viral RNA is sensed by retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA-5) in the cytoplasm and Toll-like receptor 3 (TLR3) in the endosome, which leads to downstream signaling that results in the induction of type III and I IFNs and other inflammatory cytokines [28, [36] [37] [38] [39] . Intracellular signals from RIG-I, MDA-5, and TLR3 are transmitted via mitochondrial antiviral signaling protein (MAVS) and Toll/IL-1 receptor domain-containing adaptor inducing IFN- (TRIF), respectively, which leads to the interferon regulatory factor-3 (IRF-3)-dependent induction of IFNs and NF-κB activation in HCV-infected cells [38, 39] . IFN-s activate the same JAK-STAT pathway as type I IFNs [48] [49] [50] , thereby inducing a similar set of ISGs. Although the exact source of IFN-s in HCV-infected liver remains to be clarified, it seems that the production of IFN-s by HCV-infected hepatocytes results in the expression of ISGs, presumably through autocrine and/or paracrine signaling via the IFN-λ receptor [28, [44] [45] [46] . HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons doi = 10.3390/ijms161023683 id = cord-255096-27dfbhsl author = Sweet, Michael J. title = Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date = 2016-06-19 keywords = China; OIE; PCR; Pacific; WSSV; Wang; disease; virus summary = Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. In this review, we are not listing all known diseases for the three main commercially important phyla/ sub-phyla and/or class (echinoderms, crustaceans and molluscs), but instead focus on those which likely pose a major threat and/or are infecting large populations of both wild and farmed organisms around the world. Hosts affected: Again, this disease predominantly occurs during the auricularia stages of development of many different sea cucumber species, with mortality being recorded as high as 90% in certain cases (Zhang et al., 2010) . Furthermore, diseases caused by Platyhelminthiasis have been shown to infect both aestivated juveniles (larger than 1 cm) and adults of many different sea cucumber species. doi = 10.1016/j.seares.2016.06.001 id = cord-351170-belbcrcd author = Symonds, Erin M. title = Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management date = 2014-10-16 keywords = enteric; fib; virus summary = Although this method is known to be flawed (see below), FIB are still widely used as an indicator of enteric pathogens and human health risks due to their consistent presence in wastewater and the readily available, low cost, culture-based methods for detection that require minimal laboratory training [14] [15] [16] [17] . As a result of the inadequacy of FIB monitoring to determine human health risks associated with enteric pathogens, particularly viruses, alternative approaches to traditional microbial quality monitoring have been recommended (Fig. 1C) . Finally, the utility of incorporating specific enteric viruses and/or a viral indicator to identify wastewater pollution/poor microbial quality and to better predict human health risks related to wastewater exposure has been demonstrated throughout the world [14-16, 22, 24, 25] . In conjunction with water management advances, the development of simple, affordable, lab-free tests for the rapid detection of enteric viruses and/or viral indicators is essential for ensuring worldwide improvements in microbial safety. doi = 10.1002/clen.201400235 id = cord-265642-7mu530yp author = Syomin, B. V. title = Virus-Like Particles as an Instrument of Vaccine Production date = 2019-06-17 keywords = VLP; antigen; particle; protein; vaccine; virus summary = Using protein expression systems it is possible to produce virus-like particles (VLPs), which are made up of monomers, which are able to multimerize into VLPs, and display the antigenic determinants of target pathogens on their surface. For example, in different laboratories different eukaryotic systems for viral protein expression, including plant cells, are used to produce VLPs which are used for vaccination against the hepatitis C virus (HCV) [36] . Antigen of the duck hepatitis A virus produced in the baculovirus expression system assembles into VLPs immediately in the cultured Spodoptera frugiperda (sf9) cells, while immunization of ducklings with the obtained VLPs induces a high level humoral immune response and protects them from developing the disease [46] . Expression vectors for foreign protein production in plants have been developed based on plant viruses, which allows obtaining plant-producing recombinant viruses or VLPs displaying the target antigen on their surface [101, 102] . doi = 10.1134/s0026893319030154 id = cord-004034-mjkixqhs author = Szilasi, Anna title = Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary date = 2019-12-10 keywords = FIV; feline; virus summary = doi = 10.1177/2055116919892094 id = cord-260014-q5sug7uu author = Szűcs, Zsolt title = Reprogramming of the Antibacterial Drug Vancomycin Results in Potent Antiviral Agents Devoid of Antibacterial Activity date = 2020-06-29 keywords = Table; compound; virus summary = We prepared six vancomycin aglycone hexapeptide derivatives with the aim of obtaining compounds having anti-influenza virus but no antibacterial activity. On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . On the other hand, this result is in line with our previous findings on ristocetin and teicoplanin aglycone derivatives, indicating that even minor structural differences in the peptide core can lead to significantly different anti-influenza virus activity [27] . Hence, we established, by virus yield assays, that compound 6 suppresses the replication of influenza virus and coronavirus, and for the other viruses, activity was indicated by the protection against viral CPE. Diazo transfer-click reaction route to new, lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: An aggregation and receptor binding study doi = 10.3390/ph13070139 id = cord-017287-70lk77zb author = Sánchez, Gloria title = Survival of Enteric Viruses in the Environment and Food date = 2016-08-26 keywords = HAV; enteric; virus summary = In the last decade, epidemiological reports indicate that enteric viruses, in particular human noroviruses (NoV), which cause acute gastroenteritis, and hepatitis A virus (HAV), are the leading cause of foodborne illness in developed countries (Koopmans and Duizer 2004 ; EFSA 2015 ) . While consumption of ready-to-eat foods contaminated by infected food handlers remains the major risk factor for viral foodborne outbreaks, many types of food products are being recognized as vehicles of viruses in causing gastroenteritis or hepatitis A outbreaks (Table 13 .1 ). These data suggest that temperature, and probably relative humidity, may be meaningful in the seasonal distribution of outbreaks of certain human enteric viruses (Enright 1954 ) , due to the infl uence of these factors on virus persistence. Survival of enteric viruses in the environment and different food products has been well studied employing cell-adapted virus strains. doi = 10.1007/978-3-319-30723-7_13 id = cord-009504-sn00p8iw author = Taguchi, Fumihiro title = Pathogenesis of Mouse Hepatitis Virus Infection: The Role of Nasal Epithelial Cells as a Primary Target of Low‐Virulence Virus, MHV‐S date = 2013-11-14 keywords = MHV; virus summary = The pathogenesis of mouse hepatitis virus (MHV‐S) infection in suckling and weanling mice was comparatively studied after intranasal inoculation. In the posterior part of the brain and spinal cord, virus was detected on days 3 to 4 postinoculation when viral growth was clearly demonstrable in the liver, spleen and intestines. In weanling mice, however, neither infectious virus nor viral antigen was detected in the liver or other visceral organs, while serum neutralizing antibody became detectable on day 5 postinoculation, increasing in titer thereafter. 2A and 2B , significant viral growth was observed in the brain, spinal cord ( Fig. 2A) and head without brain (Fig. 2B) , whereas no virus was demonstrated in the spleen or liver of the infected mice with a few exceptions (not included in the figures). In 4-week-old mice, however, no or little infectious virus was detected in the liver or other visceral organs, although high titered virus demonstrable in the brain was probably disseminated from the nasal mucosa as was observed in suckling mice. doi = 10.1111/j.1348-0421.1979.tb00461.x id = cord-004771-4yinnncj author = Tajima, M. title = Morphology of transmissible gastroenteritis virus of pigs: A possible member of coronaviruses date = 1970 keywords = virus summary = doi = 10.1007/bf01253886 id = cord-011106-h20vbmbo author = Takeda, Yohei title = Antiviral Activities of Hibiscus sabdariffa L. Tea Extract Against Human Influenza A Virus Rely Largely on Acidic pH but Partially on a Low-pH-Independent Mechanism date = 2019-10-16 keywords = PBS; PCA; PR8; virus summary = Here, we analyzed the antiviral activity of hibiscus (Hibiscus sabdariffa L.) tea extract against human IAV and evaluated its potential as a novel anti-IAV drug and a safe inactivating agent for whole inactivated vaccine. In addition, we assessed hibiscus tea extract''s potential as a candidate for novel anti-IAV drug and as an inactivating agent for whole-virus vaccines. PR8 virus propagated in allantoic fluid was mixed with an equal amount of neutral and acidic pH PBS, Hib[crude], frHibis, or PCA. 50 μl PBS, formalin-, β-PL-, or acidic Hib[crude]-inactivated PR8 virus vaccine was intranasally administered in mice (first vaccination) under light anesthesia with isolflurane (Intervet K.K., Tokyo, Japan). The neutralized Hib[crude] in the blood loses potent anti-IAV activity due to acid, and the low-pH-independent antiviral activity is inadequate to inactivate virus in vivo. doi = 10.1007/s12560-019-09408-x id = cord-325280-4whzcmqv author = Takizawa, Naoki title = Current landscape and future prospects of antiviral drugs derived from microbial products date = 2017-10-11 keywords = HBV; RNA; dna; virus summary = In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes. doi = 10.1038/ja.2017.115 id = cord-342151-1e6x589e author = Talbot, Pierre J. title = Hemagglutination by Murine Hepatitis Viruses date = 2008-07-29 keywords = MHV; virus summary = Erythrocytes from twelve mammalian and avian sources in ten different buffers at three incubation temperatures could not be hemagglutinated with murine hepatitis virus (MHV) strains 3, A59, or S grown on DBT cells. Viral antigen preparation in the absence of fetal calf serum, partial virus purification, or various concentrations of red blood cells still failed to yield detectable hemagglutinating activity. For use as antigen for hemag glutination assays, MHV-3 was grown in the absence of fetal calf serum (FCS) and har vested from clarified medium by precipita tion with 10% (w/v) polyethylene glycol in 0.5 M NaCl. After centrifugation at 10,000 g for 30 min, the pellet was resuspended and dialyzed against TMEN buffer: 50 mM Tris-HCi (pH 6.2), 0.1 M NaCl, 1 m M EDTA. Control hemagglutinating antigens were either rabbit enteric coronavirus (titer 1/64 with rabbit red blood cells ) or pneumonia virus of mice (titer 1/320 with CDI mouse erythrocytes). doi = 10.1159/000150083 id = cord-254100-u6x5zd4i author = Taliansky, M.E. title = Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date = 2010-10-15 keywords = Hiscox; ORF3; RNA; nucleolus; protein; virus summary = An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. doi = 10.1016/b978-0-12-385034-8.00005-3 id = cord-253143-73dsc6q3 author = Tang, Julian W. title = Emerging, Novel, and Known Influenza Virus Infections in Humans date = 2010-08-02 keywords = H1N1; H5N1; influenza; virus summary = Nevertheless, the plethora of epidemiologic, diagnostic, mathematical and phylogenetic modeling, and investigative methodologies developed since the severe acute respiratory syndrome outbreak of 2003 and the subsequent sporadic human cases of avian influenza have been applied effectively and rapidly to the emergence of this novel pandemic virus. 3 In addition, sporadic, generally mild (although there has been at least 1 recorded death because of H7N7) human infections resulting from occasional bird-to-human transmissions, with low pathogenic avian influenza strains (eg, subtypes H9N2, H7N7, H7N2, and H7N3) have been ongoing since 1997, when heightened surveillance for avian influenza viruses began (Fig. 2) . Analyses of the viruses that caused the 1957 and 1968 influenza pandemics therefore proved that zoonotic transmissions of influenza viruses (ie, from animals to man) with gene reassortment were capable of generating antigenically new influenza strains, novel to human immunity, with significant effects on the public health. doi = 10.1016/j.idc.2010.04.001 id = cord-255734-038xu4hq author = Taylor, Deborah R. title = Obstacles and advances in SARS vaccine development date = 2006-02-13 keywords = SARS; respiratory; vaccine; virus summary = The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Spike-specific monoclonal and polyclonal antibodies that neutralize the virus have been developed [51, 52] and passive transfer of immune serum into naive mice protected them from infection with SARS-CoV [18] . Mice immunized with a plasmid containing the S protein produced anti-SARS-CoV IgG [64] and developed neutralizing antibodies and a T-cell mediated response resulting in a six-fold reduction in viral titer in the lungs [65] . Inactivation of the coronavirus that induces severe acute respiratory syndrome, SARS-CoV Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets doi = 10.1016/j.vaccine.2005.08.102 id = cord-018164-h5k1zsyg author = Taylor, Milton W. title = What Is a Virus? date = 2014-07-22 keywords = Fig; RNA; cell; virus summary = Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral proteins are produced in one part of the cell, the replicated nucleic acid in another, and somehow they find each other, interact, and form virus particles that are expelled from the cell. Indirect contact spread includes cases where mucus from a runny nose may get onto the hands, or virus may be left on a surface such as a doorknob, telephone, or countertops, and is picked up by a second individual, who then touches his eyes or nose, resulting in infection. Vector transmission is a very common means of transmission; the best studied cases include yellow fever, dengue virus, and West Nile fever-viruses all transmitted by mosquitoes. As many as 400 million people are infected annually by dengue virus, which is caused by any one of four related viruses transmitted by mosquitoes. doi = 10.1007/978-3-319-07758-1_2 id = cord-018441-r6wwpfcy author = Taylor, Milton W. title = Emerging Viruses date = 2014-07-22 keywords = Ebola; SARS; virus summary = Most of these viruses are terrifying, and cause hemorrhagic fever, a complete destruction of the circulation system; they include Lassa fever, Nipah virus, Ebola, HIV, Severe acute respiratory syndrome (SARS), and, recently, Middle East respiratory syndrome (MERS), which is the latest in a series of "new" respiratory viruses infecting man. From 2001 to 2012 there were 280 cases of Nipah virus infections in humans, with 211 deaths-a mortality rate of 75 %. Ebola outbreaks occur with ferocity and suddenness, and with high mortality; they may originate from bats, and the virus spreads easily to a susceptible human population. Ebola is the most lethal human viral infection known, First identified in 1976 in Zaire and the Sudan, it causes hemorrhagic fever (internal bleeding) with a mortality rate of 88 %. The SARS epidemic also showed how international cooperation among health care experts can effectively contain the The virus spread from southern China to Singapore, Taiwan, the U.S. and Canada (Ontario). doi = 10.1007/978-3-319-07758-1_20 id = cord-278482-j5zlismf author = Taylor, Raymond title = BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date = 2016-06-30 keywords = BCX4430; RNA; virus summary = Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. In a study in cynomolgus macaques infected with MARV [5] , 0/6 controls survived compared to 17/18 animals treated with a 15 mg/kg BD dose of The maximum viral load, as measured by quantitation of viral RNA copies in the peripheral blood, was reduced by ∼600-fold (geometric mean 0.008 × 10 9 compared to 4.79 × 10 9 copies/mL, p < 0.0005). The slope of the relationship of the dose of BCX4430 to both antiviral effect and survival in nonclinical models of lethal viral infections is steep. doi = 10.1016/j.jiph.2016.04.002 id = cord-016663-qnp99m7o author = Taylor, Robert B. title = Medical Words Linked to Places date = 2017-02-01 keywords = War; Zika; cause; disease; fever; virus summary = In addition to causing fever and malaise, when the patient is pregnant, the Zika virus may also cause birth defects, notably microcephaly (from Greek words meaning "small" and "head"). In addition to mosquito-borne infection, we now have discovered sexually transmitted Zika virus disease and continue to learn more each year. The West Nile virus is a member of the family Flaviviridae, from the Latin flavus, meaning "yellow." The family was named for the yellow fever virus, which tends to cause liver damage, giving its victims a yellow jaundiced appearance ( Fig. 5.2 ). The disease is caused by Borrelia bacteria, notably Borrelia burgdorferi, and is spread by the same vector as Nantucket fever/babesiosis: the Ixodes tick, also called the deer tick. Also sometimes called tick typhus or blue disease, Rocky Mountain spotted fever was first recognized in 1896 in the Snake River Valley in the Rocky Mountains of the Western United States. doi = 10.1007/978-3-319-50328-8_5 id = cord-344576-upsc9cf8 author = Taylor-Robinson, Andrew W title = A vaccine effective against Zika virus is theoretically possible but may not be delivered anytime soon date = 2016-07-05 keywords = Zika; vaccine; virus summary = In February this year, the World Health Organization declared that further to the then unconfirmed association between the virus and the clinical manifestations of microcephaly and also Guillain-Barré syndrome, the Zika epidemic was a "public health emergency of international concern". No anti-Zika therapy, vaccine or drug, is currently available and while the production of the former has now been prioritized by multiple funding agencies, the history of infectious disease vaccine development indicates that this may take several years to reach the market place. A more rapid spread of the virus via the intercontinental travel of infected persons is an additional concern, although for Zika to become established in a location distant to an endemic area requires local transmission of the initially imported focus of infection; this is dependent on the availability of the vector. Local transmission of Zika virus infection is possible in Australia but should be contained by current vector control measures doi = 10.2147/rrtm.s108992 id = cord-017824-0pinevfc author = Tekes, Gergely title = Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses date = 2015-09-10 keywords = vaccinia; virus summary = The main focus of this chapter is the vaccinia virus-based reverse genetic system for FCoVs. Here we present protocols for (1) the generation of a full-length cDNA clone, (2) the manipulation of the FCoV genome, and (3) the rescue of recombinant FCoVs. The establishment of a reverse genetic system for feline coronaviruses (FCoVs), which allows to modify the entire coronaviral genome, was successfully achieved for the fi rst time in 2008 [ 1 ] . Regardless of the applied strategy, viral RNA serves as a starting material for the generation of all FCoV-sequence containing plasmids (sections "First Step", 3.1.1.3, "Generation of plasmids suitable for vaccinia virus-mediated homologous recombination"). In order to integrate the full-length FCoV cDNA, fragments 1-8 are introduced via four rounds of vaccinia virus-mediated homologous recombination using GPT as a positive and a negative selection marker. doi = 10.1007/978-1-4939-3414-0_7 id = cord-311382-ioemd0ij author = Tellier, Raymond title = Recognition of aerosol transmission of infectious agents: a commentary date = 2019-01-31 keywords = Ebola; airborne; transmission; virus summary = For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] . doi = 10.1186/s12879-019-3707-y id = cord-310140-h7uwl0pb author = Templeton, K.E. title = A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date = 2005-07-12 keywords = NAT; PCR; virus summary = STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. Laboratories performing respiratory molecular tests want to report accurate and reliable results regardless of the type of assay in use and one of the best ways to assess performance is to participate in proficiency programmes, enabling laboratories to evaluate their performance (Schirm et al., 2002; Schloss et al., 2003; Noordhoek et al., 2004; Verkooyen et al., 2003) . Laboratories who had expressed an interest to QCMD in participating in a proficiency programme for molecular detection of respiratory viruses were asked to complete a questionnaire detailing technical aspects of the assays they had applied. In this study, samples were grown in cell culture and dilutions were made so sensitivity and limited specificity of assays for these viruses could be assessed. doi = 10.1016/j.jcv.2005.05.005 id = cord-339288-y8woqsii author = Tews, Birke Andrea title = Self-Replicating RNA date = 2016-06-11 keywords = RNA; cdna; viral; virus summary = Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. Three years later, the performance of poliovirus cDNA clones could be significantly ameliorated through the introduction of SV40 transcription and replication signals and transfection of the resulting construct into cells expressing the SV40 large T antigen [14] , thus ensuring replication of the DNA-plasmid in eukaryotic cells leading to a higher yield of viral RNA and recovered virus (Fig. 2, left part) . The resulting virus CP7_E2alf was only able to infect pigs and thus displayed the Fig. 3 Generation of a chimeric viral genome from two parental RNAs. On the level of a cDNA construct, one protein-coding sequence is replaced by the corresponding gene of the other virus (principle used for the pestivirus vaccine CP7_E2alf [58] ). doi = 10.1007/978-1-4939-6481-9_2 id = cord-268788-jcu3pasy author = Thor, Sharmi W. title = Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date = 2011-09-23 keywords = IBV; Mass; virus summary = In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120 doi = 10.3390/v3091777 id = cord-319208-jrxz59bb author = Ting, Chun Yi title = Are identity badges and lanyards in pediatrics potentially contaminated with viral pathogens? date = 2015-11-01 keywords = virus summary = Identity (ID) badges and lanyards worn by pediatric health care workers (HCWs) have been shown to be potential vectors of nosocomial bacterial infections. This cross-sectional study determined the contamination of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses. The results showed that ID badges and lanyards are not significantly contaminated with common respiratory or gastrointestinal viruses and are unlikely to be a significant vector for nosocomial infection. The principal aim of this study was to determine the contamination rates of ID badges and lanyards worn by pediatric HCWs with common respiratory and gastrointestinal viruses to evaluate their potential as vectors for both nosocomial and patient-topatient transmission of viruses. HCW ID samples were tested for respiratory viruses using viral PCR technique after an automated DNA-RNA extraction procedure, an identical process to routine clinical samples collected from pediatric patients. doi = 10.1016/j.ajic.2015.06.024 id = cord-282628-6uoberfu author = Tiwari, Bhagyashree title = Future impacts and trends in treatment of hospital wastewater date = 2020-05-01 keywords = antibiotic; disease; emergence; human; pathogen; virus summary = The causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. Factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (AMR), and climate change. The factors responsible for the emergence of infectious diseases such as (1) the evolution of new strain, (2) the introduction of a host to enzootic, (3) translocation of infected wildlife, (4) farming practices, and (5) others were provided. Due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. Increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. Furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health. doi = 10.1016/b978-0-12-819722-6.00017-1 id = cord-280878-1kt51viz author = To, Janet title = Targeting the Channel Activity of Viroporins date = 2016-01-07 keywords = Amt; HCV; Vpu; channel; protein; virus summary = For other viroporins, these studies are still mostly in their infancy, although a highresolution structure of the hepatitis C virus (HCV) p7 protein has been recently described (Ouyang et al., 2013) that may be useful for the rational design of p7 channel inhibitors in the future. Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels NMR structure and ion channel activity of the p7 protein from hepatitis C virus Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus doi = 10.1016/bs.apcsb.2015.12.003 id = cord-340194-ibli36rq author = To, Kelvin K.W. title = Ebola virus disease: a highly fatal infectious disease reemerging in West Africa date = 2014-11-29 keywords = Africa; EVD; Ebola; ebolavirus; outbreak; virus summary = Ebolavirus has been known to cause outbreaks of severe hemorrhagic fever with high fatality in Africa since 1976 [1] . Zaire and Sudan ebolavirus are responsible for most outbreaks, and these species are associated with highest case-fatality rates, ranging from 44e100% and 41e69%, respectively. In addition to clinically apparent EVD outbreaks, seroepidemiology studies showed that there is a high prevalence seropositive individuals, suggesting that asymptomatic or mild infection can occur [15] . The only human case of ebolavirus infection in West Africa before the 2014 outbreak occurred 20 years ago. During the 1976 EVD outbreak, the index case had transmitted the virus to healthcare workers and hospitalized patients with at least 15 generations of person-to-person transmission [29] . Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis Analysis of human peripheral blood samples from fatal and nonfatal cases of Ebola (Sudan) hemorrhagic fever: cellular responses, virus load, and nitric oxide levels doi = 10.1016/j.micinf.2014.11.007 id = cord-345168-3w32v2fm author = To, Kelvin K.W. title = Viral load in patients infected with pandemic H1N1 2009 influenza A virus date = 2009-11-30 keywords = H1N1; viral; virus summary = Comparison was made between patients with pandemic H1N1 virus and seasonal influenza virus infection regarding their demographics, underlying diseases, presenting symptoms, total white blood cell counts, absolute lymphocyte counts, and initial pre-treatment viral load in respiratory specimens on the day of diagnosis. Among patients with pandemic H1N1 virus infection, the same parameters was compared between those with longer duration (!5 days) and shorter duration ( 4 days) of viral shedding, as defined by the time from onset of symptoms to the last positive sample by RT-PCR. For both pandemic H1N1 cases and seasonal influenza historical controls, respiratory specimens collected on the day of onset of symptoms (day 0) had the highest mean viral load (Fig. 1 ). For patients who presented to hospital between days 0 and 3 after onset of symptoms, the initial pre-treatment viral load in pandemic H1N1 cases was lower than the seasonal influenza historical controls. doi = 10.1002/jmv.21664 id = cord-325969-9zhmmvdg author = To, Kelvin KW title = Additional molecular testing of saliva specimens improves the detection of respiratory viruses date = 2017-06-07 keywords = NPA; PCR; virus summary = In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples. doi = 10.1038/emi.2017.35 id = cord-270772-zshjrc87 author = To, Kelvin Kai-Wang title = Host genes and influenza pathogenesis in humans: an emerging paradigm date = 2015-06-14 keywords = H1N1; IFITM3; influenza; virus summary = The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection. Specific amino acid changes in the viral proteins have been associated with increased disease severity in humans or adaptation of avian influenza viruses in humans [13] . High-throughput screening platforms have allowed researchers to systematically screen a large number of genes associated with influenza virus infection in vitro, in animals or in humans. 9 Host genetic determinants of influenza virus disease severity identified in humans. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection This study incorporated in vitro, animal and human data to prioritize genes for future research on genetic susceptibility to severe influenza doi = 10.1016/j.coviro.2015.04.010 id = cord-341923-jwckbdnb author = To, Kelvin Kai-Wang title = Pathogenesis of pandemic H1N1 2009 influenza virus infection and the implication on management date = 2010-04-28 keywords = H1N1; H5N1; influenza; virus summary = Although most patients infected with this novel strain present with mild upper respiratory tract symptoms [6] , the higher fatality rate in children and young adults clearly differentiate this virus from seasonal influenza virus [7, 8] . Known virulence factors in H5N1 virus include Lys627 of PB2, which increases the viral replication; an Asn66Ser substitution in PB1-F2, a protein that induces apoptosis, enhances inflammation in mice, and predisposes to secondary bacterial infection; NS1, which antagonizes the antiviral effect of interferon; and a multibasic HA cleavage sequence, which allows cleavage by ubiquitous proteases [36] . A higher viral load in respiratory tract samples was associated with fatal disease from H5N1 [41] and with disease severity in infection due to respiratory syncytial virus and human metapneumovirus [42] . Delayed clearance of viral load and marked cytokine activation in severe cases of pandemic H1N1 2009 influenza virus infection doi = 10.1007/s11684-010-0030-9 id = cord-351365-dc9t3vh3 author = Todt, Daniel title = Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date = 2016-10-13 keywords = HCV; HEV; RBV; RNA; virus summary = Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. Figure 1 provides an overview of a selection of RNA viruses against which RBV was shown to be active: hepatitis C virus (HCV, Flaviviridae), dengue virus (DENV, Flaviviridae), respiratory syncytial virus (RSV, Paramyxoviridae), influenza A and B virus (Orthomyxoviridae), chikungunya virus (CHIKV, Togaviridae), poliovirus (Picornaviridae), Hantaan virus (Bunyaviridae), and Lassa virus (Arenaviridae) [28, 29] ( Figure 1 ). Furthermore, mechanisms on the virus itself were described by inhibition of the capping efficiency, the viral polymerase, and a mutagenic effect on newly synthesized RNA genomes. A Mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients doi = 10.3390/v8100283 id = cord-340331-51yq1rdo author = Tonelli, Michele title = Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus date = 2017-07-28 keywords = DHFR; RSV; antiviral; compound; virus summary = We have identified a series of 1-aryl-4,6-diamino-1,2-dihydrotriazines, structurally related to the antimalarial drug cycloguanil, as new inhibitors of influenza A and B virus and respiratory syncytial virus (RSV) via targeting of the host dihydrofolate reductase (DHFR) enzyme. The compounds, object of the present study, are characterized by the 1-aryl-4,6-diamino-1,2-dihydrotriazine scaffold, such as the cited cycloguanil, which was identified by us as prototype (1) of a new class of antiviral agents exploiting a host DHFR inhibition mechanism. Since host cell DHFR inhibition seemed the plausible explanation for the observed antiviral effect, we performed a combination experiment in which RSV-infected HeLa cells were exposed to compound 14 in combination with different concentrations of the natural DHFR substrate dihydrofolic acid ( reaction has a much higher impact on virus replication than on cell growth, which concurs with the promising antiviral selectivity of our host-directed DHFR inhibitors. The interesting dual activity of the 1-aryl-4,6-diamino-1,2dihydrotriazines against influenza and respiratory syncytial viruses, via inhibition of the cellular (human) DHFR enzyme, points to this host factor as a new therapeutic target for these two respiratory viruses. doi = 10.1016/j.ejmech.2017.04.070 id = cord-271650-biq0chyn author = Torres, Juan M title = Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease date = 2000-09-15 keywords = rabbit; virus summary = title: Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease Safety evaluation of a recombinant myxoma-RHDV virus inducing horizontal transmissible protection against myxomatosis and rabbit haemorrhagic disease In order to protect wild rabbits against both myxomatosis and RHD, we constructed a recombinant virus based on the naturally attenuated MV ®eld strain 6918 [24] , that expressed the RHDV VP60 protein [25] . Groups of eight wild rabbits (2 month old, weighing around 0.8 kg) free from MV and RHDV antibodies, were inoculated at the back by intradermic (i.d.) or subcutaneous (s.c.) route with dierent doses of the vaccine (10 4 , 10 5 , 10 6 pfu of 6918VP60-T2 recombinant virus). Treated rabbits were inoculated (by s.c or i.d. route) with 10 4 pfu of 6918VP60-T2 virus, and clinical signs due to virus infection were compared with those induced in control rabbits, which were vaccinated but not treated with prednisolone (Fig 2, Table 3 ). doi = 10.1016/s0264-410x(00)00183-3 id = cord-271884-86yl9ren author = Traavik, T. title = Development of a modified immunoelectroosmophoresis method for Uukuniemi and Runde virus serology date = 1977 keywords = virus summary = In search for a suitable method for sero-ecological screenings for arboviruses in Norway, efforts were undertaken to make the immunoelectroosmophoresis technique more sensitive than here to fare in detection of antibodies. The isolation of Uukuniemi (UUK) group viruses and a new coronavirus-like agent, Runde virus, from Norwegian Ixodes ticks (19, 21, 22, 23) , were intended to be followed up promptly by sero-ecological surveys by a standard haemagglutination inhibition test (HAI). B y using a gel composed of 0.4 per cent agar and 0.6 per cent agarose, and concentrated B H K antigens, results comparable to the H A I titers were obtained for the reference sera with all the viruses tested. Provided the opportunity to concentrate the antigen, the modifications used in this work to obtain a sensitive I E O P for antibody detection might prove valuable also with other viruses. doi = 10.1007/bf01314789 id = cord-333043-fe24ezt6 author = Traavik, T. title = “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks date = 1977 keywords = Runde; culture; mouse; virus summary = uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. Until then., no arbovirus isolates had been reported from this country, although ecological and cli-nicaI/epidemiological considerations (3, 24, 26) and a limited serological survey on bovine sera (28) indicated the existence of Central-European tick-borne encephalitis virus fool. uriae ticks collected at Runde in late September 1973, three virus strains have been isolated. Cells were washed with saline, virus was diluted ~enfold from 10 -1 to t0 -6 in the medium, A volume of 0.2 ml of each dilution was inoculated into three tubes and allowed to adsorb for 1 hour at room temperature before washing with saline and addition, of new medium, Culture tubes were incubated for 8 days at 37 ° C and inspected daily for a Cytopathie effect (CPE). Virus from mouse brains and cell culture demonstrated total i d e n t i t y b y these methods. doi = 10.1007/bf01314476 id = cord-339152-wfakzb6w author = Trovato, Maria title = Viral Emerging Diseases: Challenges in Developing Vaccination Strategies date = 2020-09-03 keywords = MERS; Nile; SARS; West; Zika; dna; vaccine; virus summary = Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential. doi = 10.3389/fimmu.2020.02130 id = cord-331652-oc5s1if2 author = Trudeau, Michaela P. title = Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date = 2016-06-24 keywords = PEDV; feed; virus summary = title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. Therefore, the objective of this study was to determine if thermal and non-thermal methods of microbial inactivation, as well as the use of selected feed additives, are effective in reducing the survival of PEDV in experimentally contaminated swine feed. The PEDV showed a high thermal resistance in the dry feed samples and it was completely inactivated (3.0 log reduction) at each of the tested temperatures within 30 min. doi = 10.1371/journal.pone.0158128 id = cord-267140-vdcf6vok author = Trudel, M. title = Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide date = 1981-02-28 keywords = Sepharose; virus summary = title: Purification of infectious rubella virus by gel filtration on sepharose 2B compared to gradient centrifugation in sucrose, sodium metrizoate and metrizamide Yields were lower in sucrose and metrizamide, while sodium metrizoate reduced the infectivity of the virus below detectable levels. This report describes the application of Sepharose 2B gel fitration for the purification of infectious rubella virus in comparison to centrifugation on sucrose, metrizamide and sodium metrizoate. Aliquots of 5 ml of viruses were purified by two cycles of density gradient centrifugation in sucrose, metrizoic acid (sodium salt) or metrizamide (Sigma Chemical Co., St. Louis, MO). Density gradient centrifugation of rubella virus on sucrose, metrizamide or sodium a Virus (5 ml, 65,566 HAU and 109*6TCID,,) was purified by ultracentrifugation or chromatography as described in Material and methods. Purification of rubella virus yielded similar results in sucrose and metrizamide but the infectivity was reduced to undetectable levels in sodium metrizoate. doi = 10.1016/0166-0934(81)90032-x id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 keywords = HIV; SARS; infection; treatment; virus summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial doi = 10.1177/1759720x20947296 id = cord-007445-2folsh35 author = Tuffaha, Amjad title = THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date = 2000-06-01 keywords = RSV; infection; respiratory; virus summary = To more comprehensively evaluate the relationships among virus infection, atopy (cytokine dysregulation of Thl / Th2 imbalance), and immune system or lung developmental components, a rat model of virus-induced airway dysfunction has been studied extensively.''l'' In this model, infection with PIV type 1 during a critical developmental time period (when the animals are weaning [ 3 4 weeks of age] as opposed to when they are neonates [4-5 days] or adults) produces chronic (8-12 weeks fol-lowing infection), episodic, reversible airway inflammation and remodeling with associated alterations in airway physiology (increased resistance and rnethacholine responsiveness) that resemble human asthma in high (brown Norway strain) but not low (F344 strain) IgEantibody producing rats.62 The temporal progression of this asthma-like syndrome is associated with a Thl / Th2 imbalance within the lung, and its development can be significantly attenuated by the exogenous administration of IFN-8 just prior to and during the viral infection in the brown Norway responder strain.lo2 This model further supports the concept of both genetic (atopy; cytokine dysregulation or imbalance) and environmental factors (virus infection) being important in the inception of the asthmatic phenotype, as well as a developmental component contributing. doi = 10.1016/s0272-5231(05)70267-7 id = cord-279617-xuzu55cg author = Tuladhar, E. title = Thermal stability of structurally different viruses with proven or potential relevance to food safety date = 2012-03-30 keywords = H1N1; TFL; virus summary = Methods and Results: Suspensions with poliovirus Sabin1, adenovirus type5, parechovirus1, human norovirus (NoV) GII.4, murine NoV (MNV1) and human influenza A (H1N1) viruses were heated at 56 and 73°C. The viral stocks titres used were as follows: poliovirus Sabin 1: 6AE3 · 10 8 50% Tissue Culture Infective Dose (TCID 50 ) ml )1 (1AE6 · 10 10 PCR unit (PCRU) ml )1 ), adenovirus type 5: 6AE3 · 10 7 TCID 50 ml )1 (3AE2 · 10 9 PCRU ml )1 ), parechovirus 1: 1AE3 · 10 8 TCID 50 ml )1 (2AE0 · 10 9 PCRU ml )1 ), influenza A (H1N1) virus: 1AE3 · 10 6 TCID 50 ml )1 (1AE5 · 10 8 PCRU ml )1 ), MNV1: 1AE7 · 10 7 PFU ml )1 (5AE0 · 10 8 PCRU ml )1 ) and human NoV GII.4 was at a concentration of 1 · 10 8 PCRU ml )1 . doi = 10.1111/j.1365-2672.2012.05282.x id = cord-291707-dzmvjh7j author = Tupper, G. T. title = Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus date = 1987 keywords = FECV; FIPV; virus summary = FIPV grows to higher titer, forms larger plaques and switches off host cell protein synthesis more effectively than FECV. It was reported that both virus strains produce relatively large plaques in cell culture and grew to fairly high titers (1) . This indicated the differences were consistent and were not due to maturation artitSct. There was a cell protein band just above the nucleoprotein of the FECV 79-1683 of the radiolabelled virus. The FIPV strains produced larger plaques in CrFK cells and half a log higher titer of virus than the FECV strain. Host cell protein synthesis was also shut offby infection with murine coronavirus and different strains vary in the extent to which they do it, (25) . In this study, all 3 st, ruetural polypeptides appeared synchronously in cells infected with FIPV or FECV strains. Viral protein synthesis in mouse hepatitis virus strain A 59-infected cells: effect oftunieamyein doi = 10.1007/bf01310988 id = cord-325635-don9qjpz author = Turner, Paul title = Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date = 2013-09-16 keywords = RSV; respiratory; virus summary = Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected. doi = 10.1186/1471-2334-13-434 id = cord-280987-uhxk5b1b author = Turtle, L. title = Encephalitis, Viral date = 2014-05-01 keywords = CNS; encephalitis; virus summary = Encephalitis is inflammation and swelling of the brain, often caused by an acute viral infection, or a paraor postinfectious phenomenon known as acute disseminated encephalomyelitis (ADEM). The term includes both viral infections of the brain with predominantly gray matter disease and acute disseminated encephalomyelitis (ADEM), an immune-mediated demyelinating disease. Clinically, acute viral encephalitis and ADEM usually manifest with fever, severe headache, neck stiffness, alterations of consciousness, focal neurological signs, and often seizures, especially in children. Once permissive host cells are infected in the subcutaneous tissue, the mucous membranes, or the hematopoietic system (particularly macrophages), viruses replicate usually locally before there is invasion of the central nervous system (CNS). Enteroviruses and mumps virus infect primarily meningeal and ependymal cells; therefore, they usually cause benign meningitis and only rarely are associated with encephalitis. On rare occasions when arboviruses infect the brain, they usually cause encephalitis with a significant death rate; thus, these viruses are not highly neuroinvasive but are highly neurotropic (and neuronotropic) and neurovirulent. doi = 10.1016/b978-0-12-385157-4.00375-4 id = cord-021990-a8ku5rke author = Tyring, Stephen K. title = Syndromal Tropical Dermatology date = 2016-12-02 keywords = Fig; HIV; cause; disease; tropical; virus summary = With increasing numbers of persons from industrialized, temperate countries traveling and / or working in tropical lands, there is a marked need for physicians to be able to diagnose accurately and treat tropical diseases with mucocutaneous manifestations. An example of a mosquito-borne disease that was considered primarily "tropical" in the recent past but is now relatively common in much of North America is infection with the West Nile virus (Fig. 1-3) . When one STD is confirmed, there is an increased possibility of acquisition of additional STDs. Not only is this the case because the source partner(s) may have had multiple STDs, but also because having certain STDs makes a person more susceptible to other STDs. The best example of this phenomenon is the two-to fivefold greater risk of acquiring HIV if the person with a genital ulcer disease (GUD) has sex with an HIV-positive individual. If at least 3 months separate travel from fever / rash, the following infections should be considered: bartonellosis, filariasis, gnathostomiasis, hepatitis viruses (B and C), histoplasmosis, HIV, leishmaniasis, Lyme disease, melioidosis, penicilliosis, syphilis, trypanosomiasis, and tuberculosis. doi = 10.1016/b978-0-323-29634-2.00001-8 id = cord-298733-jole21wq author = Tyrrell, D.A.J. title = A view from the common cold unit date = 1992-06-30 keywords = Unit; cold; virus; volunteer summary = Furthermore, the old empirical idea of the existence of ''the common cold virus'' was soon replaced by data collected by epidemiologically controlled field studies in which infection was detected with a range of viruses following which their pathogenicity was confirmed and studied by inoculating them into volunteers and observing their effects. Thus, after years of frustration the work of the Unit developed to the point where relevant human infections could be produced at will and precisely documented by clinical and laboratory methods -this was the ideal setting for preliminary trials of the efficacy of antiviral drugs or vaccines without which nowadays it would rarely be justifiable to go on to a field study of naturally acquired colds. When natural and recombinant interferons were tested in this way against experimental influenza and rhinovirus infections in volunteers, they were no longer effective, possibly because by then the subject was already producing substantial amounts. doi = 10.1016/0166-3542(92)90032-z id = cord-264264-7j3xirfg author = TüRsen, Ümit title = CORONAVIRUS‐DAYS IN DERMATOLOGY date = 2020-04-15 keywords = COVID-19; soap; virus summary = Soap works better than alcohol and disinfectants at destroying the structure of viruses. Soap dissolves the fat membrane, and the virus falls apart like a house of cards and "dies," or rather, it becomes inactive as viruses aren''t really alive. Apart from alcohol and soap, antibacterial agents in those products don''t affect the virus structure much. However, it was observed that washing hands with soap is better than using alcohol-based disinfectants in removing the noroviruses, rhinovirus and H1N1 influenza virus from hands (Tuladhar 2015, Kopra 2012, Grayson 2009 ). Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Efficacy of soap and water and alcohol-based hand-rub preparations against live H1N1 influenza virus on the hands of human volunteers Single treatment with ethanol hand rub is ineffective against human rhinovirus--hand washing with soap and water removes the virus efficiently doi = 10.1111/dth.13421 id = cord-307364-j86t65qu author = Uccellini, Lorenzo title = Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) date = 2014-08-08 keywords = figure; snake; virus summary = In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses. Here we report the discovery of a novel nidovirus in a collection of ball pythons (Python regius) in upstate New York with pneumonia, tracheitis and esophagitis. Based on the phylogenetic position and the genetic distances between In situ hybridization to a 934 nt fragment of the genomic polyprotein 1ab region was used to assess viral infection and distribution in the lung tissue. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) doi = 10.1186/1743-422x-11-144 id = cord-299207-lw0cv74b author = Upadhyay, Ranjit Kumar title = Modeling the spread of bird flu and predicting outbreak diversity date = 2007-05-08 keywords = H5N1; influenza; virus summary = We have designed a statistical transmission model of bird flu taking into account the factors that affect the epidemic transmission such as source of infection, social and natural factors and various control measures are suggested. Among these researches, an important approach to study bird flu is to establish a statistical transmission model, from which the general trends of epidemics can be predicted, and the effect of various control measures can be assessed [13] . We know the major factors that play an important role in the transmission of bird flu are the way the infected poultry products are transported, air temperature, the control measures (for example, culling the poultry in the infected form, introducing compulsory vaccination to enhance the resistibility of poultry in the non-infected farms forbidding live birds being sold under crowded and unsanitary conditions, etc.), migratory birds and other infected transportation vehicles (which means the vehicles carry infected poultry or bird dropping or contaminated soil, etc.). doi = 10.1016/j.nonrwa.2007.04.009 id = cord-001985-iwfidoer author = Urayama, Syun-ichi title = FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date = 2016-02-13 keywords = FLDS; RNA; viral; virus summary = This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. We herein established a novel strategy to obtain full-length RNA virus sequences with extremely high efficiency by applying a short dsRNA full-length cloning method (8) for physically fragmented dsRNAs. The improved method, named FLDS (fragmented and loop primer ligated dsRNA sequencing), was applied to a diatom colony in a tide pool and revealed previously unidentified RNA viruses. These results indicated that FLDS effectively enriched dsRNA reads, thereby allowing the retrieval of complete genome sequences including terminal regions without the requirement for the additional rapid amplification of cDNA ends (RACE). A phylogenetic analysis of RdRp in DCASSRV-2 suggested that the RNA virus was classified into the genus Mitovirus, which has a non-segmented ssRNA genome, infects the mitochondria of fungi, and lacks viral particles (Fig. S4E) . doi = 10.1264/jsme2.me15171 id = cord-293097-poh1y6o7 author = V, Antony Aroul Raj title = The contribution of dry indoor built environment on the spread of Coronavirus: Data from various Indian states date = 2020-07-02 keywords = droplet; spread; virus summary = This concept is assessed using four major parameters such as population density, climate severity, the volume of indoor spaces, and air-conditioning usage which affect the infection spread and mortality using the data available for various states of India. Hence the major objective of the present work is to propose the mechanism of virus spread under various climates and the indoor environment conditions maintained through the existing theory of respiratory droplet drying. Further, it is aimed to perform a statistical study on the dependence of mortality and infection in the Indian States with respect to four major parameters such as population density, climate severity, volume of indoor spaces, and air-conditioning usage based on monthly data for March and April. In an environment with low humidity and low temperature, due to combined high heat and mass transfer potential leads to fast drying and size reduction of the respiratory droplets and the virus is almost active in all the locations. doi = 10.1016/j.scs.2020.102371 id = cord-003639-bjtxf1y8 author = Vahey, Michael D title = Influenza A virus surface proteins are organized to help penetrate host mucus date = 2019-05-14 keywords = IAV; figure; virus summary = doi = 10.7554/elife.43764 id = cord-283641-2u16otbf author = Vainionpää, R. title = Diagnostic Techniques: Serological and Molecular Approaches date = 2015-03-06 keywords = PCR; antibody; virus summary = For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient''s specimens or investigation of specific antibody response in serum specimens. Glossary EIA Enzyme immunoassays are methods used to estimate virus-specific IgG and IgM antibodies or virus antigens by enzyme-labeled conjugates. Nucleic acid testing has become the main approach for the demonstration of the presence of virus while cultivation is used by fewer specialized laboratories and antigen detection methods have moved to the point of care. Diagnostic applications of the measurement of the avidity of IgG antibodies against specific antigens have been developed to help distinguish serological responses due to acute infections from those of chronic or past infections. In immunofluorescence tests, cells from a clinical specimen are fixed on a glass slide and viral antigens present in the cells are detected by fluorescein-labeled virus-specific antibodies. doi = 10.1016/b978-0-12-801238-3.02558-7 id = cord-323195-buzcb8ya author = Valtonen, Maarit title = Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment date = 2019-05-29 keywords = Games; POCT; virus summary = title: Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment 13 14 The aim of our prospective observational study was to investigate the occurrence and aetiology of the common cold in Team Finland during the 2018 Winter Olympic Games. Six days later, the neighbouring team member in the aeroplane developed symptomatic respiratory syncytial virus A -infection. One subject developed nasal congestion during the 9-hour flight, later detected to be a respiratory syncytial virus B infection. First, 45% of the elite athletes and 32% of the staff members suffered from the symptoms of the common cold during the median stay of 3 weeks at the Winter Olympic Games. Our study is the first to detect the aetiology of respiratory infections in elite athletes using molecular POCT at a major event. doi = 10.1136/bjsports-2018-100487 id = cord-333655-lylt7qld author = Van Breedam, Wander title = Bitter‐sweet symphony: glycan–lectin interactions in virus biology date = 2013-12-06 keywords = HIV-1; IAV; SIGN; lectin; virus summary = In sum, it appears that the dimeric lectin galectin-1 can enhance HIV-1 infection efficiency by cross-linking viral and host cell glycans and thereby promoting firmer adhesion of the virus to the target cell surface and facilitating virus-receptor interactions (Ouellet et al., 2005; Mercier et al., 2008; St-Pierre et al., 2011; Sato et al., 2012) . As has been shown for IAV, acquisition or deletion of glycosylation sites may affect crucial steps in the viral infection/replication process (e.g. receptor binding, fusion, release of newly formed virions) (Ohuchi et al., 1997; Wagner et al., 2000; Tsuchiya et al., 2002; Kim & Park, 2012) , alter the capacity of the virus to avoid induction of/recognition by virus-specific antibodies (glycan shielding) Wei et al., 2010; Wanzeck et al., 2011; Kim & Park, 2012; Job et al., 2013; Sun et al., 2013) , and modulate viral interaction with various immune system lectins (Reading et al., 2007; Vigerust et al., 2007; Reading et al., 2009; Tate et al., 2011a, b) . doi = 10.1111/1574-6976.12052 id = cord-350964-0jtfc271 author = Van Nguyen, Dung title = Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam date = 2018-02-28 keywords = HBV; HEV; Rattus; virus summary = In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Nucleic acid that was extracted from liver samples of 157 bats (29 species; Table S1 ) and 470 rodents (six species) was screened for pegivirus and human hepatitis B, C, E viruses and their homologues ( Table 1 ) by nested and semi-nested PCR assays with degenerate primers. doi = 10.3390/v10030102 id = cord-337149-cjon7ihb author = Van Vliet, Kim M. title = The Role of the Adeno-Associated Virus Capsid in Gene Transfer date = 2008 keywords = AAV; AAV1; AAV2; AAV5; adeno; vector; virus summary = Adeno-associated virus (AAV) is one of the most promising viral gene transfer vectors that has been shown to effect long-term gene expression and disease correction with low toxicity in animal models, and is well tolerated in human clinical trials. Prior to developing a gene therapy strategy that utilizes AAV, the serotype should be carefully considered since each capsid exhibits a unique tissue tropism and transduction efficiency. Several approaches have been undertaken in an effort to target AAV vectors to specific cell types, including utilizing natural serotypes that target a desired cellular receptor, producing pseudotyped vectors, and engineering chimeric and mosaic AAV capsids. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy Adeno-associated virus serotypes 1 to 5 mediated tumor cell directed gene transfer and improvement of transduction efficiency Adeno-associated virus vectors serotyped with AAV8 capsid are more efficient than AAV-1 or -2 serotypes for widespread gene delivery to the neonatal mouse brain doi = 10.1007/978-1-59745-210-6_2 id = cord-353609-no3mbg5d author = Vandegrift, Kurt J. title = An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date = 2011-04-15 keywords = disease; host; human; population; viral; virus summary = Conducting viral surveillance in animal reservoirs and invertebrate vectors can help explain circulation within host species; observed patterns of zoonotic transmission; and even allow for the prediction of periods of increased risk of zoonotic transmission (e.g., Rift valley fever and rainfall [25] ; West Nile virus (WNV) and American robin (Turdus turdus) migration [26] ; as well as hantavirus in mice [27, 28] ). Globalization, host ecology, host-virus dynamics, climate change, and anthropogenic landscape changes all contribute to the complexity of zoonotic viral emergence and disease, and create significant conservation and public health challenges. While the lasting efficacy of wildlife vaccination efforts has yet to be demonstrated with either endangered species or in breaking the transmission cycle of human pathogens, an increasing number of researchers are drawing attention to systems where it seems feasible [99, 103] ; demonstrating that intricate knowledge of host and virus ecology can greatly reduce the amount of vaccine coverage that is necessary to control these viruses. doi = 10.3390/v3040379 id = cord-314166-79323mzd author = Vanderford, Thomas H. title = Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection date = 2006-12-11 keywords = site; virus summary = Here, employing previously unused numerical analyses and a more comprehensive phylogenetic analysis of the same viral sequence data, we detect strong RM-specific selection in the V2 loop at days 40 and 70 p.i., which underscores this region''s importance in adaptation to the RMs. Most prominently, changes in the position and frequency of an N-glyc motif in the V2 loop likely represent an adaptation either to a divergent CD4 or chemokine coreceptor or to an as-of-yet undetermined target cell population. Taken together, these data suggest that in addition to overall differences in the allelic structure of the SIVsm populations between the 2 host species, the viruses replicating in RMs are significantly more diverged from the SI than viruses replicating in the newly infected SMs. To identify specific amino acid sites that may be responsible for the disparate evolutionary patterns of viruses replicating in the 2 monkey species, we applied 3 site-bysite analyses to detect particular codons under selection. doi = 10.1093/molbev/msl194 id = cord-335647-dhcxj7cj author = Vanderlinden, Evelien title = Emerging Antiviral Strategies to Interfere with Influenza Virus Entry date = 2013-06-25 keywords = H5N1; influenza; virus summary = We here focus on emerging options to interfere with the influenza virus entry process, which consists of the following steps: attachment of the viral hemagglutinin to the sialylated host cell receptors, endocytosis, M2‐mediated uncoating, low pH‐induced membrane fusion, and, finally, import of the viral ribonucleoprotein into the nucleus. There are three conceivable strategies for inhibiting attachment of influenza virus to its target cell: (i) an antiviral compound binding to the HA RBS; (ii) an inhibitor blocking the sialic acid-containing receptors on the epithelial cell membrane; or (iii) a receptor-destroying agent. 91 Regarding potential antiviral use, design of modified forms of the porcine SP-D lectin (which has higher anti-influenza virus activity than its human counterpart) is aided by the growing insight into how its carbohydrate recognition domain (CRD) precisely interacts with the high-mannose glycans attached near the RBS of HA. doi = 10.1002/med.21289 id = cord-264291-0czphube author = Varfolomeev, S. D. title = Kinetic model of development of acute viral infection in the human body. Critical conditions, control mechanisms, “thermoheliox” date = 2020-07-20 keywords = temperature; virus summary = A kinetic model of the development of acute viral infection is proposed and the dynamic behavior of key variables, including the concentrations of viral particles, infected cells, and pathogenic microorganisms, is described. The most important parameters determining the process dynamics are the concentration of the infecting viral agent, the concentration of pathogenic microfl ora, which develops symbiotrophically on the aff ected cells, and physical conditions of the process such as temperature and pH of the medium. Quite a few publications of the last decade describe modeling of the dynamics of viral growth in the body, taking account of the production of pathogenic microfl ora and human immune system response. Most of mathematical models describe the incubation, the viral growth, activation of the immune system, and treatment of infection, but they do not consider the causes for collapse of the system, that is, molecular causes for the death of an organism related to the disease. doi = 10.1007/s11172-020-2886-4 id = cord-005876-d8sid7gd author = Varnholt, V. title = ARDS infolge schwerer RSV-Infektion Therapeutische Optionen: Therapeutische Optionen date = 1996 keywords = ECMO; HFOV; RSV; Virus summary = Wir berichten im folgenden ü ber eine auffallende Hä ufung schwerster RS-Virus-Pneumonien mit konsekutivem ARDS im Winterhalbjahr 1994/1995 in unserer Klinik und den Verlauf bei den betroffenen Patienten -nach der vergeblichen Anwendung "ü blicher" Behandlungsmethoden -wä hrend der Anwendung alternativer Therapieverfahren [NO-Inhalation, Hochfrequenzoszillationsbeatmung (HFOV), extrakorporale Membranoxygenierung (ECMO)]. Respiratory syncytial virus (RSV) -ARDS -Inhaled nitric oxide (NO) -High frequency oscillatory ventilation (HFOV) -Extracorporeal membrane oxygenation (ECMO) [10] . Krankheitsverlauf bei 10 Patienten mit RSV-Pneumonie unter alternativen Therapieverfahren wurden -in den verlegenden Institutionen -in 50 % der Fä lle eingesetzt, nach Ü bernahme von uns nur noch bei 2 Kindern: Die mö gliche obstruktive Komponente einer RSV-Infektion stand bei unseren Patienten nicht im Vordergrund, ersichtlich auch an den teilweise sehr niedrigen pCO 2 -Werten. Durch den Einsatz von NO oder/und HFOV kann bei schwer verlaufenden RSV-Infektionen -wie bei anderen Formen des kindlichen Lungenversagens -eine ECMO-Therapie manchmal vermieden werden. Ob bei beatmungspflichtigen Kindern mit RSV-Pneumonie ein frü herer Einsatz von NO und/oder HFOV zu einer weiteren Senkung der Letalität fü hrt, mü ssen weitere Beobachtungen zeigen. doi = 10.1007/s001120050095 id = cord-307046-ko3bdvo0 author = Vasilakis, Nikos title = Exploiting the Legacy of the Arbovirus Hunters date = 2019-05-23 keywords = Aedes; Australia; Institute; NGS; USSR; fever; human; isolate; isolation; mosquito; new; novel; tick; virus summary = Complete genome sequences are now available for many of the archived isolates, allowing more accurate taxonomic assignments, analysis of their phylogenetic and evolutionary relationships with other viruses, and evaluation of the potential risks they may present to humans and wild or domestic animal populations. Scientists in these field laboratories were involved in the detection and investigation of human diseases in their respective geographic regions, surveying human and animal populations for serologic evidence of past viral infection, and searching for viruses in a wide variety of arthropods, mammals, birds, reptiles, and amphibians [2] . The family contains several serious human pathogens, including dengue, yellow fever, Zika, Japanese encephalitis, West Nile, and tick-borne encephalitis viruses (all arboviruses in the genus Flavivirus) and the hepatitis C virus (a member of the genus Hepacivirus). doi = 10.3390/v11050471 id = cord-339209-oe8onyr9 author = Vasilakis, Nikos title = Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date = 2014-05-20 keywords = RNA; figure; mesoniviruse; sequence; virus summary = The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5''-untranslated region (5''-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) . doi = 10.1186/1743-422x-11-97 id = cord-023925-qrr7jcwe author = Verhoef, Jan title = A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date = 2011-07-12 keywords = HIV; cell; gram; infection; virus summary = 128 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Micro-organisms that succeed in penetrating the first line of defence are ingested, killed, and degraded by phagocytic cells [polymorphonuclear leukocytes (PMN) or neutrophils, monocytes, and macrophages], which are attracted to a microbial infection through chemotaxis. Intracellular signalling involves several kinases depending on 132 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes Phenotypical characteristics: morphology, biotyping, serotyping, antibiotic resistance Analytical characteristics: cell-wall analysis, lipid and protein analysis, enzyme typing (catalase) Gram staining positive or negative Aerobic, anaerobic: Fermentation of different sugars Naming and classification of viruses according to: Structure: size, morphology (naked, enveloped), nucleic acid (RNA, DNA) Molecular aspects: mode of replication, assembly and budding Disease: encephalitis, hepatitis Means of transmission: droplets, water, blood, insects Host range: animal, plant, bacteria Classification of fungi according to: Structure: macroscopic morphology of hyphae (mycelium); microscopic morphology of hyphae, conidophores and conidia (spores); and shape and size Cell features: nucleus, cytosol, plasmalemma (cell membrane which contains cholesterol), physiology, staining properties Sexual characteristics: sexual and /or asexual reproduction, extended dikaryotic phase, basidium formation Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes doi = 10.1007/978-3-0346-0136-8_8 id = cord-258389-1u05w7r4 author = Verma, Anju title = Animal tissue culture principles and applications date = 2020-06-26 keywords = CHO; animal; cell; culture; growth; line; medium; virus summary = The development of basic culture media has enabled scientists to work with a wide variety of cells under controlled conditions; this has played an important role in advancing our understanding of cell growth and differentiation, identification of growth factors, and understanding of mechanisms underlying the normal functions of various cell types. Many animal cells can be induced to grow outside of their organ or tissue of origin under defined conditions when supplemented with a medium containing nutrients and growth factors. With advancements in animal cell culture technology, a number of cell lines have evolved and are used for vaccine production, therapeutic proteins, pharmaceutical agents, and anticancerous agents. The animal cell culture can be grown for a wide variety of cell-based assays to investigate morphology, protein expression, cell growth, differentiation, apoptosis, and toxicity in different environments. doi = 10.1016/b978-0-12-811710-1.00012-4 id = cord-283405-aozxvxxs author = Vermillion, Meghan S. title = Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date = 2018-02-01 keywords = ZIKV; infection; maternal; pregnant; vaccine; virus summary = Pregnant women, unborn fetuses, and neonates represent three populations of high-risk individuals that can all be simultaneously protected from vaccine-preventable infectious disease with strategic maternal immunization protocols. Third are neonatal and infant infections, which are not considered to pose significant risk to pregnant women or unborn fetuses, but can cause severe, and sometimes fatal disease in neonates and infants that lack protective maternal immunity following birth. Studies in pregnant nonhuman primates have been instrumental for the identification of CD4 + T cell responses as critical for early control of CMV infection and transmission during pregnancy, 100 and studies in guinea pigs have demonstrated that a single-cycle infectious CMV vaccine induces immune responses similar to natural infection and protects against congenital infection. 125 Vaccine candidates have been developed using diverse platforms, including DNA, mRNA, and purified inactivated and live-attenuated virus, many of which have been tested in non-pregnant mouse and nonhuman primate models for their ability to generate immune responses that mimic responses to natural infection and protected against ZIKV challenge. doi = 10.1038/s41541-017-0042-4 id = cord-336929-2rnkotqy author = Vieira, Flávia Sarmento title = Host‐cell lipid rafts: a safe door for micro‐organisms? date = 2012-01-03 keywords = cell; lipid; membrane; raft; virus summary = In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) . doi = 10.1042/bc20090138 id = cord-318495-1w74wf02 author = Vignuzzi, Marco title = Defective viral genomes are key drivers of the virus–host interaction date = 2019-06-03 keywords = DVG; RNA; defective; particle; viral; virus summary = The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus doi = 10.1038/s41564-019-0465-y id = cord-264884-ydkigome author = Villarreal, Luis P. title = The Widespread Evolutionary Significance of Viruses date = 2008-07-05 keywords = HIV-1; MHV; RNA; chapter; dna; evolution; gene; host; virus summary = For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage. doi = 10.1016/b978-0-12-374153-0.00021-7 id = cord-281281-knelqmzx author = Villas-Boas, Gustavo R. title = The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date = 2020-09-07 keywords = ACE2; COVID-19; China; CoV-2; RNA; SARS; figure; virus summary = The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. doi = 10.3390/molecules25184086 id = cord-004477-qu2o2iu1 author = Vlasova, Anastasia N. title = Editorial: Porcine Anti-Viral Immunity date = 2020-03-06 keywords = PRRSV; virus summary = Immediately following viral infection, neonatal survival depends on innate immunity and passive protection by lactogenic immune factors such as pathogen-specific antibodies, until an adaptive immune response can develop. Wide-spread porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SIV) represent major health challenges in the large US swine production systems and possibly worldwide. In introducing the topic of anti-viral immunity, we emphasize the genetic diversity of viruses, the virus life cycle and the pathology that viral infection can cause. A more tedious procedure is to use only parts of the virus as the vaccine (subunit vaccines) that target the immune response to those viral epitopes that elicit VN antibodies. A second approach to vaccine development is use of live attenuated virus that has been genetically modified or cell culture adapted and cannot produce a disease in the host but can still replicate. doi = 10.3389/fimmu.2020.00399 id = cord-021375-lca26xum author = Voelkner, Nadine title = Riding the Shi: From Infection Barriers to the Microbial City date = 2019-08-23 keywords = Hong; Kong; Macphail; chinese; human; virus summary = Taking its cue from the currently accepted germ theory of disease, such mechanisms render a global city like Hong Kong not only pervasively "on alert" and under threat of unpredictable and pathogenic viruses and other microbes, it also gives rise to a hygiene and antimicrobial politics that is never entirely able to control pathogenic circulation. Considering recent advances in gene sequencing in microbiology, through which a "vast diversity of microbial life in, on and around the human body" (Lorimer 2017, 544) has been identified as residing in complex relationality with one another, how befitting is it to fight infectious diseases by indiscriminately eliminating microbes through the use of antimicrobials and practicing urban hygiene as in the case of Hong Kong? Various scholars have noted how, much like Hong Kong in the face of SARS, global public health programs adopt an antimicrobial stance to the control and/or elimination of infectious diseases, however, which might prove to be counterproductive in securing human life (Macphail 2014; Methot and Alizon 2014; Fishel 2015 Fishel , 2017 White 2015; Hinchliffe et al. doi = 10.1093/ips/olz016 id = cord-276193-cngz535o author = Volz, A. title = Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development date = 2016-08-01 keywords = Ankara; CD8; MERS; MVA; VACV; vaccine; virus summary = Safety tested Modified Vaccinia virus Ankara (MVA) is licensed as third-generation vaccine against smallpox and serves as a potent vector system for development of new candidate vaccines against infectious diseases and cancer. Immunizations with this MVA deletion mutant led to significantly enhanced virus-specific CD8+ T-cell responses and increased protective capacity against lethal challenge infection with virulent VACV strain Western Reserve (WR) . Upon prime-boost vaccinations in BALB/c mice, all four MVA-WNV candidate vaccines elicited circulating serum antibodies binding to recombinant WNV-E protein and neutralizing WNV in tissue culture infections In addition, immunizations in HLA-A2.1-/HLA-DR1-transgenic H-2 class I-/class II-knockout mice efficiently induced WNV-E-specific CD8+ T-cell responses. At the moment, recombinant MVA viruses expressing various heterologous antigens are among the most promising vector candidates to develop innovative vaccination strategies to protect against complex infections such as AIDS, tuberculosis, or malaria, or against rare but threatening emerging diseases. doi = 10.1016/bs.aivir.2016.07.001 id = cord-347727-wka9q98s author = Vong, Sirenda title = Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region date = 2016-12-01 keywords = Ebola; Health; Thailand; virus summary = OBJECTIVE: To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. 2 In January 2015, nine of the 11 countries from the WHO South-East Asia Region agreed to a joint assessment by WHO and ministries of health of their preparedness and operational readiness for Ebola virus disease. Each assessment component comprised several Objective To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. However, only seven of the countries had developed a specific, written Ebola virus disease preparedness plan (task A1), including four that had detailed a risk-based approach and some level of linkage with their pandemic influenza preparedness plans. Our review showed that risk assessment (i.e. evaluating the likelihood of Ebola virus disease being imported or introduced into a non-affected country) had been formally or informally conducted in six countries (Bhutan, Indonesia, Maldives, Sri Lanka, Thailand and Timor-Leste). doi = 10.2471/blt.16.174441 id = cord-255479-yd5cbwnx author = Vu, David M. title = Chikungunya Virus date = 2017-06-30 keywords = CHIKV; chikungunya; infection; virus summary = Anti-CHIKV antibodies directed against the envelope protein that neutralize the virus in vitro also protect neonatal mice from lethal CHIKV infection in vivo, suggesting that these proteins may be important antigenic lethal targets for development of naturally acquired, or vaccine-elicited protection. Stedman, who reported this "anomalous disease" called "dandy fever" by local residents, noted that the illness "attacked almost every individual in the town," had "extremely low mortality," and was associated with "pains in the joints for weeks after recovery from the acute stage," which were key differences between the 1827 and 1828 West Indies epidemic and previous descriptions of a "break-bone fever" (referring to modern-day dengue fever). For diagnostic confirmation of current and recent infection, a molecular test (typically polymerase chain reaction [PCR]) for the virus and an assay for the presence of specific IgM antibody are required. doi = 10.1016/j.cll.2017.01.008 id = cord-010016-fs8pjy1z author = WEBB, H. E. title = CAN VIRAL ENVELOPE GLYCOLIPIDS PRODUCE AUTO‐IMMUNITY, WITH REFERENCE TO THE CNS AND MULTIPLE SCLEROSIS? date = 2008-05-12 keywords = CNS; virus summary = In this paper it is proposed that CNS demyelination could arise in susceptible individuals (HLA type) from an immune response to glycolipids, triggered by the carrier effect of one or more enveloped neurotropic viruses. The demyelination is dependent upon T-lymphocytes probably cytotoxic cells (Jagelman et al., 1978; Fazakerley, Amor & Webb 1983; Pathak et al., 1983) and probably results from an immune reaction against viral antigens on the surface of oligodendrocytes or myelin. Since all are budding viruses they will have a similar host derived viral envelope provided the virus replicates in the same cell type. It is an intriguing possibility that CNS demyelination in diseases such as MS, arises as a result of an auto-immune reaction against specific glycolipids, induced by the carrier effect of a budding neurotropic virus. I n this way any number of enveloped neurotropic viruses could be involved in initiating and restimulating a n autoimmune response to the same brain cell membrane specific glycolipid(s). doi = 10.1111/j.1365-2990.1984.tb00335.x id = cord-000359-y0m1utug author = Walpita, Pramila title = Vaccine Potential of Nipah Virus-Like Particles date = 2011-04-06 keywords = Nipah; VLP; virus summary = Co-expression of these proteins under optimized conditions resulted in quantifiable amounts of VLPs with many virus-like/vaccine desirable properties including some not previously described for VLPs of any paramyxovirus: The particles were fusogenic, inducing syncytia formation; PCR array analysis showed NiV VLP-induced activation of innate immune defense pathways; the surface structure of NiV VLPs imaged by cryoelectron microscopy was dense, ordered, and repetitive, and consistent with similarly derived structure of paramyxovirus measles virus. Plasmid-mediated expression of selected viral proteins results in the spontaneous assembly and release of VLPs. These particles make highly effective immunogens because they possess several features of the authentic virus such as their surface structure and dimensions [31, 36] . In preliminary studies it was found that co-expression of NiV G, F and M proteins in 293T cells resulted in the formation of VLPs that bud out into the transfected cell SUP and that they can be harvested, concentrated and purified as described under Methods. doi = 10.1371/journal.pone.0018437 id = cord-347710-ff64y6ef author = Wan, Qianya title = Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date = 2020-07-13 keywords = A71; ATP; HBV; HCV; HIV-1; Heat; Hsc70; Hsp27; Hsp90; RNA; cell; dna; protein; virus summary = hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. doi = 10.1038/s41392-020-00233-4 id = cord-305263-fgwf6wy3 author = Wang, Ben X. title = The yin and yang of viruses and interferons date = 2012-02-07 keywords = HCV; IFN; SARS; response; virus summary = IFN therapy therefore has the advantage over DAA treatments in that, in addition to stimulating genes that block viral replication in infected cells, IFNs activate other innate and adaptive immune responses to combat the virus. For example, polymorphisms in host genes encoding proteins associated with regulation of an IFN response such as interferon receptor a-chain (IFNAR1) [10] , the IFN-inducible myxovirus resistance GTPase protein, Mx [11] , the IFN-inducible 2 0 ,5 0 -oligoadenylate synthetase (OAS) [12] and the suppressor of cytokine signaling (SOCS) 3 associated with regulation of an IFN response [13] , are predictive markers linked with the rate of sustained virological response (SVR) to HCV infection following IFN-a treatment. Remarkably, distinct highly pathogenic respiratory viruses, namely influenza viruses and the SARS-CoV, encode nonstructural proteins in their genomes that function as virulence factors that specifically target the host innate IFN response, further emphasizing the importance of IFNs as broad-spectrum antivirals. doi = 10.1016/j.it.2012.01.004 id = cord-278511-je1509ar author = Wang, David title = 5 challenges in understanding the role of the virome in health and disease date = 2020-03-26 keywords = virome; virus summary = An even more significant problem is that in most virome studies, more than 50% of the sequences in virus-enriched preparations have no detectable sequence similarity to any known reference sequences; these unalignable sequences are referred to as viral "dark matter" [8] and may include novel, highly divergent viruses that are unrecognizable. To illustrate this point, the United States National Institutes of Health (NIH) virology study sections address only "non-bacteriophage viral genetics, infection and replication, cellular and host responses to viral infections, and mechanisms of viral disease pathogenesis." Thus, there is a great need to bring these disparate communities together in order to collectively attack questions associated with the virome, especially as more complex trans-kingdom interactions are identified linking phages, bacteria, eukaryotic viruses, and eukaryotic cells. With new cell-culture systems and animal models for novel viruses, there will ideally be studies that attribute causal roles for some of the associations. doi = 10.1371/journal.ppat.1008318 id = cord-340610-ex2yjyum author = Wang, De-Yun title = Upper Airway Stem Cells: Understanding the Nose and Role for Future Cell Therapy date = 2014-11-28 keywords = CRS; cell; epithelial; nasal; virus summary = In addition to the physical barrier, nasal epithelial cells are known to play an active role in both the innate and acquired immune responses, which have been summarized in the European Position paper on rhinosinusitis and nasal polyps 2012 (EPOS 2012) [1••] as (l) expressing membrane-bound and cytoplasmic pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs), which are conserved molecular patterns found in parasites, viruses, yeasts, bacteria, and mycobacteria; (2) secreting a vast arsenal of host defense molecules, such as antimicrobial molecules in several classes of enzymes (lysozyme, chitinases, and peroxidases), opsonins (complement and pentraxin-3), permeabilizing proteins (A defensins, B defensins, and cathelicidins such as LL-37), collectins (surfactant protein-A, surfactant protein-D, and mannose-binding lectin), and binding proteins (lactoferrin and mucins); (3) producing a variety of inflammatory cytokines, such as IL-1, TNF-α, IFNα/β, GM-CSF, eotaxins, RANTES, IP-10, IL-6, IL-8, GRO-α, MDC, SCF, TARC, MCP-4, BAFF, osteopontin, IL-25, IL-32, IL-33, and thymic stromal lymphopoietin (TSLP), in response to stimulation of the antigens. doi = 10.1007/s11882-014-0490-0 id = cord-295445-f4p00yaw author = Wang, Hao title = Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date = 2018-02-01 keywords = PCR; USA; treatment; virus summary = Previous studies conducted in wastewater treatment plants have shown that ozone disinfection might be highly efficient in inactivating bacteria and bacteriophages after conventional sewage treatments (Kim et al., 1999; Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. The four concentrated water samples (incoming sewage, conventionally treated, ozone treated, and outlet water) from each of the three weeks were also analyzed by qPCR for 14 common enteric viruses (adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, norovirus GI, norovirus GII, norovirus GIV, parechovirus, sapovirus, aichivirus, mengovirus, torovirus, enterovirus, and rotavirus). However, in this study some viruses that were undetectable in the ozone-treated samples reoccurred in the outlet water, including parvovirus, norovirus GII, human feces pecovirus, parvovirus-like virus, gokushovirus, and HAdV-F41, although the amounts were significantly lower compared with raw sewage. doi = 10.1016/j.ijheh.2018.01.012 id = cord-030961-5gzc7193 author = Wang, Jiajun title = Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane date = 2020-08-28 keywords = adhesion; membrane; virus summary = In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R. doi = 10.1007/s42558-020-00026-3 id = cord-017568-8fnr4zzv author = Wang, Lin-Fa title = Disease Outbreaks Caused by Emerging Paramyxoviruses of Bat Origin date = 2008 keywords = Malaysia; Nipah; virus summary = They are Hendra virus (HeV), Nipah virus (NiV), and Menangle virus (MenV), isolated from infected horses and humans in Australia in 1994 , humans and pigs in Malaysia in 1999 , and pigs in Australia in 1997 , respectively (Chua et al., 2000 Murray et al., 1995b; Philbey et al., 1998) . In addition to the emergence of paramyxoviruses from frugivorous Pteropus bats, insectivorous Rhinolophus species have been identified as natural hosts of SARS-like viruses (Lau et al., 2005; Li et al., 2005) , and Ebola virus has been shown to have fruit bat reservoir hosts (Leroy et al., 2005) . The identification of fruit bats in the genus Pteropus as the reservoir hosts of HeV and NiV in Australia and Malaysia, respectively, prompted searches for related viruses in other nations in the region. Case-control study of risk factors for human infection with a new zoonotic paramyxovirus, Nipah virus, during a 1998-1999 outbreak of severe encephalitis in Malaysia doi = 10.1007/978-0-387-75722-3_12 id = cord-270803-jtv5jmkn author = Wang, Lin-Fa title = Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date = 2011-11-09 keywords = bat; host; rate; virus summary = This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. Bats (order Chiroptera), one of the most abundant, diverse and geographically dispersed vertebrates on earth, have recently been shown to be reservoir hosts of a number of emerging viruses responsible for severe disease outbreaks in humans and livestock [1 ,2,3]. doi = 10.1016/j.coviro.2011.10.013 id = cord-277309-kelebqr6 author = Wang, Lin-Fa title = Viruses in bats and potential spillover to animals and humans date = 2019-01-18 keywords = Pteropus; SARS; bat; human; virus summary = While it is not easy to assess the spillover potential of many SARS-CoV related bat CoVs due to unsuccessful attempts to isolate the viruses, it should be noted that a ''consensus'' virus constructed via reverse genetics pointed to a high probability of human infection [19] . Further study is required to determine the true zoonotic potential of SADS-CoV and closely related bat CoVs. For unknown reasons, despite of the wide presence of CoVs in bats of different locations and species with relative high viral genome levels, multiple attempts by different international groups to isolate bat CoVs have been largely unsuccessful. The genetic and functional Viruses in bats and potential spillover to animals and humans Wang and Anderson 81 Aside from MenPV and TioPV, other paramyxoviruses from the genus Rubulavirus have been isolated from or detected in bats without evidence of zoonotic transmission. doi = 10.1016/j.coviro.2018.12.007 id = cord-103688-n7hzpbyf author = Wang, Lina title = VirusDIP: Virus Data Integration Platform date = 2020-06-09 keywords = Yang; virus summary = Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. For data compatibility, the virus data standard integrates the virus and pathogen sample data standard of The International Nucleotide Sequence Database Collaboration (INSDC) (Karsch-Mizrachi et al., 2018) , the hCoV-19 data standard of GISAID, and the sample data standard of COVID-19 Genomics UK (COG-UK) Consortium. VirusDIP is committed to building a comprehensive virus data platform for archive, integration, access, and analysis. doi = 10.1101/2020.06.08.139451 id = cord-268593-rvxxv1dn author = Wang, Mingyang title = Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus date = 2015-07-28 keywords = HEF; influenza; virus summary = Influenza C virus is unique since it contains only one spike protein, the hemagglutinin-esterase-fusion glycoprotein HEF that possesses receptor binding, receptor destroying and membrane fusion activities, thus combining the functions of Hemagglutinin (HA) and Neuraminidase (NA) of influenza A and B viruses. While influenza A and B virus contain the two glycoproteins Hemagglutinin (HA) and Neuraminidase (NA) inserted into the viral membrane, influenza C virus possesses only one spike designated Hemagglutinin-Esterase-Fusion (HEF) protein which combines the functions of both HA and NA (Herrler et al., 1988a; Herrler and Klenk, 1991) . Although there is only 12% amino acid identity between HA and HEF, the overall structure of both molecules as well as folds of individual segments are quite similar, except an additional bulge, which is located at the lower part of the globular domain and contains the esterase region that is not present in HA (Fig. 3) . doi = 10.1007/s13238-015-0193-x id = cord-306983-6w2fvtfy author = Wang, Siye title = Influenza Virus—Cytokine-Protease Cycle in the Pathogenesis of Vascular Hyperpermeability in Severe Influenza date = 2010-10-01 keywords = TNF; figure; influenza; virus summary = Influenza A virus infection resulted in significant increases in TNF-α, IL-6, IL-1β, viral hemagglutininprocessing protease trypsin levels, and viral replication with vascular hyperpermeability in lung and brain in the first 6 days of infection. The present study reports several new observations: (1) proinflammatory cytokines, TNF-a, IL-1b, and IL-6, when upregulated by influenza A virus infection, induce trypsin expression in various organs and human endothelial cells; (2) the upregulated trypsin induces [Ca 2+ ] i mobilization via activation of the PAR-2, followed by loss of zonula occludens-1 and vascular hyperpermeability; (3) inhibitors of NF-kB and activator protein 1 effectively suppress the upregulation of proinflammatory cytokines and trypsin and improve the survival rates of infected mice. The present results allow us to propose a new mechanism of junctional permeability regulation: upregulated trypsin by influenza A virus and/or proinflammatory cytokines induces increase in [Ca 2+ ] i and loss of zonula occludens-1 in endothelial cells via PAR-2 signaling. doi = 10.1086/656044 id = cord-295640-mhfu0e9r author = Wang, Wenling title = Improving Cross-Protection against Influenza Virus Using Recombinant Vaccinia Vaccine Expressing NP and M2 Ectodomain Tandem Repeats date = 2019-06-25 keywords = Fig; RVJ; virus summary = Therefore, the cross-protection potentially correlates with both NP and M2e-specific humoral and cellular immune responses induced by RVJ-4M2eNP, which expresses a fusion antigen of full-length NP preceded by four M2e repeats. Previously, we expressed a fusion protein of NP and M2e (NM2e) in Escherichia coli and showed that immunization with NM2e formulated with aluminum hydroxide gel protected mice from a lethal challenge with heterologous influenza virus . BALB/c mice were immunized with the recombinant viruses to measure NP-and M2e-specific humoral and cellular immune responses as well as protective effect against lethal challenge with a heterologous influenza virus. Mice immunized with the recombinant vaccinia virus RVJ-NPM2e and RVJ-M2eNP showed strong antibody responses against NP, with lower titers of antibodies against M2e (Fig. 3A) . The recombinant vaccinia virus expressing 4M2e and full-length NP fusion antigen induced strong cross-protection (92%) against a lethal heterosubtypic PR8 challenge at 20 MLD 50 and thus regarded as the optimal one among the four constructs. doi = 10.1007/s12250-019-00138-9 id = cord-260554-nao59qx4 author = Wargo, Andrew R title = Viral fitness: definitions, measurement, and current insights date = 2012-09-15 keywords = fitness; viral; virus summary = Important recent trends include increasing use of in vivo systems to assess vertebrate virus fitness, and a broadening of research beyond replicative fitness to also investigate transmission fitness and epidemiologic fitness. The majority of viral fitness study systems are based on RNA viruses, and the highest numbers of publications in recent years involves human pathogens associated with major disease emergence events, such as human immunodeficiency virus-1 (HIV-1), influenza virus, and dengue virus (DENV). In many cases the ultimate goal of replicative and transmission fitness studies is to understand the epidemiology 540 Virus evolution and population level processes governing viral evolution, emergence, and displacement in the field. For vertebrate viruses the recent increase of in vivo virus fitness research is encouraging, but the majority of studies still remain in vitro. doi = 10.1016/j.coviro.2012.07.007 id = cord-002932-5e7xrd1y author = Watanabe, Tokiko title = Experimental infection of Cynomolgus Macaques with highly pathogenic H5N1 influenza virus through the aerosol route date = 2018-03-19 keywords = H5N1; aerosol; method; virus summary = In the ferret model, these studies demonstrated that the inoculation of animals with highly pathogenic avian influenza H5N1 virus via the aerosol route led to higher nasal wash virus titers, earlier onset of clinical signs, and/or a broader spectrum of disease compared with infection via intranasal inoculation despite no difference in lethality [9] [10] [11] . On day 3 post-infection, VN3040 virus was recovered from nasal swabs of two and three animals in the conventional and aerosol method groups, respectively, and the mean virus titers were comparable between the two groups. Cynomolgus macaques were inoculated with 4 ml of a 10 7 PFU/ml solution of the highly pathogenic H5N1 avian influenza virus A/Vietnam/ UT3040/2004 strain (VN3040) through the aerosol route by using the ultrasonic nebulizer NE-U17 (defined as "the aerosol method group"). In contrast, VN3040 replicated well in the right-and left-lower lung lobes of the infected animals in the conventional method group [the virus mean titers were 3.51 and 4.75 log 10 (PFU/g), respectively]. doi = 10.1038/s41598-018-23022-0 id = cord-290548-0wezrr1b author = Watanabe, Tokiko title = Villains or heroes? The raison d''être of viruses date = 2020-02-19 keywords = host; human; virus summary = For example, Ebola virus disease and acquired immunodeficiency syndrome emerged in 1976 and 1981, respectively, 5-9 and more recently, severe acute respiratory syndrome (SARS), highly pathogenic avian influenza viruses and Middle East respiratory syndrome (MERS) have appeared in human society. In traditional virology, most viruses found in humans are considered to be pathogenic to their hosts; however, recent studies have shown that there are some viruses that have symbiotic relationships with their hosts and do not cause disease. 44 In the last a few decades, emerging infectious diseases caused by newly identified viruses, such as Ebola virus, 5-8 SARS and MERS coronaviruses, [10] [11] [12] human immunodeficiency virus (HIV), 9 Nipah virus and Hendra virus, [45] [46] [47] [48] have appeared in human society. To date, the PREDICT programme has found over 1100 viruses in animals and humans, including a new Ebola virus and MERSand SARS-like coronaviruses. doi = 10.1002/cti2.1114 id = cord-281061-uoszpnst author = Watanabe, Yohei title = A novel immunochromatographic system for easy-to-use detection of group 1 avian influenza viruses with acquired human-type receptor binding specificity date = 2015-03-15 keywords = Sia; virus summary = A biotinylated anti-hemagglutinin antibody that bound a broad range of group 1 influenza A viruses and latex-conjugated α2,3 (blue) and α2,6 (red) sialylglycopolymers were used in an immunochromatographic strip test, with avidin and lectin immobilized on a nitrocellulose membrane at test and control lines, respectively. The strip test could detect the receptor binding specificity of a wide range of influenza viruses, as well as small increases in the binding affinity of variant H5N1 viruses to α2,6 sialylglycans at viral titers >128 hemagglutination units. In conclusion, the immunochromatographic strip test developed in this study should be useful for monitoring potential changes in the receptor binding specificity of group 1 influenza A viruses in the field. In this study, we developed a new easy-to-use immunochoromatographic strip test to detect the emergence of AI viruses with increased human-type receptor specificity and confirmed the applicability of this test using AI viruses isolated in several different geographic areas. doi = 10.1016/j.bios.2014.10.036 id = cord-321481-vrfwczve author = Watashi, Koichi title = NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date = 2014-02-19 keywords = HBV; NTCP; infection; virus summary = Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. HBV infection into host hepatocytes follows a multiple step process: (1) initially, HBV reversibly attaches to host cell surface proteoglycans with a low affinity; (2) this is followed by the process involving more specific receptor(s) with high affinity to mediate the early entry step; and (3) after endocytosis-mediated internalization, the virus fuses with the cellular membrane compartment, probably in an endosomal compartment, although the mechanisms are not fully understood. A myristoylated peptide encompassing amino acids 2-48 of the preS1 region turned out to be the most efficient in infection inhibition of HBV and also the envelope protein-related hepatitis D virus (HDV) [30, 31] . Cyclosporin A and its analogs inhibit hepatitis B virus entry into cultured hepatocytes through targeting a membrane transporter NTCP doi = 10.3390/ijms15022892 id = cord-271122-3fsl5589 author = Wathes, D. Claire title = Importance of Viral Disease in Dairy Cow Fertility date = 2019-07-24 keywords = BVDV; bovine; effect; infection; virus summary = Acute infection with non-cytopathic bovine viral diarrhea virus (BVDV) in mid-gestation increases abortion rates or causes the birth of persistently infected calves. In cultured bovine endometrial cells, experimental infection with ncp BVDV inhibited a variety of immune pathways normally activated in response to a challenge with bacterial lipopolysaccharide (LPS), including downregulation of many interferon-stimulated genes (ISGs), which are an important part of uterine defense mechanisms [40, 41] . Establishment of persistent infection with non-cytopathic bovine viral diarrhoea virus in cattle is associated with a failure to induce type I interferon A field investigation of the effects of bovine viral diarrhea virus infection around the time of insemination on the reproductive performance of cattle The effect of infection with bovine viral diarrhea virus on the fertility of Swiss dairy cattle Embryos produced from fertilization with bovine viral diarrhea virus (BVDV)-infected semen and the risk of disease transmission to embryo transfer (ET) recipients and offspring doi = 10.1016/j.eng.2019.07.020 id = cord-275602-cog4nma0 author = Watkins, Kevin title = Emerging Infectious Diseases: a Review date = 2018-06-22 keywords = East; Middle; RNA; disease; virus summary = SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. In 1992, an expert committee that produced the Institute of Medicine report on emerging infections defined them as "new, reemerging, or drug-resistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future." Additionally, six major contributors to these diseases were presented and included changes in human demographics and behavior, advances in technology and changes in industry practices, economic development and changes in land-use patterns, dramatic increases in volume and speed of international travel and commerce, microbial adaptation and change, and breakdown of public health capacity [1] . The World Health Organization has prioritized a number of infectious diseases as requiring urgent need for research and development given the concern for potential of severe outbreaks. doi = 10.1007/s40138-018-0162-9 id = cord-339062-tq0f6d01 author = Weaver, Scott C. title = Transmission cycles, host range, evolution and emergence of arboviral disease date = 2004 keywords = JEV; United; VEEV; venezuelan; virus summary = RNA viruses, including HIV 1,2 , dengue virus (DENV) 3, 4 and possibly the severe acute respiratory syndrome (SARS) coronavirus [5] [6] [7] , have caused recent pandemics by changing their host range to amplify in humans. In this review, we focus on selected viruses such as Venezuelan equine and Japanese encephalitis viruses (VEEV and JEV, respectively), which cause epidemics by adapting to domestic animals and exploiting them as amplification hosts. After identification of VEEV as a cause of human disease, experimental animal models revealed that equine infection results in a high titre VIRAEMIA; the animals therefore serve as highly efficient amplification hosts in the presence of abundant competent mosquito vectors 12 However, studies of dengue virus ecology in sylvatic habitats of west Africa 72 and Malaysia 73, 74 have identified transmission cycles involving non-human primates as reservoir hosts and arboreal, tree-hole dwelling Aedes (Stegomyia) spp. doi = 10.1038/nrmicro1006 id = cord-274112-6t0wpiqy author = Webby, RJ title = Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines date = 2004-04-03 keywords = H5N1; Hong; vaccine; virus summary = INTERPRETATION: The ability to produce a candidate reference virus in such a short period of time sets a new standard for rapid response to emerging infectious disease threats and clearly shows the usefulness of reverse genetics for influenza vaccine development. The agent must be handled only under conditions of at least biosafety level 3 (BSL3), and it can kill fertilised chicken eggs, the standard medium for the reassortment and Responsiveness to a pandemic alert: use of reverse genetics for rapid development of influenza vaccines propagation of influenza virus before its inactivation and formulation for use in vaccines. The vaccine-candidate reference virus stock described in this report has been produced entirely on a cell substrate licensed for the manufacture of human vaccine, and as such, is-to our knowledge-the first reverse genetically derived influenza vaccine suitable for testing in clinical trials. Recombinant influenza A virus vaccines for the pathogenic human A/Hong Kong/97 (H5N1) viruses doi = 10.1016/s0140-6736(04)15892-3 id = cord-280130-ewqe9edq author = Weber, Friedemann title = Viral suppression of the interferon system date = 2007-01-27 keywords = IFN; RNA; virus summary = In most nucleated body cells, viral infections activate transcription of the ''''classic'''' IFN-b gene [1] by a signaling chain which is initiated by the RNA sensors RIG-I and MDA-5, which in turn act trough the adaptor IPS-1 and the kinases TBK-1 and IKK-3 to activate the transcription factor IRF-3 (see reviews by P. Many RNA and DNA viruses therefore express proteins which bind this key molecule to avoid both IFN induction and activation of dsRNA-dependent antiviral enzymes [7, 8] . Binding of the influenza virus NS1 protein to double-stranded RNA inhibits the activation of the protein kinase that phosphorylates the elF-2 translation initiation factor Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon doi = 10.1016/j.biochi.2007.01.005 id = cord-018078-clxzp1ph author = Weber, Olaf title = Coronavirus infections in veterinary medicine date = 2005 keywords = TGEV; coronavirus; virus summary = Some important viruses that are discussed below belong to group I and include the canine enteric coronavirus (CECoV), the transmissible gastroenteritis virus (TGEV) of swine, the porcine epidemic diarrhoea virus (PEDV), the porcine respiratory coronavirus (PRCoV) and the feline coronaviruses (FCoVs). The clinical symptoms of endemic/enzootic TGE are usually less severe in the older pigs, making a clinical differentiation between TGE and other infectious enteric diseases, like that caused by rotaviruses and/or clostridia, impossible. Bovine coronavirus (BCoV) is an important cause of neonatal calf diarrhea [33] but may also infect the respiratory tract and has been recognized as the causing agent especially for winter dysentery in adult cattle. As for other coronaviruses, seasonal changes in temperature, environmental factors but also the immune status play an important role in the transmission of the virus and the clinical outcome of the infection. Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism doi = 10.1007/3-7643-7339-3_2 id = cord-019051-gtruu1op author = Weber, Olaf title = The role of viruses in the etiology and pathogenesis of common cold date = 2009-11-10 keywords = RNA; RSV; infection; respiratory; virus summary = Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells doi = 10.1007/978-3-7643-9912-2_5 id = cord-266138-yibbiiij author = Wege, Helmut title = Immunopathological aspects of coronavirus infections date = 1995 keywords = JHM; MHV; cell; virus summary = Murine coronaviruses (mouse hepatitis virus, MHV) can spread inapparently or may hide as persistent infections that modulate the immune response [38, 100] . Suppression of immune response induction in Peyer''s patch lymphoid cells from mice infected with mouse hepatitis virus Infection of BALB/cByJ mice with the JHM strain of mouse hepatitis virus alters in vitro splenic T cell proliferation and cytokine production Interaction of immune and central nervous systems: contribution of anti-viral Thy-1 + cells to demyelination induced by coronavirus JHM Impaired T and B cell subpopulations involved in a chronic disease induced by mouse hepatitis virus type 3 Identification of antigenic sites mediating antibody-dependent enhancement of feline infectious peritonitis virus infectivity The pathogenic role of virus-specific antibody-secreting cells in the central nervous system of rats with different susceptibility to coronavirus-induced demyelinating encephalitis Demyelination induced by murine hepatitis virus JHM strain (MHV-4) is immunologically mediated doi = 10.1007/bf00196162 id = cord-272981-8gahvdt0 author = Wege, Helmut title = Relapsing subacute demyelinating encephalomyelitis in rats during the course of coronavirus JHM infection date = 1984-08-31 keywords = CNS; JHM; SDE; virus summary = These results demonstrate that mutants of JHM virus can induce a relapsing demyelinating disease process, associated with a persistent infection, which possesses some similarities to chronic experimental allergic encephalomyelitis. It has been shown that an autoimmune reaction against CNS tissue can lead to 6hronic relapsing demyelination as seen in chronic experimental allergic encephalomyelitis (EAE) whereas the role of a virus infection in the induction of such a condition has not so far been directly demonstrated (McFarlin et al. After virus infection in rats inflammatory disseminating CNS lesions of marked demyelination develop accompanied by clinical signs of a subacute disease after varying incubation times. The induction of a progressive demyelinating, or relapsing demyelinating, disease process, in JHM virus-infected rats has ~me parallels to chronic EAE, an animal model based on sensitation ~8ainst CNS tissue extracts or myelin basic protein (McFarlin et al. doi = 10.1016/0165-5728(84)90022-5 id = cord-276212-ys5njiw0 author = Wei, L. title = Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date = 2015-05-30 keywords = IFVA; virus summary = authors: Wei, L.; Chan, K.-H.; Ip, D.K.M.; Fang, V.J.; Fung, R.O.P.; Leung, G.M.; Peiris, M.J.S.; Cowling, B.J. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong In this study, we aimed to investigate the burden of ARIs caused by different respiratory viral pathogens among children aged 15 years in a community outpatient setting, to describe their seasonal patterns of occurrence, and to characterize their clinical characteristics at presentation. The specimens were tested for eight common respiratory viruses (including types and subtypes), namely IFVA (subtypes H1 and H3), influenza virus B (IFVB), RSV (subtypes A and B), PIV (types 1-4), metapneumovirus (MPV), enterovirus (EnV)/RhV, AdV, bocavirus (BoV), and coronavirus (CoV) (types NL63, HKU1, 229E, and OC43), with the xTAG RVP FAST version 2.0 multiplex assay (Luminex Molecular Diagnostics, Toronto, Ontario, Canada), and this was followed by product detection and identification with a Luminex suspension microarray [7] . doi = 10.1016/j.cmi.2015.05.027 id = cord-004775-foaf3vyl author = Weiss, Marianne title = The proposed family toroviridae: Agents of enteric infections date = 1987 keywords = BEV; BRV; Breda; virus summary = A morphologically similar virus (Lyon 4 virus) detected in cattle in Lyon, France (6, 7) , was shown later to possess an antigenic relatedness to the Berne (BEV) and Breda (BRV) viruses. In thin sections through BEV infected cells (horse kidney, embryonic mule skin, equine dermal cells) densely staining spherical, elliptieM and elongated particles were detected (2, 9) . Thin sections through BRV infected intestinal cells of calves (10, 11, 12) showed elongated viral particles with rounded ends measuring 42 × 100.5 nm. The high molecular weight virion protein in the range of 75-100 kD of BEV is glycosylated, probably by N-linked oligosaccharides since tunicamycin, an antibiotic known to inhibit N-linked oligosaccharide synthesis, prevented the formation of infectious virus as well as appearance of the 75-100 kD band in PAGE of infected cells (20) . Evidence of a reaction of the particles in human feces with sera containing antibodies against BRV and BEV, respectively, were obtained in IEM (8), (Flewett personal communication). doi = 10.1007/bf01310058 id = cord-290133-4ou7ubb4 author = Weiss, Martin M. title = Rethinking Smallpox date = 2004-12-01 keywords = case; smallpox; vaccination; virus summary = The last recorded death due to smallpox, according to World Health Organization investigators, was likely associated with virus that had been transmitted by aerosol [16] . Such observations-along with the long incubation period of smallpox (mean, 12-14 days; range, 7-21 days)suggest that there would be adequate time to vaccinate the public and prevent a more widespread outbreak. Nonetheless, these masks, if distributed to the public, could prove to be critical for the control of a smallpox epidemic that was overwhelming our health care system, and they might also prove to be effective in limiting contagion of smaller viruses, such as influenza virus (either natural virus, as in 1918, or engineered virus [61] ). Because of the possibility of an attack involving bioengineered smallpox virus that is resistant to the current vaccine, methisazone should be reexamined, and research should be continued on other antiviral agents. doi = 10.1086/425745 id = cord-008333-1wepke2o author = Weisz, Ora A. title = Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology date = 2008-02-28 keywords = cell; dna; vaccinia; virus summary = The recombinant virus is selected, expanded, and used to infect cells, which then express high levels of the foreign protein. Transfection of cells immediately after infection with a vector containing the gene of interest cloned behind a T7 promoter results in rapid and efficient expression of the encoded protein. The use of an early vaccinia promoter to drive the foreign gene is essential for cell biology applications, since the protein will be expressed before most of the cytopathic effects of the virus infection become evident. Before growing a large-scale preparation of the recombinant, we also test that the expressed protein is the correct size by immunoprecipitation from radiolabeled infected cells, followed by electrophoresis in SDS polyacrylamide gels (see Section IV,C,l). Expression is mediated by co-infecting the cells with another vaccinia virus encoding T7 RNA polymerase (vTF7-3). This chapter has discussed the preparation and use of recombinant vaccinia viruses to express proteins in mammalian cells. doi = 10.1016/s0091-679x(08)60602-0 id = cord-002874-9rxv6fy9 author = Welch, David title = Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases date = 2018-02-09 keywords = irradiation; light; uvc; virus summary = Here we applied this approach to test the efficacy of the 222-nm far-UVC light to inactivate influenza A virus (H1N1) carried by aerosols in a benchtop aerosol UV irradiation chamber, which generated aerosol droplets of sizes similar to those generated by human coughing and breathing. If these results are confirmed in other scenarios, it follows that the use of overhead low-level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases such as influenza and tuberculosis. In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. doi = 10.1038/s41598-018-21058-w id = cord-277010-2iecsho0 author = Wen, Xiaohong title = Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study date = 2019-01-08 keywords = China; virus summary = title: Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Similarly, the positive rate of cases with a single virus infection was highest in the young children (65.5%) and lowest in adults of 18-60 years of age (38.5%). The proportion of respiratory viruses notably differed across different age groups; the virus positive rate was the highest in young children under 5 years but was lowest in adults (18~60 years) in this study. Therefore, all positive RhV and/or EV specimens and 10 FluA virus specimens with random selection were identified Table 2 Age distribution of viruses from outpatients with ARIs ARIs, acute respiratory infections by sequencing assay, respectively, and among them, four RhV positive and 3 EV positive specimens were not sequenced due to low viral load in the specimens. In summary, this study provides important epidemiologic data regarding the clinical characteristics, viral spectrum, age distribution and seasonality of viruses in outpatients with ARIs in Huzhou, China. doi = 10.1186/s12879-018-3668-6 id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 keywords = BALB; C57BL/6; Control; Fig; Helicobacter; LCMV; MHV; PCR; SCID; animal; cell; complication; diagnosis; disease; dna; infection; laboratory; medicine; mouse; sign; strain; virus summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. doi = 10.1016/b978-0-12-409527-4.00003-1 id = cord-341765-ml6eo8r3 author = Widhidewi, Ni Wayan title = Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia date = 2020-03-25 keywords = ARTI; respiratory; virus summary = title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In this study, throat swab specimens were collected from patients with respiratory symptoms to identify viral etiological agents of ARTI. Singleplex PCR assays were used for detection of a panel of respiratory viruses using family-level primers for Paramyxoviridae, Herpesviridae, Coronaviridae, Hantaviridae, Adenoviridae, Arenaviridae; genus-level primers for Enterovirus, Henipavirus, Influenza A virus, Bocavirus; and Pneumovirinae sub-family primer including respiratory syncytial virus (RSV) and human metapneumovirus (HMPV). In addition to the influenza virus routinely screened in ARTI studies, other viral agents associated with severity like Herpesviridae, Enterovirus and RSV should be screened in respiratory illnesses. doi = 10.1099/acmi.0.000120 id = cord-263017-rh86g4jk author = Wigginton, Krista Rule title = Virus disinfection mechanisms: the role of virus composition, structure, and function date = 2011-12-09 keywords = inactivation; structure; virus summary = Non-culturable virus disinfection kinetics must be either determined with human charge studies or predicted using surrogate viruses that can be cultured in vitro but that differ in composition, structure, and function. Coupling structure and composition information aids in our understanding of virus reactivity X-ray crystal structures have been published for numerous enteric viruses [25,26 ,27] and with these reports have come a windfall of valuable information including the location and orientation of capsid protein residues. Specific questions include: 1) Which virus protein residues are involved with fundamental functions and how do these vary amongst different strains and species; 2) What specific chemical modifications take place in the genome and capsid during disinfection and what effects do these modifications have on virus structure and function; 3) How similar are disinfectant-induced modifications amongst various enteric viruses? doi = 10.1016/j.coviro.2011.11.003 id = cord-278465-tjjkz16y author = Wille, Michelle title = Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date = 2017-03-18 keywords = IAV; virus summary = Recent studies have been instrumental in starting to describe dynamics and ecology of AMPV-1 and CoV in wild birds; 9-12% of migrating Mallards have CoV infections, compared to a lower prevalence (2%) of AMPV-1 towards the end of the migratory season in Sweden (Tolf et al., 2013b; Wille et al., 2015) . In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting. In comparing prevalence [Sept-Dec] between our urban dataset and a wild bird dataset from southern Sweden using the same qPCR methods (Wille et al., 2015) , autumnal prevalence for IAV (p b 0.0010) and CoV (p b 0.0010) is significantly different, where prevalence for both these viruses is lower in urban Mallards (Fig. 2) . doi = 10.1016/j.meegid.2017.03.019 id = cord-302047-vv5gpldi author = Willemsen, Anouk title = On the stability of sequences inserted into viral genomes date = 2019-11-14 keywords = Gene; RNA; genome; insert; stability; virus summary = Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Viruses genera covered in relevant studies Conclusions of this review All viruses • Inserted sequences are often unstable and rapidly lost upon passaging of an engineered virus • The position at which a sequence is integrated in the genome can be important for stability • Sequence stability is not an intrinsic property of genomes because demographic parameters, such as population size and bottleneck size, can have important effects on sequence stability • The multiplicity of cellular infection affects sequence stability, and can in some cases directly affect whether there is selection for deletion variants • Deletions are not the only class of mutations that can reduce the cost of inserted sequences, although they are the most common I: dsDNA doi = 10.1093/ve/vez045 id = cord-337659-x4oywbrj author = Wilson, Brenda A. title = Global biosecurity in a complex, dynamic world date = 2008-07-31 keywords = BSE; HIV; U.S.; disease; food; human; virus summary = Although one might argue that the principal difference in the infectious disease threat today versus say 10, 25, or 50 years ago is bioterrorism, the resources spend on preparing for a bioterror attack is viewed by most scientists as grossly exorbitant [6] , particularly considering the small numbers of individuals who have been or could be affected by this type of attack and considering the relatively low medical relevance or prevalence of the diseases caused by the limited number of highpriority bioterror bioagents, the socalled ''''category A select agents.'''' And, while admittedly the preparedness and surveillance measures put in place for one has certainly helped to protect against the other (the improved global response to and curtailment of SARS coming after the anthrax bioterrorist attacks is a prime example of this), most scientists feel that the limited resources available from an already overburdened system should instead be used for studying and preparing against the looming and potentially more devastating infectious disease threats from natural or accidental exposure [7] , which could affect millions of people and animals and could have huge health and economic consequences. doi = 10.1002/cplx.20246 id = cord-281332-5mddyv0n author = Wilson, Michael R. title = A novel cause of chronic viral meningoencephalitis: Cache Valley virus date = 2017-07-25 keywords = CVV; Cache; Valley; patient; virus summary = Interpretation: Cache Valley virus, a mosquito-borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Here, we report the effective deployment of metagenomic next generation sequencing (mNGS) to diagnose Cache Valley virus (CVV), a mosquito-borne orthobunyavirus, 4 in an Australian patient with a primary immunodeficiency suffering from chronic meningoencephalitis. 41 Because CVV is rarely identified as a cause of human disease and has not been reported in Australia previously, there are no traditional candidate-based diagnostic tests for this virus available in Australia. doi = 10.1002/ana.24982 id = cord-018463-a6qu0cuv author = Wimmer, Eckard title = Synthetic Biology, Dual Use Research, and Possibilities for Control date = 2018-03-23 keywords = agent; virus summary = The anthrax attack coincided with the first report in 2002 of the de novo synthesis in the test tube of a pathogenic human virus, poliovirus, that was equally shocking because it indicated that dangerous infectious agents could be produced in laboratories outside of government control. These events were synchronous with the advent of a new discipline, Synthetic Biology, which was an emerging area of research that can broadly be described "as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems." The synthesis of viruses, or more broadly expressed: each experiment in Synthetic Biology, fits the definition of "Dual Use Research" – the dual use dilemma in which the same technologies can be used for the good of humans and misused for bioterrorism. doi = 10.1007/978-94-024-1263-5_2 id = cord-350151-s75d1hat author = Wiramus, S. title = Rianimazione e influenza grave: pandemia influenzale A (H1N1) date = 2013-04-30 keywords = H1N1; dei; pazienti; virus summary = A causa delle mutazioni costanti dei virus influenzali, la composizione del vaccino è generalmente diversa da un anno all''altro: ogni anno, l''Organizzazione Mondiale della Sanità (OMS) emette una raccomandazione sui ceppi che devono essere inclusi nel vaccino. • personale paramedico e medico: rischio importante di riduzione del personale disponibile negli ospedali e rischio maggiore di infettare dei pazienti fragili; • donne gravide: rischio elevato di complicanze gravi e di morte; • bambini di meno di 6 mesi e persone che se ne occupano; • persone da 6 mesi a 24 anni; • persone da 25 a 64 anni che hanno delle comorbilità: enfisema polmonare, broncopneumopatia cronica ostruttiva (BPCO), asma, obesità patologica, insufficienza cardiaca, diabete instabile, immunodepressione e malattie neurologiche. Solo i soggetti poco o non immuni nei confronti del virus sono suscettibili di essere colpiti in questa maniera ed è per questo che la vaccinazione contro l''influenza stagionale sembra conferire una protezione contro queste forme più gravi [6] . doi = 10.1016/s1283-0771(13)64502-8 id = cord-325915-dw989txm author = Wolf, Michael W title = Downstream processing of cell culture-derived virus particles date = 2014-01-09 keywords = dna; high; membrane; particle; process; purification; vector; virus summary = The number of publications [24, [38] [39] [40] [41] [42] [43] [44] [45] [46] and patents [301] [302] [303] describing the purification or concentration of virus particles by centrifugation methods demonstrates that these procedures are extensively used at industrial-and small-scale levels for viral vectors and vaccine production processes. In summary, the main advantages of ultrafiltration compared with other methods are their high-throughput and (for the concentration of active virus particles) the gentle processing at optimal operating conditions [43, 47] that results in improved efficacies for purification of viral vectors for gene therapy. Considering a complete purification train for the production of vaccines or gene therapy vectors (Figure 1) , current improvements of the dynamic binding capacities in chromatography media might facilitate the removal of the initial concentration step within the downstream process. doi = 10.1586/erv.11.111 id = cord-327660-p1b07b4t author = Wolf, Yuri I. title = Origins and Evolution of the Global RNA Virome date = 2018-11-27 keywords = Fig; RNA; SJR; branch; virus; ϪRNA summary = The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . doi = 10.1128/mbio.02329-18 id = cord-303186-2hxlx1j2 author = Won, Hokeun title = Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus date = 2019-07-09 keywords = Aram; PEDV; TCID; virus summary = In this study, we generated a cold-adapted live attenuated vaccine candidate (Aram-P29-CA) by short-term passage of a virulent PEDV isolate at successively lower temperatures in Vero cells. In this study, we sought to create a cold-adapted attenuated G2b PEDV low-passage strain by progressively decreasing growth temperatures to 32°C in Vero cells and then attempted to evaluate its protective efficacy on neonatal piglets against virulent PEDV challenge. Overall, the quantities of viruses in the feces of animals of group 2 significantly declined compared to those in group 1, with wide Ct ranges of 34.46-24.34 ( Efficacy of cold-adapted attenuated PEDV vaccine All animals in the parental Aram-P5-infected group were necropsied upon death at 4 or 5 DPI, while piglets in the remaining groups were euthanized at the end of the study for postmortem examinations (Fig. 7) . doi = 10.4142/jvs.2019.20.e32 id = cord-276364-zyw5aukk author = Wong, Ho Him title = Manipulation of autophagy by (+) RNA viruses date = 2019-08-08 keywords = DENV; HCV; RNA; autophagy; virus summary = Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. doi = 10.1016/j.semcdb.2019.07.013 id = cord-343963-99rd3o79 author = Wong, Mun-Teng title = Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date = 2014-12-29 keywords = HCV; IFN; NS5A; PKR; RNA; rig; table; virus summary = 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. doi = 10.1038/cmi.2014.127 id = cord-330647-w1bpeqzg author = Wong, Samson Sai-Yin title = Ebola virus disease in nonendemic countries date = 2015-05-31 keywords = EBOV; EVD; Ebola; FHF; Marburg; fever; virus summary = The largest outbreak of Ebola virus disease (EVD) in history has renewed interest in filoviruses and has provided an unprecedented impetus to the development of new therapeutics and vaccines for this highly lethal infection. Nucleic acid amplification is the diagnostic test of choice because of its high sensitivity (especially in the early phase of illness); its ability to differentiate between different agents of viral hemorrhagic fever; and its relatively lower biohazard, if the viruses are appropriately inactivated; and because antigen and antibody assays are often unavailable in laboratories in nonendemic countries. 119e123 Animal studies also demonstrate the efficacy of favipiravir in the treatment of Junín virus, arenavirus, and EBOV hemorrhagic fevers, and the drug was used to treat human EVD in the 2014 West African epidemic. doi = 10.1016/j.jfma.2015.01.012 id = cord-293387-0m1ngob3 author = Wood, A. title = The action of three antiseptics/disinfectants against enveloped and non-enveloped viruses date = 1998-04-30 keywords = virus summary = Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidme and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Four antiseptic/disinfectant solutions with chloroxylenol, benzalkonium chloride, cetrimide/ chlorhexidine and povidone-iodine were also assessed for antiviral effect against human immunodeficiency virus in the presence of whole human blood. Virucidal activity of the antiseptic/disinfectants in the presence of albumin/ yeast extract The virucidal activity of Dettol, Dettol Hospital Concentrate and Savlon was compared to that of water of standard hardness against all the test viruses. The exception was Dettol Hospital Concentrate (active agent benzalkonium chloride) which was effective in the inactivation of the non-enveloped human coxsackie virus with a reduction of >5 log,,, after the 1 min timepoint. In conclusion, the solutions tested at their recommended concentrations for antiseptic use were very effective in inactivating the non-enveloped viruses, human immunodeficiency virus type 1 and herpes simplex virus type 1 in the presence of significant levels of organic soil. doi = 10.1016/s0195-6701(98)90077-9 id = cord-009846-o6wj8z6e author = Wroblewska, Zofia title = Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells date = 2005-12-06 keywords = TOC; virus summary = title: Rat tracheal organ culture supports replication of parainfluenza 1 (6/94) virus and promotes 6/94 virus rescue from latently infected human brain cells For example, Cytochalasin treatment of indicator cells has been shown to enhance the rescue of 6/94 virus from latently infected human brain cells [Wroblewska et al, 19781 after cocultivation. For these reasons, we decided to study the replication of 6/94 virus in rat TOC and to determine its applicability for rescue of 6/94 virus from latently infected human brain cell cultures. The ability of rat TOC to promote 6/94 virus rescue from latently infected human brain cells is shown in Table 1 . Transfer of rat TOC that had been cocultivated with normal human brain cells to CV, cells did not result in 6/94 virus detection. TOC provides a favorable growth environment for a large number of viruses as well as a system that is capable of rescuing virus from latently infected human brain cells. doi = 10.1002/jmv.1890030204 id = cord-337673-1nau263l author = Wu, Chang-Jer title = Antiviral applications of RNAi for coronavirus date = 2006-01-24 keywords = RNA; SARS; viral; virus summary = Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . doi = 10.1517/13543784.15.2.89 id = cord-309635-1tgovkr7 author = Wu, Nicholas C. title = Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure date = 2020-09-22 keywords = RBS; influenza; virus summary = Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Similarly, RBS of influenza B HA is composed of the 140-loop, 190-helix, and 240-loop, which are structurally equivalent to the 130-loop, 150-loop, and 190-helix Receptor specificity can also continue to evolve when seasonal viruses circulate in the human population, due to natural mutations that are likely a response to immune selection pressure. A broadly neutralizing human monoclonal antibody that recognizes a conserved, novel epitope on the globular head of the influenza H1N1 virus hemagglutinin Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin Design of nanoparticulate group 2 influenza virus hemagglutinin stem antigens that activate unmutated ancestor B cell receptors of broadly neutralizing antibody lineages doi = 10.3390/v12091053 id = cord-268645-5op2m7pu author = Wu, Zhiqiang title = Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date = 2015-08-11 keywords = SARS; Supplementary; Table; bat; virus summary = However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) . doi = 10.1038/ismej.2015.138 id = cord-307632-x9bxnrtn author = Wu, Zhiqiang title = Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases date = 2018-10-03 keywords = China; additional; rodent; table; virus summary = Five virus strains identified from Microtus clarkei, Eothenomys inez, Eothenomys melanogaster, Myodes rufocanus, and Cricetulus longicaudatus in five provinces appeared to be closely related to porcine reproductive and respiratory syndrome virus (PRRSV) with higher sequence similarity than those with other members of the family Arteriviridae (60.1-73.7% versus 25.7-54.2% aa identity for ORF1b, compared with equine arteritis virus, lactate dehydrogenase-elevating virus (LDV) of mice, simian hemorrhagic fever virus, and wobbly possum disease virus; Additional file 1: Table S6 ). Pairwise similarity and phylogenetic analysis ( Fig. 5a and Additional file 3: Figure S6 ) revealed that 29 viruses formed diverse evolutionary clades in lineage A under the genus Betacoronavirus, with sequence identities between 88.1 and 98.9% (RdRp aa identity). doi = 10.1186/s40168-018-0554-9 id = cord-354035-i3sl2r0k author = Wylie, Kristine M. title = The Virome of the Human Respiratory Tract date = 2016-12-10 keywords = HTS; PCR; virus summary = Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. However, as characterization of the respiratory tract virome using molecular methods is a relatively new area of exploration, these studies can be useful in order to determine if viruses beyond the common, known respiratory pathogens are detected. In a study of 71 patients, viruses were assessed in nasal swabs using a panel of targeted PCR assays for common respiratory pathogens. Another study tested 89 nasopharyngeal swabs from adults with upper respiratory tract infections using reverse transcription (RT)-PCR assays for a series of common viruses, including human rhinoviruses, coronaviruses, influenza viruses and others, and by RNA sequencing. doi = 10.1016/j.ccm.2016.11.001 id = cord-352200-i05h8csb author = Xu, Yi title = Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date = 2012-04-27 keywords = RNA; SRBSDV; WBPH; gene; virus summary = title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. doi = 10.1371/journal.pone.0036238 id = cord-262748-v4xue7ha author = Xu, Yongtao title = Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date = 2015-12-04 keywords = SVM; peptide; protein; virus summary = Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The predictive support vector machine model for selfderived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process. In view of the important role of E proteins in virus fusion process and common mechanism of action of self-derived peptides, we developed a SVM model to predict the antiviral activities of self-derived peptides using sequence-based statistical scores as input features. Because similar sequences are often associated with similar structure and function, the sequence-based property AVPalign would account for the activities of the self-derived peptide inhibitors which regulate the virus fusion by mimicking the binding to E proteins. The prominent performance of EAPscoring model indicates the sequence-based stability feature of self-derived peptides may reflect their potential of binding to E proteins so as to regulate the virus entry process. doi = 10.1371/journal.pone.0144171 id = cord-018706-gykw2nvt author = Yadav, Mahendra Pal title = Emerging and Transboundary Animal Viral Diseases: Perspectives and Preparedness date = 2020-02-23 keywords = FMD; H5N1; India; OIE; animal; disease; virus summary = The factors driving the emergence of different emerging infectious disease (EID) interfaces include global travel, urbanisation and biomedical manipulations for human EIDs; agricultural intensification for domestic animal EIDs; translocation for wildlife EIDs; human encroachment, ex situ contact and ecological manipulation for wildlife–human EIDs; encroachment, new introductions and ''spill-over'' and ''spill-back''; and technology and industry for domestic animal–human EIDs. The concepts of sanitary and phytosanitary (SPS) measures and biosecurity have gained recognition globally in almost all the realms of human activities, including livestock health and production management. Among the TADs having zoonotic manifestations, a number of infectious diseases, such as highly pathogenic avian influenza (HPAI), BSE (Mad cow disease caused by prion), West Nile fever, Rift Valley fever, SARS coronavirus, Hendra virus, Nipah virus, Ebola virus, Zika virus and CCHF, to name a few, adversely affecting animal and human health have been in the news in recent times (Malik and Dhama 2015; Munjal et al. doi = 10.1007/978-981-15-0402-0_1 id = cord-276052-gk6n8slx author = Yadav, Pragya title = Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date = 2016-09-09 keywords = India; Pteropus; bat; virus summary = During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line. doi = 10.1016/j.meegid.2016.09.010 id = cord-014908-jys1y0k9 author = Yadav, Rakesh title = Trends and Perspectives of Biosensors for Food and Environmental Virology date = 2010-05-19 keywords = RNA; biosensor; detection; dna; virus summary = Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions. doi = 10.1007/s12560-010-9034-5 id = cord-010189-makhaypd author = Yamashita, Teruo title = VI, 3. Molecular biology and epidemiology of Aichi virus and other diarrhoeogenic enteroviruses date = 2004-09-14 keywords = Aichi; Yamashita; virus summary = Stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were examined for variation, based on their reactivity with a monoclonal antibody raised against the standard strain (A486/88) and on reverse transcription–polymerase chain reactions (RT-PCR) of three genomic regions. Aichi virus was isolated in Vero cells from 7 (12.5%) of 56 patients in 6 gastroenteritis outbreaks, 5 (0.7%) of 722 Japanese travelers returning from tours to Southeast Asian countries and complaining of gastrointestinal symptoms at the quarantine station of Nagoya International Airport in Japan, and 5(2.3%) of 222 Pakistani children with gastroenteritis (Yamashita et al., 1993; Yamashita et al., 1995) . In the ELISA, 15 (26.8%) of 56 stool samples from adult patients in six oyster-associated gastroenteritis outbreaks were found to be positive for Aichi virus. The Aichi virus RNA was detected in 54 (55%) of 99 fecal specimens from patients in 12 (32%) of 37 outbreaks of gastroenteritis in Japan. doi = 10.1016/s0168-7069(03)09040-2 id = cord-277107-gs7j6fxo author = Yamin, Mohammad title = Counting the cost of COVID-19 date = 2020-05-13 keywords = COVID-19; cause; pandemic; virus summary = Coronavirus disease 2019 (COVID-19) is the name given by the World Health Organization (WHO) to the highly contagious and infectious disease caused by the Novel Corona Virus or SARS-CoV-2, which was first reported on 31 December 2019 in Wuhan city of the capital of China''s Hubei province. In recent years we have witnessed an increased growth and spread of communicable and highly contagious viruses and diseases like EBOLA [3] , HIV Aids [4] , Swine Influenza (H1N1, H1N2) [5] , various strands of Flu [6] , Severe Acute Respiratory Syndrome (SARS) [7] and Middle Eastern Respiratory Syndrome (MERS) [8] in Africa, the Middle East and several other parts of the world. The coronavirus disease COVID-19 is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ( Fig. 1) , which is resulting in a heavy toll on people''s lives and colossal economic damage. doi = 10.1007/s41870-020-00466-0 id = cord-308385-bcph664h author = Yan, Zishuo title = Modeling COVID-19 infection in a confined space date = 2020-07-15 keywords = Fig; virus summary = In our model, states of individuals with diverse physiological conditions are subject to dynamic changes according to their interaction with viruses in a closed environment, where spatial factors play an essential role in that the spreading of the virus and the infection of human are tightly correlated in both space and time. Based on the SEIR model, Joseph T Wu [7] estimated the basic regeneration number as 2.68 and the doubling time as 6.4 days; Qun Li [18] analyzed data on the first 425 confirmed cases in the early stage and found that the epidemic is doubled in size every 7.4 days with a mean serial interval of 7.5 days. Through the newly constructed virus infection model, we provide useful guidance for effective prevention and control of the COVID-19 spreading, such as restricting the movement of people and placing the ventilation opening in the right position, reducing the releasing of the virus and the contact of susceptibles with unfriendly environment. doi = 10.1007/s11071-020-05802-4 id = cord-254090-x8tnweih author = Yang, Szu-Chi title = Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses date = 2015-12-09 keywords = Fig; H3N2; microwave; virus summary = It is interesting to notice that the required threshold electric field magnitudes at the resonant frequency (86.9 V/m) to fracture H3N2 viruses as shown in Fig. 3 (c) are within the IEEE Microwave Safety Standard (106 V/m), indicating high SRET efficiency, even though the quality factor of the H3N2 virus is low. To further investigate the efficiency of this SRET effect from microwave to virus and the threshold effect, we further measured the inactivation ratio of H3N2 virus with different power densities at the resonant frequency ~8 GHz of the confined acoustic dipolar mode. Second, at the resonant frequency, we do observe H3N2 virus inactivation by illuminating 82 W/m 2 (lower than the IEEE safety standard in public space) 8 GHz microwaves on our viral solution, corresponding to an average 87 V/m electric field intensity inside the solution, confirming that our proposed simple model to estimate the field threshold (86.9 V/m) to structurally fracture the virus is quantitatively correct, especially combining the observed threshold effect as discussed above. doi = 10.1038/srep18030 id = cord-355259-779czzzx author = Yang, Xiaoyun title = A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date = 2014-10-15 keywords = Fig; SIV; mucus; virus summary = Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract. To this purpose, we applied swine influenza virus to a model we previously set up using porcine respiratory mucus, pseudorabies virus (PRV) and single particle tracking (SPT) [20] . This does not only confirm the beneficial effect of neuraminidase on releasing SIV from respiratory mucus, but also highlights bidirectional synergistic interactions between influenza virus and bacterial infections. doi = 10.1371/journal.pone.0110026 id = cord-297662-slmlhqnb author = Yap, Sally S. L. title = Dengue Virus Glycosylation: What Do We Know? date = 2017-07-25 keywords = DENV; NS1; virus summary = In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement doi = 10.3389/fmicb.2017.01415 id = cord-322748-a5131tv9 author = Yates, Mary K. title = Flex-nucleoside analogues – Novel therapeutics against filoviruses date = 2017-06-15 keywords = EBOV; virus summary = Most recently GS-5734, a monophosphoramidate prodrug adenosine analogue which targets EBOV RNA-dependent RNA polymerase (RdRp), exhibited very potent activity against both EBOV and MARV, 17, 18 further demonstrating the potential for finding effective nucleoside inhibitors of filoviruses. After the successful synthesis of the three Flex-analogues 1, 2, and 3, the compounds were screened against a panel of filoviruses including EBOV, MARV, and SUDV, as well as other hemorrhagic fever viruses such as Lassa and Rift Valley Fever. The second series of assays utilized Huh7 cells infected with recombinant reporter EBOV, Lassa, and Rift Valley Fever viruses. Within this study we found that both compounds 1 and 3 exhibited antiviral activity against a recombinant reporter EBOV in Huh7 cells, though surprisingly the McGuigan prodrug was 10-fold less potent (EC 50 = 2.2 ± 0.3 lM and 27.2 ± 2.2 lM respectively). doi = 10.1016/j.bmcl.2017.04.069 id = cord-003961-gs75ebo4 author = Yin, Xin title = Hepatitis E Virus Entry date = 2019-09-20 keywords = HEV; ORF3; virus summary = doi = 10.3390/v11100883 id = cord-255137-utg8k7qs author = Yinda, Claude Kwe title = Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date = 2019-01-23 keywords = Cameroon; Fig; bat; cameroonian; human; strain; virus summary = Previously, we identified a plethora of known and novel eukaryotic viruses in Cameroonian fruit bats using a viral metagenomics approach, including viruses known to cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) and Astroviridae (Mamastrovirus), Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viral families known to cause gastroenteritis in humans, were identified in both bat and human pools from the same region. In this study, we focused on viruses from which near-complete genomes were obtained, particularly those that are known to cause viral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovirus] , Picornaviridae [enterovirus, parechovirus, cosavirus] , Parvoviridae, Reoviridae, and Adenoviridae [human mastadenovirus]). Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon (20) (21) (22) (23) 63) and showed the presence of many novel and divergent eukaryotic viral families, including viruses known to cause gastroenteritis in humans. doi = 10.1128/msphere.00585-18 id = cord-307813-elom30nx author = Yip, Tsz-Fung title = Advancements in Host-Based Interventions for Influenza Treatment date = 2018-07-10 keywords = IAV; IFN; TNF; cell; infection; influenza; viral; virus summary = Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. A recent study using RNAi also demonstrated that cholesterol homeostasis can be regulated via acid phosphatase 2 (ACP2)-mediated Niemann-Pick C2 activity and impaired the membrane fusion of IAV and influenza B virus (IBV) (52) , further suggesting the importance of controlling cholesterol homeostasis in the release of viral genome to cytoplasm. Furthermore, FPR2 antagonists have been described to possess antiviral activity against not only IAV but also IBV infection (111) , promoting the idea that antagonizing FPR2 to suppress Raf/MEK/ERK signaling cascade could potentially be a novel approach for the treatment of a broad spectrum of influenza viruses. doi = 10.3389/fimmu.2018.01547 id = cord-252466-usrpodjx author = Yun, Nadezhda E. title = Pathogenesis of Lassa Fever date = 2012-10-09 keywords = LASV; Lassa; RNA; fever; virus summary = Apparently, failure to develop the cellular immune response that would control dissemination of LASV, which is indicated by high serum virus titers, combined with disseminated replication in tissues and absence of neutralizing antibodies, leads to the development of fatal Lassa fever [64] . Downregulation of immune responses caused by LASV infection demonstrated in vitro is also in agreement with the results of clinical observations showing that fatal outcome of Lassa fever correlates with low levels or absence of interleukin (IL) 8 and IFN inducible protein 10 (IP-10) in circulation [70] . These data indicate that T cells are essential for rapid resolution of LASV infection; however, if the host fails to control virus replication due to inadequate activation of the immune system, T lymphocytes may play a key role in Lassa fever pathogenesis. doi = 10.3390/v4102031 id = cord-272829-i4jh6bcn author = ZANETTI, A. R. title = Emerging and re‐emerging infections at the turn of the millennium date = 2010-01-04 keywords = disease; human; infectious; virus summary = Globalization changes promote the emergence of new infections and pandemics; international deliveries and travelling facilitate the dissemination of infectious agents; man‐induced environmental changes create new opportunities for contacts between species, leading to infections in aberrant hosts, including man; global warming enables insects, a major vector of pathogens, to thrive in more countries. What is more, a number of other factors promote not only the dissemination but also the emergence of new infectious diseases: intensive farming and breeding associated with crowding promote the development of foci of infection; global warming has modified the climate, making insects, a major vector of pathogens, able to thrive in countries where the climate was previously hostile; the exploitation of natural resources has produced environmental changes that create opportunities for new contacts between species leading to emergence of infections in new hosts. doi = 10.1111/j.1365-2516.2009.02174.x id = cord-292286-ygomb3oi author = Zakaryan, Hovakim title = Flavonoids: promising natural compounds against viral infections date = 2017-05-25 keywords = EGCG; HIV-1; activity; antiviral; virus summary = Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. The antiviral activity of flavones is known from the 1990s, when it was showed that the simultaneous application of apigenin with acyclovir resulted in an enhanced antiviral effect on herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) in cell culture [92] . Besides these DNA viruses, apigenin was found to exert antiviral effect against African swine fever virus (ASFV), by suppressing the viral protein synthesis and reducing the ASFV yield by 3 log [46]. Besides these viruses, EGCG has been found to exert antiviral activity against HCV by preventing the attachment of the virus to the cell surface and suppressing RNA replication steps [8, 15] . Antiviral activity of baicalin against influenza A (H1N1/ H3N2) virus in cell culture and in mice and its inhibition of neuraminidase doi = 10.1007/s00705-017-3417-y id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 keywords = CMV; Fig; HSV; Nipah; SARS; cell; human; infection; pneumonia; respiratory; virus summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. doi = 10.1007/978-0-387-68792-6_11 id = cord-340907-j9i1wlak author = Zarai, Yoram title = Evolutionary selection against short nucleotide sequences in viruses and their related hosts date = 2020-04-27 keywords = ZIKV; sequence; supplementary; virus summary = Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. Figure 3A and B depicts the average number of under-represented sequences of size m ¼ 3, 4, and 5 nucleotides, identified in few subsets of viruses in both the original and random variants of the virus. A sampling analysis that we performed (see Supplementary document, Section 2.8) suggests that the number of under-represented sequences identified in dsDNA viruses matches their genomic size, when compared with RNA viruses. To show that the correspondence between selection against short palindromic sequences in viruses and restriction sites cannot be explained by basic coding region features such as amino-acid content and order, codon usage bias and dinucleotide distribution, we also evaluated the overlap between restriction sites and common under-represented sequences of random variants of viruses. doi = 10.1093/dnares/dsaa008 id = cord-348867-c0xpzd4d author = Zhai, Jun-Qiong title = First complete genome sequence of parainfluenza virus 5 isolated from lesser panda date = 2017-01-30 keywords = PIV5; virus summary = In this study, a PIV5 variant (named ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Sequence alignment and genetic analysis revealed that ZJQ-221 shared a close relationship with a PIV5 strain of canine-origin (1168-1) from South Korea. In this study, a novel variant of PIV5 (designated as ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Fourteen samples were tested for the possible presence of three respiratory-related pathogens (including PIV5, canine distemper virus, and coronavirus) by RT-PCR according to previous studies [27, 28] . In summary, we have identified a novel PIV5 isolate in lesser panda and performed whole genome sequencing, indicating that this mammal may act as a possible natural reservoir for this virus. The complete genome sequencing and analysis of canine parainfluenza virus strain CC-14 doi = 10.1007/s00705-017-3245-0 id = cord-339885-mpzgrogd author = Zhan, Yangqing title = Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls date = 2014-09-02 keywords = cap; patient; virus summary = title: Respiratory virus is a real pathogen in immunocompetent community-acquired pneumonia: comparing to influenza like illness and volunteer controls In order to better understand the real role of respiratory virus in pneumonia and better manage the patients, we conducted a prospective observational study to reveal the viral etiology of adult CAP in Guangzhou, as compared with etiology of patients diagnosed with influenza like illness (ILI) and with volunteer controls. Obviously, considering the high prevalence of viral CAP in Guangzhou and influenza infection as an independent variable in the severe disease model, routine laboratory detection should be taken in hospitalized CAP patients at admission for an adequate diagnosis of respiratory viruses, especially influenza virus in severe individuals. Another question was that did all patients with viral community-acquired pneumonia, especially those without evidence of bacteria infection, need to be treated with antibiotics? doi = 10.1186/1471-2466-14-144 id = cord-319814-tyqb473m author = Zhang, Dingmei title = Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date = 2014-06-11 keywords = RSV; respiratory; virus summary = METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. doi = 10.1016/j.ijid.2014.02.019 id = cord-344782-ond1ziu5 author = Zhang, Jing title = Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date = 2018-10-24 keywords = PCR; RNA; River; sequence; virus summary = Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. doi = 10.1371/journal.pone.0205209 id = cord-299549-bjqwwzam author = Zhang, Lei title = Against Ebola: type I interferon guard risk and mesenchymal stromal cell combat sepsis date = 2015-01-01 keywords = Ebola; IFN; virus summary = When the viral infection proceeds to the terminal stage, the key factor would be applying a non-specific immune modulation approach to suppress the cytokine storm that causes multiple organ failure, in an attempt to open a time window for the host''s immune system to recover. In most patients, Ebola viral burden elevates by time and triggers an extremely strong immune attack-a phenomenon called ''cytokine storm'' (Sullivan et al., 2003) , during which monocytes and/or macrophages produce a massive amount of pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukins (ILs), and The virus burden, inflammatory response, and specific antibodies are the main contributors to different outcomes: mortality, survival, or symptomless infection (Fig. 2) , suggesting that the appropriate intervention strategy in each stage would accordingly be able to control the Ebola virus. Nonetheless, this phenomenon does give clues to the treatment against Ebola virus disease (EVD)-early activated innate immune responses may prevent the viral infection. doi = 10.1631/jzus.b1400365 id = cord-263785-0iift8zy author = Zhang, Xiaorong title = Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date = 2020-07-31 keywords = IBV; virus summary = title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. doi = 10.1186/s13567-020-00819-4 id = cord-317412-f3ua8ks3 author = Zhang, Xing title = Characterization of the lipidomic profile of BmN cells in response to Bombyx mori cytoplasmic polyhedrosis virus infection date = 2020-08-15 keywords = cell; lipid; virus summary = Here, the lipid metabolism in BmCPV-infected BmN cells was studied by lipidomics analysis. Our previous studies have found alterations in a large number of genes related to important signaling pathways, including those associated with innate immunity, development and metabolism following BmCPV infection [3, 5] . An increasing number of studies in recent years have demonstrated changes of lipid metabolism in host cells after virus infection. It has been shown that infection by some single-stranded RNA(ssRNA) viruses can alter the lipid metabolism and other biological processes of the host cells to facilitate the completion of the virus life cycle [11] . Analysis of differential expressed circRNAs has revealed changes in the metabolism of fatty acids upon BmCPV infection [5] . In addition, fatty acid metabolism has been observed to be significantly changed by the differentially expressed circRNAs in the midgut of silkworms infected by BmCPV [5] . doi = 10.1016/j.dci.2020.103822 id = cord-000539-uh3q65we author = Zhang, Yi title = Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date = 2012-01-03 keywords = ARDS; H1N1; mouse; virus summary = BACKGROUND: Acute respiratory distress syndrome (ARDS) induced by pandemic 2009 H1N1 influenza virus has been widely reported and was considered the main cause of death in critically ill patients with 2009 H1N1 infection. Mice infected with SD/09 virus showed typical ARDS symptoms characterized by 60% lethality on days 8–10 post-inoculation, highly edematous lungs, inflammatory cellular infiltration, alveolar and interstitial edema, lung hemorrhage, progressive and severe hypoxemia, and elevated levels of proinflammatory cytokines and chemokines. In the present mouse model, the number of leukocytes observed in the BALF of virus-infected mice significantly increased compared with the control mice on day 8 p.i. Different counts in BALF showed that the proportion of neutrophils dramatically increased. doi = 10.1371/journal.pone.0029347 id = cord-257652-ndt8f812 author = Zhang, Yong-Zhen title = The diversity, evolution and origins of vertebrate RNA viruses date = 2018-08-13 keywords = RNA; vertebrate; virus summary = In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. However, following the extensive use of PCR and the Sanger sequencing methods for virus identification over the past decade, the number of RNA viruses sampled from lower vertebrates has steadily increased [28] , with notable examples being arenavirus and paramyxoviruses in reptiles [29] , and novirhabdoviruses and other RNA viruses from fish [30] , although these numbers were still very limited compared to the viruses described in birds and mammals. doi = 10.1016/j.coviro.2018.07.017 id = cord-011438-imbpgsub author = Zhang, Yun title = Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date = 2020-03-29 keywords = IAV; IFN; Influenza; infection; virus summary = Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. Host innate immunity, including phagocytic cells, interferons (IFNs), proinflammatory cytokines, etc., applies multiple mechanisms in defending IAV infection [105] . Influenza A virus nucleoprotein induces apoptosis in human airway epithelial cells: Implications of a novel interaction between nucleoprotein and host protein Clusterin Antiviral response elicited against avian influenza virus infection following activation of toll-like receptor (TLR)7 signaling pathway is attributable to interleukin (IL)-1β production The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm Cell death regulation during influenza A virus infection by matrix (M1) protein: A model of viral control over the cellular survival pathway doi = 10.3390/v12040376 id = cord-348876-v55piprx author = Zhao, Guangyu title = An M2e-based multiple antigenic peptide vaccine protects mice from lethal challenge with divergent H5N1 influenza viruses date = 2010-01-18 keywords = H5N1; MAP; virus summary = In the present study, we designed a tetra-branched multiple antigenic peptide (MAP)-based vaccine, designated M2e-MAP, which contains the sequence overlapping the highly conserved extracellular domain of matrix protein 2 (M2e) of a HPAI H5N1 virus, and investigated its immune responses and cross-protection against different clades of H5N1 viruses. In the present study, we designed and synthesized a tetra-branched multiple antigenic peptide (MAP) derived from the M2e sequence of H5N1 virus VN/1194 strain, denoted as M2e-MAP, with an aim to develop a M2e-based vaccine for induction of M2e-specific immune responses and cross-protection of the vaccinated animals against lethal challenge of divergent H5N1 virus strains. After receiving the lethal dose (10 LD 50 ) of two H5N1 virus strains, the M2e-MAP vaccinated mice were further evaluated in terms of cross-protective ability by daily observation of the clinical symptoms, including weight loss and survival rate for two weeks, and then histopathological examination following removal of lung tissues. doi = 10.1186/1743-422x-7-9 id = cord-000902-ew8orn0z author = Zhao, Xiangyan title = Coevolution between simple sequence repeats (SSRs) and virus genome size date = 2012-08-30 keywords = additional; genome; ssr; virus summary = The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. While, relative abundance and relative density were examined to make the SSRs comparison parallel among differently sized species genomes; principal component analysis (PCA) was designed to investigate which repeat class(es) made a greater contribution to the variance among virus species as well as the relationships between repeat classes. Therefore, the 257 genome sequences were selected as samples for the analysis of relationship between SSRs distribution and genome size in the level of the whole virus. We surveyed the distribution of different SSR classes in virus genomes to investigate the relationship between repeat classes (mono-, di-, tri-, tetra-, penta-and hexa-) and genome sequence length. Coevolution between simple sequence repeats (SSRs) and virus genome size doi = 10.1186/1471-2164-13-435 id = cord-321112-w7x1dkds author = Zhao, Xuesen title = IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date = 2019-01-08 keywords = IAV; IFITM3; virus summary = Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Similar to many other host defense genes that evolve under the selective pressure of microorganism infection, IFITM genes evolved in an accelerated speed in vertebrates and many single-nucleotide polymorphisms (SNPs) have been identified in the human population, some of which have been associated with severity and prognosis of viral infection (e.g., influenza A virus). Among the number of single-nucleotide polymorphisms (SNPs) in IFITM3 gene that have been identified in human populations, several are associated with disease severity and prognosis of influenza A virus (IAV) and other viral infections (Everitt et al., 2012; Zhang et al., 2015; Xu-Yang et al., 2016; Allen et al., 2017) . doi = 10.3389/fmicb.2018.03228 id = cord-355535-01h8yyqj author = Zheng, Xue-yan title = Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review date = 2018-01-11 keywords = RSV; virus summary = The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study. doi = 10.1007/s00705-017-3700-y id = cord-025181-eg108wcd author = Zheng, Zhihang title = Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date = 2020-05-25 keywords = DENV-2; IFN; RNA; pfu; virus summary = In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. Further, we compared the infectivity of these two viral variants in a self-limited infection model, in which type I IFN receptor of wild-type Balb/c mice had been transiently blocked before infection, and found only the virus strain exhibiting larger plaque size caused infectious viral particles in sera. We have recently developed a ZIKV infection model in Balb/c mice with transient blockage of type I IFN Fig. 2 Phylogenetic analysis of DENV-2 1D4-5-SP and DENV-2 8H2-7-LP with representative serotype-2 dengue viruses of different genotypes isolated from different geographical regions. doi = 10.1007/s12250-020-00229-y id = cord-270911-z637eh2z author = Zhou, Jie title = Differentiated human airway organoids to assess infectivity of emerging influenza virus date = 2018-06-26 keywords = H7N9; human; virus summary = title: Differentiated human airway organoids to assess infectivity of emerging influenza virus airway organoid | proximal differentiation | influenza virus | infectivity I nfluenza A viruses (IAVs) can infect a diversity of avian and mammalian species, including humans, and have the remarkable capacity to evolve and adapt to new hosts (1) . Current in vitro models for studying influenza infection in the human respiratory tract involve shortterm cultures of human lung explants and primary airway epithelial cells. We chose to compare the infectivity of H7N2 with that of H7N9/Ah in the PD organoids as a proof of concept, to verify that the differentiated AOs can indeed simulate human airway epithelium in the context of influenza virus infection. Fig. 4 shows that viral loads in the cell lysate and medium of H7N9/ Ah-infected organoids increased gradually after inoculation; the viral titer increased more than 3 log 10 units within 24 h, indicating a robust viral replication. doi = 10.1073/pnas.1806308115 id = cord-255075-6azu6k3h author = Zhuang, Jianjian title = Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date = 2020-05-12 keywords = HIV; chip; detection; virus summary = Multiplexed efficient on-chip sample preparation 613 and sensitive amplification-free detection of Ebola virus A bead-based 689 immunofluorescence-assay on a microfluidic dielectrophoresis platform for rapid dengue virus 690 detection Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable 770 An integrated self-driven microfluidic device for rapid 781 detection of the influenza A (H1N1) virus by reverse transcription loop-mediated isothermal 782 amplification Paper-based RNA detection and 785 multiplexed analysis for Ebola virus diagnostics Multiplex microfluidic paper-based 805 immunoassay for the diagnosis of hepatitis C virus infection Simultaneous and automated detection of influenza A virus hemagglutinin H7 and H9 based on 965 magnetism and size mediated microfluidic chip A 1026 point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute D: Schematic of a 1149 paper-based chip for the detection of HIV developed by Li et al. doi = 10.1016/j.bios.2020.112291 id = cord-264916-c4n0kyog author = Zimmerman, Keith title = Natural protection of ocular surface from viral infections – a hypothesis date = 2020-07-09 keywords = SARS; infection; ocular; virus summary = A pandemic outbreak of a viral respiratory infection (COVID-19) caused by a coronavirus (SARS-CoV-2) prompted a multitude of research focused on various aspects of this disease. In this work, we discuss the significance of natural protective factors related to anatomical and physiological properties of the eyes and preventing the deposition of large number of virus-loaded particles on the ocular surface. Specifically, we advance the hypothesis that the standing potential of the eye plays an important role in repelling aerosol particles (microdroplets) from the surface of the eye and discuss factors associated with this hypothesis, possible ways to test it and its implications in terms of prevention of ocular infections. This hypothesis could be tested by measuring the electrical charge of bioaerosol generated by normal breathing in healthy subjects and in patients with viral infections caused by different viruses, causing respiratory infections or with suspected aerosol transmission pathway. doi = 10.1016/j.mehy.2020.110082 id = cord-284523-lknyehsa author = da Mata, Élida Cleyse Gomes title = Antiviral activity of animal venom peptides and related compounds date = 2017-01-06 keywords = CD4; HIV; HIV-1; cell; peptide; virus summary = This review provides a panorama of peptides described from animal venoms that present antiviral activity, thereby reinforcing them as important tools for the development of new therapeutic drugs. Synthetic hybrid peptides, namely cecropin A (1-8)-magainin 2 (1-12), exhibited potent antiviral activity by a mechanism mainly based on the compound hydrophobicity and α-helical content, inhibiting the virushost cell fusion [85] (Table 2) . Other peptides from marine sponges that inhibit HIV-1 entry into host cells are: callipeltin A, isolated from sponges of the genus Callipelta, which displayed antiviral activity with a high selectivity index (29) between the virus and host cells (SI ratio 50% cytotoxic dose [CD 50 ]/ED 50 ) [109] ; celebesides A-C from Siliquariaspongia mirabilis [108] ; neamphamide A, from Neamphius huxleyi, a compound with structural similarities to callipeptins and papuamides that exhibited low toxicity to host cells and a selectivity index above 10 [110] ; and microspinosamide, isolated from Sidonops microspinosa [111] . doi = 10.1186/s40409-016-0089-0 id = cord-350925-1h6pbfwp author = da Silva, Priscilla Gomes title = Airborne spread of infectious SARS-CoV-2: moving forward using lessons from SARS-CoV and MERS-CoV date = 2020-10-08 keywords = MERS; SARS; virus summary = Transmission of viruses through air can happen via droplets or aerosols generated during coughing, sneezing, talking, singing or breathing (Jones and CoV-2 is that most studies performed only focused on the detection of viral RNA and do not correlate to the infectivity of these viral particles. Therefore, in this systematic review, the viability/stability of aerosols containing SARS-CoV and MERS-CoV viruses will be discussed to provide information on potential mitigation strategies for SARS-CoV-2 airborne transmission. The presence of MERS-CoV was also confirmed by RT-PCR of viral cultures of 4 out of 7 air samples from two hospitals in South Korea (Kim et al., 2016) , and showed to be very stable in aerosol at 20°C and 40% relative humidity (van Doremalen et al., 2013) . doi = 10.1016/j.scitotenv.2020.142802 id = cord-259233-smmhhroe author = de Armas‐Rillo, Laura title = Membrane dynamics associated with viral infection date = 2016-01-28 keywords = ESCRT; HIV-1; RNA; figure; viral; virus summary = Several RNA viruses induce the formation of these autophagosome-like vesicles (also referred to as DMVs) to enhance viral replication and non-lytic egression, such as poliovirus and CVB3, HIV-1 and HCV. Indeed, autophagosome-like vesicles may represent a trafficking pathway for these viruses, connecting to multivesicular bodies (MVBs), and assuring virus assembly and budding at the cell surface while protecting them from intrinsic antiviral factors and immune responses. Trogocytosis involves the exchange of cell surface membrane patches that may contain receptor clusters associated to viral particles, while exosomes are vesicles formed from MVBs that could participate in viral infection and spreading between cells of the Alphavirus group of this family [12] , couple their RNA synthesis to endosome and lysosome membranes modified by the association of virus specific components. It remains unclear how proteins from distinct viruses and host cells use the same intracellular membrane compartments or events (e.g. autophagy) to achieve viral replication, without affecting important cellular processes. doi = 10.1002/rmv.1872 id = cord-289593-81vu2kbu author = de Blic, J. title = Interactions micro-organismes et voies aériennes distales : spécificités pédiatriques date = 2017-03-03 keywords = VRS; des; virus summary = Les relations entre bronchiolites virales et asthme, la place des virus à tropisme respiratoire dans l''histoire naturelle de l''asthme ont fait l''objet de nombreuses études, d''abord concentrées sur le virus respiratoire syncytial humain (hVRS) et plus récemment sur le rhinovirus humain (hRV). D''autres IAV aviaires ont pu contaminer l''homme ces dernières années, mais c''est du porc en 2009 qu''une pandémie grippale a éclos avec un virus influenza A triple réassortant (H 1 N 1pdm09 ), heureusement d''une pathogénicité moindre que celle imaginée lors des premières transmissions au Mexique puis de son expansion pandémique dans l''hémisphère sud [3] . En effet, à partir de la cohorte Childhood Origins of ASThma (COAST) constituée de 285 nouveau-nés, ayant au moins un parent atopique (1 Prick test positif) et/ou asthmatique, les auteurs ont évalué la prévalence des manifestations sifflantes dans les 6 premières années de la vie, en regard des antécédents de bronchiolite à VRS et à hRV [17, 28] . doi = 10.1016/j.rmr.2016.02.012 id = cord-256510-orr2roxz author = de Castro, Isabel Fernández title = Virus factories: biogenesis and structural design date = 2012-10-04 keywords = Fig; RNA; virus summary = For example, transmission electron microscopy (TEM) of cells infected with coxsackievirus showed intracellular organized lattices (Fig. 1E) , very similar to those assembled by the viral RNA polymerase in vitro (Kemball et al., 2010) close relationship between self-interaction and replication activity is reported for viral polymerases of other viruses such as FHV (Dye et al., 2005) , hepatitis C virus (Qin et al., 2002) and RUBV (Risco et al., 2012) . For viral genome replication, the virus first assembles cytoplasmic mini-nuclei with attached mitochondria (Tolonen et al., 2001) ; virus morphogenesis then starts an aggresome-like structure (Risco et al., 2002) , where immature viruses assemble using an atypical membrane remodelling mechanism that has been characterized by ET (Chlanda et al., 2009) . Although we are beginning to understand how replication organelles are assembled, information is still limited about how cell organelles are recruited, about the mechanisms of macromolecular transport between compartments, and about the signals that regulate the major structural changes in the factory during distinct stages in the virus life cycle. doi = 10.1111/cmi.12029 id = cord-290352-0pc5eji4 author = de Jong, Menno D. title = Avian influenza A (H5N1) date = 2005-10-06 keywords = H5N1; Hong; Kong; influenza; virus summary = Since their reemergence in 2003, highly pathogenic avian influenza A (H5N1) viruses have reached endemic levels among poultry in several southeast Asian countries and have caused a still increasing number of more than 100 reported human infections with high mortality. However, occurrences of direct bird-to-human transmission of avian influenza viruses have increasingly been reported in recent years, culminating in the ongoing outbreak of influenza A (H5N1) among poultry in several Asian countries with associated human infections. The "Asian influenza" pandemic of 1957 was caused by an H2N2 virus that had acquired three genes (H2, N2, and PB1) from avian viruses infecting wild ducks, in a backbone of the circulating H1N1 human influenza strain. Furthermore, these infections were associated with severe hemorrhagic pneumonia and the induction of high levels of macrophage-derived cytokines and chemokines, strikingly reminiscent of clinical observations in humans during the Spanish flu pandemic, as well as of recent in vitro and in vivo observations of infections with highly pathogenic avian influenza H5N1 viruses (Cheung et al., 2002; Oxford, 2000; Peiris et al., 2004; To et al., 2001) . doi = 10.1016/j.jcv.2005.09.002 id = cord-020756-d9f5fd7x author = de Jong, Menno Douwe title = Avian Influenza Viruses and Pandemic Influenza date = 2007 keywords = H5N1; Hong; Kong; avian; human; influenza; virus summary = This is illustrated by the fact that during its evolution in humans, the NA of H2N2 viruses, which were of avian origin and therefore highly specific for hydrolization of α2,3-linked sialic acids, acquired high affinity for the human α2,6-linked sialic acids (Baum and Paulson, 1991) In addition to the surface glycoproteins, laboratory experiments with reassortant viruses suggest that the genes encoding internal proteins, such as M, NP, PB1 and PB2, may also play a role in determining the host range (Almond 1977; Scholtissek et al., 1978a; Snyder et al., 1987; Subbarao et al., 1993) . By reverse genetics experiments, it has been shown that a lysine residue at position 627 (Lys627) of PB2 seems essential for high virulence and systemic replication in mice of highly pathogenic influenza H5N1 viruses responsible for the outbreak among poultry and humans in Hong Kong in 1997 (H5N1/97) (Hatta et al., 2001) . doi = 10.1007/978-0-387-32830-0_9 id = cord-259235-p0yj9qug author = de Lamballerie, Xavier title = Diagnostic et traitement des viroses émergentes : comment aller de l’avant ? date = 2016-12-31 keywords = virus summary = (ii) l''émergence dans une population donnée d''un pathogène déjà impliqué en pathologie humaine dans un contexte épidémiologique différent (on parle ici plus proprement de pathologie « ré-émergente » et l''arrivée des virus Chikungunya [2] ou Zika [3] dans le Nouveau Monde constituent des exemples récents ayant provoqué des épidémies massives) ; À titre d''exemple, le seul arbovirus dont la circulation avait été prouvée en République du Congo jusqu''à une période récente était le virus de la fièvre jaune, alors qu''une simple étude de séroprévalence a permis de préciser l''importance de la circulation de la dengue, du chikungunya, de la fièvre de la vallée du Rift, de la fièvre de West Nile (Dr. Nanikaly Moyen, données personnelles Un cas particulier de thérapeutique antivirale applicable aux infections émergentes et ré-émergentes est constitué par la sérothérapie au sens large qui inclut l''usage d''immunoglobulines humaines ou animales (ces dernières pouvant être « humanisées ») monoclonales ou polyclonales [19] . doi = 10.1016/s0001-4079(19)30571-0 id = cord-332992-8rmqg4rf author = de Vries, A. A. F. title = SARS-CoV-2/COVID-19: a primer for cardiologists date = 2020-07-15 keywords = COVID-19; CoV-2; RNA; SARS; cell; patient; virus summary = Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . doi = 10.1007/s12471-020-01475-1 id = cord-002327-tocqabgu author = de Vries, Rory D. title = Viral vector-based influenza vaccines date = 2016-07-25 keywords = A(H5N1; H5N1; MVA; virus summary = doi = 10.1080/21645515.2016.1210729 id = cord-326160-mf0vh6iu author = de Wit, Emmie title = Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques date = 2014-08-12 keywords = Fig; H7N9; anhui/1/2013; influenza; virus summary = Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. To elucidate global host responses specifically associated with sites of virus-induced airway injury in influenza virus A/Anhui/1/2013-infected macaques, we used microarrays to assess transcriptional profiles induced in lung lesions compared to the adjacent lung tissue. We identified ten compounds in IPA (Table 1) , four of which were perturbagens listed in CMap. We identified two compounds that met our criteria in IPA and CMap, rosiglitazone and simvastatin, predicted to have inhibitory effects on pathological host responses associated with lesions in influenza virus A/Anhui/1/2013-infected animals ( Table 1) . doi = 10.1128/mbio.01331-14 id = cord-332457-gan10za0 author = de Ángel Solá, David E. title = Weathering the pandemic: How the Caribbean Basin can use viral and environmental patterns to predict, prepare and respond to COVID‐19 date = 2020-04-10 keywords = Caribbean; SARS; virus summary = On March 12, 2020, the World Health Organization (WHO) declared a pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the pathogen responsible for the clinical disease known as COVID-19. Recently, a pattern favoring cold, dry weather was also observed in Hong Kong in a 6-year-long study, though in this case coronaviruses were found yearround 48 Therefore, data from other coronaviruses and the similar portal of infection discussed above do support the idea that SARS-CoV-2 may follow the same patterns as influenza, and that timing interventions around influenza peaks in the Caribbean would be reasonable. If SARS-CoV-2 interacts with climate and weather as theorized above, it is likely that areas in the Greater Caribbean with Air Surface Temperatures (AST) >25°C and RH>70% might be considered areas of relatively decreased environmental risk (Figure 1 ) 53 . doi = 10.1002/jmv.25864 id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 keywords = A(H1N1; CDC; China; ELISA; H1N1; H3N2; H5N1; H9N2; HAI; Health; Hong; ILI; Influenza; Kong; LAIV; MDCK; PB1-F2; PCR; RNA; TCID; USA; cell; figure; infection; ns1; pandemic; table; virus summary = The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. doi = 10.1111/j.1750-2659.2011.00209.x id = cord-004608-3u00cpsc author = nan title = Arboviren—durch Arthropoden übertragbare Viren: Stellungnahmen des Arbeitskreises Blut des Bundesministeriums für Gesundheit und Soziale Sicherung date = 2004 keywords = Arboviren; Infektionen; Virus; WNV summary = Unter dem Oberbegriff Arboviren (arthropod-borne viruses) werden diejenigen Viren zusammengefasst, die sich sowohl in Arthropoden wie Mücken oder Zecken als auch in Vertebraten (Vögeln, Säugetieren) vermeh-ren. Hantaviren, die zum Genus Hantavirus der Bunyaviridae gehören, werden dagegen nicht von Arthropoden auf den Menschen übertragen, sondern durch dessen Kontakt mit Ausscheidungen der natürlichen Wirte, Mäuse und Ratten. In Deutschland spielt nach dem heutigen Wissensstand nur das Virus der Frühsommermeningoenzephalitis (FSME), das durch Zecken (Ixodes ricinus) übertragen wird, epidemiologisch eine wesentliche Rolle. Für einige Viren, wie etwa West-Nil-Virus (WNV) und St.-Louis-Enzephalitis-Virus (SLEV), wurde nachgewiesen, dass die Virusvermehrung in den Mücken abhängig ist von der durchschnittlichen Umgebungstemperatur. Für verschiedene Erreger wurde gezeigt, dass einerseits infizierte Mücken überwintern können; annahme an Krankheitsfällen bei Menschen in den USA Das Verhältnis von Infektionen zu Erkrankungen wird dabei je nach Erreger und untersuchtem Kollektiv mit 20:1 bis 1.000:1 angegeben. doi = 10.1007/s00103-004-0890-8 id = cord-008764-j9qmw4zy author = nan title = Chapter 1 The need for chemotherapy and prophylaxis against viral diseases date = 2008-05-29 keywords = USA; chapter; disease; virus summary = We shall examine the methods developed for the prevention of measles, influenza, polio and rotaviruses later on (Chapters 8, 7, 4 and 9, respectively) but it may be mentioned here that live polio vaccines used so successfully in industrialized countries are much more difficult to apply successfully in third world countries where problems of vaccine administration, heat lability control and viral interference become very important. The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). The greatest challenges and probably the most difficult and medically important areas for prophylaxis and therapy of viral diseases are those viruses which are rapidly changing in antigenic composition and/or viruses with animal reservoirs (influenza and arboviruses) and also those forming latent infections (herpesviruses). doi = 10.1016/s0168-7069(08)70009-0 id = cord-014462-11ggaqf1 author = nan title = Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date = 2011-04-21 keywords = BTV; CMV; CTV; ELISA; India; PCR; Pradesh; RNA; RTBV; disease; dna; gene; isolate; plant; protein; sequence; study; vaccine; virus summary = Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. doi = 10.1007/s13337-011-0027-2 id = cord-015619-msicix98 author = nan title = Virus Structure & Assembly date = 2009-02-24 keywords = SARS; dna; structure; virus summary = The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. doi = 10.1016/s0006-3495(08)79065-9 id = cord-017752-ofzm3x3a author = nan title = Theories of Carcinogenesis date = 2007 keywords = cancer; cause; cell; dna; gene; human; theory; tumor; virus summary = Others attributed the simplified enzyme patterns of cancerous cells to a regression of the tumor tissues to early embryonal stages of development. Viral DNA is frequently integrated into the cancer cells, but additional agents or factors may be involved at various stages of the progression to invasive carcinoma. The encounter with a family, in which many members developed breast or liver cancer, led Pierre Paul Broca to hypothesize, in 1866, that an inherited abnormality within the affected tissue caused the tumor development [Broca 1866 Theodor Boveri (1862 Boveri ( -1915 then proposed that defects in chromosomes lead to malignancy [Boveri 1914 ]. Any mutation of cancer associated genes can be handed on to following generations and predispose the affected cells to malignant transformation in the case of additional DNA damage. Further developments in tumor immunology have led to models of selection and evolution of cancer cells. doi = 10.1007/978-1-4020-6016-8_1 id = cord-020010-q58x6xb0 author = nan title = 19th ICAR Abstracts: date = 2006-03-13 keywords = CDV; Department; HCMV; HCV; HIV; HIV-1; Institute; REP; RNA; Research; ST-246; Sciences; USA; University; Virology; WNV; activity; antiviral; cell; compound; dna; infection; virus summary = In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. doi = 10.1016/j.antiviral.2006.02.001 id = cord-020087-gs0pc6ee author = nan title = Cumulative Contents for 2010 date = 2010-11-18 keywords = virus summary = Myristoylation of the small envelope protein of porcine reproductive and respiratory syndrome virus is non-essential for virus infectivity but promotes its growth 294 Porcine reproductive and respiratory syndrome virus (PRRSV) could be sensed by professional beta interferon-producing Hikichi (Japan) The 126-and/or 183-kDa replicases or their coding regions are responsible both for inefficient local and for systemic movements of Paprika mild mottle virus Japanese strain in tomato plants USA) Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection Porcine reproductive and respiratory syndrome virus (PRRSV) in serum and oral fluid samples from individual boars: Will oral fluid replace serum for PRRSV surveillance USA) Use of a production region model to assess the efficacy of various air filtration systems for preventing airborne transmission of porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae: Results from a 2-year study 177 Morrison (USA) Control and elimination of porcine reproductive and respiratory syndrome virus 185 Cumulative Author Index for doi = 10.1016/s0168-1702(10)00397-7 id = cord-020097-eh5deunk author = nan title = Cumulative Author Index for 2006 (Volumes 115–122) date = 2006-10-27 keywords = cell; protein; virus summary = Modulation of PKR activity in cells infected by bovine viral diarrhea virus Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein A deletion and point mutation study of the human papillomavirus type 16 major capsid gene Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus doi = 10.1016/s0168-1702(06)00318-2 id = cord-020101-5rib7pe8 author = nan title = Cumulative Author Index for 2008 date = 2008-11-17 keywords = HIV-1; gene; protein; virus summary = Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors doi = 10.1016/s0168-1702(08)00367-5 id = cord-020235-stcrozdw author = nan title = Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date = 2012-03-15 keywords = HSV; Inst; RNA; Univ; cell; dna; protein; viral; virus summary = Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). doi = 10.1016/s0174-3031(82)80128-5 id = cord-022822-7346069t author = nan title = Infections, Immunity & their Effects on Asthma date = 2006-10-02 keywords = RSV; virus summary = The mechanisms underlying the association between RSV bronchiolitis and the later development of wheezing are incompletely understood, though there is increasing evidence that impaired antiviral immunity is likely to play an important role in increasing susceptibility to virus infections early in life, as well as perhaps the later development of asthma [3] . Areas that particularly require attention include interplay between the innate and acquired immune responses in host defence; the role of viral persistence in development of wheezing illness and asthma; the roles of antigen presenting cells and other specific cell compartments such as epithelial cells, T cells, neutrophils, eosinophils and non T cell lymphocytes in host protection and disease severity. Further studies investigating the importance of different virus types in the association between lower respiratory infection in infancy and wheezing illness in asthma are required to clarify the relationships, including rhinovirus, human metapneumoviruses, coronaviruses and bocaviruses. doi = 10.1111/j.1365-2222.2006.02583_7.x id = cord-022980-tkii8se4 author = nan title = Diarrhea date = 2008-03-05 keywords = virus summary = Nevertheless, until recently gastro-enteritis provided a poor hunting ground for virologists for, although such viruses as adenoviruses, echoviruses and Coxsackie viruses could be isolated from the stools of patients with acute gastro-enteritis, they could often be recovered with almost equal frequency from those without diarrhoeal disease, particularly in developing countries. However, the examination of negatively stained faecal preparations from patients witb gastro-enteritis by electron microscopy has resulted in the discovery of many viruses, some of which, for example, rotaviruses and such parovirus-like viruses as the Norwalk agent, are undoubtedly the cause of acute gastroenteritis. In general, in vitro cultivation of viruses causing gastroenteritis in humans is either not possible or extremely difficult and of little value for routine diagnostic purposes but, since they are often excreted in very high titres, they may be detected without difficulty by electron microscopic examination of faecal extracts,-Banatvala jE: Viruses and Diarrhoes, Trans R Soc Trop Med Hyg 73: 503, 1979. doi = 10.1111/j.1365-4362.1980.tb00268.x id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 keywords = CD4; CD8; CNS; CTL; HIV; HIV-1; HLA; IFN; LCMV; MHC; cell; infection; mouse; protein; response; viral; virus summary = Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. doi = 10.1002/jcb.240591009 id = cord-023564-kpqvyxxe author = nan title = Viral gastroenteritis: Causes, pathophysiology, immunology, treatment, and epidemiology date = 2004-09-14 keywords = virus summary = This chapter discusses the causes, pathophysiology, immunology, treatment, and epidemiology of viral gastroenteritis. Infection with gastroenteritis agents can be asymptomatic or can be followed by mild or severe disease, including vomiting or diarrhea or both, and can be fatal because of severe dehydration. Infection with gastroenteritis agents can be asymptomatic, or be followed by mild or severe disease including vomiting or diarrhoea or both, and can be fatal as a consequence of severe dehydration. The main diarrhoeogenic agents comprise four virus families: rotaviruses, enteric adenoviruses, human caliciviruses (Norwalk-and Sapporo-like viruses, now termed noro-and sapoviruses) and astroviruses, and cause diarrhoea at frequencies of 20-30%, 5%, 5-10%, and 5%, respectively. By contrast, epidemic disease is found in all ages, mainly caused by Norwalk-and Sapporo-like viruses (human caliciviruses), rotaviruses of group B (in China), and sometimes astroviruses. Systemic and intestinal antibody secreting cell responses and correlates of protective immunity to human rotaviruses in a gnotobiotic pigs model of disease doi = 10.1016/s0168-7069(03)09001-3 id = cord-023608-w2g7v7g1 author = nan title = ISAR News date = 2017-10-20 keywords = ICAR; ISAR; RNA; Society; dengue; virus summary = ICAR retains its flavor and personality, providing an interdisciplinary forum at which investigators involved in basic, translational, and clinical research worldwide meet to review recent developments in all areas of antiviral research, drug and vaccine development. Additionally, satellite activities such as the Women in Science Roundtable, the Career Development Panel and the New Member and First Time Attendee luncheon (The Happy Hour) provided an opportunity to discuss other issues of relevance. With so many different competing conferences and meetings to attend and a long economic crisis of which scientific research did not escape, ISAR has gone through great financial efforts to continue supporting the participation of students, postdocs and young investigators. The TCFF Awards support the professional development of women with potential to make significant contributions to the field of Antiviral Research by providing funds to attend a conference, visit another laboratory, take a course, or acquire specialized training. doi = 10.1016/s0166-3542(17)30664-2 id = cord-023622-tul7bonh author = nan title = Rotaviruses of Man and Animals date = 1975-02-01 keywords = patient; virus summary = Certainly bacterial pathogens may cause both sporadic and epidemic gastroenteritis in children, but they cannot be isolated in up to 75% of cases.2, 3 Whilst it is true that some investigations suggest that enteroviruses or adenoviruses may occasionally cause localised outbreaks of gastroenteritis,4-7 others have shown that these viruses may be detected almost as frequently in controls as among patients. Employing negativestaining techniques on fsecal extracts, FLEWETT and his colleagues found similar particles in children with gastroenteritis in Birmingham 13; indeed, if virologists had only looked at such simply prepared specimens, there is no technical reason why these viruses could not have been detected, say, 15 years ago. Thus, existing evidence suggests that rotaviruses are the most important cause of infantile gastroenteritis throughout the world, but as yet only a limited number of specimens have been examined from those tropical areas where mortality-rates are particularly high. doi = 10.1016/s0140-6736(75)91148-4 id = cord-327883-s9nbr5y8 author = nan title = Section Virology date = 1990-03-31 keywords = EBV; HCMV; HSV; antibody; cell; dna; protein; virus summary = By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC). doi = 10.1016/s0934-8840(11)80039-3 id = cord-340489-yo3cp5vs author = nan title = KAPITEL 13 Infektionskrankheiten date = 2008-12-31 keywords = AIDS; CMV; Erkrankung; Erreger; Fieber; HIV; Infektion; Jahren; Nachweis; Patienten; RNA; Substanzen; Symptome; Therapie; Viren; Virus; Zellen; auch; bei; der; des; die; durch; eine; ist; mit; oder; sind; und; von; werden summary = Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. doi = 10.1016/b978-3-437-42831-9.10013-0 id = cord-350703-vrqltz3s author = nan title = ISAR News date = 2016-01-31 keywords = Ebola; ICAR; ISAR; Institute; University; antiviral; drug; research; virus summary = She is studying the response of primary human mononuclear cells to dengue virus infection, aiming to establish a more relevant in vitro model for antiviral drug testing and to identify potential new antiviral targets, using genome-wide transcriptomic analysis. According to ISAR member Robert Jordan, who heads the Gilead team developing antivirals against respiratory viruses, the parent compound was originally discovered as part of the hepatitis C program, targeting the HCV polymerase, but the strong clinical efficacy of sofosbuvir, especially in combination with ledipasvir, resulted in the molecule being evaluated for other indications, including respiratory viruses such as respiratory syncytial virus (RSV). ISAR members know Andrea (standing, above, with Cardiff colleague Salvatore Ferla) as the winner of the 2013 Prusoff Young Investigator Award, but not all of us are familiar with the direction of his career, which has increasingly explored the use of computer-based methods to design new antivirals and anticancer drugs. doi = 10.1016/s0166-3542(15)00286-7 id = cord-257019-lj1yzjn0 author = ter MEULEN, V. title = Mechanisms and Consequences of Virus Persistence in the Human Nervous System date = 2006-12-16 keywords = virus summary = Virus penetration may result in acute encephalitis, but occasionally a persistent infection is established that leads to a fatal slowly progressing disease, subacute sclerosing panencephalitis (SSPE). However, virus expression may sometimes be rescued from this infected tissue by co-cultivation procedure^.''^ These experiments have therefore confirmed that measles virus is the etiological agent of SSPE and also indicated that virus persistence may be based on some defect in the virus maturation process that could involve some form of host effect. The case of PRP is an exception; infectious virus may be isolated directly despite a strong antibody response in both serum and CSF.M Similarly, the cell-mediated immune system does not show any specific deficien~y.*~.~'' However, the site of rubella virus antigen expression has not yet been identified during this disease process. Similarly, chronic echovirus infection is associated with immune deficiency, and although inflammatory processes are observed in extraneural tissue, it seems unlikely that C N S damage is largely caused by virus-mediated cell destruction. doi = 10.1111/j.1749-6632.1984.tb14778.x id = cord-288111-0ufc54kw author = ter MEULEN, VOLKER title = Autoimmune Reactions Against Myelin Basic Protein Induced by Corona and Measles Viruses date = 2006-12-17 keywords = CNS; Lewis; virus summary = What apparently happens is that the viruses themselves induce Ia expression on the astrocytes, enabling these cells to present the viral antigens to the lymphocytes and allowing the host to mount an effective immune response to control the infection. However, in extremely high constitutive levels of class I1 expression on astrocytes, an inappropriate or excessive presentation of self-antigens and viral antigens may develop, similar to that in autoimmune processes directed against the thyroid gland.''" This mechanism could well play a role in the JHM-and measles-virus-induced CNS disease in Lewis rats, because as recently shown by us," these hyperexpressions of Ia molecules on astrocytes after contact with gamma-interferon or viral particles are genetically regulated. JHM and measles virus infections in rats are models of a persistent viral infection of the CNS with and without demyelination, associated with a cell-mediated immune reaction to MBP. doi = 10.1111/j.1749-6632.1988.tb27062.x id = cord-354151-psog34u3 author = van Asten, Liselotte title = Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections date = 2015-12-11 keywords = early; influenza; virus summary = METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. [1] [2] [3] [4] A few population-level studies in Europe were based on observations in one respiratory season only (the 2009 H1N1 pandemic) in which the annually recurring influenza epidemic occurred relatively early. Almost all of the included respiratory viruses (influenza A and B virus, RSV, coronavirus) except rhinovirus showed very clear seasonality in their reporting over time. Viruses that showed a shifted trend of reporting during years with early influenza A epidemics were of respiratory nature with clear winter seasonality and with epidemics occurring relatively close in time to influenza A virus epidemics. doi = 10.1111/irv.12348 id = cord-261241-eqf6ame6 author = van Beek, Josine title = Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date = 2017-08-15 keywords = ILI; influenza; virus summary = The aim of this prospective observational study was to determine the relative contribution of influenza virus and other respiratory pathogens to ILI in older adults (aged ≥60 years) in 2 consecutive seasons in the Netherlands. In 60.8% (2011-2012) and 44.7% (2012-2013) of ILI samples, potential pathogens other than influenza virus were detected (Figure 3 ; Supplementary Table 1 ). Coronaviruses of all 4 common human subtypes (18.2% in 2011-2012 and 11.3% in 2012-2013), human metapneumovirus (hMPV) (20.3% and 3.6%), rhinoviruses (8.4% and 21.1%), respiratory syncytial virus (RSV) (4.9% and 6.5%), and parainfluenza viruses (2.8% and 5.1%) were detected in >5% of the ILI samples in at least 1 season. In this study in a cohort of community-dwelling older adults in the Netherlands, we show that influenza virus was present in 18.9% and 34.2% of ILI cases in 2 consecutive seasons and that influenza vaccination significantly reduced laboratory-confirmed influenza virus infection. Effectiveness of seasonal influenza vaccine in community-dwelling elderly people: a meta-analysis of test-negative design case-control studies doi = 10.1093/infdis/jix268 id = cord-291860-dw1sfzqx author = van Boheemen, Sander title = Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date = 2019-12-16 keywords = PCR; RNA; dna; virus summary = Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI''s nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. doi = 10.1016/j.jmoldx.2019.10.007 id = cord-330508-uilejxmi author = van den Hoogen, Bernadette title = Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date = 2020-07-28 keywords = initiate; virus summary = While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. doi = 10.1016/j.virusres.2020.198094 id = cord-295792-hajvtzj9 author = Álvez, Fernando title = SARS-CoV2 coronavirus: So far polite with children. Debatable immunological and non-immunological evidence date = 2020-07-03 keywords = ACE2; SARS; child; virus summary = In short, the purpose of this first defensive barrier for early control during the incubation period and the first symptoms of SAR-CoV2 infection is to inhibit viral replication, promote elimination of the virus, induce tissue repair and trigger a specific adaptive immune response (AIR) (12) . Furthermore, this enzyme also plays an important role in the immune response, especially in inflammation, and is involved in the defensive mechanisms of the lung -protecting it from severe injury induced by respiratory viruses (11, 18) . However, serological studies evaluating the immune response to respiratory infections including CovH have shown steadily increasing seroprevalence of antibodies to CovH in both children and young adults, as well as cross-reactivity, such as between antibodies to the previous SARS-CoV and CovH (25) (26) . Cell Responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-Infected mice doi = 10.1016/j.aller.2020.05.003 id = cord-258027-f3rr5el1 author = Østby, Anne‐Cathrine title = Respiratory virology and microbiology in intensive care units: a prospective cohort study date = 2013-05-18 keywords = ICU; patient; virus summary = Our aim was to determine the frequency of 12 common respiratory viruses in patients admitted to intensive care units with respiratory symptoms, evaluate the clinical characteristics and to compare the results to routine microbiological diagnostics. The information included the following: age, gender, underlying comorbidity, use of immunosuppressant drugs, respiratory symptoms, diagnoses on admission, diagnoses on discharge, length of hospital stay, ICU stay and intubation, Simplified Acute Physiology Score II (SAPS II)scores, administration of antibiotics, non-invasive ventilation, chest x-ray, laboratory analyses and results of the physical examination, which included temperature, saturation, stethoscopic findings and clinical signs of respiratory infection or distress. Viruses -Of the 122 patients included in the study group, 19 (16%) were positive for a virus, of which the most frequently detected were influenza A (n = 9) and RSV (n = 3, Fig. 2 ). doi = 10.1111/apm.12089 id = cord-278635-vwdxr1bl author = Świętoń, Edyta title = Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date = 2020-08-28 keywords = PCR; RNA; defective; virus summary = In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). doi = 10.1186/s13567-020-00833-6