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?' ---------------------------------------------------------- 145 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 8146 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 44 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 144 viral 72 virus 55 RNA 22 SARS 20 cell 17 infection 16 protein 14 dna 13 HIV-1 12 respiratory 10 HIV 8 PCR 7 patient 7 IFN 7 HCV 6 host 5 sequence 5 disease 5 Fig 4 genome 4 figure 4 child 4 COVID-19 3 receptor 3 particle 3 mutant 3 drug 3 asthma 3 antiviral 3 H1N1 2 vaccine 2 translation 2 siRNA 2 sample 2 resistance 2 population 2 plasma 2 nanoparticle 2 metagenomic 2 influenza 2 human 2 cap 2 bacterial 2 antibody 2 animal 2 PKR 2 NCBI 2 MHC 2 IRES 2 HSV Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 14926 virus 7448 cell 5938 infection 5487 protein 3001 host 2474 replication 2460 study 2432 disease 2342 patient 2071 genome 1779 influenza 1772 % 1743 gene 1707 response 1704 sequence 1610 type 1340 mechanism 1298 factor 1264 receptor 1243 membrane 1194 effect 1172 role 1159 activity 1151 expression 1147 treatment 1138 drug 1138 dna 1133 interaction 1085 case 1061 antibody 1049 analysis 1034 mouse 1015 sample 1014 system 1008 particle 1003 site 985 vaccine 962 result 938 level 938 function 926 translation 918 time 896 acid 885 method 855 structure 847 target 846 inhibitor 840 child 815 process 808 population Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 4480 RNA 2675 al 2174 et 2017 . 1063 SARS 859 HIV-1 830 HIV 670 C 633 PCR 542 HCV 526 Fig 514 CoV-2 489 IFN 408 HRV 399 T 398 A 376 B 349 siRNA 309 mRNA 296 CTL 274 DNA 267 Virus 262 HBV 261 COVID-19 260 CoV 255 IAV 241 Table 237 miRNA 228 Influenza 226 RSV 225 miRNAs 225 II 219 H1N1 211 BVDV 201 Viral 196 RT 196 CD4 187 L 166 Ebola 164 simplex 164 Hepatitis 161 MHC 161 Golgi 161 EBV 160 vivo 159 IRES 158 mRNAs 158 VSV 154 RNAi 150 hepatitis Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2304 it 1578 we 930 they 585 i 275 them 89 itself 84 us 47 one 42 themselves 40 he 21 mrnas 10 you 10 she 5 me 4 him 4 gh625 3 rssc 2 mg 2 hunovs 2 clustalx 1 theirs 1 s 1 pdcs 1 p6gag 1 ourselves 1 ours 1 orf2 1 nsp15 1 ns3/4a 1 n.m.we 1 mirna-28 1 mine 1 l~ 1 isgf3 1 ilc1s 1 ikkb/ 1 icam-5 1 i8r 1 himself 1 hcrm1 1 grasp55 1 gate16 1 em 1 eif4g-4a 1 c08-c09 1 benzo-1,2,4thiadiazine 1 a1-antitrypsin 1 _ 1 621114mice 1 's Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 31019 be 6317 have 3193 use 1528 show 1422 include 1394 associate 1292 induce 1203 infect 1137 bind 1033 base 961 identify 954 find 943 require 909 increase 892 do 840 cause 819 target 793 provide 781 report 761 mediate 761 contain 758 suggest 756 detect 745 inhibit 723 involve 717 result 717 know 689 occur 682 follow 671 develop 631 lead 617 encode 579 reduce 571 determine 568 describe 567 produce 554 demonstrate 531 express 525 allow 518 compare 500 make 458 remain 448 observe 444 reveal 443 see 436 prevent 412 indicate 410 regulate 405 perform 399 affect Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 11441 viral 2802 not 2329 also 2057 human 2039 - 1932 respiratory 1684 other 1638 such 1523 high 1477 antiviral 1475 immune 1452 cellular 1361 specific 1350 more 1168 clinical 1161 different 1068 however 1064 most 983 well 982 new 964 only 890 acute 862 low 829 several 781 important 761 early 751 many 717 severe 696 molecular 691 large 679 first 659 infectious 658 as 655 thus 632 non 631 single 621 small 612 infected 612 anti 599 long 597 bacterial 590 common 579 further 570 dependent 568 novel 558 positive 550 genetic 515 similar 499 multiple 475 structural Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 391 most 150 least 127 Most 78 good 62 high 43 large 19 low 18 vRNA 18 great 12 simple 10 early 9 small 7 late 6 strong 6 flat 5 common 5 close 4 fit 4 big 3 short 2 young 2 new 2 near 2 hvPPI 2 fast 2 clear 2 bad 2 -which 1 wilcox_t 1 slow 1 slight 1 safe 1 old 1 nt9300 1 narrow 1 long 1 healthy 1 easy 1 broad 1 AuNPs 1 -particulates 1 -A1b Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 673 most 105 least 45 well 2 α2-ar 2 vrna 2 -i 1 poorest 1 highest 1 aunps Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 31 doi.org 7 www.ncbi.nlm.nih.gov 6 github.com 4 www 3 www.frontiersin.org 2 www.virologyj.com 2 www.google.org 2 www.ebi.ac.uk 2 viralzone.expasy.org 2 earthmicrobiome.org 1 www.wma.net 1 www.weather.gov.sg 1 www.uniprot.org 1 www.synapse-web.org 1 www.singstat.gov.sg 1 www.rostlab.org 1 www.promedmail.org 1 www.predictprotein.org 1 www.picornastudygroup.com 1 www.oxfordjournals.org 1 www.ncbi.nlm.nih 1 www.mg-rast.org 1 www.international-rhinovirus-consortium.org 1 www.iedb.org 1 www.expasy.ch 1 www.epa.gov 1 www.biorxiv.org 1 www.be-md.ncbi.nlm.nih.gov 1 www.r-project 1 www.454.com 1 viralzone.expasy 1 urldefense.proofpoint.com 1 rotac.regatools.be 1 pubs.acs.org 1 opal.biology 1 lsbr.niams.nih.gov 1 lalashan 1 healthmap.org 1 figshare.com 1 evolution.genetics.washington.edu 1 data 1 clinicaltrials.gov 1 cgc.sbgenomics.com 1 blast.ncbi.nlm.nih.gov 1 bibiserv.techfak 1 amira.zib.de Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 10 http://doi.org/10.1101/2020.04 6 http://github.com/ICBI/viGEN/ 6 http://doi.org/10.1101/2020.06.17.20132076 4 http://www 4 http://doi.org/10.1101/2020.04.04.20047886 2 http://www.virologyj.com/content/2/1/70 2 http://www.frontiersin.org/articles/10.3389/fimmu 2 http://www.ebi.ac.uk/ena/data/view/ 2 http://earthmicrobiome.org/protocols-and-standards/16s/ 1 http://www.wma.net 1 http://www.weather.gov.sg/climate-historical-daily/ 1 http://www.uniprot.org/ 1 http://www.synapse-web.org/tools/index.stm/ 1 http://www.singstat.gov.sg/statistics/browse-by-theme/ 1 http://www.rostlab.org/ 1 http://www.promedmail.org 1 http://www.predictprotein.org/ 1 http://www.picornastudygroup.com/ 1 http://www.oxfordjournals.org/nar/database/ 1 http://www.ncbi.nlm.nih.gov/sutils/pasc 1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394299/ 1 http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ 1 http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses 1 http://www.ncbi.nlm.nih.gov/genome/viruses/ 1 http://www.ncbi.nlm.nih.gov/genome 1 http://www.ncbi.nlm.nih.gov/Entrez/ 1 http://www.ncbi.nlm.nih 1 http://www.mg-rast.org/linkin.cgi? 1 http://www.international-rhinovirus-consortium.org/ 1 http://www.iedb.org 1 http://www.google.org/flutrends 1 http://www.google.org/denguetrends 1 http://www.frontiersin.org/articles/10.3389/fmicb 1 http://www.expasy.ch/ 1 http://www.epa.gov/microbes/moldtech.htm 1 http://www.biorxiv.org/content/10.1101/2020.04.17.045161v1 1 http://www.be-md.ncbi.nlm.nih.gov/projects/geo/query/acc 1 http://www.R-project 1 http://www.454.com/ 1 http://viralzone.expasy.org/886 1 http://viralzone.expasy.org 1 http://viralzone.expasy 1 http://urldefense.proofpoint.com/v2/url?u= 1 http://rotac.regatools.be/ 1 http://pubs.acs.org/10.1021/acsnano.0c04117 1 http://opal.biology 1 http://lsbr.niams.nih.gov/bsoft/ 1 http://lalashan 1 http://healthmap.org 1 http://figshare.com/articles/Supplementary_Data_Alignment_Files/12649109 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 sbraun@afm-telethon.fr 1 philip.efron@surgery.ufl.edu 1 moreho17@msu.edu.ethi 1 kkhafizov@gmail.com 1 g.reina@ibmc-cnrs.unistra.fr 1 a.bianco@ibmc-cnrs.unistra.fr Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 18 viruses do not 10 rna binding proteins 9 receptor binding domain 9 rna binding protein 9 viruses are not 8 viruses have also 7 proteins are also 7 virus infected cells 7 virus was not 7 viruses are capable 6 cells are not 6 virus does not 6 viruses are also 6 viruses are highly 5 cell mediated immunity 5 cells is not 5 infection does not 5 protein is also 5 virus is not 5 virus is present 5 viruses are able 4 cells are important 4 cells was also 4 disease is usually 4 drugs are available 4 genomes are not 4 infection has also 4 infection is not 4 mechanism is still 4 protein does not 4 protein inhibits host 4 response is not 4 rna is then 4 studies did not 4 studies have also 4 study are available 4 study did not 4 study has several 4 virus was also 4 viruses are common 4 viruses are frequently 4 viruses are intracellular 4 viruses are now 4 viruses are often 4 viruses were also 3 cell mediated immune 3 cells were not 3 disease are often 3 disease is not 3 effect was not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 response is not significantly 2 studies are not homologous 1 % was not similar 1 activities are not commonly 1 activity was not equivalent 1 cells are not primary 1 cells are not rapidly 1 cells are not susceptible 1 cells are not well 1 cells had no effect 1 cells have not yet 1 cells is not cor 1 cells showed no significant 1 cells were not able 1 cells were not completely 1 cells were not immunoreactive 1 disease are not well 1 disease does not systematically 1 disease is not comprehensive 1 disease is not necessarily 1 effect was not satisfactory 1 effects are not short 1 expression is not as 1 expression is not necessary 1 factors are not homologous 1 genes were not available 1 genome had no significant 1 genomes are not infectious 1 genomes are not naked 1 genomes are not robust 1 genomes contain no poly(a 1 host is not that 1 infection had no difference 1 infection had not yet 1 infection include not only 1 infection is not cytotoxic 1 infection is not well 1 infection occurs not only 1 infection requires not only 1 infection was not significantly 1 infections are not uncommon 1 infections were not previously 1 mechanism is not completely 1 mechanisms do not wholly 1 mechanisms have not yet 1 patients have not yet 1 protein does not substantially 1 protein had no observable 1 protein is not functional 1 proteins are not targets A rudimentary bibliography -------------------------- id = cord-307354-dkwcheu0 author = Abernathy, Emma title = Emerging roles for RNA degradation in viral replication and antiviral defense date = 2015-05-31 keywords = NMD; RNA; viral summary = Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus doi = 10.1016/j.virol.2015.02.007 id = cord-287459-k9x3z2h1 author = Abu-Farha, Mohamed title = The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date = 2020-05-17 keywords = COVID-19; SARS; lipid; viral summary = doi = 10.3390/ijms21103544 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 = doi = 10.1038/nrmicro2452 id = cord-318751-4v2tl0gi author = Arias, Armando title = Progress towards the prevention and treatment of norovirus infections date = 2013-11-17 keywords = MNV; Norwalk; RNA; norovirus; viral summary = doi = 10.2217/fmb.13.109 id = cord-329162-6w8qcv1c author = Ayginin, Andrey A. title = The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date = 2018-08-12 keywords = PCR; primer; sample; viral summary = The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format. doi = 10.1155/2018/3248285 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-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-315130-8g2ih8zl author = Bax, Adriaan title = SARS-CoV-2 transmission via speech-generated respiratory droplets date = 2020-09-11 keywords = droplet; viral summary = doi = 10.1016/s1473-3099(20)30726-x 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-022349-z8w1wkm8 author = Beeler, Judy A. title = Human and Animal Viruses date = 2007-09-02 keywords = freeze; vaccine; viral; virus summary = doi = 10.1016/b978-012361946-4/50010-7 id = cord-271495-5906wju4 author = Beldomenico, Pablo M. title = Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date = 2020-05-11 keywords = SARS; viral summary = doi = 10.1016/j.ijid.2020.05.025 id = cord-342660-xigv4u3f author = Benotmane, I. title = In-depth virological assessment of kidney transplant recipients with COVID-19 date = 2020-06-19 keywords = SARS; viral summary = We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. We thus conducted a retrospective cohort study in kidney transplant recipients (KTR) in Alsace, Grand-Est France, to determine the dynamics of nasopharyngeal and plasma viral loads and SARS-CoV-2 serology and to study their association with mortality and severe forms of COVID-19. . https://doi.org/10.1101/2020.06.17.20132076 doi: medRxiv preprint positive viral load greater than 3 log10 copies/reaction after D10, and ten patients (24.4 %) In this retrospective study conducted in a sample of 40 immunocompromised KTR hospitalized for COVID-19, we precisely determined the temporal evolution of nasopharyngeal and plasma SARS-CoV-2 loads, as well as the serological response to the virus. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China doi = 10.1101/2020.06.17.20132076 id = cord-003045-r707jl16 author = Bhuvaneshwar, Krithika title = viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date = 2018-06-05 keywords = Hepatitis; RNA; viral summary = The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format. doi = 10.3389/fmicb.2018.01172 id = cord-279716-kxfc4npg author = Blachere, Francoise M. title = Bioaerosol sampling for the detection of aerosolized influenza virus date = 2007-10-22 keywords = particle; viral summary = Background Influenza virus was used to characterize the efficacy of a cyclone‐based, two‐stage personal bioaerosol sampler for the collection and size fractionation of aerosolized viral particles. Results Based on qPCR results, we demonstrate that aerosolized viral particles were efficiently collected and separated according to aerodynamic size using the two‐stage bioaerosol sampler. In order to quantify the relative amount of viral particles or fungal spores collected at each stage of the bioaerosol sampler, qPCR was performed in parallel using either serial 10-fold dilutions of cDNA generated from a single dose of non-aerosolized FluMist Ò containing approximately 10 7 TCID 50 per influenza strain or genomic DNA isolated from 10 7 spores. In this study, by aerosolizing FluMist Ò , we demonstrate the recovery of aerosolized viral particles using the bioaerosol sampler and detection of influenza by qPCR. doi = 10.1111/j.1750-2659.2007.00020.x 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-323404-3mw4q7m3 author = Bomsel, Morgane title = Entry of viruses through the epithelial barrier: pathogenic trickery date = 2003 keywords = cell; epithelial; receptor; viral; virus summary = doi = 10.1038/nrm1005 id = cord-281916-v6u5mr2i author = Bonnin, Paul title = Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date = 2016-08-09 keywords = respiratory; sample; viral summary = doi = 10.1186/s12879-016-1730-9 id = cord-018526-rz7id5mt author = Braun, Serge title = Non-viral Vector for Muscle-Mediated Gene Therapy date = 2018-12-14 keywords = dna; gene; muscle; non; viral summary = Nevertheless, the local production of therapeutic proteins that may act distantly from the injected site and/or the hydrodynamic perfusion of safe plasmids remains a viable basis for the non-viral gene therapy of muscle disorders, cachexia, as well as peripheral neuropathies. In humans, intramuscular injections of naked plasmid encoding angiogenic factors (such as VEGF165 or HGF) were used in small numbers of patients with critical limb ischemia and did demonstrate promising clinical efficacy for the treatment of peripheral arterial disease. A meta-analysis of 12 clinical trials (1494 patients total) of local administration of pro-angiogenic growth factors (VEGF, FGF, HGF, Del-1, HIF-1alpha) using plasmid or viral gene transfer by intra-arterial or intramuscular injections showed that, despite promising results in single studies, no clear benefit could be identified in peripheral artery disease patients, irrespective of disease severity [51] . doi = 10.1007/978-3-030-03095-7_9 id = cord-334127-wjf8t8vp author = Brister, J. Rodney title = NCBI Viral Genomes Resource date = 2015-01-28 keywords = NCBI; Viral; sequence summary = This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets. Whereas primary databases are archival repositories of sequence data, reference databases provide curated datasets that enable a number of activities, among them are transfer annotation to related genomes (11) (12) (13) , sequence assembly and virus discovery (14) (15) (16) (17) , viral dynamics and evolution (18) (19) (20) and pathogen detection (14, (21) (22) (23) . The second model captures and standardizes host information for all viruses, and whenever a new RefSeq record is created, a manually curated ''viral host'' property is assigned to the relevant species within the NCBI Taxonomy database. The link to the Retrovirus Resource (http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses) provides access to the Retrovirus Genotyping Tool and HIV-1, Human Interaction Database (50, 51) . doi = 10.1093/nar/gku1207 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-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 = doi = 10.1016/j.biologicals.2004.07.001 id = cord-266147-s8rxzm0t author = Burnouf, Thierry title = Modern Plasma Fractionation date = 2007-03-28 keywords = FVIII; plasma; product; protein; treatment; viral summary = Modern plasma product production technology remains largely based on the ethanol fractionation process, but much has evolved in the last few years to improve product purity, to enhance the recovery of immunoglobulin G, and to isolate new plasma proteins, such as α1-protease inhibitor, von Willebrand factor, and protein C. A complete set of measures-and, most particularly, the use of dedicated viral inactivation and removal treatments-has been implemented throughout the production chain of fractionated plasma products over the last 20 years to ensure optimal safety, in particular, and not exclusively, against HIV, hepatitis B virus, and hepatitis C virus. In the last few years, the complexity of the fractionation process has increased by (a) the introduction of chromatography to isolate new proteins from existing fractions such as cryoprecipitate, cryo-poor plasma, and Cohn fractions; (b) the integration of chromatography to the ethanol fractionation process to increase IgG recovery; and (c) the implementation of dedicated viral inactivation or removal steps. doi = 10.1016/j.tmrv.2006.11.001 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-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-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 = doi = 10.3390/cells3020386 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-103460-5thh6syt author = Carlson, Colin J. title = Climate change will drive novel cross-species viral transmission date = 2020-07-14 keywords = bat; viral summary = doi = 10.1101/2020.01.24.918755 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 = doi = 10.3390/v3101959 id = cord-326273-6rp12py3 author = Chow, Kuan-Chih title = Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date = 2004-04-01 keywords = SARS; cell; viral summary = doi = 10.1309/c0edu0raqbtxbhce 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-270205-fw555w1u author = Cillóniz, Catia title = Pure Viral Sepsis Secondary to Community-Acquired Pneumonia in Adults: Risk and Prognostic Factors date = 2019-10-01 keywords = cap; viral summary = doi = 10.1093/infdis/jiz257 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 = According to the literature data results, namomaterials designed with different shapes and morphologies display numerous advantages for use in antiviral therapy, namely: nanometric size that permits drug delivery through impermeable barriers [88] , large surface area to volume ratios for large drug payloads incorporation [117] and improved efficacy, surface modification and/or backbone functionalization versatility that facilitates cellular membranes passage [118] or enhancing stability and bioavailability [119] , virucidal activity against a series of viruses (HIV, HSV, HBV, etc.) due to biomimetic properties [120] , increased specificity, improved antiviral delivery and controlled drug release to the target [121] through engineered moieties, decrease the emergence of drug resistance, personalized therapy possibility, protection of the drugs and low adverse drug side effects mainly due to the composition. doi = 10.3390/pharmaceutics12020171 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-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 = doi = 10.1016/j.jped.2014.07.001 id = cord-292335-al6v3b9x author = Crotty, Matthew P. title = Impact of antibacterials on subsequent resistance and clinical outcomes in adult patients with viral pneumonia: an opportunity for stewardship date = 2015-11-18 keywords = MDRO; patient; viral summary = doi = 10.1186/s13054-015-1120-5 id = cord-022439-8wy7rpqv author = DENMAN, A.M. title = Viral Etiology of Polymyositis/Dermatomyositis date = 2013-11-17 keywords = antibody; cell; viral; virus summary = doi = 10.1016/b978-0-409-95191-2.50010-0 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-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 = doi = 10.1016/j.semcdb.2020.08.002 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-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-318749-k91oku7h author = Dong, Hui-Jun title = Selective regulation in ribosome biogenesis and protein production for efficient viral translation date = 2020-10-29 keywords = IRES; RNA; protein; viral summary = Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Similarly, ribosomes are required for the protein synthesis of host cells and viruses, but the biogenesis factor RBFs can also impact the proliferation of virus and cell-intrinsic immune responses. The multifunctional nucleolar phosphoprotein nucleophosmin (NPM) plays a lead role in ribosome biogenesis to stimulate RNA Pol I-dependent transcription (Li and Hann 2013) and regulates SARS-CoV, IBV, HIV-1, HCV Recruited by viral proteins to facilitate viral replication Chen et al. RPS25 deletion in yeast or mammalian cells has minimal effects on cellular protein synthesis, which implies that this ribosomal protein may be selectively required for viral IRES-mediated translation (Jack et al. Conservation of multifunctional ribosomal protein metallopanstimulin-1 (RPS27) through complex evolution demonstrates its key role in growth regulation in Archaea, eukaryotic cells, DNA repair, translation and viral replication doi = 10.1007/s00203-020-02094-5 id = cord-269194-b1wlr3t7 author = Engstrom-Melnyk, Julia title = Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date = 2015-12-31 keywords = CMV; FDA; HCV; HIV; HIV-1; PCR; RNA; viral summary = Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. doi = 10.1016/bs.mim.2015.04.005 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 = 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-293038-pjjvfdnq author = Fontana, Juan title = The unique architecture of Bunyamwera virus factories around the Golgi complex date = 2008-06-10 keywords = Fig; Golgi; RNA; tube; viral summary = We propose that this new structure, unique among enveloped viruses, assembles in association with the most stable component of Golgi stacks, the actin‐containing matrix scaffold, connecting viral replication and morphogenesis inside viral factories. Modified membranes harbouring viral replication complexes (RCs) frequently integrate into a complex structure known as the ''viral factory'' where the cytoskeleton participates, cell organelles are recruited and the different steps of the virus life cycle are sequentially connected. We propose that this new multifunctional structure associates with the actin-containing matrix of the Golgi stacks providing a stable scaffold for viral replication and early morphogenesis. LtA and CyD had very little or no effect, respectively, on viral replication and assembly as determined by measurement of infectious viral particles released to the culture supernatants at 6 and 10 h p.i. Complete tubes, virus budding profiles and viral particles assembled in Golgi stacks of cells treated with LtA, as observed in thin sections of treated cells studied by EM (not shown). doi = 10.1111/j.1462-5822.2008.01184.x 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 = 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-274680-6pui91uu author = Gao, Chun title = Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date = 2020-10-14 keywords = SARS; viral summary = doi = 10.1016/j.clim.2020.108611 id = cord-347731-eqxn6auk author = Garcia‐Cremades, Maria title = Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date = 2020-05-12 keywords = HCQ; SARS; viral summary = The data sources included were (i) longitudinal clinical, pharmacokinetic (PK), and virologic data from patients with severe acute respiratory syndrome‐2 (SARS‐CoV‐2) infection who received HCQ with or without azithromycin (n = 116), (ii) in vitro viral replication data and SARS‐CoV‐2 viral load inhibition by HCQ, (iii) a population PK model of HCQ, and (iv) a model relating chloroquine PKs to corrected QT (QTc) prolongation. 12 The drug effect over time on viral replication rate was established by simulating unbound plasma concentrations or unbound lung tissue concentrations using a previously defined partition coefficient (10 2.45 ; HCQ unbound fraction assumed to be ~ 50%) and using the established in vitro sigmoidal efficacy parameters. 3, 9, 10 Viral kinetics were estimated from in vitro replication rate of severe acute respiratory syndrome-coronavirus (SARS-CoV)-1 and unbound drug concentration in plasma and lungs were simulated with HCQ PK model. doi = 10.1002/cpt.1856 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 = 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 = doi = 10.1186/1297-9686-28-5-385 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 = doi = 10.1016/j.micinf.2018.06.002 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 = doi = 10.1002/ana.410220502 id = cord-314024-n6l2804j author = Gonçalves, Antonio title = Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date = 2020-04-07 keywords = SARS; viral summary = We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer 39 viral growth parameters and predict the effects of antiviral treatments. We 162 considered a simple case where the drug effectiveness is assumed to be constant after therapy 163 initiation (see methods) and we calculated the minimal efficacy that would be needed to 164 generate more than 2 logs of viral decline at peak viral load in the 13 studied patients (Fig. 1) . For a putative 167 treatment initiated at the time of infection, symptom onset, or 3 days post symptom onset, a 168 median efficacy of at least 60, 90 and 99% in reducing viral replication would be needed, 169 respectively, to generate more than 2 log of decline in the peak viral load (Fig. 1) . doi = 10.1101/2020.04.04.20047886 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-319675-mwy3t1ny author = Gu, Li title = Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date = 2016-08-17 keywords = respiratory; viral summary = doi = 10.1371/journal.pone.0160777 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-328259-3g4klpyg author = Guajardo-Leiva, Sergio title = Metagenomic Insights into the Sewage RNA Virosphere of a Large City date = 2020-09-21 keywords = NCBI; RNA; Rotavirus; Trebal; sequence; viral summary = Despite the overrepresentation of dsRNA viruses, our results show that Santiago''s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Viral sequences identified as Partitiviridae-like viruses included in the "unclassified RNA viruses ShiM-2016" category in the NCBI taxonomy (~25% abundance; Figure 2B ) and Totiviriade family were also highly abundant in treated and untreated sewage samples from the EU [5, 7] . Therefore, the abundance of these viruses in the Trebal metagenome can expand the known sequence space associated with this family (only 10 genomes are currently available in the NCBI database) and contribute to a better understanding of the bacteriophage biology related to RNA genomes. Taken together, our results show that metagenomic surveys of RNA viruses in sewage samples and the use of HMMs could uncover extraordinary viral diversity through the detection of remote homologs in these human-impacted environments. doi = 10.3390/v12091050 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 = doi = 10.1002/slct.202001709 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 = doi = 10.1016/j.ymeth.2020.06.013 id = cord-286337-qk90xb3a author = Hanada, Shigeo title = Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date = 2018-11-16 keywords = URT; bacterial; infection; respiratory; viral summary = While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. doi = 10.3389/fimmu.2018.02640 id = cord-258685-ayek8zbo author = Har-Noy, Michael title = Allo-priming as a universal anti-viral vaccine: protecting elderly from current COVID-19 and any future unknown viral outbreak date = 2020-05-12 keywords = CTL; IFN-ϒ; Th1; cell; viral summary = Allo-priming healthy elderly adults is proposed to provide universal protection from progression of any type of viral infection, including protection against progression of the current outbreak of COVID-19 infection, and any future variants of the causative SARS-CoV-2 virus or the next ''Disease X''. The lysis of viral infected cells by activated innate effector cells and cross-reactive allo-specific memory CTL releases "danger signals" [18] and heat shock proteins (HSP) [19] which chaperone viral antigens (e.g., GRP78, HSP70) [20, 21] into the microenvironment, creating the conditions for "in situ vaccination", which leads to development of viral-specific cellular immunity. Modulating the immune system of elderly individuals through alloantigen priming to provide high titers of non-exhausted Th1/ CTL memory cells that can be non-specifically activated upon encounter with any virus to cause release type 1 cytokines may provide an immediate anti-viral immune response upon viral exposure and could also reinstate responsiveness to viral vaccines [85] . doi = 10.1186/s12967-020-02363-3 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-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 = doi = 10.1007/bf03256383 id = cord-000346-9b6yz3f4 author = Holder, Benjamin P. title = Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model date = 2011-03-24 keywords = H1N1; H275Y; viral summary = In order to obtain two complementary views of the infection kinetics for the A/Brisbane/59/2007 WT and H275Y mutant strains, virus growth over time was observed in two different in vitro systems: the viral plaque assay and the multiple-cycle viral yield assay. We are left then with two experimental measures -the viral titer growth rate and the plaque velocity -whose values may depend on three unknown infection kinetics parameters: the infecting time, t inf ; the latent infection period, t L ; and the infectious lifespan of a cell, t I . To demonstrate this concept using the A/ Brisbane/59/2007 (H1N1) WT and H275Y mutant strains, we have plotted the experimentally-measured values of plaque velocity and viral titer growth rate as functions of the infecting time and latent infection period, using the model dependence determined above ( Figure 6 ). doi = 10.1371/journal.pone.0014767 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-274780-fmnro0kw author = Hoshino, Y. title = Detection of astroviruses in feces of a cat with diarrhea date = 1981 keywords = particle; viral summary = doi = 10.1007/bf01320252 id = cord-262585-5vjqrnwh author = Hraber, Peter title = Resources to Discover and Use Short Linear Motifs in Viral Proteins date = 2019-08-16 keywords = ELM; host; motif; protein; viral summary = doi = 10.1016/j.tibtech.2019.07.004 id = cord-330200-l6bnxi40 author = Huang, Jianping title = Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date = 2020-04-27 keywords = RNA; SARS; viral summary = title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. doi = 10.1101/2020.04.22.20071258 id = cord-022156-mm8en4os author = Isaiah, Amal title = Tracheal Infections date = 2015-07-14 keywords = bacterial; child; croup; uenza; viral summary = Tracheal infections have a signifi cantly lower incidence compared to infections of the upper respiratory tract, with 1-5 % of all children requiring outpatient evaluation for viral croup within the fi rst 3 years of life. In 1958, the fi rst evidence for association between croup and two newly isolated myxoviruses, parainfl uenza virus types 1 and 2, resulted in separation of two categories of cases-mild, requiring only outpatient follow up, and severe, requiring hospitalization [ 12 ] . Among other important viral pathogens causing tracheal infections, RSV was studied in isolates from sentinel practices in England and Wales from 1975 to 1990, during which an increase in mortality, by as much as 60-80 %, was observed in comparison with parainfl uenza and infl uenza viruses [ 13 ] . [ 31 ] studied the clinical courses of croup caused by parainfl uenza and infl uenza viruses to highlight the differences in morbidity caused by the different viral strains in hospitalized children. doi = 10.1007/978-3-319-21744-4_12 id = cord-021146-wdnnjlcw author = Jandrić, Petar title = Postdigital Research in the Time of Covid-19 date = 2020-03-21 keywords = covid-19; pandemic; viral summary = doi = 10.1007/s42438-020-00113-8 id = cord-308126-wpxhk0pf author = Jaume, Francesca title = Common Cold and Acute Rhinosinusitis: Up-to-Date Management in 2020 date = 2020-06-03 keywords = ABRS; ARS; viral summary = doi = 10.1007/s11882-020-00917-5 id = cord-270294-g95skuik author = Johnstone, Jennie title = Viral Infection in Adults Hospitalized With Community-Acquired Pneumonia Prevalence, Pathogens, and Presentation date = 2008-12-31 keywords = infection; patient; viral summary = Furthermore, viral etiology studies in pneumonia are difficult to interpret as noninvasive viral detection methods are often considered to be only markers of infection rather than the cause of pneumonia." Clearly, much better knowledge of the potential role of respiratory viruses present in patients with pneumonia is needed. More recently, the introduction of highly sensitive nucleic acid amplification tests (NATs) has dramatically improved our ability to detect multiple viral pathogens such as influenza, respiratory syncytial virus (RSV), rhinovirus, parainfluenza, and adenovirus. [13] [14] [15] To date, there have been few studies, 5, 7, [9] [10] [11] 16 ,17 reported in patients with pneumonia using NATs to detect viral infection, and these studies have either not included clinical data 7.9.11 or have not tested for all potentially important respiratory viruses in a comprehensive manner.lv-!? doi = 10.1378/chest.08-0888 id = cord-006450-si5168pb author = Jouneau, S. title = Which patients should be tested for viruses on bronchoalveolar lavage fluid? date = 2012-12-14 keywords = BALF; PCR; viral summary = The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). The variables significantly associated with positive viral tests on univariate analysis were immunosuppression (i.e., HIV infection, corticosteroids >10 mg/day for ≥3 weeks, and/or other immunosuppressive therapy), ground-glass attenuations on chest CT scans, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) ICU stay, and (iii) mechanical ventilation before BAL was performed (p<0.01 for each comparison). This advocates for the systematic use of PCR techniques for viral tests in BALF, in accordance with previous studies [27, 28] , in the situations where viruses may reasonably be suspected (i.e., acute lower tract respiratory disease in immunocompromised patients and/or patients with unexplained bilateral ground-glass attenuations on CT scan). doi = 10.1007/s10096-012-1791-7 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-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 = doi = 10.1016/j.cvsm.2008.02.009 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-343377-6muareue author = Kidszun, André title = Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date = 2016-05-16 keywords = PCR; viral summary = Objective The aim of our study was to evaluate the occurrence of viral infections in infants with suspected late-onset bacterial sepsis in a neonatal intensive care unit. Methods In a prospective study, infants with suspected late-onset bacterial sepsis underwent viral testing alongside routine blood culture sampling. Bennett et al performed a surveillance study of viral respiratory infections in two NICUs. All infants of a gestational age < 33 weeks were tested twice a week using multiplex RT-PCR ELISA. Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units Viral respiratory tract infections in the Neonatal Intensive Care Unit doi = 10.1055/s-0036-1584150 id = cord-329306-p5wmqmvj author = Kim, Kiwook title = Rhinovirus Associated Severe Respiratory Failure in Immunocompetent Adult Patient date = 2014-09-30 keywords = respiratory; viral summary = Rhinovirus infection is typically associated with the common cold and has rarely been reported as a cause of severe pneumonia in immunocompetent adults. Rhinovirus infection can extend to lower respiratory tract in children [4] [5] [6] or immunocompromised hosts 7, 8 , but is generally not concerned as singular cause of severe pneumonia, especially in immunocompetent adults. Although technical advances have allowed for increased detection of viral pneumonia, viral infections other than influenza are generally not considered as causes of severe respiratory tract infection in immunocompetent hosts, because viral clearance usually occurs rapidly in healthy individuals. Therefore, it is still believed that severe viral pneumonia caused by frequently exposed rhinovirus could hardly occurs in immunocompetent adults. On the contrary, our relatively young immunocompetent patient suffered severe rhinovirus pneumonia without bacterial co-infection, which was confirmed by BAL fluid analysis, and not by the nasopharyngeal specimen. Rhinovirus associated with severe lower respiratory tract infections in children doi = 10.4046/trd.2014.77.3.132 id = cord-317037-1qydcc5e author = Kumar, Asit title = Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date = 2020-08-13 keywords = Exosomes; Extracellular; HIV; RNA; SARS; Vesicles; viral summary = doi = 10.3390/v12080887 id = cord-329710-vqorb6j7 author = Kumar, Krishna title = Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date = 2020-05-27 keywords = RNA; SARS; viral summary = We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. doi = 10.1021/acsmedchemlett.0c00254 id = cord-001340-kqcx7lrq author = Ladner, Jason T. title = Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing date = 2014-06-17 keywords = genome; sequence; viral summary = doi = 10.1128/mbio.01360-14 id = cord-274749-ji91qq9q author = Lagare, Adamou title = Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger date = 2015-11-14 keywords = Niger; respiratory; viral summary = The viruses most frequently detected in children with ARIs include respiratory syncytial virus (RSV), influenza virus (INF) types A and B, adenovirus (AV), parainfluenza virus (PIV), human metapneumovirus (HMPV) and rhinovirus (RV) [3] [4] [5] ; however, the clinical presentations of respiratory tract infections are similar, making it difficult to distinguish between etiologic agents without a laboratory diagnosis [6] . We aimed to document the prevalence of selected viral and bacterial infections among children <5 years of age hospitalized with severe acute respiratory illness (SARI) at selected hospitals in Niger from January 2010 through December 2012. We report the detection rate of selected viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger. This study reports the detection rate of viral and bacterial pathogens among children <5 years of age hospitalized with SARI in Niger. doi = 10.1186/s12879-015-1251-y id = cord-286328-ap0wfjhq author = Lewis, Toby C. title = Nasal cytokine responses to natural colds in asthmatic children date = 2012-11-26 keywords = IFN; asthma; infection; viral summary = CONCLUSIONS & CLINICAL RELEVANCE: We conclude that, in children with asthma, naturally-occurring viral infections apparently induce a robust innate immune response including expression of specific chemokines, IFNs and IFN-responsive genes. To further examine the innate immune response to viral infection in children with asthma, we measured nasal aspirate cytokine levels in 16 asthmatic children before and after upper respiratory tract infections. We also examined the effects of upper respiratory tract infection on mRNA levels of selected markers of viral infection, including IFNs. Finally, we evaluated a new method of virus detection using a single polymerase chain reaction-ligation detection reaction (PCR-LDR) multiplex assay. We performed home measurements of respiratory symptoms and collected nasal secretions (for detection of viral RNA by PCR and host biomarkers by PCR and ELISA) on 3 days during a week when children were healthy (not reporting upper respiratory tract infection or asthma symptoms), and again during a week when they experienced cold or flu-like symptoms. doi = 10.1111/cea.12005 id = cord-319215-8tdtia5w author = Li, Iris W. title = The Natural Viral Load Profile of Patients With Pandemic 2009 Influenza A(H1N1) and the Effect of Oseltamivir Treatment date = 2010-04-30 keywords = A(H1N1; H1N1; NPA; viral summary = doi = 10.1378/chest.09-3072 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 = doi = 10.1016/j.tips.2013.11.006 id = cord-265900-7lj4bfli author = Luo, Honglin title = Interplay between the virus and the ubiquitin–proteasome system: molecular mechanism of viral pathogenesis date = 2015-09-29 keywords = UPS; isg15; viral summary = Several proteins encoded by DNA tumor viruses, such as the human papillomavirus (HPV) E6 and E7 proteins [14, 15] and the adenovirus E1B55k/E4orf6 proteins [16] , have been shown to induce the assembly of an E3 ligase complex that contains both viral protein and cellular E3 to catalyze the ubiquitination of p53 and subsequent degradation by the proteasome. In addition to its pro-viral function usurped by viruses as discussed above, the UPS-mediated cellular protein degradation may also represent a host defense mechanism against viral infection. ISG15 and the ISGylation conjugation system represent an important host defense mechanism against infection of a broad spectrum of viruses, including Sindbis virus, Viral interaction with the host ubiquitin-proteasome system (UPS): pro-viral and anti-viral function of the UPS in viral pathogenesis. The UPS, including modification of key signaling molecules involved in innate immunity by ubiquitin or ubiquitin-like modifiers (e.g. SUMO and ISG15), represents an important host anti-viral defense mechanism. doi = 10.1016/j.coviro.2015.09.005 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-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-303330-zh8wzza5 author = Magleby, Reed title = Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date = 2020-06-30 keywords = COVID-19; SARS; viral summary = doi = 10.1093/cid/ciaa851 id = cord-314560-rswa5zdn author = Manjunath, N. title = Interfering antiviral immunity: application, subversion, hope? date = 2006-06-06 keywords = HIV; RNA; siRNA; viral summary = RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. However, in recent years, a new type of genomic immunity mediated by RNA interference (RNAi) has emerged and has sparked intense interest as a potential treatment strategy for a variety of diseases, including viral infections, cancer and degenerative diseases [1] [2] [3] [4] . In RNAi, long double-stranded (ds) RNA generated during viral infection is cleaved by an enzyme termed Dicer into short, 21-23 nucleotide (nt) dsRNA molecules termed small interfering (si)RNAs that mediate sequence-specific gene silencing [5, 6] . A landmark development in the field occurred with the discovery that the introduction of 21-nt-long synthetic RNA resembling the Dicer-processed siRNA into mammalian cells induces sequence-specific gene silencing without evoking the interferon response [10] . doi = 10.1016/j.it.2006.05.006 id = cord-018430-u3k8pds6 author = Mason, Jay W. title = Myocarditis date = 2007 keywords = Chagas; DCM; acute; biopsy; cardiac; disease; heart; myocardial; myocarditis; patient; ventricular; viral summary = The classification states that "myocarditis is diagnosed by established histological, immunological and immunohistochemical criteria." The Dallas criteria 5 provide consensus-derived histologic criteria: "an inflammatory infiltrate of the myocardium with necrosis and/or degeneration of adjacent myocytes not typical of ischemic damage associated with coronary artery disease." However, many have speculated that less pronounced histologic abnormalities may be present and that additional molecular, immunologic, and immunohistochemical diagnostic criteria can be used productively. 330 These criteria define active myocarditis (see also Fig. 59 .7A) as "an inflammatory infiltrate of the myocardium with necrosis and/or degeneration of adjacent myocytes not typical of ischemic damage associated with coronary artery disease." Furthermore, other causes of inflammation (e.g., connective tissue disorders, infection, drugs) should be excluded. 392 An interesting hypothesis to explain the high frequency of dilated heart muscle disease is the presence of myocarditis in HIV-infected patients with left ventricular dysfunction. The ECG abnormalities suggesting myocardial involvement are present in a high proportion of patients, 414 but clinical evidence of cardiac dysfunction occurs in only 10% to 25% of cases. doi = 10.1007/978-1-84628-715-2_62 id = cord-011095-79ce5900 author = Meskill, Sarah D. title = Respiratory Virus Co-infection in Acute Respiratory Infections in Children date = 2020-01-24 keywords = RSV; infection; respiratory; viral summary = doi = 10.1007/s11908-020-0711-8 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-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-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-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-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-010233-772e35kx author = Monto, Arnold S. title = Respiratory illness caused by picornavirus infection: a review of clinical outcomes date = 2002-01-03 keywords = infection; respiratory; viral summary = doi = 10.1016/s0149-2918(01)80133-8 id = cord-337636-3yc0ribg author = Morehouse, Zachary P. title = A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date = 2020-08-25 keywords = PCR; SARS; viral summary = Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. Using human coronavirus 229E (HCoV-229E) as our model organism, we developed a novel two-step methodology of optimized shaker-mill homogenization parameters that allowed for direct-to-PCR viral detection. doi = 10.1186/s12985-020-01405-y id = cord-294592-zwvr57a0 author = Mukherjee, Moumita title = Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date = 2020-08-11 keywords = RNA; SARS; UTR; viral summary = doi = 10.1371/journal.pone.0237559 id = cord-287758-da11ypiy author = Mônica Vitalino de Almeida, Sinara title = COVID-19 therapy: what weapons do we bring into battle? date = 2020-09-10 keywords = ACE2; COVID-19; CoV-2; Coronavirus; FDA; FIG; MERS; RNA; SARS; drug; patient; viral summary = The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. doi = 10.1016/j.bmc.2020.115757 id = cord-262753-jld1ygxt author = Neidermyer, William J. title = Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date = 2019-06-21 keywords = Fig; RNA; VSV; cell; polysome; viral summary = doi = 10.1371/journal.ppat.1007875 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-306921-3afgpunj author = Owino, Collins Oduor title = Recent advances on the role of host factors during non-poliovirus enteroviral infections date = 2019-06-19 keywords = A71; D68; Enterovirus; RNA; viral summary = A small siRNA screen targeting human membrane trafficking genes identified vasolin-containing protein (VCP-p97) as an important protein essential after PV viral replication and it interacts and colocalizes with 2 BC/2C as well as 3AB/3B in poliovirus infected cells [83] . Human host factors-viral protein studies identified nuclear factor; adenosine-uridine (AU)-rich element RNA binding factor 1 (AUF1) is targeted for cleavage by CV-B3 viral 3C protease upon translocation to the cytoplasm for enhanced stability of the IRES dependent viral RNA production [112] , similar antiviral observations were made for poliovirus, coxsackievirus and human rhinovirus [113] . A subsequent study by Mohamud and colleagues demonstrated that SQSTM1 and another host factor calcium binding and coiled-coil domain-containing protein 2/nuclear dot 10 protein 52 (CALCOCO2) regulate CV-B3 virus infection by targeting autophagy receptors; via their interaction with viral protein 1 [177] . doi = 10.1186/s12929-019-0540-y 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-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-342133-khrljehj author = Principi, Nicola title = Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date = 2015-08-12 keywords = child; infection; respiratory; viral summary = To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children doi = 10.1371/journal.pone.0135640 id = cord-007255-jmjolo9p author = Pulliam, Juliet R. C. title = Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses date = 2009-02-15 keywords = model; viral summary = The database contains information on the 3 molecular characteristics hypothesized to influence the potential of a virus to cross host species: site of replication (X SR ; whether replication is completed in the cytoplasm or requires nuclear entry), genomic material (X GM ; RNA or DNA), and segmentation of the viral genome (X Seg ; segmented or nonsegmented). Hypothesis testing allowed us to determine how likely it was that the observed patterns were due to chance, whereas model-based prediction allowed us to determine what trait or set of traits was the best predictor of a livestock virus''s ability to infect humans and to estimate the probability that a particular virus species would be able to jump host species, given knowledge of the traits of interest. To examine the magnitude and relative importance of the effects that the 3 molecular characteristics of interest have on the ability of the viral species in the database to infect humans, we developed a set of logistic regression models. doi = 10.1086/596510 id = cord-286843-8qh1pblc author = Quah, Jessica title = Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date = 2018-09-04 keywords = cap; patient; severe; viral summary = doi = 10.1186/s12879-018-3366-4 id = cord-305195-e41yfo89 author = Rainwater-Lovett, Kaitlin title = Viral Epidemiology: Tracking Viruses with Smartphones and Social Media date = 2016-02-12 keywords = Google; HIV; disease; internet; viral summary = doi = 10.1016/b978-0-12-800964-2.00018-5 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-272655-qeojdpez author = Remolina, Yuly Andrea title = Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia date = 2015-11-17 keywords = Influenza; patient; viral summary = doi = 10.1371/journal.pone.0143152 id = cord-330684-3hxau5vt author = Richard, A title = Caspase cleavage of viral proteins, another way for viruses to make the best of apoptosis date = 2012-03-08 keywords = caspase; cleavage; viral summary = Several unrelated viruses have been described to take advantage of apoptosis induction by expressing proteins targeted by caspases, the key effectors of apoptotic cell death. Based on the well-described case of AMDV, we can In some cases, apoptosis induction by the host cell leads to exactly what is expected, namely viral attenuation, but surprisingly with the help of viral protein cleavages. However H-1PV is able to activate caspases in non-transformed cells, leading to the cleavage of NS1, a non-structural protein (NS) notably involved in viral DNA replication and gene expression by transactivating P38 promoter, which controls the synthesis of capsid proteins. In HRT18jap1 cells, the infection causes apoptosis but is not productive, suggesting that caspase activation (and possibly N caspase cleavage) prevents progeny virion generation. Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection doi = 10.1038/cddis.2012.18 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-275683-1qj9ri18 author = Roux, Simon title = Metagenomics in Virology date = 2019-06-12 keywords = RNA; genome; viral; virus summary = doi = 10.1016/b978-0-12-809633-8.20957-6 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-015893-e0fofgxq author = Ryhal, Bruce title = Viral Disease, Air Pollutants, Nanoparticles, and Asthma date = 2011-05-03 keywords = HRV; asthma; child; respiratory; viral summary = doi = 10.1007/978-1-4419-6836-4_11 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 = doi = 10.1186/1743-422x-2-70 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-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 = doi = 10.1016/j.cytogfr.2017.05.007 id = cord-252763-gy8f1oyt author = Shetty, Mamatha title = Viral Diarrhoea in a Rural Coastal Region of Karnataka India date = 1995-10-17 keywords = India; viral summary = A total of 106 children below 5 years of age admitted to the Kasturba Medical College Hospital Manipal Karnataka (South India) were investigated over a period of 6 months to determine the aetiologkal role of viruses in acute diarrhoea. 1 " 3 In view of the recent recognition of some viral aetiological agents of acute infantile diarrhoea, we conducted the present study to identify viruses as the causative agents of infantile diarrhoea in Manipal, a place in Coastal Karanataka (South India). One-hundred-and-six children aged below 5 years, suffering from acute watery diarrhoea of less than 4 days'' duration who attended the out patient clinic of paediatric dept of the Kasturba Medical College Hospital, Karanataka, South India were included in the study. Enteric adenoviruses are well established as respiratory viruses and are second to Rotavirus as the most common cause of pediatric viral gastroenteritis. doi = 10.1093/tropej/41.5.301 id = cord-002608-zn7tm1ww author = Sokoloski, Kevin J. title = Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date = 2017-06-29 keywords = Fig; RNA; SINV; interaction; viral summary = A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. This report details our efforts to identify and characterize the sites of interaction between the viral capsid protein and the genomic RNA using the model alphavirus Sindbis virus (SINV). C) The infectivity of the individual SINV C:R interaction site mutants and parental wild type virus as reported as the ratio of total particles per infectious unit as determined using BHK-21 cells. doi = 10.1371/journal.ppat.1006473 id = cord-009101-376snefs author = Strodtbeck, Frances title = Viral Infections of the Newborn date = 2015-12-16 keywords = Strodtbeck; infection; viral summary = doi = 10.1111/j.1552-6909.1995.tb02548.x id = cord-353810-mf753ae9 author = Tan, Cedric Chih Shen title = A novel method for the capture-based purification of whole viral native RNA genomes date = 2019-04-08 keywords = PCR; RNA; capture; viral summary = This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. Based on the mapping rates to human and DENV1 reference genomes for pre and post-capture groups, shown in Table 2 , purification factor was calculated to be 272-fold. The minimum coverage required for variant calling was, as described above, benchmarked to that of Illumina reads so that the effectiveness of our capture-based purification method could be more accurately evaluated based on the higher error read rates of direct RNA sequencing technology. Indeed, after comparison of the postcapture and concentrated post-capture sequencing runs (Table 2) , the 2.5-fold increase in the percentage of reads mapping to DENV1 suggests that scaling our method greatly improved the signal-to-noise ratio of this particular downstream RNA assay. doi = 10.1186/s13568-019-0772-y 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-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-254478-scc9wee0 author = To, Kelvin Kai-Wang title = Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date = 2020-03-23 keywords = SARS; load; patient; viral summary = title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses. We present findings of an observational cohort study of the temporal profile of viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from posterior oropharyngeal saliva samples and serum antibody responses, dated by symptom onset and correlated with clinical findings. doi = 10.1016/s1473-3099(20)30196-1 id = cord-343470-w215pzdc author = Tsai, Kevin title = Epigenetic and epitranscriptomic regulation of viral replication date = 2020-06-12 keywords = HIV-1; PML; RNA; dna; viral summary = Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs). doi = 10.1038/s41579-020-0382-3 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 = doi = 10.1264/jsme2.me15171 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-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 = doi = 10.1038/s41564-019-0465-y 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 = doi = 10.1016/j.coviro.2012.07.007 id = cord-327444-y2464gjh author = Wilson, M.R. title = Meningitis, Viral date = 2014-05-01 keywords = CSF; meningitis; viral summary = doi = 10.1016/b978-0-12-385157-4.00384-5 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-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 = doi = 10.3389/fimmu.2018.01547 id = cord-325626-r7k7u7ro author = Yu, Xia title = SARS-CoV-2 viral load in sputum correlates with risk of COVID-19 progression date = 2020-04-23 keywords = viral summary = doi = 10.1186/s13054-020-02893-8 id = cord-353554-98uzivsk author = Zhang, Zheng title = Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date = 2018-03-08 keywords = receptor; viral summary = title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. 64 The virus-receptor interaction was reported to be a principal determinant of viral host 65 range, tissue tropism and cross-species infection [11, 16, 22] . However, we found the viral receptor tended not to interact with each 248 other ( Figure S3D 270 Since the virus has to compete with other proteins for binding to the receptor, proteins (Table S5) . doi = 10.1101/271171 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 = doi = 10.1002/rmv.1872 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 = doi = 10.1016/s0174-3031(82)80128-5 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-018325-k69h9cc5 author = Çatlı, Tolgahan title = Acute Viral Rhinitis date = 2019-05-14 keywords = AVR; nasal; viral summary = doi = 10.1007/978-3-030-21217-9_23