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?' ---------------------------------------------------------- 89 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 6416 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 47 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 13 figure 12 SARS 10 RNA 8 PCR 7 cell 7 IFN 6 virus 5 respiratory 5 protein 4 dna 4 HCV 4 COVID-19 3 RSV 3 PEDV 2 strain 2 pneumoniae 2 peptide 2 infection 2 covid-19 2 ZIKV 2 Vero 2 United 2 UPR 2 Mycoplasma 2 Illumina 2 IFITM3 2 HRV 2 HIV-1 2 HCT 2 EBV 2 DENV 1 viral 1 tag 1 table 1 student 1 stat1 1 social 1 slam 1 rig 1 resistance 1 pneumonia 1 plant 1 phage 1 pdcov 1 pcv2 1 patient 1 mv.1.lu 1 membrane 1 lncRNAs 1 individual Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 4395 virus 4191 cell 3076 protein 2983 infection 1436 % 1347 study 1067 figure 966 host 955 gene 926 analysis 874 expression 842 disease 833 patient 822 sequence 797 type 728 sample 725 replication 711 response 710 genome 700 strain 677 group 674 peptide 665 detection 663 antibody 653 result 638 activity 616 time 604 level 581 membrane 581 datum 565 role 537 treatment 534 assay 524 mouse 511 control 501 domain 481 site 476 region 470 effect 465 pathway 456 receptor 447 pathogen 441 factor 441 case 439 phage 438 acid 435 interaction 431 specie 428 p 427 method Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 7179 al 6276 . 5658 et 918 RNA 602 C 578 SARS 548 IFN 500 PCR 407 HCV 346 CoV-2 279 HEV 270 β 248 PEDV 236 China 235 ER 229 Figure 209 M. 192 United 187 Table 184 COVID-19 181 Vero 181 States 179 • 179 RSV 179 EGR1 176 RT 175 A 174 HIV-1 172 | 172 B 167 CoV 165 ZIKV 165 ERAD 159 LG 157 PMO 157 CYPA 155 G. 151 AR 150 HRV 146 PRRSV 144 PBS 144 KSHV 144 E 140 T 139 IGF1 136 TGEV 132 IFITM3 130 DENV 128 M 128 L Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1080 we 916 it 321 i 291 they 122 them 52 us 22 itself 22 he 14 themselves 10 ifitm3 9 one 5 you 5 me 3 ypk30 2 she 2 myself 2 himself 2 herself 1 λr1 1 z2-cy5 1 z"ikv 1 yourself 1 thee 1 ourselves 1 nur77 1 leu415 1 ire1mrna 1 imagej 1 ifitms 1 him 1 hacats 1 eks 1 cidr1α 1 's Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 15728 be 2431 have 1996 use 1135 show 781 induce 726 infect 723 associate 719 include 634 detect 561 base 519 bind 492 find 485 identify 484 increase 461 suggest 458 inhibit 444 do 432 cause 429 perform 417 indicate 413 compare 406 report 388 mediate 376 target 369 follow 357 involve 357 contain 351 describe 347 require 346 provide 328 signal 328 observe 322 reduce 311 result 309 express 296 obtain 291 regulate 291 demonstrate 288 treat 286 produce 283 reveal 275 determine 261 develop 260 know 258 analyze 246 relate 246 lead 239 activate 225 occur 225 consider Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1935 viral 1256 not 1194 - 1172 human 1076 also 1073 respiratory 859 high 758 other 643 such 598 different 565 clinical 551 specific 550 however 524 more 476 low 474 antiviral 469 immune 455 well 450 only 393 anti 390 cellular 387 most 385 further 379 positive 375 non 363 important 362 then 361 new 360 molecular 350 bacterial 334 several 328 acute 325 as 318 thus 306 respectively 300 significant 300 severe 298 significantly 298 first 274 like 271 potential 269 novel 265 therefore 257 porcine 249 antimicrobial 248 recent 248 previously 247 single 245 similar 244 many Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 108 most 56 least 43 high 41 good 40 Most 26 close 15 late 14 large 7 small 7 low 6 strong 6 great 4 old 2 long 2 early 2 deep 2 MOST 2 -I 1 young 1 vRNA 1 tremeGENE 1 short 1 safe 1 ofinter 1 new 1 near 1 https://web.mit.edu/$\sim$csvoss/Public/usabo/stats_handout.pdf 1 bottommost 1 big 1 Rab7-positive 1 GRP58 1 -t 1 -q Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 279 most 62 least 11 well 2 fast 1 lowest 1 early 1 -biotin Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 28 www.frontiersin.org 10 github.com 7 journal.frontiersin.org 4 www.youtube.com 4 www 4 clinicaltrials.gov 2 www.targetscan 2 www.ncbi.nlm.nih.gov 2 www.ebi.ac.uk 2 gph.niid.go.jp 1 www.who 1 www.uniprot.org 1 www.targetscan.org 1 www.sqlite.org 1 www.sealinksproject.com 1 www.rcsb 1 www.nih.go.jp 1 www.gisaid 1 www.genome.jp 1 www.cytoscape.org 1 www.compbio.dundee.ac 1 www.ch.embnet.org 1 www.cbs.dtu.dk 1 www.broadinstitute.org 1 www.r-project 1 web.mit.edu 1 string-db.org 1 string-db 1 proline.bic.nus.edu.sg 1 primerexplorer.jp 1 figshare.com 1 cgc.sbgenomics.com 1 aps.unmc.edu 1 alfred.med.yale.edu 1 r-project.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 23 http://www.frontiersin.org/articles/10.3389/fmicb 7 http://journal.frontiersin.org/article/10.3389/fmicb 6 http://github.com/ICBI/viGEN/ 4 http://www 3 http://www.frontiersin.org/articles/10.3389/fmicb.2020 2 http://www.targetscan 2 http://www.frontiersin.org/articles/10.3389/fmicb.2018 2 http://www.ebi.ac.uk/ena/data/view/ 2 http://gph.niid.go.jp/geograph/dengue/content/genomemap 1 http://www.youtube.com/watch?v=jFCD8Q6qSTM&t=176s 1 http://www.youtube.com/watch?v=fCd6B5HRaZ8 1 http://www.youtube.com/watch?v=Jnk_4Maf5Fk 1 http://www.youtube.com/channel/UCfJyQ3P2k_SuqfxVdqIEQNw 1 http://www.who 1 http://www.uniprot.org/ 1 http://www.targetscan.org 1 http://www.sqlite.org/ 1 http://www.sealinksproject.com/ 1 http://www.rcsb 1 http://www.nih.go.jp/niid/en/iasr-e.html 1 http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/ 1 http://www.ncbi.nlm.nih.gov/tools/primer-blast/ 1 http://www.gisaid 1 http://www.genome.jp/kegg/ 1 http://www.cytoscape.org/ 1 http://www.compbio.dundee.ac 1 http://www.ch.embnet.org/software/TMPRED_form.html 1 http://www.cbs.dtu.dk/services/TMHMM/ 1 http://www.broadinstitute.org/ 1 http://www.R-project 1 http://web.mit.edu/$\sim$csvoss/Public/usabo/stats_handout.pdf 1 http://string-db.org 1 http://string-db 1 http://proline.bic.nus.edu.sg/denvdb/ 1 http://primerexplorer.jp/elamp4.0.0/index 1 http://github.com/jfouret/scaff2links 1 http://github.com/jfouret/pMed_ 1 http://github.com/glennhickey/progressiveCactus 1 http://github.com/ 1 http://figshare.com/articles/dataset_for_the_ 1 http://clinicaltrials.gov/ct2/show/NCT03481244 1 http://clinicaltrials.gov/ct2/show/NCT02367313 1 http://clinicaltrials.gov/ct2/show/NCT02032381 1 http://clinicaltrials.gov/ct2/show/NCT01502072 1 http://cgc.sbgenomics.com 1 http://aps.unmc.edu/AP/ 1 http://alfred.med.yale.edu/alfred/high 1 http://R-project.org Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 13 cells were co 13 cells were then 13 group was significantly 8 studies have also 6 cells was significantly 6 expression was also 6 results are consistent 6 study are available 5 cells did not 4 cells do not 4 cells were also 4 cells were further 4 cells were not 4 cells were transiently 4 group were significantly 4 samples were further 4 studies involving human 4 virus infected cells 3 activity is not 3 cells is dependent 3 cells showed little 3 cells were always 3 expression was not 3 expression was significantly 3 genes were also 3 group was higher 3 infection has not 3 infection is dependent 3 infections are generally 3 protein is essential 3 protein is important 3 proteins were detectable 3 proteins were up 3 results were also 3 samples were then 3 virus is essential 3 virus is highly 3 virus is not 3 virus was first 2 activities were also 2 activity was also 2 analyses do not 2 antibodies using whole 2 cells are not 2 cells containing empty 2 cells using lipofectamine 2 cells was also 2 cells was not 2 cells was rapidly 2 cells were cultured Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 3 study caused no significant 2 study suggests not only 1 activity is not present 1 analysis showed no obvious 1 antibodies were not present 1 cells are not natural 1 cells are not susceptible 1 cells did not significantly 1 cells were no longer 1 cells were not apparently 1 diseases are not physically 1 expression does not effectively 1 expression had no obvious 1 expression was not only 1 genes does not necessarily 1 genome is not randomly 1 group showed no significant 1 group was not statistically 1 group were not obvious 1 groups had no significant 1 groups have not enough 1 groups was not significant 1 hosts does not necessarily 1 infection are not reliably 1 infection induced no obvious 1 infection is not available 1 infection is not fully 1 peptides had no detectable 1 protein is not essential 1 proteins were not significantly 1 results are not valid 1 results was not statistically 1 results were not stratified 1 results were not valid 1 sample was not successful 1 strains are not consistent 1 studies is not clear 1 study is not far 1 study showed no protective 1 virus is not critical 1 viruses is not common 1 viruses is not only 1 viruses was not due 1 viruses was not significantly 1 viruses were not part A rudimentary bibliography -------------------------- id = cord-302928-nnly9ju8 author = Adachi, Akio title = Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date = 2020-03-18 keywords = HIV-1 summary = Most cited articles and most viewed RTs in the human/animal virus field of the section (top 5, as of February 3, 2020) are as follows, respectively: articles, "Epidemiological aspects and world distribution of HTLV-1 infection" (Gessain and Cassar, 2012) , "Pathology of asthma" (Kudo et al., 2013) , "Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data" (Beerenwinkel et al., 2012) , "ER stress, autophagy, and RNA viruses" (Jheng et al., 2014) , and "Zika virus: the latest newcomer" (Saiz et al., 2016) ; RTs, "Highly mutable animal RNA viruses: adaptation and evolution" , "Virus discovery by metagenomics: the (im)possibilities" (Dutilh et al., 2017) , "Zika virus research" (Bueno-Marí et al., 2018), "Pathophysiology and epidemiology of virus-induced asthma" (Kimura and Ryo, 2014) , and "Forefront studies on HTLV-1 oncogenesis" (Mahieux and Watanabe, 2013) . doi = 10.3389/fmicb.2020.00431 id = cord-319614-4qi59pbz author = Benej, Martin title = Quantitative Proteomics Reveal Peroxiredoxin Perturbation Upon Persistent Lymphocytic Choriomeningitis Virus Infection in Human Cells date = 2019-10-25 keywords = Akt; LCMV; ROS; cell; protein summary = Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. These data suggest that LCMV maintains its replication in persistently infected cells by regulating redox signaling through modulation of local levels of H 2 O 2 and subsequent activation of cellular processes that it uses for its own benefit. Notably, the treatment with antioxidants also resulted in reduced levels of viral NP in HeLa, as well as in A549 LCMV-infected cells, suggesting a link between ROS-dependent signaling and virus replication (Figures 7B,D and Supplementary Figure S2B ). doi = 10.3389/fmicb.2019.02438 id = cord-319460-n4ezxnjc author = Bertasio, Cristina title = Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date = 2016-12-15 keywords = PCR; PEDV; Table summary = doi = 10.3389/fmicb.2016.02009 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-333309-21czobqy author = Byun, Hyewon title = ERAD and how viruses exploit it date = 2014-07-03 keywords = CD4; ERAD; MHC; Rem; protein summary = Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins doi = 10.3389/fmicb.2014.00330 id = cord-264071-hg0qslyx author = Camelo-Castillo, Anny title = Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date = 2019-01-28 keywords = 16S; IPD; PCR; Streptococcus summary = doi = 10.3389/fmicb.2019.00011 id = cord-298240-vcph52gn author = Chan, Shiu-Wan title = The unfolded protein response in virus infections date = 2014-09-30 keywords = UPR summary = This research topic collated a number of review articles and original research article, in an attempt to highlight how viruses interact with the host UPR in the establishment of acute, chronic and latent infections. The relationship between virus and UPR and its associated autophagy is being addressed in three reviews focusing on RNA viruses, as their life cycles are closely associated with the ER (Blazquez et al., 2014; Fung and Liu, 2014; Jheng et al., 2014) . An important question remains as to whether UPR represents a new tool for sensing viruses or select UPR molecules are merely being co-opted in "microbial stress response." This is being addressed in Judith Smith''s review, in which she provides a critique on the intersection of the UPR with the inflammatory pathways and innate immunity and offers an insight into UPR-PRR synergy as an evolutionary adaptation to ensure specificity of anti-viral responses (Smith, 2014) . doi = 10.3389/fmicb.2014.00518 id = cord-343132-qqhivgkq author = Chang-Liao, Wan-Ping title = Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains date = 2020-07-15 keywords = PEDV; Vero; YPK30 summary = The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. As shown in Figure 3 , the metabolic activity of Vero cells pretreated with the intracellular extracts of Ln. mesenteroides, regardless of which strain, were similar to those pretreated with IFN-α2b (p > 0.05) but were significantly higher than the un-pretreated cells (p < 0.05), indicating that all the Ln. mesenteroides strains isolated from kefir grains possessed in vitro prophylactic effects against PEDV. durans, Lb. kefiri, Lc. lactis, and Ln. mesenteroides , were isolated from kefir grains, and the in vitro prophylactic effects of the intracellular extracts of these four species against PEDV infection in Vero cells were compared. Therefore, the in vitro prophylactic and therapeutic effects of the intracellular extracts of Ln. mesenteroides YPK30 against PEDV in Vero cells seem not be attributed to the direct interaction of bacterial components or metabolites with virus. doi = 10.3389/fmicb.2020.01578 id = cord-278540-gy65bvot author = Chen, I-Yin title = Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome date = 2019-01-29 keywords = NLRP3; SARS summary = doi = 10.3389/fmicb.2019.00050 id = cord-329003-ovnzlpa2 author = Chen, Mengmeng title = Rabbit Hemorrhagic Disease Virus Non-structural Protein 6 Induces Apoptosis in Rabbit Kidney Cells date = 2019-01-09 keywords = NSP6; RHDV; RK13; cell summary = doi = 10.3389/fmicb.2018.03308 id = cord-353957-0pjg25kn author = Chen, Shilong title = Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date = 2017-04-20 keywords = ATMUV; DF-1; IFITM3; IFN; PCR summary = Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. Interestingly, we observed that ATMUV infection could trigger duck innate immune response including robust expression of particular type I and type III IFNs and IFITM family proteins. Our previous studies had shown that ATMUV infection effectively triggers the host innate immune response, including robust upregulation of type I and type III IFNs and some critical ISGs in chicken and CEF (Chen et al., 2016a) . To confirm these findings, DF-1 cell lines expressing specific shRNA targeting each of these IFITMs were infected with ATMUV and harvested at 36 hpi, followed by qRT-PCR assay to detect mRNA expression of viral genes. doi = 10.3389/fmicb.2017.00672 id = cord-337198-4sors3bg author = Clementi, Nicola title = Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date = 2020-07-10 keywords = CPE; HCQ; PCR; SARS summary = In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . doi = 10.3389/fmicb.2020.01704 id = cord-000914-d0bk9gu5 author = Conant, Katelyn L. title = Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria date = 2013-03-12 keywords = CD147; CD36; EBV; KSHV; Kaposi summary = In this article, we highlight emerging evidence supporting the proposition that the signaling pathways anchored by Basigin/CD147 and CD36, two of the known host receptors that control Pf invasion and cyto-adherence, respectively, are also targets for functional subversion by Kaposi''s sarcoma (KS)-associated herpesvirus (KSHV), an inherently persistent cancer-associated herpesvirus that is prevalent in malaria-endemic regions. Remarkably, we have also discovered that cross-linking of CD36 on the surface of KSHV-infected cells with MC179, a recombinant peptide derived from the CIDR1α domain of PfEMP-1 that normally interacts with CD36 to mediate cyto-adherence (Ockenhouse et al., 1989 (Ockenhouse et al., , 1991 Baruch et al., 1997) , not only upregulated CD36 expression (Figure 2A ) but also reactivated the virus from latency through transcriptional activation of KSHV RTA (Figure 2B) , and that the molecular mechanisms that control this process overlap with those that putatively regulate PfEMP-1dependent EBV reactivation from latently infected cells (Chene et al., 2007) . doi = 10.3389/fmicb.2013.00035 id = cord-316176-rqc6kvsl author = Crémet, Lise title = Evaluation of the FilmArray(®) Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients date = 2020-08-25 keywords = ETA; FAPP summary = The FilmArray(®) Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. The FilmArray R Pneumonia plus Panel (FAPP) is a new panel for HAP, which offers potential advantage to detect and quantify in a single test, 27 respiratory pathogens (18 bacteria, 9 viruses) and 7 antibiotic resistance genes. At the time of HAP diagnosis, FAPP yielded positive results with significant levels (i.e., ≥ 10 4 bin in BAL and ≥ 10 5 bin in ETA for semi-quantified bacteria) in 82/100 patients. In this study, this test was compared to routine microbiological methods using 237 prospectively collected BAL and ETA specimens obtained from 100 ICU patients at the time of suspected HAP and, if possible, at a later timepoint during follow-up. doi = 10.3389/fmicb.2020.02080 id = cord-331973-avjw4kx1 author = Das, Shubhagata title = Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date = 2018-10-18 keywords = RSV; respiratory summary = Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) . doi = 10.3389/fmicb.2018.02478 id = cord-344970-ud1lhkyi author = Fecchi, Katia title = Coronavirus Interplay With Lipid Rafts and Autophagy Unveils Promising Therapeutic Targets date = 2020-08-11 keywords = COVID-19; SARS; virus summary = Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ). doi = 10.3389/fmicb.2020.01821 id = cord-002068-e071ciil author = Feng, Min title = Innate Immune Responses in ALV-J Infected Chicks and Chickens with Hemangioma In Vivo date = 2016-05-25 keywords = ALV; IFN; figure summary = In the current study we analyzed the transcriptional level of selected immune-response genes we had previously identified from whole-transcriptome profiling of ALV-J-induced tumors in chicken spleen samples (Li et al., 2015) . According to the transcriptome profiles of ALV-J-induced tumor spleen samples and healthy spleen samples from White (Recessive) Plymouth Rock chickens in our previous experiments (Li et al., 2015) , we analyzed the transcriptional level of related innate immune genes. Taken together these results indicated that ALV-J early infection induced no obvious antiviral innate immunity responses in chicks sampled from 1 to 7 d.p.i. However, this was not the case for late infections and there were significant increases in Type I IFN, pro-inflammatory cytokines as well as IL-10. doi = 10.3389/fmicb.2016.00786 id = cord-314567-purplsjn author = Fernández-Ponce, Cecilia title = Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date = 2018-01-04 keywords = HCV; RNA; core; protein summary = doi = 10.3389/fmicb.2017.02595 id = cord-295121-4xemmaqt author = Ferreira, Eliane de Oliveira title = Should We Be Worried About Clostridioides difficile During the SARS-CoV2 Pandemic? date = 2020-09-29 keywords = CDI; COVID-19; SARS summary = doi = 10.3389/fmicb.2020.581343 id = cord-324651-8teb5jrn author = Filippini, Antonio title = Could the Inhibition of Endo-Lysosomal Two-Pore Channels (TPCs) by the Natural Flavonoid Naringenin Represent an Option to Fight SARS-CoV-2 Infection? date = 2020-04-30 keywords = SARS; TPC2 summary = doi = 10.3389/fmicb.2020.00970 id = cord-317595-siwzjeea author = Forni, Diego title = Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV date = 2018-05-01 keywords = CD81; EHV; HCV; figure summary = Herein, we apply an evolutionary approach to shed light into HCV origin, to analyze its adaptation to human populations, and to verify if the emergence of drug-resistant variants is a result of positive selection. We used Single-Likelihood Ancestor Counting (SLAC) and fixed effects likelihood (FEL) (Kosakovsky Pond and Frost, 2005) to calculate the rates of nonsynonymous and synonymous changes at each site in the structural and in the non-structural region alignments (analyses were performed on alignments split on the basis of the recombination breakpoint detected by GARD). The observation that the positively selected sites are involved in HCV binding and infectivity suggests that hepaciviruses contributed to shape the genetic diversity of CD81 in bats. Using an evolutionary model that accounts for variation in the pressure of natural selection across sites and branches, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago, with a lower bound estimate of ∼5200 years before present. doi = 10.3389/fmicb.2018.00854 id = cord-312336-784izxqd author = Fouret, Julien title = Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding date = 2020-07-29 keywords = Illumina; Pteropus; dna; figure summary = doi = 10.3389/fmicb.2020.01807 id = cord-003261-fz8ucwwm author = Freundt, Eric C. title = Innate Immune Detection of Cardioviruses and Viral Disruption of Interferon Signaling date = 2018-10-12 keywords = EMCV; IFN; MDA5; PKR summary = L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) . doi = 10.3389/fmicb.2018.02448 id = cord-289623-7oc1ykds author = Gendy, Sherif title = Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018 date = 2020-08-20 keywords = SRS-8-S-2018; Serratia; strain summary = doi = 10.3389/fmicb.2020.01923 id = cord-353454-zq51hpjs author = Gouda, Sushanto title = Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance date = 2016-09-29 keywords = endophytic; plant summary = While plant sources are being extensively explored for the discovery of new chemical entities for various therapeutic purposes, endophytic microorganisms play an important role in this search for natural bioactive compounds, with potential use in the health sector and in drug discovery (Lam, 2007) . Bacterial endophytes are diverse in nature and are known to produce different bioactive metabolites that act as antimicrobial and anticancer compounds, for example, with 76% of them reported from the single genus, Streptomyces (Berdy, 2012) . Endophytes are reported to produce a number of bioactive metabolites in a single plant or microbe which served as an excellent source of drugs for treatment against various diseases and with potential applications in agriculture, medicine, food and cosmetics industries (Strobel and Daisy, 2003; Jalgaonwala et al., 2011; Godstime et al., 2014; Shukla et al., 2014) . doi = 10.3389/fmicb.2016.01538 id = cord-263162-37fvlhuo author = Guo, Kangkang title = A Host Factor GPNMB Restricts Porcine Circovirus Type 2 (PCV2) Replication and Interacts With PCV2 ORF5 Protein date = 2019-01-08 keywords = Cyclin; GPNMB; ORF5; figure; pcv2 summary = doi = 10.3389/fmicb.2018.03295 id = cord-315834-ashjw2xs author = Guo, Lingxi title = Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score date = 2019-12-03 keywords = patient; pneumonia summary = title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score OBJECTIVE: The aim of this study was to further clarify clinical characteristics and predict mortality risk among patients with viral pneumonia. CONCLUSION: Here, we designed an easy-to-use clinically predictive tool for assessing 90-day mortality risk of viral pneumonia. Influenza and other respiratory viruses are common reasons of acute pneumonia which can result in significant morbidity or mortality in the setting of high-risk factors such as extremes of age, pregnancy, obesity or chronic pre-existing conditions. Other reported risk factors for influenza pneumonia such as PO2/FiO2, lymphocyte count, and antigen-specific T cells are likewise useful in predicting mortality and deciding on appropriate management (Viasus et al., 2011; Shi et al., 2017) . In patients hospitalized with viral pneumonia, a simple prognostic tool was made for overall mortality which is useful for prediction several days after admission upon obtaining culture results. doi = 10.3389/fmicb.2019.02752 id = cord-262682-gsvswr7v author = Hedblom, Grant A. title = Segmented Filamentous Bacteria – Metabolism Meets Immunity date = 2018-08-24 keywords = SFB; Th17; host summary = doi = 10.3389/fmicb.2018.01991 id = cord-343357-5nhyumxl author = Heegaard, Peter M. H. title = Animal Models for COVID-19: More to the Picture Than ACE2, Rodents, Ferrets, and Non-human Primates. A Case for Porcine Respiratory Coronavirus and the Obese Ossabaw Pig date = 2020-09-25 keywords = ACE2; SARS; covid-19 summary = We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research. doi = 10.3389/fmicb.2020.573756 id = cord-001726-d7iwkatn author = Henry, Kevin A. title = Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold date = 2015-08-04 keywords = M13; antibody; display; filamentous; peptide; phage; protein summary = doi = 10.3389/fmicb.2015.00755 id = cord-281836-j1r771nq author = Hernando-Amado, Sara title = Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health date = 2020-08-28 keywords = Global; Health; antibiotic; arg; human; individual; resistance; social summary = doi = 10.3389/fmicb.2020.01914 id = cord-267960-r5m7o9dp author = Hourdel, Véronique title = Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100(TM) System date = 2020-09-25 keywords = Illumina; SARS; United summary = doi = 10.3389/fmicb.2020.571328 id = cord-269957-vd9ctqro author = Hua, Chen title = The Underlying Mechanism of 3-Hydroxyphthalic Anhydride-Modified Bovine Beta-Lactoglobulin to Block Human Papillomavirus Entry Into the Host Cell date = 2019-09-26 keywords = 3HP; HPV summary = doi = 10.3389/fmicb.2019.02188 id = cord-353815-w35spqqt author = Huan, Yuchen title = Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields date = 2020-10-16 keywords = acid; activity; amp; antimicrobial; cell; effect; gram; membrane; peptide summary = This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane''s abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) . doi = 10.3389/fmicb.2020.582779 id = cord-282797-thywse7g author = Hwang, Yoon Jung title = Engineered Bacteriophage T7 as a Potent Anticancer Agent in vivo date = 2020-09-24 keywords = CSF; b16f10; figure summary = doi = 10.3389/fmicb.2020.491001 id = cord-003207-ow3aez9v author = Ismail, Ashrafali M. title = Adenoviromics: Mining the Human Adenovirus Species D Genome date = 2018-09-11 keywords = Robinson; adenovirus; dna summary = doi = 10.3389/fmicb.2018.02178 id = cord-336074-76ca1cfy author = Izumida, Mai title = Fragments of Target Cells are Internalized into Retroviral Envelope Protein-Expressing Cells during Cell-Cell Fusion by Endocytosis date = 2016-01-19 keywords = Env; MLV; cell summary = doi = 10.3389/fmicb.2015.01552 id = cord-276493-hoaxv5e0 author = Jeong, Gi Uk title = Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date = 2020-07-14 keywords = COVID-19; RBD; RNA; SARS summary = doi = 10.3389/fmicb.2020.01723 id = cord-285868-fz5utxss author = Jheng, Jia-Rong title = ER stress, autophagy, and RNA viruses date = 2014-08-05 keywords = ATF6; HCV; RNA; UPR summary = doi = 10.3389/fmicb.2014.00388 id = cord-001933-rnjnxymc author = Kariithi, Henry M. title = Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies date = 2016-02-09 keywords = Alla; Glossina; SGH; table summary = Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus whose 190 kb genome encodes more than 60 confirmed proteins (Abd-Alla et al., 2008 , 2009b Kariithi et al., 2013a) . However, detection of hytrosavirus-like infection symptoms, i.e., the salivary gland hypertrophy syndrome (SGH) in the Narcissus bulb fly Merodon equestris (Diptera; Syrphidae; Amargier et al., 1979) and in male accessory gland filaments of the parasitic wasp Diachasmimorpha longicuadata (Hymenoptera; Braconidae; Luo and Zeng, 2010) implies that the Hytrosaviridae potentially contains other members. We hypothesized that GpSGHV infection in Glossina is under the control of host-and/or virus-encoded factors (proteins/peptides) whose interactions influence the expression or lack of overt SGH symptoms. The host (and viral) proteins identified in this study are potential targets for control of GpSGHV infections in tsetse fly mass production facilities. The clear GpSGHV-induced differential modulation of SG protein expression in Glossina raises the question of what host pathways are potentially globally regulated to facilitate successful virus infection. doi = 10.3389/fmicb.2016.00089 id = cord-295240-76ee00i0 author = Kruchten, Anne E. title = A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R date = 2020-09-10 keywords = Excel; course; student summary = doi = 10.3389/fmicb.2020.578600 id = cord-332221-6ea6gz9s author = Li, Guiping title = Insulin-Like Growth Factor 1 Regulates Acute Inflammatory Lung Injury Mediated by Influenza Virus Infection date = 2019-11-26 keywords = AKT; IGF1; PBS; PPP; PR8 summary = The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. To explore the mechanism by which IGF1 regulates acute inflammatory lung injury induced by IAV infection, a Western blot was used to detect the expression of molecules in key signaling pathways in the lung tissue of PR8-infected mice (50LD 50 PR8). doi = 10.3389/fmicb.2019.02541 id = cord-286779-si3qml42 author = Li, Hai-yan title = Modulation of Gut Microbiota, Short-Chain Fatty Acid Production, and Inflammatory Cytokine Expression in the Cecum of Porcine Deltacoronavirus-Infected Chicks date = 2020-06-04 keywords = HNZK-02; group; pdcov summary = doi = 10.3389/fmicb.2020.00897 id = cord-000708-iuo2cw23 author = Lippé, Roger title = Deciphering Novel Host–Herpesvirus Interactions by Virion Proteomics date = 2012-05-28 keywords = cell; protein; virus summary = These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection doi = 10.3389/fmicb.2012.00181 id = cord-347917-fmb5nyxu author = Liu, Junli title = Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date = 2020-01-28 keywords = RNA; gene; lncRNAs summary = In this study, genome-wide profiling of lncRNAs in swine testicular (ST) cells infected with PDCoV was performed using RNA-seq. An integrative analysis of lncRNA alterations suggested their putative role in regulating the expression of several key genes in metabolic and TNF signaling pathways during infection. There have been reports of using genome-wide association analysis between lncRNAs and the co-expressed and/or co-regulated protein-coding genes to characterize the function of the lncRNA (Huarte et al., 2010) . GO and KEGG pathway enrichment analysis of target genes revealed that lncRNAs may act in cis or trans to participate in the regulation of expression of multiple important genes in different processes including protein binding, DNA transcription, metabolism, and immune response. The functional association between regulatory lncRNA and protein-coding gene transcripts can be determined by performing expression correlation analysis coupled with ascertaining their putative role in related physiological processes. doi = 10.3389/fmicb.2019.03036 id = cord-257656-z7zx46gd author = Ljubin-Sternak, Sunčanica title = The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date = 2019-12-03 keywords = respiratory summary = doi = 10.3389/fmicb.2019.02737 id = cord-316537-f5rto51t author = Loens, Katherine title = Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date = 2016-03-31 keywords = Mycoplasma; PCR; pneumoniae summary = doi = 10.3389/fmicb.2016.00448 id = cord-003908-wbawzbhz author = Matsushima, Yuki title = Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date = 2019-09-27 keywords = GII.P17-GII.17; VP1; figure; strain summary = doi = 10.3389/fmicb.2019.02189 id = cord-296495-9v0sq8k6 author = Meyer Sauteur, Patrick M. title = Infection with and Carriage of Mycoplasma pneumoniae in Children date = 2016-03-23 keywords = Mycoplasma; pneumoniae summary = Mycoplasma pneumoniae causes both upper and lower respiratory tract infections, with community-acquired pneumonia (CAP) as the major burden of disease. pneumoniae infections were first reported in 1960 when 16% of 110 children with lower respiratory tract disease were tested positive by a fourfold rise in antibody titers against the Eaton agent (Chanock et al., 1960) . This study described 20 patients with CAP, of which 19 were children 4-15 years of age, diagnosed by a significant rise in antibody titers against M. Emergence of macrolide-resistant strains during an outbreak of Mycoplasma pneumoniae infections in children Results of molecular detection of Mycoplasma pneumoniae among patients with acute respiratory infection and in their household contacts reveals children as human reservoirs Antibiotics for community-acquired lower respiratory tract infections secondary to Mycoplasma pneumoniae in children Role of Mycoplasma pneumoniae and Chlamydia pneumoniae in children with community-acquired lower respiratory tract infections doi = 10.3389/fmicb.2016.00329 id = cord-322649-c99lszcu author = Miao, Faming title = Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus date = 2019-05-15 keywords = ASFV; RPA; african summary = title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus doi = 10.3389/fmicb.2019.01004 id = cord-002376-970934vm author = Mikel, Pavel title = Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date = 2016-12-01 keywords = MS2; PCR; PLP; RNA summary = The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. doi = 10.3389/fmicb.2016.01911 id = cord-032614-hp07ky6q author = Minich, Jeremiah J. title = The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment date = 2020-08-24 keywords = MKL; PZQ; SBT; figure summary = In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, ranched SBT were sampled to characterize the microbial diversity associated with mucosal body sites, including gill, skin, and gut, providing the first assessment of microbiome diversity in this ecologically and commercially important fish species. In this study we set out to describe how the fish mucosal microbiome is associated by parasitic infection and treatment with praziquantel (PZQ) across three body sites including the gill, skin, and digesta of Southern Bluefin Tuna (SBT). doi = 10.3389/fmicb.2020.02015 id = cord-298032-3zlu8g8y author = Nan, Yuchen title = Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date = 2018-04-20 keywords = PMO; PPMO; RNA; Vivo; virus summary = doi = 10.3389/fmicb.2018.00750 id = cord-298233-qqhgmqrg author = Nan, Yuchen title = Molecular Biology and Infection of Hepatitis E Virus date = 2016-09-07 keywords = HEV; ORF1; ORF2; RNA; VP13; hepatitis summary = More interestingly, a remarkable HEV strain Kernow-C1, which was originally isolated from an HIV-positive patient with chronic HEV infection, contains an insertion of a 174 nt gene fragment of human ribosomal protein S17 in the Pro region (Shukla et al., 2011) . Furthermore, other studies indicate that the expression of viral macro domain in liver cells inhibits apoptosis since it is functionally related to poly(ADP-ribose) polymerase-1 (PARP-1; Allen et al., 2003; Chen et al., 2009) , suggesting a role in apoptosis during viral infection. Identification of critical residues in hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins ORF3 protein of hepatitis E virus is not required for replication, virion assembly, or infection of hepatoma cells in vitro A PSAP motif in the ORF3 protein of hepatitis E virus is necessary for virion release from infected cells The ORF2 protein of hepatitis E virus binds the 5 region of viral RNA ORF3 protein of hepatitis E virus is essential for virion release from infected cells doi = 10.3389/fmicb.2016.01419 id = cord-277400-w7mvk3x4 author = Nasir, Arshan title = Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification date = 2017-03-10 keywords = Abrescia; FSF; SCOP; virus summary = doi = 10.3389/fmicb.2017.00380 id = cord-351719-xqmir1ca author = Olaimat, Amin N. title = Food Safety During and After the Era of COVID-19 Pandemic date = 2020-08-04 keywords = COVID-19; SARS; food summary = doi = 10.3389/fmicb.2020.01854 id = cord-003970-3e58229u author = Paploski, Igor Adolfo Dexheimer title = Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus date = 2019-11-01 keywords = PRRSV; States; United summary = Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection doi = 10.3389/fmicb.2019.02486 id = cord-300379-db79kb5c author = Park, Jun-Gyu title = Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid date = 2019-04-12 keywords = ATA; Vero; ZIKV; figure summary = doi = 10.3389/fmicb.2019.00718 id = cord-305973-i3raopi6 author = Perley, Casey C. title = Anti-HFRS Human IgG Produced in Transchromosomic Bovines Has Potent Hantavirus Neutralizing Activity and Is Protective in Animal Models date = 2020-05-07 keywords = HTNV; Hooper; PUUV; SAB-159; dna summary = These data demonstrate that DNA vaccines combined with the TcB-based manufacturing platform can be used to rapidly produce potent, human, polyclonal, escape-resistant anti-HTNV, and anti-PUUV neutralizing antibodies that are protective in animal models. Here, we demonstrate that it is possible to combine DNA vaccine technology with the TcB platform to produce potent human polyclonal IgG for use as a pre-or post-exposure prophylactic for HFRS caused by HTNV and PUUV infection. Previous experiments to produce anti-ANDV and anti-SNV TcB human IgG have demonstrated that including an SAB-adj-1 adjuvant at the injection sight increased immunogenicity of the ANDV and SNV DNA vaccines resulting in higher titer virusspecific neutralizing antibodies (Hooper et al., 2014a) . To determine the dose of SAB-159 required to protect against infection, hamsters were administered decreasing concentrations of neutralizing antibody ranging from 12.23 mg/kg to 0.39 mg/kg SAB-159 subcutaneously 1 day prior to a 10 PFU HTNV challenge. doi = 10.3389/fmicb.2020.00832 id = cord-290505-omszep7u author = Pochon, Cécile title = Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients date = 2019-01-09 keywords = HCT; LRI; PIV; RSV; respiratory summary = doi = 10.3389/fmicb.2018.03294 id = cord-302854-buzyani0 author = Prabakaran, Ponraj title = Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing date = 2012-08-02 keywords = HIV-1; figure summary = doi = 10.3389/fmicb.2012.00277 id = cord-254115-hwy962a4 author = Reslova, Nikol title = xMAP Technology: Applications in Detection of Pathogens date = 2017-01-25 keywords = DDH; MBMI; PCR; assay; detection; dna; tag summary = doi = 10.3389/fmicb.2017.00055 id = cord-326217-ji0njeha author = Saleh, Maged title = Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date = 2018-11-27 keywords = GSK3; HCV; RNA summary = We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon. doi = 10.3389/fmicb.2018.02949 id = cord-317499-mxt7stat author = Saraya, Takeshi title = Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date = 2014-05-26 keywords = HRV; IFN; infection summary = Table 1 shows the frequency of HRV infection in various adult respiratory diseases such as exacerbation of asthma (Nicholson et al., 1993; Atmar et al., 1998; Tan et al., 2003) , common cold (Makela et al., 1998; van Gageldonk-Lafeber et al., 2005) , exacerbation of COPD (Seemungal et al., 2001; Rohde et al., 2003; Tan et al., 2003; Beckham et al., 2005; Papi et al., 2006; Hutchinson et al., 2007; Ko et al., 2007; McManus et al., 2008; Kherad et al., 2010; Dimopoulos et al., 2012; Perotin et al., 2013) , community acquired pneumonia (Jennings et al., 2008; Johnstone et al., 2008; Johansson et al., 2010; Lieberman et al., 2010; Fry et al., 2011; Wootton et al., 2011; Luchsinger et al., 2013; Takahashi et al., 2013; Huijskens et al., 2014) , exacerbation of idiopathic pulmonary fibrosis (Wootton et al., 2011) , and asymptomatic infection (Fry et al., 2011) . doi = 10.3389/fmicb.2014.00226 id = cord-271557-xic32wxh author = Sato, Hiroki title = Morbillivirus Receptors and Tropism: Multiple Pathways for Infection date = 2012-03-01 keywords = CD46; cell; slam summary = doi = 10.3389/fmicb.2012.00075 id = cord-310392-fmobf1f1 author = Sekizuka, Tsuyoshi title = SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise date = 2020-06-05 keywords = Egypt; SARS summary = doi = 10.3389/fmicb.2020.01316 id = cord-260336-kwzo8puo author = Si, Lulu title = A Peptide-Based Virus Inactivator Protects Male Mice Against Zika Virus-Induced Damage of Testicular Tissue date = 2019-09-27 keywords = ZIKV; Zika; figure summary = Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student''s unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility. doi = 10.3389/fmicb.2019.02250 id = cord-277731-thazunob author = Smith, Matthew L. title = Biosurfactants: A Covid-19 Perspective date = 2020-06-09 keywords = SARS; biosurfactant summary = doi = 10.3389/fmicb.2020.01341 id = cord-267735-y3832u9e author = Sun, Wuping title = Management of Immunity Alteration-Induced Chronic Pain During the Coronavirus Disease-2019 (COVID-19) Pandemic date = 2020-09-24 keywords = SARS; covid-19 summary = doi = 10.3389/fmicb.2020.572318 id = cord-002806-mu9jt1ul author = Tong, Mingwei title = Quantitative Analysis of Cellular Proteome Alterations in CDV-Infected Mink Lung Epithelial Cells date = 2017-12-22 keywords = CDV; cell; mv.1.lu summary = Many studies have reported the effects of CDV infections on the host cell proteins, such as inhibiting STAT1 and STAT2 nuclear import (Rothlisberger et al., 2010) , inducing cytokine responses in PBMCs (Nielsen et al., 2009) , and inducing lymphocytes apoptosis (Kumagai et al., 2004) . Based on iTRAQ combined with LC-MS/MS, a quantitative proteomic analysis was performed to identify differentially expressed proteins (DEPs) in mink lung epithelial cells (Mv.1.Lu cells) infected with CDV at 24 hours post infection (hpi). Therefore, we utilized an iTRAQ approach to identify the DEPs to further explore the pathogenic mechanism and immunomodulation of CDV infection through an analysis of the effects on host cell proteins in the mink. Collectively, the findings suggested that activation of the innate immune NF-κB signaling pathway and the NLR signaling pathway was involved in mink immune responses against CDV infection, and the NF-κB signaling was associated with the pathological respiratory or other symptoms FIGURE 5 | Confirmation of the iTRAQ-MS data by western blotting or real-time RT-PCR. doi = 10.3389/fmicb.2017.02564 id = cord-284889-hth8nf5b author = Tsukagoshi, Hiroyuki title = Molecular epidemiology of respiratory viruses in virus-induced asthma date = 2013-09-12 keywords = HRV; RSV; respiratory summary = doi = 10.3389/fmicb.2013.00278 id = cord-330942-x238hq9b author = Versluys, Anne Birgitta title = Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? date = 2018-11-21 keywords = CARV; HCT summary = doi = 10.3389/fmicb.2018.02795 id = cord-252772-f3fctcru author = Wang, Changlin title = The Coronavirus PEDV Evades Type III Interferon Response Through the miR-30c-5p/SOCS1 Axis date = 2020-05-22 keywords = IFN; PEDV; SOCS1 summary = doi = 10.3389/fmicb.2020.01180 id = cord-003976-05tf6oqa author = Wang, Kai title = Anti-TGEV Miller Strain Infection Effect of Lactobacillus plantarum Supernatant Based on the JAK-STAT1 Signaling Pathway date = 2019-11-06 keywords = IPEC; TGEV; stat1 summary = doi = 10.3389/fmicb.2019.02540 id = cord-003357-4qrg6lqu author = Wang, Yingchen title = Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date = 2018-11-27 keywords = China; Harbin; infection; respiratory summary = doi = 10.3389/fmicb.2018.02919 id = cord-338773-ilir895i author = Wu, Zhiqiang title = Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces date = 2018-10-24 keywords = Pestivirus summary = Novel sequencing reads related to pestivirus were found in samples collected from different bat and rodent species. Genomic and phylogenetic analyses of these viruses revealed the presences of six novel pestivirus species in bat and rodent hosts. Each peptide of BPV species 1 and 2 aligned best with those of APPV, even when the overall identities FIGURE 1 | Occurrence of pestivirus-related reads in bats and rodents from different locations. This study described the identification of novel BPVs and RPVs in different bat and rodent species across several Chinese regions, which revealed that these two mammals served as natural hosts for pestiviruses. Considering their divergent phylogenetic positions, different genome sizes and structures, and the minimal sequence similarities of BPVs and RPVs when compared to other pestiviruses, we propose classifying members of the genus Pestivirus into three main lineages; bat-swine, rodent, and artiodactylous lineages, based on the order level of their hosts. doi = 10.3389/fmicb.2018.02562 id = cord-291295-7og5umiq author = Xin, Shuyu title = Epstein-Barr Virus Nuclear Antigen 1 Recruits Cyclophilin A to Facilitate the Replication of Viral DNA Genome date = 2019-12-13 keywords = Barr; CYPA; EBNA1; EBV; figure summary = doi = 10.3389/fmicb.2019.02879 id = cord-002085-e7xwb03g author = Yamashita, Akifumi title = DGV: Dengue Genographic Viewer date = 2016-06-07 keywords = DENV; DGV; genotype summary = We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. The second database is the Dengue virus genotyping database 2 (Yamashita et al., 2013) , which provides a summary table containing the DENV serotype/genotype, year and country of collection and accession number. The Dengue Virus Resource 3 facilitates the retrieval of DENV sequences deposited in GenBank according to serotype, disease symptom, host, region/country, genome region, and collection and/or release data (Resch et al., 2009) . DGV provides a search engine for the assignment of the DENV serotype, genotype, and origin country according to the most homologous sequence on the basis of a blastn search against the DENV database. doi = 10.3389/fmicb.2016.00875 id = cord-002795-i1qcanti author = Yang, Jing title = Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date = 2017-12-12 keywords = GPV; PCR summary = Isolated pathogen was detected by polymerase chain reaction (PCR) assay, and the result showed that only GPV was positive; Genomic sequence analysis showed that this new pathogen shared 90.8-94.6% of nucleotide identity with goose parvovirus (GPV). In addition, LAMP has been considered as a time-saving, lowcost, highly specific and sensitive method (Chotiwan et al., 2017) , which can be completed within 60 min under condition of constant temperature, and it has been established to detect GPV, Muscovy duck parvovirus (MDPV), porcine parvovirus (PPV), canine parvovirus (CPV), and others targeting at VP gene (Cho et al., 2006; Chen et al., 2009; Ji et al., 2010; JinLong et al., 2010) . Quantitative loop-mediated isothermal amplification assay was carried out using different viruses including GPV, duck plague virus, duck tembusu virus, duck hepatitis virus, duck reovirus, Muscovy duck parvovirus, and H9N2-AIV to validate specificity of this method. doi = 10.3389/fmicb.2017.02472 id = cord-297662-slmlhqnb author = Yap, Sally S. L. title = Dengue Virus Glycosylation: What Do We Know? date = 2017-07-25 keywords = DENV; NS1; virus summary = In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement doi = 10.3389/fmicb.2017.01415 id = cord-252485-cxi3cr15 author = Yoshida, Asuka title = IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date = 2015-08-04 keywords = IFN; RNA; figure; rig summary = We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not. doi = 10.3389/fmicb.2015.00804 id = cord-344200-ev4707pq author = Yu, Qing title = Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis date = 2020-06-19 keywords = Cy5-Q5; MCP; Q5-MCP; SGIV summary = title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. In this study, an aptamer (Q5)-based specific probe was used to investigate the trafficking mechanism and endocytotic pathway of MCP in host cells during SGIV infection. We analyzed the effects of various inhibitors on the binding of aptamer Cy5-Q5 to its target protein, MCP, in the membranes of SGIV-infected cells with flow cytometry. Relative to the control group of normal GS cells, the GS cells incubated with the safe working concentration of each inhibitor in L-15 medium retained their normal FIGURE 7 | Caveolae/raft-dependent endocytosis is not involved in MCP entry during SGIV infection. doi = 10.3389/fmicb.2020.01206 id = cord-282305-l5r67gte author = Zhang, Xuejiao title = Crystal Structure of Refolding Fusion Core of Lassa Virus GP2 and Design of Lassa Virus Fusion Inhibitors date = 2019-08-13 keywords = HR1; HR2; LASV; figure summary = doi = 10.3389/fmicb.2019.01829 id = cord-321112-w7x1dkds author = Zhao, Xuesen title = IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections date = 2019-01-08 keywords = IAV; IFITM3; virus summary = doi = 10.3389/fmicb.2018.03228 id = cord-003239-nph2ezii author = Zhu, Zixiang title = Early Growth Response Gene-1 Suppresses Foot-and-Mouth Disease Virus Replication by Enhancing Type I Interferon Pathway Signal Transduction date = 2018-09-27 keywords = EGR1; FMDV; IFN; SAP summary = doi = 10.3389/fmicb.2018.02326