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?' ---------------------------------------------------------- 101 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5382 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 51 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 16 RNA 15 Fig 14 SARS 10 virus 10 IBV 8 cell 8 PEDV 7 protein 7 PRRSV 5 dna 5 PCR 4 Vero 3 UTR 3 MERS 3 HIV-1 3 China 2 strain 2 infection 2 covid-19 2 codon 2 antiviral 2 WNV 2 TGEV 2 PID 2 ORF 2 NL63 2 MHV 2 Jung 2 IFN 2 HIV 2 HBV 2 FIPV 2 ELISA 2 COVID-19 2 ACE2 1 vr-2332 1 viral 1 usage 1 type 1 stress 1 site 1 severe 1 ribavirin 1 recombinant 1 protease 1 porcine 1 pdcov 1 patient 1 nsp4 1 novel Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 5904 virus 4467 cell 3791 protein 2023 infection 1647 gene 1581 sequence 1423 coronavirus 1382 % 1345 strain 1220 study 1182 genome 1161 replication 931 antibody 865 analysis 830 expression 828 site 805 acid 801 region 765 type 725 activity 670 disease 658 result 650 host 626 vaccine 604 response 580 domain 569 group 559 cleavage 551 effect 549 structure 537 assay 535 pig 528 c 517 interaction 512 h 503 sample 498 receptor 484 control 483 time 475 mutation 472 mouse 470 coronaviruse 464 syndrome 463 role 450 system 444 codon 430 membrane 430 datum 426 level 425 dna Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 6687 al 6133 . 5279 et 2146 RNA 1200 Fig 1021 SARS 707 IBV 701 PEDV 554 PCR 534 CoV 530 C 529 PRRSV 498 S 491 N 467 M 330 China 322 CoV-2 310 RT 303 CCR5 290 HIV-1 269 TGEV 248 PBS 245 aa 218 Vero 210 II 208 HCoV 201 HIV 200 Table 183 S1 182 B 179 T 175 ORF 168 UTR 164 COVID-19 164 CH 162 MERS 160 A 151 USA 150 mRNA 150 HCV 150 ACE2 148 G 147 siRNA 146 Coronavirus 144 ELISA 139 NL63 139 Li 139 Chen 137 TCoV 135 RNA3 Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 877 it 869 we 289 they 259 i 82 them 37 he 27 us 23 itself 13 you 12 themselves 11 one 6 nsp10 5 mrnas 4 iga+ 3 she 2 nsp15 2 ccr5Δ32 1 thee 1 psip409-pgsa 1 ourselves 1 nsp7-nsp8 1 nsp7 1 nsp4 1 nsp1 1 ms2vlps 1 microrna-130a 1 me 1 l2-vlps 1 jx220982 1 http://dx.doi.org/10.1016/j.virusres.2017.05.003 1 hav-2 1 cpms Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 16353 be 2361 have 2023 use 1276 show 858 infect 695 induce 646 contain 622 bind 563 express 559 include 540 suggest 536 find 521 identify 503 base 488 isolate 458 detect 455 indicate 445 describe 442 associate 440 do 429 increase 418 observe 411 determine 387 inhibit 385 encode 382 report 373 compare 364 perform 361 follow 338 require 328 mediate 319 cause 300 involve 295 neutralize 292 result 288 reveal 282 provide 267 treat 253 incubate 252 confirm 250 analyze 249 generate 247 demonstrate 244 reduce 242 occur 239 obtain 232 inoculate 230 produce 229 know 217 conserve Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1915 viral 1387 not 1236 - 1088 also 931 other 923 human 818 porcine 746 respiratory 679 infectious 626 high 610 specific 610 recombinant 565 different 519 however 516 only 494 like 479 more 469 non 448 antiviral 445 severe 424 infected 419 then 413 immune 412 genetic 406 well 398 such 387 positive 386 structural 386 cellular 384 respectively 382 new 378 most 377 clinical 366 anti 353 similar 352 further 339 first 338 molecular 337 low 336 acute 332 novel 326 small 321 previously 302 large 280 genomic 279 same 279 dependent 278 several 269 single 265 thus Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 141 most 66 least 63 high 43 large 34 Most 30 good 17 low 8 great 8 close 6 small 6 late 4 ClustalW 3 early 2 strong 2 short 2 NC8 2 -proximal 1 ® 1 vvIBV 1 vRNA 1 tremeGENE 1 simple 1 severe 1 safe 1 pdqu 1 pSARS 1 outermost 1 old 1 new 1 near 1 AF488-Tf 1 -subunit 1 -ACGUGA Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 237 most 45 least 8 well 1 shortest 1 clustalw 1 -cccctc Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 17 dx.doi.org 10 www.ncbi.nlm.nih.gov 6 doi.org 4 www.who.int 3 www.ebi.ac.uk 2 www.megasoftware.net 2 mobyle.pasteur.fr 2 initiate-itn.eu 1 www2.eur.nl 1 www.uhnresearch.ca 1 www.tree-puzzle.de 1 www.rscb.org 1 www.nlm.nih.gov 1 www.nihclinicalcollection.com 1 www.moseslab 1 www.mif.dfci.harvard 1 www.matrixscience.com 1 www.kazusa.or.jp 1 www.intl-pag.org 1 www.ictvonline 1 www.hiv.lanl.gov 1 www.gesundheitsforschungbmbf.de 1 www.drugbank 1 www.covid19cellatlas.org 1 www.compbio.dundee.ac 1 www.cbs.dtu.dk 1 www.access.gpo.gov 1 www 1 tree.bio.ed.ac.uk 1 talk.ictvonline.org 1 talk 1 scholar.google.com.br 1 mafft.cbrc.jp 1 initiateitn.eu 1 genomes.urv.es 1 drive.google.com 1 clustalw.ddbj.nig.ac.jp 1 beast.bio.ed.ac.uk 1 arsa.ddbj.nig.ac.jp 1 arcg.is 1 150.216 Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://dx.doi.org/10.1016/j.virusres 3 http://doi.org/10 2 http://www.ncbi.nlm.nih.gov/gorf/gorf.html 2 http://www.ncbi.nlm.nih.gov 2 http://mobyle.pasteur.fr 2 http://initiate-itn.eu/ 2 http://dx.doi.org/10.1016/j.virusres.2017.08.008 1 http://www2.eur.nl/fgg/kgen/primer/Overlapping 1 http://www.who.int/emergencies/diseases/novel-coronavirus-2019 1 http://www.who.int/csr/sars/en/ 1 http://www.who.int/csr/disease/coronavirus 1 http://www.who.int/ 1 http://www.uhnresearch.ca/facilities/wcif/imagej/ 1 http://www.tree-puzzle.de/ 1 http://www.rscb.org/pdb 1 http://www.nlm.nih.gov/learn-about-drugs.html 1 http://www.nihclinicalcollection.com 1 http://www.ncbi.nlm.nih.gov/gorf/gorf 1 http://www.ncbi.nlm.nih.gov/genbank/sars-cov-2seqs/ 1 http://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/] 1 http://www.ncbi.nlm.nih.gov/blast 1 http://www.ncbi.nlm.nih.gov/BLAST/ 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.moseslab 1 http://www.mif.dfci.harvard 1 http://www.megasoftware.net/index.html 1 http://www.megasoftware.net/ 1 http://www.matrixscience.com/ 1 http://www.kazusa.or.jp/codon/ 1 http://www.intl-pag.org/11/abstracts/P2c 1 http://www.ictvonline 1 http://www.hiv.lanl.gov/ 1 http://www.gesundheitsforschungbmbf.de/de/1721.php#SARS 1 http://www.ebi.ac.uk/interpro/ 1 http://www.ebi.ac.uk/embl/Access/index.html 1 http://www.ebi.ac.uk 1 http://www.drugbank 1 http://www.covid19cellatlas.org/ 1 http://www.compbio.dundee.ac 1 http://www.cbs.dtu.dk/services/NetNGlyc/ 1 http://www.access.gpo.gov/nara/cfr/waisidx 1 http://www 1 http://tree.bio.ed.ac.uk/software/tracer/ 1 http://talk.ictvonline.org/files/ictv 1 http://talk 1 http://scholar.google.com.br/ 1 http://mafft.cbrc.jp/alignment/software/ 1 http://initiateitn.eu/early-stage-researchers/ 1 http://genomes.urv.es/CAIcal 1 http://dx.doi.org/10.1016/j.virusres.2017.05.006 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 yves.mely@unistra.fr 1 vonbrunn@mvp.uni-muenchen.de 1 rlloyd@bcm.tmc.edu 1 paulo7926@usp.br 1 parkx026@snu.ac.kr 1 mjackwoo@uga.edu 1 doljav@science.oregonstate.edu 1 chingho@ntu.edu.tw 1 abinash-padhi@utulsa.edu 1 pierre.talbot@iaf.inrs.ca Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 16 cells were then 8 cells were co 8 virus is not 6 sequences are available 5 cells were also 5 cells were cultured 5 protein did not 5 virus does not 4 cells were further 4 cells were mock 4 infection is not 4 protein was not 4 results were consistent 4 sequences are unable 3 acid binding properties 3 acid has also 3 antibodies did not 3 cells were kindly 3 cells were more 3 cells were simultaneously 3 cells were subsequently 3 gene showed only 3 infection was not 3 infections were also 3 pedv isolate knu-141112 3 protein does not 3 protein induces antibodies 3 protein is important 3 protein was lower 3 protein were dispensable 3 proteins are not 3 proteins were not 3 rna binding protein 3 sequences are also 3 virus are essential 3 virus induces apoptosis 3 virus induces protection 3 virus is currently 3 virus was not 3 virus was then 2 % showed surface 2 acid binding activity 2 activity was not 2 analysis was not 2 antibodies are present 2 antibodies were first 2 antibodies were not 2 cells are not 2 cells are susceptible 2 cells did not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 4 virus is not essential 1 . indicated not significant 1 acid had no virucidal 1 analysis was not only 1 antibodies were no longer 1 antibodies were not significantly 1 cells are not entirely 1 cells do not only 1 cells is not only 1 cells were not permissive 1 coronavirus were not common 1 disease is not yet 1 expression has no effect 1 infection had no statistical 1 infection is not completely 1 infection is not coronavirus 1 infection is not currently 1 infections are not contagious 1 pedv is not well 1 protein did not fully 1 protein was not further 1 protein was not sufficient 1 proteins are not essential 1 proteins are not ideal 1 proteins do not always 1 region had no detectable 1 region is not essential 1 result is not conclusive 1 results were not conclusive 1 results were not surprising 1 rna is not sufficient 1 sequence found no homology 1 sites are not present 1 sites were not due 1 strain contained not only 1 strain is not necessarily 1 strain was not due 1 strains showed no possible 1 type were no vaccine 1 virus is not necessarily 1 virus is not sufficient 1 viruses are no match 1 viruses do not readily 1 viruses had no changes 1 viruses showed no signs 1 viruses were not detectable A rudimentary bibliography -------------------------- id = cord-303111-iv4lzpev author = Almazán, Fernando title = Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date = 2014-12-19 keywords = BAC; RNA; SARS summary = Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. doi = 10.1016/j.virusres.2014.09.006 id = cord-312489-ywep0c08 author = Andoh, Kiyohiko title = Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date = 2015-10-02 keywords = IBV; protein; recombinant summary = We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Native S1 ELISA detected similar titers in the sera of animals immunized with recombinant S1 protein compared to those in sera of chickens immunized with inactivated virus (Fig. 6b ) (Control experiments (data not shown) demonstrated that mock and unvaccinated control groups did not differ from each other in VN and ELISA tests of anti-S1 activity.) These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus doi = 10.1016/j.virusres.2015.06.019 id = cord-279969-5nlmljcw author = Bastien, Nathalie title = Sequence analysis of the N, P, M and F genes of Canadian human metapneumovirus strains() date = 2003-04-03 keywords = APV summary = doi = 10.1016/s0168-1702(03)00065-0 id = cord-346104-18x8u2oe author = Black, Wendy title = Identification of gammaherpesvirus infection in free-ranging black bears (Ursus americanus) date = 2019-01-02 keywords = Fig; PCR; dna summary = Herpesvirus infection in the bear tissues and tissue cultures were detected by PCR using degenerate primers specific to the DNA polymerase gene (DPOL) and glycoprotein B gene (gB). To determine whether the observed viral particles are herpesviruses, tissues collected from the two NV black bears B1 and B2 were examined by nested PCR using panherpesvirus primers (Pozo et al., 2016 ) and herpesvirus consensus primers (VanDevanter et al., 1996) . To determine how common this UrHV-1 like virus is in black bear population, various tissues from 15 bears collected from Nevada, California, and Oregon were analyzed by this hybrid nested PCR with panherpesvirus primers in primary reaction and UrHV-1specific primers in the secondary reactions. Positive amplification with UrHV-1 specific primers was observed in total DNA of white blood cells (WBC) from two black bears from Nevada and one from Oregon. doi = 10.1016/j.virusres.2018.10.016 id = cord-304137-vxqkztio author = Bueno, Carlos A. title = A natural tetranortriterpenoid with immunomodulating properties as a potential anti-HSV agent date = 2009-01-20 keywords = CDM; HSV-1 summary = We have reported that meliacine (MA), an antiviral principle present in partially purified leaf extracts of Melia azedarach L., exerts an antiviral action on the development of herpetic stromal keratitis (HSK) in mice by causing a significant decrease in the viral load in the eye of Herpes simplex virus type 1 (HSV-1) infected animals, as well as in the incidence and severity of lesions due to a virus-induced immunopathological reaction (Pifarré et al., 2002) . We have found that CDM is able to block HSV-1 induced activation of NF-B by inhibiting its translocation to the nucleus of infected human conjunctival cells (NHC), and postulated that CDM would be able to abolish murine HSK by controlling viral spread and the associated immunopathology as well (Barquero et al., 2006) . The aim of the present study was to determine whether CDM displays an antiviral activity in infected corneal cells, the target of HSV-1 multiplication in vivo, as well as its effect on the translocation of NF-B to the nucleus. doi = 10.1016/j.virusres.2008.12.013 id = cord-320331-wtxja5i9 author = Cabbab, Iris Louise N. title = Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection date = 2020-10-08 keywords = ACE2; Ang; COVID-19; RAAS; SARS summary = doi = 10.1016/j.virusres.2020.198190 id = cord-257487-xanqvdhn author = Carbajo-Lozoya, Javier title = Replication of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E is inhibited by the drug FK506 date = 2012-02-10 keywords = NL63; SARS; fk506 summary = Knockdown of the cellular FK506-binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. Here we demonstrate that the drug FK506 (Tacrolimus) inhibited strongly the growth of human coronaviruses SARS-CoV, HCoV-NL63 and HCoV-229E at low, non-cytotoxic concentrations in cell culture. Knockdown of the cellular FK506binding proteins FKBP1A and FKBP1B in CaCo2 cells prevented replication of HCoV-NL63, suggesting the requirement of these members of the immunophilin family for virus growth. To examine whether FK506 exerts an inhibitory activity on other human coronaviruses, CaCo2 cells were infected with HCoV-NL63 at MOI = 0.004 (Herzog et al., 2008) in the presence of increasing inhibitor concentrations. In order to examine whether the cellular FK506-binding proteins FKBP1A and FKBP1B are required for virus replication, CaCo2 knockdown cell lines were established using lentiviral expression of shRNA (Sirion GmbH, Martinsried, Germany). doi = 10.1016/j.virusres.2012.02.002 id = cord-330260-xuw31zfn author = Chen, Hui-Wen title = Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan date = 2009-01-20 keywords = China; IBV; Taiwan summary = All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Phylogenetic analyses were performed based on the nucleotide sequence alignment using each ORF from the S to N genes among eight Taiwan and reference strains (Fig. 1) . Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan doi = 10.1016/j.virusres.2008.11.012 id = cord-272408-8flsy5o1 author = Chen, Rui title = Identification of the immunodominant neutralizing regions in the spike glycoprotein of porcine deltacoronavirus date = 2020-01-15 keywords = CTD; NTD summary = The neutralizing activity of the rabbit and mouse anti -NTD, -CTD, and -S2 polyclonal antisera was assessed 4 weeks after the initial inoculation by a FFN assay, as previously described (Okda et al., 2015) . Sera from rabbits inoculated with NTD, CTD, and S2 were tested for neutralizing antibodies against PDCoV by ELISA, virus neutralization (VN), and fluorescent focus neutralization (FFN) assays. These results demonstrate that the NTD, CTD, and S2 proteins induced potent anti-PDCoV neutralizing antibody responses in the immunized animals. We found that three regions in PDCOV S protein, including NTD (aa 50-286), CTD (aa 278-616), and S2 (aa 601-1087), can induce neutralizing antibody responses, and the specific polyclonal mouse and rabbit sera efficiently inhibit PDCoV entry and infection in ST cells. Cell attachment domains of the porcine epidemic diarrhea virus spike protein are key targets of neutralizing antibodies doi = 10.1016/j.virusres.2019.197834 id = cord-326320-flfrdrbi author = Choudhary, Shalki title = Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 date = 2020-08-29 keywords = ACE2; SARS summary = title: Scaffold morphing of arbidol (umifenovir) in search of multi-targeting therapy halting the interaction of SARS-CoV-2 with ACE2 and other proteases involved in COVID-19 The multi-targeting potential of generated analogues was explored against various targets involved in the pathogenesis of COVID-19 including SARS-CoV-2 SP, ACE2, furin, TMPRSS2 (in viral attachment) and 3CLPro (in viral replication). A cutoff value of 3 was used for the screening of compounds based on synthetic possibility and topranked molecules were submitted to structure-guided drug binding analysis such as molecular docking studies. All these molecules were docked against SARS-CoV-2 SP-ACE2 complex, furin, TMPRSS2 and main protease (3CLPro) and the binding affinity of their docked complexes was also calculated in terms of MM-GBSA score. J o u r n a l P r e -p r o o f 44 A combination of scaffold morphing and a structure-based drug designing approach was successfully utilized to identify putative multi-targeting analogues of arbidol against COVID-19. doi = 10.1016/j.virusres.2020.198146 id = cord-258546-1tf5ggfo author = Chung, Hee-Chun title = New emergence pattern with variant porcine epidemic diarrhea viruses, South Korea, 2012–2015 date = 2016-12-02 keywords = Korea; PEDV summary = Since outbreaks of porcine epidemic diarrhea virus (PEDV) in the United States in 2013, explosive outbreaks of PED in South Korea have infected all age groups of pigs in 2014–2015 year. PED outbreaks re-occurred in Korea in 2013, however, it was demonstrated that the emerging PEDVs were not variants of old Korean isolates or attenuated vaccine strains (Chung et al., 2015) . This study tested whether PEDV isolated recently was crossed neutralized by serum of pigs which were vaccinated with Korean PED oral vaccine (Attenuated DR13 strain, Green Cross Veterinary Product Co., Ltd., Yong-In, Korea). Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea ISolation of porcine epidemic diarrhea virus during outbreaks in South Korea Isolation of porcine epidemic diarrhea virus (PEDV) in Korea Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea doi = 10.1016/j.virusres.2016.06.013 id = cord-299904-i5c6nf18 author = Cornelissen, E. title = Absence of antibody-dependent, complement-mediated lysis of feline infectious peritonitis virus-infected cells date = 2009-04-07 keywords = ADCML; FIPV; cell summary = authors: Cornelissen, E.; Dewerchin, H.L.; Van Hamme, E.; Nauwynck, H.J. title: Absence of antibody-dependent, complement-mediated lysis of feline infectious peritonitis virus-infected cells ADCML consists of virus-specific antibodies that bind to cell surface expressed viral proteins which result in complement activation and cell lysis. ADCML consists of virus-specific antibodies that bind to cell surface expressed viral proteins which result in complement activation and cell lysis. Surprisingly, no lysis was observed in the CrFK cells and the monocytes that do show surface-expressed viral proteins, while controls showed that the ADCML assay was functional. Surprisingly, no lysis was observed in the CrFK cells and the monocytes that do show surface-expressed viral proteins, while controls showed that the ADCML assay was functional. Absence of surface expression of feline infectious peritonitis virus (FIPV) antigens on infected cells isolated from cats with FIP Feline infectious peritonitis virus-infected monocytes internalize viral membrane-bound proteins upon antibody addition doi = 10.1016/j.virusres.2009.03.017 id = cord-275182-cmjfqkjz author = Cruz, Jazmina L.G. title = Vectored vaccines to protect against PRRSV date = 2010-06-25 keywords = Fig; GP5; PRRSV summary = doi = 10.1016/j.virusres.2010.06.017 id = cord-279849-zzkliu76 author = DaPalma, T. title = A systematic approach to virus–virus interactions date = 2010-01-20 keywords = HIV; VVI; infection; virus summary = doi = 10.1016/j.virusres.2010.01.002 id = cord-295187-konm26x5 author = Decaro, Nicola title = Full-length genome analysis of canine coronavirus type I date = 2015-12-02 keywords = CCoV; Decaro summary = However, two distinct features were observed in the CCoV-I genome: (i) the presence of an additional ORF between the spike (S) protein gene and ORF3a; (ii) the diversity of the S protein, which is more closely related to that of feline coronavirus type I and presents a furin cleavage site. Canine coronavirus (CCoV) is usually responsible for mild enteritis in young dogs Buonavoglia, 2008, 2011) , although fatal disease has been associated to a pantropic variant of the virus (Decaro et al., , 2010a Marinaro et al., 2010; Zicola et al., 2012; Ntafis et al., 2012) . Alignment of complete genome sequences of CCoV-I strain 23/03 and reference alphacoronaviruses showed the closest genetic relatedness with CCoV-IIa isolates (83.82-84.98% nt identity), followed by TGEV (82.81%) and . Molecular characterization of a canine coronavirus NA/09 strain detected in a dog''s organs doi = 10.1016/j.virusres.2015.07.018 id = cord-272458-72dybi7t author = Desforges, Marc title = Activation of human monocytes after infection by human coronavirus 229E date = 2007-07-31 keywords = Fig; MOI; OC43; THP-1; cell summary = Moreover, like primary monocytes and macrophages, the THP-1 cells were highly susceptible to HCoV-229E-induced cell death, regardless of the state of differentiation, as mitochondrial metabolic activity dropped significantly at 72 hpi ( Fig. 1C) , suggesting that the decrease in infectious titers may in part be due to a lower number of viable cells. Also, similarly to primary monocytes and macrophages, the PMA-differentiated THP-1 cells restricted HCoV-OC43 replication, with no detection of production of infectious virus (Fig. 1B ) or viral antigens (data not shown). When HCoV-229E infection of human primary monocytes/macrophages was performed at a MOI of 1, infectious virus was under the detection limit at 3 dpi but viral antigens were still easily detected within the infected cells until at least 5 dpi (data not shown). When HCoV-229E infection of both primary monocytes and THP-1 cells was performed at a MOI of 0.1, the kinetics of infection was similar, as shown by infectious virus production ( Fig. 2A) and detection of viral antigens (Fig. 3A) . doi = 10.1016/j.virusres.2007.06.016 id = cord-294764-v28wbrqp author = Deval, Jerome title = Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses date = 2017-04-15 keywords = Fig; Norwalk; RNA; norovirus summary = doi = 10.1016/j.virusres.2016.12.018 id = cord-326349-59566vqe author = Ding, Li title = Transmissible gastroenteritis virus infection induces cell cycle arrest at S and G2/M phases via p53-dependent pathway date = 2013-12-26 keywords = TGEV summary = In addition, TGEV infection of the cells synchronized in various stages of cell cycle showed that viral genomic RNA and subgenomic RNA, and virus titer were higher in the cells released from S-phaseor G2/M phase-synchronized cells than that in the cells released from the G0/G1 phase-synchronized or asynchronous cells after 18 h p.i. Taken together, our data suggested that TGEV infection induced S and G2/M phase arrest in host cells, which might provide a favorable condition for viral replication. To further determine the roles of p53 in TGEV-induced cell cycle arrest, we investigated the effects of PFT-␣, a specific inhibitor of p53 that does not affect the mRNA levels of TGEV genes (Huang et al., 2013) , on the cell cycle profiles and the expression of p21, cdks and cyclins in TGEV-infected PK-15 and ST cells. As shown in Fig. 6B , pre-incubation of PK-15 and ST cells with PFT-␣ attenuated cell cycle arrest at S and G2/M phase induced by TGEV infection. doi = 10.1016/j.virusres.2013.09.036 id = cord-290481-i2ppvsh5 author = Dolja, Valerian V. title = Comparative and functional genomics of closteroviruses date = 2006-03-09 keywords = BYV; Fig; RNA; virus summary = It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . doi = 10.1016/j.virusres.2006.02.002 id = cord-284866-66azyje4 author = D’ Andrea, Lucía title = A detailed comparative analysis on the overall codon usage patterns in Hepatitis A virus date = 2011-02-04 keywords = HAV; codon; usage summary = The first axis in COA is highly correlated with the GC 3 S and GC 12 values in HAV ORFs. This result reveals that nucleotide composition plays an important key role in the codon usage bias observed in HAV ORFs (see Table 2 ). These observations indicate that the composition of dinucleotides also plays a key role in the variation found in synonymous codon usage among HAV ORFs. To study the possible effects of CpG under-representation on codon usage bias of HAV ORFs, the RSCU value of the eight codons that contain CpG (CCG, GCG, UCG, ACG, CGC, CGG, CGU, CGA) were analyzed. The results of these studies revealed that codon usage in HAV ORFs is quite different from that of human genes (see Table 1 ). Positions of the 30 HAV ORFs in the plot of the first two major axes by correspondence analysis (COA) of relative synonymous codon usage (RSCU) values. doi = 10.1016/j.virusres.2011.01.012 id = cord-344084-z4t2wkgk author = Ellwanger, Joel Henrique title = Beyond HIV infection: neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases date = 2020-05-30 keywords = CCR5; CCR5Δ32; HBV; HCV; HIV; WNV; infection summary = The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals. In this context, this review discusses the involvement of CCR5 and the effects of the CCR5Δ32 in human infections caused by the following pathogens: West Nile virus, Influenza virus, Human papillomavirus, Hepatitis B virus, Hepatitis C virus, Poliovirus, Dengue virus, Human cytomegalovirus, Crimean-Congo hemorrhagic fever virus, Enterovirus, Japanese encephalitis virus, and Hantavirus. In agreement with studies showing that CCR5Δ32 homozygous genotype is a risk factor for symptomatic WNV infection in humans, Ccr5-/-WNV-infected mice showed a reduced capacity of viral control, increased disease severity, impaired leukocyte trafficking towards the brain, and high mortality rates than Ccr5 wild-type mice. In conclusion, although tissue analysis and evidence obtained in vitro suggest that the CCR5 is potentially involved in the pathogenesis of HPV, most studies point to a lack of involvement of CCR5Δ32 in susceptibility to HPV infection or HPV-associated diseases. doi = 10.1016/j.virusres.2020.198040 id = cord-311628-ep795pil author = Fu, Yu title = A novel delivery platform based on Bacteriophage MS2 virus-like particles date = 2016-01-04 keywords = MS2; RNA; VLP summary = Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. A series of research findings showed that an MS2 VLP-based vaccine can effectively induce innate and cognate immune responses and can be used as a specific preventive intervention in some diseases, such as foot-and-mouth disease (Bittle et al., 1982; Dong et al., 2015; Van Lierop et al., 1992; Wong et al., 2000) , prostate cancer (Li et al., 2014) , and illnesses caused by human papilloma virus (HPV) (Tumban et al., 2012) . These particles offer an effective and convenient way to package RNAs, DNAs, epitope peptides, and drugs into bacteriophage capsids, forming different kinds of VLPs. MS2 VLPs can not only deliver various kinds of agents with a good safety profile and strong immunogenicity but also ensure tissue-specific targeting, which is determined by the species of the virus. doi = 10.1016/j.virusres.2015.08.022 id = cord-338602-6n309bnp author = Gadotti, Ana Carolina title = IFN-γ is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection date = 2020-09-23 keywords = IFN; covid-19; patient summary = title: IFN-γ is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection We proposed a study in patients with moderate to severe COVID-19 infection to evaluate the interleukin patterns and its role as prognosis factors. A reasonable hypothesis is that (i) pro-inflammatory innate immunity and (ii) anti-inflammatory system are related to disease severity or death once IL-6, IL-8, and IL10 are closely described as prognostic factors in patients diagnosed with COVID-19 1, 3, 7 . Previous studies have not reported the association between IFN-γ and death, even evaluating the COVID-19-reactive CD69+ expressing IFN-γ producing CD8+ T in 25 patients with severe and moderate disease 22 . Suppressed T cell-mediated immunity in patients with COVID-19: A clinical retrospective study in Wuhan Levels of cytokines from patients with moderate and severe COVID-19 infection according to the outcome (data in the median with IQR) doi = 10.1016/j.virusres.2020.198171 id = cord-258294-ny3xrjzc author = Gao, Xiang title = Characterization, Pathogenicity and Protective efficacy of a Cell Culture-Derived Porcine Deltacoronavirus date = 2020-04-02 keywords = China; LLC; pdcov summary = Compared with nonvaccinated pigs, conventional weaned pigs given the inactivated vaccine developed a potent humoral immune response and showed no clinical signs or viral shedding after challenge, indicating a potent protective effect of the vaccine against PDCoV infection. Piglets in the infection group and mock control group were separately inoculated with 3 ml of MEM containing 1.0×10 4 TCID50 of the cell culture-adapted PDCoV strain CH/XJYN/2016-P6. To determine a standardized and validated dose for the subsequent pig challenge experiments, the median pig diarrhea dose (PDD50) of P6 of the cell culture-adapted PDCoV strain, CH/XJYN/2016, was determined by using conventional weaned pigs as described in our previous study (Zhang et al., 2019a) . Therefore, the infectious titer (PDD50) of PDCoV in two-month-old conventional pigs and the protection efficacity of an inactivated vaccine based on the cell-adapted strain CH/XJYN/2016 were determined for the first time in the present study. doi = 10.1016/j.virusres.2020.197955 id = cord-284479-75zgljet author = García-Serradilla, Moisés title = Drug repurposing for new, efficient, broad spectrum antivirals date = 2019-04-15 keywords = antiviral; drug; virus summary = Thus, the antiviral activity of cyclosporine A (CsA) and some of its nonimmunosuppressive analogs against these viruses has been shown to be related to its ability to bind cellular cyclophilins and inhibiting the interaction with the viral proteins (Bienkowska-Haba et al., 2009; Bose et al., 2003; Damaso and Moussatche, 1998; Franke et al., 1994; Kaul et al., 2009; Nakagawa et al., 2004; Thali et al., 1994; Wainberg et al., 1988; Yang et al., 2008) . CsA has also been reported to inhibit the propagation of several strains of influenza A virus in cell cultures blocking a late step of the replication cycle by mechanisms that might implicate CypA-dependent and -independent pathways (Hamamoto et al., 2013; Liu et al., 2012a; Ma et al., 2016) . Therefore, further studies are needed to better understand the mode of action of AgNPs, their cell specificity and toxicological issues in order to generate new and more effective compounds as well as the use in combination with other drugs in the treatment of different viral diseases. doi = 10.1016/j.virusres.2019.02.011 id = cord-260422-z22t57ju author = Godet, Julien title = Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date = 2012-06-26 keywords = HIV-1; RNA; Tat; dna summary = Today''s view is that RNA chaperones are nucleic acid binding proteins present in all living organisms, including viruses, where they Abbreviations: HIV-1, human immunodeficiency virus-type I; NCp7, nucleocapsid protein of HIV-1; ZF, zinc finger; NA, nucleic acid; TAR, transactivation response element; PBS, primer binding site; AA, amino acids. The substantial nucleic acid chaperone properties exhibited by Tat may account for its ability to promote the annealing of the primer tRNA to the viral RNA (Kameoka et al., 2002) and intervene in the first strand transfer (Boudier et al., 2010) and by this way, to stimulate RTion as does NCp7 (Harrich et al., 1997; Ulich et al., 1999; Apolloni et al., 2007) . Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minusstrand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site doi = 10.1016/j.virusres.2012.06.021 id = cord-286473-sl5zy8nj author = Gomaa, M.H. title = Complete genomic sequence of turkey coronavirus date = 2008-05-12 keywords = IBV; ORF summary = doi = 10.1016/j.virusres.2008.03.020 id = cord-329183-s0zrvn9o author = Graham, Robert I. title = Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae)() date = 2008-04-10 keywords = Graham; Reoviridae summary = title: Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae)() When the protein encoded by ObRV Seg-10 was expressed (by inserting the open reading frame into a baculovirus expression vector) no ''occlusion bodies'' were observed in the recombinant baculovirus infected insect cell cultures. Seg-1 of ObRV is 4170 nt in length (Table 1) , with a single large ORF between nt 33 and 4109 (stop codon TGA), coding for a predicted protein of 1358 aa (155.7 kDa), which is identified as VP1. Although the lack of sequence information from this genus (particularly the RdRp), makes it difficult to make further comparisons, the data presented here, together with the detection of an eleventh genome segment in female wasps (Graham et al., 2006) , suggest that ObRV represents a new member (a new species) within the genus Idnoreovirus, which contains other non-occluded insect reoviruses. doi = 10.1016/j.virusres.2008.02.005 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 = doi = 10.1016/j.virusres.2017.10.014 id = cord-314415-yr0uxok2 author = Guo, Zijing title = Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China date = 2018-08-15 keywords = Circo; dna summary = In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The result showed that Bo-Circo-like virus CH is clustered into a independent branch with seven reported strains of proposed family Kirkoviridae and eight CRESS-DNA virus strains recently submitted to GenBank database; Bo-Circo-like virus CH is more closely related to Po-Circo-like virus and shows significant genetic differences with viruses in the families Circoviridae, Nanoviridae, Geminiviridae Genomoviridae, Bacilladnaviridae and Smacoviridae (Fig. 3) . The sequence alignments included strain Bo-Circo-like virus CH in this study, representative members of the Circoviridae, Geminiviridae, Nanoviridae, Genomoviridae, Bacilladnaviridae and Smacoviridae families, the proposed new genera of krikoviruses, and still unassigned novel CRESS-DNA viruses with the best BLASTp matchs in GenBank database. The sequence alignments included five Bo-Circo-like virus strains detected in this study and seven reported strains of the proposed family Kirkoviridae. doi = 10.1016/j.virusres.2018.07.015 id = cord-267228-g2tf1jz6 author = Huang, Ke-Yan title = Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide date = 2018-03-02 keywords = Ctrlpep; Fig summary = Mice were immunized by lavage administration of the recombinant NC8-pSIP409-pgsA''-S-DCpep, which was observed to induce DC activation and high production of sIgA and IgG antibodies in experimental animals, while also eliciting production of significantly more IgA(+)B220(+) B cells. Compared with the saline group, the expression level of CD11c + CD40 + of DCs surface molecules in the LP cells of the small intestine was significantly increased in the NC8-pSIP409-pgsA''-S-DCpep group (P < 0.01) and NC8-pSIP409-pgsA''-S-Ctrlpep group (P < 0.05) experimental groups (Fig. 2B) . Unexpectedly, the level of IFN-γ in the supernatant of MLN cells cultured with the strains expressing S-DCpep was significantly higher in the group of mice orally immunized with recombinant NC8-pSIP409-pgsA''-S-Dcpep compare to the group of mice orally administered with saline (P < 0.01), NC8-pSIP409-pgsA''-S-Ctrlpep and NC8-pSIP409-pgsA'' groups (P < 0.05) (Fig. 6B ). doi = 10.1016/j.virusres.2017.12.011 id = cord-290948-cuu78cvl author = Imbert, Isabelle title = The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date = 2008-02-05 keywords = GST; RNA; SARS summary = Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. doi = 10.1016/j.virusres.2007.11.017 id = cord-293562-69nnyq8p author = Imran, Mudassar title = Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever date = 2018-08-15 keywords = Zika; model summary = We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. Since the only way to control the disease is to isolate patients who have been infected with the Zika virus, we included a new population compartment consisting of hospitalized individuals. doi = 10.1016/j.virusres.2018.07.002 id = cord-290801-dv6aak01 author = Ivanyi-Nagy, Roland title = Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro() date = 2012-09-27 keywords = Fig; RNA; UTR; WNV summary = Since the core protein of flaviviruses is also endowed with potent RNA chaperone activities, we decided to examine the effect of West Nile virus (WNV) core on 5′–3′ genomic RNA annealing in vitro. These results indicate that core protein – besides its function in viral particle formation – might be involved in the regulation of flavivirus genomic RNA cyclization, and thus virus replication. In this study, we examined the effect of WNV core protein chaperoning on viral 5 -3 UTR annealing, using an in vitro model system with separate 5 and 3 RNAs. We found that core protein binding greatly increases the rate of 5 -3 complex formation, and is required for the interaction when full-length 3 UTR RNAs are used (Fig. 2) . doi = 10.1016/j.virusres.2012.09.009 id = cord-271568-qgpi2kcs author = Jackwood, M.W. title = Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date = 2010-01-21 keywords = IBV; bird; challenge; virus summary = Genomic diversity and the Abbreviations: CPE, cytopathic effects; EID50, 50% embryo infectious dose; ELISA, enzyme linked immunosorbent assay; HMA, hexamethylene amiloride; IBV, infectious bronchitis virus; MHV, mouse hepatitis virus; PBS, phosphate buffered saline; RFLP, restriction fragment length polymorphism; RT-PCR, reverse transcriptasepolymerase chain reaction; SARS-CoV, Severe Acute Respiratory Syndrome virus; SPF, specific pathogen free; TCID50, 50% tissue culture infectious dose. Clinical signs were observed in all of the Mass41 virus challenged groups of birds regardless of treatment but in the intranasal and spray treated groups, fewer birds had signs and the signs were milder, as reflected by lower average scores (Table 1) . Virus was detected in 1 of 5 vaccinated birds in the treated group at 7 days post-vaccination Table 3 Experiment 4: clinical signs a in broiler chickens challenged with IBV at various times after treatment with QR448(a) at 1 day of age. doi = 10.1016/j.virusres.2010.01.006 id = cord-286658-9kco7qad author = Jiang, Lei title = Characterization of the complete genome, antigenicity, pathogenicity, tissue tropism, and shedding of a recombinant avian infectious bronchitis virus with a ck/CH/LJL/140901-like backbone and an S2 fragment from a 4/91-like virus date = 2018-01-15 keywords = I1101/16; IBV; LJL/140901 summary = Recently, numerous IBV strains have been identified and new genotypes/serotypes have emerged from existing viruses via point mutations, insertions, and deletions in the viral genome, especially in the S1 subunit of the spike protein gene. There have been several episodes of infectious bronchitis (IB) in Chinese chicken flocks, and the genotypes/serotypes of IBVs were previously classified based mainly on the nucleotide sequences of genes encoding the S1 subunit of the spike protein (Han et al., 2011) , and in some cases based on cross virus-neutralization Chen et al., 2017) in China. In addition, it is very interesting to note that the/I1101/16 isolate exhibited decreased replication levels in both the tracheal and kidney tissues (two target tissues for most IBVs) compared with one of its parental viruses (the ck/CH/LHLJ/140901 strain, which does not cause severe clinical disease in SPF chickens), but it exhibited prolonged replication and shedding post-challenge in a Table 3 Pairwise comparisons of the nucleotide sequences of the S2 subunit of the spike genes between the 4/91 vaccine strain, I1101/16 isolate, and pathogenic 4/91 strain a . doi = 10.1016/j.virusres.2017.11.007 id = cord-291962-rp172ugk author = Jing, Huiyuan title = Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 date = 2019-07-15 keywords = NLRX1; Nsp9; PRRSV; RNA summary = title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 To test this, increasing dose of NLRX1 was transfected into Marc-145 cells followed by PRRSV infection, qPCR was then performed to test the total viral RNA levels. On the other hand, recent literature indicated that the interaction of Nsp9 with SUMO E2 conjugating enzyme Ubc9 and cellular protein interleukin-2 enhancer binding factor 2 (ILF2) through its RdRp domain resulted in a significantly decrease of virus titers, indicating that cells utilize host antiviral factors as defense mechanisms to limit PRRSV infection Wen et al., 2017) . An intracellularly expressed Nsp9-specific nanobody in MARC-145 cells inhibits porcine reproductive and respiratory syndrome virus replication Porcine reproductive and respiratory syndrome virus nucleocapsid protein interacts with Nsp9 and cellular DHX9 to regulate viral RNA synthesis The DEADbox RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro doi = 10.1016/j.virusres.2019.05.011 id = cord-268010-1m5h3krw author = Jung, Kwonil title = Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis date = 2016-12-02 keywords = Jung; PEDV; PID summary = However, a recent study reported evidence of antigenic cross-reactivity between PDCoV Michigan/8977/2014 strain and PEDV, possibly sharing at least one conserved or similar epitope on their N proteins, as determined by enzyme-linked immunosorbent assay (ELISA) and western blot using monoclonal PEDV and PDCoV N-specific antibodies, whereas no cross-reactivity was detected when virus neutralization, indirect immunofluorescence, and immunostaining assays were conducted on either virus-infected cells or intestinal tissues using pig hyperimmune antisera to PEDV or PDCoV (Ma et al., 2016) . Another study using conventional 5-day-old pigs and a cell culture-adapted PDCoV USA/IL/2014 strain (P11) reported the onset of diarrhea at PID 5 in 5 of 5 pigs orally inoculated with 3 × 10 4 TCID 50 /pig of the virus, which was 1 day later or coincided with the detection of viral RNA in feces at PID 4 (3/5 pigs tested) or 5 (2/5 pigs tested) (Chen et al., 2015b) . doi = 10.1016/j.virusres.2016.04.009 id = cord-302083-9q1i20o6 author = Jung, Kwonil title = Porcine epidemic diarrhea virus (PEDV): An update on etiology, transmission, pathogenesis, and prevention and control date = 2020-06-02 keywords = INDEL; Jung; PEDV; PID summary = PEDV infection of neonatal pigs causes fecal virus shedding (alongside frequent detection of PEDV RNA in the nasal cavity), acute viremia, severe atrophic enteritis (mainly jejunum and ileum), and increased pro-inflammatory and innate immune responses. Detection of viremia where viral RNA in serum ranged from 4.5-8.6 log10 genomic equivalents (GE)/ml was identified in gnotobiotic neonatal (5/5; 100%), or conventional 9-dayold nursing (16/16; 100%) and 26-day-old weaned pigs (11/20; 55%) infected with a US non-S INDEL PEDV strain at PID 1-5 (Jung et al., 2015a; Jung et al., 2014) . Cross protective immune responses in nursing piglets infected with a US spike-insertion deletion porcine epidemic diarrhea virus strain and challenged with an original US PEDV strain Goblet cell depletion in small intestinal villous and crypt epithelium of conventional nursing and weaned pigs infected with porcine epidemic diarrhea virus. doi = 10.1016/j.virusres.2020.198045 id = cord-260835-ck9z5xsd author = Kamau, Anthony Ndirangu title = Porcine amino peptidase N domain VII has critical role in binding and entry of porcine epidemic diarrhea virus date = 2017-01-02 keywords = NIH3T3; PEDV; cell summary = Results showed PEDV infection was restricted to pAPN and pAPN domain VII expressing NIH3T3 cells. Also, PEDV harvested from pAPN or domain VII expressing NIH3T3 cells was induced indirect plaques in Vero cells confirming successful entry and replication. In the current study, by constitutive expression of pAPN in non-susceptible NIH3T3 cells, we have sought to annotate the previous findings stipulating pAPN receptor function for PEDV. Susceptibility assays showed infection in pAPN domain-VII expressing cells but virus entry was abrogated in absence of seventh domain (pAPN DI-VI ) as shown in (Fig. 5A) . PEDV was also reported to interact with pAPN in porcine enterocytes (Li et al., 2009) , and is capable of infecting MDCK and ST cells expressing the pAPN receptor (Oh et al., 2003; Nam and Lee, 2010) . In our study, to determine the specific interactive point of pAPN wt with PEDV, domain mutants were expressed stably in NIH3T3 cells. doi = 10.1016/j.virusres.2016.10.004 id = cord-345999-iiw4cs8p author = Khare, Prashant title = Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection date = 2020-09-24 keywords = SARS; Wen summary = Since it is a newly emerging viral disease and obviously there is a lack of anti-SARS-CoV-2 therapeutic agents, it is urgently required to develop an effective anti-SARS-CoV-2-agent.Through recent advancements in computational biology and biological assays, several natural compounds and their derivatives have been reported to confirm their target specific antiviral potential against Middle East respiratory syndrome coronavirus (MERS-CoV) or Severe Acute Respiratory Syndrome(SARS-CoV).These targets including an important host cell receptor, i.e., angiotensin-converting enzyme ACE2 and several viral proteins e.g. spike glycoprotein (S) containing S1 and S2 domains, SARS CoV Chymotrypsin-like cysteine protease (3CL(pro)), papain-like cysteine protease (PL(pro)), helicases and RNA-dependent RNA polymerase (RdRp). For the management J o u r n a l P r e -p r o o f of COVID-19 infection, various molecular targets playing important role in the SARS-CoV-2 life cycle including host cell receptor-Angiotensin-converting enzyme ACE2 (PDB ID 3D0G) and viral proteins such as S protein (containing S1 and S2 domains) (PDB ID 6XM0); various cysteine proteases such as papain-like cysteine protease (PL pro ) (PDB ID 6WX4) or Chymotrypsin like nprotease (3CL pro ) (PDB ID 1P9U), helicases and RNA-dependent RNA polymerase (RdRp) (PDB ID 6M71) could be evaluated . doi = 10.1016/j.virusres.2020.198169 id = cord-272729-nbgdmavr author = Kim, Youngnam title = Ribavirin efficiently suppresses porcine nidovirus replication date = 2012-10-27 keywords = PEDV; PRRSV; RNA; Vero; ribavirin summary = Investigations into the mechanism of action of ribavirin against PRRSV and PEDV revealed that the addition of guanosine to the ribavirin treatment significantly reversed the antiviral effects, suggesting that depletion of the intracellular GTP pool by inhibiting IMP dehydrogenase may be essential for ribavirin activity. Further experiments revealed that suppression of ribavirin affects post-entry steps of the replication cycle of PRRSV and PEDV, including viral genomic and sg RNA synthesis, viral protein expression, and virus production. Several mechanisms of action for the antiviral activity of ribavirin have been suggested, including a reduction in cellular GTP pools via inosine monophosphate dehydrogenase (IMPDH) inhibition and increased mutation frequency on the virus genome leading to error catastrophe (Graci and Cameron, 2006) . Treatment of cells with ribavirin resulted in significant attenuation of postentry steps during the replication of porcine nidovirus, as determined by lower progeny production, diminished viral protein expression, and decreased synthesis of genomic RNA and sg mRNA. doi = 10.1016/j.virusres.2012.10.018 id = cord-260107-gqbtkf0x author = Lee, Sunhee title = Isolation and characterization of a Korean porcine epidemic diarrhea virus strain KNU-141112 date = 2015-10-02 keywords = KNU-141112; Lee; PEDV; Vero; korean summary = In the present study, one Korean PEDV strain, KOR/KNU-141112/2014, was successfully isolated and serially propagated in Vero cells for over 30 passages. Our genomic analyses indicated that the Korean isolate KNU-141112 is genetically stable during the first 30 passages in cell culture and is grouped within subgroup G2b together with the recent re-emergent Korean strains. Our data indicated that KNU-141112 isolate is relatively stable during the first 30 passages in cell culture and is classified into subgroup G2b that includes PEDV strains responsible for recent severe outbreaks in Korea and the US. Although virus isolation in cell culture from clinical samples of naturally or experimentally infected pigs is fastidious, recent studies reported the successful isolation and propagation of several US original PEDV strains using Vero cells (Chen et al., 2014; Oka et al., 2014) . Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene doi = 10.1016/j.virusres.2015.07.010 id = cord-285180-32bxx94u author = Lee, Sunhee title = Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus date = 2015-10-02 keywords = Invitrogen; cell; protein summary = doi = 10.1016/j.virusres.2015.06.013 id = cord-309428-qkjjxr6p author = Li, Liwei title = Host miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by upregulating type I interferons date = 2015-01-02 keywords = Fig; IFN; PRRSV summary = doi = 10.1016/j.virusres.2014.08.012 id = cord-268337-o6lo55o8 author = Lloyd, Richard E. title = Translational control by viral proteinases date = 2005-11-21 keywords = PABP; RNA summary = Human immunodeficiency virus-1 (HIV-1) infection of cells resulted in partial cleavages of eIF4GI that was mapped to three sites in two regions on either side of the eIF3-binding domain ( Fig. 1) (Ohlmann et al., 2002; Ventoso et al., 2001) . Translation assays based on luciferase reporter constructs in cells indicated that expression of HIV protease (HIV PR) primarily inhibited translation of capped mRNAs. Interestingly, comparison of translation function of eIF4GI C-terminal cleavage products produced by L pro and HIV PR revealed that the slightly shorter HIV PR-derived fragment was defective in supporting translation of the PV-IRES but not the EMCV IRES. Demonstration in vitro that eucaryotic initiation factor 3 is active but a cap-binding protein complex is inactive in poliovirus-infected HeLa cells Eukaryotic initiation factor 4GII (eIF4GII), but not eIF4GI, cleavage correlates with inhibition of host cell protein synthesis after human rhinovirus infection Cleavage of eukaryotic initiation factor eIF4G and inhibition of host-cell protein synthesis during feline calicivirus infection doi = 10.1016/j.virusres.2005.10.016 id = cord-347270-x05tfkgx author = Lu, Shuai title = Discovery of a novel canine respiratory coronavirus support genetic recombination among betacoronavirus1 date = 2017-06-02 keywords = Betacoronavirus; K37; bj232 summary = doi = 10.1016/j.virusres.2017.05.006 id = cord-259671-7de21oaq author = Madhugiri, Ramakanth title = RNA structure analysis of alphacoronavirus terminal genome regions date = 2014-12-19 keywords = MHV; RNA; UTR summary = Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alphaand betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements. Other internal cis-acting elements include specific RNA signals required for genome packing, which have been characterized in a small number of coronaviruses Escors et al., 2003; Morales et al., 2013; Penzes et al., 1994) , and a complex RNA pseudoknot structure located in the ORF1a-ORF1b overlap region that mediates a (−1) ribosomal frameshift event and thus controls the expression of the second large ORF on the coronavirus genome RNA (ORF1b) (Brierley et al., 1987 (Brierley et al., , 1989 de Haan et al., 2002; Namy et al., 2006) . doi = 10.1016/j.virusres.2014.10.001 id = cord-278939-z6kiee09 author = Mani, Janice S. title = Natural product-derived phytochemicals as potential agents against coronaviruses: a review date = 2020-04-30 keywords = EC50; MERS; SARS; antiviral summary = As previous work has highlighted the potential of traditional Chinese medicines as a source of potential novel drugs (Ling, 2020) , we have not included details on such studies investigating the antiviral activity of remedies comprising portions of numerous plant species in this review. (2020) virtually screened 83 compounds found in Chinese traditional medicines for activity against the RNA-dependent RNA polymerase of SARS-CoV-2, identifying theaflavin, an antioxidant polyphenol, as a potential inhibitor. Several authors have utilised virtual computer docking models to screen for potential compounds that could bind to and inhibit key proteins present in SARS-CoV (Liu and Zhou, 2005; Toney et al., 2004; Wang et al., 2007) , highlighting the potential antiviral activity of compounds such as sabadinine and aurantiamide acetate. Several large in vitro screening studies searching for inhibitory activity of naturally occurring compounds against SARS-CoV have been performed, mainly on Chinese medicinal herbs (Li et al., 2005; Wang et al., 2003) . doi = 10.1016/j.virusres.2020.197989 id = cord-252048-ftbjsoup author = McKinley, Enid T. title = Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date = 2011-04-22 keywords = Conn; IBV; Mass; virus summary = The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. doi = 10.1016/j.virusres.2011.04.006 id = cord-301301-ilsenpus author = Mihalov-Kovács, Eszter title = Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission date = 2017-03-15 keywords = ORF2; UTR; canine; strain summary = Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3′UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. A total of 63 samples obtained from 50 animals were tested for AstV by using a pan-astrovirus specific primer set (Chu et al., 2008) as described elsewhere (Mihalov-Kovács et al., 2014) and 37 (from 33 dogs) were randomly selected for viral metagenomics. The complete ORF1b was 1530 nt long in all canine AstVs, except the partially sequenced strain, HUN/2012/8, where a 770 nt long portion was determined. In addition, upon sequence comparison and phylogenetic analysis, strain HUN/2012/8 differed markedly from other canine AstVs concerning the partial ORF1b and the full-length ORF2 (Table 3) . doi = 10.1016/j.virusres.2016.12.005 id = cord-279827-921kvrrz author = Murata, Takayuki title = Growth behavior of bovine herpesvirus-1 in permissive and semi-permissive cells date = 1999-06-11 keywords = BHV-1; MDBK; dna summary = doi = 10.1016/s0168-1702(99)00023-4 id = cord-325973-e3rxr6oq author = Navarro, Ryan title = Molecular characterization of canine parvovirus and canine enteric coronavirus in diarrheic dogs on the island of St. Kitts: First report from the Caribbean region date = 2017-08-15 keywords = CPV; KNA; caribbean summary = Although the current CPV vaccines, derived from the original CPV-2 strains, or CPV-2b strains, have been shown to confer protective immunity against CPV disease, and post-vaccination reactions have rarely been encountered in immunized dogs, the emergence of new genetic and antigenic variants underscores the importance of constant http://dx.doi.org/10.1016/j.virusres.2017.08.008 Received 16 May 2017; Received in revised form 10 July 2017; Accepted 21 August 2017 monitoring of evolution patterns of CPV strains circulating in dogs throughout the world (Decaro and Buonavoglia, 2012; Miranda and Thompson, 2016) . Although the prevalence and genetic diversity of CPV and CCoV in dogs have been extensively studied in different parts of the world including nearby Latin American countries, there are no reports on these important canine viruses from the Caribbean region so far. We report here the detection and molecular characterization of CPV and CCoV strains in dogs with diarrhea on the Caribbean island of St. Kitts (KNA). doi = 10.1016/j.virusres.2017.08.008 id = cord-333180-xevie6tm author = Neumann, Simon title = How do viruses control mitochondria-mediated apoptosis? date = 2015-11-02 keywords = Bak; Bax; Bcl-2; Fig; cell summary = doi = 10.1016/j.virusres.2015.02.026 id = cord-263439-oquk4t96 author = Park, Jung-Eun title = Clathrin- and serine proteases-dependent uptake of porcine epidemic diarrhea virus into Vero cells date = 2014-10-13 keywords = PEDV; Vero; cell summary = Similar to other coronaviruses, PEDV spike protein mediates its cell entry by binding to cellular receptors and inducing membrane fusion between viral envelopes and cellular membranes. Taken together, our findings reveal that PEDV enters Vero cells via clathrin-mediated endocytosis and requires serine proteolysis during infection. Based on these observations, we concluded that an exogenous protease, like trypsin, was necessary to induce cell-cell fusion in PEDV-infected Vero cells but not essentially required for virus-cell entry. So, we hypothesized that PEDV entry into Vero cells under the trypsin-free condition most likely occurred inside endosomal compartments where cellular proteases might operate similar to trypsin, facilitating S-mediated fusion of PEDV with the endosomal membrane. The infection inhibition assay using various substrates that interfere with endocytosis or lysosomotropic agents revealed that PEDV enters Vero cells via clathrin-mediated endocytic uptake and delivery of virus to an acidic intracellular compartment. doi = 10.1016/j.virusres.2014.07.022 id = cord-288253-wqrhiq08 author = Park, Jung-Eun title = Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus date = 2015-02-02 keywords = APN; PCR; PEDV; mouse; porcine summary = Because the major pathological changes of the porcine coronaviruses (e.g., TGEV and PEDV) involves enteric diseases, we measured porcine APN expression in the small intestine by RT-PCR, immunoblotting, and IHC. An immunohistochemical analysis, with both anti-Flag and anti-porcine APN antibodies, clearly confirmed porcine APN expression in the brush borders of the absorptive cells in the small intestines of the mouse model (Fig. 4C) . For these purposes, many transgenic mouse models have been developed to study viral pathogenesis, immune responses, and vaccines (Darling et Both wild type and porcine APN transgenic mice were infected with PEDV (5X TCID5010 6 ) orally on day 0. Although significant clinical illness was not observed when the transgenic mice were infected with PEDV, their susceptibility to the virus was confirmed by the detection of viral RNA in various organs with RT-PCR and viral proteins in the small intestines with IHC. doi = 10.1016/j.virusres.2014.12.024 id = cord-285580-gq7400tq author = Pieretti, Joana C. title = Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections date = 2020-10-18 keywords = COVID-19; SARS summary = In this mini-review, we discuss recent progress concerning the antivirus activity of NO in clinical, pre-clinical and research settings, and its beneficial effects in the treatment of clinical complications in patients infected with coronaviruses and other respiratory viral diseases, including COVID-19. Although positive biological effects have been reported for the administration of NO donors, further studies are required to better evaluate the levels of inflammatory mediators and the activity of important heme-containing enzymes, such as indoleamine 2,3-dioxygenase (IDO), directly involved in the inflammatory responses in respiratory viral infections (Anderson and Russel, 2020) . In other words, NO demonstrates potential for the treatment of patients infected with COVID-19 both in severe and nonsevere conditions, improving oxygenation and antiviral mechanisms, and preventing aggravation of the disease (Ferrari et al., 2020; Parikh et al., 2020) . Protocol of a randomized controlled trial testing inhaled nitric oxide in mechanically ventilated patients with severe acute respiratory syndrome in COVID-19 (SARS-CoV-2) doi = 10.1016/j.virusres.2020.198202 id = cord-257715-pbcr81qm author = Pignatelli, J. title = Molecular characterization of a new PToV strain. Evolutionary implications date = 2009-03-20 keywords = BEV; BRES; ELISA summary = Thus, there have been a few reports where indirect ELISA using partially purified BToV or BEV particles were used for torovirus serodiagnosis, but purification procedures are not affordable by all laboratories and, in addition, this assay would also provide low sensitivity for detection of antibodies to human and porcine toroviruses (Brown et al., 1987) . Lack of cross-reactivity between PToV and antibodies to other related viruses infecting pigs was confirmed by ELISA, Western blot and virus neutralization tests using ␣PRRSV, ␣PRCV, and ␣BRES serum samples, purified PToV N protein or BEV particles as toroviral antigens, and purified PRRSV and TGEV virions as related viruses (data not shown). In order to evaluate the potential use of the PToV-N protein as antigen for diagnostic ELISA to detect antibodies against porcine torovirus, 45 serum samples were collected from three Spanish farms located in Galicia, Navarra and Aragon and were analyzed by ELISA, virus neutralization assay and/or Western blot. Recombinant PToV-BRES-N protein was used to develop an ELISA assay to detect antibodies against torovirus in swine serum samples. doi = 10.1016/j.virusres.2009.02.019 id = cord-287324-ecpicv5v author = Qiu, Yuan title = Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date = 2017-06-02 keywords = RNA; method summary = In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. In this study, we detected the viromes of RNA viruses of one mock sample and two pooled authentic samples, using the libraries prepared by the three methods on the Personal Genome Machine (PGM) platform, with the aim to generate data of significance for virome detection of RNA viruses and characterize the viromes of RNA viruses in ducks and minks. In the future, it is of significance to compare methods 2 and 3 in detecting viromes of RNA viruses in some clinical samples containing limited viral RNA. Detection of viromes of ducks and minks increases our understanding of the viral diversity in the animals, and provides novel clues for further studies regarding diagnosis of infectious diseases, identification of novel viruses and research of host-virus relationships. doi = 10.1016/j.virusres.2017.05.003 id = cord-272383-pzivb0ro author = Reddy, P.Seshidhar title = Optimization of bovine coronavirus hemagglutinin-estrase glycoprotein expression in E3 deleted bovine adenovirus-3 date = 2000-11-08 keywords = BAV-3; BCV summary = In an effort to optimize the expression, we have constructed several BAV-3 recombinants carrying the hemagglutinin esterase (HE) gene of bovine coronavirus (BCV) in the E3 region with or without exogenous transcription control elements. During infection of bovine cell lines, such recombinant BAVs produced large amounts of glycoprotein gD (a DNA virus gene), which has been shown to undergo proper post-translational modifications . This new transfer vector has two unique restriction enzyme sites (SrfI and SalI) for cloning of foreign genes and an overlap of 1992 bp on the left side and 3866 bp on the right side of the E3 region for efficient homologous recombination with plasmid pFBAV-302 , which dramatically increased the frequency of recombination in BJ 5183 cells. Our initial attempts to insert the BCV HE gene in the E3 region of plasmid pFBAV302 (E3 deleted full length BAV-3 genomic clone; Zakhartchouk et al., 1998) by homologous recombination in E. doi = 10.1016/s0168-1702(00)00209-4 id = cord-275413-e2rhioty author = Rowland, Raymond R.R. title = The interaction between PRRSV and the late gestation pig fetus date = 2010-09-09 keywords = IFN-; PCR; PRRSV; TNF-; fetus summary = The purpose of this study was to characterize the interaction between PRRSV and the pig fetus by (1) identifying sites of virus replication, (2) measuring immune and inflammatory cytokines in different compartments, and (3) evaluating the response of lymph nodes. Maternal, accessory and fetal tissues were collected and stored in formalin for histological staining and immunohistochemistry (IHC), or storage in RNAlater (Ambion) for RT-PCR of cytokine mRNAs. PRRSV-specific antibody was measured in sera using the HerdCheck ® PRRS ELISA (IDEXX) and performed by personnel at Kansas State University Veterinary Diagnostic Laboratory. As shown in Fig. 4A , IFN-␥ and TNF-␣ PCR products were not detected in lung, lymph node or placenta from the non-infected fetuses. To determine if cytokine gene expression was the direct result of PRRSV infection, RT-PCR for IFN-␥ and TNF-␣ was performed on the same tissues from fetuses of infected dam no. doi = 10.1016/j.virusres.2010.09.001 id = cord-327682-i3uim0zi author = Santti, Juhana title = Molecular detection and typing of human picornaviruses date = 1999-08-25 keywords = PCR summary = It has been shown in a number of studies that virtually all the enterovirus serotypes and most of the HRV isolates can be detected using these primer sequences (Hyypiä et , 1989; Horsnell et al., 1995; Pulli et al., 1995; Arola et al., 1996; Huttunen et al., 1996; Pitkäranta et al., 1997; Hyypiä et al., 1998; Oberste et al., 1998) The authors became convinced of the usefulness of this technique during a recent outbreak of aseptic meningitis in Finland. Partial sequence analysis of virtually all enterovirus serotypes has shown that they belong to these four clusters (Pulli et al., 1995; Huttunen et al., 1996) and that the VP4/VP2 region sequence can be used for molecular typing of clinical isolates (Arola et al., 1996) . In hepatitis A virus infections, the molecular epidemiology has been investigated by many reseach groups and an extensive analysis of partial sequences from different geographic locations has been used to establish a useful database for further studies (Robertson et al., 1992) . doi = 10.1016/s0168-1702(99)00036-2 id = cord-263178-lvxxdvas author = Shan, Dan title = Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus date = 2018-05-02 keywords = Beaudette; IBV; Vero summary = To study the roles of hypervariable regions (HVRs) in receptor-binding subunit S1 of the spike protein, we manipulated the genome of the IBV Beaudette strain using a reverse genetics system to construct seven recombinant strains by separately or simultaneously replacing the three HVRs of the Beaudette strain with the corresponding fragments from a QX-like nephropathogenic isolate ck/CH/LDL/091022 from China. We could not detect the replication with ck/CH/ LDL/091022 in Vero cells, so the neutralization tests were performed in 9-day-old SPF embryonated eggs to confirm whether the serotypes of the recombinant IBVs belonged to ck/CH/LDL/091022. Viral antigen was observed in Vero cells infected with the Beaudette strain and the seven recombinant IBVs (Fig. 1b) . S1 gene sequencing results confirmed that the heterogenous HVRs were stably maintained in the recombinant IBVs (Sup Fig. 1) , and no additional mutations were detected in the S protein after three passages in cells or eggs. doi = 10.1016/j.virusres.2018.04.013 id = cord-281101-gv1sgbk1 author = Shin, Gu-Choul title = Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein date = 2006-08-30 keywords = ELISA; SARS; protein summary = doi = 10.1016/j.virusres.2006.07.004 id = cord-309205-l8vjtrjq author = Shirato, Kazuya title = Differential susceptibility of macrophages to serotype II feline coronaviruses correlates with differences in the viral spike protein date = 2018-08-15 keywords = FECV; FIPV; Fig; feline summary = The ability to infect and replicate in monocytes/macrophages is a critically distinguishing feature between the two feline coronavirus (FCoV) pathotypes: feline enteric coronavirus (FECV; low-virulent) and feline infectious peritonitis virus (FIPV; lethal). Previously, by comparing serotype II strains FIPV 79-1146 and FECV 79-1683 and recombinant chimeric forms thereof in cultured feline bone marrow macrophages, we mapped this difference to the C-terminal part of the viral spike (S) protein (S2). Despite some concerns relating to the precise identity of the FCoV strains 79-1683 and 79-1146, to be discussed later, but lacking better options to address this critical issue in the pathogenesis of FIP, we continued in the present study with investigating the contributions of the amino acids in the spike S2 domain differing between the prototypic strains to the distinguishing macrophage tropism of these viruses. There are eleven amino acid differences in the C-terminal domain of the S proteins of FIPV 79-1146 and FECV 79-1683 to which we mapped these viruses'' differential ability to infect macrophages (Fig. 1c) . doi = 10.1016/j.virusres.2018.06.010 id = cord-275016-ij5yaqkx author = Someya, Yuichi title = Characterization of the norovirus 3C-like protease date = 2005-03-08 keywords = like; protease summary = The recombinant 3C-like protease of Chiba virus, a Norovirus, expressed in Escherichia coli cells was purified and characterized as to effects of pH, temperature, salt contents, and SH reagents on its proteolytic activity. The DNA fragment encoding all residues (Ala1 to Glu181) of the Chiba virus 3C-like protease was amplified by PCR, in that NdeI and Aor51HI restriction sites were introduced at the 5 and 3 ends, respectively. In order to observe proteolysis at the cleavage site between the 3C and 3D, we at first used the His-3CD-C139A mutant protein expressed from pT7His3CD-C139A as a substrate, which was the N-terminal His-tagged 3CD fragment containing the Ala mutation of active-site Cys139 of the 3C-like protease (Fig. 1B) . They used bacterially expressed 3C-like protease with its C-terminus His-tagged as an enzyme and the entire ORF1 protein or 3CD fragment containing the active-site Cys mutation as a substrate which was expressed in the in vitro transcription/translation reaction. doi = 10.1016/j.virusres.2005.02.002 id = cord-295099-ghc85pf5 author = Sun, Zehua title = Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date = 2018-01-02 keywords = HIV-1; antibody; cell summary = Antibody responses to neutralize human immunodeficiency virus-1 (HIV-1) are mediated by direct binding to viral spikes, which are trimers composed of glycoproteins gp120 and gp41 (Pincus et al., 2017a; Pincus et al., 2017b; Blair et al., 2007; Morris et al., 2000; Micoli et al., 2000; Pegu et al., 2017; Haynes and Mascola, 2017; Liao et al., 2004; Brodine et al., 2003; Ward and Wilson, 2017; Debnath et al., 1994; Moore et al., 1993) . M43 and m44 are HIV-1 cross-reactive human monoclonal antibodies isolated from a recombinant phage display library by competitive antigen panning (Zhang et al., 2012; Zhang et al., 2008; Zhang et al., 2006; Zhang et al., 2004a; Zhang et al., 2004b) . HIV-1 specific antibodies isolated by display techniques are less potent than those isolated by micro neutralization or single B cell sorting and cloning. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries doi = 10.1016/j.virusres.2017.10.011 id = cord-266453-v1hbust8 author = Sztuba-Solińska, Joanna title = Mutations in the coat protein-binding cis-acting RNA motifs debilitate RNA recombination of Brome mosaic virus date = 2012-10-16 keywords = BMV; Bbox; RNA3 summary = We have previously described the efficient homologous recombination system between 5′ subgenomic RNA3a (sgRNA3a) and genomic RNA3 of Brome mosaic virus (BMV) in barley protoplasts (Sztuba-Solińska et al., 2011a). A structured region near the 3 sgRNA3a polyA tail, referred to as the intergenic Bbox motif, participates in the assembly of the BMV replicase complex on RNA3 via interactions with protein 1a (Baumstrak and Ahlquist, 2001) , and it binds CP molecules via a specific peptide domains, as mapped by Yi et al. In a separate experiment, the Bbox-RNA3 was co-transfected with SG construct to determine whether the presence of the wt Bbox motif in sgRNA3a could rescue the previously reported high recombination frequency for unmutated RNAs. Indeed, among 100 cDNA clones, there were 42 recombinants (Fig. 2B) , of which the majority carried all three marker restriction sites (74%, 32 clones), while few had either single (BamHI -four clones) or double (BamHI/HindIII -three clones, BamHI/PstI -one clone, HindIII/PstI -two clones) restriction sites. doi = 10.1016/j.virusres.2012.10.001 id = cord-335706-lopcb77c author = Tan, Feifei title = Identification of non-essential regions in nucleocapsid protein of porcine reproductive and respiratory syndrome virus for replication in cell culture date = 2011-03-24 keywords = Fig; PRRSV summary = doi = 10.1016/j.virusres.2011.03.011 id = cord-266025-bkm486jd author = Tao, Ying title = Genomic characterization of seven distinct bat coronaviruses in Kenya() date = 2012-04-26 keywords = Kenya; PCR summary = Based on available data, bats appear to harbor a great diversity of CoVs. The frequency and diversity of CoV detection in bats, now in multiple continents, suggest that bats are likely a source for CoV introduction into other species globally and possibly play an important role in the ecology and evolution of CoVs. Recently we reported the identification of 41 divergent CoVs in bats from Kenya, based on limited ORF1b sequences (Tong et al., 2009) . The aa distances in the 816 bp fragment of the RdRp gene from the Kenya bat CoVs described in this study were compared to the aa sequences from their close reference viruses (Table S2) . In conclusion, sequence data for the structural and nonstructural ORFs in the 3 -end of the genome of seven Kenya bat CoVs confirmed the high diversity and their phylogenetical placement into Alphacoronavirus and Betacoronavirus genera. Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences doi = 10.1016/j.virusres.2012.04.007 id = cord-261388-d56ci0hl author = Tibbles, K.W title = Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus date = 1999-05-28 keywords = IBV summary = Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. The bacterial expression system described utilises the minimum processing unit identified in our previous studies which established that, in addition to the 3CLP domain, MP2 protein sequence between the Q/S 4 cleavage target and a point delimited by an NcoI restriction site (ntd position 10118) was that minimally required for processing. Identification of a 24-kDa polypeptide processed from the coronavirus infectious bronchitis virus 1a polyprotein by the 3C-like proteinase and determination of its cleavage sites doi = 10.1016/s0168-1702(99)00011-8 id = cord-270064-hidirfkv author = Tort, Fernando L. title = A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES date = 2020-04-12 keywords = CAI; SARS; codon summary = In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. In order to gain insight into the emergence, evolution, adaptation and spread of the SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. To gain insight into the biology and evolution of emerging SARS-CoV-2, a comprehensive analysis of genome composition, codon and amino acid usage of βCoV strains isolated in China from humans, bats, civets and ferret hosts was performed, including SARS-CoV-2 strains recently isolated from current outbreak. The results of these studies revealed that SARS-CoV-2 strains enrolled in these analyses have a distinct genome composition in relation to other βCoV strains isolated from human (SARS-CoV), bats, civets and ferrets (see Fig. 1 ). doi = 10.1016/j.virusres.2020.197976 id = cord-286416-8eu6wp9b author = Valiente-Echeverría, Fernando title = Viral modulation of stress granules date = 2012-06-14 keywords = RNA; stress summary = If deadenylation (e.g., CCR4/Not1), destabilization (e.g., TTP/XRN1) and decapping (e.g., DCP1/DCP2) complex; and even RISC (Ago) complex are recruited to mRNA, these will be targeted to PBs. Conversely, if TIA-1/TIAR or proteins such as G3BP/USP10 are recruited to the stalled initiation complexes, these will be directed to SGs. Different pathways in SG assembly are described (in red): (i) phosphorylation of eIF2␣ induced by the exposure to different stress inducers (e.g., arsenite and thapsigargin) (Fig. 1) ; (ii) Hippuristanol and Pateamine A, drugs that inhibit the helicase activity of eIF4A altering ATP binding or ATPase activity; and (iii) the overexpression of SG markers, such as G3BP or TIA-1. West Nile virus infections suppress early viral RNA synthesis and avoid inducing the cell stress granule response Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly doi = 10.1016/j.virusres.2012.06.004 id = cord-276198-psjua913 author = V’kovski, Philip title = New insights on the role of paired membrane structures in coronavirus replication date = 2015-04-16 keywords = MHV; RNA; TM2 summary = doi = 10.1016/j.virusres.2014.12.021 id = cord-291086-goidlh08 author = Walker, Peter J. title = Rhabdovirus accessory genes date = 2011-09-14 keywords = ORF; protein summary = doi = 10.1016/j.virusres.2011.09.004 id = cord-259935-xyo2pe4g author = Wang, Ching-Ying title = SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling date = 2017-05-02 keywords = Fig; SARS; TGF; type summary = To examine the association of SARS-CoV PLpro-induced TGF-β1 production with the collagen up-regulation, A549 lung epithelial cells transiently transfected with pcDNA3.1 and pSARS-PLpro were analyzed the production of TGF-β1 and type I collagen using Western blot, realtime RT-PCR and Sirius red staining assays (Fig. 1) . To examine whether SMAD-dependent pathways involve in TGF-β1mediated up-regulation of Type I collagen in response SARS-CoV PLpro, subcellular localization of receptor-regulated SMAD3 and inhibitory SMAD7 in transfected cells were detected using the immunofluorescent and DAPI staining (Fig. 4) . To examine the possible pathways involved in TGF-β1-dependent up-regulation of Type I collagen by SARS-CoV PLpro, the profiles of ubiquitin-conjugated proteins in transfected cells with vector control and pSARS-PLpro were determined using immune-precipitation and nanoLC-MS/MS. Subcellular localization analysis demonstrated that SMAD3 was predominant in cytoplasmic, but not in the nucleus in transfected cells with pSARS-PLpro compared to vector control (Fig. 4) , revealing that canonical Smad-dependent signaling pathway was not involved in PLpro-induced TGF-β1-dependent upregulation of Type I collagen. doi = 10.1016/j.virusres.2017.04.008 id = cord-332075-gxmae2rs author = Wang, Jianzhong title = Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings date = 2015-05-04 keywords = GPV; NDV; Newcastle; VP3 summary = title: Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings In this study, we generated a recombinant rmNA-VP3, expressing GPV VP3 using a modified goose-origin NDV NA-1 by changing the multi-basic cleavage site motif RRQKR↓F of the F protein to the dibasic motif GRQGR↓L as that of the avirulent strain LaSota as a vaccine vector. This is the first study demonstrating that recombinant NDV has the potential to serve as bivalent live vaccine against Goose parvovirus and Newcastle disease virus infection in birds. To evaluate whether this genotype VII isolate could be used as a vaccine vector for geese we generated a recombinant virus rmNA-VP3 expressing VP3 protein of GPV after modifying the polybasic F cleavage site of NA-1 to the dibasic motif of LaSota. doi = 10.1016/j.virusres.2015.04.006 id = cord-262760-mf1pn587 author = Weber, Stefanie title = Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world date = 2020-09-24 keywords = China; SARS; Table summary = By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. More specifically, the absence of the distinct hotspot mutations in the majority of sequences from samples isolated in China, convincingly argues against the possibility of technical problems during the generation of SARS-CoV-2 nucleotide sequences. and predominate in human populations with different geographic, societal, and genetic backgrounds At the time of beginning our analyses, about 2.500 nucleotide sequences of SARS-CoV-2 had been published of which 570 were randomly selected and compared to the reference sequence of the Wuhan isolate from late 2019 (NCBI Reference Sequence: NC_045512.2). The data on the analyses of 112 isolates from the US confirmed the steady rise in mutation frequencies as SARS-CoV-2 spread to different parts of the world (Table S4 ). doi = 10.1016/j.virusres.2020.198170 id = cord-347924-w06ho8sn author = Wen, Jin-Sheng title = Computational prediction and identification of dengue virus-specific CD4(+) T-cell epitopes date = 2007-12-03 keywords = CD4; PBMC summary = In this study, we tried to identify dengue virus-specific CD4(+) T-cell epitopes, which can induce PBMC (peripheral blood mononuclear cells) isolated from DF convalescent patients (dengue virus type 1 infection) to secrete IFN-γ. Currently, many studies suggested that dengue-specific T-cell immune response are hypothesized to play an important role in the immunopathogenesis of DHF during a secondary DEN virus infection, and induction of immunopathology by T lymphocytes may occur by various mechanisms, including cell-mediated cytotoxicity and/or cytokine production (Miskovsky et al., 1994; Vergelli et al., 1997) . In the present study, a combination of bioinformatics tools (epitope-prediction programs RANKpep) and in vitro assays (enzyme-linked immunospot assay (ELISPOT) and intracel-lular cytokine staining assay (ICS)) was used to screen and select antigen sequences as potential DEN-specific CD4 + T-cell epitopes, then the selected sequences are tested for biological function by their activation of T cells of DEN infected populations. doi = 10.1016/j.virusres.2007.10.010 id = cord-259044-mubjm22l author = Weng, Jing-Ru title = Antiviral activity of Sambucus FormosanaNakai ethanol extract and related phenolic acid constituents against human coronavirus NL63 date = 2019-09-24 keywords = HCoV; NL63; Sambucus; acid summary = The study indicated the inhibitory activity of Sambucus FormosanaNakai extract and its phenolic acid constituents on HCoV-NL63 induced cytopathic effect, virus yield, and the early stage of HCoV-NL63 replication in concentration-dependent and cell-type independent manners. LLC-MK2 cells (3 × 10 4 cells/well) were cultured in the 96-well plates overnight, quintuplicate treated with Sambucus Formosana Nakai stem ethanol extract or its phenolic acid constituents (caffeic acid, chlorogenic acid, coumaric acid, ferulic acid, and gallic acid) for 2 days, and then incubated with 0.5 mg/ml 3-(4,5-Dimethylthiazol-2-yl)-2,5diphenyltetrazolium bromide (MTT) for additional 4 h. For minimizing the antiviral effect of indicated agents in the cells, 100 μl (near 200 pfu HCoV-NL63) of the 10000-fold dilution from the mixtures of virus and the extract or phenolic acids was added to the MK2 cell monolayer in the 6-well plate to determining the residual viral infectivity using the plaque assay described above. To examine the antiviral mechanism of caffeic acid and chlorogenic acid against HCoV-NL63, the assays of plaque formation, virucidal activity and virus attachment were subsequently performed (Fig. 5 , Table 1 ). doi = 10.1016/j.virusres.2019.197767 id = cord-317061-0bx704ao author = Wu, Andong title = Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus date = 2015-10-02 keywords = Fig; MERS; cleavage; site summary = doi = 10.1016/j.virusres.2015.05.018 id = cord-280643-n8qjorqk author = Wu, Kai-Lang title = Inhibition of Hepatitis B virus gene expression by single and dual small interfering RNA treatment date = 2005-04-26 keywords = Fig; HBS; HBV summary = To circumvent the problem that mutation in HBV genome may result in resistance when siRNA is further developed as an anti-viral drug, in this study, we established a dual small interfering RNA (siRNA) expression system, which could simultaneously express two different siRNA molecules that can specifically target two genes. To test the effectiveness of this system, we applied this new approach to express simultaneously two different 21-bp hairpin siRNA duplexes that specifically attack the HBs and HBx genes of HBV, respectively, in Bel-7402 and HepG2.2.15 cells. Results indicated that dual siRNA could simultaneously inhibit the expression of HBs and HBx gene by 83.7% and 87.5%, respectively, based on luciferase assays. Results indicated that the levels of HBV core associ-ated DNA were significantly decreased in the cells transfected by HBSXsiRNA, HBS 1 siRNA, HBS 2 siRNA, and HBX 2 siRNA with reduction rate of 90.2%, 85.7 %, 81.3%, and 60.4%, respectively, compared with that of vector control (Fig. 5a) . doi = 10.1016/j.virusres.2005.04.001 id = cord-318319-efqf5e1i author = Yamasaki, Yukitaka title = The peripheral lymphocyte count as a predictor of severe COVID-19 and the effect of treatment with ciclesonide date = 2020-07-03 keywords = covid-19; severe summary = The lymphocyte count after ciclesonide treatment in the non-severe pneumonia group was significantly higher (p = 0. Many patients with coronavirus infection disease 2019(COVID-19) are subclinical, and it has been reported that people are J o u r n a l P r e -p r o o f contagious even when asymptomatic [1, 2] , which means preventing the spread of SARS-CoV-2 is challenging [3] . Risk factors of severe pneumonia include age, comorbidities, smoking, reduced lymphocyte count, elevated ferritin levels, and elevated C-reactive protein (CRP) levels [4] [5] [6] [7] [8] [9] . In addition, we examined whether ciclesonide could prevent the development of severe COVID-19 among patients with these predictors. Moreover, the lymphocyte count after ciclesonide therapy in the non-severe pneumonia group was significantly higher (p=0.0156) compared to before treatment (mean 6.14 days, SD 2.17) (Figure 3b ). doi = 10.1016/j.virusres.2020.198089 id = cord-281526-7t9e4lgn author = Yin, Lijuan title = Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens date = 2016-09-02 keywords = IBV; m41 summary = title: Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens To investigate whether the recombinant proteins could induce better immune response against IBV infection, we detected IBVspecific antibody in the sera of vaccinated chicken using indirect ELISA. Two weeks after booster vaccination (day 28), the levels of anti-IBV antibodies increased further in chickens immunized with inactivated M41 virus, rS1, rS1-H3(TM) and rS1-HA2. After challenged with virulent IBV M41 strain, our results demonstrated that fusion proteins performed better protection compared with inactivated M41 vaccine and recombinant rS1 protein alone, while the latter groups presented similar protection ratio. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus doi = 10.1016/j.virusres.2016.07.010 id = cord-255857-y9wjp0aj author = Yuan, Shishan title = Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date = 2001-11-05 keywords = PRRSV; RespPRRS; strain; vr-2332 summary = Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions. doi = 10.1016/s0168-1702(01)00295-7 id = cord-332317-wrztpeb8 author = Zhang, Xin title = Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus date = 2015-03-16 keywords = TGEV; protein summary = doi = 10.1016/j.virusres.2014.12.013 id = cord-291754-1zxztadu author = Zhao, Ye title = Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date = 2019-10-15 keywords = BHK-21; IBV; RNA summary = In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. doi = 10.1016/j.virusres.2019.197726 id = cord-301151-f6vya3qh author = Zhu, Xiaojuan title = Co-infection with respiratory pathogens among COVID-2019 cases date = 2020-05-11 keywords = SARS summary = In this study, the clinical features of COVID-19 patients were analyzed, then 39 respiratory pathogens in their throat swab were detected by specific real-time RT-PCR. 257 patients were diagnosed with the SARS-CoV-2 infection and their clinical severity was classified according to National Health Commission of the People''s Republic of China revised criteria for diagnosis and treatment of novel coronavirus infection pneumonia (trial version fifth, revised version). Below 15 years of age, a total of 11 (4.3 %) were diagnosed with the SARS-CoV-2 infection and there were no case in severe/critical category. In our study, 94.2 % of COVID-19 patients could be co-infected with one or more other pathogens, including 9 viruses, 11 bacteria and 4 fungi. Along with the course of disease, both the rates and pathogen species of co-infection among COVID-19 patients were decreased significantly, which may due to the treatment X. doi = 10.1016/j.virusres.2020.198005 id = cord-286703-ipoj13va author = de Wilde, Adriaan H. title = Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model date = 2017-01-15 keywords = ALV; MERS; SARS summary = Data from cell culture infection models (Chan et al., 2013a (Chan et al., , 2013b de Wilde et al., 2013b; Falzarano et al., 2013a; Kindler et al., 2013; Zielecki et al., 2013) and experiments in rhesus macaques (Falzarano et al., 2013b) and marmosets (Chan et al., 2015) suggested that interferons (IFNs) are potent inhibitors of MERS-CoV replication. As ribavirin has previously been reported to inhibit MERS-CoV replication (Falzarano et al., 2013a) and ALV and ribavirin have been used together during clinical trials for hepatitis C treatment (Pawlotsky et al., 2015) , this combination was tested in LLC-MK2 cells. (e, f) SARS-CoV-infected (e) Vero or (f) VeroE6 cells (MOI 0.01) were treated with various concentrations of ALV from 1 h p.i. onwards, and virus titers in the culture medium at 32 h p.i. were determined by plaque assay. doi = 10.1016/j.virusres.2016.11.011 id = cord-020087-gs0pc6ee author = nan title = Cumulative Contents for 2010 date = 2010-11-18 keywords = virus summary = Myristoylation of the small envelope protein of porcine reproductive and respiratory syndrome virus is non-essential for virus infectivity but promotes its growth 294 Porcine reproductive and respiratory syndrome virus (PRRSV) could be sensed by professional beta interferon-producing Hikichi (Japan) The 126-and/or 183-kDa replicases or their coding regions are responsible both for inefficient local and for systemic movements of Paprika mild mottle virus Japanese strain in tomato plants USA) Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection Porcine reproductive and respiratory syndrome virus (PRRSV) in serum and oral fluid samples from individual boars: Will oral fluid replace serum for PRRSV surveillance USA) Use of a production region model to assess the efficacy of various air filtration systems for preventing airborne transmission of porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae: Results from a 2-year study 177 Morrison (USA) Control and elimination of porcine reproductive and respiratory syndrome virus 185 Cumulative Author Index for doi = 10.1016/s0168-1702(10)00397-7 id = cord-020097-eh5deunk author = nan title = Cumulative Author Index for 2006 (Volumes 115–122) date = 2006-10-27 keywords = cell; protein; virus summary = Modulation of PKR activity in cells infected by bovine viral diarrhea virus Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Efficient inhibition of hepatitis B virus replication by small interfering RNAs targeted to the viral X gene in mice Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein A deletion and point mutation study of the human papillomavirus type 16 major capsid gene Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus doi = 10.1016/s0168-1702(06)00318-2 id = cord-020101-5rib7pe8 author = nan title = Cumulative Author Index for 2008 date = 2008-11-17 keywords = HIV-1; gene; protein; virus summary = Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors doi = 10.1016/s0168-1702(08)00367-5 id = cord-268930-y1cm58r6 author = van Aken, Danny title = Expression, purification, and in vitro activity of an arterivirus main proteinase date = 2006-03-09 keywords = EAV; Fig; MBP; nsp4 summary = To allow the biochemical and structural characterization of the chymotrypsin-like "main proteinase" (non-structural protein 4; nsp4) of the arterivirus prototype Equine Arteritis Virus (EAV), we developed protocols for the large-scale production of recombinant nsp4 in Escherichia coli. In a synthetic peptide-based activity assay, the potential of the recombinant proteinase to cleave peptides mimicking the P9–P7′ residues of six nsp4 cleavage sites was investigated. To test whether active recombinant proteinases had been isolated, the proteolytic activity of purified MBP-nsp4 and nsp4His was tested in cleavage assays using in vitro synthesized substrates as described in Section 2. Although it was reported that the addition of six His residues strongly inhibited the enzymatic activity of the human coronavirus 229E 3CL pro proteinase (Ziebuhr et al., 1997) , in both our assays the catalytic activity of nsp4His was very comparable to that of partially purified uncleaved or cleaved MBP-nsp4. doi = 10.1016/j.virusres.2006.01.025 id = cord-330508-uilejxmi author = van den Hoogen, Bernadette title = Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network date = 2020-07-28 keywords = initiate; virus summary = While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. While molecular details of the innate immune response are well characterized, this research field is now being revolutionized with the recognition that cell metabolism has a major impact on the antiviral and inflammatory responses to virus infections. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. A detailed understanding of the role of metabolic regulation with respect to antiviral and inflammatory responses, together with knowledge of the strategies used by viruses to exploit immunometabolic pathways, will ultimately change our understanding and treatment of pathogenic viral diseases. doi = 10.1016/j.virusres.2020.198094