# bib

id: cord-020097-eh5deunk
title: Cumulative Author Index for 2006 (Volumes 115–122)
date: 2006-10-27
extension: .txt
mime: text/plain
words: 1485
sentence: 4
flesch: -330
cache: cache/cord-020097-eh5deunk.txt
txt: txt/cord-020097-eh5deunk.txt
summary:
  An endornavirus from a hypovirulent strain of the violet root rot fungus Importance of the extracellular and cytoplasmic/transmembrane domains of the haemagglutinin protein of rinderpest virus for recovery of viable virus from cDNA copies Envelope gene capture and insect retrovirus evolution: The relationship between errantivirus and baculovirus envelope proteins Multiclonal pattern of Jaagsiekte sheep retrovirus integration sites in ovine pulmonary adenocarcinoma Venezuelan equine encephalitis virus complex-specific monoclonal antibody provides broad protection, in murine models, against airborne challenge with viruses from serogroups I, II and III Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in human immunodeficiency virus type Phylogenetic analysis of the gag region encoding the matrix protein of small ruminant lentiviruses: Comparative analysis and molecular epidemiological applications Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life HIV-l and the microRNA-guided silencing pathway: An intricate and multifaceted encounter A modified viral satellite DNA-based gene silencing vector is effective in association with heterologous begomoviruses TATAbinding protein and TBP-associated factors during herpes simplex virus type 1 infection: Localization at viral DNA replication sites Immunohistochemical examination of the role of Fas ligand and lymphocytes in the pathogenesis of human liver yellow fever Complete sequence and organization of the human adenovirus serotype 46 genome Molecular characterization and phylogenetic study of Maedi Visna and Caprine Arthritis Encephalitis viral sequences in sheep Lymphocytopathogenic activity in vitro correlates with high virulence in vivo for BVDV type 2 strains: Criteria for a third biotype of BVDV Inactivation of White Spot Syndrome Virus (WSSV) by normal rabbit serum: Implications for the role of the envelope protein VP28 in WSSV infection of shrimp Low prevalence of primary antiretroviral resistance mutations and predominance of HIV-1 clade C at polymerase gene in newly diagnosed individuals from south Brazil Characterization of a highly virulent feline calicivirus and attenuation of this virus Interaction of the hepatitis B virus protein HBx with the human transcription regulatory protein p120E4F in vitro Translation reinitiation and leaky scanning in plant viruses Phylogenetic analysis of recent isolates of classical swine fever virus from Colombia Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein Rabies virus-induced apoptosis involves caspase-dependent and caspase-independent pathways Translational control during virus infection Epstein-Barr virus immunossuppression of innate immunity mediated by phagocytes Binding of shrimp cellular proteins to Taura syndrome viral capsid proteins VP1 Collaborative study to evaluate a new ELISA test to monitor the effectiveness of rabies vaccination in domestic carnivores 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 The kinetics of proinflammatory cytokines in murine peritoneal macrophages infected with envelope protein-glycosylated or non-glycosylated West Nile virus Members of adenovirus species B utilize CD80 and CD86 as cellular attachment receptors Exogenous nitric oxide inhibits Crimean Congo hemorrhagic fever virus Structural and antigenic analysis of the yellow head virus nucleocapsid protein p20 Efficient expression of the 15-kDa form of infectious pancreatic necrosis virus VP5 by suppression of a UGA codon Phylogenetic relationships of Brazilian bovine respiratory syncytial virus isolates and molecular homology modeling of attachment glycoprotein Genetic manipulation of two fowlpox virus late transcriptional regulatory elements influences their ability to direct expression of foreign genes A new RNA virus found in black tiger shrimp Penaeus monodon from Thailand Conformational maturation of the nucleoprotein synthesized in influenza C virus-infected cells HIV-1-mediated syncytium formation promotes cell-to-cell transfer of Tax protein and Systemic antiviral silencing in plants Sequencing and comparative analysis of a pig bovine viral diarrhea virus genome EsiRNAs inhibit Hepatitis B virus replication in mice model more efficiently than synthesized siRNAs Chronological and geographical variations in the small RNA segment of the teratogenic Akabane virus HCV NS2 protein inhibits cell proliferation and induces cell cycle arrest in the S-phase in mammalian cells through down-regulation of cyclin A expression Pepper mild mottle virus pathogenicity determinants and cross protection effect of attenuated mutants in pepper Hepatitis E virus genotyping based on full-length genome and partial genomic regions Location and phylogenetic analysis of the region immediately upstream of the granulin gene of the Clostera anachoreta granulovirus Molecular characterization of rabies virus isolates in China during Proteolytic cleavage and shedding of the bovine prion protein in two cell culture systems Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus Generation of virus-like particles consisting of the major capsid protein VP1 of goose hemorrhagic polyomavirus and their application in serological tests Amino acid changes in the recombinant Dengue 3 Envelope domain III determine its antigenicity and immunogenicity in mice


id: cord-020101-5rib7pe8
title: Cumulative Author Index for 2008
date: 2008-11-17
extension: .txt
mime: text/plain
words: 2143
sentence: 10
flesch: -170
cache: cache/cord-020101-5rib7pe8.txt
txt: txt/cord-020101-5rib7pe8.txt
summary:
  Murine leukemia virus reverse transcriptase: Structural comparison with HIV-1 reverse transcriptase The GPRLQPY motif located at the carboxy-terminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus Detection of ovine herpesvirus 2 major capsid gene transcripts as an indicator of virus replication in shedding sheep and clinically affected animals Genetic characterization of equine influenza viruses isolated in Italy between A new living cell-based assay system for monitoring genome-length hepatitis C virus RNA replication Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus The contribution of feathers in the spread of chicken anemia virus Cloning and subcellular localization of the phosphoprotein and nucleocapsid proteins of Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus The p26 gene of the Autographa californica nucleopolyhedrovirus: Timing of transcription, and cellular localization and dimerization of product Complete genomic sequence of turkey coronavirus Recombinant L and P protein complex of Rinderpest virus catalyses mRNA synthesis in vitro Molecular divergence of Grapevine virus A (GVA) variants associated with Shiraz disease in South Africa Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae SARS coronavirus replicase proteins in pathogenesis Virus-induced gene silencing in Medicago truncatula and Lathyrus odorata Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery HBx modulates iron regulatory protein 1-mediated iron metabolism via reactive oxygen species Pathogenetic mechanisms of severe acute respiratory syndrome Detection of a novel circovirus in mute swans (Cygnus olor) by using nested broadspectrum PCR Chimaeric HIV-1 subtype C Gag molecules with large in-frame C-terminal polypeptide fusions form virus-like particles Cross-species recombination in the haemagglutinin gene of canine distemper virus Sapovirus-like particles derived from polyprotein Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Adenovirus vector induced innate immune responses: Impact upon efficacy and toxicity in gene therapy and vaccine applications Interfering with cellular signaling pathways enhances sensitization to combined sodium butyrate and GCV treatment in EBV-positive tumor cells Evidence for recombination between PCV2a and PCV2b in the field Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): A comparison of their molecular and biochemical properties Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening Appearance of intratypic recombination of enterovirus 71 in Taiwan from The circulation of subgenogroups B5 and C5 of enterovirus 71 in Taiwan from In vitro replication of Bamboo mosaic virus satellite Characterization of the interaction of domain III of the envelope protein of dengue virus with putative receptors from CHO cells 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 The SARS-Coronavirus PLnc domain of nsp3 as a replication/ transcription scaffolding protein Limited compatibility between the RNA polymerase components of influenza virus type A and B Serotype-specificity of recombinant fusion proteins containing domain III of dengue virus Very virulent infectious bursal disease virus isolated from wild birds in Korea: Epidemiological implications Genetic analysis and evaluation of the reassortment of influenza B viruses isolated in Taiwan during the Enhanced immune responses of mice inoculated recombinant adenoviruses expressing GP5 by fusion with GP3 and/or GP4 of PRRS virus Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus Novel HIV-1 reverse transcriptase inhibitors Synthesis of recombinant human parainfluenza virus 1 and 3 nucleocapsid proteins in yeast Saccharomyces cerevisiae Evolutionary analyses of European H1N2 swine influenza


id: cord-295187-konm26x5
author: Decaro, Nicola
title: Full-length genome analysis of canine coronavirus type I
date: 2015-12-02
extension: .txt
mime: text/plain
words: 3181
sentence: 89
flesch: 40
cache: cache/cord-295187-konm26x5.txt
txt: txt/cord-295187-konm26x5.txt
summary:
  The RNA extract was subjected to a previously-established TaqMan-based real-time RT-PCR assay for rapid detection and quantification of CCoV RNA , with minor modifications. 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


id: cord-287324-ecpicv5v
author: Qiu, Yuan
date: 2017-06-02
extension: .txt
mime: text/plain
words: 3739
sentence: 132
flesch: 46
cache: cache/cord-287324-ecpicv5v.txt
txt: txt/cord-287324-ecpicv5v.txt
title:
  Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

summary:
  Virome detection has been widely applied to identification of novel RNA viruses and research of RNA viruses (Masson et al., 2014; Paez-Espino et al., 2016; Webster et al., 2015) . key: cord-287324-ecpicv5v authors: Qiu, Yuan; Chen, Ji-Ming; Wang, Tong; Hou, Guang-Yu; Zhuang, Qing-Ye; Wu, Run; Wang, Kai-Cheng title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date: 2017-06-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.05.003 sha: doc_id: 287324 cord_uid: ecpicv5v Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization.


id: cord-261388-d56ci0hl
author: Tibbles, K.W
date: 1999-05-28
extension: .txt
mime: text/plain
words: 3915
sentence: 129
flesch: 43
cache: cache/cord-261388-d56ci0hl.txt
txt: txt/cord-261388-d56ci0hl.txt
title:
  Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus

summary:
  The 3CLP domain was first identified as a possible component of IBV polyproteins (Gorbalenya et al., 1989) due to sequence similarity to picornavirus 3C proteinases (reviewed in Ryan and Flint, 1997) . A simple method for displaying the hydropathic character of a protein Screening for membrane-permeabilizing mutants of the poliovirus protein 3AB The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase A 100-kilodalton polypeptide encoded by open reading frame (ORF) 1b of the coronavirus infectious bronchitis virus is processed by ORF 1a products Proteolytic mapping of the coronavirus infectious bronchitis virus 1b polyprotein: Evidence for the presence of four cleavage sites of the 3C-like proteinase and identification of two novel cleavage products Identification, expression, and processing of an 87-kDa polypeptide encoded by ORF 1a of the coronavirus infectious bronchitis virus Proteolytic processing of the coronavirus infectious bronchitis virus 1a polyprotein: identification of a 10-kilodalton polypeptide and determination of its cleavage sites Intracellular and in vitro-translated 27-kDa proteins contain the 3C-like proteinase activity of the coronavirus MHV-A59 Identification and characterization of a serine-like proteinase of the murine coronavirus MHV-A59 Recombination of protein domains facilitated by co-translational folding in eukaryotes 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 Virus-encoded proteinases of the picornavirus super-group Expression and characterization of a recombinant murine coronavirus 3C-like proteinase Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system Use of T7 RNA polymerase to direct expression of cloned genes Characterization in vitro of an autocatalytic processing activity associated with the predicted 3C-like proteinase domain of the coronavirus avian infectious bronchitis virus A region of the infectious bronchitis virus 1a polyprotein encoding the 3C-like protease domain is subject to rapid turnover when expressed in rabbit reticulocyte lysate Characterization of a human coronavirus (strain 229E) 3C-like proteinase activity Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase


id: cord-266025-bkm486jd
author: Tao, Ying
title: Genomic characterization of seven distinct bat coronaviruses in Kenya()
date: 2012-04-26
extension: .txt
mime: text/plain
words: 3917
sentence: 121
flesch: 43
cache: cache/cord-266025-bkm486jd.txt
txt: txt/cord-266025-bkm486jd.txt
summary:
  The four clusters of Kenya bat CoVs represented by BtKY22, BtKY41, BtKY43, and BtKY24 respectively, most likely belonged to novel CoV species, the two clusters represented by BtKY27 and BtKY33 were likely members of Bat-CoV 1A, and the cluster represented by BtKY06 was likely a member of Bat-CoV HKU9 species. However, because of the examples of host switching among CoVs after relatively minor sequence changes in S1 domain of spike protein, a further surveillance in animal reservoirs and understanding the interface between host susceptibility is critical for predicting and preventing the potential threat of bat CoVs to public health.


id: cord-255857-y9wjp0aj
author: Yuan, Shishan
date: 2001-11-05
extension: .txt
mime: text/plain
words: 4291
sentence: 151
flesch: 45
cache: cache/cord-255857-y9wjp0aj.txt
txt: txt/cord-255857-y9wjp0aj.txt
title:
  Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains”

summary:
  key: cord-255857-y9wjp0aj authors: Yuan, Shishan; Mickelson, Daniel; Murtaugh, Michael P.; Faaberg, Kay S. title: Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date: 2001-11-05 journal: Virus Res DOI: 10.1016/s0168-1702(01)00295-7 sha: doc_id: 255857 cord_uid: y9wjp0aj 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. Initially, several standard 5%-RACE was performed on passage 2 from the original VR-2332 field isolate brain homogenate, passage 31 of strain VR-2332 and passage 4 of RespPRRS vaccine strain (Frohman, 1994) .


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
extension: .txt
mime: text/plain
words: 4321
sentence: 150
flesch: 49
cache: cache/cord-270064-hidirfkv.txt
txt: txt/cord-270064-hidirfkv.txt
summary:
  Comparative genomic analysis MERS CoV isolated from humans and camels with special reference to virus encoded helicase The Galaxy platform for accessible, reproducible and collaborative biomedical analyses On the biased nucleotide composition of the human coronavirus RNA genome The evolution of codon usage in structural and non-structural viral genes: the case of Avian coronavirus and its natural host Gallus gallus Genome-wide analysis of codon usage bias in Bovine Coronavirus Coronavirus avian infectious bronchitis virus A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster Genomic characterization of the 2019 Microbes & Infec Emerging coronaviruses: genome structure, replication, and pathogenesis Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus Bovine coronavirus Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus Origin and evolution of pathogenic coronaviruses Severe acute respiratory syndrome-related coronavirus: The species and its viruses -a statement of the Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales The extent of codon usage bias in human RNAviruses and its evolutionary origin From SARS and MERS CoVs to SARS-CoV-2, moving toward more biased codon usage in viral structural and nonstructural genes To sense or not to sense viral RNA-essentials of coronavirusinnate immune evasion MEGA-X: Molecular evolutionary genetics analysis across computing platforms Extensive diversity of coronaviruses in bats from China Severe acute respiratory syndrome CAIcal: a combined set of tools to assess codon usage adaptation E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI) Genome structure and transcriptional regulation of human coronavirus NL63 Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Clustvis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap Posterior summarization in Bayesian phylogenetics using Tracer MACSE: Multiple alignment of coding sequences accounting for frameshifts and stop codons The codon adaptation index -a measure of directional synonymous codon usage bias, and its potential applications Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design Epidemiology, genetic recombination, and pathogenesis of coronaviruses Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evol. 4,vey016 Analysis of codon usage bias and base compositional constraints in iridovirus genomes The biased nucleotide composition of HIV-1 triggers type I interferon response and correlates with subtype D increased pathogenicity On the nucleotide compositionand structure of retroviral RNA genomes The A-nucleotide preference of HIV-1 in the context of its structured RNA genome Free Statistics Software, Office for Research Development and Education, version 1.1.23-r7 Analysis of codon usage in bovine viral diarrhea virus Global Epidemiology of Bat Coronaviruses World Health Organization (2020) Coronavirus disease (COVID-19) outbreak.


id: cord-262760-mf1pn587
author: Weber, Stefanie
date: 2020-09-24
extension: .txt
mime: text/plain
words: 4672
sentence: 177
flesch: 50
cache: cache/cord-262760-mf1pn587.txt
txt: txt/cord-262760-mf1pn587.txt
title:
  Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world

summary:
  Hence, the consequences of an increase in the number of viral mutations on its pathogenicity will be very difficult to predict. Additionally, in sequence positions 28854 and 28863 a few C → T point mutations were apparent.


id: cord-285580-gq7400tq
author: Pieretti, Joana C.
date: 2020-10-18
extension: .txt
mime: text/plain
words: 4886
sentence: 166
flesch: 37
cache: cache/cord-285580-gq7400tq.txt
txt: txt/cord-285580-gq7400tq.txt
title:
  Nitric oxide (NO) and nanoparticles – potential small tools for the war against COVID-19 and other human coronavirus infections

summary:
  The use of NO donors and nanomaterials increases the stability of NO and enables targeted, controlled NO release at desirable concentrations, which is fundamental for NO bioactivity (Quinn et al., 2015) . NO has already been reported as a potential candidate for the treatment against coronaviruses and other respiratory viral diseases, such as influenza (Arabi et al., 2015; Keyaerts et al., 2004; Murphy et al., 1998) .


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
extension: .txt
mime: text/plain
words: 5417
sentence: 201
flesch: 40
cache: cache/cord-263439-oquk4t96.txt
txt: txt/cord-263439-oquk4t96.txt
summary:
  To confirm the role of exogenous proteases in PEDV infection, PEDV infected cells were treated with trypsin and evaluated viral infectivity by immunocytochemistry. Both approaches provided similar conclusions on the mechanism of PEDV cell entry.


id: cord-259044-mubjm22l
author: Weng, Jing-Ru
date: 2019-09-24
extension: .txt
mime: text/plain
words: 5629
sentence: 181
flesch: 39
cache: cache/cord-259044-mubjm22l.txt
txt: txt/cord-259044-mubjm22l.txt
title:
  Antiviral activity of Sambucus FormosanaNakai ethanol extract and related phenolic acid constituents against human coronavirus NL63

summary:
  Chlorogenic acid specifically inhibited the neuraminidase activity of influenza A viruses H1N1 and H3N2 that was the crucial mechanism of chlorogenic acid for blocking the release of progeny virions from infected cells (Ding et al., 2017) . Among the phenolic acid constituents in Sambucus FormosanaNakai extract, caffeic acid, chlorogenic acid and gallic acid sustained the anti-HCoV-NL63 activity that was ranked in the following order of virus yield reduction: caffeic acid (IC(50) = 3.54 μM) > chlorogenic acid (IC(50)


id: cord-291962-rp172ugk
author: Jing, Huiyuan
date: 2019-07-15
extension: .txt
mime: text/plain
words: 5750
sentence: 217
flesch: 40
cache: cache/cord-291962-rp172ugk.txt
txt: txt/cord-291962-rp172ugk.txt
title:
  Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9

summary:
  Western blot analysis further showed that si-NLRX1-2 # reduced the level of NLRX1 protein by ∼87% compared to the controls cells transfected with NC siRNA (Fig. 3B) . NLRX1 protein levels measured by Western blotting reflected the changes in mRNA observed, suggesting that endogenous NLRX1 expression was upregulated by PRRSV infection (Fig. 1C) .


id: cord-275413-e2rhioty
author: Rowland, Raymond R.R.
title: The interaction between PRRSV and the late gestation pig fetus
date: 2010-09-09
extension: .txt
mime: text/plain
words: 6192
sentence: 241
flesch: 42
cache: cache/cord-275413-e2rhioty.txt
txt: txt/cord-275413-e2rhioty.txt
summary:
  The IHC staining procedure included two sets of negative controls: tissue thin sections from non-infected fetuses and from infected fetuses stained with only secondary antibody. This scenario as a cause of severe interstitial pnuemonia in the PRRSV-infected newborn requires further investigation, but has obvious implications in the etiology of postnatal pulmonary complications following virus infections of the fetus.


id: cord-252048-ftbjsoup
author: McKinley, Enid T.
date: 2011-04-22
extension: .txt
mime: text/plain
words: 6386
sentence: 201
flesch: 44
cache: cache/cord-252048-ftbjsoup.txt
txt: txt/cord-252048-ftbjsoup.txt
title:
  Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus

summary:
  To examine sequence changes not only in spike but also over the entire length of the genome, we sequenced the full-length genomes of 5 Mass type, 4 Conn type and 2 CAL type IBV field viruses that were isolated over a 41, 25 and 8 year period respectively. It has been shown that vaccine usage can result in faster evolutionary rates in IBV field viruses (Lee and Jackwood, 2001; Wang Fig. 4 .


id: cord-272408-8flsy5o1
author: Chen, Rui
date: 2020-01-15
extension: .txt
mime: text/plain
words: 6081
sentence: 239
flesch: 47
cache: cache/cord-272408-8flsy5o1.txt
txt: txt/cord-272408-8flsy5o1.txt
title:
  Identification of the immunodominant neutralizing regions in the spike glycoprotein of porcine deltacoronavirus

summary:
  Inoculation with PDCoV S protein may therefore be able to inhibit PDCoV infection and induce neutralizing antibodiess against PDCoV infection. Recently, Li et al. demonstrated that the porcine aminopeptidase N, previously known to be a functional receptor for transmissible gastroenteritis virus (TGEV), also interacts with the B domain of PDCoV S1 subunit and functions as a major cell entry receptor for PDCoV. Therefore, in this study, we aimed to identify the immunodominant region of PDCoV S protein, and its neutralizing epitopes.


id: cord-267228-g2tf1jz6
author: Huang, Ke-Yan
date: 2018-03-02
extension: .txt
mime: text/plain
words: 6560
sentence: 216
flesch: 40
cache: cache/cord-267228-g2tf1jz6.txt
txt: txt/cord-267228-g2tf1jz6.txt
title:
  Construction and immunogenicity analysis of Lactobacillus plantarum expressing a porcine epidemic diarrhea virus S gene fused to a DC-targeting peptide

summary:
  Meanwhile, CD80 + and CD86 + of activated B cells could combine with CD28 expressed on the surface of T cells, which involved in co-stimulatory signal transduction. DCs are involved in regulating the function of B cells and promoting the differentiation of B cells into plasma cells to produce IgG .


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
extension: .txt
mime: text/plain
words: 6530
sentence: 170
flesch: 32
cache: cache/cord-290801-dv6aak01.txt
txt: txt/cord-290801-dv6aak01.txt
summary:
  A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication The molecular biology of West Nile Virus: a new invader of the western hemisphere Sequence and secondary structure analysis of the 5 -terminal region of flavivirus genome RNA The 3 -nucleotides of flavivirus genomic RNA form a conserved secondary structure A La protein requirement for efficient pre-tRNA folding The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication Fine mapping of a cis-acting sequence element in yellow fever virus RNA that is required for RNA replication and cyclization The ubiquitous nature of RNA chaperone proteins The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro Translation elongation factor-1alpha, La, and PTB interact with the 3 untranslated region of dengue 4 virus RNA The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealingcompetent conformation West Nile virus core protein; tetramer structure and ribbon formation Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein Attenuation and immunogenicity in humans of a live dengue virus type-4 vaccine candidate with a 30 nucleotide deletion in its 3 -untranslated region Small noncoding RNA modulates Japanese encephalitis virus replication and translation in trans RNA sequences and structures required for the recruitment and activity of the dengue virus polymerase A 5 RNA element promotes dengue virus RNA synthesis on a circular genome Interplay of RNA elements in the dengue virus 5 and 3 ends required for viral RNA replication Composition of the sequence downstream of the dengue virus 5 cyclization sequence (dCS) affects viral RNA replication The 5 and 3 downstream AUG region elements are required for mosquito-borne flavivirus RNA replication RNA structures required for production of subgenomic flavivirus RNA La protein binds to NS5 and NS3 and to the 5 and 3 ends of Dengue 4 virus RNA Functional RNA elements in the dengue virus genome Autochthonous dengue fever in Croatia Impact of climate change and other factors on emerging arbovirus diseases Pathogenic flaviviruses Viral encephalomyelitis Origin and evolution of flavivirus 5 UTRs and panhandles: trans-terminal duplications? Flaviviruses constitute a large and diverse group within the Flaviviridae family of positive-strand enveloped RNA viruses (Lindenbach et al., 2007) .


id: cord-267363-5qri915n
author: Shi, Mang
title: Meta-transcriptomics and the evolutionary biology of RNA viruses
date: 2018-01-02
extension: .txt
mime: text/plain
words: 6387
sentence: 186
flesch: 32
cache: cache/cord-267363-5qri915n.txt
txt: txt/cord-267363-5qri915n.txt
summary:
  9 The genomics of emerging pathogens Predicting virus emergence amidst evolutionary noise Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families Commensal viruses of mosquitoes: host restriction, transmission, and interaction with arboviral pathogens The Evolution and Emergence of RNA Viruses The double-stranded DNA virosphere as a modular hierarchical network of gene sharing Virus discovery and recent insights into virus diversity in arthropods Virus world as an evolutionary network of viruses and capsidless selfish elements. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history.


id: cord-286658-9kco7qad
author: Jiang, Lei
date: 2018-01-15
extension: .txt
mime: text/plain
words: 7028
sentence: 224
flesch: 46
cache: cache/cord-286658-9kco7qad.txt
txt: txt/cord-286658-9kco7qad.txt
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

summary:
  The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Infectious bronchitis virus: evidence for recombination within the Massachusetts serotype Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China The avian coronavirus infectious bronchitis virus undergoes direct low-pH-dependent fusion activation during entry into host cells The long view: 40 years of infectiousbronchitis research Sequence and structure of the coronavirus peplomer protein Cooperative involvement f the S1 and S2 subunits of the murine coronavirus spike protein in receptor binding and extended host range Infectious bronchitis virus variants: a review of the history, current situation and control measures Recommendations for a standardized avian coronavirus (AvCoV) nomenclature: outcome from discussions within the framework of the European Union COST Action FA1207: towards control of avian coronaviruses: strategies for vaccination, diagnosis and surveillance Molecular investigation of a full-length genome of a Q1-like IBV strain isolated in Italy in 2013 Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China Fine level epitope mapping and conservation analysis of two novel linear B-cell epitopes of the avian infectious bronchitis coronavirus nucleocapsid protein Genetic, antigenic, and pathogenic characteristics of avian infectious bronchitis viruses genotypically related to 793/B in China Molecular and serologic characterization pathogenicity, and protection studies with infectious bronchitis virus field isolates from California Molecular evolution and emergence of avian gammacoronaviruses Genome characterization, antigenicity and pathogenicity of a novel infectious bronchitis virus type isolated from south China Antigenic domains on thepeplomer protein of avian infectious bronchitis virus: correlation with biologicalfunctions Phylogeny of antigenic variants of avian coronavirus IBV Full-length genome sequencing analysis of avian infectious bronchitis virus isolate associated with nephropathogenic infection Antigenicity of the peplomer protein of infectious bronchitis virus infectious bronchitis virus isolates in southern china A novel variant of the infectious bronchitis virus resulting from recombination events in Italy L Mulan: multiple-sequence local alignment and visualization for studying function and evolution Contributions of the S2 spike ectodomain to attachment and host range of infectious bronchitis virus Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin A simple method of estimating fifty percent endpoints Why do RNA viruses recombine? Recombination in avian gamma-coronavirus infectious bronchitis virus S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification Australian infectious bronchitis viruses: identification of nine subtypes by a neutralisation test Binding of avian coronavirus spike proteins to host factors reflects virus tropism and pathogenicity Emergence of novel nephropathogenic infectious bronchitis viruses currently circulating in Chinese chicken flocks Serotype shift of a 793/B genotype infectious bronchitis coronavirus by natural recombination Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China Complete genome sequence of a novel infectious bronchitis virus strain circulating in China with a distinct S gene Identification of a novel recombinant virulent avian infectious bronchitis virus This work was supported by grants from the China Agriculture Research Systerm (No. CARS-40-K18) and National Twelfth Five-Year Plan for Science and Technology Support (2015BAD12B03).


id: cord-271568-qgpi2kcs
author: Jackwood, M.W.
date: 2010-01-21
extension: .txt
mime: text/plain
words: 7617
sentence: 285
flesch: 52
cache: cache/cord-271568-qgpi2kcs.txt
txt: txt/cord-271568-qgpi2kcs.txt
title:
  Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo

summary:
  Tracheas were scored as described in Section 2 with 1 being normal and 4 being severe, and the birds that did not receive challenge virus had an average lesion score of 1.06. A less pronounced response was observed in birds treated 2 h after virus challenge.


id: cord-268930-y1cm58r6
author: van Aken, Danny
title: Expression, purification, and in vitro activity of an arterivirus main proteinase
date: 2006-03-09
extension: .txt
mime: text/plain
words: 7547
sentence: 246
flesch: 48
cache: cache/cord-268930-y1cm58r6.txt
txt: txt/cord-268930-y1cm58r6.txt
summary:
  PCP␤, nsp1 papain-like Cys proteinase; CP, nsp2 Cys proteinase; SP, nsp4 Ser proteinase; RdRp, RNA-dependent RNA polymerase; Z, zinc finger; Hel, helicase; N, nidovirus-specific endoribonuclease (NendoU). Using an identical experimental set-up, partially purified cleaved and uncleaved MBP-nsp4 were also tested for proteinase activity.


id: cord-272458-72dybi7t
author: Desforges, Marc
title: Activation of human monocytes after infection by human coronavirus 229E
date: 2007-07-31
extension: .txt
mime: text/plain
words: 7564
sentence: 224
flesch: 35
cache: cache/cord-272458-72dybi7t.txt
txt: txt/cord-272458-72dybi7t.txt
summary:
  Our results clearly indicate that susceptibility of THP-1 cells to HCoV-229E infection correlates very well with results on primary cells. The pro-inflammatory cytokine TNF-␣ was constitutively produced at very low levels in THP-1 and primary cells (Fig. 5A) , consistent with reports for THP-1 cells (Heidinger et al., 2006) and primary monocytes (Nguyen et al., 2006) .


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
extension: .txt
mime: text/plain
words: 7710
sentence: 262
flesch: 46
cache: cache/cord-260107-gqbtkf0x.txt
txt: txt/cord-260107-gqbtkf0x.txt
summary:
  All original feces and passaged PEDV viruses through passages 30 were classified into subgroup 2b along with the recent Korean field isolates, which were most closely clustered together with the emergent US strains in an adjacent clade with the same subgroup. Animal studies showed that KNU-141112 virus causes severe diarrhea and vomiting, fecal shedding, and acute atrophic enteritis, indicating that strain KNU-141112 is highly enteropathogenic in the natural host.


id: cord-284479-75zgljet
author: García-Serradilla, Moisés
title: Drug repurposing for new, efficient, broad spectrum antivirals
date: 2019-04-15
extension: .txt
mime: text/plain
words: 7588
sentence: 236
flesch: 29
cache: cache/cord-284479-75zgljet.txt
txt: txt/cord-284479-75zgljet.txt
summary:
  Although it seems to act at several steps of the viral life cycle, the isomerase activity of CypA does not seem to be implicated (Liu et al., 2009) . Overexpression of CypA inhibits M1 translocation into the nucleus (Liu et al., 2009 ) while depletion of CypA accelerated the replication of the virus (Liu et al., 2012b) .


id: cord-266453-v1hbust8
author: Sztuba-Solińska, Joanna
date: 2012-10-16
extension: .txt
mime: text/plain
words: 7865
sentence: 260
flesch: 43
cache: cache/cord-266453-v1hbust8.txt
txt: txt/cord-266453-v1hbust8.txt
title:
  Mutations in the coat protein-binding cis-acting RNA motifs debilitate RNA recombination of Brome mosaic virus

summary:
  RNA recombination Role of RNA structure in heteroduplex-mediated and sitespecific nonhomologous recombination in brome mosaic virus A mutation in the putative RNA polymerase gene inhibits nonhomologous, but not homologous, genetic recombination in an RNA virus Mutations in the N terminus of the brome mosaic virus polymerase affect genetic RNA-RNA recombination Mutual interference between genomic RNA replication and subgenomic mRNA transcription in brome mosaic virus Template sequence near the initiation nucleotide can modulate Brome mosaic virus RNA accumulation in plant protoplasts Retroviral recombination: review of genetic analyses An interaction between the nucleocapsid protein and a component of the replicase-transcriptase complex is crucial for the infectivity of coronavirus genomic RNA High efficiency T7 polymerase synthesis of infectious RNA from cloned Brome mosaic virus cDNA and effects of 5 extensions of transcript infectivity Defined mutations in a small region of the Brome mosaic virus 2 gene cause diverse temperature-sensitive RNA replication phenotypes Targeting the site of RNA-RNA recombination in Brome mosaic virus with antisense sequences Efficient system of homologous RNA recombination in Brome mosaic virus: sequence and structure requirements and accuracy of crossovers Homologous RNA recombination in Brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers Engineering of homologous recombination hotspots with AU-rich sequences in Brome mosaic virus Silencing homologous RNA recombination hot spots with GC-rich sequences in Brome mosaic virus Copy-choice recombination by reverse transcriptases: reshuffling of genetic markers mediated by RNA chaperones RNA recombination in brome mosaic virus: effects of strand-specific stem-loop inserts Mutations in the RNA-binding domains of tombusvirus replicase proteins affect RNA recombination in vivo Requirements for ICR-like sequences in the replication of brome mosaic virus genomic RNA Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases Genome packaging by spherical plant RNA viruses Preparation and inoculation of mesophyll protoplasts from monocotyledonous and dicotyledenous hosts Role of the reverse transcriptase, nucleocapsid protein, and template structure in the two-step transfer mechanism in retroviral recombination Molecular Cloning: A Laboratory Manual A physical interaction between viral replicase and capsid protein is required for genome packaging specificity in an RNA virus Alternate, virusinduced membrane rearrangements support positive-strand RNA virus genome replication The AU-rich RNA recombination hot spot sequence of Brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination Requirements for Brome mosaic virus subgenomic RNA synthesis in vivo and replicase-core promoter interactions in vitro RNA recombination between cucumoviruses: possible role of predicted stem-loop structures and an internal subgenomic promoter-like motif Recombination of 5 subgenomic RNA3a with genomic RNA3 of Brome mosaic bromovirus in vitro and in vivo RNA-RNA recombination in plant virus replication and evolution Dissecting the requirement for subgenomic promoter sequences by RNA recombination of brome mosaic virus in vivo: evidence for functional separation of transcription and recombination Characterization of a novel 5 subgenomic RNA3a derived from RNA3 of Brome mosaic bromovirus Brome mosaic virus capsid protein regulates accumulation of viral replication proteins by binding to the replicase assembly RNA element RNA binding by the Brome mosaic virus capsid protein and the regulation of viral RNA accumulation RNA-binding proteins that inhibit RNA virus infection Coronavirus nucleocapsid protein facilitates template switching and is required for efficient transcription We would like to thank Stuart Hill for comments and discussions and Barbara Ball for assistance with figures. Our study offers novel insight into BMV RNA recombination and indicates that associations of CP with the RNA cis-acting motifs can mediate RNA recombination process.


id: cord-257715-pbcr81qm
author: Pignatelli, J.
title: Molecular characterization of a new PToV strain. Evolutionary implications
date: 2009-03-20
extension: .txt
mime: text/plain
words: 8284
sentence: 275
flesch: 44
cache: cache/cord-257715-pbcr81qm.txt
txt: txt/cord-257715-pbcr81qm.txt
summary:
  In addition, since the nucleocapsid proteins are usually highly conserved, serodiagnosis tests based on the use of PToV N protein may prove useful for detection of antibodies against other toroviruses. A baculovirus recombinant that contains the nucleotide coding sequence for PToV N protein fused at its 5 -end to a sequence encoding a 6-histidine tag was generated by using the Bac-to-Bac system (Invitrogen, Corp.) .


id: cord-278939-z6kiee09
author: Mani, Janice S.
title: Natural product-derived phytochemicals as potential agents against coronaviruses: a review
date: 2020-04-30
extension: .txt
mime: text/plain
words: 8177
sentence: 237
flesch: 30
cache: cache/cord-278939-z6kiee09.txt
txt: txt/cord-278939-z6kiee09.txt
summary:
  The antiviral activity of extracts from plant species against the avian IBV viral strains have been extensively studied (Chen et al., 2014; Jackwood et al., 2010; Lelesius et al., 2019; Li et al., 2011; Nguyen et al., 2015; Yang et al., 2010; Yang et al., 2011; Yin et al., 2011) . Recent reviews have suggested that traditional Chinese medicine could be used for the prevention or treatment (Yang et al., 2020a ) of COVID-19; while still acknowledging that many studies involving clinical trials are poorly designed or controlled, and the choice of treatments is largely empirically based.


id: cord-301151-f6vya3qh
author: Zhu, Xiaojuan
title: Co-infection with respiratory pathogens among COVID-2019 cases
date: 2020-05-11
extension: .txt
mime: text/plain
words: 2603
sentence: 133
flesch: 56
cache: cache/cord-301151-f6vya3qh.txt
txt: txt/cord-301151-f6vya3qh.txt
summary:
  In addition to bacteria, fungi was also a major factor of co-infection secondary to viral infections such as seen in influenza infection in which A. baumannii, Aspergillus, Candida and KP were discovered as common secondary infections (Gao, et al. 2013; Guo, et al. 2019) . The current outbreaks of coronavirus infection remind us that CoVs are still a severe and critical threats to global public health.


id: cord-260422-z22t57ju
author: Godet, Julien
date: 2012-06-26
extension: .txt
mime: text/plain
words: 9194
sentence: 234
flesch: 29
cache: cache/cord-260422-z22t57ju.txt
txt: txt/cord-260422-z22t57ju.txt
title:
  Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1

summary:
  Later, a similar chaperone activity was shown for the HIV-1 NC protein (Darlix et al., 1990; De Rocquigny et al., 1992; Barat et al., 1993; Dib-Hajj et al., 1993; Lapadat-Tapolsky et al., 1993) . In sharp contrast to NCp7, multimerization of Gag or Gag-related proteins dramatically compromises reverse transcription since the cooperative binding and the slow dissociation rate of the multimerized Gag proteins impaired RT processivity (Wu et al., 2010) .


id: cord-268337-o6lo55o8
author: Lloyd, Richard E.
title: Translational control by viral proteinases
date: 2005-11-21
extension: .txt
mime: text/plain
words: 9429
sentence: 311
flesch: 38
cache: cache/cord-268337-o6lo55o8.txt
txt: txt/cord-268337-o6lo55o8.txt
summary:
  The major apoptotic pathway activated and suppressed by poliovirus Foot-and-mouth disease virus 3C protease induces cleavage of translation initiation factors eIF4A and eIF4G within infected cells Picornavirus IRESes and the poly(A) Translational repression by a novel partner of human poly(A) binding protein, Paip2 Foot-and-mouth disease virus leader proteinase: purification of the lb form and determination of its cleavage site on eIF-4 gamma Loss of a phosphorylated form of transcription factor CREB/ATF in poliovirus-infected cells Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase Structure and function of the C-terminal PABC domain of human poly(A)-binding protein Calicivirus 3C-like proteinase inhibits cellular translation by cleavage of poly(A)-binding protein Efficient cleavage of ribosome-associated poly(A)-binding protein by enterovirus 3C protease Cleavage of poly(A)-binding protein by poliovirus 3C protease inhibits host cell translation: a novel mechanism for host translation shutoff Mapping of functional domains in eukaryotic protein synthesis initiation factor 4G (eIF4G) with picornaviral proteases -implications for cap-dependent and cap-independent translational initiation Mapping the cleavage site in protein synthesis initiation factor-eIF-4G of the 2A proteases from human Coxsackievirus and rhinovirus Isolation and structural characterization of cap-binding proteins from poliovirus-infected HeLa cells Purification of two picornaviral 2A proteinases -interaction with eIF-4G and influence on in vitro translation Homeostasis in mRNA initiation: wheat germ poly(A)-binding protein lowers the activation energy barrier to initiation complex formation Capdependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G Eukaryotic translation initiation factor 4G is targeted for proteolytic cleavage by caspase 3 during inhibition of translation in apoptotic cells A cellular protein that binds to the 5 -noncoding region of poliovirus RNA: implications for internal translation initiation La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate Cap-dependent and cap-independent translation in eukaryotic systems Messenger RNA turnover in eukaryotes: pathways and enzymes Messenger RNA poly(A) tail, a 3 enhancer of translational initiation An internal ribosome entry segment promotes translation of the simian immunodeficiency virus genomic RNA In vitro cleavage of eIF4GI but not eIF4GII by HIV-1 protease and its effects on translation in the rabbit reticulocyte lysate system The C-terminal domain of eukaryotic protein synthesis initiation factor (eIF) 4G is sufficient to support cap-independent translation in the absence of eIF4E Dominant negative mutants of mammalian translation initiation factor eIF-4A define a critical role for eIF-4F in cap-dependent and cap-independent initiation of translation Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes Haemoglobin synthesis and polysomes in intact reticulocytes A cell cycle-dependent protein serves as a template-specific translation initiation factor Cell-specific proteins regulate viral RNA translation and virus-induced disease Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast Starting the protein synthesis machine: eukaryotic translation initiation Poly(A)-tail-promoted translation in yeast: implications for translational control Characterization of a novel RNA-binding region of eIF4GI critical for ribosomal scanning Lack of direct correlation between p220 cleavage and the shut-off of host translation after poliovirus infection ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors Caspases are not involved in the cleavage of translation initiation factor eIF4GI during picornavirus infection eIF4A: the godfather of the DEAD box helicases Variability in apoptotic response to poliovirus infection Paip1 interacts with poly(A) binding protein through two independent binding motifs Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F Infection of HeLa cells with poliovirus results in modification of a complex that binds to the rRNA promoter The poly(A)-binding protein is required for poly(A) shortening and 60S ribosomal subunit dependent translation initiation Eukaryotic translation initiation: there are (at least) two sides to every story Translation initiation and viral tricks Nuclear entry of poliovirus protease-polymerase precursor 3CD: implications for host cell transcription shut-off


id: cord-290481-i2ppvsh5
author: Dolja, Valerian V.
title: Comparative and functional genomics of closteroviruses
date: 2006-03-09
extension: .txt
mime: text/plain
words: 9321
sentence: 323
flesch: 39
cache: cache/cord-290481-i2ppvsh5.txt
txt: txt/cord-290481-i2ppvsh5.txt
summary:
  Nevertheless, RNA viruses play a prominent role in our understanding of life's origin and evolution. Because RNA is widely believed to predate DNA as the genetic material, RNA viruses could be living fossils of the primordial RNA world (Joyce, 2002; Koonin and Martin, 2005) .


id: cord-281526-7t9e4lgn
author: Yin, Lijuan
date: 2016-09-02
extension: .txt
mime: text/plain
words: 4537
sentence: 168
flesch: 40
cache: cache/cord-281526-7t9e4lgn.txt
txt: txt/cord-281526-7t9e4lgn.txt
title:
  Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens

summary:
  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 overall protein concentrations of recombinant proteins and inactivated IBV were determined using BCA protein assay kit (Pierce, Company); and the protein concentrations of the three recombinant proteins (rS1 protein, rS1-H3(TM) protein and rS1-HA2 protein) and S1 protein concentration of inactivated IBV were determined using SDS-PAGE gel electrophoresis by GeneSnap and GeneTools from SynGene software with BSA as standard.


id: cord-286703-ipoj13va
author: de Wilde, Adriaan H.
date: 2017-01-15
extension: .txt
mime: text/plain
words: 3357
sentence: 109
flesch: 38
cache: cache/cord-286703-ipoj13va.txt
txt: txt/cord-286703-ipoj13va.txt
title:
  Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model

summary:
  The outcome of the clinical use of interferons was variable, with some reports questioning the long-term survival benefits (Al-Tawfiq et al., 2014; Omrani et al., 2014; Shalhoub et al., 2015) , whereas others suggested that further investigation is warranted (Khalid et al., 2016) , possibly in combination with the use of lopinavir/ritonavir (Kim et al., 2015) . Among these, alisporivir (ALV) showed increased sustained viral response during treatment of chronic hepatitis C virus (HCV) infection in phase III clinical trials, when treatment with ribavirin and pegylated interferon was combined with ALV (Buti et al., 2015; Flisiak et al., 2012; Pawlotsky et al., 2015; Zeuzem et al., 2015) .


id: cord-275016-ij5yaqkx
author: Someya, Yuichi
title: Characterization of the norovirus 3C-like protease
date: 2005-03-08
extension: .txt
mime: text/plain
words: 3248
sentence: 121
flesch: 51
cache: cache/cord-275016-ij5yaqkx.txt
txt: txt/cord-275016-ij5yaqkx.txt
summary:
  The smallest chymotrypsinlike proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole Purification, properties, and mutagenesis of poliovirus 3C protease In vitro proteolytic processing of the MD145 norovirus ORF1 non-structural polyprotein yields stable precursors and products similar to those detected in calicivirus-infected cells The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition Identification and characterization of a 3C-like protease from rabbit hemorrhagic disease virus, a calicivirus A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of proteindye binding Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases Expression and partial purification of recombinant tomato ringspot nepovirus 3C-like proteinase: comparison of the activity of the mature proteinase and the VPg-proteinase precursor Human enteric RNA viruses: caliciviruses and astroviruses Expression and purification of recombinant rhinovirus 14 3CD proteinase and its comparison to the 3C proteinase Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes Norwalk and related diarrhea viruses Cysteine proteases of positive strand RNA viruses and chymotrypsinlike serine proteases A distinct protein superfamily with a common structural fold Identification of active-site residues in protease 3C of hepatitis A virus by site-directed mutagenesis Site-directed mutagenesis of the putative catalytic triad of poliovirus 3C proteinase Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein Recent advances in the treatment of rhinovirus infections Active efflux of tetracycline encoded by four genetically different tetracycline resistance determinants in Escherichia coli Refined X-ray crystallographic structure of the poliovirus 3C gene product Structural basis for the substrate specificity of tobacco etch virus protease Complete nucleotide sequence of the chiba virus genome and functional expression of the 3C-like protease in Escherichia coli Identification of active-site amino acid residues in the Chiba virus 3C-like protease The treatment of rhinovirus infections: progress and potential Effects of temperature on protease activity.


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
extension: .txt
mime: text/plain
words: 3715
sentence: 154
flesch: 49
cache: cache/cord-330260-xuw31zfn.txt
txt: txt/cord-330260-xuw31zfn.txt
summary:
  In this study, the 3 7.3 kb genomes from Taiwan IBV strains were investigated to elucidate the genetic diversity of viruses. Evidence of circulation of a Chinese strain of infectious bronchitis virus (QXIBV) in Italy Molecular epizootiology of avian infectious bronchitis in Russia Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination Genes 3 and 5 of infectious bronchitis virus are accessory protein genes Comparisons of envelope through 5B sequences of infectious bronchitis coronaviruses indicates recombination occurs in the envelope and membrane genes Infectious bronchitis virus S2 gene sequence variability may affect S1 subunit specific antibody binding Co-circulation of four types of infectious bronchitis virus (793/B, 624/I, B1648 and Massachusetts)


id: cord-338602-6n309bnp
author: Gadotti, Ana Carolina
date: 2020-09-23
extension: .txt
mime: text/plain
words: 2892
sentence: 145
flesch: 49
cache: cache/cord-338602-6n309bnp.txt
txt: txt/cord-338602-6n309bnp.txt
title:
  IFN-γ is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection

summary:
  Besides it, cytokine storm is also present in severe patients due to elevation of interleukins such as TNF-α, IL-6, IL-8, and IL-10 2, 3 . Lancet Profiling serum cytokines in COVID-19 patients reveals IL-6 and IL-10 are disease severity predictors.


id: cord-314415-yr0uxok2
author: Guo, Zijing
date: 2018-08-15
extension: .txt
mime: text/plain
words: 3774
sentence: 137
flesch: 45
cache: cache/cord-314415-yr0uxok2.txt
txt: txt/cord-314415-yr0uxok2.txt
title:
  Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China

summary:
  Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand Identification of a novel circovirus in Australian ravens (Corvus coronoides) with feather disease Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae Smacoviridae: a new family of animal-associated singlestranded DNA viruses Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Mfold web server for nucleic acid folding and hybridization prediction In addition to six recognized CRESS DNA viral families, a large number of novel CRESS DNA viruses, waiting to be classified by ICTV, have been rapidly discovered in faeces of humans and animals through viral metagenomics in recent years.


id: cord-259671-7de21oaq
author: Madhugiri, Ramakanth
title: RNA structure analysis of alphacoronavirus terminal genome regions
date: 2014-12-19
extension: .txt
mime: text/plain
words: 11177
sentence: 307
flesch: 34
cache: cache/cord-259671-7de21oaq.txt
txt: txt/cord-259671-7de21oaq.txt
summary:
  Despite major progress in the characterization of proteins and cis-acting RNA elements involved in coronavirus RNA synthesis, the molecular mechanisms that mediate specific steps of coronavirus RNA replication and transcription are far from being understood. A conserved RNA pseudoknot in a putative molecular switch domain of the 3 -untranslated region of coronaviruses is only marginally stable Leader switching occurs during the rescue of defective RNAs by heterologous strains of the coronavirus infectious bronchitis virus Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10 Dependence of coronavirus RNA replication on an NH2-terminal partial nonstructural protein 1 in cis Severe acute respiratory syndrome coronavirus nsp1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Genome organization and reverse genetic analysis of a type I feline coronavirus A mobile genetic element with unknown function found in distantly related viruses Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus Suppression of host gene expression by nsp1 proteins of group 2 bat coronaviruses Expression and functions of SARS coronavirus replicative proteins Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain Evolution of virus and defective-interfering RNAs in BHK cells persistently infected with Sindbis virus LocARNA-P: accurate boundary prediction and improved detection of structural RNAs Analysis of a hypervariable region in the 3 non-coding end of the infectious bronchitis virus genome A phylogenetically conserved hairpin-type 3 untranslated region pseudoknot functions in coronavirus RNA replication Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Reselection of a genomic upstream open reading frame in mouse hepatitis coronavirus 5 -untranslatedregion mutants Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavirus molecules Regulation of coronaviral poly(A) tail length during infection Bovine coronavirus 5 -proximal genomic acceptor hotspot for discontinuous transcription is 65 nucleotides wide Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity Mouse hepatitis virus stem-loop 4 functions as a spacer element required to drive subgenomic RNA synthesis Strategy for systematic assembly of large RNA and DNA genomes: transmissible gastroenteritis virus model Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis Coronavirus replicative proteins Characterization of a human coronavirus (strain 229E) 3C-like proteinase activity


id: cord-272729-nbgdmavr
author: Kim, Youngnam
title: Ribavirin efficiently suppresses porcine nidovirus replication
date: 2012-10-27
extension: .txt
mime: text/plain
words: 6673
sentence: 226
flesch: 37
cache: cache/cord-272729-nbgdmavr.txt
txt: txt/cord-272729-nbgdmavr.txt
summary:
  Our results demonstrated that ribavirin treatment dose-dependently inhibited the replication of both nidoviruses. N protein staining revealed that the number of cells expressing viral antigen, as quantified by N protein staining results, was also reduced during ribavirin treatment, resulting in a maximum of ∼80% inhibition in response to 50 M and 200 M for PRRSV and PEDV, respectively ( Fig.


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
extension: .txt
mime: text/plain
words: 2074
sentence: 90
flesch: 55
cache: cache/cord-258546-1tf5ggfo.txt
txt: txt/cord-258546-1tf5ggfo.txt
summary:
  Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States 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 Sequence of the spike protein of the porcine epidemic diarrhoea virus Coronavirus spike proteins in viral entry and pathogenesis Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States Pathology of US porcine epidemic diarrhea virus strain PC21A in gnotobiotic pigs Isolation of porcine epidemic diarrhea virus (PEDV) in Korea Genetic characterization of porcine epidemic diarrhea virus in Korea from Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea Suchard.


id: cord-299904-i5c6nf18
author: Cornelissen, E.
date: 2009-04-07
extension: .txt
mime: text/plain
words: 3619
sentence: 132
flesch: 35
cache: cache/cord-299904-i5c6nf18.txt
txt: txt/cord-299904-i5c6nf18.txt
title:
  Absence of antibody-dependent, complement-mediated lysis of feline infectious peritonitis virus-infected cells

summary:
  Opsonization of the virus with complement proteins can promote phagocytosis, virolysis and interference with attachment, internalization or uncoating of the virions (Hirsch, 1982) . The fact that neutralizing antibodies are present in a cat with FIP, together with the observed enhancement of neutralization by complement in this study, indicates that cell free virus does not play an important role in the pathogenesis of FIP (de Groot-Mijnes et al., 2005) .


id: cord-256343-dtfw8o4g
author: Brandão, Paulo Eduardo
date: 2013-12-26
extension: .txt
mime: text/plain
words: 4921
sentence: 117
flesch: 37
cache: cache/cord-256343-dtfw8o4g.txt
txt: txt/cord-256343-dtfw8o4g.txt
title:
  The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus

summary:
  These results provide evidence that A. coronavirus genes have taken different codon evolution pathways depending on the function that each protein possesses. The most probable reason for the fact that non-100% conserved amino acid positions coded by a preferred codon for that amino acid (noted as NC in Table 1 ) were only found in A. coronavirus genes and not in the G. gallus genes is that host genes are less susceptible to both the occurrence of putative amino acids and codon usage polymorphisms, contrary to what is observed and expected for virus genes.


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
extension: .txt
mime: text/plain
words: 2962
sentence: 118
flesch: 40
cache: cache/cord-257487-xanqvdhn.txt
txt: txt/cord-257487-xanqvdhn.txt
summary:
  The EC 50 inhibitory concentration for HCoV-NL63 was about 5.1 M and replication was completely inhibited at 36 M FK506 (Fig. 1C) , reflecting a 732-fold reduction of virus replication (Fig. 1D) . 1E and F shows percentage and log reductions of inhibition of virus replication, respectively.


id: cord-327682-i3uim0zi
author: Santti, Juhana
title: Molecular detection and typing of human picornaviruses
date: 1999-08-25
extension: .txt
mime: text/plain
words: 2440
sentence: 94
flesch: 36
cache: cache/cord-327682-i3uim0zi.txt
txt: txt/cord-327682-i3uim0zi.txt
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; The outcome of enterovirus infections in man varies from minor respiratory illnesses to paralysis, myocarditis, meningoencephalitis and generalized infections with multiorgan failure in newborns (Grist et al., 1978) .


id: cord-020087-gs0pc6ee
title: Cumulative Contents for 2010
date: 2010-11-18
extension: .txt
mime: text/plain
words: 483
sentence: 7
flesch: -19
cache: cache/cord-020087-gs0pc6ee.txt
txt: txt/cord-020087-gs0pc6ee.txt
summary:
  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 The capsid protein of Grapevine rupestris stem pitting-associated virus contains a typical nuclear localization signal and targets to the nucleus 212 Distinct propagation efficiencies of H5N1 influenza virus Thai isolates in newly established murine respiratory region-derived cell clones 218 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 Cumulative Subject Index for Cumulative Contents for Molecular anatomy of subcellular localization of HSV-1 tegument protein US11 in living cells 71 ) Mapping of amino acid residues responsible for adhesion of cell culture-adapted foot-and-mouth disease SAT type viruses 82 Renault (France) Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas Kotait (Brazil, Ecuador) Human rabies transmitted by vampire bats: Antigenic and genetic characterization of rabies virus isolates from the Amazon region China)


id: cord-312848-vbadg8ki
author: Jeong, Jae-Ho
date: 2004-08-26
extension: .txt
mime: text/plain
words: 2953
sentence: 94
flesch: 45
cache: cache/cord-312848-vbadg8ki.txt
txt: txt/cord-312848-vbadg8ki.txt
title:
  Molecular analysis of S gene of spike glycoprotein of winter dysentery bovine coronavirus circulated in Korea during 2002–2003

summary:
  In the present study, the aa sequences of the S2 subunit of Korean WD strains were comparatively well conserved compared with the S1 subunit of the Mebus strain. at aa 510, 531, 543, and 578 can be predictive and Mabsspecific strains for this region may also be distinguished among respiratory, enteric, and vaccine BCoV strains.


id: cord-279827-921kvrrz
author: Murata, Takayuki
title: Growth behavior of bovine herpesvirus-1 in permissive and semi-permissive cells
date: 1999-06-11
extension: .txt
mime: text/plain
words: 7154
sentence: 268
flesch: 57
cache: cache/cord-279827-921kvrrz.txt
txt: txt/cord-279827-921kvrrz.txt
summary:
  Confluent monolayer cultures of MDBK cells or HmLu-1 cells were infected with BHV-1 at an moi of 5 and at 3, 6, 12, 24, and 48 h p.i., DNA was extracted as described in Section 2. Therefore it might be possible that HmLu-1 cells might lacked the HVEM like factor for BHV-1 gD while MDBK cells express such a factor allowing the penetration and the nuclear transport of BHV-1.


id: cord-260835-ck9z5xsd
author: Kamau, Anthony Ndirangu
date: 2017-01-02
extension: .txt
mime: text/plain
words: 4538
sentence: 170
flesch: 49
cache: cache/cord-260835-ck9z5xsd.txt
txt: txt/cord-260835-ck9z5xsd.txt
title:
  Porcine amino peptidase N domain VII has critical role in binding and entry of porcine epidemic diarrhea virus

summary:
  Also, PEDV harvested from pAPN or domain VII expressing NIH3T3 cells was induced indirect plaques in Vero cells confirming successful entry and replication. Cells were blocked with 4% skim milk for 30 min at room temperature and detection of viral antigens was performed using mouse anti-PEDV polysera for 1 h at 37 • C. After 3 times wash with 200 l of 1 X PBS, cells were incubated with horseradish peroxidase (HRP) -conjugated anti-mouse IgG (Santa-Cruz) for 1 h, 37 • C.


id: cord-258294-ny3xrjzc
author: Gao, Xiang
date: 2020-04-02
extension: .txt
mime: text/plain
words: 6071
sentence: 213
flesch: 45
cache: cache/cord-258294-ny3xrjzc.txt
txt: txt/cord-258294-ny3xrjzc.txt
title:
  Characterization, Pathogenicity and Protective efficacy of a Cell Culture-Derived Porcine Deltacoronavirus

summary:
  Virus inactivation was verified by the absence of viral growth in LLC-PK cell cultures, and no obvious CPEs were observed in cell cultures within 96 h after inoculation (data not shown). Subsequently, the pigs were challenged orally with 3 mL of 1000 PDD50 cell culture-adapted J o u r n a l P r e -p r o o f USDA to require reports of PED Age-dependent variation in innate immune responses to porcine epidemic diarrhea virus infection in suckling versus weaned pigs Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 Porcine deltacoronavirus in mainland China Vaccines for porcine epidemic diarrhea virus and other swine coronaviruses Isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the United States Isolation and characterization of Korean porcine deltacoronavirus strain KNU16-07 Porcine deltacoronavirus infection: etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis Susceptibility of porcine IPEC-J2 intestinal epithelial cells to infection with porcine deltacoronavirus (PDCoV) and serum cytokine responses of gnotobiotic pigs to acute infection with IPEC-J2 cell culture-passaged PDCoV Porcine epidemic diarrhea virus: an emerging and re-emerging epizootic swine virus Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04/2014 Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus Determination of the infectious titer and virulence of an original US porcine epidemic diarrhea virus PC22A strain A newly isolated Chinese virulent genotype GIIb porcine epidemic diarrhea virus strain: biological characteristics, pathogenicity and immune protective effects as an inactivated vaccine candidate Complete genome sequence of porcine deltacoronavirus isolated in Thailand Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus Different lineage of porcine deltacoronavirus in Thailand, Vietnam and Lao PDR in 2015 Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province MEGA6: molecular evolutionary genetics analysis version 6.0 Detection and genetic characterization of deltacoronavirus in pigs Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from mainland China Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5'-untranslated region Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus Porcine deltacoronavirus: overview of infection dynamics, diagnostic methods, prevalence and genetic evolution Biological characterization and pathogenicity of a newly isolated Chinese highly virulent genotype GIIa porcine epidemic diarrhea virus strain Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China Detection and spike gene characterization in porcine deltacoronavirus in China during Characterization and Pathogenicity of the Porcine Deltacoronavirus Isolated in Southwest China


id: cord-301301-ilsenpus
author: Mihalov-Kovács, Eszter
date: 2017-03-15
extension: .txt
mime: text/plain
words: 4874
sentence: 187
flesch: 47
cache: cache/cord-301301-ilsenpus.txt
txt: txt/cord-301301-ilsenpus.txt
title:
  Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission

summary:
  Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics Nineteen New Species in the Genus Mamastrovirus in the Astroviridae Family Complete genome sequence of canine astrovirus with molecular and epidemiological characterisation of UK strains Novel astroviruses in insectivorous bats Astrovirus infections in humans and animals-molecular biology, genetic diversity, and interspecies transmissions Viral genome sequencing by random priming methods Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea Human stool contains a previously unrecognized diversity of novel astroviruses Complete sequence of a duck astrovirus associated with fatal hepatitis in ducklings Prevalence and risk factors of astrovirus infection in puppies from French breeding kennels Avian Nephritis Virus (ANV) as a new member of the family Astroviridae and construction of infectious ANV cDNA Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server Viruses and virus-like particles in the faeces of dogs with and without diarrhoea Astroviruses in dogs Detection and characterization of canine astroviruses Enteric disease in dogs naturally infected by a novel canine astrovirus Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system Astroviruses Characterization of human astrovirus cell entry Enteric viral infections of sheltered dogs in Hungary Candidate new rotavirus species in sheltered dogs Molecular characterisation of the 3'-end of the astrovirus genome Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus) Astrovirus Research. Essential Ideas, Everyday Impacts, Future Directions Detection and characterization of avastrovirus associated with diarrhea isolated from minks in China Detection of canine astrovirus in dogs with diarrhea in Japan MEGA6: molecular evolutionary genetics analysis version 6.0 Genetic characterization of a new astrovirus detected in dogs suffering from diarrhoea Electron microscopic demonstration of viruses in feces of dogs with diarrhea Astrovirus infection in children Astrovirus-like, coronavirus-like, and parvovirus-like particles detected in the diarrheal stools of beagle pups Isolation and characterization of canine astrovirus in China


id: cord-329183-s0zrvn9o
author: Graham, Robert I.
date: 2008-04-10
extension: .txt
mime: text/plain
words: 4595
sentence: 168
flesch: 50
cache: cache/cord-329183-s0zrvn9o.txt
txt: txt/cord-329183-s0zrvn9o.txt
title:
  Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae)()

summary:
  No homology was found with other virus sequences. Out-break populations of O. brumata larvae have recently been observed on heather moorland on Orkney, in northern Scotland (Graham et al., 2004 (Graham et al., , 2006 Kerslake et al., 1996) .


id: cord-286473-sl5zy8nj
author: Gomaa, M.H.
title: Complete genomic sequence of turkey coronavirus
date: 2008-05-12
extension: .txt
mime: text/plain
words: 7986
sentence: 297
flesch: 54
cache: cache/cord-286473-sl5zy8nj.txt
txt: txt/cord-286473-sl5zy8nj.txt
summary:
  Similar results were obtained with a large number of IBV sequences and five TCoV sequences with the M protein (data not shown). The 3 end of TCoV genome had been done using the 3 race system for rapid amplification of cDNA ends (Invitrogen) according to the instruction of the kite.


id: cord-312489-ywep0c08
author: Andoh, Kiyohiko
title: Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells
date: 2015-10-02
extension: .txt
mime: text/plain
words: 5052
sentence: 175
flesch: 35
cache: cache/cord-312489-ywep0c08.txt
txt: txt/cord-312489-ywep0c08.txt
summary:
  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. Results showed that the recombinant S1 protein was highly glycosylated, and the neutralizing antigenicity of recombinant S1 protein was lower than that of inactivated virus.


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
extension: .txt
mime: text/plain
words: 3782
sentence: 132
flesch: 46
cache: cache/cord-280643-n8qjorqk.txt
txt: txt/cord-280643-n8qjorqk.txt
summary:
  To study the effects of dual RNAi on HBV gene expression in a cell culture model, we used a derivative of the human HepG2 hepatoma cell line, HepG2.2.15, which has been stably transformed with several copies of the HBV genome and used as an in vitro model for HBV replication. The effects of dual siRNA system on HBV gene expression were investigated in this study.


id: cord-303111-iv4lzpev
author: Almazán, Fernando
title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons()
date: 2014-12-19
extension: .txt
mime: text/plain
words: 7077
sentence: 179
flesch: 25
cache: cache/cord-303111-iv4lzpev.txt
txt: txt/cord-303111-iv4lzpev.txt
summary:
  Molecular genetic analysis of the structure and function of RNA virus genomes has been profoundly advanced by the availability of full-length cDNA clones. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses.


id: cord-309205-l8vjtrjq
author: Shirato, Kazuya
date: 2018-08-15
extension: .txt
mime: text/plain
words: 6696
sentence: 206
flesch: 38
cache: cache/cord-309205-l8vjtrjq.txt
txt: txt/cord-309205-l8vjtrjq.txt
title:
  Differential susceptibility of macrophages to serotype II feline coronaviruses correlates with differences in the viral spike protein

summary:
  The prevalence of types I and II feline coronavirus infections in cats Protease-mediated entry via the endosome of human coronavirus 229E Deletions in the 7a ORF of feline coronavirus associated with an epidemic of feline infectious peritonitis Feline infectious peritonitis: still an enigma? Sites of feline coronavirus persistence in healthy cats Feline coronavirus serotypes 1 and 2: seroprevalence and association with disease in Switzerland Retargeting of coronavirus by substitution of the spike glycoprotein ectodomain: crossing the host cell species barrier Cellular entry of the porcine epidemic diarrhea virus Mutation in spike protein cleavage site and pathogenesis of feline coronavirus Field strain feline coronaviruses with small deletions in ORF7b associated with both enteric infection and feline infectious peritonitis Genetic diversity and correlation with feline infectious peritonitis of feline coronavirus type I and II: a 5-year study in Taiwan Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis Isolation of feline coronaviruses from two cats with diverse disease manifestations Host cell proteases: critical determinants of coronavirus tropism and pathogenesis The paradox of feline coronavirus pathogenesis: a review Receptor-bound porcine epidemic diarrhea virus spike protein cleaved by trypsin induces membrane fusion A review of feline infectious peritonitis virus infection: 1963-2008 An update on feline infectious peritonitis: virology and immunopathogenesis Pathogenic differences between various feline coronavirus isolates Pathogenicity studies of feline coronavirus isolates 79-1146 and 79-1683 Pathogenesis of feline enteric coronavirus infection Pathogenesis of feline enteric coronavirus infection Significance of coronavirus mutants in feces and diseased tissues of cats suffering from feline infectious peritonitis Feline infectious peritonitis: role of the feline coronavirus 3c gene in intestinal tropism and pathogenicity based upon isolates from resident and adopted shelter cats Two related strains of feline infectious peritonitis virus isolated from immunocompromised cats infected with a feline enteric coronavirus Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis Utilization of DC-SIGN for entry of feline coronaviruses into host cells Differential role for low pH and cathepsin-mediated cleavage of the viral spike protein during entry of serotype II feline coronaviruses Feline lectin activity is critical for the cellular entry of feline infectious peritonitis virus Acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein Clinical isolates of human coronavirus 229E bypass the endosome for cell entry Intrinsic resistance of feline peritoneal macrophages to coronavirus infection correlates with in vivo virulence Intriguing interplay between feline infectious peritonitis virus and its receptors during entry in primary feline monocytes Genetic drift and genetic shift during feline coronavirus evolution Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses Pathogenic characteristics of persistent feline enteric coronavirus infection in cats Proteolytic activation of the porcine epidemic diarrhea coronavirus spike fusion protein by trypsin in cell culture Several genes, including the S gene and the accessory genes 3a, 3b, 3c, 7a, and 7b, have been considered (Balint et al., 2012; Chang et al., 2010; Kennedy et al., 2001; Licitra et al., 2013; Pedersen et al., 2012; Rottier et al., 2005; Vennema et al., 1998) .


id: cord-272383-pzivb0ro
author: Reddy, P.Seshidhar
date: 2000-11-08
extension: .txt
mime: text/plain
words: 4187
sentence: 150
flesch: 44
cache: cache/cord-272383-pzivb0ro.txt
txt: txt/cord-272383-pzivb0ro.txt
title:
  Optimization of bovine coronavirus hemagglutinin-estrase glycoprotein expression in E3 deleted bovine adenovirus-3

summary:
  The expression studies suggest that the introduction of a 137 bp chimeric intron upstream of the HE cDNA is able to increase the level of HE gene expression. In addition, as the development of a quality immune response would correlate with levels of antigen produced by the recombinant adenovirus vectors, we investigated ways of increasing HE gene expression in the BAV-3 expression system.


id: cord-288253-wqrhiq08
author: Park, Jung-Eun
date: 2015-02-02
extension: .txt
mime: text/plain
words: 5336
sentence: 194
flesch: 42
cache: cache/cord-288253-wqrhiq08.txt
txt: txt/cord-288253-wqrhiq08.txt
title:
  Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus

summary:
  We thus generated porcine APN transgenic mice expressing porcine APN in the brush borders of their small intestines and various tissues (lungs and kidneys). PEDV replication in the small intestines of porcine APN transgenic mice Both wild type and porcine APN transgenic mice were infected with PEDV orally on day 0.


id: cord-326320-flfrdrbi
author: Choudhary, Shalki
date: 2020-08-29
extension: .txt
mime: text/plain
words: 4678
sentence: 168
flesch: 45
cache: cache/cord-326320-flfrdrbi.txt
txt: txt/cord-326320-flfrdrbi.txt
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

summary:
  The entry of coronavirus in the host cell depends on the binding of the viral spike proteins (SP) to cellular receptors and its priming by host cell proteases (Hoffmann et al., 2020) . The S1/S2 domain of SP in newly emerged coronavirus (SARS-CoV-2) harbor potential protease cleavage site (PCS), NSPRRAR ^ SVA (^ is cleavage site), having four distinct amino acids (in bold), which is absent in SARS-CoV of the same clade and thereby became a keyhole for viral invasion J o u r n a l P r e


id: cord-263178-lvxxdvas
author: Shan, Dan
date: 2018-05-02
extension: .txt
mime: text/plain
words: 6895
sentence: 239
flesch: 44
cache: cache/cord-263178-lvxxdvas.txt
txt: txt/cord-263178-lvxxdvas.txt
title:
  Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus

summary:
  The pathogenesis of virulent and avirulent avian infectious bronchitis virus Fine level epitope mapping and conservation analysis of two novel linear B-cell epitopes of the avian infectious bronchitis coronavirus nucleocapsid protein Recombinant infectious bronchitis coronavirus beaudette with the spike protein gene of the pathogenic M41 strain remains attenuated but induces protective immunity The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Identification of previously unknown antigenic epitopes on the S and N proteins of avian infectious bronchitis virus A recombinant fowl adenovirus expressing the S1 gene of infectious bronchitis virus protects against challenge with infectious bronchitis virus Development and validation of RT-PCR tests for the detection and S1 genotyping of infectious bronchitis virus and other closely related gammacoronaviruses within clinical samples Location of antigenic sites defined by neutralizing monoclonal antibodies on the S1 avian infectious bronchitis virus glycopolypeptide Antigenic domains on the peplomer protein of avian infectious bronchitis virus: correlation with biological functions Analysis of an immunodominant region of infectious bronchitis virus Antigenicity of the peplomer protein of infectious bronchitis virus Altered pathogenesis of a mutant of the murine coronavirus MHV-A59 is associated with a Q159L amino acid substitution in the spike protein Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens Identification of a trypsin-like serine proteinase domain encoded by ORF 1a of the coronavirus IBV Proteolytic mapping of the coronavirus infectious bronchitis virus 1b polyprotein: evidence for the presence of four cleavage sites of the 3C-like proteinase and identification of two novel cleavage products Infectious bronchitis virus: S1 gene characteristics of vaccines used in China and efficacy of vaccination against heterologous strains from China Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between Identification of a newly isolated avian infectious bronchitis coronavirus variant in China exhibiting affinity for the respiratory tract Molecular characterization and pathogenicity of infectious bronchitis coronaviruses: complicated evolution and epidemiology in china caused by cocirculation of multiple types of infectious bronchitis coronaviruses Characterization of a recombinant coronavirus infectious bronchitis virus with distinct S1 subunits of spike and nucleocapsid genes and a 3' untranslated region Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Identification of amino acids involved in a serotype and neutralization specific epitope within the s1 subunit of avian infectious bronchitis virus Epitopes on the peplomer protein of infectious bronchitis virus strain M41 as defined by monoclonal antibodies Multiple regions of the murine coronavirus spike glycoprotein influence neurovirulence Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Assessment of molecular and genetic evolution, antigenicity and virulence properties during the persistence of the infectious bronchitis virus in broiler breeders Development and immunogenicity of recombinant GapA(+) Mycoplasma gallisepticum vaccine strain ts-11 expressing infectious bronchitis virus-S1 glycoprotein and chicken interleukin-6 Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus Singleamino-acid substitutions in open reading frame (ORF) 1b-nsp14 and ORF 2a proteins of the coronavirus mouse hepatitis virus are attenuating in mice Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and Persistent antigenic variation of influenza A viruses after incomplete neutralization in ovo with heterologous immune serum The replicase gene of avian coronavirus infectious bronchitis virus is a determinant of pathogenicity Evidence of circulation of a Chinese strain of infectious bronchitis virus (QXIBV) in Italy Molecular epizootiology of avian infectious bronchitis in Russia Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus Coronavirus IBV: removal of spike glycopolypeptide S1 by urea abolishes infectivity and haemagglutination but not attachment to cells Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus Molecular and antigenic characteristics of Massachusetts genotype infectious bronchitis coronavirus in China Evidence for a coiled-coil structure in the spike proteins of coronaviruses Induction of cystic oviducts and protection against early challenge with infectious bronchitis virus serotype D388 (genotype QX) by maternally derived antibodies and by early vaccination Mouse hepatitis virus liver pathology is dependent on ADP-ribose-10phosphatase, a viral function conserved in the alpha-like supergroup Selection of and recombination between minor variants lead to the adaptation of an avian coronavirus to primate cells An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells Functional and genetic studies of the substrate specificity of coronavirus infectious bronchitis virus 3C-like proteinase Coronavirus-induced ER stress response and its involvement in regulation of coronavirus-host interactions


id: cord-345999-iiw4cs8p
author: Khare, Prashant
date: 2020-09-24
extension: .txt
mime: text/plain
words: 3295
sentence: 138
flesch: 49
cache: cache/cord-345999-iiw4cs8p.txt
txt: txt/cord-345999-iiw4cs8p.txt
title:
  Current approaches for target-specific drug discovery using natural compounds against SARS-CoV-2 infection

summary:
  Triterpenes [betulinic acid (22) and savinin (23)] were reported to possess anti 3CLpro activity (Wen et al., 2007) . 4.00 μM (Wen et al., 2007)


id: cord-259935-xyo2pe4g
author: Wang, Ching-Ying
date: 2017-05-02
extension: .txt
mime: text/plain
words: 4679
sentence: 159
flesch: 41
cache: cache/cord-259935-xyo2pe4g.txt
txt: txt/cord-259935-xyo2pe4g.txt
title:
  SARS coronavirus papain-like protease up-regulates the collagen expression through non-Samd TGF-β1 signaling

summary:
  The expression of SARS-PLpro in lung tissues of mice was determined using IHC staining with anti-E. coli synthesized PLpro serum, and IHC positivity for PLpro expression within lung tissues was observed in the group infected with pSARS-PLpro ( Fig. 2A) . PLpro expression caused the STAT6 expression and induced the translation of STAT6 in the nucleus.


id: cord-332075-gxmae2rs
author: Wang, Jianzhong
date: 2015-05-04
extension: .txt
mime: text/plain
words: 5221
sentence: 183
flesch: 44
cache: cache/cord-332075-gxmae2rs.txt
txt: txt/cord-332075-gxmae2rs.txt
title:
  Generation and evaluation of a recombinant genotype VII Newcastle disease virus expressing VP3 protein of Goose parvovirus as a bivalent vaccine in goslings

summary:
  I. Epidemiological, clinical, pathological and aetiological studies Newcastle disease virus, a host range-restricted virus, as a vaccine vector for intranasal immunization against emerging pathogens Newcastle disease virus-vectored vaccines expressing the hemagglutinin or neuraminidase protein of H5N1 highly pathogenic avian influenza virus protect against virus challenge in monkeys Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus Newcastle disease virus-based live attenuated vaccine completely protects chickens and mice from lethal challenge of homologous and heterologous H5N1 avian influenza viruses Novel in-ovo chimeric recombinant Newcastle disease vaccine protects against both Newcastle disease and infectious bursal disease Isolation and identification of goose parvovirus in the UK Studies with a duck embryo adapted goose parvovirus vaccine A vaccine candidate of attenuated genotype VII Newcastle disease virus generated by reverse genetics Generation of a genotype VII Newcastle disease virus vaccine candidate with high yield in embryonated chicken eggs Genomic sequence of an isolate of Newcastle disease virus isolated from an outbreak in geese: a novel six nucleotide insertion in the non-coding region of the nucleoprotein gene Recombinant Newcastle disease virus as a vaccine vector A recombinant Newcastle disease virus (NDV) expressing VP2 protein of infectious bursal disease virus (IBDV) protects against NDV and IBDV Epidemiologic investigation of an outbreak of goose parvovirus infection in Sweden A goose-sourced paramyxovirus isolated from southern China Goose parvovirus structural proteins expressed by recombinant baculoviruses self-assemble into virus-like particles with strong immunogenicity in goose Modified Newcastle disease virus vectors expressing the H5 hemagglutinin induce enhanced protection against highly pathogenic H5N1 avian influenza virus in chickens Immunological aspects of Derzsy's disease in goslings Expression of muscovy duck parvovirus capsid proteins (VP2 and VP3) in a baculovirus expression system and demonstration of immunity induced by the recombinant proteins Biochemical and genomic characterization of muscovy duck parvovirus CpG oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by a goose parvovirus vaccine in ducks Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during Newcastle disease: evolution of genotypes and the related diagnostic challenges Evolutionary dynamics of Newcastle disease virus Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge Newcastle disease virus in pakistan: genetic characterization and implication in molecular diagnosis Role of fusion protein cleavage site in the virulence of Newcastle disease virus Rescue of Newcastle disease virus from cloned cDNA: evidence that cleavability of the fusion protein is a major determinant for virulence Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: efficacy of field vaccination A simple method of estimating fifty per cent endpoints Virus hepatitis of geese. Host range of goose hepatitis virus An outbreak of goose parvovirus infection in Japan Cloning of the genome of a goose parvovirus vaccine strain SYG61v and rescue of infectious virions from recombinant plasmid in embryonated goose eggs Development of a reverse genetics system based on RNA polymerase II for Newcastle disease virus genotype VII Genotyping of Newcastle disease viruses isolated from 2002 to 2004 in China Generation by reverse genetics of an effective, stable, live-attenuated Newcastle disease virus vaccine based on a currently circulating, highly virulent Indonesian strain Genomic analysis of Newcastle disease virus strain NA-1 isolated from geese in China


id: cord-311628-ep795pil
author: Fu, Yu
title: A novel delivery platform based on Bacteriophage MS2 virus-like particles
date: 2016-01-04
extension: .txt
mime: text/plain
words: 6025
sentence: 177
flesch: 36
cache: cache/cord-311628-ep795pil.txt
txt: txt/cord-311628-ep795pil.txt
summary:
  In order to determine the role of MS2 RNA in capsid stability, the experiment was repeated with wild-type phage particles, prepared for electron microscopy in the same way as the empty capsids. The use of armored RNA as a multi-purpose internal control for RT-PCR A simple, RNA-mediated allosteric switch controls the pathway to formation of a T = 3 viral capsid Molecular mechanism of RNA phage morphogenesis Molecular mechanism of RNA-phage morphogenesis Effects of amino acid substitution on the thermal stability of MS2 capsids lacking genomic RNA Crystal structures of MS2 capsids with mutations in the subunit FG loop Ribonucleoprotein complexes formed between bacteriophages MS2 RNA and MS2 protein in vitro A new RNA vaccine platform based on MS2 virus-like particles produced in saccharomyces cerevisiae MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly Visualising a viral RNA genome poised for release from its receptor complex VLPs displaying a single L2 epitope induce broadly cross-neutralizing antibodies against human papilloma virus A coat for all sequences RNA-based vaccines Structure determination of the bacteriophage MS2 The three-dimensional structure of the bacterial virus MS2 Proliferative lymphocyte responses to foot-and-mouth disease virus and three FMDV peptides after vaccination or immunization with these peptides in cattle mRNA: from a chemical blueprint for protein production to an off-the-shelf therapeutic mRNA: delivering an antitumor message External quality assessment of molecular detection of ebola virus in China Delivery of siRNA therapeutics: barriers and carriers Development of an antisense RNA delivery system using conjugates of the MS2 bacteriophage capsids and HIV-1 TAT cell-penetrating peptide RNase-resistant virus-like particles containing long chimeric RNA sequences produced by two-plasmid coexpression system Plasmids encoding foot-and-mouth disease virus VP1 epitopes elicited immune responses in mice and swine and protected swine against viral infection Delivery of antisense oligonucleotides to leukemia cells by RNA bacteriophage capsids Using a novel MicroRNA delivery system to inhibit osteoclastogenesis Cancer therapy using a self-replicating RNA vaccine Construction and characterization of virus-like particles: a review Armored long RNA controls or standards for branched DNA assay for detection of human immunodeficiency virus type 1 External quality assessment for the detection of measles virus by reverse transcription-PCR using armored RNA A novel method to produce armored double-stranded DNA by encapsulation of MS2 viral capsids RNA melanoma vaccine: induction of antitumor immunity by human glycoprotein 100 mRNA immunization Virus assembly, allostery and antivirals This work was supported by the grant from the National Natural Science Foundation of China (No. 81171981).


id: cord-300883-rws11uel
author: Padhi, Abinash
title: Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein
date: 2007-10-10
extension: .txt
mime: text/plain
words: 3542
sentence: 102
flesch: 30
cache: cache/cord-300883-rws11uel.txt
txt: txt/cord-300883-rws11uel.txt
summary:
  Maximum likelihood (ML)-based codon substitution models, which account for variable ω ratios among codon sites and detect codon sites that are subjected to positive selection (Yang et al., 2000) , have been widely used in detecting positive selection in a number of respiratory viral groups (e.g., Zlateva et al., 2004; Zhang et al., 2006) . (Yang et al., 2000) , and M8a (β + ω = 1) (Swanson et al., 2003) .


id: cord-293562-69nnyq8p
author: Imran, Mudassar
date: 2018-08-15
extension: .txt
mime: text/plain
words: 5874
sentence: 287
flesch: 51
cache: cache/cord-293562-69nnyq8p.txt
txt: txt/cord-293562-69nnyq8p.txt
title:
  Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever

summary:
  The dynamics of Zika fever epidemic model have been considered. Susceptible individuals get infected with Zika fever virus (due to contact with infected vectors) at a rate λ h and thus enter the exposed class E h .


id: cord-267362-l4288mxw
author: Shi, Xibao
date: 2010-08-06
extension: .txt
mime: text/plain
words: 3910
sentence: 137
flesch: 44
cache: cache/cord-267362-l4288mxw.txt
txt: txt/cord-267362-l4288mxw.txt
title:
  Porcine reproductive and respiratory syndrome virus (PRRSV) could be sensed by professional beta interferon-producing system and had mechanisms to inhibit this action in MARC-145 cells

summary:
  It is a coincidence that PRRSV nsp1 also contained papain-like protease domain (den Boon et al., 1995) and the crystal structure of PRRSV N protein was similar to that of SARS-CoV N protein (Yu et al., 2006) . Since PRRSV nsp1 also contains papain-like protease domain (den Boon et al., 1995) and the crystal structure of PRRSV N protein was similar to that of SARS-CoV N protein (Yu et al., 2006) , PRRSV nsp1 and N proteins were chosen to probe which component of PRRSV could inhibit IFN-␤ production.


id: cord-330508-uilejxmi
author: van den Hoogen, Bernadette
date: 2020-07-28
extension: .txt
mime: text/plain
words: 1782
sentence: 58
flesch: 22
cache: cache/cord-330508-uilejxmi.txt
txt: txt/cord-330508-uilejxmi.txt
title:
  Immunometabolism pathways as the basis for innovative anti-viral strategies (INITIATE): A Marie Sklodowska-Curie innovative training network

summary:
  The research program is divided into 3 work packages (Figure 2 The objective of WP1 is to obtain in-depth knowledge of the roles of different organelles and signaling complexes (such as mitochondria, signalosomes, stress granules, replication organelles) in modulation of immune-and metabolic pathways in response to RNA virus infections, including influenza virus, pneumoviruses and coronaviruses. In WP3, innate lymphoid cells, natural killer cells, hepatocytes, dendritic cells and in vivo animal models relevant for RNA virus infection will be used to investigate the regulatory interface between immune and metabolic pathways on antiviral immunity.


id: cord-268010-1m5h3krw
author: Jung, Kwonil
date: 2016-12-02
extension: .txt
mime: text/plain
words: 7592
sentence: 235
flesch: 44
cache: cache/cord-268010-1m5h3krw.txt
txt: txt/cord-268010-1m5h3krw.txt
title:
  Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis

summary:
  Of the 14 PDCoV-positive samples, 7 (50%) were also positive for PEDV; and 2 were co-infected with PEDV, TGEV, and PDCoV. In infected nursing pigs, similar to PEDV and TGEV infections Saif et al., 2012) , gross lesions are limited to the gastrointestinal tract and are characterized by thin and transparent intestinal walls (proximal jejunum to colon) with accumulation of large amounts of yellow fluid in the intestinal lumen (Chen et al., 2015b; Hu et al., 2016; Jung et al., 2015c; Ma et al., 2015) . In infected nursing pigs, similar to PEDV and TGEV infections Saif et al., 2012) , histological lesions are characterized by acute, multifocal to diffuse, mild to severe atrophic enteritis in the proximal jejunum to ileum (Chen et al., 2015b; Hu et al., 2016; Jung et al., 2015c; Ma et al., 2015; Wang et al., 2015a) , occasionally accompanied by mild vacuolation of superficial epithelial cells in the cecum and colon that coincided with a few PDCoV antigen-positive cecal and colonic epithelial cells (Jung et al., 2015c) .


id: cord-320331-wtxja5i9
author: Cabbab, Iris Louise N.
date: 2020-10-08
extension: .txt
mime: text/plain
words: 10078
sentence: 314
flesch: 32
cache: cache/cord-320331-wtxja5i9.txt
txt: txt/cord-320331-wtxja5i9.txt
title:
  Anti-Inflammatory Drugs and the Renin-Angiotensin-Aldosterone System: Current Knowledge and Potential Effects on Early SARS-CoV-2 Infection

summary:
  Hence, the reduction in prostaglandin E 2 and I 2 syntheses is the main mechanism by which NSAIDs directly contribute to increased ACE2 expression, which can be utilized by SARS-CoV-2 (Fig. 2) . This may suggest the promotion of coronavirus replication secondary to immunosuppression, or of increased ACE2 expression secondary to osmotic diuresis, which we hypothesized earlier above (Fig. 4) .


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
extension: .txt
mime: text/plain
words: 7117
sentence: 233
flesch: 43
cache: cache/cord-290948-cuu78cvl.txt
txt: txt/cord-290948-cuu78cvl.txt
summary:
  Interestingly, nsp10 also interacts with nsp9, a single-stranded RNA binding protein (Egloff et al., 2004; Su et al., 2006; Sutton et al., 2004) that in turn interacts with nsp8, the putative RNA primase (Imbert et al., 2006) . One of them reveals a unique spherical dodecamer architecture (Su et al., 2006) and the other shows a monomer (Joseph et al., 2006) .


id: cord-318319-efqf5e1i
author: Yamasaki, Yukitaka
date: 2020-07-03
extension: .txt
mime: text/plain
words: 2137
sentence: 108
flesch: 54
cache: cache/cord-318319-efqf5e1i.txt
txt: txt/cord-318319-efqf5e1i.txt
title:
  The peripheral lymphocyte count as a predictor of severe COVID-19 and the effect of treatment with ciclesonide

summary:
  Of the 30 included patients, 12, 14, and 4 were allocated to severe pneumonia, non-severe pneumonia, and non-pneumonia groups, respectively. Patients were divided into three groups: severe pneumonia, non-severe pneumonia, and non-pneumonia.


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
extension: .txt
mime: text/plain
words: 5442
sentence: 188
flesch: 51
cache: cache/cord-279969-5nlmljcw.txt
txt: txt/cord-279969-5nlmljcw.txt
summary:
  The N protein of hMPV is similar in size to the ones of other pneumoviruses (391 Á/394 residues), which is relatively smaller than those reported for the other members of the Paramyxoviridae family (489 Á/583 residues) (Barr et al., 1991; Collins et al., 1985; Curran and Kolakofsky, 1999; Dar et al., 2001; Spriggs and Collins, 1986) . When compared to the other pneumovirus members, the hMPV N gene showed 69 Á/89% aa identity with APV members, 42 Á/44% with RSV members and 45% with PVM ( Barr et al., 1991; Buchholz et al., 1999; Dar et al., 2001; Karron et al., 1997; Li et al., 1996; Venkatesan et al., 1983) (Table 4 ).


id: cord-286416-8eu6wp9b
author: Valiente-Echeverría, Fernando
title: Viral modulation of stress granules
date: 2012-06-14
extension: .txt
mime: text/plain
words: 5583
sentence: 163
flesch: 34
cache: cache/cord-286416-8eu6wp9b.txt
txt: txt/cord-286416-8eu6wp9b.txt
summary:
  While the details on the mechanisms by which viruses elicit favorable environments in which to replicate will require further work, the sequestration of critical factors for the induction of SGs by viral proteins appears to be an increasingly studied area of research and should yield important new information on how viruses gain control over host cell biology. This observation likely indicates that viral proteins or viral RNA could locally disassemble SG to favor viral translation and this was shown to correlate with increased vRNA levels (McInerney et al., 2005) .


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
extension: .txt
mime: text/plain
words: 4740
sentence: 146
flesch: 38
cache: cache/cord-304137-vxqkztio.txt
txt: txt/cord-304137-vxqkztio.txt
summary:
  This increase was significantly reduced by half when CDM was added to HSV-1 infected cells (p < 0.005). (NF-κB) activation in HSV-1 infected conjunctival cells.


id: cord-309428-qkjjxr6p
author: Li, Liwei
date: 2015-01-02
extension: .txt
mime: text/plain
words: 5108
sentence: 189
flesch: 42
cache: cache/cord-309428-qkjjxr6p.txt
txt: txt/cord-309428-qkjjxr6p.txt
title:
  Host miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by upregulating type I interferons

summary:
  We then analyzed the kinetics of miR-26 expression in PRRSV infected PAM cells. Indirect immunofluorescence assays (IFA) were performed as described previously (Tian et al., 2011) for the detection of nucleocapsid (N) protein in PRRSV vJX143 infected MARC-145 cells or PAMs pre-transfected with miR-26 family or mutant mimics.


id: cord-326349-59566vqe
author: Ding, Li
date: 2013-12-26
extension: .txt
mime: text/plain
words: 4896
sentence: 176
flesch: 51
cache: cache/cord-326349-59566vqe.txt
txt: txt/cord-326349-59566vqe.txt
title:
  Transmissible gastroenteritis virus infection induces cell cycle arrest at S and G2/M phases via p53-dependent pathway

summary:
  Since the proportion of cells in the S and G2/M phases was greater in TGEV infected cells compared to mock-infected cells, to investigate the effects of cell accumulation at S and G2/M phases on TGEV replication, synchronized cells in G2/M phase, G0/G1 phase, G1/S phase or asynchronous cells were simultaneously released from their different phase of cell cycle, and then either mock infected or infected with 0.5 MOI of TGEV, cell cycle profiles were determined by flow cytometry and TGEV gRNA and sgRNAs levels were determined by qRT-PCR at 18 h p.i. key: cord-326349-59566vqe authors: Ding, Li; Huang, Yong; Dai, Meiling; Zhao, Xiaomin; Du, Qian; Dong, Feng; Wang, Lili; Huo, RuiChao; Zhang, Wenlong; Xu, Xingang; Tong, Dewen title: Transmissible gastroenteritis virus infection induces cell cycle arrest at S and G2/M phases via p53-dependent pathway date: 2013-12-26 journal: Virus Res DOI: 10.1016/j.virusres.2013.09.036 sha: doc_id: 326349 cord_uid: 59566vqe p53 signaling pathway plays an important role in the regulation of cell cycle.


id: cord-291754-1zxztadu
author: Zhao, Ye
date: 2019-10-15
extension: .txt
mime: text/plain
words: 6873
sentence: 225
flesch: 43
cache: cache/cord-291754-1zxztadu.txt
txt: txt/cord-291754-1zxztadu.txt
title:
  Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure

summary:
  The cDNA samples were submitted for SYBR Green I real-time RT-qPCR to detect the viral load for IBV N gene as described before (Zhao et al., 2015) . 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.


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
extension: .txt
mime: text/plain
words: 3857
sentence: 130
flesch: 42
cache: cache/cord-284866-66azyje4.txt
txt: txt/cord-284866-66azyje4.txt
summary:
  Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? Ribosome traffic in E. coli and regulation of gene expression Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts Hepatitis A virus: from discovery to vaccines Bayesian coalescent inference of Hepatitis A virus populations: evolutionary rates and patterns Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity Identification of amino acids located in the antibody binding sites of human hepatitis A virus Antigenic structure of human hepatitis A virus defined by analysis of escape mutants selected against murine monoclonal antibodies Codon usage and replicative strategies of hepatitis A virus Picornaviridae: the viruses and their replication Mononucleotide and dinucleotide frequencies, and codon usage in poliovirus RNA Evidence for quasispecies distributions in the human Hepatitis A virus genome Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity Codon usage in regulatory genes in Escherichia coli not reflect selection for rare codons An evolutionary perspective on synonymous codon usage in unicellular organisms Neutralization escape mutants define a dominant immunogenic neutralization site on Hepatitis A virus Analysis of synonymous codon usage in classical swine fever virus Analysis of codon usage bias and base compositional constraints in iridovirus genomes Genome rhetoric and the emergence of compositional bias Free Statistics Software, Office for Research Development and Education, version 1.1.23-r5 Low efficiency of the 5 nontranslated region of hepatitis A virus RNA in directing cap-independent translation in permissive monkey kidney cells Hepatitis A and the molecular biology of picornaviruses: a case for a new genus of the family Picornaviridae Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in Coronaviruses The effective number of codons used in a gene Analysis of synonymous codon usage in 11 Human Bocavirus isolates Mutation pressures shapes codon usage in the GC-rich genome of foot-and-mouth disease virus Analysis of synonymous codon usage in H5N1 virus and Genomic analysis of Influenza A viruses, including Avian Flu (H5N1) strains Activity of the Hepatitis A virus IRES requires association between the Cap-binding translation initiation factor (eIF4E) and eIF4G Fine-tuning translation kinetics selection as the driving force of codon usage bias in the Hepatitis A virus capsid Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability Coding biases and viral fitness Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region Virus attenuation by genome-scale changes in codon pair bias An evaluation of measures of synonymous codon usage bias Genetic variability and molecular evolution of Hepatitis A virus MUSCLE: a multiple sequence alignment method with reduced time and space complexity Theory and Applications of Correspondence Analysis Initial sequencing and analysis of the human genome Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus What drives codon choices in human genes?


id: cord-275182-cmjfqkjz
author: Cruz, Jazmina L.G.
title: Vectored vaccines to protect against PRRSV
date: 2010-06-25
extension: .txt
mime: text/plain
words: 8365
sentence: 327
flesch: 38
cache: cache/cord-275182-cmjfqkjz.txt
txt: txt/cord-275182-cmjfqkjz.txt
summary:
  A recombinant PRV, based on the attenuated Bartha strain, was constructed expressing PRRSV GP5 protein (Qiu et al., 2005) . Animals inoculated with the recombinant PRV expressing PRRSV proteins developed NAbs before the challenge.


id: cord-346264-hnwgzt6v
author: Nagai, Makoto
title: Porcine sapoviruses: Pathogenesis, epidemiology, genetic diversity, and diagnosis
date: 2020-05-26
extension: .txt
mime: text/plain
words: 2019
sentence: 71
flesch: 50
cache: cache/cord-346264-hnwgzt6v.txt
txt: txt/cord-346264-hnwgzt6v.txt
summary:
  Porcine SaV replicated in the villous epithelial cells, but not crypt cells, mainly in duodenum, less in jejunum and the least in ileum, but not in the large intestines as determined by immunofluorescent assays (IFA) using pig hyperimmune antisera against porcine SaV Cowden strain. The binding of porcine SaV or virus-like particles or bile acids alone to LLC-PK cells caused the dissociation of TJs and exposed occludin for PoSaV binding.


id: cord-335706-lopcb77c
author: Tan, Feifei
date: 2011-03-24
extension: .txt
mime: text/plain
words: 6418
sentence: 241
flesch: 46
cache: cache/cord-335706-lopcb77c.txt
txt: txt/cord-335706-lopcb77c.txt
title:
  Identification of non-essential regions in nucleocapsid protein of porcine reproductive and respiratory syndrome virus for replication in cell culture

summary:
  N protein is assembled into an icosahedral nucleocapsid in the form of disulfide-linked homodimer , and the Cterminal half of PRRSV N protein is believed to be the dimerization domain (Spilman et al., 2009) . In this study, serial N- and C-terminal truncations of N protein were performed in the context of type 2 PRRSV infectious cDNA clone, and our results revealed that a stretch of inter-genotypic variable N terminal residues aa 5–13 ((5)NGKQQKKK(13)K) and the last four inter-genotypic variable aa residues ((120)SPS(123)A) at the C terminus of N protein were dispensable for type 2 PRRSV infectivity.


id: cord-285180-32bxx94u
author: Lee, Sunhee
date: 2015-10-02
extension: .txt
mime: text/plain
words: 7663
sentence: 240
flesch: 33
cache: cache/cord-285180-32bxx94u.txt
txt: txt/cord-285180-32bxx94u.txt
title:
  Functional characterization and proteomic analysis of the nucleocapsid protein of porcine deltacoronavirus

summary:
  These observations demonstrated that, like N proteins of other coronaviruses, PDCoV N protein is mostly distributed in the nucleolus along with the cytoplasm and has a conserved subcellular localization property. Similar to N proteins of other coronaviruses, the PDCoV N protein was found to interact with itself to form non-covalently linked oligomers and was mainly localized to the nucleolus.


id: cord-325973-e3rxr6oq
author: Navarro, Ryan
date: 2017-08-15
extension: .txt
mime: text/plain
words: 3836
sentence: 144
flesch: 51
cache: cache/cord-325973-e3rxr6oq.txt
txt: txt/cord-325973-e3rxr6oq.txt
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

summary:
  The clustering patterns of KNA CCoV strains were validated by creating ML trees with other mathematical models, such as the Jukes-Cantor model, Kimura 2-parameter model, and Hasegawa-Kishino-Yano model (data not shown). Based on analysis of the M-and/or S-protein encoding genes, CCoV strains have been classified into at least two genotypes, CCoV-I and CCoV-II Buonavoglia, 2008, 2011) .


id: cord-332317-wrztpeb8
author: Zhang, Xin
date: 2015-03-16
extension: .txt
mime: text/plain
words: 3986
sentence: 168
flesch: 42
cache: cache/cord-332317-wrztpeb8.txt
txt: txt/cord-332317-wrztpeb8.txt
title:
  Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus

summary:
  To confirm the interaction between N protein of TGEV and cellular vimentin, immunoprecipitation assay was utilized to identify whether TGEV N protein interacted with cellular vimentin in TGEVinfected ST cells. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication.


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
extension: .txt
mime: text/plain
words: 6097
sentence: 176
flesch: 30
cache: cache/cord-276198-psjua913.txt
txt: txt/cord-276198-psjua913.txt
summary:
  related to the replication of potato virus M (PVM) Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1 -phosphate dephosphorylation by a conserved domain of nsP3 Properly folded nonstructural polyprotein directs the semliki forest virus replication complex to the endosomal compartment Functional and genetic analysis of coronavirus replicase-transcriptase proteins A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids Alternate, virusinduced membrane rearrangements support positive-strand RNA virus genome replication Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3 Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I-and EDEM1-containing membranes Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex Lymphoid organ virus of Penaeus monodon from Australia Genetic analysis of Murine hepatitis virus nsp4 in virus replication A new cistron in the murine hepatitis virus replicase gene Remodeling the endoplasmic reticulum by poliovirus infection and by individual viral proteins: an autophagy-like origin for virus-induced vesicles The SARS-unique domain (SUD) of SARS coronavirus contains two macrodomains that bind G-quadruplexes Induction of intracellular membrane rearrangements by HAV proteins 2C and 2BC A new nidovirus (NamDinh virus NDiV): its ultrastructural characterization in the C6/36 mosquito cell line Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells Mouse hepatitis coronavirus RNA replication depends on GBF1-mediated ARF1 activation Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome Composition and threedimensional architecture of the dengue virus replication and assembly sites Structure of the X (ADRP) domain of nsp3 from feline coronavirus Papain-like protease 1 from transmissible gastroenteritis virus: crystal structure and enzymatic activity toward viral and cellular substrates Electron microscopic study of tissue cultures infected with simian haemorrhagic fever virus Crystal structures of two coronavirus ADP-ribose-1 -monophosphatases and their complexes with ADP-Ribose: a systematic structural analysis of the viral ADRP domain Crystal structure of the C-terminal cytoplasmic domain of non-structural protein 4 from mouse hepatitis virus A59 Coronavirus replication does not require the autophagy gene ATG5 Recent progress in studies of arterivirus-and coronavirus-host interactions An insect nidovirus emerging from a primary tropical rainforest This work was supported by the Swiss National Science Foundation (SNF; project 149784; VT and PV) and a studentship from the Iraqi Ministry of Higher Education and Scientific Research (HA). These observations parallel the ones seen for MHV but raise further questions whether this feature is even more widespread amongst +RNA viruses.


id: cord-347270-x05tfkgx
author: Lu, Shuai
date: 2017-06-02
extension: .txt
mime: text/plain
words: 3165
sentence: 105
flesch: 42
cache: cache/cord-347270-x05tfkgx.txt
txt: txt/cord-347270-x05tfkgx.txt
title:
  Discovery of a novel canine respiratory coronavirus support genetic recombination among betacoronavirus1

summary:
  Another previously described CRCoV strain, K37, was identified to have arisen from recombination between CRCoV-BJ232 and BCoV. key: cord-347270-x05tfkgx authors: Lu, Shuai; Wang, Yanqun; Chen, Yingzhu; Wu, Bingjie; Qin, Kun; Zhao, Jincun; Lou, Yongliang; Tan, Wenjie title: Discovery of a novel canine respiratory coronavirus support genetic recombination among betacoronavirus1 date: 2017-06-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.05.006 sha: doc_id: 347270 cord_uid: x05tfkgx


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
extension: .txt
mime: text/plain
words: 3335
sentence: 123
flesch: 48
cache: cache/cord-347924-w06ho8sn.txt
txt: txt/cord-347924-w06ho8sn.txt
summary:
  The levels of circulating CD4 + T cells of 10 patients ranged from 10.89 to 21.46% while the levels of circulating CD8 + T cells ranged from 6.66 to 21.03%. T cells were measured by using ELISPOT assay and ICS assay (intracellular cytokine straining), respectively.


id: cord-281101-gv1sgbk1
author: Shin, Gu-Choul
date: 2006-08-30
extension: .txt
mime: text/plain
words: 5936
sentence: 191
flesch: 42
cache: cache/cord-281101-gv1sgbk1.txt
txt: txt/cord-281101-gv1sgbk1.txt
title:
  Preparation and characterization of a novel monoclonal antibody specific to severe acute respiratory syndrome-coronavirus nucleocapsid protein

summary:
  SARS N proteins exist as phosphorylated forms in mature viral particles, whereas, in host cells, this protein exists in both the dephosphorylated form and the phosphorylated form (Kalicharran and Dales, 1995; Surjit et al., 2005) . Three IgG(2b) mAbs were recognized within the N-terminus of N protein, whereas the epitope of two IgG(1) mAbs localized within the C-terminus.


id: cord-317061-0bx704ao
author: Wu, Andong
date: 2015-10-02
extension: .txt
mime: text/plain
words: 6019
sentence: 197
flesch: 45
cache: cache/cord-317061-0bx704ao.txt
txt: txt/cord-317061-0bx704ao.txt
title:
  Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus

summary:
  The substrate specificity of coronaviruses 3CLpro is determined by the residues from P4 to P2 positions of cleavage sites, especially depending on the P1, P2 and P1 positions, which would benefit the prediction of cleavage site and design the broadspectrum inhibitors of coronaviruses 3CLpro (Chuck et al., 2011; Hegyi and Ziebuhr, 2002) . Our study points out a new direction regarding the prediction and identification of cleavage sites of proteases and contributes to understanding the mechanism of coronaviral polyprotein processing.


id: cord-346104-18x8u2oe
author: Black, Wendy
title: Identification of gammaherpesvirus infection in free-ranging black bears (Ursus americanus)
date: 2019-01-02
extension: .txt
mime: text/plain
words: 5167
sentence: 211
flesch: 49
cache: cache/cord-346104-18x8u2oe.txt
txt: txt/cord-346104-18x8u2oe.txt
summary:
  Interestingly, black bear herpesvirus infections were also found in bears without neurological signs. shown in Fig. 6 , the amplicons from bear tissues and UrHV-1 branch out together and have smaller distance to members of Rhadinvirus, such as HHV-8 and Rhadinovirus 1 (RHV-1).


id: cord-302083-9q1i20o6
author: Jung, Kwonil
date: 2020-06-02
extension: .txt
mime: text/plain
words: 9129
sentence: 231
flesch: 35
cache: cache/cord-302083-9q1i20o6.txt
txt: txt/cord-302083-9q1i20o6.txt
title:
  Porcine epidemic diarrhea virus (PEDV): An update on etiology, transmission, pathogenesis, and prevention and control

summary:
  In infected conventional weaned to feeder pigs (21-56-day-old), a few (<5%) to all of the inoculated pigs began to show diarrhea at PID 1-4, which coincided with or was detected 1-2 days later than the first detection of viral RNA in feces (Gallien et al., 2018a; Gerber et al., 2016; Jung et al., 2015a; Lohse et al., 2017; Madson et al., 2014; Niederwerder et al., 2016; Thomas et al., 2015a) (Table 1) . PEDV antigens were also frequently detected in the intestinal crypt cells or antigen presenting cells, such as macrophages, in the lamina propria or Peyer's patches (Debouck et al., 1981; Jung et al., 2014; Lin et al., 2015a; Madson et al., 2016; Stevenson et al., 2013; Sueyoshi et al., 1995) .


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
extension: .txt
mime: text/plain
words: 7476
sentence: 200
flesch: 22
cache: cache/cord-295099-ghc85pf5.txt
txt: txt/cord-295099-ghc85pf5.txt
summary:
  The gp120 or gp41 proteins are not ideal probes, because they are reactive with many HIV-1 antibodies, including non-neutralizing but strong binding antibodies (Wu et al., 2010; Wu et al., 2015; Zhou et al., 2015) . This observation suggests that extraordinary variation in antibody immunity may only occur within a few antibody lineages − or even a single lineage (Wu et al., 2015) .


id: cord-279849-zzkliu76
author: DaPalma, T.
title: A systematic approach to virus–virus interactions
date: 2010-01-20
extension: .txt
mime: text/plain
words: 8236
sentence: 243
flesch: 24
cache: cache/cord-279849-zzkliu76.txt
txt: txt/cord-279849-zzkliu76.txt
summary:
  on a worldwide geographical scale Upregulation of human cytomegalovirus by HIV type 1 in human lymphoid tissue ex vivo An equine infectious anemia virus variant superinfects cells through novel receptor interactions Specific inhibition of the PKR-mediated antiviral response by the murine cytomegalovirus proteins m142 and m143 Herpes simplex virus types 1 and 2 completely help adenovirus-associated virus replication Recombination in HIV: an important viral evolutionary strategy A prospective study of dengue infections in Bangkok Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection Genital herpes and human immunodeficiency virus: double trouble The interaction between herpes simplex virus and human immunodeficiency virus Nonreciprocal pseudotyping: murine leukemia virus proteins cannot efficiently package spleen necrosis virus-based vector RNA Memory CD8+ T cells in heterologous antiviral immunity and immunopathology in the lung Specific history of heterologous virus infections determines anti-viral immunity and immunopathology in the lung Anatomical mapping of human herpesvirus reservoirs of infection Systemic movement of a movement-deficient strain of Cucumber mosaic virus in zucchini squash is facilitated by a cucurbit-infecting potyvirus Reactivation and recombination of multiple cytomegalovirus strains from individual organ donors A viral epitope that mimics a self antigen can accelerate but not initiate autoimmune diabetes Coxsackie B virus infection and onset of childhood diabetes Dynamic effects of antibody-dependent enhancement on the fitness of viruses A case-control study of group B Coxsackievirus immunoglobulin M antibody prevalence and HLA-DR antigens in newly diagnosed cases of insulin-dependent diabetes mellitus Maternal enteroviral infection during pregnancy as a risk factor for childhood IDDM. The phenomenon of ADE is not unique to dengue virus infections.


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
extension: .txt
mime: text/plain
words: 8333
sentence: 251
flesch: 32
cache: cache/cord-294764-v28wbrqp.txt
txt: txt/cord-294764-v28wbrqp.txt
summary:
  Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin Characterization of lethal Zika virus infection in AG129 mice Development of a reverse-genetics system for murine norovirus 3: long-term persistence occurs in the caecum and colon Favipiravir elicits antiviral mutagenesis during virus replication in vivo Norovirus polymerase fidelity contributes to viral transmission in vivo Norovirus vaccine against experimental human Norwalk virus illness In vitro proteolytic processing of the MD145 norovirus ORF1 nonstructural polyprotein yields stable precursors and products similar to those detected in calicivirus-infected cells Norovirus proteinase-polymerase and polymerase are both active forms of RNA-dependent RNA polymerase Chronic norovirus gastroenteritis in a double hematopoietic stem cell and lung transplant recipient Rapid evolution of pandemic noroviruses of the GII.4 lineage Caliciviruses differ in their functional requirements for eIF4F components High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors Chronic diarrhea associated with persistent norovirus excretion in patients with chronic lymphocytic leukemia: report of two cases Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late Interferons and ribavirin effectively inhibit Norwalk virus replication in replicon-bearing cells Stable expression of a Norwalk virus RNA replicon in a human hepatoma cell line Structural basis for initiation of transcription from an RNA polymerase-promoter complex Norovirus infection as a cause of diarrhea-associated benign infantile seizures Organization and expression of calicivirus genes Antiviral activity of nucleoside analogues against norovirus Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases The genome-linked protein VPg of the Norwalk virus binds eIF3, suggesting its role in translation initiation complex recruitment Antiviral, antimetabolic and antineoplastic activities of 2 -or 3 -amino or -azido-substituted deoxyribonucleosides Viral shape-shifting: norovirus evasion of the human immune system Failure to detect norovirus in a large group of asymptomatic individuals by Adjuvanted intranasal Norwalk virus-like particle vaccine elicits antibodies and antibody-secreting cells that express homing receptors for mucosal and peripheral lymphoid tissues A fluorescence-based high-throughput screen to identify small compound inhibitors of the genotype 3a hepatitis C virus RNA polymerase Nonnucleoside inhibitors of norovirus RNA polymerase: scaffolds for rational drug design Norwalk virus nonstructural protein p48 forms a complex with the SNARE regulator VAP-A and prevents cell surface expression of vesicular stomatitis virus G protein Replication of human noroviruses in stem cell-derived human enteroids Norwalk virus N-terminal nonstructural protein is associated with disassembly of the golgi complex in transfected cells Poly(A)-and primer-independent RNA polymerase of Norovirus Mechanism of action of T-705 against influenza virus T-705 (favipiravir) and related compounds: novel broad-spectrum inhibitors of RNA viral infections Favipiravir (T-705), a novel viral RNA polymerase inhibitor The genome-linked protein VPg of vertebrate viruses-a multifaceted protein Epidemiology of foodborne norovirus outbreaks Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase Lack of norovirus replication and histo-blood group antigen expression in 3-dimensional intestinal epithelial cells The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity Development of a microsphere-based serologic multiplexed fluorescent immunoassay and a reverse transcriptase PCR assay to detect murine norovirus 1 infection in mice Persistent infection with and serologic cross-reactivity of three novel murine noroviruses Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants Inhibition of human immunodeficiency virus type I reverse transcriptase by suramin-related compounds The ambiguous base-pairing and high substrate efficiency of T-705 (favipiravir) ribofuranosyl 5 -triphosphate towards influenza A virus polymerase Biochemical evaluation of the inhibition properties of favipiravir and 2 -C-methyl-cytidine triphosphates against human and mouse norovirus RNA polymerases New mouse model for dengue virus vaccine testing Enteric bacteria promote human and mouse norovirus infection of B cells Human norovirus culture in B cells Murine norovirus (MNV-1) exposure in vitro to the purine nucleoside analog Ribavirin increases quasispecies diversity Comparative murine norovirus studies reveal a lack of correlation between intestinal virus titers and enteric pathology STAT1-dependent innate immunity to a Norwalk-like virus Treatment of norovirus infections: moving antivirals from the bench to the bedside De novo initiation of viral RNA-dependent RNA synthesis Gastrointestinal norovirus infection associated with exacerbation of inflammatory bowel disease Inhibition of human norovirus by a viral polymerase inhibitor in the B cell culture system and in the mouse model Norwalk virus does not replicate in human macrophages or dendritic cells derived from the peripheral blood of susceptible humans Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases Increase in viral gastroenteritis outbreaks in Europe and epidemic spread of new norovirus variant Environmental transmission of norovirus gastroenteritis The evolution and transmission of epidemic GII.17 noroviruses Trends in statin use and low-density lipoprotein cholesterol levels among US adults: impact of the 2001 National Cholesterol Education Program guidelines Structure-based inhibition of norovirus RNA-dependent RNA polymerases Delivery of suramin as an antiviral agent through liposomal systems Norovirus regulation of the innate immune response and apoptosis occurs via the product of the alternative open reading frame 4 Norovirus RNA in the blood of a child with gastroenteritis and convulsions-a case report Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (−)sense genomic RNA: mapping of a subgenomic promoter The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site Crystal structure of norwalk virus polymerase reveals the carboxyl terminus in the active site cleft Suramin prevents duck hepatitis B virus infection in vivo Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins Challenges of culturing human norovirus in three-dimensional organoid intestinal cell culture models Noroviruses: a comprehensive review Picornaviral polymerase structure, function and fidelity modulation Synthesis and pharmacokinetics of valopicitabine (NM283), an efficient prodrug of the potent anti-HCV agent 2 -C-methylcytidine X-ray crystallographic structure of the Norwalk virus capsid The approved pediatric drug suramin identified as a clinical candidate for the treatment of EV71 infection-suramin inhibits EV71 infection in vitro and in vivo Norovirus virus-like particle vaccines for the prevention of acute gastroenteritis Inhibition of norovirus replication by the nucleoside analogue 2 -C-methylcytidine Favipiravir (T-705) inhibits in vitro norovirus replication The norovirus RdRp (NS7) is the central enzyme in norovirus RNA replication.


id: cord-333180-xevie6tm
author: Neumann, Simon
title: How do viruses control mitochondria-mediated apoptosis?
date: 2015-11-02
extension: .txt
mime: text/plain
words: 9416
sentence: 261
flesch: 31
cache: cache/cord-333180-xevie6tm.txt
txt: txt/cord-333180-xevie6tm.txt
summary:
  They are present in various members of the Poxviridae (F1L, N1L, M11L, A179L, ORFV125), Herpesviridae (BHRF1, BALF1, vMIA, KSBcl-2, MHVBcl-2), Adenoviridae (E1B-19K) and Birnaviridae (VP5) family of viruses ( Fig. 2) (Benedict et al., 2002; Galluzzi et al., 2008; Postigo and Ferrer, 2009 ). But while the L4-100K protein also potently inhibited granzyme B-mediated cell death (Andrade et al., 2001) , this could not be effectively observed with cells overexpressing CrmA or Serp2 or infected with poxviruses (Müllbacher et al., 1999; Barry et al., 2000; Screpanti et al., 2001; Pardo et al., 2009a Pardo et al., , 2009b .


id: cord-291086-goidlh08
author: Walker, Peter J.
title: Rhabdovirus accessory genes
date: 2011-09-14
extension: .txt
mime: text/plain
words: 12151
sentence: 358
flesch: 33
cache: cache/cord-291086-goidlh08.txt
txt: txt/cord-291086-goidlh08.txt
summary:
  Is not required for viral replication Endogenous viral elements in animal genomes Antiviral immunity in drosophila Kotonkan, a new rhabdovirus related to Mokola virus of the rabies serogroup Complete nucleotide sequence of the hirame rhabdovirus, a pathogen of marine fish Matrix protein and another viral component contribute to induction of apoptosis in cells infected with vesicular stomatitis virus Normal replication of vesicular stomatitis virus without C proteins Molecular cloning of the six mRNA species of infectious hematopoietic necrosis virus, a fish rhabdovirus, and gene order determination by R-loop mapping Distribution and variation of NV genes in fish rhabdoviruses Characterization of infectious hematopoietic necrosis virus mRNA species reveals a nonvirion rhabdovirus protein Sendai virus C proteins are categorically nonessential gene products but silencing their expression severely impairs viral replication and pathogenesis Isolation and characterization of a tupaia rhabdovirus Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences Shimoni bat virus, a new representative of the Lyssavirus genus The rhabdoviruses: biodiversity, phylogenetics, and evolution Complete genomes of Aravan, Khujand Irkut and West Caucasian bat viruses, with special attention to the polymerase gene and non-coding regions Gene 2 of the sigma rhabdovirus genome encodes the P protein, and gene 3 encodes a protein related to the reverse transcriptase of retroelements The origins of defective interfering particles of the negative-strand RNA viruses Vesicular stomatitis Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny Rhabdoviruses in two species of Drosophila: vertical transmission and a recent sweep Evidence for recombination in Crimean-Congo hemorrhagic fever virus Sequence of mouse hepatitis virus A59 mRNA 2 Indications for RNA recombination between coronaviruses and influenza C virus Analysis of nucleotide sequence of Iranian maize mosaic virus confirms its identity as a distinct nucleorhabdovirus Genome organization and transcription strategy in the complex GNS-L intergenic region of bovine ephemeral fever rhabdovirus The '30K' superfamily of viral movement proteins A host-factor interaction and localization map for a plant-adapted rhabdovirus implicates cytoplasm-tethered transcription activators in cell-to-cell movement Structure and transcription of the glycoprotein gene of attenuated HEP-Flury strain of rabies virus The glycoprotein of Thogoto virus (a tick-borne orthomyxo-like virus) is related to the baculovirus glycoprotein GP64 Nucleocytoplasmic distribution of rabies virus P protein is regulated by phosphorylation adjacent to C-terminal nuclear import and export signals Dual modes of rabies P-protein association with microtubules: a novel strategy to suppress the antiviral response Isolation of chikungunya virus from Aedes aegypti mosquitoes collected in the town of Yawat Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein Accessory genes of the paramyxoviridae, a large family of nonsegmented negative-strand RNA viruses, as a focus of active investigation by reverse genetics Nucleocytoplasmic shuttling of the rabies virus P protein requires a nuclear localization signal and a CRM1-dependent nuclear export signal Vesicular stomatitis virus induces apoptosis primarily through Bak rather than Bax by inactivating Mcl-1 and Bcl-XL Identification of a set of proteins (C and C) encoded by the bicistronic P gene of the Indiana serotype of vesicular stomatitis virus and analysis of their effect on transcription by the viral RNA polymerase Origin and replication of defective interfering particles Translational termination-reinitiation in RNA viruses F gene recombination between genotype II and VII Newcastle disease virus A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh Rabies virus glycoprotein gene contains a long 3 noncoding region which lacks pseudogene properties Plant rhabdoviruses Shotgun sequencing of the negative-sense RNA genome of the rhabdovirus maize mosaic virus Taro vein chlorosis virus: characterization and variability of a new nucleorhabdovirus Genetic dissection of interferon-antagonistic functions of rabies virus phosphoprot inhibition of interferon regulatory factor 3 activation. Secondary structure predictions have shown that the SYNV sc4, LNYV 4b, LYMoV P3, MMV P3, MFSV P4, RYSV P3 and PYDV Y proteins have some structural similarities in common with those of the '30K' superfamily of plant virus movement proteins (Melcher, 2000) .


id: cord-304424-048xo7jn
author: Greninger, Alexander L.
title: A decade of RNA virus metagenomics is (not) enough
date: 2018-01-15
extension: .txt
mime: text/plain
words: 9614
sentence: 265
flesch: 26
cache: cache/cord-304424-048xo7jn.txt
txt: txt/cord-304424-048xo7jn.txt
summary:
  Mining of publicly available transcriptome data has contributed greatly to the discovery of novel RNA viruses (Basler et al., 2005; Schomacker et al., 2004) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates.


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
extension: .txt
mime: text/plain
words: 15779
sentence: 492
flesch: 32
cache: cache/cord-344084-z4t2wkgk.txt
txt: txt/cord-344084-z4t2wkgk.txt
summary:
  Besides, the regulation of multiple aspects of the immune system is strongly influenced by EVs (O'Neill and Quah, 2008; Colombo et al., 2014; Ellwanger et al., 2016) . This knowledge gap should be addressed in further studies since the reemergence of ROCV in Brazil is a concern in terms of public health (Figueiredo, 2007; Ellwanger et al., 2017b) .


