# bib

id: cord-254291-y8xvh6hs
author: Yamanaka, Miles
title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus
date: 1998
extension: .txt
mime: text/plain
words: 833
sentence: 38
flesch: 63
cache: cache/cord-254291-y8xvh6hs.txt
txt: txt/cord-254291-y8xvh6hs.txt
summary:
  A related sequence, CTAAAT, is present upstream of FIPV ORF 3b. In contrast, an amber codon limits FIPV ORF 3b to only 40 residues while ORF 3b of the Purdue strain of TGEV extends 244 amino acids (3) .


id: cord-303834-yqysedne
author: Ducatez, Mariette F.
title: Full genome sequence of guinea fowl coronavirus associated with fulminating disease
date: 2015-02-25
extension: .txt
mime: text/plain
words: 1260
sentence: 57
flesch: 54
cache: cache/cord-303834-yqysedne.txt
txt: txt/cord-303834-yqysedne.txt
summary:
  GfCoV S gene was indeed more closely related to TCoV S than to IBV S genes but also more distinct to both viruses on the S gene than on the rest of its genome (\50 % identity for IBV and 65-90 % identity with TCoV S genes, Fig. 1b) , suggesting a recombination event as was hypothesized for the origin of TCoV The sequences generated that matched with avian CoVs sequences, as determined using GAAS software [7] , were extracted for further analysis and visualized using integrative genomics viewer (IGV) with the closest blast hit as reference genome: TCoV MG10 (accession number: EU095850)


id: cord-288239-ca5uthvd
author: Jeoung, Hye-Young
title: Three clusters of bovine kobuvirus isolated in Korea, 2008–2010
date: 2011-03-12
extension: .txt
mime: text/plain
words: 1268
sentence: 57
flesch: 62
cache: cache/cord-288239-ca5uthvd.txt
txt: txt/cord-288239-ca5uthvd.txt
summary:
  The nucleotide sequences of Korean bovine kobuvirus strains were deposited in GenBank as accession numbers HQ650164-HQ650200 (Table 1) . The results indicated that Korean bovine kobuvirus has diverse lineages regardless of disease status and species.


id: cord-333914-c150ki1n
author: Koba, Ryota
title: Identification and characterization of a novel bat polyomavirus in Japan
date: 2020-08-20
extension: .txt
mime: text/plain
words: 1687
sentence: 70
flesch: 46
cache: cache/cord-333914-c150ki1n.txt
txt: txt/cord-333914-c150ki1n.txt
summary:
  The aims of this study were to (i) determine the presence of PyVs in Japanese bats, (ii) characterize the genomic structure of bat PyVs, and (iii) analyze the evolutionary relationships between the bat PyV detected in this study and other known bat PyVs. The nucleotide sequence identity of the genome with those of other bat PyVs was less than 80%.


id: cord-295554-0pzjyrdf
author: Lima, Francisco Esmaile de Sales
date: 2013-03-16
extension: .txt
mime: text/plain
words: 1788
sentence: 76
flesch: 52
cache: cache/cord-295554-0pzjyrdf.txt
txt: txt/cord-295554-0pzjyrdf.txt
title:
  Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil

summary:
  In this initial study, samples were restricted in location and variety of bat species, and we found only alphacoronaviruses. Additional studies with larger numbers of bats and bat species, as well as the continued vigilance on the occurrence of viral infections in bats over the years is required to follow the evolution of bat coronaviruses in its interactions with the different bat host species.


id: cord-269340-o9jdt86j
author: Callison, Scott Andrew
date: 1999
extension: .txt
mime: text/plain
words: 2118
sentence: 85
flesch: 54
cache: cache/cord-269340-o9jdt86j.txt
txt: txt/cord-269340-o9jdt86j.txt
title:
  Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding

summary:
  This suggests that the interaction between S1 and S2 subunits may determine the shape or availability of S1 subunit speci®c epitopes. Whether the S2 subunit is actually involved in S1 subunit speci®c antibody recognition, sterically hinders antibody from binding to the S1 subunit, or effects the presentation of S1 subunit epitopes is not known.


id: cord-005207-02wmt2e9
author: Lee, Hee-Kyung
title: Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99
date: 2003
extension: .txt
mime: text/plain
words: 2171
sentence: 83
flesch: 55
cache: cache/cord-005207-02wmt2e9.txt
txt: txt/cord-005207-02wmt2e9.txt
summary:
  [10] previously cloned a gene of 1326 nucleotides in a single large ORF capable of encoding a 441 amino acid protein of 49 kDa from PEDV CV777 and Br1/87, which were very similar Nucleotide Sequence of PEDV N gene in both length and sequence to coronavirus N proteins, and therefore represented it as the PEDV N gene. Chinju99 N gene also had 96.8% amino acid sequence identity with that of CV777 and Br1/87


id: cord-282126-gmjnbnx5
author: Yang, Limin
date: 2012-08-07
extension: .txt
mime: text/plain
words: 2140
sentence: 94
flesch: 55
cache: cache/cord-282126-gmjnbnx5.txt
txt: txt/cord-282126-gmjnbnx5.txt
title:
  Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1

summary:
  After a comparison of different DHAV-1 subgroup genomes, the conserved domain 2C of the genome was selected as the domain for LAMP primer design and was used for screening a group of primers with good amplification efficiency. DHAV-1 total RNA concentration was measured spectrophotometrically at A260 and A280.


id: cord-299573-vq6ckqtd
author: Lee, Meong-Hun
title: Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea
date: 2012-09-11
extension: .txt
mime: text/plain
words: 1966
sentence: 119
flesch: 63
cache: cache/cord-299573-vq6ckqtd.txt
txt: txt/cord-299573-vq6ckqtd.txt
summary:
  It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well. The clinical significance of PAstV infection remains to be clarified.


id: cord-311204-fc12f845
author: Zhou, Ling
title: Full-length genomic characterization and molecular evolution of canine parvovirus in China
date: 2016-04-02
extension: .txt
mime: text/plain
words: 2237
sentence: 120
flesch: 62
cache: cache/cord-311204-fc12f845.txt
txt: txt/cord-311204-fc12f845.txt
summary:
  To further examine CPV-2 isolates, we used a larger dataset composed only of VP2 protein sequences. In this study, molecular phylogenetic analysis of CPV-NY-14 and other CPV-2 isolates in GenBank revealed that CPV-NY-14 is closely related to isolates s5, SC02-11, LZ1, LZ2, and nj01-06, especially isolate LZ2.


id: cord-266634-bww62vx8
author: Gopinath, M.
date: 2015-10-07
extension: .txt
mime: text/plain
words: 2307
sentence: 90
flesch: 50
cache: cache/cord-266634-bww62vx8.txt
txt: txt/cord-266634-bww62vx8.txt
title:
  Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

summary:
  In the present work, we present evidence for N 7 guanine methyl transferase activity of RPV L protein and further demonstrate that this activity is localized to aa 1717-2183 of L protein indicating the modular nature of the RdRP. Sequence alignment of RPV L protein with 2 0 -O-methyl transferase from other species revealed the conservation of KDKE tetrad suggesting the presence of this motif in domain III of RPV L protein (Fig. 1a) .


id: cord-263489-i4tkdgy4
author: Suo, Siqingaowa
date: 2015-05-27
extension: .txt
mime: text/plain
words: 2222
sentence: 107
flesch: 61
cache: cache/cord-263489-i4tkdgy4.txt
txt: txt/cord-263489-i4tkdgy4.txt
title:
  Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential

summary:
  Herein, we use similar technology and advance previous work by using the rS-AD as an immobilizing target to select phages from a peptide display library, with diagnostic potential for TGEV. key: cord-263489-i4tkdgy4 authors: Suo, Siqingaowa; Wang, Xue; Zarlenga, Dante; Bu, Ri-e; Ren, Yudong; Ren, Xiaofeng title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 journal: Virus Genes DOI: 10.1007/s11262-015-1208-7 sha: doc_id: 263489 cord_uid: i4tkdgy4 The spike (S) protein of porcine transmissible gastroenteritis virus (TGEV) is located within the viral envelope and is the only structural protein that possesses epitopes capable of inducing virus-neutralizing antibodies.


id: cord-257122-h3zi8k8g
author: Lin, Chao-Nan
title: Full genome analysis of a novel type II feline coronavirus NTU156
date: 2012-12-14
extension: .txt
mime: text/plain
words: 2384
sentence: 108
flesch: 58
cache: cache/cord-257122-h3zi8k8g.txt
txt: txt/cord-257122-h3zi8k8g.txt
summary:
  When the sequences around the putative recombination sites were examined, i.e., one located in the 5 0 region (strain 79-1146) and two in the 3 0 region (strain 79-1146, and 79-1683), porcine coronavirus (TGEV) was also found to contribute to the evolution of type II FCoV (in addition to CCoV) This finding is not surprising because the receptor for type II FCoV, feline aminopeptidase N, has been found to serve as a receptor for several CoVs, including canine, porcine, and human CoVs [30] .


id: cord-328518-umvk59dc
author: Lee, Dana N.
title: Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma
date: 2019-12-03
extension: .txt
mime: text/plain
words: 2384
sentence: 99
flesch: 51
cache: cache/cord-328518-umvk59dc.txt
txt: txt/cord-328518-umvk59dc.txt
summary:
  Phylogenetic analysis of these fragments confirmed our isolates were from the genus Mastadenovirus and had genetic diversity ranging from 20 to 50% when compared to other bat adenoviruses. Viruses in bats can switch hosts to other bat species [4] and they are known to carry pathogenic viruses that can infect humans such as rabies, lyssaviruses, nipah and hendra viruses, ebola, and


id: cord-012091-3bo88tux
author: Ibrahim, Madiha Salah
title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1)
date: 2011-02-17
extension: .txt
mime: text/plain
words: 2497
sentence: 92
flesch: 44
cache: cache/cord-012091-3bo88tux.txt
txt: txt/cord-012091-3bo88tux.txt
summary:
  The scale bar represents the distance unit between sequence pairs b Virus Genes (2011) 42:363-368 367 Avian influenza virus (H5N1) outbreaks, Kuwait Epidemiological findings of outbreaks of disease caused by highly pathogenic H5N1 Avian influenza virus in poultry in Egypt during Characterization of an avian influenza virus H5N1 Egyptian isolate Highly pathogenic avian influenza virus subtype H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates Genomic signature of human versus avian influenza A viruses Properties and dissemination of H5N1 viruses isolated during an influenza outbreak in migratory waterfowl in western China Establishment of multiple sub-lineages of H5N1 influenza virus in Asia-implications for pandemic control Molecular and antigenic evolution and geographical spread of H5N1 highly pathogenic avian influenza viruses in western X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptors analogs BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Universal primer set for the full-length amplification of all influenza A viruses Pathology, molecular biology, and pathogenesis of avian influenza A (H5N1) infection in humans Selection of H5N1 influenza virus PB2 during replication in humans Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia Molecular characterization of the hemagglutinin and neuraminidase genes of H5N1 influenza A viruses isolated from poultry in Vietnam from OIE, Update on highly pathogenic avian influenza in animals (TYPE H5 and H7) A single amino acid in the PB2 gene of influenza A virus is a determinant of host range Emergence of amantadine-resistant influenza A viruses: epidemiological study MEGA 4: Molecular Evolutionary Genetic analysis (MEGA) software version 4.0 WHO, Continuing progress towards a unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses WHO, Cumulative number of confirmed human cases of Avian Influenza A/(H5N1) reported to WHO Acknowledgments This study was supported by the JSPS Postdoctoral Fellowship for Foreign Researchers and the Grant-in-Aid (Scientific Research (B) (Overseas Academic Research)), Japanese Society for the Promotion of Science, Japan. In this article, we directly sequenced and analyzed the complete genome sequences of H5N1 virus from the tissues of two host species; chicken and duck.


id: cord-322475-i29t7ce8
author: Chen, Xi
date: 2012-07-29
extension: .txt
mime: text/plain
words: 2810
sentence: 110
flesch: 49
cache: cache/cord-322475-i29t7ce8.txt
txt: txt/cord-322475-i29t7ce8.txt
title:
  Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China

summary:
  The underlines indicate amino acid mutations between strains Experimental infection of pigs with a new porcine enteric coronavirus, CV777 Porcine epidemic diarrhea, in Diseases of Swine Porcine epidemic diarrhoea virus as a cause of persistent diarrhoea in a herd of breeding and finishing pigs Letter to the Editor An immunoelectron microscopic and immunofluorescent study on the antigenic relationship between the coronavirus-like agent, CV777, and several coronaviruses Chinese-like strain of porcine epidemic diarrhea virus An outbreak of swine diarrhea of a new-type associated with coronavirus-like particles in Japan Molecular epidemiology of porcine epidemic diarrhea virus in China A new coronavirus-like particle associated with diarrhea in swine Propagation of the virus of porcine epidemic diarrhea in cell culture The genome organization of the Nidovirales: similarities and differences between arteri-, toro-, and coronaviruses The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus Major receptorbinding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein Sequence analysis of the partial spike glycoprotein gene of porcine epidemic diarrhea viruses isolated in Korea Coronaviruses: structure and genome expression The group-specific murine coronavirus genes are not essential, but their deletion, by reverse genetics, is attenuating in the natural host Efficacy of a transmissible gastroenteritis coronavirus with an altered ORF-3 gene Cloning and further sequence analysis of the ORF3 gene of wild-and attenuated-type porcine epidemic diarrhea viruses Porcine epidemic diarrhea Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses Differentiation of a Vero cell adapted porcine epidemic diarrhea virus from Korean field strains by restriction fragment length polymorphism analysis of ORF 3 Complete genome sequences of a Korean virulent porcine epidemic diarrhea virus and its attenuated counterpart Complete genome sequence of transmissible gastroenteritis coronavirus PUR46-MAD clone and evolution of the purdue virus cluster Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Acknowledgments This work was supported by Project Management for Agricultural Science and Technology Achievements Transformation Fund (2010GB2C400209), Science and Technology Major Project of Fujian (2010NZ0002-3), and National Spark Program (2011GA720005).


id: cord-303672-ujp78213
author: Gu, Wen-yuan
date: 2019-08-28
extension: .txt
mime: text/plain
words: 2705
sentence: 115
flesch: 47
cache: cache/cord-303672-ujp78213.txt
txt: txt/cord-303672-ujp78213.txt
title:
  Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells

summary:
  A conserved domain in the coronavirus membrane protein tail is important for virus assembly Heterogeneity in membrane protein genes of porcine epidemic diarrhea viruses isolated in China Modular organization of SARS coronavirus nucleocapsid protein Identification of a specific interaction between the coronavirus mouse hepatitis virus A59 nucleocapsid protein and packaging signal Effective inhibition of porcine epidemic diarrhea virus by RNA interference in vitro Small interfering RNA targeting M2 gene induces effective and long term inhibition of influenza A virus replication Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene A transgenic Marc-145 cell line of piggyBac transposon-derived targeting shRNA interference against porcine reproductive and respiratory syndrome virus Characterization and evolution of porcine deltacoronavirus in the United States Complete genome sequence of porcine deltacoronavirus isolated in Thailand in 2015 Porcine deltacoronavirus: overview of infection dynamics, diagnostic methods, prevalence and genetic evolution In-vitro inhibition of spring viremia of carp virus replication by RNA interference targeting the RNAdependent RNA polymerase gene Potential and development of inhaled RNAi therapeutics for the treatment of pulmonary tuberculosis Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 The cytopathogenicity assays demonstrated that pGenesil-M and pGenesil-N protected ST cells against pathological changes with high specificity and efficacy.


id: cord-268627-nnx46nwf
author: Ren, Xiaofeng
date: 2011-02-01
extension: .txt
mime: text/plain
words: 2777
sentence: 137
flesch: 55
cache: cache/cord-268627-nnx46nwf.txt
txt: txt/cord-268627-nnx46nwf.txt
title:
  Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus

summary:
  To the knowledge, this is the first report regarding the establishment and optimization of a RT-LAMP for PEDV N gene. Using PEDV RNA and six primers targeting the PEDV N gene, an RT-LAMP was done at 65°C in a water bath for 1 h.


id: cord-346643-os2kyvvf
author: Wang, Li
date: 2016-11-15
extension: .txt
mime: text/plain
words: 2959
sentence: 137
flesch: 53
cache: cache/cord-346643-os2kyvvf.txt
txt: txt/cord-346643-os2kyvvf.txt
title:
  Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene

summary:
  Non-transfected cells were used as a Virus Genes (2017) 53:226-232 227 control. The analysis of cytopathic effects demonstrated that pRNAT-2 and pRNAT-3 could protect PK-15 cells against pathological changes specifically and efficiently.


id: cord-259398-s8qsjkj2
author: Chouljenko, Vladimir N.
date: 1998
extension: .txt
mime: text/plain
words: 3190
sentence: 122
flesch: 54
cache: cache/cord-259398-s8qsjkj2.txt
txt: txt/cord-259398-s8qsjkj2.txt
title:
  Nucleotide and Predicted Amino Acid Sequences of All Genes Encoded by the 3′ Genomic Portion (9.5 kb) of Respiratory Bovine Coronaviruses and Comparisons Among Respiratory and Enteric Coronaviruses

summary:
  Strategy for cDNA construction and assembly of the 9.5 Kb cDNA sequence representing the 3 H -end of different BCV strains. Light-gray boxes contain RBCV-speci®c, dark boxes contain virulent-speci®c, and clear boxes contain EBCV-speci®c aa changes.


id: cord-348896-a2mjj5dt
author: Abid, Nabil Ben Salem
date: 2010-12-28
extension: .txt
mime: text/plain
words: 3298
sentence: 153
flesch: 53
cache: cache/cord-348896-a2mjj5dt.txt
txt: txt/cord-348896-a2mjj5dt.txt
title:
  Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein

summary:
  The nucleotide and the amino acid sequences of TGEV TMK22 strains were compared with the corresponding sequences of TGEV strains, available in GenBank database. Cell culture adapted TGEV TMK22 strain (the collection of microorganism strains of the Federal Governmental Institute, All-Russian Research Institute for Animal Health, FGI ARRIAH) was used in this study.


id: cord-269720-o81j3d1j
author: Page, Kevin W.
date: 1990
extension: .txt
mime: text/plain
words: 3559
sentence: 125
flesch: 51
cache: cache/cord-269720-o81j3d1j.txt
txt: txt/cord-269720-o81j3d1j.txt
title:
  Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus

summary:
  An oligonucleotide, oligo 58, was synthesised that was complementary to the 5' end of the TGEV and PRCV leader RNA sequences (Fig. 1) . In this paper we describe the elucidation of the leader RNA sequences from the porcine coronaviruses TGEV and PRCV, the first leader sequence to be described from the TGEV serogroup of coronaviruses.


id: cord-307580-nokd5kmx
author: Yang, Guang
date: 1999
extension: .txt
mime: text/plain
words: 3407
sentence: 125
flesch: 57
cache: cache/cord-307580-nokd5kmx.txt
txt: txt/cord-307580-nokd5kmx.txt
title:
  D-RNA Molecules Associated with Subisolates of the VT Strain of Citrus Tristeza Virus which Induce Different Seedling-Yellows Reactions

summary:
  The virus titers were considerably higher in sour orange plants infected with nSY than in those infected with SY subisolates. There have been reports of spontaneous recovery from SY infection by sour orange plants which initially showed SY symptoms, and of the elimination of the SY causal agent by the passage of SY-inducing CTV subisolates through SY-sensitive citrus hosts such as grapefruit and sour orange (12) , which has led to the emergence of non-SY (nSY) isolates.


id: cord-302584-fwdpzv85
author: Zhu, Ying
date: 2005-01-01
extension: .txt
mime: text/plain
words: 3432
sentence: 155
flesch: 52
cache: cache/cord-302584-fwdpzv85.txt
txt: txt/cord-302584-fwdpzv85.txt
title:
  Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates

summary:
  In this report, we described the isolation of a new SARS-CoV strain (WHU) from a patient in Hubei Province, China during the late period of SARS outbreak. He worked in Beijing during that time when SARS outbreak was occurring.


id: cord-005252-m02inmc4
author: Kwon, Hyuk Moo
date: 1995
extension: .txt
mime: text/plain
words: 4420
sentence: 470
flesch: 90
summary: A T T T C T G C T A T G A G T G T C G T G T G
cache: cache/cord-005252-m02inmc4.txt
txt: txt/cord-005252-m02inmc4.txt
title:
  Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus


id: cord-283168-kl1hoa1x
author: Farkas, Tibor
title: Molecular detection of novel picornaviruses in chickens and turkeys
date: 2011-12-13
extension: .txt
mime: text/plain
words: 4036
sentence: 170
flesch: 49
cache: cache/cord-283168-kl1hoa1x.txt
txt: txt/cord-283168-kl1hoa1x.txt
summary:
  However, RdRps of RNA viruses because of their common evolutionary origin share several conserved motifs. Indeed, using P289/P290 for the detection of caliciviruses in several previous studies resulted in the unintentional detection of RNA viruses including rotavirus, porcine kobuvirus and astrovirus


id: cord-331919-6kistim2
author: Song, Daesub
date: 2012-01-22
extension: .txt
mime: text/plain
words: 4270
sentence: 219
flesch: 54
cache: cache/cord-331919-6kistim2.txt
txt: txt/cord-331919-6kistim2.txt
title:
  Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines

summary:
  ORF3 genes have been used to divide Chinese field strains and PEDV reference strains into 3 groups; further, Chinese field strains appear to be closely related to Korean strains, but genetically different from PEDV vaccine strains. Immunochromatographic assay kits can be used at farms in order to detect PEDV S proteins with 92% sensitivity and 98% specificity.


id: cord-311712-lkvt9slp
author: Barrett, John W.
date: 2006
extension: .txt
mime: text/plain
words: 4902
sentence: 208
flesch: 51
cache: cache/cord-311712-lkvt9slp.txt
txt: txt/cord-311712-lkvt9slp.txt
title:
  Optimization of Codon Usage of Poxvirus Genes allows for Improved Transient Expression in Mammalian Cells

summary:
  It has been suggested that codon bias reflects the level of gene expression and/or length of gene Finally there was no correlation between level of gene expression and codon bias in NPV or between gene length and codon bias, and patterns of codon usage appeared to be a direct function of GC content of the virus encoded genes [12] .


id: cord-265095-lf5j4ic7
author: Ten Dam, Edwin B.
title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs
date: 1990
extension: .txt
mime: text/plain
words: 5156
sentence: 215
flesch: 59
cache: cache/cord-265095-lf5j4ic7.txt
txt: txt/cord-265095-lf5j4ic7.txt
summary:
  key: cord-265095-lf5j4ic7 authors: Ten Dam, Edwin B.; Pleij, Cornelius W. A.; Bosch, Leendert title: RNA pseudoknots: The characteristics of RNA pseudoknots and their prediction and detection have been reviewed (12, 14) .


id: cord-287748-co9j3uig
author: Kobayashi, Tomoya
title: Detection of bat hepatitis E virus RNA in microbats in Japan
date: 2018-05-29
extension: .txt
mime: text/plain
words: 1390
sentence: 60
flesch: 52
cache: cache/cord-287748-co9j3uig.txt
txt: txt/cord-287748-co9j3uig.txt
summary:
  Although there is no information about migration of E. japonensis and P. sacrimontis, bat species closely related to them were reported to migrate only a few kilometers from their colonies per night key: cord-287748-co9j3uig authors: Kobayashi, Tomoya; Murakami, Shin; Yamamoto, Terumasa; Mineshita, Ko; Sakuyama, Muneki; Sasaki, Reiko; Maeda, Ken; Horimoto, Taisuke title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 journal: Virus Genes DOI: 10.1007/s11262-018-1577-9 sha: doc_id: 287748 cord_uid: co9j3uig Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV).


id: cord-284675-7zv449sc
author: Yew, Tan Do
title: Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus
date: 2004
extension: .txt
mime: text/plain
words: 5518
sentence: 286
flesch: 57
cache: cache/cord-284675-7zv449sc.txt
txt: txt/cord-284675-7zv449sc.txt
summary:
  Cutting the tree at 0.05 linkage distance, it was clear that VP5 gene and its non-overlapping region formed different clusters compared with other viral genes. The very virulent IBDV strain (vvIBDV) can cause up to 100% mortality and severe bursal lesions in specific-pathogen-free (SPF


id: cord-279863-5kxgu4t9
author: Oem, Jae-Ku
title: Phylogenetic analysis of bovine astrovirus in Korean cattle
date: 2013-11-23
extension: .txt
mime: text/plain
words: 1633
sentence: 94
flesch: 62
cache: cache/cord-279863-5kxgu4t9.txt
txt: txt/cord-279863-5kxgu4t9.txt
summary:
  Nine of 115 fecal samples from Korean cattle were positive for BAstV and all of the BAstVs were related to diarrhea. Nonambulatory cattle which are commonly referred to as ''downer'' cattle are unable to stand or walk.


id: cord-272693-432ixb7g
author: Phillips, J. E.
date: 2011-09-10
extension: .txt
mime: text/plain
words: 6285
sentence: 243
flesch: 52
cache: cache/cord-272693-432ixb7g.txt
txt: txt/cord-272693-432ixb7g.txt
title:
  Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus

summary:
  The percent amino acid identity for the S glycoprotein is 97.8% for Ark viruses, 96.6% for GA98 viruses, and 97.2% for Mass 41 viruses (Fig. 3) . To examine the sequence changes in individual genes associated with attenuation of IBV for chickens, we sequenced and compared the full-length consensus genomes of pathogenic IBV viruses and egg-passaged attenuated (for chickens) viruses from three different serotypes.


id: cord-340438-9q3ic0ye
author: Zhang, Jianqiang
date: 2018-02-21
extension: .txt
mime: text/plain
words: 1728
sentence: 76
flesch: 59
cache: cache/cord-340438-9q3ic0ye.txt
txt: txt/cord-340438-9q3ic0ye.txt
title:
  Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States

summary:
  Subsequent PEDV S gene-based differential rRT-PCR revealed that these samples were negative for S INDEL PEDV (C T > 40) but positive for non-S INDEL PEDV. PEDV S protein has multiple functions including (1) mediating receptor binding through its S1 subunit (aa 1-729) and fusion of the viral and cellular membranes during cell entry through its S2 subunit (aa 730-1386); (2) harboring neutralization epitopes.


id: cord-344558-1jgqofbr
author: Kocherhans, Rolf
title: Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence
date: 2001
extension: .txt
mime: text/plain
words: 2841
sentence: 147
flesch: 61
cache: cache/cord-344558-1jgqofbr.txt
txt: txt/cord-344558-1jgqofbr.txt
summary:
  Later, a mixture of up to six antigenome sense primers based on PEDV specific sequences or the degenerate primers and random hexamer primer (purchased from Schmidheini AG; Balgach, Switzerland) was used for first strand cDNA synthesis. The multiple sequence alignments revealed several putative functional domains common to coronavirus sequences [23, 26] located on the deduced amino acid sequence of ORF1ab of PEDV.


id: cord-011794-ejoufvvj
author: Binder, Florian
title: Isolation and characterization of new Puumala orthohantavirus strains from Germany
date: 2020-04-23
extension: .txt
mime: text/plain
words: 5994
sentence: 253
flesch: 47
cache: cache/cord-011794-ejoufvvj.txt
txt: txt/cord-011794-ejoufvvj.txt
summary:
  Phylogenetic analysis of the concatenated S, M and L segment coding sequences grouped the novel isolates together with Astrup prototype strain in sister relationship to PUUV sequences from France (Fig. 4a) . Moreover, the hybrid-capture-based enrichment of PUUV sequences allows a rapid determination of the complete genome and underlines the value of this workflow for hantavirus surveillance and molecular evolution studies [35] .


id: cord-296791-h8ftslps
author: Junwei, Ge
title: Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03
date: 2006-10-01
extension: .txt
mime: text/plain
words: 2346
sentence: 92
flesch: 54
cache: cache/cord-296791-h8ftslps.txt
txt: txt/cord-296791-h8ftslps.txt
summary:
  A phylogenetic tree was prepared to further examine relationships between PEDV and other coronaviruses based on a comparison of N protein amino acid sequences (Fig. 3) . The N protein is highly immunogenic, more then, the cellular immune response against N protein of some animal coronaviruses can enhance the recovery from the virus infection


id: cord-005253-8qja4j9h
author: Li, Weike
title: Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China
date: 2014-04-02
extension: .txt
mime: text/plain
words: 3396
sentence: 116
flesch: 53
cache: cache/cord-005253-8qja4j9h.txt
txt: txt/cord-005253-8qja4j9h.txt
summary:
  The hemoagglutinin (H) protein is one of the most important antigens for inducing protective immunity against CD, and antigenic variation of recent CDV strains may explain vaccination failure. Analysis of CDV strains detected globally and from a variety of host species will provide a more in-depth understanding of the global ecology of CDV and will provide the basis for the improvement of current CDV vaccines.


id: cord-310298-26x2p9wc
author: Tao, Pan
title: Analysis of synonymous codon usage in classical swine fever virus
date: 2008-10-29
extension: .txt
mime: text/plain
words: 3420
sentence: 168
flesch: 55
cache: cache/cord-310298-26x2p9wc.txt
txt: txt/cord-310298-26x2p9wc.txt
summary:
  This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage.


id: cord-025704-icedihm2
author: Pawestri, Hana A.
date: 2020-06-01
extension: .txt
mime: text/plain
words: 6557
sentence: 257
flesch: 38
cache: cache/cord-025704-icedihm2.txt
txt: txt/cord-025704-icedihm2.txt
title:
  Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015

summary:
  In summary, we performed genetic and antigenic analyses of H5N1 influenza viruses isolated from humans between 2008 and 2015. Pedoman Pengambilan dan Pengiriman Spesimen Yang Berhubungan Dengan Flu Burung CDC realtime RTPCR (rRTPCR) protocol for detection and characterization of Swine Influenza (version Antigenic variation in H5N1 clade 2.1 viruses in Indonesia from Universal primer set for the full-length amplification of all influenza A viruses Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus Genome analysis linking recent European and African influenza (H5N1) viruses Genetic diversity and host adaptation of avian H5N1 influenza viruses during human infection BioEdit: an important software for molecular biology RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees Using RAxML to infer phylogenies Continued evolution of highly pathogenic avian influenza A(H5N1): updated nomenclature World Health Organization/World Organisation for Animal HF, Agriculture Organization HEWG.


