        item: #1 of 40
          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
       words: 2171
      flesch: 55
     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
    keywords: chinju99; gene; pedv; protein
       cache: cord-005207-02wmt2e9.txt
  plain text: cord-005207-02wmt2e9.txt

        item: #2 of 40
          id: cord-005252-m02inmc4
      author: Kwon, Hyuk Moo
       title: Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus
        date: 1995
       words: 4420
      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
    keywords: c c; c g; c t; g g; t g; t ppi; t t
       cache: cord-005252-m02inmc4.txt
  plain text: cord-005252-m02inmc4.txt

        item: #3 of 40
          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
       words: 3396
      flesch: 53
     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.
    keywords: amino; cdv; protein; strains
       cache: cord-005253-8qja4j9h.txt
  plain text: cord-005253-8qja4j9h.txt

        item: #4 of 40
          id: cord-011794-ejoufvvj
      author: Binder, Florian
       title: Isolation and characterization of new Puumala orthohantavirus strains from Germany
        date: 2020-04-23
       words: 5994
      flesch: 47
     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] .
    keywords: antibodies; bank; cells; germany; hantavirus; isolates; isolation; monoclonal; novel; osnabrück; puuv; rna; strain; v29; veroe6; virus; vole
       cache: cord-011794-ejoufvvj.txt
  plain text: cord-011794-ejoufvvj.txt

        item: #5 of 40
          id: cord-012091-3bo88tux
      author: Ibrahim, Madiha Salah
       title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1)
        date: 2011-02-17
       words: 2497
      flesch: 44
     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.
    keywords: analysis; cl6/07; d2br10/07; h5n1; influenza; sequences; viruses
       cache: cord-012091-3bo88tux.txt
  plain text: cord-012091-3bo88tux.txt

        item: #6 of 40
          id: cord-025704-icedihm2
      author: Pawestri, Hana A.
       title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015
        date: 2020-06-01
       words: 6557
      flesch: 38
     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.
    keywords: antigenic; avian; h5n1; hpai; human; indonesia; influenza; isolates; poultry; protein; receptor; substitutions; virulence; viruses
       cache: cord-025704-icedihm2.txt
  plain text: cord-025704-icedihm2.txt

        item: #7 of 40
          id: cord-254291-y8xvh6hs
      author: Yamanaka, Miles
       title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus
        date: 1998
       words: 833
      flesch: 63
     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) .
    keywords: fipv; orf
       cache: cord-254291-y8xvh6hs.txt
  plain text: cord-254291-y8xvh6hs.txt

        item: #8 of 40
          id: cord-257122-h3zi8k8g
      author: Lin, Chao-Nan
       title: Full genome analysis of a novel type II feline coronavirus NTU156
        date: 2012-12-14
       words: 2384
      flesch: 58
     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] .
    keywords: fcov; nsp; ntu156; recombination; type
       cache: cord-257122-h3zi8k8g.txt
  plain text: cord-257122-h3zi8k8g.txt

        item: #9 of 40
          id: cord-259398-s8qsjkj2
      author: Chouljenko, Vladimir N.
       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
        date: 1998
       words: 3190
      flesch: 54
     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.
    keywords: acid; amino; kda; rbcv; speci; strains
       cache: cord-259398-s8qsjkj2.txt
  plain text: cord-259398-s8qsjkj2.txt

        item: #10 of 40
          id: cord-263489-i4tkdgy4
      author: Suo, Siqingaowa
       title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential
        date: 2015-05-27
       words: 2222
      flesch: 61
     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.
    keywords: elisa; phage; tgev
       cache: cord-263489-i4tkdgy4.txt
  plain text: cord-263489-i4tkdgy4.txt

        item: #11 of 40
          id: cord-265095-lf5j4ic7
      author: Ten Dam, Edwin B.
       title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs
        date: 1990
       words: 5156
      flesch: 59
     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) .
    keywords: downstream; hairpin; nucleotides; pseudoknot; rna; rnas; sequence
       cache: cord-265095-lf5j4ic7.txt
  plain text: cord-265095-lf5j4ic7.txt

        item: #12 of 40
          id: cord-266634-bww62vx8
      author: Gopinath, M.
       title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus
        date: 2015-10-07
       words: 2307
      flesch: 50
     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) .
    keywords: cap; methyl; mrna; protein; transferase
       cache: cord-266634-bww62vx8.txt
  plain text: cord-266634-bww62vx8.txt

        item: #13 of 40
          id: cord-268627-nnx46nwf
      author: Ren, Xiaofeng
       title: Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus
        date: 2011-02-01
       words: 2777
      flesch: 55
     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.
    keywords: dna; lamp; pcr; pedv; reaction; virus
       cache: cord-268627-nnx46nwf.txt
  plain text: cord-268627-nnx46nwf.txt

        item: #14 of 40
          id: cord-269340-o9jdt86j
      author: Callison, Scott Andrew
       title: Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding
        date: 1999
       words: 2118
      flesch: 54
     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.
    keywords: amino; sequence; strains; subunit
       cache: cord-269340-o9jdt86j.txt
  plain text: cord-269340-o9jdt86j.txt

        item: #15 of 40
          id: cord-269720-o81j3d1j
      author: Page, Kevin W.
       title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus
        date: 1990
       words: 3559
      flesch: 51
     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.
    keywords: leader; leader rna; mrna; prcv; rna; sequence; species; tgev
       cache: cord-269720-o81j3d1j.txt
  plain text: cord-269720-o81j3d1j.txt

        item: #16 of 40
          id: cord-272693-432ixb7g
      author: Phillips, J. E.
       title: Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus
        date: 2011-09-10
       words: 6285
      flesch: 52
     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.
    keywords: acid; amino; ark; changes; differences; ga98; ibv; mass; nsp; pathogenic; virus; viruses
       cache: cord-272693-432ixb7g.txt
  plain text: cord-272693-432ixb7g.txt

        item: #17 of 40
          id: cord-279863-5kxgu4t9
      author: Oem, Jae-Ku
       title: Phylogenetic analysis of bovine astrovirus in Korean cattle
        date: 2013-11-23
       words: 1633
      flesch: 62
     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.
    keywords: bastvs; bovine; cattle; pig; samples
       cache: cord-279863-5kxgu4t9.txt
  plain text: cord-279863-5kxgu4t9.txt

        item: #18 of 40
          id: cord-282126-gmjnbnx5
      author: Yang, Limin
       title: Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1
        date: 2012-08-07
       words: 2140
      flesch: 55
     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.
    keywords: assay; dhav-1; lamp; pcr
       cache: cord-282126-gmjnbnx5.txt
  plain text: cord-282126-gmjnbnx5.txt

        item: #19 of 40
          id: cord-283168-kl1hoa1x
      author: Farkas, Tibor
       title: Molecular detection of novel picornaviruses in chickens and turkeys
        date: 2011-12-13
       words: 4036
      flesch: 49
     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
    keywords: chicken; genus; picornaviruses; rna; samples; sequences; turkey; viruses
       cache: cord-283168-kl1hoa1x.txt
  plain text: cord-283168-kl1hoa1x.txt

        item: #20 of 40
          id: cord-284675-7zv449sc
      author: Yew, Tan Do
       title: Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus
        date: 2004
       words: 5518
      flesch: 57
     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
    keywords: analysis; base; cpg; dinucleotide; gene; ibdv; isolates; pca; sequences; usage; virus; vp5
       cache: cord-284675-7zv449sc.txt
  plain text: cord-284675-7zv449sc.txt

        item: #21 of 40
          id: cord-287748-co9j3uig
      author: Kobayashi, Tomoya
       title: Detection of bat hepatitis E virus RNA in microbats in Japan
        date: 2018-05-29
       words: 1390
      flesch: 52
     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).
    keywords: bat; bats; bthev; species
       cache: cord-287748-co9j3uig.txt
  plain text: cord-287748-co9j3uig.txt

        item: #22 of 40
          id: cord-288239-ca5uthvd
      author: Jeoung, Hye-Young
       title: Three clusters of bovine kobuvirus isolated in Korea, 2008–2010
        date: 2011-03-12
       words: 1268
      flesch: 62
     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.
    keywords: bovine; kobuvirus
       cache: cord-288239-ca5uthvd.txt
  plain text: cord-288239-ca5uthvd.txt

        item: #23 of 40
          id: cord-295554-0pzjyrdf
      author: Lima, Francisco Esmaile de Sales
       title: Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil
        date: 2013-03-16
       words: 1788
      flesch: 52
     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.
    keywords: bats; brazil; coronavirus; rna; species; viruses
       cache: cord-295554-0pzjyrdf.txt
  plain text: cord-295554-0pzjyrdf.txt

        item: #24 of 40
          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
       words: 2346
      flesch: 54
     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
    keywords: gene; ljb/03; nucleotide; pedv; phosphorylation; protein; sequence
       cache: cord-296791-h8ftslps.txt
  plain text: cord-296791-h8ftslps.txt

        item: #25 of 40
          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
       words: 1966
      flesch: 63
     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.
    keywords: astrovirus; pastv; pigs; porcine; samples; study
       cache: cord-299573-vq6ckqtd.txt
  plain text: cord-299573-vq6ckqtd.txt

        item: #26 of 40
          id: cord-302584-fwdpzv85
      author: Zhu, Ying
       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
        date: 2005-01-01
       words: 3432
      flesch: 52
     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.
    keywords: cov; genome; isolates; mutations; period; sars; viral; virus
       cache: cord-302584-fwdpzv85.txt
  plain text: cord-302584-fwdpzv85.txt

        item: #27 of 40
          id: cord-303672-ujp78213
      author: Gu, Wen-yuan
       title: Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells
        date: 2019-08-28
       words: 2705
      flesch: 47
     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.
    keywords: cells; pdcov; pgenesil; porcine; shrna; virus
       cache: cord-303672-ujp78213.txt
  plain text: cord-303672-ujp78213.txt

        item: #28 of 40
          id: cord-303834-yqysedne
      author: Ducatez, Mariette F.
       title: Full genome sequence of guinea fowl coronavirus associated with fulminating disease
        date: 2015-02-25
       words: 1260
      flesch: 54
     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)
    keywords: covs; genome; gfcov; tcov
       cache: cord-303834-yqysedne.txt
  plain text: cord-303834-yqysedne.txt

        item: #29 of 40
          id: cord-307580-nokd5kmx
      author: Yang, Guang
       title: D-RNA Molecules Associated with Subisolates of the VT Strain of Citrus Tristeza Virus which Induce Different Seedling-Yellows Reactions
        date: 1999
       words: 3407
      flesch: 57
     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.
    keywords: ctv; plants; rnas; subisolates
       cache: cord-307580-nokd5kmx.txt
  plain text: cord-307580-nokd5kmx.txt

        item: #30 of 40
          id: cord-310298-26x2p9wc
      author: Tao, Pan
       title: Analysis of synonymous codon usage in classical swine fever virus
        date: 2008-10-29
       words: 3420
      flesch: 55
     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.
    keywords: bias; codon; codon usage; csfv; usage; viruses
       cache: cord-310298-26x2p9wc.txt
  plain text: cord-310298-26x2p9wc.txt

        item: #31 of 40
          id: cord-311204-fc12f845
      author: Zhou, Ling
       title: Full-length genomic characterization and molecular evolution of canine parvovirus in China
        date: 2016-04-02
       words: 2237
      flesch: 62
     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.
    keywords: china; dogs; genome; pcr; samples; test
       cache: cord-311204-fc12f845.txt
  plain text: cord-311204-fc12f845.txt

        item: #32 of 40
          id: cord-311712-lkvt9slp
      author: Barrett, John W.
       title: Optimization of Codon Usage of Poxvirus Genes allows for Improved Transient Expression in Mammalian Cells
        date: 2006
       words: 4902
      flesch: 51
     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] .
    keywords: bias; codon; content; expression; genes; position; poxvirus; usage
       cache: cord-311712-lkvt9slp.txt
  plain text: cord-311712-lkvt9slp.txt

        item: #33 of 40
          id: cord-322475-i29t7ce8
      author: Chen, Xi
       title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China
        date: 2012-07-29
       words: 2810
      flesch: 49
     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).
    keywords: diarrhea; gene; p55; pedv; protein; strains
       cache: cord-322475-i29t7ce8.txt
  plain text: cord-322475-i29t7ce8.txt

        item: #34 of 40
          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
       words: 2384
      flesch: 51
     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
    keywords: adenoviruses; advs; bats; guano; samples; species; viruses
       cache: cord-328518-umvk59dc.txt
  plain text: cord-328518-umvk59dc.txt

        item: #35 of 40
          id: cord-331919-6kistim2
      author: Song, Daesub
       title: Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines
        date: 2012-01-22
       words: 4270
      flesch: 54
     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.
    keywords: antibodies; diarrhoea; gene; pedv; piglets; pigs; protein; virus
       cache: cord-331919-6kistim2.txt
  plain text: cord-331919-6kistim2.txt

        item: #36 of 40
          id: cord-333914-c150ki1n
      author: Koba, Ryota
       title: Identification and characterization of a novel bat polyomavirus in Japan
        date: 2020-08-20
       words: 1687
      flesch: 46
     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%.
    keywords: bat; bats; dna; mfpyv; pyvs; sequences; virus
       cache: cord-333914-c150ki1n.txt
  plain text: cord-333914-c150ki1n.txt

        item: #37 of 40
          id: cord-340438-9q3ic0ye
      author: Zhang, Jianqiang
       title: Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States
        date: 2018-02-21
       words: 1728
      flesch: 59
     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.
    keywords: gene; indel; pedv
       cache: cord-340438-9q3ic0ye.txt
  plain text: cord-340438-9q3ic0ye.txt

        item: #38 of 40
          id: cord-344558-1jgqofbr
      author: Kocherhans, Rolf
       title: Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence
        date: 2001
       words: 2841
      flesch: 61
     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.
    keywords: acid; amino; hcov-229e; orf1a; pedv; sequence; tgev
       cache: cord-344558-1jgqofbr.txt
  plain text: cord-344558-1jgqofbr.txt

        item: #39 of 40
          id: cord-346643-os2kyvvf
      author: Wang, Li
       title: Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene
        date: 2016-11-15
       words: 2959
      flesch: 53
     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.
    keywords: cells; gene; infection; prnat-2; tgev; virus
       cache: cord-346643-os2kyvvf.txt
  plain text: cord-346643-os2kyvvf.txt

        item: #40 of 40
          id: cord-348896-a2mjj5dt
      author: Abid, Nabil Ben Salem
       title: Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein
        date: 2010-12-28
       words: 3298
      flesch: 53
     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.
    keywords: infection; piglets; prcv; protein; strain; tgev; tmk22; virus
       cache: cord-348896-a2mjj5dt.txt
  plain text: cord-348896-a2mjj5dt.txt

