About: Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015

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About: Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015 Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015
Creator	Feng, Li Guo, Donghua Li, Chunqiu Liu, Qiujin Sun, Dongbo Wang, Enyu Wang, Zhihui Wei, Shan Kong, Fanzhi Zhang, Bei Li, Guo Liu, Wang
source	Medline; PMC
abstract	In an effort to trace the evolution of porcine epidemic diarrhea virus (PEDV), S1 and ORF3 genes of viruses identified in 41 pig farms from seven regions (North, Northeast, Northwest, Central, East, South West, and South, respectively) of China in 2015 were sequenced and analyzed. Sequence analysis revealed that the 41 ORF3 genes and 29 S1 genes identified in our study exhibited nucleotide homologies of 98.2%–100% and 96.6%–100%, respectively; these two genes exhibited low nucleotide sequence similarities with classical CV777 strain and early Chinese strain LZC. Phylogenetic analysis indicated that the identified PEDV strains belonged to global non S-INDEL strains, and exhibited genetic diversity; S1 gene of the HLJ2015/DP1-1 strain harbored an unique deletion of 12 nucleotides (A(1130)CAACTCCACTG(1141)); while the Chinese PEDV S-INDEL reference strains included two types of the “CV777” S-INDEL as well as the “US” S-INDEL, and all co-circulated with Chinese non S-INDEL strains. Of 29 identified S1 genes, the SS2 epitope (Y(748)SNIGVCK(755)) was highly conserved, while the SS6 epitope (L(764)QDGQVKI(771)) and pAPN receptor-binding region (aa 490–615) exhibited amino substitutions. Nine possible recombination events were identified between the 29 identifed S1 genes and the 3 S1 reference genes from early Chinese PEDV strains. The complete S genes of selected Chinese PEDV field strains (2011–2015) showed 5.18%–6.07% nucleotide divergence, which is far higher than the divergence observed in early Chinese PEDV strains (3.1%) (P<0.05). Our data provide evidence that PEDV non S-INDEL strains with genetic diversities and potential recombination circulate in seven regions of China in 2015; Chinese PEDV S-INDEL strains exhibit genetic diversity and co-circulate with non S-INDEL strains.
has issue date	2016-08-05(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0160561
bibo:pmid	27494026
has license	cc-by
sha1sum (hex)	a286c95345592981acce2ffe297605fd083d9fe7
schema:url	https://doi.org/10.1371/journal.pone.0160561
resource representing a document's title	Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015
has PubMed Central identifier	PMC4975444
has PubMed identifier	27494026
schema:publication	PLoS One
resource representing a document's body	covid:a286c95345592981acce2ffe297605fd083d9fe7#body_text
is schema:about of	named entity 'ORF3' named entity 'CHARACTERIZATION' named entity 'PORCINE EPIDEMIC DIARRHEA VIRUS' named entity 'PROVIDE' named entity 'SS2' named entity 'GENETIC' named entity 'CHINESE' named entity 'INDEL' named entity 'CHINA' named entity 'GENES' named entity 'SEVEN' named entity 'AMINO' named entity 'EVIDENCE' named entity 'NORTHEAST' named entity 'FAR' named entity 'NUCLEOTIDES' named entity '615' named entity 'DATA' named entity 'S1 GENE' named entity 'OUR' named entity '764' named entity 'INDICATED' named entity '28A' named entity '28P' named entity 'VIRUSES' named entity 'GENETIC DIVERSITY' named entity 'REFERENCE' named entity '1130' named entity 'RECEPTOR' named entity 'EVENTS' named entity 'CHINA' named entity 'CIRCULATED' named entity 'STRAINS' named entity '748' named entity 'POSSIBLE' named entity 'SS6' named entity 'LOW' named entity 'ANALYZED' named entity 'REGIONS' named entity 'MOLECULAR' named entity 'INCLUDED' named entity 'NORTHWEST' named entity 'NON' named entity 'DELETION' named entity 'NON' named entity 'INDEL' named entity 'POTENTIAL' named entity 'STRAIN' named entity 'GLOBAL' named entity 'TRACE' named entity 'EAST' named entity 'HARBORED' named entity 'EVOLUTION' named entity 'GENES' named entity 'CONSERVED' named entity 'EARLY' named entity 'REGIONS' named entity 'EFFORT' named entity 'STUDY' named entity 'BINDING REGION' named entity 'SELECTED' named entity 'THESE' named entity 'COMPLETE' named entity 'PHYLOGENETIC ANALYSIS' named entity 'EXHIBIT' named entity '100%' named entity 'ORF3' named entity 'FARMS' named entity 'PIG' named entity 'CLASSICAL'

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