About: Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011

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About: Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011–2013 in Guangdong, China Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011–2013 in Guangdong, China
Creator	Cao, Yongchang Wang, Yang Hao, Jianwei Chunyi, • Liangliang, Xue
source	Medline; PMC
abstract	Three strains of porcine epidemic diarrhea virus (PEDV) were isolated from dead or diseased pigs at different swine farms in Guangdong during 2011–2013, and their S genes were sequenced. In the same period, seven PEDV strains were also isolated in Guangdong by other laboratories. The spike sequences of 10 Guangdong isolates were compared with vaccine strains and reference pathogenic isolates using six bioinformatics tools. The results revealed that 10 Guangdong strains, excluding strain GDS03, had distinct characteristics in terms of primary structure, secondary structure, high-specificity N-glycosylation sites, potential phosphorylation sites, and palmitoylation sites. Phylogenetic analysis also confirmed these findings and revealed that all PEDV strains were clustered into three distinct groups. Ten Guangdong strains, not including GDS03, belong to Group 1, whereas four vaccine strains and GDS03 belong to Group 3, which is evolutionarily distant from Group 1. Alignment analysis of the neutralizing region amino acid sequences indicated that the amino acid substitutions of Y/D766S, T549S, and G594S that are present in the Guangdong strains, not including GDS03, were a sign of predominant genetic changes among the isolated strains. GDS03 is closely related to the 83P-5 vaccine strain, which suggests that it might represent re-isolation of the vaccine strain or vaccine variants. Taken together, these results indicate that there have been predominant new strains circulating in Guangdong from 2011 to 2013, and the circulating PEDV strains have a genetic composition that is distant from reference strains, especially the vaccine strains; however, the vaccinations might also provide some level of cross-protection, as there have been no changes in the neutralizing epitopes of SS2 and 2C10. This explains why there have been constant but infrequent outbreaks recently in comparison to late 2010 in which PEDV outbreaks were more frequent and severe. In addition, the USA-Colorado-2013 strain had the same amino acid substitutions in the neutralizing regions as the Guangdong strains except GDS03, which suggests that the information and strategies in this study may play role in PEDV variant research in other countries.
has issue date	2014-04-26(xsd:dateTime)
bibo:doi	10.1007/s11262-014-1055-y
bibo:pmid	24771495
has license	no-cc
sha1sum (hex)	a2c85702169970687f328e35a66d62c16eac33d8
schema:url	https://doi.org/10.1007/s11262-014-1055-y
resource representing a document's title	Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011–2013 in Guangdong, China
has PubMed Central identifier	PMC7088867
has PubMed identifier	24771495
schema:publication	Virus Genes
resource representing a document's body	covid:a2c85702169970687f328e35a66d62c16eac33d8#body_text
is schema:about of	named entity 'VARIANT' named entity 'BUT' named entity 'ISOLATION' named entity 'RECENTLY' named entity 'VACCINATIONS' named entity 'CLUSTERED' named entity 'CONFIRMED' named entity 'SECONDARY STRUCTURE' named entity 'SEVERE' named entity 'COMPOSITION' named entity 'PROVIDE' named entity 'EPITOPES' named entity 'ADDITION' named entity 'PRIMARY STRUCTURE' named entity 'ALIGNMENT ANALYSIS' named entity 'PATHOGENIC' named entity 'USA' named entity 'NEW' named entity 'THEIR' named entity 'SWINE' named entity '2011' named entity 'DISTANT FROM' named entity 'distant' named entity 'level' named entity 'epitopes' named entity 'genetic' named entity 'Guangdong' named entity 'Guangdong' named entity 'neutralizing' named entity 'sequenced' named entity 'diseased' named entity 'INSIGHT' named entity 'GROUP 1' named entity 'DISEASED' named entity 'STRATEGIES' named entity 'REVEALED' named entity 'RESULTS' named entity 'STRAINS' named entity 'CHARACTERISTICS' named entity 'PHOSPHORYLATION SITES' named entity 'FIELD' named entity 'GENE' named entity 'CONSTANT' named entity 'FREQUENT' named entity 'RELATED' named entity 'CIRCULATING' named entity 'COUNTRIES' named entity 'SS2' named entity 'POTENTIAL' named entity 'COMPARISON' named entity 'REFERENCE' named entity 'VARIANTS' named entity 'PORCINE EPIDEMIC DIARRHEA VIRUS' named entity 'PALMITOYLATION' named entity 'USING' named entity 'RESEARCH' named entity 'OUTBREAKS' named entity 'SEQUENCES' named entity 'GENETIC' named entity 'DISTINCT' named entity 'VACCINE STRAIN' named entity 'PREDOMINANT' named entity 'TAKEN' named entity 'THESE' named entity 'BIOINFORMATICS' named entity 'STRAINS' named entity 'PORCINE EPIDEMIC DIARRHEA' named entity 'LATE' named entity 'EXCEPT' named entity 'AMINO ACID SEQUENCES' named entity 'PRESENT' named entity 'SEVEN' named entity 'REPRESENT' named entity 'PERIOD' named entity 'COMPARED' named entity 'LEVEL' named entity 'COLORADO'

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